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article stringlengths 4.36k 149k | summary stringlengths 32 3.35k | section_headings listlengths 1 91 | keywords listlengths 0 141 | year stringclasses 13
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|---|---|---|---|---|---|
Nontuberculous mycobacteria ( NTM ) have been reported to be increasing worldwide and its geographic distribution differs by region . The aim of this study was to describe the epidemiology and distribution of NTM in the eastern part of China . Sputum samples were collected from 30 surveillance sites for tuberculosis dr... | Nontuberculous mycobacteria ( NTM ) exist ubiquitously in the environment and cause many kinds of diseases including pulmonary infection . Despite this , NTM does not match compulsory report policy in many countries , such as China . Thus , the epidemiology of NTM is generally unknown . Furthermore , misdiagnosis of no... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | The Epidemiology and Geographic Distribution of Nontuberculous Mycobacteria Clinical Isolates from Sputum Samples in the Eastern Region of China |
Ribosomal RNAs ( rRNAs ) in budding yeast are encoded by ~100–200 repeats of a 9 . 1kb sequence arranged in tandem on chromosome XII , the ribosomal DNA ( rDNA ) locus . Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis . Despite the importance o... | Eukaryotic genomes contain many copies of ribosomal DNA ( rDNA ) genes , usually far in excess of the requirement for cellular ribosome biogenesis . rDNA array size is highly variable , both within and across species . Although it is becoming increasingly evident that the rDNA locus serves extra-coding functions , and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"chemical",
"compounds",
"dna-binding",
"proteins",
"carbohydrates",
"galactose",
"organic",
"compounds",
"dna",
"damage",
"fungi",
"polymerases",
"dna",
"replication",
"dna",
"mammalian",
"genomics",
"molecular",
"biology",
"techniques",
"research",
"and",
"analysis",
... | 2017 | DNA replication stress restricts ribosomal DNA copy number |
Mycobacterium tuberculosis ( Mtb ) mutants lacking rv1411c , which encodes the lipoprotein LprG , and rv1410c , which encodes a putative efflux pump , are dramatically attenuated for growth in mice . Here we show that loss of LprG-Rv1410 in Mtb leads to intracellular triacylglyceride ( TAG ) accumulation , and overexpr... | Of the estimated 2 billion people worldwide currently infected with Mycobacterium tuberculosis ( Mtb ) , surprisingly few go on to develop active tuberculosis ( TB ) disease . The vast majority , 95 percent , of infected individuals develop latent TB , remaining infected but without disease . Despite its importance in ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | Mycobacterial Metabolic Syndrome: LprG and Rv1410 Regulate Triacylglyceride Levels, Growth Rate and Virulence in Mycobacterium tuberculosis |
Cryptococcus neoformans and Cryptococcus gattii are responsible globally for almost one million cryptococcosis cases yearly , mostly in immunocompromised patients , such as those living with HIV . Infections due to C . gattii have mainly been described in tropical and subtropical regions , but its adaptation to tempera... | Cryptococcus neoformans and Cryptococcus gattii are fungal agents responsible globally for almost one million cryptococcosis cases yearly , mostly in immunocompromised patients , such as those living with HIV . Cryptococcosis is a life-threatening mycosis , frequently causing meningoencephalitis . Infections due to C .... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing",
"techniques",
"cryptococcus",
"gattii",
"medicine",
"and",
"health",
"sciences",
"cryptococcus",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"population",
"genetics",
"geographical",
"locations",
"microbiology",
"north",
"america",
"fungi",
"p... | 2016 | Population Genetic Analysis Reveals a High Genetic Diversity in the Brazilian Cryptococcus gattii VGII Population and Shifts the Global Origin from the Amazon Rainforest to the Semi-arid Desert in the Northeast of Brazil |
Buruli ulcer ( BU ) , a necrotizing skin infection caused by Mycobacterium ulcerans is the third most important mycobacterial disease globally after tuberculosis and leprosy in immune competent individuals . This study reports on the retrospective analyses of microbiologically confirmed Buruli ulcer ( BU ) cases in sev... | Buruli ulcer ( BU ) , a necrotizing skin disease caused by Mycobacterium ulcerans , is currently reported in 33 countries , with the greatest disease burden mostly in West African countries along the gulf of Guinea . The lack of pain associated with BU disease enhances delay in seeking medical treatment that could resu... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"tropical",
"diseases",
"geographical",
"locations",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"bacterial",
"diseases",
"signs",
"and",
"symptoms",
"ulcers",
"neglected"... | 2018 | Laboratory confirmation of Buruli ulcer cases in Ghana, 2008-2016 |
Echinostoma caproni ( Trematoda: Echinostomatidae ) is an intestinal trematode that has been extensively used as experimental model to investigate the factors determining the expulsion of intestinal helminths or , in contrast , the development of chronic infections . Herein , we analyze the changes in protein expressio... | Intestinal helminth infections are among the most prevalent parasitic diseases and about 1 billion people are currently infected with intestinal helminths . Incidence of intestinal helminth infections is high due to both socio-economic factors that facilitates continuous re-infections and the lack of effective vaccines... | [
"Abstract",
"Introduction",
"Material",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Altered Protein Expression in the Ileum of Mice Associated with the Development of Chronic Infections with Echinostoma caproni (Trematoda) |
The conserved internal trimeric coiled-coil of the N-heptad repeat ( N-HR ) of HIV-1 gp41 is transiently exposed during the fusion process by forming a pre-hairpin intermediate , thus representing an attractive target for the design of fusion inhibitors and neutralizing antibodies . In previous studies we reported a se... | Membrane fusion of HIV-1 with its target cells represents the first step in viral infection . This process involves a series of conformational changes in two viral envelope glycoproteins , gp120 and gp41 , subsequent to binding of gp120 to the CD4 receptor and the chemokine coreceptor on the target cell membrane . Duri... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/hiv",
"infection",
"and",
"aids"
] | 2010 | Structural Basis of HIV-1 Neutralization by Affinity Matured Fabs Directed against the Internal Trimeric Coiled-Coil of gp41 |
The branch point ( BP ) is one of the three obligatory signals required for pre-mRNA splicing . In mammals , the degeneracy of the motif combined with the lack of a large set of experimentally verified BPs complicates the task of modeling it in silico , and therefore of predicting the location of natural BPs . Conseque... | From transcription to translation , the events underlying protein production from DNA sequence are paramount to all aspects of cellular function . Pre-mRNAs in eukaryotes undergo several processing steps prior to their export to the cytoplasm . Among these , splicing – the process of intron removal and exon ligation – ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/alternative",
"splicing",
"computational",
"biology/genomics"
] | 2010 | Genome-Wide Association between Branch Point Properties and Alternative Splicing |
Leptospirosis has emerged as an urban health problem as slum settlements have rapidly spread worldwide and created conditions for rat-borne transmission . Prospective studies have not been performed to determine the disease burden , identify risk factors for infection and provide information needed to guide interventio... | Leptospirosis is a disease that is transmitted by human contact with an environment contaminated with urine from animals , such as rodents , infected by the Leptospira bacteria . Human illness due to these bacteria can be mild , or can have very severe complications . Residents of urban slum settlements are at high ris... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"leptospirosis",
"bacterial",
"diseases",
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonoses",
"medicine",
"and",
"health",
"sciences",
"environmental",
"epidemiology",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"neglected",
"tropical",
"diseases",
... | 2014 | Prospective Study of Leptospirosis Transmission in an Urban Slum Community: Role of Poor Environment in Repeated Exposures to the Leptospira Agent |
Multispecificity–the ability of a single receptor protein molecule to interact with multiple substrates–is a hallmark of molecular recognition at protein-protein and protein-peptide interfaces , including enzyme-substrate complexes . The ability to perform structure-based prediction of multispecificity would aid in the... | Across biology , many proteins that recognize peptides are multispecific; they interact with multiple binding partners of disparate sequence . Computational prediction of these multiple peptide partners would enable greater understanding of individual protein-recognition domains . Additionally , the ability to customiz... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"crystal",
"structure",
"pathology",
"and",
"laboratory",
"medicine",
"protein",
"interactions",
"chemical",
"compounds",
"enzymes",
"pathogens",
"condensed",
"matter",
"physics",
"enzymology",
"microbiology",
"organic",
"compounds... | 2017 | MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory |
The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically . We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination ( NAHR ) mediated by low-copy repeats ( LCRs ) . Combined evidence ... | The human genome contains many loci with high incidence of structural mutations , including insertions and deletions of chromosomal segments . This excessive mutability has accelerated evolution and contributed to human disease but has yet to be explained . Segments of DNA repeated in low-copy numbers ( LCRs ) have bee... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"biology",
"computational",
"biology"
] | 2012 | Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome |
Sphingosine-1-phosphate ( S1P ) is a crucial regulator of a wide array of cellular processes , such as apoptosis , cell proliferation , migration , and differentiation , but its role in Leishmania donovani infection is unknown . In the present study , we observed that L . donovani infection in THP-1 derived macrophages... | Leishmania donovani is an intracellular parasite which is internalized by host macrophages by subverting several intracellular signaling events . During infection suppression of p38 MAPK and activation of ERK1/2 MAPK have been acclaimed for survival and proliferation of these protozoan parasites . In this study , we sh... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"phosphorylation",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"immunology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"physiological",
"processes",
"development... | 2018 | Sphingosine-1-phosphate signaling in Leishmania donovani infection in macrophages |
Mitosis in eukaryotic cells employs spindle microtubules to drive accurate chromosome segregation at cell division . Cells lacking spindle microtubules arrest in mitosis due to a spindle checkpoint that delays mitotic progression until all chromosomes have achieved stable bipolar attachment to spindle microtubules . In... | The process of cell division , mitosis , ensures that chromosomes are accurately segregated to generate two daughter cells , each with a complete genome . Eukaryotic cells use a microtubule-based mitotic spindle to ensure proper chromosome segregation . In the fission yeast Schizosaccharomyces pombe , mitosis is “close... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/cell",
"growth",
"and",
"division",
"cell",
"biology",
"cell",
"biology/cytoskeleton"
] | 2010 | Fission Yeast Cells Undergo Nuclear Division in the Absence of Spindle Microtubules |
The Saccharomyces cerevisiae RNA-binding protein Nab4/Hrp1 is a component of the cleavage factor complex required for 3′ pre-mRNA processing . Although the precise role of Nab4/Hrp1 remains unclear , it has been implicated in correct positioning of the cleavage site in vitro . Here , we show that mutation or overexpres... | A fundamental step in gene expression is the generation of the terminal edge ( 3′ end ) of the mRNA transcript by appropriate cleavage of the longer pre-mRNA . In general , the processing site that emerges first is used , but there are interesting examples where alternative sites are used . Because the choice of altern... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology",
"eukaryotes",
"molecular",
"biology",
"genetics",
"and",
"genomics",
"saccharomyces"
] | 2007 | Alternative 3′ Pre-mRNA Processing in Saccharomyces cerevisiae Is Modulated by Nab4/Hrp1 In Vivo |
The peroxide response transcriptional regulator , PerR , is thought to contribute to virulence of group A Streptococcus ( GAS ) ; however , the specific mechanism through which it enhances adaptation for survival in the human host remains unknown . Here , we identify a critical role of PerR-regulated gene expression in... | Group A Streptococcus ( GAS ) is the leading cause of bacterial pharyngitis ( strep throat ) in children . It is also associated with the life-threatening conditions of necrotizing fasciitis , streptococcal toxic shock , and the post-streptococcal autoimmune syndrome of rheumatic fever and heart disease . The peroxide ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis",
"infectious",
"diseases/respiratory",
"infections"
] | 2008 | PerR Confers Phagocytic Killing Resistance and Allows Pharyngeal Colonization by Group A Streptococcus |
The flavivirus NS5 harbors both a methyltransferase ( MTase ) and an RNA-dependent RNA polymerase ( RdRP ) . Both enzyme activities of NS5 are critical for viral replication . Recently , the full-length NS5 crystal structure of Japanese encephalitis virus reveals a conserved MTase-RdRP interface that features two conse... | Flaviviruses , such as Japanese encephalitis virus ( JEV ) and dengue virus 1-4 ( DENV1-4 ) , are important arthropod-borne pathogens causing major public health threats worldwide . For example , JEV is the most common cause of viral encephalitis in eastern and southern Asia , affecting over 50 , 000 patients , and lea... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"and",
"Discussions"
] | [
"viruses",
"infectious",
"diseases",
"infectious",
"diseases",
"of",
"the",
"nervous",
"system",
"medicine",
"and",
"health",
"sciences",
"japanese",
"encephalitis",
"rna",
"viruses",
"viral",
"classification",
"virology",
"dengue",
"fever",
"neglected",
"tropical",
"... | 2014 | The Interface between Methyltransferase and Polymerase of NS5 Is Essential for Flavivirus Replication |
Post Kala-azar Dermal Leishmaniasis ( PKDL ) develops in patients apparently cured of Visceral Leishmaniasis ( VL ) , and is the strongest contender for being the disease reservoir . Therefore , existence of a few cases is sufficient to trigger an epidemic of VL in a given community , emphasizing the need for its activ... | Post Kala-azar Dermal Leishmaniasis ( PKDL ) is a dermal condition that occurs in South Asia in 10–20% of patients after apparent cure from Visceral Leishmaniasis ( VL ) . It presents with macular or papulonodular lesions that harbor Leishmania parasites , thus playing a major role in the transmission cycle . According... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"kala-azar",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"tropical",
"diseases",
"geographical",
"locations",
"india",
"parasitic",
"diseases",
"signs",
"and",
"symptoms",
"neglected",
"tropical",
"diseases",
"public",
"and",
... | 2019 | Active surveillance identified a neglected burden of macular cases of Post Kala-azar Dermal Leishmaniasis in West Bengal |
Wolbachia infections confer protection for their insect hosts against a range of pathogens including bacteria , viruses , nematodes and the malaria parasite . A single mechanism that might explain this broad-based pathogen protection is immune priming , in which the presence of the symbiont upregulates the basal immune... | Wolbachia is a commonly occurring bacterium or symbiont that lives inside the cells of insects . Recently , Wolbachia was artificially introduced into the mosquito vector dengue virus that was naturally Wolbachia-free . Wolbachia limits the growth of a range of pathogens transmitted to humans , including viruses , bact... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"zoology",
"genetics",
"biology",
"microbiology"
] | 2013 | Wolbachia-Associated Bacterial Protection in the Mosquito Aedes aegypti |
Profiling of DNA and histone modifications has recently allowed the establishment of reference epigenomes from several model organisms . This identified a major chromatin state for active genes that contains monoubiquitinated H2B ( H2Bub ) , a mark linked to transcription elongation . However , assessment of dynamic ch... | In eukaryotes , chromatin-based mechanisms overlay with DNA sequence information to determine the transcriptional output of the genome . Evaluating the role of chromatin state variations in the regulation of gene expression is therefore key to understanding their contribution to development . Several transcriptional co... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"biology",
"signaling",
"in",
"selected",
"disciplines",
"histone",
"modification",
"plant",
"science",
"model",
"organisms",
"developmental",
"signaling",
"plant",
"ecology",
"chromatin",
"arabidopsis",
"thaliana",
"plant",
"signaling",
"gene",
"expression",
"... | 2012 | Histone H2B Monoubiquitination Facilitates the Rapid Modulation of Gene Expression during Arabidopsis Photomorphogenesis |
The ability of Plasmodium falciparum–infected red blood cells ( IRBCs ) to bind to vascular endothelium , thus enabling sequestration in vital host organs , is an important pathogenic mechanism in malaria . Adhesion of P . falciparum IRBCs to platelets , which results in the formation of IRBC clumps , is another cytoad... | Adhesion of Plasmodium falciparum–infected red blood cells ( IRBCs ) to the endothelium lining the capillaries of vital host organs can obstruct blood circulation and is an important pathogenic mechanism in malaria . Adhesion of P . falciparum IRBCs to platelets results in the formation of IRBC clumps that can also obs... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology",
"infectious",
"diseases",
"plasmodium"
] | 2007 | Plasmodium falciparum Uses gC1qR/HABP1/p32 as a Receptor to Bind to Vascular Endothelium and for Platelet-Mediated Clumping |
The reservoir and mode of transmission of Mycobacterium ulcerans , the causative agent of Buruli ulcer , remain unknown . Ecological , genetic and epidemiological information nonetheless suggests that M . ulcerans may reside in aquatic protozoa . We experimentally infected Acanthamoeba polyphaga with M . ulcerans and f... | Buruli ulcer ( BU ) is a devastating skin disease caused by Mycobacterium ulcerans , an environmental bacterium that is probably linked to slow-running water . It is unlikely to occur free-living , but even though M . ulcerans DNA has been detected in quite a few different organisms ( with most studies focusing on inse... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"microbiology",
"bacterial",
"diseases",
"emerging",
"infectious",
"diseases",
"neglected",
"tropical",
"diseases",
"applied",
"microbiology",
"infectious",
"diseases",
"buruli",
"ulcer",
"mycobacterium",
"epidemiology"... | 2012 | Amoebae as Potential Environmental Hosts for Mycobacterium ulcerans and Other Mycobacteria, but Doubtful Actors in Buruli Ulcer Epidemiology |
Detrimental inflammation of the lungs is a hallmark of severe influenza virus infections . Endothelial cells are the source of cytokine amplification , although mechanisms underlying this process are unknown . Here , using combined pharmacological and gene-deletion approaches , we show that plasminogen controls lung in... | Influenza viruses , including H5N1 bird influenza viruses continue to form a major threat for public health . Available antiviral drugs for the treatment of influenza are effective to a limited extent and the emergence of resistant viruses may further undermine their use . The symptoms associated with influenza are cau... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunopathology",
"medicine",
"pulmonology",
"virology",
"immunology",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"immunomodulation",
"respiratory",
"medicine",
"hematology"
] | 2013 | Plasminogen Controls Inflammation and Pathogenesis of Influenza Virus Infections via Fibrinolysis |
The phylum Apicomplexa comprises a group of obligate intracellular parasites that alternate between intracellular replicating stages and actively motile extracellular forms that move through tissue . Parasite cytosolic Ca2+ signalling activates motility , but how this is switched off after invasion is complete to allow... | Central to pathogenesis and infectivity of Toxoplasma and related parasites is their ability to move through tissue , invade host cells , and establish a replicative niche . Ca2+-dependent signalling pathways are important for activating motility , host cell invasion , and egress , yet how this signalling is turned off... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"motility",
"parasite",
"groups",
"medicine",
"and",
"health",
"sciences",
"viral",
"transmission",
"and",
"infection",
"enzymes",
"microbiology",
"enzymology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"in",
"vivo",
"imaging",
"parasitology",
"apicomp... | 2018 | Protein kinase A negatively regulates Ca2+ signalling in Toxoplasma gondii |
Innate and type 1 cell-mediated cytotoxic immunity function as important extracellular control mechanisms that maintain cellular homeostasis . Interleukin-12 ( IL12 ) is an important cytokine that links innate immunity with type 1 cell-mediated cytotoxic immunity . We recently observed in vitro that tumor-derived Wnt-i... | Effective anti-tumor immunity is proportional to the number and to the cytotoxic activity of immune cells that enter the tumor microenvironment . Recent advances in cancer immunotherapy stem from increasing the number of tumor-infiltrating immune cells by inhibiting immune checkpoints or adoptive T cell therapy . Here ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bioengineering",
"systems",
"biology",
"biomedical",
"engineering",
"medicine",
"oncology",
"forms",
"of",
"evolution",
"microevolution",
"immune",
"evasion",
"immunotherapy",
"basic",
"cancer",
"research",
"cancer",
"treatment",
"biology",
"computational",
"biology",
"e... | 2014 | Induction of Wnt-Inducible Signaling Protein-1 Correlates with Invasive Breast Cancer Oncogenesis and Reduced Type 1 Cell-Mediated Cytotoxic Immunity: A Retrospective Study |
The human cytomegalovirus ( HCMV ) is extremely prevalent in the human population . Infection by HCMV is life threatening in immune compromised individuals and in immune competent individuals it can cause severe birth defects , developmental retardation and is even associated with tumor development . While numerous mec... | The human cytomegalovirus ( HCMV ) infects a high percentage of the human population . HCMV infection is life threatening to immune-compromised individuals and when transmitted to the fetus can cause severe birth defects . Thus , it is crucial to understand the anti-viral strategies that are induced in response to HCMV... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"infectious",
"diseases",
"immune",
"cells",
"nk",
"cells",
"immunology",
"cytomegalovirus",
"infection",
"biology",
"viral",
"diseases"
] | 2014 | MicroRNA Editing Facilitates Immune Elimination of HCMV Infected Cells |
The Joint Evolutionary Trees ( JET ) method detects protein interfaces , the core residues involved in the folding process , and residues susceptible to site-directed mutagenesis and relevant to molecular recognition . The approach , based on the Evolutionary Trace ( ET ) method , introduces a novel way to treat evolut... | Information obtained on the structure of macromolecular complexes is important for identifying functionally important partners but also for determining how such interactions will be perturbed by natural or engineered site mutations . Hence , to fully understand or control biological processes we need to predict in the ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/macromolecular",
"structure",
"analysis",
"molecular",
"biology/molecular",
"evolution",
"computational",
"biology/evolutionary",
"modeling",
"molecular",
"biology/bioinformatics",
"computational",
"biology/macromolecular",
"sequence",
"analysis",
"evolution... | 2009 | Joint Evolutionary Trees: A Large-Scale Method To Predict Protein
Interfaces Based on Sequence Sampling |
Human papillomaviruses are causally associated with 5% of human cancers . The recent discovery of a papillomavirus ( MmuPV1 ) that infects laboratory mice provides unique opportunities to study the life cycle and pathogenesis of papillomaviruses in the context of a genetically manipulatable host organism . To date , Mm... | Epidemiological studies have implicated that ultraviolet radiation ( UVR ) from sunlight drive papillomavirus-induced disease in healthy as well as immunocompromised humans . In this report we demonstrate that treatment of immunocompetent mice with UVR renders them susceptible to papillomas and associated squamous cell... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"dermatology",
"urology",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"ultraviolet",
"radiation",
"ears",
"immunology",
"immune",
"suppression",
"cancers",
"and",
"neoplasms",
"light",
"electromagnetic",
"radiation",
"oncology",
... | 2016 | Role of Ultraviolet Radiation in Papillomavirus-Induced Disease |
In the last few million years , the hominin brain more than tripled in size . Comparisons across evolutionary lineages suggest that this expansion may be part of a broader trend toward larger , more complex brains in many taxa . Efforts to understand the evolutionary forces driving brain expansion have focused on clima... | Humans have extraordinarily large brains , which tripled in size in the last few million years . Other animals also experienced a significant , though smaller , increase in brain size . These increases are puzzling , because brain tissue is energetically expensive—a smaller brain is easier to maintain in terms of calor... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"learning",
"organismal",
"evolution",
"ecology",
"and",
"environmental",
"sciences",
"hominin",
"evolution",
"sociology",
"human",
"evolution",
"social",
"sciences",
"vertebrates",
"neuroscience",
"learning",
"and",
"memory",
"animals",
"mammals",
"primates",
"cultural",... | 2018 | The Cultural Brain Hypothesis: How culture drives brain expansion, sociality, and life history |
The endoplasmic reticulum ( ER ) is the site of synthesis of secreted and membrane proteins . To exit the ER , proteins are packaged into COPII vesicles through direct interaction with the COPII coat or aided by specific cargo receptors . Despite the fundamental role of such cargo receptors in protein traffic , only a ... | All cells sense their environment , respond to it , and communicate with neighboring cells . To perform these functions , cells use an impressive array of proteins that they display on their surface membranes and secrete into their external environment . Newly synthesized proteins destined for the surface of nucleated ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biochemistry",
"genetics",
"biology",
"proteomics",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | A Systematic Approach to Pair Secretory Cargo Receptors with Their Cargo Suggests a Mechanism for Cargo Selection by Erv14 |
Chagas Disease ( CD ) is an anthropozoonosis caused by Trypanosoma cruzi . With complex pathophysiology and variable clinical presentation , CD outcome can be influenced by parasite persistence and the host immune response . Complement activation is one of the primary defense mechanisms against pathogens , which can be... | The heterogeneity of clinical progression during chronic Trypanosoma cruzi infection and the mechanisms determining why some individuals develop symptoms whereas others remain asymptomatic are still poorly understood . The pathogenesis of chronic Chagas Disease ( CD ) has been attributed mainly to the persistence of th... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cardiomyopathies",
"medicine",
"and",
"health",
"sciences",
"variant",
"genotypes",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"genetic",
"mapping",
"protozoans",
"neglected",
"tropical",
"diseases",
"cardiology",
"proteins",
"protozoan",
... | 2019 | Human collectin-11 (COLEC11) and its synergic genetic interaction with MASP2 are associated with the pathophysiology of Chagas Disease |
Loa loa infection is endemic in limited areas of West-Central Africa . Loiasis has been associated with excess mortality , but clinical studies on its treatment are scant , particularly outside endemic areas , due to the rarity of cases diagnosed . With this retrospective TropNet ( European Network for Tropical Medicin... | Loa loa is a worm which infects millions of people living in wide forested areas of central Africa . The infection is rarely diagnosed outside Africa , and cases are mainly referred to referral centers on tropical medicine . Aim of this study was to describe the treatment and management of patients diagnosed with loias... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pruritus",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"parasitic",
"diseases",
"animals",
"neuroscience",
"parasitology",
"nematode",
"infections",
"pharmaceutics",
"drug",
"administr... | 2018 | Comparison of different drug regimens for the treatment of loiasis—A TropNet retrospective study |
The toxicity of available drugs for treatment of leishmaniasis , coupled with emerging drug resistance , make it urgent to find new therapies . Antimicrobial peptides ( AMPs ) have a strong broad-spectrum antimicrobial activity with distinctive modes of action and are considered as promising therapeutic agents . The de... | In Iran , cutaneous leishmaniasis ( CL ) is a widespread and highly endemic disease in young individuals . To date , treatment strategy is based on chemotherapy accompanied with high incidence of toxicity and drug resistance . Distinctive mode of action of defensins ( members of antimicrobial peptides ) with low suscep... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Human Neutrophil Peptide-1 (HNP-1): A New Anti-Leishmanial Drug Candidate |
Using a transgenic mouse model harboring a mutation reporter gene that can be efficiently recovered from genomic DNA , we previously demonstrated that mutations accumulate in aging mice in a tissue-specific manner . Applying a recently developed , similar reporter-based assay in Drosophila melanogaster , we now show th... | DNA mutations are changes in the DNA sequence , including basepair substitutions and genome rearrangements . Mutations are inevitable and are a consequence of errors made in replicating DNA during cell division or repairing damage . Aging is a complex process of functional decline and increased disease risk that has of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics"
] | 2010 | Age- and Temperature-Dependent Somatic Mutation Accumulation in Drosophila melanogaster |
Anopheles balabacensis of the Leucospyrus group has been confirmed as the primary knowlesi malaria vector in Sabah , Malaysian Borneo for some time now . Presently , knowlesi malaria is the only zoonotic simian malaria in Malaysia with a high prevalence recorded in the states of Sabah and Sarawak . Anopheles spp . were... | Anopheles balabacensis has been incriminated as the primary vector of zoonotic simian malaria , P . knowlesi in Malaysian Borneo with a high prevalence recorded in the states of Sabah and Sarawak . In this study , Anopheles spp . were sampled using human landing catch ( HLC ) method at Paradason village in Kudat distri... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"taxonomy",
"invertebrates",
"parasite",
"groups",
"medicine",
"and",
"health",
"sciences",
"evolutionary",
"biology",
"plasmodium",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"parasitic",
"protozoans",
"parasitology",
"apicomplexa",
"phylogenetics",
"data"... | 2017 | Phylogenetic analysis of simian Plasmodium spp. infecting Anopheles balabacensis Baisas in Sabah, Malaysia |
AMPA receptors ( AMPARs ) and their associations with auxiliary transmembrane proteins are bulky structures with large steric-exclusion volumes . Hence , self-crowding of AMPARs , depending on the local density , may affect their lateral diffusion in the postsynaptic membrane as well as in the highly crowded postsynapt... | The transmembrane AMPA receptors ( AMPARs ) prominently exhibit lateral diffusion in the postsynaptic membrane at excitatory synapses . Steric obstructions to AMPAR diffusion due to the crowd of other relatively static transmembrane proteins and binding of AMPARs to the submembranous scaffold proteins in the specialize... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"classical",
"mechanics",
"nervous",
"system",
"electrophysiology",
"neuroscience",
"simulation",
"and",
"modeling",
"membrane",
"proteins",
"mathematics",
"statistics",
"(mathematics)",
"reflection",
"cellular",
"structures",
"and",... | 2018 | Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion |
Quantifying human mobility has significant consequences for studying physical activity , exposure to pathogens , and generating more realistic infectious disease models . Location-aware technologies such as Global Positioning System ( GPS ) -enabled devices are used increasingly as a gold standard for mobility research... | Being able to quantify human movement is important for studying activity patterns , exposure to pathogens and developing realistic infectious disease models . We compared fine-scale human mobility data obtained by Global Positioning System ( GPS ) -enabled devices and semi-structured interviews ( SSI ) from 160 individ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"and",
"occupational",
"health",
"infectious",
"diseases",
"geography",
"medicine",
"and",
"health",
"sciences",
"global",
"health",
"earth",
"sciences",
"social",
"sciences"
] | 2014 | Strengths and Weaknesses of Global Positioning System (GPS) Data-Loggers and Semi-structured Interviews for Capturing Fine-scale Human Mobility: Findings from Iquitos, Peru |
Coding of multiple proteins by overlapping reading frames is not a feature one would associate with eukaryotic genes . Indeed , codependency between codons of overlapping protein-coding regions imposes a unique set of evolutionary constraints , making it a costly arrangement . Yet in cases of tightly coexpressed intera... | A textbook human gene encodes a protein using a single reading frame . Alternative splicing brings some variation to that picture , but the notion of a single reading frame remains . Although this is true for most of our genes , there are exceptions . Like viral counterparts , some eukaryotic genes produce structurally... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology",
"homo",
"sapiens",
"genetics",
"and",
"genomics",
"computational",
"biology"
] | 2007 | A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes |
Cytotoxic T lymphocytes ( CTLs ) are the major killer of virus-infected cells . Granzyme B ( GrB ) from CTLs induces apoptosis in target cells by cleavage and activation of substrates like caspase-3 and Bid . However , while undergoing apoptosis , cells are still capable of producing infectious viruses unless a mechani... | Lymphocytes , a type of white blood cell , are the major killer of virus-infected cells . Lymphocytes secrete proteins like granzyme B that are responsible for the destruction of the virus-infected host cell . However , killing an infected cell through this pathway may take several hours , thus allowing viral replicati... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"immune",
"cells",
"viral",
"transmission",
"and",
"infection",
"immunology",
"microbiology",
"gene",
"expression",
"t",
"cells",
"biology",
"jurkat",
"cells",
"molecular",
"biology",
"host",
"cells",
"cell",
"biology",
"clinical",
"immunology",
"virology"... | 2011 | Granzyme B Inhibits Vaccinia Virus Production through Proteolytic Cleavage of Eukaryotic Initiation Factor 4 Gamma 3 |
Contact patterns strongly influence the dynamics of disease transmission in both human and non-human animal populations . Domestic dogs Canis familiaris are a social species and are a reservoir for several zoonotic infections , yet few studies have empirically determined contact patterns within dog populations . Using ... | For communicable infections , variations in contact rates determine the flow of disease through populations . Therefore , describing contact patterns within populations could help to better predict and prevent disease outbreaks . Free-ranging domestic dogs are susceptible to a number of zoonotic infections yet few stud... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"animal",
"types",
"medicine",
"and",
"health",
"sciences",
"infectious",
"disease",
"epidemiology",
"binomials",
"domestic",
"animals",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"dogs",
"animals",
"mammals",
"rabies",
"mathematics",
"algebra",
... | 2019 | High-resolution contact networks of free-ranging domestic dogs Canis familiaris and implications for transmission of infection |
Antiretroviral therapy ( ART ) can reduce HIV levels in plasma to undetectable levels , but rather little is known about the effects of ART outside of the peripheral blood regarding persistent virus production in tissue reservoirs . Understanding the dynamics of ART-induced reductions in viral RNA ( vRNA ) levels throu... | Antiretroviral therapy ( ART ) improves the quality of life for HIV infected individuals . However , ART is currently a lifelong commitment because HIV persists during treatment despite being suppressed below detection . If therapy is stopped , the HIV reappears . A concerted effort is ongoing to develop new eradicatio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"preclinical",
"models",
"hiv",
"diagnosis",
"and",
"management",
"clinical",
"research",
"design",
"immunity",
"hiv",
"drugs",
"and",
"devices",
"hiv",
"clinical",
"manifestations",
"immunology",
"drug",
"distribution",
"biology",
... | 2014 | Targeted Cytotoxic Therapy Kills Persisting HIV Infected Cells During ART |
Stigma plays in an important role in the lives of persons affected by neglected tropical diseases , and assessment of stigma is important to document this . The aim of this study is to test the cross-cultural validity of the Community Stigma Scale ( EMIC-CSS ) and the Social Distance Scale ( SDS ) in the field of lepro... | Persons affected by neglected tropical diseases , such as , Buruli ulcer , lymphatic filariasis , onchocerciasis , leishmaniasis and leprosy , can experience stigma . One important source of stigma are members in the community . Neighbours , religious leaders , and community leaders can exclude , reject , blame or deva... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"epidemiological",
"statistics",
"public",
"and",
"occupational",
"health",
"bacterial",
"diseases",
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"disabilities",
"epidemiology",
"leprosy",
"neglected",
"tropical",
"diseases",
"tropical",
"diseases",
... | 2014 | The Cultural Validation of Two Scales to Assess Social Stigma in Leprosy |
The intricate interactions between viruses and hosts include exploitation of host cells for viral replication by using many cellular resources , metabolites and energy . Tomato bushy stunt virus ( TBSV ) , similar to other ( + ) RNA viruses , induces major changes in infected cells that lead to the formation of large r... | Positive-strand ( + ) RNA viruses build replication organelles with the help of many co-opted cellular factors and by usurping cellular metabolites and energy , which frequently lead to disease states in plants , animals and humans . The authors discovered that tomato bushy stunt virus ( TBSV ) co-opts the glycolytic A... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"plant",
"anatomy",
"protein",
"interactions",
"molecular",
"probe",
"techniques",
"microbiology",
"fluorophotometry",
"northern",
"blot",
"fungi",
"plant",
"science",
"model",
"organisms",
"experimental",
"organism",
"systems",
"molecular",
"biology",
"techniques",
"gel"... | 2017 | Co-opting ATP-generating glycolytic enzyme PGK1 phosphoglycerate kinase facilitates the assembly of viral replicase complexes |
High throughput mRNA expression profiling can be used to characterize the response of cell culture models to perturbations such as pharmacologic modulators and genetic perturbations . As profiling campaigns expand in scope , it is important to homogenize , summarize , and analyze the resulting data in a manner that cap... | The effects of small molecules or biologics can be measured via their effect on cells’ gene expression profiles . Such experiments have been performed with small , focused sample sets for decades . Technological advances now permit this approach to be used on the scale of tens of thousands of samples per year . As data... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods",
"Availability",
"of",
"supporting",
"materials"
] | [
"chemical",
"compounds",
"neural",
"networks",
"neuroscience",
"optimization",
"mathematics",
"mapk",
"signaling",
"cascades",
"discrete",
"mathematics",
"combinatorics",
"computer",
"and",
"information",
"sciences",
"cluster",
"compounds",
"gene",
"expression",
"chemistry"... | 2017 | Representing high throughput expression profiles via perturbation barcodes reveals compound targets |
Guided migrations of cells and developing axons along the dorso-ventral ( D/V ) and antero-posterior ( A/P ) body axes govern tissue patterning and neuronal connections . In C . elegans , as in vertebrates , D/V and A/P graded distributions of UNC-6/Netrin and Wnts , respectively , provide instructive polarity informat... | While ample information was gathered in past decades on identifying guidance cues and their downstream mediators , very little is known about how the information from multiple extracellular cues is integrated within the cell to generate normal patterning . Netrin and Wnt signaling pathways are both critical to multiple... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"cell",
"motility",
"caenorhabditis",
"neuroscience",
"animals",
"gene",
"function",
"animal",
"models",
"developmental",
"biology",
"mutation",
"caenorhabditis",
"elegans",
"model",
"organisms",
"organism",
"development",
"molecular",
"development",
"molec... | 2014 | Netrins and Wnts Function Redundantly to Regulate Antero-Posterior and Dorso-Ventral Guidance in C. elegans |
The site frequency spectrum ( SFS ) has long been used to study demographic history and natural selection . Here , we extend this summary by examining the SFS conditional on the alleles found at the same site in other species . We refer to this extension as the “phylogenetically-conditioned SFS” or cSFS . Using recent ... | The site frequency spectrum ( SFS , i . e . , the distribution of allele frequencies ) is a summary of natural variation , used to study demographic history and natural selection . Here , we extended the SFS by conditioning on phylogenetic divergence patterns . We refer to this extension as the “phylogenetically-condit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"demography",
"computational",
"biology",
"vertebrates",
"animals",
"mammals",
"primates",
"substitution",
"mutation",
"mutation",
"genome",
"analysis",
"mammalian",
"genomics",
"epigenetics",
"dna",
"chromatin",
"dna",
"methylation",
"research",
"and",
"analysis",
"metho... | 2016 | Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans |
Currently , there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature . According to a previous evaluation of 441 biomedical journals articles published in 2000–2014 , the biomedical literature largely lacked transparency in important dimensions . Here , we surv... | Currently , there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature . According to a previous evaluation of 441 biomedical articles published from 2000–2014 , the majority of studies did not share protocols and raw data or disclose funding or potential conflic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"open",
"science",
"open",
"access",
"publishing",
"research",
"funding",
"publication",
"practices",
"replication",
"studies",
"research",
"design",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"meta-research",
"article",
"bioinformatics",
"governmen... | 2018 | Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017 |
The X chromosome ( chrX ) represents one potential source for the “missing heritability” for complex phenotypes , which thus far has remained underanalyzed in genome-wide association studies ( GWAS ) . Here we demonstrate the benefits of including chrX in GWAS by assessing the contribution of 404 , 862 chrX SNPs to lev... | The X chromosome ( chrX ) analyses have often been neglected in large-scale genome-wide association studies . Given that chrX contains a considerable proportion of DNA , we wanted to examine how the variation in the chromosome contributes to commonly studied phenotypes . To this end , we studied the associations of ove... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"x",
"chromosome",
"inactivation",
"genetics",
"epigenetics",
"biology"
] | 2014 | Chromosome X-Wide Association Study Identifies Loci for Fasting Insulin and Height and Evidence for Incomplete Dosage Compensation |
Apicomplexan parasites are global killers , being the causative agents of diseases like toxoplasmosis and malaria . These parasites are known to be hypersensitive to redox imbalance , yet little is understood about the cellular roles of their various redox regulators . The apicoplast , an essential plastid organelle , ... | To survive , apicomplexan parasites must adjust to the redox insults they experience . These parasites undergo redox stresses induced by the host cell within which they live , by the host immune system , and by their own metabolic activities . Yet the myriad of cellular processes that are affected by redox changes and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"taxonomy",
"plastids",
"parasite",
"groups",
"plant",
"cell",
"biology",
"light",
"microscopy",
"parasitology",
"apicomplexa",
"plant",
"science",
"phylogenetics",
"data",
"management",
"microscopy",
"sequence",
"motif",
"analysis",
"research",
"and",
"analysis",
"meth... | 2018 | Two essential Thioredoxins mediate apicoplast biogenesis, protein import, and gene expression in Toxoplasma gondii |
Mechanisms underlying the dramatic patterns of genome size variation across the tree of life remain mysterious . Effective population size ( Ne ) has been proposed as a major driver of genome size: selection is expected to efficiently weed out deleterious mutations increasing genome size in lineages with large ( but no... | Genome size ( the amount of nuclear DNA ) varies tremendously across organisms but is not necessarily correlated with organismal complexity . For example , genome sizes just within the grasses vary nearly 20-fold , but large-genomed grass species are not obviously more complex in terms of morphology or physiology than ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology",
"genetics",
"and",
"genomics/population",
"genetics",
"genetics",
"and",
"genomics",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics"
] | 2010 | Did Genetic Drift Drive Increases in Genome Complexity? |
Two small quorum sensing ( QS ) peptides regulate competence in S . mutans in a cell density dependent manner: XIP ( sigX inducing peptide ) and CSP ( competence stimulating peptide ) . Depending on the environmental conditions isogenic S . mutans cells can split into a competent and non-competent subpopulation . The o... | Streptococcus mutans is a bacterium of the human dental plaque that contributes to caries development . It controls two important survival mechanisms via a cell-density dependent communication system ( quorum sensing ) : The synthesis of peptide antibiotics , and of a membrane apparatus for genetic competence , i . e .... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | The Alternative Sigma Factor SigX Controls Bacteriocin Synthesis and Competence, the Two Quorum Sensing Regulated Traits in Streptococcus mutans |
Access to laboratory diagnosis can be a challenge for individuals suspected of Buruli Ulcer ( BU ) . Our objective was to develop a clinical score to assist clinicians working in resource-limited settings for BU diagnosis . Between 2011 and 2013 , individuals presenting at Akonolinga District Hospital , Cameroon , were... | In most Buruli ulcer ( BU ) endemic areas , laboratory diagnosis is hard to access and comes at a high cost . Clinicians are in need of new tools to assist them in identifying which patients truly require additional work-up and which can be treated directly . We analyzed the clinical data of all patients with ulcerativ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"smell",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"neuroscience",
"bacterial",
"diseases",
"research",
"design",
"mathematics",
"signs",
"and",
"symp... | 2016 | The “Buruli Score”: Development of a Multivariable Prediction Model for Diagnosis of Mycobacterium ulcerans Infection in Individuals with Ulcerative Skin Lesions, Akonolinga, Cameroon |
The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage . As an alternative to costly phenotypic assays , computational methods aim at predicting virus tropism based on the sequence and structure of the V3 ... | Human Immunodeficiency Virus ( HIV ) requires one of the chemokine coreceptors CCR5 or CXCR4 for entry into the host cell . The capacity of the virus to use one or both of these coreceptors is termed tropism . Monitoring HIV tropism is of high importance due to the relationship of the emergence of CXCR4-tropic virus wi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"sequence",
"analysis",
"protein",
"structure",
"biology",
"computational",
"biology",
"macromolecular",
"structure",
"analysis"
] | 2013 | Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage |
Influenza viruses elude immune responses and antiviral chemotherapeutics through genetic drift and reassortment . As a result , the development of new strategies that attack a highly conserved viral function to prevent and/or treat influenza infection is being pursued . Such novel broadly acting antiviral therapies wou... | Influenza viruses constantly challenge our ability to prevent and treat their resulting infection . From a survivor of the H5N1 influenza we have discovered an antibody that is effective against both H5N1 and seasonal H1N1 influenza viruses . Here we show the antibody is effective against 2009 pandemic influenza in a c... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"immunology/antigen",
"processing",
"and",
"recognition",
"infectious",
"diseases",
"immunology/immune",
"response",
"infectious",
"diseases/viral",
"infections",
"infectious",
"diseases/respiratory",
"infections",
"immunology/immunity",
"to",
"infections",
"bioc... | 2010 | Protection from the 2009 H1N1 Pandemic Influenza by an Antibody from Combinatorial Survivor-Based Libraries |
Bacterial biodiversity at the species level , in terms of gene acquisition or loss , is so immense that it raises the question of how essential chromosomal regions are spared from uncontrolled rearrangements . Protection of the genome likely depends on specific DNA motifs that impose limits on the regions that undergo ... | Availability of bacterial “pan genomes , ” based on multiple genome sequences of a given species , has revealed the existence of core genomes , but also of high levels of variable , nonconserved regions . The nature of bacterial strategies that assure genome organization while permitting biodiversity remains an intrigu... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"microbiology",
"computational",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics",
"eubacteria"
] | 2007 | Identification of DNA Motifs Implicated in Maintenance of Bacterial Core Genomes by Predictive Modeling |
Dengue is endemic in the Western Pacific and Oceania and the region reports more than 200 , 000 cases annually . Outbreaks of dengue and severe dengue occur regularly and movement of virus throughout the region has been reported . Disease surveillance systems , however , in many areas are not fully established and deng... | Dengue virus ( DENV ) was first identified in Papua New Guinea ( PNG ) in 1944 . Dengue is currently assumed to be an endemic disease in PNG although there is little incidence or prevalence data , and the evidence consensus for dengue presence is low . Routine surveillance is not undertaken and dengue is not a notifiab... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"reverse",
"transcriptase-polymerase",
"chain",
"reaction",
"geomorphology",
"taxonomy",
"dengue",
"virus",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"landforms",
"engineering",
"and",
"technology",
"pathogens",
"topography",
"... | 2018 | Hyperendemic dengue transmission and identification of a locally evolved DENV-3 lineage, Papua New Guinea 2007-2010 |
Symbionts can have mutualistic effects that increase their host’s fitness and/or parasitic effects that reduce it . Which of these strategies evolves depends in part on the balance of their costs and benefits to the symbiont . We have examined these questions in Wolbachia , a vertically transmitted endosymbiont of inse... | Arthropods are commonly infected with heritable bacteria , and some of these symbionts can protect their hosts against infection and/or be reproductive parasites . Which of these traits evolves will depend on whether the trait is costly to the symbiont and the host . Using a panel of strains of the symbiont Wolbachia i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Should Symbionts Be Nice or Selfish? Antiviral Effects of Wolbachia Are Costly but Reproductive Parasitism Is Not |
Fatty-acid metabolism plays a key role in acquired and inborn metabolic diseases . To obtain insight into the network dynamics of fatty-acid β-oxidation , we constructed a detailed computational model of the pathway and subjected it to a fat overload condition . The model contains reversible and saturable enzyme-kineti... | Lipid metabolism plays an important role in the development of metabolic syndrome , a major risk factor for cardiovascular disease and diabetes . Furthermore , inborn errors in lipid oxidation cause rare , but severe diseases in children . To obtain more insight into the response of lipid oxidation to dietary and medic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biochemistry",
"enzymes",
"metabolic",
"networks",
"biology",
"computational",
"biology"
] | 2013 | Biochemical Competition Makes Fatty-Acid β-Oxidation Vulnerable to Substrate Overload |
Rhesus macaques are unusual among schistosome hosts , self-curing from an established infection and thereafter manifesting solid immunity against a challenge , an ideal model for vaccine development . Previously , the immunological basis of self-cure was confirmed; surviving worms had ceased feeding but how immunologic... | Rhesus macaques can self-cure from a schistosome infection . Antibody is crucial to drive this process and adult worm elimination is preceded by cessation of blood feeding . Recently we have shown that the schistosome esophagus plays a central role in blood processing . We first confirm the self-cure process in rhesus ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Evidence That Rhesus Macaques Self-Cure from a Schistosoma japonicum Infection by Disrupting Worm Esophageal Function: A New Route to an Effective Vaccine? |
Exhausted T cells express multiple co-inhibitory molecules that impair their function and limit immunity to chronic viral infection . Defining novel markers of exhaustion is important both for identifying and potentially reversing T cell exhaustion . Herein , we show that the ectonucleotidse CD39 is a marker of exhaust... | Chronic viral infection induces an acquired state of T cell dysfunction known as exhaustion . Discovering surface markers of exhausted T cells is important for both to identify exhausted T cells as well as to develop potential therapies . We report that the ectonucleotidase CD39 is expressed by T cells specific for chr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | CD39 Expression Identifies Terminally Exhausted CD8+ T Cells |
A central issue of myogenesis is the acquisition of identity by individual muscles . In Drosophila , at the time muscle progenitors are singled out , they already express unique combinations of muscle identity genes . This muscle code results from the integration of positional and temporal signalling inputs . Here we i... | In Drosophila , as in vertebrates , the muscular system consists of different types of muscles that must act in coordination with the nervous system to control the adequate release of contraction power required for the proper functioning of the organism . Therefore , the acquisition of specific identities by individual... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"model",
"organisms",
"genetics",
"biology",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2011 | Drosophila Araucan and Caupolican Integrate Intrinsic and Signalling Inputs for the Acquisition by Muscle Progenitors of the Lateral Transverse Fate |
RNA modification plays an important role in modulating host-pathogen interaction . Flavivirus NS5 protein encodes N-7 and 2′-O methyltransferase activities that are required for the formation of 5′ type I cap ( m7GpppAm ) of viral RNA genome . Here we reported , for the first time , that flavivirus NS5 has a novel inte... | We report that flavivirus NS5 has a novel internal RNA methylation activity . Recombinant proteins of NS5 and its N-terminal methyltransferase domain of West Nile virus and Dengue virus ( DENV ) specifically methylates polyA , but not polyG , polyC , or polyU . RNAs with internal adenosines substituted with 2′-O-methyl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"biology",
"microbiology",
"molecular",
"cell",
"biology"
] | 2012 | 2′-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase |
Peptidoglycan hydrolases are a double-edged sword . They are required for normal cell division , but when dysregulated can become autolysins lethal to bacteria . How bacteria ensure that peptidoglycan hydrolases function only in the correct spatial and temporal context remains largely unknown . Here , we demonstrate th... | Peptidoglycan ( PG ) is a major component of the bacterial cell wall , which forms a flexible , but strong mesh around the cell to oppose osmotic pressure and prevent lysis . PG is also dynamically modified , continually being disassembled and polymerized as the cell elongates and divides . It remains poorly understood... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"microbial",
"physiology",
"biology",
"microbiology",
"microbial",
"growth",
"and",
"development",
"bacterial",
"pathogens"
] | 2013 | Protein Complexes and Proteolytic Activation of the Cell Wall Hydrolase RipA Regulate Septal Resolution in Mycobacteria |
Despite worldwide mass drug administration , it is estimated that 68 million individuals are still infected with lymphatic filariasis with 19 million hydrocele and 17 million lymphedema reported cases . Despite the staggering number of pathology cases , the majority of LF-infected individuals do not develop clinical sy... | Regulation of the host`s immune system by filarial nematodes is crucial for the fertility and survival of the nematode . Indeed , the majority of W . bancrofti-infected individuals are characterized by a regulated state including increased regulatory T cells ( Treg ) , IL-10 , TGF-β and filarial-specific IgG4 and suppr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"parasitic",
"diseases",
"animals",
"signs",
"and",
"symptoms",
"edema",
"white",
"blood",
"c... | 2019 | Wuchereria bancrofti-infected individuals harbor distinct IL-10-producing regulatory B and T cell subsets which are affected by anti-filarial treatment |
Pleiotropy has been suggested as a novel mechanism for stabilising cooperation in bacteria and other microbes . The hypothesis is that linking cooperation with a trait that provides a personal ( private ) benefit can outweigh the cost of cooperation in situations when cooperation would not be favoured by mechanisms suc... | Recent research into microbial communities has revealed that the cooperative secretion of molecules—which are produced by individual cells and benefit neighbouring cells—is linked to the production of privately beneficial intracellular enzymes . This pleiotropic link between commonly and privately beneficial traits has... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"organismal",
"evolution",
"gene",
"regulation",
"microbiology",
"developmental",
"biology",
"regulator",
"genes",
"microbial",
"evolution",
"gene",
"types",
"population",
"biology",
"fecundity",
"kin",
"selection",
"gene",
"expression",
"life",
"cycles",
"evolutionary",
... | 2018 | Pleiotropy, cooperation, and the social evolution of genetic architecture |
Loss-of-function mutations in PINK1 or PARKIN are the most common causes of autosomal recessive Parkinson's disease . Both gene products , the Ser/Thr kinase PINK1 and the E3 Ubiquitin ligase Parkin , functionally cooperate in a mitochondrial quality control pathway . Upon stress , PINK1 activates Parkin and enables it... | Parkinson's disease ( PD ) is a devastating neurological condition caused by the selective and progressive degeneration of dopaminergic neurons in the brain . Loss-of-function mutations in the PINK1 or PARKIN genes are the most common causes of recessively inherited PD . Together the encoded proteins coordinate a prote... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"movement",
"disorders",
"biochemistry",
"molecular",
"neuroscience",
"computer",
"and",
"information",
"sciences",
"cellular",
"neuroscience",
"medicine",
"and",
"health",
"sciences",
"computer",
"modeling",
"cell",
"biology",
"neurology",
"neurodegenerative",
"diseases",
... | 2014 | Phosphorylation by PINK1 Releases the UBL Domain and Initializes the Conformational Opening of the E3 Ubiquitin Ligase Parkin |
The series of events that occurs immediately after pathogen entrance into the body is largely speculative . Key aspects of these events are pathogen dissemination and pathogen interactions with the immune response as the invader moves into deeper tissues . We sought to define major events that occur early during infect... | The earliest stage of any infection takes place when a pathogen enters the body ( inoculation ) at an initial site of contact . From this point , the pathogen can spread into deeper tissues where the pathogen itself and the immune responses against it cause disease . Very little is known about the events that follow in... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Dissemination of a Highly Virulent Pathogen: Tracking The Early Events That Define Infection |
In metabolism research , thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway . However , the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the ... | Given data about enzyme kinetics and reaction thermodynamics , traditional metabolic control analysis ( MCA ) can pinpoint the enzymes whose expression will have the largest effect on steady-state flux through the pathway . These analyses can aid experimentalists in tuning enzyme expression levels along a metabolic pat... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"systems",
"biology",
"biochemistry",
"enzymes",
"metabolic",
"pathways",
"biology",
"enzyme",
"kinetics",
"metabolism",
"computational",
"biology"
] | 2014 | Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism |
Self-incompatibility ( SI ) is the flowering plant reproductive system in which self pollen tube growth is inhibited , thereby preventing self-fertilization . SI has evolved independently in several different flowering plant lineages . In all Brassicaceae species in which the molecular basis of SI has been investigated... | Self-incompatibility ( SI ) is a pollen recognition system that enables plants to avoid the inbreeding caused by self-pollination . It involves a pair of tightly linked genes known as the S locus . The product of one of these genes acts as the receptor and recognizes the pollen protein produced by the same plant , whil... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"evolution",
"gene",
"function",
"genome",
"sequencing",
"plant",
"science",
"plant",
"genomics",
"plants",
"flowering",
"plants",
"plant",
"genetics",
"comparative",
"genomics",
"biology",
"evolutionary",
"genetics",
"flowers",
"angiosperms",
"plant",
"evolut... | 2013 | Secondary Evolution of a Self-Incompatibility Locus in the Brassicaceae Genus Leavenworthia |
Tumor necrosis factor ( TNF ) is critical for controlling many intracellular infections , but can also contribute to inflammation . It can promote the destruction of important cell populations and trigger dramatic tissue remodeling following establishment of chronic disease . Therefore , a better understanding of TNF r... | Many parasitic diseases are associated with the generation of potent inflammatory responses . These are often needed to control infection , but can also cause tissue damage if not appropriately regulated . IL-10 has emerged as an important immune regulator that protects tissues by dampening inflammation . Recently , so... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2016 | Blimp-1-Dependent IL-10 Production by Tr1 Cells Regulates TNF-Mediated Tissue Pathology |
Control of axial polarity during regeneration is a crucial open question . We developed a quantitative model of regenerating planaria , which elucidates self-assembly mechanisms of morphogen gradients required for robust body-plan control . The computational model has been developed to predict the fraction of heteromor... | Understanding how large-scale anatomy emerges from the activity of cellular pathways is a key goal of evolutionary developmental biology . Elucidating the rules of body-wide morphogenesis is especially essential for transitioning molecular signaling data at the cellular level into advances in regenerative biomedicine .... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"rna",
"interference",
"cell",
"processes",
"animals",
"nerve",
"regeneration",
"head",
"regeneration",
"developmental",
"biology",
"organism",
"development",
"network",
"analysis",
"molecular",
"development",
"epigenetics",
"morphogenesis",
"tail",
"regene... | 2019 | Neural control of body-plan axis in regenerating planaria |
Graph theory has evolved into a useful tool for studying complex brain networks inferred from a variety of measures of neural activity , including fMRI , DTI , MEG and EEG . In the study of neurological disorders , recent work has discovered differences in the structure of graphs inferred from patient and control cohor... | In this paper we show that within modular networks ( that is , networks with multiple scales of connections ) , two distinct mechanisms may drive the emergence of synchrony at the global level . We term the first of these mechanisms “network-driven synchrony” , which is characterized by the presence of cycles within th... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"epilepsy",
"computer",
"and",
"information",
"sciences",
"medicine",
"and",
"health",
"sciences",
"computer",
"modeling",
"systems",
"science",
"network",
"analysis",
"neurology",
"epileptic",
"seizures"
] | 2014 | Dynamics on Networks: The Role of Local Dynamics and Global Networks on the Emergence of Hypersynchronous Neural Activity |
Computer science has become ubiquitous in many areas of biological research , yet most high school and even college students are unaware of this . As a result , many college biology majors graduate without adequate computational skills for contemporary fields of biology . The absence of a computational element in secon... | We have designed and implemented a curriculum to teach basic computational biology to advanced high school students . The curriculum includes an introduction to the concept of algorithms , an overview of the Basic Local Alignment Search Tool ( BLAST ) algorithm used to compare DNA sequences , and methods for building p... | [
"Abstract",
"Introduction",
"Methods",
"Results/Discussion",
"Conclusions"
] | [
"education",
"biology",
"computational",
"biology"
] | 2011 | A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms |
Telomere length ( TL ) predicts health and survival across taxa . Variation in TL between individuals is thought to be largely of genetic origin , but telomere inheritance is unusual , because zygotes already express a TL phenotype , the TL of the parental gametes . Offspring TL changes with paternal age in many specie... | Telomeres are DNA-protein structures at chromosome ends and a short telomere length predicts reduced survival in humans , birds and other organisms . Variation in telomere length between individuals is thought to be largely of genetic origin , but telomere inheritance may be unusual because not only genes regulating te... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"animal",
"genetics",
"chromosome",
"structure",
"and",
"function",
"population",
"genetics",
"reproductive",
"physiology",
"germ",
"cells",
"telomeres",
"clutches",
"epigenetics",
"population",
"biology",
"bird",
"genetics",
"sp... | 2019 | Epigenetic inheritance of telomere length in wild birds |
Entomological surveys of Simulium vectors are an important component in the criteria used to determine if Onchocerca volvulus transmission has been interrupted and if focal elimination of the parasite has been achieved . However , because infection in the vector population is quite rare in areas where control has succe... | The absence of infective larvae of Onchocerca volvulus in the black fly vector of this parasite is a major criterion used to certify that transmission has been eliminated in a focus . This process requires screening large numbers of flies . Currently , this is accomplished by screening pools of flies using a PCR-based ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"neglected",
"tropical",
"diseases",
"onchocerciasis"
] | 2012 | Oligonucleotide Based Magnetic Bead Capture of Onchocerca volvulus DNA for PCR Pool Screening of Vector Black Flies |
The near exclusive use of praziquantel ( PZQ ) for treatment of human schistosomiasis has raised concerns about the possible emergence of drug-resistant schistosomes . We measured susceptibility to PZQ of isolates of Schistosoma mansoni obtained from patients from Kisumu , Kenya continuously exposed to infection as a c... | The emergence of drug resistant pathogens is a great challenge to the control of infectious diseases . Schistosomiasis is one of the world's greatest neglected tropical diseases , and it is primarily controlled with the drug praziquantel . This drug is often used by repeatedly treating patients to maintain reduced worm... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"evolutionary",
"biology",
"infectious",
"diseases/helminth",
"infections",
"infectious",
"diseases/antimicrobials",
"and",
"drug",
"resistance"
] | 2009 | Reduced Susceptibility to Praziquantel among Naturally Occurring Kenyan Isolates of Schistosoma mansoni |
Break-induced replication ( BIR ) has been implicated in restoring eroded telomeres and collapsed replication forks via single-ended invasion and extensive DNA synthesis on the recipient chromosome . Unlike other recombination subtypes , DNA synthesis in BIR likely relies heavily on mechanisms enabling efficient fork p... | Chromatin poses a barrier to the recombination process . Chromatin modification is therefore a prerequisite factor for the efficient execution of the recombination event . Chromatin remodeling and several unique histone modifications at or near DNA double strand breaks ( DSBs ) facilitate early recombination processes ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Hyper-Acetylation of Histone H3K56 Limits Break-Induced Replication by Inhibiting Extensive Repair Synthesis |
Several regulators are involved in the control of cell cycle progression in the bacterial model system Caulobacter crescentus , which divides asymmetrically into a vegetative G1-phase ( swarmer ) cell and a replicative S-phase ( stalked ) cell . Here we report a novel functional interaction between the enigmatic cell c... | Methylation of genomic DNA at a specific regulatory site can impact a myriad of processes in eukaryotic cells . In bacteria , methylation at the N6 position of adenosine ( m6A ) is known to mediate a non-adaptive immunity response to protect cells from foreign DNA . While m6A marks are not known to govern expression of... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"prokaryotic",
"models",
"model",
"organisms",
"caulobacter",
"crescentus",
"gene",
"expression",
"genetics",
"epigenetics",
"biology",
"dna",
"modification",
"microbiology",
"gene",
"networks",
"dna",
"transcription"
] | 2013 | DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria |
Netherton syndrome ( NS ) is a severe skin disease caused by the loss of protease inhibitor LEKTI , which leads to the dysregulation of epidermal proteases and severe skin-barrier defects . KLK5 was proposed as a major protease in NS pathology , however its inactivation is not sufficient to rescue the lethal phenotype ... | Netherton syndrome ( NS ) is a genetic skin disorder caused by the loss of protease inhibitor LEKTI , which leads to the dysregulation of epidermal proteases and severe skin-barrier defects . In this work , we aimed to explore the molecular mechanisms underlying this disease using a novel mutant mouse model for NS , wh... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"skin",
"medicine",
"and",
"health",
"sciences",
"integumentary",
"system",
"pathology",
"and",
"laboratory",
"medicine",
"enzymes",
"immunology",
"enzymology",
"animal",
"models",
"developmental",
"biology",
"model",
"organisms",
"signs",
"and",
"symptoms",
"experiment... | 2017 | KLK5 and KLK7 Ablation Fully Rescues Lethality of Netherton Syndrome-Like Phenotype |
Differentiation of CD4+ T cells into effector or regulatory phenotypes is tightly controlled by the cytokine milieu , complex intracellular signaling networks and numerous transcriptional regulators . We combined experimental approaches and computational modeling to investigate the mechanisms controlling differentiatio... | CD4+ T cells can differentiate into different phenotypes depending on the cytokine milieu . Due to the complexity of this process , we have constructed a computational and mathematical model with sixty ordinary differential equations representing a CD4+ T cell differentiating into either Th1 , Th2 , Th17 or iTreg cells... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"computer",
"science",
"adaptive",
"immunity",
"computer",
"modeling",
"immune",
"cells",
"immunity",
"gastroenterology",
"and",
"hepatology",
"t",
"cells",
"inflammatory",
"bowel",
"disease",
"immunology",
"biology",
"immunoregulation",
"immunomodulation"
] | 2013 | Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity |
In the short-germ beetle Tribolium castaneum , waves of pair-rule gene expression propagate from the posterior end of the embryo towards the anterior and eventually freeze into stable stripes , partitioning the anterior-posterior axis into segments . Similar waves in vertebrates are assumed to arise due to the modulati... | One of the most popular problems in development is how the anterior-posterior axis of vertebrates , arthropods and annelids is partitioned into segments . In vertebrates , and recently shown in the beetle Tribolium castaneum , segments are demarcated by means of gene expression waves that propagate from posterior to an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"genetic",
"oscillators",
"animal",
"genetics",
"invertebrate",
"genetics",
"gene",
"regulatory",
"networks",
"genetics",
"biology",
"and",
"life",
"sciences",
"gene",
"disruption",
"molecular",
"genetics",
"computational",
"biology",
"evolutio... | 2014 | Caudal Regulates the Spatiotemporal Dynamics of Pair-Rule Waves in Tribolium |
Many human diseases , arising from mutations of disease susceptibility genes ( genetic diseases ) , are also associated with viral infections ( virally implicated diseases ) , either in a directly causal manner or by indirect associations . Here we examine whether viral perturbations of host interactome may underlie su... | Many “virally implicated human diseases” - diseases for which there is scientific consensus of viral involvement - are associated with genetic alterations in particular disease susceptibility genes . We proposed and demonstrated that for two human viruses , Epstein-Barr virus and human papillomavirus , topological prox... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"microarrays",
"systems",
"biology",
"biology",
"computational",
"biology",
"metabolic",
"networks",
"genetics",
"and",
"genomics"
] | 2012 | Viral Perturbations of Host Networks Reflect Disease Etiology |
Candida parapsilosis and Candida albicans are human fungal pathogens that belong to the CTG clade in the Saccharomycotina . In contrast to C . albicans , relatively little is known about the virulence properties of C . parapsilosis , a pathogen particularly associated with infections of premature neonates . We describe... | Candida species are among the most common causes of fungal infection worldwide . Infections can be both community-based and hospital-acquired , and are particularly associated with immunocompromised individuals . Candida albicans is the most commonly isolated species and is the best studied . However , other species ar... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"molecular",
"biology",
"biology",
"and",
"life",
"sciences",
"mycology"
] | 2014 | Comparative Phenotypic Analysis of the Major Fungal Pathogens Candida parapsilosis and Candida albicans |
Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation . In order to detect genetic variations affecting gene expression , we performed association analysis of single nucleotide polymorphisms ( SNPs ) and copy number variants ( CNVs ) with... | Humans differ in their genetic sequences at millions of positions but only a subset of these differences have a functional effect . In order to detect functional genetic differences , we assessed the impact of common genetic variants on gene expression in 869 individuals and discovered that the expression of many genes... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"genomics",
"functional",
"genomics",
"gene",
"regulatory",
"networks",
"genome",
"analysis",
"gene",
"expression",
"genetics",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"human",
"genetics"
] | 2014 | Cis and Trans Effects of Human Genomic Variants on Gene Expression |
Fatal human respiratory disease associated with the 1918 pandemic influenza virus and potentially pandemic H5N1 viruses is characterized by severe lung pathology , including pulmonary edema and extensive inflammatory infiltrate . Here , we quantified the cellular immune response to infection in the mouse lung by flow c... | Patients who succumbed to influenza during the 1918 pandemic had severe lung pathology marked by extensive inflammatory infiltrate , indicating a robust immune response in the lung . Similar findings have been reported from H5N1-infected patients , raising the question as to why people expire in the presence of a stron... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/animal",
"models",
"of",
"infection",
"virology"
] | 2008 | H5N1 and 1918 Pandemic Influenza Virus Infection Results in Early and Excessive Infiltration of Macrophages and Neutrophils in the Lungs of Mice |
Enterococcus faecium has become a nosocomial pathogen of major importance , causing infections that are difficult to treat owing to its multi-drug resistance . In particular , resistance to the β-lactam antibiotic ampicillin has become ubiquitous among clinical isolates . Mutations in the low-affinity penicillin bindin... | Enterococcus faecium has emerged as an important nosocomial pathogen around the world . Clinical E . faecium isolates are often resistant to multiple antibiotics , thereby complicating therapeutic interventions . However , the molecular mechanisms that contribute to the recent emergence of E . faecium as a nosocomial p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"functional",
"genomics",
"genetic",
"mutation",
"microbiology",
"gene",
"function",
"bacterial",
"diseases",
"genome",
"analysis",
"tools",
"enterococcus",
"infection",
"bacterial",
"pathogens",
"infectious",
"diseases",
"microbial",
"pathogens",
"biology",
"... | 2012 | Genome-Wide Identification of Ampicillin Resistance Determinants in Enterococcus faecium |
Health institutions may choose to screen newly admitted patients for the presence of disease in order to reduce disease prevalence within the institution . Screening is costly , and institutions must judiciously choose which patients they wish to screen based on the dynamics of disease transmission . Since potentially ... | Healthcare associated infections are a major cause of morbidity and mortality . Screening patients on admission to the hospital may reduce prevalence by identifying infected individuals; infected individuals can then be treated or isolated to prevent further spread . Because screening is costly , institutions must weig... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"social",
"and",
"behavioral",
"sciences",
"health",
"economics",
"infectious",
"disease",
"epidemiology",
"epidemiology",
"epidemiological",
"methods",
"economics"
] | 2014 | Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting |
In response to DNA damage during S phase , cells slow DNA replication . This slowing is orchestrated by the intra-S checkpoint and involves inhibition of origin firing and reduction of replication fork speed . Slowing of replication allows for tolerance of DNA damage and suppresses genomic instability . Although the me... | Faithful duplication of the genome is essential for genetic stability of organisms and species . To ensure faithful duplication , cells must be able to replicate damaged DNA . To do so , they employ checkpoints that regulate replication in response to DNA damage . However , the mechanisms by which checkpoints regulate ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"flow",
"cytometry",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"enzymology",
"dna-binding",
"proteins",
"organisms",
"dna",
"damage",
"fungi",
"model",
"organisms",
"polymerases",
"dna",
"replication",
"experimental",
"organism",
"systems",
"dna... | 2017 | Replication fork slowing and stalling are distinct, checkpoint-independent consequences of replicating damaged DNA |
Despite recent progress in proteomics most protein complexes are still unknown . Identification of these complexes will help us understand cellular regulatory mechanisms and support development of new drugs . Therefore it is really important to establish detailed information about the composition and the abundance of p... | Most proteins are biologically active only when part of a complex with other proteins of the same or other type . Hence , to unravel biological functions of proteins , it is important to identify the type of complexes they can form . Multiple copies of each protein are present in cells and some of these could be involv... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations |
Presented here is a genome sequence of an individual human . It was produced from ∼32 million random DNA fragments , sequenced by Sanger dideoxy technology and assembled into 4 , 528 scaffolds , comprising 2 , 810 million bases ( Mb ) of contiguous sequence with approximately 7 . 5-fold coverage for any given region . ... | We have generated an independently assembled diploid human genomic DNA sequence from both chromosomes of a single individual ( J . Craig Venter ) . Our approach , based on whole-genome shotgun sequencing and using enhanced genome assembly strategies and software , generated an assembled genome over half of which is rep... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"primates",
"mammals",
"human",
"genetics",
"and",
"genomics"
] | 2007 | The Diploid Genome Sequence of an Individual Human |
The advent of induced pluripotent stem cells ( iPSCs ) revolutionized human genetics by allowing us to generate pluripotent cells from easily accessible somatic tissues . This technology can have immense implications for regenerative medicine , but iPSCs also represent a paradigm shift in the study of complex human phe... | Induced pluripotent stem cells ( iPSCs ) are a new and powerful cell type that provides scientists the ability to model complex human diseases in vitro . These cells can be cryopreserved and later expanded , providing a renewable source of cells from the same individual . iPSCs can be made from a variety of somatic cel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"fibroblasts",
"cytoplasmic",
"staining",
"viruses",
"stem",
"cells",
"dna",
"viruses",
"connective",
"tissue",
"cells",
"epigenetics",
"dna",
"dna",
"m... | 2016 | Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs |
Much of the complexity of biochemical networks comes from the information-processing abilities of allosteric proteins , be they receptors , ion-channels , signalling molecules or transcription factors . An allosteric protein can be uniquely regulated by each combination of input molecules that it binds . This “regulato... | The complexity of biochemical networks challenges our ability to create quantitative and predictive models of cellular responses to extracellular changes . In these networks , the regulation of allosteric receptors and proteins by multiple drugs or endogenous ligands introduces “regulatory complexity” because a large n... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biophysics/macromolecular",
"assemblies",
"and",
"machines",
"biophysics/membrane",
"proteins",
"and",
"energy",
"transduction",
"computational",
"biology/synthetic",
"biology",
"computational",
"biology/transcriptional",
"regulation",
"biophysics/theory",
"and",
"simulation",
"... | 2010 | Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks |
Disassembly of the nuclear lamina is essential in mitosis and apoptosis requiring multiple coordinated enzymatic activities in nucleus and cytoplasm . Activation and coordination of the different activities is poorly understood and moreover complicated as some factors translocate between cytoplasm and nucleus in prepar... | Parvoviruses are small non-enveloped DNA viruses successfully used in gene therapy . Their nuclear replication requires transit of the nuclear envelope . Analyzing the interaction between parvoviruses and the nucleus , we showed that despite their small size , they did not traverse the nuclear pore , but attached direc... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Parvoviruses Cause Nuclear Envelope Breakdown by Activating Key Enzymes of Mitosis |
Personal exome and genome sequencing provides access to loss-of-function and rare deleterious alleles whose interpretation is expected to provide insight into individual disease burden . However , for each allele , accurate interpretation of its effect will depend on both its penetrance and the trait's expressivity . I... | Gene expression is a fundamental cellular process that contributes to phenotypic diversity . Gene expression can vary between alleles of an individual through differences in genomic imprinting or cis-acting regulatory variation . Distinguishing allelic activity is important for informing the abundance of altered mRNA a... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"sequencing",
"techniques",
"genome",
"sequencing",
"genome",
"expression",
"analysis",
"genomics",
"functional",
"genomics",
"genome",
"analysis",
"gene",
"expression",
"transcriptome",
"analysis",
"genetics",
"biology",
"and",
"life",
"sciences",
"molecular",
"biology",... | 2014 | Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues |
Atrial fibrillation ( AF ) is the most frequent form of arrhythmia occurring in the industrialized world . Because of its complex nature , each identified form of AF requires specialized treatment . Thus , an in-depth understanding of the bases of these arrhythmias is essential for therapeutic development . A variety o... | A fundamentally important element in cardiac in silico research is a model for the cardiac cell . It provides a link between measurable characteristics at the subcellular level and biological processes at the whole cell level , thereby allowing the researcher to study mechanisms of cardiac arrhythmias from a molecular ... | [
"Abstract",
"Introduction",
"Discussion",
"Methods"
] | [
"carbachol",
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"neurochemistry",
"acetylcholine",
"drugs",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"fibroblasts",
"connective",
"tissue",
"cells",
"cardiac",
"pacing",
"pharmacology",
"neur... | 2016 | A Mathematical Model of Neonatal Rat Atrial Monolayers with Constitutively Active Acetylcholine-Mediated K+ Current |
The taxonomic distinctiveness of Ascaris lumbricoides and A . suum , two of the world's most significant nematodes , still represents a much-debated scientific issue . Previous studies have described two different scenarios in transmission patterns , explained by two hypotheses: ( 1 ) separated host-specific transmissi... | Ascaris lumbricoides , the world's most common human nematode , and A . suum , the pig roundworm , are two of the most important soil-transmitted helminthes of public health and socio-economic concern . However , previously documented similarities at the morphological and genetic level , coupled with evidence for hybri... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"taxonomy",
"medicine",
"public",
"health",
"and",
"epidemiology",
"population",
"genetics",
"parasitic",
"diseases",
"phylogenetics",
"molecular",
"systematics",
"neglected",
"tropical",
"diseases",
"ascariasis",
"infectious",
"diseases",
"soil-transmitted",
"helminths",
"... | 2013 | Phylogeographical Studies of Ascaris spp. Based on Ribosomal and Mitochondrial DNA Sequences |
Vpx is a small virion-associated adaptor protein encoded by viruses of the HIV-2/SIVsm lineage of primate lentiviruses that enables these viruses to transduce monocyte-derived cells . This probably reflects the ability of Vpx to overcome an as yet uncharacterized block to an early event in the virus life cycle in these... | Monocyte-derived tissue macrophages play crucial roles in infection by primate lentiviruses . Human and simian lentiviruses of the HIV-2 and SIVsm/mac lineages encode a virion-bound virulence factor termed Vpx . Vpx is required to establish infection specifically of monocyte-derived cells , but the underlying molecular... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/virulence",
"factors",
"and",
"mechanisms",
"virology/immunodeficiency",
"viruses",
"infectious",
"diseases/hiv",
"infection",
"and",
"aids",
"biochemistry/macromolecular",
"assemblies",
"and",
"machines",
"chemical",
"biology/protein",
"chemistry",
"and",
"proteomics... | 2008 | Lentiviral Vpx Accessory Factor Targets VprBP/DCAF1 Substrate Adaptor for Cullin 4 E3 Ubiquitin Ligase to Enable Macrophage Infection |
The dynamics of dengue virus ( DENV ) circulation depends on serotype , genotype and lineage replacement and turnover . In São José do Rio Preto , Brazil , we observed that the L6 lineage of DENV-1 ( genotype V ) remained the dominant circulating lineage even after the introduction of the L1 lineage . We investigated v... | Since 2008 L6 is the endemic lineage that has circulated in SJRP . In 2010 , the L1 lineage was first identified in the city . For a period , both lineages co-circulated , and then in 2013 , L1 began to diminish until it was no longer detected in the population . Differences in replicative fitness are usually the main ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"invertebrates",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"immune",
"cells",
"cytokines",
"immunology",
"microbiology",
"animals",
"developmental",
"biology",
"molecular",
"development",
"insect",
"... | 2018 | Viral immunogenicity determines epidemiological fitness in a cohort of DENV-1 infection in Brazil |
During development , animals usually undergo a rapid growth phase followed by a homeostatic stage when growth has ceased . The increase in cell size and number during the growth phase requires a large amount of lipids; while in the static state , excess lipids are usually stored in adipose tissues in preparation for nu... | During development , animals undergo a rapid increase in cell size and number , which requires large amounts of lipids , in the form of phospholipids , for the expansion of cell membranes . Once the growth phase ends , excess lipids are usually stored as body fat , in the form of triacylglycerol ( TAG ) , for use when ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"signaling",
"cell",
"growth",
"molecular",
"development",
"biology",
"molecular",
"cell",
"biology"
] | 2014 | CDP-Diacylglycerol Synthetase Coordinates Cell Growth and Fat Storage through Phosphatidylinositol Metabolism and the Insulin Pathway |
Circadian clocks coordinate time-of-day-specific metabolic and physiological processes to maximize organismal performance and fitness . In addition to light and temperature , which are regarded as strong zeitgebers for circadian clock entrainment , metabolic input has now emerged as an important signal for clock entrai... | Circadian clocks are self-sustained , endogenous pacemakers that enable organisms to anticipate daily environmental changes and resource abundance to perform specific time-of-day activities and achieve optimal survival . Multiple time cues are interpreted by circadian clocks to facilitate synchrony between organisms an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"invertebrates",
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"animals",
"circadian",
"oscillators",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"immunoprecipitation",
"experimental",
"organism",
"sy... | 2019 | O-GlcNAcylation of PERIOD regulates its interaction with CLOCK and timing of circadian transcriptional repression |
Mycobacterium tuberculosis ( Mtb ) and helminth infections elicit antagonistic immune effector functions and are co-endemic in several regions of the world . We therefore hypothesized that helminth infection may influence Mtb-specific T-cell immune responses . We evaluated the cytokine profile of Mtb-specific T cells i... | Mycobacterium tuberculosis ( Mtb ) and helminth infections are co-endemic in several regions of the world and their immune responses may be mutually antagonistic . We therefore hypothesized that helminth infection would impact and potentially shape Mtb-specific T-cell responses and systemic inflammation in patients suf... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"t",
"helper",
"cells",
"invertebrates",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"helminths",
"immunology",
"tropical",
"diseases",
"parasitic",
"diseases",
"anima... | 2017 | Mixed Th1 and Th2 Mycobacterium tuberculosis-specific CD4 T cell responses in patients with active pulmonary tuberculosis from Tanzania |
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