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The HIV-1 envelope protein gp120 is both the target of neutralizing antibodies and a major focus of vaccine efforts; however how it is delivered to B cells to elicit an antibody response is unknown . Here , we show that following local gp120 injection lymph node ( LN ) SIGN-R1+ sinus macrophages located in interfollicu...
The human immune system contains many different cell types , which play specific roles in defending the body from invading pathogens , such as bacteria and viruses . For example , macrophages engulf and digest foreign material , whereas specialized B cells termed plasma cells produce molecules called antibodies that he...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "immunology", "and", "inflammation" ]
2015
The HIV-1 envelope protein gp120 is captured and displayed for B cell recognition by SIGN-R1+ lymph node macrophages
To successfully guide limb movements , the brain takes in sensory information about the limb , internally tracks the state of the limb , and produces appropriate motor commands . It is widely believed that this process uses an internal model , which describes our prior beliefs about how the limb responds to motor comma...
The human brain is widely hypothesized to construct “inner beliefs” about how the world works . It is thought that we need this conception to coordinate our movements and anticipate rapid events that go on around us . A driver , for example , needs to predict how the car should behave in response to every turn of the s...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2015
Internal models for interpreting neural population activity during sensorimotor control
Prior experience accelerates acquisition of novel , related information through processes like assimilation into mental schemas , but the underlying neuronal mechanisms are poorly understood . We investigated the roles that prior experience and hippocampal CA3 N-Methyl-D-aspartate receptor ( NMDAR ) -dependent synaptic...
Learning is an inherent feature of the living animals . During development and childhood we learn a large repertoire of items that we encounter for the first time in our life , such as the names of things and how to perform certain tasks . This de novo learning process takes a relatively long time and generally require...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2013
Development of schemas revealed by prior experience and NMDA receptor knock-out
T cell expansion and differentiation are critically dependent on the transcription factor c-Myc ( Myc ) . Herein we use quantitative mass-spectrometry to reveal how Myc controls antigen receptor driven cell growth and proteome restructuring in murine T cells . Analysis of copy numbers per cell of >7000 proteins provide...
T cells are white blood cells that form an important part of our immune defence , acting to attack disease-causing microbes and cancer and directing other immune cells to help in this fight . T cells spend most of their time in a resting state , small and inactive , but when an infection strikes , they transform into l...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "immunology", "and", "inflammation" ]
2020
Quantitative analysis of how Myc controls T cell proteomes and metabolic pathways during T cell activation
Plants constantly renew during their life cycle and thus require to shed senescent and damaged organs . Floral abscission is controlled by the leucine-rich repeat receptor kinase ( LRR-RK ) HAESA and the peptide hormone IDA . It is unknown how expression of IDA in the abscission zone leads to HAESA activation . Here we...
Plants can shed their leaves , flowers or other organs when they no longer need them . But how does a leaf or a flower know when to let go ? A receptor protein called HAESA is found on the surface of the cells that surround a future break point on the plant . When its time to shed an organ , a hormone called IDA instru...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "plant", "biology", "structural", "biology", "and", "molecular", "biophysics" ]
2016
Mechanistic insight into a peptide hormone signaling complex mediating floral organ abscission
Disparate redox activities that take place beyond the bounds of the prokaryotic cell cytosol must connect to membrane or cytosolic electron pools . Proteins post-translationally flavinylated by the enzyme ApbE mediate electron transfer in several characterized extracytosolic redox systems but the breadth of functions o...
In bacteria , certain chemical reactions required for life do not take place directly inside the cells . For instance , ‘redox’ reactions essential to gather minerals , repair proteins and obtain energy are localised in the membranes and space that surround a bacterium . These chemical reactions involve electrons being...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "biochemistry", "and", "chemical", "biology" ]
2021
Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life
Exosomes are small vesicles that are secreted from metazoan cells and may convey selected membrane proteins and small RNAs to target cells for the control of cell migration , development and metastasis . To study the mechanisms of RNA packaging into exosomes , we devised a purification scheme based on the membrane mark...
Human cells release molecules into their surroundings via membrane-bound packets called exosomes . These molecules can then circulate throughout the body and are protected from degradation . Among the cargos carried by exosomes are small molecules of RNA known as microRNAs , which are involved in regulating gene activi...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "biochemistry", "and", "chemical", "biology", "cancer", "biology" ]
2016
Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction
How host and microbial factors combine to structure gut microbial communities remains incompletely understood . Redox potential is an important environmental feature affected by both host and microbial actions . We assessed how antibiotics , which can impact host and microbial function , change redox state and how this...
The gut is home to a large and diverse community of bacteria and other microbes , known as the gut microbiota . The makeup of this community is important for the health of both the host and its residents . For instance , many gut bacteria help to digest food or keep disease-causing bacteria in check . In return , the h...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "microbiology", "and", "infectious", "disease" ]
2018
Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut
The perception and response to cellular death is an important aspect of multicellular eukaryotic life . For example , damage-associated molecular patterns activate an inflammatory cascade that leads to removal of cellular debris and promotion of healing . We demonstrate that lysis of Pseudomonas aeruginosa cells trigge...
Bacteria live in diverse and changing environments where resources such as nutrients and space are often limited . They have thus evolved many survival strategies , including competitive and cooperative behaviors . In the first case , bacteria antagonize or prevent the growth of other microorganisms competing with them...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "microbiology", "and", "infectious", "disease" ]
2015
Kin cell lysis is a danger signal that activates antibacterial pathways of Pseudomonas aeruginosa
The general transcription factor TFIID comprises the TATA-box-binding protein ( TBP ) and approximately 14 TBP-associated factors ( TAFs ) . Here we find , unexpectedly , that undifferentiated human embryonic stem cells ( hESCs ) contain only six TAFs ( TAFs 2 , 3 , 5 , 6 , 7 and 11 ) , whereas following differentiatio...
Embryonic stem cells have two characteristic properties: they are able to differentiate into any type of cell , a property known as pluripotency , and they are able to replicate themselves indefinitely to produce an endless supply of new stem cells . Different genes code for the various proteins associated with these t...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "chromosomes", "and", "gene", "expression" ]
2012
Non-canonical TAF complexes regulate active promoters in human embryonic stem cells
Collision avoidance is critical for survival , including in humans , and many species possess visual neurons exquisitely sensitive to objects approaching on a collision course . Here , we demonstrate that a collision-detecting neuron can detect the spatial coherence of a simulated impending object , thereby carrying ou...
Whether you are a flying insect or a driver on a freeway , your survival will depend on avoiding collisions . Many species have nerve cells or neurons within their visual system that respond to objects headed towards them on a collision course . In locusts , for example , a neuron called the lobula giant movement detec...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2018
Biophysics of object segmentation in a collision-detecting neuron
Small heat shock proteins ( sHSPs ) are essential ‘holdase’ chaperones that form large assemblies and respond dynamically to pH and temperature stresses to protect client proteins from aggregation . While the alpha-crystallin domain ( ACD ) dimer of sHSPs is the universal building block , how the ACD transmits structur...
Proteins are composed of one or more long chain-like molecules that must fold into complex three-dimensional shapes in order to work properly . Incorrectly folded proteins cannot function and often aggregate into toxic states that are associated with a number of neurological diseases including Alzheimer's , Huntington'...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "biochemistry", "and", "chemical", "biology", "structural", "biology", "and", "molecular", "biophysics" ]
2015
A conserved histidine modulates HSPB5 structure to trigger chaperone activity in response to stress-related acidosis
The level of copy number alteration ( CNA ) , termed CNA burden , in the tumor genome is associated with recurrence of primary prostate cancer . Whether CNA burden is associated with prostate cancer survival or outcomes in other cancers is unknown . We analyzed the CNA landscape of conservatively treated prostate cance...
Cancer cells carry different types of mutations that are associated with the cell starting to multiply uncontrollably . Certain changes only affect one or a few letters of the genetic code . Others , known as copy number alterations , or CNA , involve larger portions of the genome that can either be lost ( deletions ) ...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "medicine", "cancer", "biology" ]
2018
Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death
Fidaxomicin ( Fdx ) is an antimicrobial RNA polymerase ( RNAP ) inhibitor highly effective against Mycobacterium tuberculosis RNAP in vitro , but clinical use of Fdx is limited to treating Clostridium difficile intestinal infections due to poor absorption . To identify the structural determinants of Fdx binding to RNAP...
Tuberculosis ( TB ) is an infectious disease that affects over ten million people every year . The Mycobacterium tuberculosis bacteria that cause the disease spread through the air from one person to another and mainly infect the lungs . Although curable , TB is difficult to eradicate because it is remarkably widesprea...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "structural", "biology", "and", "molecular", "biophysics" ]
2018
Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts
Pioneer transcription factors recognise and bind their target sequences in inaccessible chromatin to establish new transcriptional networks throughout development and cellular reprogramming . During this process , pioneer factors establish an accessible chromatin state to facilitate additional transcription factor bind...
All cells in your body contain the same genetic information in the form of genes encoded within DNA . Yet , cells use this information in different ways so that the activities of individual genes within that DNA can vary from cell to cell . This allows identical cells to become different to each other and to adapt to c...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "stem", "cells", "and", "regenerative", "medicine", "chromosomes", "and", "gene", "expression" ]
2017
The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells
The simultaneous imaging and manipulating of neural activity could enable the functional dissection of neural circuits . Here we have combined two-photon optogenetics with simultaneous volumetric two-photon calcium imaging to measure and manipulate neural activity in mouse neocortex in vivo in three-dimensions ( 3D ) w...
Modern microscopy provides a window into the brain . The first light microscopes were able to magnify cells only in thin slices of tissue . By contrast , today’s light microscopes can image cells below the surface of the brain of a living animal . Even so , this remains challenging for several reasons . One is that the...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "tools", "and", "resources", "neuroscience" ]
2018
Simultaneous two-photon imaging and two-photon optogenetics of cortical circuits in three dimensions
During transcription elongation , RNA polymerase has been assumed to attain equilibrium between pre- and post-translocated states rapidly relative to the subsequent catalysis . Under this assumption , recent single-molecule studies proposed a branched Brownian ratchet mechanism that necessitates a putative secondary nu...
The production of a protein inside a cell starts with a region of the DNA inside the cell nucleus being transcribed to form a molecule of messenger RNA . This process involves an enzyme called RNA polymerase that moves along the DNA , reading the bases and making a complementary strand of messenger RNA from molecules c...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "structural", "biology", "and", "molecular", "biophysics" ]
2013
Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism
Feeding and oviposition deterrents help phytophagous insects to identify host plants . The taste organs of phytophagous insects contain bitter gustatory receptors ( GRs ) . To explore their function , the GRs in Plutella xylostella were analyzed . Through RNA sequencing and qPCR , we detected abundant PxylGr34 transcri...
Plant-eating insects use their sense of taste to decide where to feed and where to lay their eggs . They do this using taste sensors called gustatory receptors which reside in the antennae and legs of adults , and in the mouthparts of larvae . Some of these sensors detect sugars which signal to the insect that the plan...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "ecology" ]
2020
A gustatory receptor tuned to the steroid plant hormone brassinolide in Plutella xylostella (Lepidoptera: Plutellidae)
Coat protein complex II ( COPII ) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum . The inner COPII proteins bind to cargo and membrane , linking them to the outer COPII components that form a cage around the vesicle . Regulated flexibility in coat archi...
Proteins often need to move between different compartments within cells . To do this they are packaged into transport pods called vesicles . Many trafficked proteins are synthesized in an organelle called the endoplasmic reticulum , or ER; these proteins are transported away from the ER in ‘COPII’ vesicles , which are ...
[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]
[ "biochemistry", "and", "chemical", "biology", "structural", "biology", "and", "molecular", "biophysics" ]
2013
The structure of the COPII transport-vesicle coat assembled on membranes
Sprouting angiogenesis is a well-coordinated process controlled by multiple extracellular inputs , including vascular endothelial growth factor ( VEGF ) . However , little is known about when and how individual endothelial cell ( EC ) responds to angiogenic inputs in vivo . Here , we visualized endothelial Ca2+ dynamic...
Throughout life , new blood vessels grow out like branches from existing vessels in a process called “sprouting angiogenesis” . This involves some of the endothelial cells that line the inner surface of the blood vessel migrating outwards , creating a vessel sprout made up of tip cells and stalk cells . Sprouting is co...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology" ]
2015
Endothelial Ca2+ oscillations reflect VEGFR signaling-regulated angiogenic capacity in vivo
Neutralizing antibodies elicited by prior infection or vaccination are likely to be key for future protection of individuals and populations against SARS-CoV-2 . Moreover , passively administered antibodies are among the most promising therapeutic and prophylactic anti-SARS-CoV-2 agents . However , the degree to which ...
The new coronavirus , SARS-CoV-2 , which causes the disease COVID-19 , has had a serious worldwide impact on human health . The virus was virtually unknown at the beginning of 2020 . Since then , intense research efforts have resulted in sequencing the coronavirus genome , identifying the structures of its proteins , a...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "microbiology", "and", "infectious", "disease", "immunology", "and", "inflammation" ]
2020
Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants
Domesticated animals experienced profound changes in diet , environment , and social interactions that likely shaped their gut microbiota and were potentially analogous to ecological changes experienced by humans during industrialization . Comparing the gut microbiota of wild and domesticated mammals plus chimpanzees a...
Living inside our gastrointestinal tracts is a large and diverse community of bacteria called the gut microbiota that plays an active role in basic body processes like metabolism and immunity . Much of our current understanding of the gut microbiota has come from laboratory animals like mice , which have very different...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "ecology", "evolutionary", "biology" ]
2021
Effects of domestication on the gut microbiota parallel those of human industrialization
Pneumococcal whole cell vaccines ( WCVs ) could cost-effectively protect against a greater strain diversity than current capsule-based vaccines . Immunoglobulin G ( IgG ) responses to a WCV were characterised by applying longitudinally-sampled sera , available from 35 adult placebo-controlled phase I trial participants...
Streptococcus pneumoniae is a bug that causes pneumonia and meningitis , killing around a million people each year . Vaccines now exist to protect young children against these diseases , but they are expensive and do not work against all the strains of the bacteria . This is because these shots train the body’s immune ...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "microbiology", "and", "infectious", "disease", "immunology", "and", "inflammation" ]
2018
Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination
DNA is a remarkably precise medium for copying and storing biological information . This high fidelity results from the action of hundreds of genes involved in replication , proofreading , and damage repair . Evolutionary theory suggests that in such a system , selection has limited ability to remove genetic variants t...
DNA is a molecule that contains the information needed to build an organism . This information is stored as a code made up of four chemicals: adenine ( A ) , guanine ( G ) , cytosine ( C ) , and thymine ( T ) . Every time a cell divides and copies its DNA , it accidentally introduces ‘typos’ into the code , known as mu...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "evolutionary", "biology" ]
2017
Rapid evolution of the human mutation spectrum
Chronic infection perturbs immune homeostasis . While prior studies have reported dysregulation of effector and memory cells , little is known about the effects on naïve T cell populations . We performed a cross-sectional study of chronic hepatitis C ( cHCV ) patients using tetramer-associated magnetic enrichment to st...
Long-lasting or “chronic” infections massively perturb the immune system as a way to favor their own growth . In particular , they can stop T cells – a subtype of immune cells that help to destroy viruses – from working well . For example , HIV and hepatitis C viruses can overwork T cells and cause them to die . This c...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "immunology", "and", "inflammation" ]
2015
Bystander hyperactivation of preimmune CD8+ T cells in chronic HCV patients
Morphogen gradients expose cells to different signal concentrations and induce target genes with different ranges of expression . To determine how the Nodal morphogen gradient induces distinct gene expression patterns during zebrafish embryogenesis , we measured the activation dynamics of the signal transducer Smad2 an...
How a cell can tell where it is in a developing embryo has fascinated scientists for decades . The pioneering computer scientist and mathematical biologist Alan Turing was the first person to coin the term ‘morphogen’ to describe a protein that provides information about locations in the body . A morphogen is released ...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology" ]
2015
Response to Nodal morphogen gradient is determined by the kinetics of target gene induction
Chemokines are secreted proteins that regulate a range of processes in eukaryotic organisms . Interestingly , different chemokine receptors control distinct biological processes , and the same receptor can direct different cellular responses , but the basis for this phenomenon is not known . To understand this property...
Every process in the body is regulated by a complex network of interactions between different molecules and cells . Chemokines , for example , are tiny molecules produced by a cell that are involved in a range of processes , from development to immune responses and cancer . When chemokines bind to a specific protein on...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology", "immunology", "and", "inflammation" ]
2018
Spatio-temporal regulation of concurrent developmental processes by generic signaling downstream of chemokine receptors
We have developed an open-source software called bi-channel image registration and deep-learning segmentation ( BIRDS ) for the mapping and analysis of 3D microscopy data and applied this to the mouse brain . The BIRDS pipeline includes image preprocessing , bi-channel registration , automatic annotation , creation of ...
Mapping all the cells and nerve connections in the mouse brain is a major goal of the neuroscience community , as this will provide new insights into how the brain works and what happens during disease . To achieve this , researchers must first capture three-dimensional images of the brain . These images are then proce...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "computational", "and", "systems", "biology", "neuroscience" ]
2021
Bi-channel image registration and deep-learning segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain
Hippocampal firing is organized in theta sequences controlled by internal memory processes and by external sensory cues , but how these computations are coordinated is not fully understood . Although theta activity is commonly studied as a unique coherent oscillation , it is the result of complex interactions between d...
In the brain , a vast number of neurons coordinate their activity to support complex cognitive processes . One of the best places to see this in action is the hippocampus , a brain structure with a key role in memory and navigation . The hippocampus shows waves of electrical activity , which represent the synchronized ...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2020
Different theta frameworks coexist in the rat hippocampus and are coordinated during memory-guided and novelty tasks
Gastrulation generates three layers of cells ( ectoderm , mesoderm , endoderm ) from a single sheet , while large scale cell movements occur across the entire embryo . In amniote ( reptiles , birds , mammals ) embryos , the deep layers arise by epithelial-to-mesenchymal transition ( EMT ) at a morphologically stable mi...
A key process during the development of an embryo involves a single layer of cells reorganizing into three ‘germ layers’: the ectoderm , which becomes the skin and nervous system; the mesoderm , which gives rise to the skeleton , muscles and the circulatory and urinogenital systems , and the endoderm , which gives rise...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology" ]
2014
Local cell interactions and self-amplifying individual cell ingression drive amniote gastrulation
Signaling pathways often transmit multiple signals through a single shared transcription factor ( TF ) and encode signal information by differentially regulating TF dynamics . However , signal information will be lost unless it can be reliably decoded by downstream genes . To understand the limits on dynamic informatio...
The way that a cell responds to an external stimulus is governed by a sequence of events called a signalling pathway . While cells are exposed to a wide range of external stimuli—such as different types of chemicals and different forms of radiation—the last stage of the signalling pathway usually involves a gene being ...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology", "computational", "and", "systems", "biology" ]
2015
Limits on information transduction through amplitude and frequency regulation of transcription factor activity
Adenosine triphosphate ( ATP ) , the chemical energy currency of biology , is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase . ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalyti...
A molecule called adenosine triphosphate ( ATP ) is the energy currency in cells . Most of the ATP used by cells is made by the membrane-embedded enzyme ATP synthase . This enzyme is found in membranes inside specialized compartments known as mitochondria . ATP synthase is made up of many protein subunits that work tog...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "biochemistry", "and", "chemical", "biology", "structural", "biology", "and", "molecular", "biophysics" ]
2015
Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM
Novel regenerative therapies may stem from deeper understanding of the mechanisms governing cardiovascular lineage diversification . Using enhancer mapping and live imaging in avian embryos , and genetic lineage tracing in mice , we investigated the spatio-temporal dynamics of cardiovascular progenitor populations . We...
As an animal embryo develops , it establishes a circulatory system that includes the heart , vessels and blood . Vessels and blood initially form in the yolk sac , a membrane that surrounds the embryo . These yolk sac vessels act as a rudimentary circulatory system , connecting to the heart and blood vessels within the...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology" ]
2017
Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aorta
Centrioles are microtubule-based organelles crucial for cell division , sensing and motility . In Caenorhabditis elegans , the onset of centriole formation requires notably the proteins SAS-5 and SAS-6 , which have functional equivalents across eukaryotic evolution . Whereas the molecular architecture of SAS-6 and its ...
Most animal cells contain structures known as centrioles . Typically , a cell that is not dividing contains a pair of centrioles . But when a cell prepares to divide , the centrioles are duplicated . The two pairs of centrioles then organize the scaffolding that shares the genetic material equally between the newly for...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology", "structural", "biology", "and", "molecular", "biophysics" ]
2015
The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation
CaV1 . 3 channels regulate excitability in many neurons . As is the case for all voltage-gated channels , it is widely assumed that individual CaV1 . 3 channels behave independently with respect to voltage-activation , open probability , and facilitation . Here , we report the results of super-resolution imaging , opto...
The electrical charge inside a cell is different from that outside of the cell . Neurons rely on this difference to send signals via electrical impulses . This process involves ions moving across the neuron’s membrane through proteins called ion channels . Cav1 . 3 channels are ion channels that open when the membrane’...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "structural", "biology", "and", "molecular", "biophysics", "neuroscience" ]
2016
Ca2+ entry into neurons is facilitated by cooperative gating of clustered CaV1.3 channels
Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells . Despite its profound effects , the cellular processes affected by aneuploidy are not well characterized . Here , we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains . We show that al...
Nearly all tumor cells contain abnormal number of chromosomes . This state is called aneuploidy , and can also cause embryos to be miscarried , or to be born with severe developmental disorders . Proteins are produced from the genes contained within chromosomes , and so cells with too many chromosomes produce too many ...
[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]
[ "chromosomes", "and", "gene", "expression", "cell", "biology" ]
2014
Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast
Hippocampal place cells encode an animal's past , current , and future location through sequences of action potentials generated within each cycle of the network theta rhythm . These sequential representations have been suggested to result from temporally coordinated synaptic interactions within and between cell assemb...
When we explore a new place , we naturally create a mental map of the location as we go . This mental map is stored in a region of the brain called the hippocampus , which contains cells called place cells . These cells can carry information about our past , present , and future location in the form of electrical signa...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2015
Independent theta phase coding accounts for CA1 population sequences and enables flexible remapping
When pathogens enter the host , sensing of environmental cues activates the expression of virulence genes . Opposite transition of pathogens from activating to non-activating conditions is poorly understood . Interestingly , variability in the expression of virulence genes upon infection enhances colonization . In orde...
Bacteria typically cope with harsh and changing environments by activating specific genes or accumulating those mutations that change genes in a beneficial way . Recently , it was also shown that the levels of gene activity can vary between otherwise identical bacteria in a single population . This provides an alternat...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "computational", "and", "systems", "biology", "microbiology", "and", "infectious", "disease" ]
2017
A long-term epigenetic memory switch controls bacterial virulence bimodality
Single-cell transcriptomes are established by transcription factors ( TFs ) , which determine a cell's gene-expression complement . Post-transcriptional regulation of single-cell transcriptomes , and the RNA binding proteins ( RBPs ) responsible , are more technically challenging to determine , and combinatorial TF-RBP...
All the cells in the human nervous system contain the same genetic information , and yet there are many kinds of neurons , each with different features and roles in the body . Proteins known as transcription factors help to establish this diversity by switching on different genes in different types of cells . A mechani...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology", "genetics", "and", "genomics" ]
2019
Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors
Hallucinations occur in both normal and clinical populations . Due to their unpredictability and complexity , the mechanisms underlying hallucinations remain largely untested . Here we show that visual hallucinations can be induced in the normal population by visual flicker , limited to an annulus that constricts conte...
Hallucinations can occur in both healthy and unwell people . Drugs , sleep deprivation , loss of vision , and migraines can all trigger visual hallucinations in people with no psychiatric illness . We have known for more than 200 years that flickering light can induce hallucinations in almost anyone . However , the unp...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2016
Sensory dynamics of visual hallucinations in the normal population
Inserted ( I ) domains function as ligand-binding domains in adhesins that support cell adhesion and migration in many eukaryotic phyla . These adhesins include integrin αβ heterodimers in metazoans and single subunit transmembrane proteins in apicomplexans such as TRAP in Plasmodium and MIC2 in Toxoplasma . Here we sh...
Malaria is an infectious disease caused by single-celled parasites known as Plasmodium . Humans and other animals with backbones – such as birds , reptiles and rodents – can become hosts for these parasites if an infected female mosquito feeds on their blood . Likewise , healthy mosquitoes can in turn become infected w...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "microbiology", "and", "infectious", "disease" ]
2020
Evolutionarily distant I domains can functionally replace the essential ligand-binding domain of Plasmodium TRAP
The robust representation of the environment from unreliable sensory cues is vital for the efficient function of the brain . However , how the neural processing captures the most reliable cues is unknown . The interaural time difference ( ITD ) is the primary cue to localize sound in horizontal space . ITD is encoded i...
The ability to locate where a sound is coming from is an essential survival skill for both prey and predator species . A major cue used by the brain to infer the sound's location is the difference in arrival time of the sound at the left and right ears; for example , a sound coming from the left side will reach the lef...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2014
Spatial cue reliability drives frequency tuning in the barn Owl's midbrain
Regulation of animal development in response to nutritional cues is an intensely studied problem related to disease and aging . While extensive studies indicated roles of the Target of Rapamycin ( TOR ) in sensing certain nutrients for controlling growth and metabolism , the roles of fatty acids and lipids in TOR-invol...
Animals require nutrients , including carbohydrates , lipids , and amino acids , for development and growth , and to maintain the normal functioning of cells . However , in most natural environments , the availability of food tends to fluctuate . Some animals have therefore acquired the ability to dramatically reduce t...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology" ]
2013
A novel sphingolipid-TORC1 pathway critically promotes postembryonic development in Caenorhabditis elegans
Biological membranes create compartments , and are usually formed by lipid bilayers . However , in hyperthermophilic archaea that live optimally at temperatures above 80°C the membranes are monolayers which resemble fused bilayers . Many double-stranded DNA viruses which parasitize such hosts , including the filamentou...
Virtually every environment on the planet is home to some form of life , even places that , at first glance , appear to be too harsh for any organism to survive in . For example , a microscopic organism known as Acidianus hospitalis thrives in highly acidic environments that are hotter than 80°C , conditions that would...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "structural", "biology", "and", "molecular", "biophysics" ]
2017
Model for a novel membrane envelope in a filamentous hyperthermophilic virus
The adult mammalian brain is mainly composed of mature neurons . A limited amount of stem cell-driven neurogenesis persists in postnatal life and is reduced in large-brained species . Another source of immature neurons in adult brains is cortical layer II . These cortical immature neurons ( cINs ) retain developmentall...
To acquire new skills or recover after injuries , the mammalian brain relies on plasticity , the ability for the brain to change its architecture and its connections during the lifetime of an animal . Creating new nerve cells is one way to achieve plasticity , but this process is rarer in humans than it is in mammals w...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2020
Phylogenetic variation in cortical layer II immature neuron reservoir of mammals
Nanobodies are single-domain antibodies of camelid origin . We generated nanobodies against the vertebrate nuclear pore complex ( NPC ) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement . For this , we introduced cysteines at specific positions in the nanobody sequen...
Antibodies not only protect humans and other animals against disease-causing bacteria and viruses . They can also be used as tools for medical diagnostics and basic research . Conventional antibodies consist of light and heavy protein chains , and both are required to bind to target molecules ( or antigens ) . Alpacas ...
[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]
[ "biochemistry", "and", "chemical", "biology", "cell", "biology", "tools", "and", "resources" ]
2015
Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation
Transcriptional feedback loops are key to circadian clock function in many organisms . Current models of the Arabidopsis circadian network consist of several coupled feedback loops composed almost exclusively of transcriptional repressors . Indeed , a central regulatory mechanism is the repression of evening-phased clo...
We live in a world with a 24-hr cycle in which day follows night follows day with complete predictability . Life on earth has evolved to take advantage of this predictability by using circadian clocks to prepare for the coming of night ( or day ) , and plants are no exception . Even in constant darkness , characteristi...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "plant", "biology" ]
2013
Accurate timekeeping is controlled by a cycling activator in Arabidopsis
Dopamine neurons are thought to encode novelty in addition to reward prediction error ( the discrepancy between actual and predicted values ) . In this study , we compared dopamine activity across the striatum using fiber fluorometry in mice . During classical conditioning , we observed opposite dynamics in dopamine ax...
New experiences trigger a variety of responses in animals . We are surprised by , move towards , and often explore new objects . But how does the brain control these responses ? Dopamine is a molecule that controls many processes in the brain and plays critical roles in various mental disorders , diseases that affect m...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2017
Opposite initialization to novel cues in dopamine signaling in ventral and posterior striatum in mice
Neural patterning involves regionalised cell specification . Recent studies indicate that cell dynamics play instrumental roles in neural pattern refinement and progression , but the impact of cell behaviour and morphogenesis on neural specification is not understood . Here we combine 4D analysis of cell behaviours wit...
The inner ear is responsible for our senses of hearing and balance , and is made up of a series of fluid-filled cavities . Sounds , and movements of the head , cause the fluid within these cavities to move . This activates neurons that line the cavities , causing them to increase their firing rates and pass on informat...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology", "neuroscience" ]
2017
Pioneer neurog1 expressing cells ingress into the otic epithelium and instruct neuronal specification
Giant viruses are ecologically important players in aquatic ecosystems that have challenged concepts of what constitutes a virus . Herein , we present the giant Bodo saltans virus ( BsV ) , the first characterized representative of the most abundant group of giant viruses in ocean metagenomes , and the first isolate of...
In oceans , rivers and lakes , there are about a million viruses in every milliliter of water . Most of these viruses are tiny , often 10 or 100 times smaller than bacteria . However , a few reach a similar size and complexity to bacteria , and so stand out as relative giants . Relative to other viruses , Giant Viruses...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "microbiology", "and", "infectious", "disease" ]
2018
The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea
Cerebellar granule cell progenitors ( GCP ) proliferate extensively in the external granule layer ( EGL ) of the developing cerebellum prior to differentiating and migrating . Mechanisms that regulate the appropriate timing of cell cycle withdrawal of these neuronal progenitors during brain development are not well def...
Many proteins control how cells are organised in your body . For example , a group of proteins called the neurotrophins help to control the life and death of brain cells . After a brain injury , neurotrophins can cause nerve cells to die by working together with another protein called p75NTR . The p75NTR protein is als...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology", "neuroscience" ]
2016
Proneurotrophin-3 promotes cell cycle withdrawal of developing cerebellar granule cell progenitors via the p75 neurotrophin receptor
How transcription factor dimerization impacts DNA-binding specificity is poorly understood . Guided by protein dimerization properties , we examined DNA binding specificities of 270 human bZIP pairs . DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined h...
Most cells in our body contain the same DNA blueprint , which encodes all the genes needed for every process in the body . However , only certain genes need to be active in a particular cell at any given time . Proteins known as transcription factors control the activity of genes by binding to DNA near the start of the...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "chromosomes", "and", "gene", "expression", "computational", "and", "systems", "biology" ]
2017
Combinatorial bZIP dimers display complex DNA-binding specificity landscapes
The transcription factor SOX2 is central in establishing and maintaining pluripotency . The processes that modulate SOX2 activity to promote pluripotency are not well understood . Here , we show SOX2 is O-GlcNAc modified in its transactivation domain during reprogramming and in mouse embryonic stem cells ( mESCs ) . Up...
Embryos develop from stem cells , which have the ability to mature into any type of cell in the body . The activity of proteins called transcription factors determines whether a stem cell will become a specialized cell type or remain in an immature “pluripotent” state that has the potential to become any cell type . Th...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "stem", "cells", "and", "regenerative", "medicine", "biochemistry", "and", "chemical", "biology" ]
2016
SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells
Transcriptional gene silencing ( TGS ) can serve as an innate immunity against invading DNA viruses throughout Eukaryotes . Geminivirus code for TrAP protein to suppress the TGS pathway . Here , we identified an Arabidopsis H3K9me2 histone methyltransferase , Su ( var ) 3-9 homolog 4/Kryptonite ( SUVH4/KYP ) , as a bon...
Many viruses can infect plants and cause diseases that can reduce crop yields . The Geminiviruses are a family of plant viruses that are transmitted by insects and infect tomato , cabbage , and many other crop plants . These viruses hijack the plant cells that they infect and force the plant cells to make viral protein...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "chromosomes", "and", "gene", "expression", "plant", "biology" ]
2015
Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense
During transcription initiation , RNA polymerase ( RNAP ) binds to promoter DNA , unwinds promoter DNA to form an RNAP-promoter open complex ( RPo ) containing a single-stranded ‘transcription bubble , ’ and selects a transcription start site ( TSS ) . TSS selection occurs at different positions within the promoter reg...
Genes store the information needed to build and repair cells . This information is written in a chemical code within the structure of DNA molecules . To make use of the information , cells copy sections of a gene into a DNA-like molecule called RNA . An enzyme called RNA polymerase makes RNA molecules from DNA template...
[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]
[ "chromosomes", "and", "gene", "expression", "structural", "biology", "and", "molecular", "biophysics" ]
2017
The mechanism of variability in transcription start site selection
Most age-related human diseases are accompanied by a decline in cellular organelle integrity , including impaired lysosomal proteostasis and defective mitochondrial oxidative phosphorylation . An open question , however , is the degree to which inherited variation in or near genes encoding each organelle contributes to...
Getting older increases our risk of experiencing a wide range of diseases , such as diabetes , heart disease and neurodegenerative disease . The genetic variations that we inherit from our parents play a major role in predicting this risk . However , the biological networks involved in this process are extremely comple...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "genetics", "and", "genomics" ]
2021
Human genetic analyses of organelles highlight the nucleus in age-related trait heritability
The fibroblast growth factor FGF21 was labeled with molecularly defined gold nanoparticles ( AuNPs ) , applied to human adipocytes , and imaged by cryo-electron tomography ( cryo-ET ) . Most AuNPs were in pairs about 80 Å apart , on the outer cell surface . Pairs of AuNPs were also abundant inside the cells in clathrin...
Following a molecule’s movement around a cell is a bit like looking for a needle in a haystack . Cells contain thousands of different components that can be difficult to distinguish between when viewed using a microscope . It helps to have a method to tag the molecule of interest to make it more easily visible . Electr...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "structural", "biology", "and", "molecular", "biophysics", "cell", "biology", "tools", "and", "resources" ]
2019
FGF21 trafficking in intact human cells revealed by cryo-electron tomography with gold nanoparticles
The mutualistic endosymbiosis between cnidarians and dinoflagellates is mediated by complex inter-partner signaling events , where the host cnidarian innate immune system plays a crucial role in recognition and regulation of symbionts . To date , little is known about the diversity of thrombospondin-type-1 repeat ( TSR...
Cnidarians , such as corals and sea anemones , often form a close relationship with microscopic algae that live inside their cells – a partnership , on which the entire coral reef ecosystem depends . These microalgae produce sugars and other compounds that the cnidarians need to survive , while the cnidarians protect t...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "ecology", "microbiology", "and", "infectious", "disease" ]
2017
A diverse host thrombospondin-type-1 repeat protein repertoire promotes symbiont colonization during establishment of cnidarian-dinoflagellate symbiosis
Convergent evidence suggests that the basal ganglia support reinforcement learning by adjusting action values according to reward prediction errors . However , adaptive behavior in stochastic environments requires the consideration of uncertainty to dynamically adjust the learning rate . We consider how cholinergic ton...
One of the keys to successful learning is being able to adjust behavior on the basis of experience . In simple terms , it pays to repeat behaviors with positive outcomes and avoid those with negative outcomes . A group of brain regions known collectively as the basal ganglia supports this process by guiding behavior ba...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "computational", "and", "systems", "biology", "neuroscience" ]
2015
A cholinergic feedback circuit to regulate striatal population uncertainty and optimize reinforcement learning
During inflammation and infection , hematopoietic stem and progenitor cells are stimulated to proliferate and differentiate into mature immune cells , especially of the myeloid lineage . MicroRNA-146a ( miR-146a ) is a critical negative regulator of inflammation . Deletion of miR-146a produces effects that appear as dy...
Hematopoietic stem cells are cells that both renew themselves and develop into any type of blood cell , including red blood cells and the several classes of immune cells . When an injury or infection occurs , it is vital that hematopoietic stem cells replenish themselves in addition to developing into the new blood cel...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "stem", "cells", "and", "regenerative", "medicine", "immunology", "and", "inflammation" ]
2013
MicroRNA-146a acts as a guardian of the quality and longevity of hematopoietic stem cells in mice
Multicellular development produces patterns of specialized cell types . Yet , it is often unclear how individual cells within a field of identical cells initiate the patterning process . Using live imaging , quantitative image analyses and modeling , we show that during Arabidopsis thaliana sepal development , fluctuat...
Plant and animal organs contain several types of cells that perform different roles . As a plant or animal develops , these different cell types can form intricate patterns . To start the pattern , a few cells within a group of identical cells must somehow become different from their neighbors . Some patterns of cells ...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "plant", "biology" ]
2017
Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal
Exceptionally high rates of tooth fracture in large Pleistocene carnivorans imply intensified interspecific competition , given that tooth fracture rises with increased bone consumption , a behavior that likely occurs when prey are difficult to acquire . To assess the link between prey availability and dental attrition...
Gray wolves roam many European and American landscapes , where they prey on large animals such as elk and moose . A healthy dentition is essential for these predators to kill , eat and defend themselves . As a result , they tend to avoid biting down on tough body parts , such as bones , so that their teeth do not break...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "ecology", "evolutionary", "biology" ]
2019
Tooth fracture frequency in gray wolves reflects prey availability
The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells , yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood . Here we investigate how the smallest unit of chromatin , a nucleosome , constrain...
CRISPR is a method of editing the genetic material inside living cells and has enabled dramatic advances in a broad variety of research fields in recent years . The method relies on a bacterial enzyme called Cas9 that can be programmed , via short guide molecules made from RNA , to target specific sites in the cell’s D...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "chromosomes", "and", "gene", "expression", "short", "report", "biochemistry", "and", "chemical", "biology" ]
2016
Nucleosome breathing and remodeling constrain CRISPR-Cas9 function
The multi-domain splicing factor RBM5 regulates the balance between antagonistic isoforms of the apoptosis-control genes FAS/CD95 , Caspase-2 and AID . An OCRE ( OCtamer REpeat of aromatic residues ) domain found in RBM5 is important for alternative splicing regulation and mediates interactions with components of the U...
The information required to produce proteins is encoded within genes . In the first step of creating a protein , its gene is “transcribed” to form a pre-messenger RNA molecule ( called pre-mRNA for short ) . Both the gene and the pre-mRNA contain regions called exons that code for protein , and regions called introns t...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "Accession", "codes" ]
[ "biochemistry", "and", "chemical", "biology", "structural", "biology", "and", "molecular", "biophysics" ]
2016
Structural basis for the recognition of spliceosomal SmN/B/B’ proteins by the RBM5 OCRE domain in splicing regulation
Following learning , increased coupling between spindle oscillations in the medial prefrontal cortex ( mPFC ) and ripple oscillations in the hippocampus is thought to underlie memory consolidation . However , whether learning-induced increases in ripple-spindle coupling are necessary for successful memory consolidation...
Sleep contributes to the strengthening of memories . During non-dreaming sleep , neurons in regions of the brain that form and store memories – such as the hippocampus and prefrontal cortex – fire in rhythmic waves . The neurons in the hippocampus tend to fire during a wave that repeats up to 250 times per second , cal...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2017
Parvalbumin-positive interneurons mediate neocortical-hippocampal interactions that are necessary for memory consolidation
Organizers play important roles during the embryonic development of many animals . The most famous example is the Spemann organizer that sets up embryonic axes in amphibian embryos . In spiders , a group of BMP secreting mesenchymal cells ( the cumulus ) functions as an organizer of the dorsoventral axis . Similar to e...
At the earliest stages of animal development , embryos consisting of only a handful of cells must figure out where each part of their body will come from . The first step in this process is to determine what will be their head versus their tail , and what will be their front versus their back . Many animals use special...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology" ]
2017
A novel role for Ets4 in axis specification and cell migration in the spider Parasteatoda tepidariorum
Cardiac neural crest cells contribute to important portions of the cardiovascular system including the aorticopulmonary septum and cardiac ganglion . Using replication incompetent avian retroviruses for precise high-resolution lineage analysis , we uncover a previously undescribed neural crest contribution to cardiomyo...
Before birth , unspecialized stem cells go through a process called differentiation to form the many types of cells found in the adult . Neural crest cells are a group of these stem cells found in all animals with backbones ( i . e . vertebrates ) including humans . These cells migrate extensively during development to...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "developmental", "biology", "short", "report" ]
2019
Cardiac neural crest contributes to cardiomyocytes in amniotes and heart regeneration in zebrafish
The Drosophila midgut is maintained throughout its length by superficially similar , multipotent intestinal stem cells that generate new enterocytes and enteroendocrine cells in response to tissue requirements . We found that the midgut shows striking regional differentiation along its anterior-posterior axis . At leas...
Many cells in the body accumulate wear and tear over time , and a fraction of them are always nearing the end of their lives . However , in some tissues there are stem cells that can divide into daughter cells which then differentiate and replace the damaged cells . Unlike embryonic stem cells , these ‘adult tissue ste...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "stem", "cells", "and", "regenerative", "medicine" ]
2013
Physiological and stem cell compartmentalization within the Drosophila midgut
Passage through mitosis is driven by precisely-timed changes in transcriptional regulation and protein degradation . However , the importance of translational regulation during mitosis remains poorly understood . Here , using ribosome profiling , we find both a global translational repression and identified ∼200 mRNAs ...
The human body contains billions of cells , most of which formed via a process called mitosis in which a single cell divides to produce two new daughter cells . Actively dividing cells pass through a series of events ( or phases ) that are collectively known as the cell cycle . These phases allow the cell to grow in si...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology", "computational", "and", "systems", "biology" ]
2015
Regulation of mRNA translation during mitosis
Regulation of cell wall assembly is essential for bacterial survival and contributes to pathogenesis and antibiotic tolerance in Mycobacterium tuberculosis ( Mtb ) . However , little is known about how the cell wall is regulated in stress . We found that CwlM , a protein homologous to peptidoglycan amidases , coordinat...
Bacterial cells are surrounded by a protective cell wall . Some bacteria , including the species Mycobacterium tuberculosis that causes tuberculosis , have the ability to change the properties of their cell wall when exposed to stressful conditions . These changes may also help the bacteria to resist the antibiotics us...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "biochemistry", "and", "chemical", "biology", "microbiology", "and", "infectious", "disease" ]
2016
A cytoplasmic peptidoglycan amidase homologue controls mycobacterial cell wall synthesis
Notch is a critical regulator of T cell differentiation and is activated through proteolytic cleavage in response to ligand engagement . Using murine myelin-reactive CD4 T cells , we demonstrate that proximal T cell signaling modulates Notch activation by a spatiotemporally constrained mechanism . The protein kinase PK...
The body’s immune system recognizes and responds to foreign agents such as bacteria and viruses . Immune cells known as T cells recognize foreign substances through a protein on their surface called the T cell receptor . Specifically , the T cell receptor binds to fragments of foreign proteins displayed on the surface ...
[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]
[ "short", "report", "cell", "biology", "immunology", "and", "inflammation" ]
2017
PKCθ links proximal T cell and Notch signaling through localized regulation of the actin cytoskeleton
Store-operated calcium entry ( SOCE ) by calcium release activated calcium ( CRAC ) channels constitutes a primary route of calcium entry in most cells . Orai1 forms the pore subunit of CRAC channels and Stim1 is the endoplasmic reticulum ( ER ) resident Ca2+ sensor . Upon store-depletion , Stim1 translocates to domain...
Calcium is an essential element for many biological functions . In particular , the movement of calcium ions through the cell membrane has a central role in many of the signalling pathways that cells use to communicate with other cells . Signals are produced by calcium ions both entering and leaving the cell , with inf...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology" ]
2013
An essential and NSF independent role for α-SNAP in store-operated calcium entry
The brain displays a remarkable ability to adapt following injury by altering its connections through neural plasticity . Many of the biological mechanisms that underlie plasticity are known , but there is little knowledge as to when , or where in the brain plasticity will occur following injury . This knowledge could ...
The brain has the ability to adapt after injury , a process known as plasticity . When one area sustains damage , for example following a car accident or stroke , other areas change their activity and structure to compensate . Understanding how this happens is critical to helping people recover from brain injuries . Ce...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2018
Macro-connectomics and microstructure predict dynamic plasticity patterns in the non-human primate brain
In several neurodegenerative diseases and myelin disorders , the degeneration profiles of myelinated axons are compatible with underlying energy deficits . However , it is presently impossible to measure selectively axonal ATP levels in the electrically active nervous system . We combined transgenic expression of an AT...
The brain contains an intricate network of nerve cells that receive , process , send and store information . This information travels as electrical impulses along a long , thin part of each nerve cell known as the nerve fiber or axon . The act of sending these electrical signals requires a lot of energy , and energy in...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2017
Monitoring ATP dynamics in electrically active white matter tracts
Over 170 different mutations in the gene encoding SOD1 all cause amyotrophic lateral sclerosis ( ALS ) . Available studies have been primarily focused on the mechanisms underlying mutant SOD1 cytotoxicity . How cells defend against the cytotoxicity remains largely unknown . Here , we show that misfolding of ALS-linked ...
Amyotrophic lateral sclerosis ( ALS ) is a disease that leads to muscle weakness and paralysis . The symptoms become progressively worse over time to the point that patients die because they become unable to breathe . Over 170 different genetic mistakes ( or mutations ) in a gene that encodes a protein called SOD1 are ...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology" ]
2017
Nuclear export of misfolded SOD1 mediated by a normally buried NES-like sequence reduces proteotoxicity in the nucleus
Low-density lipoprotein receptor-related protein 1 ( LRP1 ) is a multifunctional cell surface receptor with diverse physiological roles , ranging from cellular uptake of lipoproteins and other cargo by endocytosis to sensor of the extracellular environment and integrator of a wide range of signaling mechanisms . As a c...
Atherosclerosis is a disease in which “plaques” build up inside the walls of arteries . Plaques consist of a fatty substance called cholesterol , together with immune cells such as macrophages and other material from the blood . Over time , the plaque narrows and hardens the arteries . This restricts the flow of blood ...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology" ]
2017
LRP1 integrates murine macrophage cholesterol homeostasis and inflammatory responses in atherosclerosis
Emerging evidence points to an unexpected diversification of core promoter recognition complexes that serve as important regulators of cell-type specific gene transcription . Here , we report that the orphan TBP-associated factor TAF9B is selectively up-regulated upon in vitro motor neuron differentiation , and is requ...
Almost all the cells in an organism contain the same genetic information , but they develop into many different types of cells that perform a variety of specialized functions in the body . Brain cells , for example , have a very different shape and function from red blood cells . A small group of proteins act inside ce...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "chromosomes", "and", "gene", "expression", "developmental", "biology" ]
2014
Core promoter factor TAF9B regulates neuronal gene expression
Gene transcription can be activated by decreasing the duration of RNA polymerase II pausing in the promoter-proximal region , but how this is achieved remains unclear . Here we use a ‘multi-omics’ approach to demonstrate that the duration of polymerase pausing generally limits the productive frequency of transcription ...
Genes can contain the coded instructions to make proteins . These instructions must first be copied , or transcribed , into an intermediate molecule called a messenger RNA by an enzyme known as RNA polymerase II . Shortly after it begins , this enzyme – which is called Pol II for short – pauses , and it only starts aga...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "computational", "and", "systems", "biology" ]
2017
CDK9-dependent RNA polymerase II pausing controls transcription initiation
Rodents are emerging as increasingly popular models of visual functions . Yet , evidence that rodent visual cortex is capable of advanced visual processing , such as object recognition , is limited . Here we investigate how neurons located along the progression of extrastriate areas that , in the rat brain , run latera...
Everyday , we see thousands of different objects with many different shapes , colors , sizes and textures . Even an individual object – for example , a face – can present us with a virtually infinite number of different images , depending on from where we view it . In spite of this extraordinary variability , our brain...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2017
Emergence of transformation-tolerant representations of visual objects in rat lateral extrastriate cortex
Economic theories posit reward probability as one of the factors defining reward value . Individuals learn the value of cues that predict probabilistic rewards from experienced reward frequencies . Building on the notion that responses of dopamine neurons increase with reward probability and expected value , we asked h...
Learning to choose the most fulfilling reward from a number of options requires the ability to infer the value of each option from unpredictable and changing environments . Neurons in the brain that produce a chemical called dopamine are critical for this learning process . They broadcast a 'prediction error' signal th...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2016
Dopamine neurons learn relative chosen value from probabilistic rewards
Antifreeze proteins ( AFPs ) protect certain cold-adapted organisms from freezing to death by selectively adsorbing to internal ice crystals and inhibiting ice propagation . The molecular details of AFP adsorption-inhibition is uncertain but is proposed to involve the Gibbs–Thomson effect . Here we show by using unbias...
Water expands as it freezes . If this happens to the water inside plants and animals , the resulting ice crystals can rupture cells . To prevent this , many plants and animals that live in cold climates have evolved ‘antifreeze proteins’ . When a small particle of ice first starts to form , the antifreeze proteins bind...
[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]
[ "structural", "biology", "and", "molecular", "biophysics", "computational", "and", "systems", "biology" ]
2015
The biological function of an insect antifreeze protein simulated by molecular dynamics
Perforin-2 ( MPEG1 ) is a pore-forming , antibacterial protein with broad-spectrum activity . Perforin-2 is expressed constitutively in phagocytes and inducibly in parenchymal , tissue-forming cells . In vitro , Perforin-2 prevents the intracellular replication and proliferation of bacterial pathogens in these cells . ...
An effective defense against foreign invaders is fundamental to an organism's survival . It is likely that immunity began to develop shortly after the emergence of Earth's first single-celled organisms and a remnant of that distant past still exists in our present day immune system in the form of Perforin-2 . This anci...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "microbiology", "and", "infectious", "disease", "immunology", "and", "inflammation" ]
2015
Perforin-2 is essential for intracellular defense of parenchymal cells and phagocytes against pathogenic bacteria
The functional communication of neurons in cortical networks underlies higher cognitive processes . Yet , little is known about the organization of the single neuron network or its relationship to the synchronization processes that are essential for its formation . Here , we show that the functional single neuron netwo...
The network of neurons in our brain generates all of our actions , yet it is not well understood how these neurons coordinate their activity with each other . Rhythmic electrical activity that happens at the same time across many different neurons is thought to be crucial for allowing different areas of the brain to co...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2016
Uniting functional network topology and oscillations in the fronto-parietal single unit network of behaving primates
The circadian clock interacts with other regulatory pathways to tune physiology to predictable daily changes and unexpected environmental fluctuations . However , the complexity of circadian clocks in higher organisms has prevented a clear understanding of how natural environmental conditions affect circadian clocks an...
Living things face daily , predictable challenges due to the regular day and night cycle imposed by the Earth’s rotation . Many of them have evolved an internal ‘circadian’ clock to anticipate daily changes in the environment . However , nature can also change in unpredictable ways , and in order to survive , organisms...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "chromosomes", "and", "gene", "expression", "computational", "and", "systems", "biology" ]
2017
Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria
The genetic code has been proposed to be a ‘frozen accident , ’ but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree . Since most examples were found anecdotally , it is difficult to draw general conclusions about the evolutionary trajectories of codon re...
All life forms rely on a ‘code’ to translate their genetic information into proteins . This code relies on limited permutations of three nucleotides – the building blocks that form DNA and other types of genetic information . Each ‘triplet’ of nucleotides – or codon – encodes a specific amino acid , the basic component...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "computational", "and", "systems", "biology", "genetics", "and", "genomics" ]
2021
A computational screen for alternative genetic codes in over 250,000 genomes
Brainstem and cerebellar neurons implement an internal model to accurately estimate self-motion during externally generated ( ‘passive’ ) movements . However , these neurons show reduced responses during self-generated ( ‘active’ ) movements , indicating that predicted sensory consequences of motor commands cancel sens...
When seated in a car , we can detect when the vehicle begins to move even with our eyes closed . Structures in the inner ear called the vestibular , or balance , organs enable us to sense our own movement . They do this by detecting head rotations , accelerations and gravity . They then pass this information on to spec...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2017
A unified internal model theory to resolve the paradox of active versus passive self-motion sensation
Alternative pre-mRNA splicing expands the complexity of the transcriptome and controls isoform-specific gene expression . Whether alternative splicing contributes to metabolic regulation is largely unknown . Here we investigated the contribution of alternative splicing to the development of diet-induced obesity . We fo...
The process of building a protein from the information encoded in a gene begins when the gene is copied to form a pre-messenger RNA molecule . This molecule is then edited to produce a final messenger RNA that is “translated” to form the protein . Different segments of the pre-messenger RNA molecule can be removed to c...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology" ]
2016
An alternative splicing program promotes adipose tissue thermogenesis
Venom toxins are invaluable tools for exploring the structure and mechanisms of ion channels . Here , we solve the structure of double-knot toxin ( DkTx ) , a tarantula toxin that activates the heat-activated TRPV1 channel . We also provide improved structures of TRPV1 with and without the toxin bound , and investigate...
Humans and other mammals sense heat using a protein called the transient receptor potential vanilloid ( TRPV1 ) channel . This protein is found in the membranes of a particular type of nerve cell , and it forms a pore that allows certain ions to pass through the membrane . Along with sensing heat , TRPV1 can also be ac...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "structural", "biology", "and", "molecular", "biophysics" ]
2016
Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin
Adolescents are particularly vulnerable to nicotine , the principal addictive component driving tobacco smoking . In a companion study , we found that reduced activity of the translation initiation factor eIF2α underlies the hypersensitivity of adolescent mice to the effects of cocaine . Here we report that nicotine po...
Nicotine addiction is a serious public health problem . People who start using nicotine during adolescence are more likely to become addicted to it during adulthood , but the reasons for this are not well understood . Nicotine causes long-lasting changes in the brain that are responsible for the feelings of pleasure an...
[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]
[ "short", "report", "neuroscience" ]
2016
Translational control of nicotine-evoked synaptic potentiation in mice and neuronal responses in human smokers by eIF2α
Photoactivation ( 'uncaging’ ) is a powerful approach for releasing bioactive small-molecules in living cells . Current uncaging methods are limited by the random distribution of caged molecules within cells . We have developed a mitochondria-specific photoactivation method , which permitted us to release free sphingos...
Fatty or oily molecules called lipids are essential components of the membranes of cells and important signaling molecules too . They are made in specific compartments of the cell , but most are found in all membranes , albeit in varying amounts . Their widespread distribution suggests that there are extensive networks...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "biochemistry", "and", "chemical", "biology", "cell", "biology", "tools", "and", "resources" ]
2018
Mitochondria-specific photoactivation to monitor local sphingosine metabolism and function
Serotonin is implicated in mood and affective disorders . However , growing evidence suggests that a core endogenous role is to promote flexible adaptation to changes in the causal structure of the environment , through behavioral inhibition and enhanced plasticity . We used long-term photometric recordings in mice to ...
Serotonin is a molecule that plays various roles in the human body . In the brain , it is involved in regulating mood and emotions . Growing evidence suggests that serotonin also helps animals – including humans – adapt their behavior to changes in their environment . To allow for such behavioral flexibility , serotoni...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "neuroscience" ]
2017
Activity patterns of serotonin neurons underlying cognitive flexibility
Entosis is a form of epithelial cell cannibalism that is prevalent in human cancer , typically triggered by loss of matrix adhesion . Here , we report an alternative mechanism for entosis in human epithelial cells , driven by mitosis . Mitotic entosis is regulated by Cdc42 , which controls mitotic morphology . Cdc42 de...
For over a century , scientists looking down microscopes at samples from human cancers have noticed cells eating other cells – in other words , cell cannibalism . The causes and mechanisms involved in this unusual process , which is also known as entosis , are not well understood and its relationship to cancer is compl...
[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]
[ "cell", "biology", "cancer", "biology" ]
2017
Mitosis can drive cell cannibalism through entosis
The etiological underpinnings of amyotrophic lateral sclerosis ( ALS ) are complex and incompletely understood , although contributions to pathogenesis by regulators of proteolytic pathways have become increasingly apparent . Here , we present a novel variant in UBQLN4 that is associated with ALS and show that its expr...
Amyotrophic lateral sclerosis , or ALS for short , is a disease in which parts of the brain and spinal cord progressively degenerate . Specifically , the condition causes the nerve cells that control movement – called motor neurons – to die . As a result , people with ALS lose control of their muscles . The cause of AL...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "short", "report", "cell", "biology", "neuroscience" ]
2017
A novel ALS-associated variant in UBQLN4 regulates motor axon morphogenesis
Spontaneous DNA breaks instigate genomic changes that fuel cancer and evolution , yet direct quantification of double-strand breaks ( DSBs ) has been limited . Predominant sources of spontaneous DSBs remain elusive . We report synthetic technology for quantifying DSBs using fluorescent-protein fusions of double-strand ...
Cells have developed a variety of mechanisms for repairing DNA molecules when breaks occur in one or both of the DNA strands . However , we know relatively little about the causes of these breaks , which often occur naturally , or even about how common they are . Learning more about the most common forms of DNA breakag...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "chromosomes", "and", "gene", "expression" ]
2013
Engineered proteins detect spontaneous DNA breakage in human and bacterial cells
In response to Ca2+ influx , a synapse needs to release neurotransmitters quickly while immediately preparing for repeat firing . How this harmonization is achieved is not known . In this study , we found that the Ca2+ sensor synaptotagmin 1 orchestrates the membrane association/disassociation cycle of Rab3 , which fun...
Neurons communicate with one another at junctions called synapses . The arrival of an electrical signal called an action potential causes calcium ions to enter the first cell , which in turn triggers the release of molecules called neurotransmitters into the gap between the neurons . The binding of these molecules to r...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology", "neuroscience" ]
2015
Synaptotagmin 1 directs repetitive release by coupling vesicle exocytosis to the Rab3 cycle
Modulation of synaptic vesicle retrieval is considered to be potentially important in steady-state synaptic performance . Here we show that at physiological temperature endocytosis kinetics at hippocampal and cortical nerve terminals show a bi-phasic dependence on electrical activity . Endocytosis accelerates for the f...
Neurons communicate with each other at specialized junctions called synapses . When signals travelling along a neuron reach the presynaptic cell , this triggers small packages ( vesicles ) containing neurotransmitter molecules to release their contents into the synapse , and these molecules then cross the gap and bind ...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "cell", "biology", "neuroscience" ]
2013
Dynamin phosphorylation controls optimization of endocytosis for brief action potential bursts
Large herbivores influence ecosystem functioning via their effects on vegetation at different spatial scales . It is often overlooked that the spatial distribution of large herbivores results from their responses to interacting top-down and bottom-up ecological gradients that create landscape-scale variation in the str...
In almost every ecosystem on Earth , communities of herbivores are kept in check by both predators and the availability of the plants they eat . As herbivores move in response to these pressures , they shape local plant communities and impact vegetation across entire landscapes . Yet the role of large plant-eating mamm...
[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]
[ "ecology" ]
2019
Linking spatial patterns of terrestrial herbivore community structure to trophic interactions
Enzymes can increase the rate of biomolecular reactions by several orders of magnitude . Although the steps of substrate capture and product release are essential in the enzymatic process , complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conf...
Enzymes are proteins that catalyse biochemical reactions . They bind to their target molecules—known as substrates—and help to change them to make ‘products’ . Afterwards , the products are released and the enzymes are free to bind to the next molecules . To perform this activity , an enzyme can change its structure se...
[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]
[ "short", "report", "structural", "biology", "and", "molecular", "biophysics" ]
2015
Structure of a low-population intermediate state in the release of an enzyme product
A founding paradigm in virology is that the spatial unit of the viral replication cycle is an individual cell . Multipartite viruses have a segmented genome where each segment is encapsidated separately . In this situation the viral genome is not recapitulated in a single virus particle but in the viral population . Ho...
Many viruses are small particles consisting of genetic material surrounded by a coat made of proteins . They are unable to multiply on their own and so they must enter a host cell and trick it into reading their genetic information to produce new virus particles . It is generally thought that the process of making new ...
[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]
[ "short", "report", "microbiology", "and", "infectious", "disease" ]
2019
A multicellular way of life for a multipartite virus
The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor ( TF ) binding to crucial DNA sequence elements . However , it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template . In...
Cells contain thousands of genes that are encoded by molecules of DNA . In yeast and other eukaryotic organisms , this DNA is wrapped around proteins called histones to make structures called nucleosomes . This compacts the DNA and allows it to fit inside the tiny nucleus within the cell . The positioning of the nucleo...
[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]
[ "biochemistry", "and", "chemical", "biology" ]
2015
Dynamic regulation of transcription factors by nucleosome remodeling