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Post-translational modifications of histones play a key role in DNA-based processes , like transcription , by modulating chromatin structure . N-terminal acetylation is unique among the numerous histone modifications because it is deposited on the N-alpha amino group of the first residue instead of the side-chain of am...	The genome of eukaryotic cells is packaged into nucleosomes consisting of an octamer of histone proteins that is wrapped around by DNA . Histone proteins are often modified with chemical groups that can influence the arrangement of nucleosomes and thereby affect DNA-based processes like transcription . Histone N-termin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	N-alpha-terminal Acetylation of Histone H4 Regulates Arginine Methylation and Ribosomal DNA Silencing
The epidemiology of Chagas disease , until recently confined to areas of continental Latin America , has undergone considerable changes in recent decades due to migration to other parts of the world , including Spain . We studied the prevalence of Chagas disease in Latin American patients treated at a health center in ...	Chagas disease is a parasitic infection caused by the protozoan Trypanosoma cruzi , and is becoming an emerging health problem in non-endemic areas because of growing population movements . The clinical manifestations of chronic T . cruzi infection include the latent form ( the indeterminate chronic form ) , the cardia...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "health", "screening", "public", "health", "and", "epidemiology", "chagas", "disease", "primary", "care", "neglected", "tropical", "diseases", "public", "health" ]	2011	Chagas Disease among the Latin American Adult Population Attending in a Primary Care Center in Barcelona, Spain
During the pachytene stage of meiosis in male mammals , the X and Y chromosomes are transcriptionally silenced by Meiotic Sex Chromosome Inactivation ( MSCI ) . MSCI is conserved in therian mammals and is essential for normal male fertility . Transcriptomics approaches have demonstrated that in mice , most or all prote...	During male germ cell formation , the X and the Y chromosomes are inactivated . This process is conserved and it is essential for germ cell generation . It is believed that X/Y silencing affects all protein-coding genes , but the status of miRNAs and other non-coding genes needs further investigation . MicroRNAs from t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Silencing of X-Linked MicroRNAs by Meiotic Sex Chromosome Inactivation
An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures . We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies . Genome sequence data from 142 individuals across 17 species identified narrow regions associated...	Butterflies show an amazing diversity of patterns on their wings . In fact , most of the 18 , 000 species of butterfly can be distinguished on the basis of their wing pattern . Much of this diversity is thought to arise through novel switches in the genome that turn genes on in new contexts during wing development , th...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling
Neonates , including mice and humans , are highly susceptible to cytomegalovirus ( CMV ) infection . However , many aspects of neonatal CMV infections such as viral cell tropism , spatio-temporal distribution of the pathogen as well as genesis of antiviral immunity are unknown . With the use of reporter mutants of the ...	Neonates are highly susceptible to a number of infections that usually cause disease only in immunocompromised individuals , most likely because of their incompletely developed immune system . Although this phenomenon has been frequently observed , immune responses of neonates remain largely undefined upon infections w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Nodular Inflammatory Foci Are Sites of T Cell Priming and Control of Murine Cytomegalovirus Infection in the Neonatal Lung
Prion diseases are infectious neurodegenerative disorders of humans and animals caused by misfolded forms of the cellular prion protein PrPC . Prions cause disease by converting PrPC into aggregation-prone PrPSc . Chronic wasting disease ( CWD ) is the most contagious prion disease with substantial lateral transmission...	Chronic wasting disease ( CWD ) is a prion disease which affects wild and captive cervids . Prion diseases are infectious neurodegenerative disorders , and the causative agent consists of abnormally folded prion protein termed PrPSc . Prions replicate without genetic information , and their three-dimensional structure ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chronic", "wasting", "disease", "animal", "diseases", "medicine", "and", "health", "sciences", "deer", "molecular", "dynamics", "ruminants", "engineering", "and", "technology", "vertebrates", "animals", "mammals", "animal", "models", "animal", "prion", "diseases", "m...	2017	Destabilizing polymorphism in cervid prion protein hydrophobic core determines prion conformation and conversion efficiency
Microsporidia ( Fungi ) have been repeatedly identified as the cause of opportunistic infections predominantly in immunodeficient individuals such as AIDS patients . However , the global epidemiology of human microsporidiosis is poorly understood and the ability of microsporidia to survive and multiply in immunocompete...	Microsporidia are a group of obligate intracellular parasitic fungi that have risen over the past two decades from obscure organisms to well recognized human pathogens . Out of 14 species reported to infect humans and causing more severe symptoms in immunocompromised individuals , microsporidia of the species Encephali...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology", "veterinary", "science" ]	2011	Latent Microsporidial Infection in Immunocompetent Individuals – A Longitudinal Study
While the static magnitude of thermal pain perception has been shown to follow a power-law function of the temperature , its dynamical features have been largely overlooked . Due to the slow temporal experience of pain , multiple studies now show that the time evolution of its magnitude can be captured with continuous ...	We propose a model of thermal pain perception that accounts for its dynamical behavior , and can be used to predict subjective responses to thermal stimulation on individual subjects with high accuracy , close to 90% averaged over subjects ( over 65% for the null hypothesis ) . The model is based on behavioral consider...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "cognitive", "neuroscience", "fmri", "computational", "neuroscience", "biology", "computational", "biology", "pain", "neuroscience", "neuroimaging" ]	2012	Predictive Dynamics of Human Pain Perception
Autophagy plays a crucial role in health and disease , regulating central cellular processes such as adaptive stress responses , differentiation , tissue development , and homeostasis . However , the role of autophagy in human physiology is poorly understood , highlighting a need for a model human organ system to asses...	Human scalp hair follicles ( HFs ) experience a massive growth for years , until they spontaneously enter into a rapid , apoptosis-driven organ involution process , orchestrated by an organ-intrinsic “hair cycle clock , ” the molecular control of which remains unclear . Human HFs maintain in vivo–like characteristics ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "fluorescence", "imaging", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "keratinocytes", "hair", "growth", "integumentary", "system", "catagen", "phase", "scalp", "cell", "processes", "epithelial", "cells", "physiological", ...	2018	Autophagy is essential for maintaining the growth of a human (mini-)organ: Evidence from scalp hair follicle organ culture
The visual system must learn to infer the presence of objects and features in the world from the images it encounters , and as such it must , either implicitly or explicitly , model the way these elements interact to create the image . Do the response properties of cells in the mammalian visual system reflect this cons...	When we look at a visual scene , neurons in our eyes “fire” short , electrical pulses in a pattern that encodes information about the visual world . This pattern passes through a series of processing stages within the brain , eventually leading to cells whose firing encodes high-level aspects of the scene , such as the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/natural", "and", "synthetic", "vision", "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems" ]	2009	A Structured Model of Video Reproduces Primary Visual Cortical Organisation
Across diverse taxa , seminal fluid proteins ( Sfps ) transferred at mating affect the reproductive success of both sexes . Such reproductive proteins often evolve under positive selection between species; because of this rapid divergence , Sfps are hypothesized to play a role in speciation by contributing to reproduct...	Across many species , males transfer both sperm and seminal proteins to their mates . These proteins increase male reproductive success by improving sperm competitive ability and modifying female behavior . In Drosophila , seminal proteins increase female rates of egg-laying and sperm storage and reduce a female's will...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2008	Proteomics Reveals Novel Drosophila Seminal Fluid Proteins Transferred at Mating
Bacterial growth in multicellular communities , or biofilms , offers many potential advantages over single-cell growth , including resistance to antimicrobial factors . Here we describe the interaction between the biofilm-promoting components curli fimbriae and cellulose of uropathogenic E . coli and the endogenous ant...	Most infections of the urinary tract are caused by uropathogenic E . coli . On abiotic surfaces , these bacteria are able to form biofilms , which protect them from various adverse environmental conditions . In this study , we sought to investigate whether two E . coli biofilm components , curli fimbriae and cellulose ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases/urological", "infections", "urology/urological", "infections", "immunology/immune", "response", "immunology/innate", "immunity", "infectious", "diseases/bacterial", "infections", "immunology/immunit...	2010	Uropathogenic Escherichia coli Modulates Immune Responses and Its Curli Fimbriae Interact with the Antimicrobial Peptide LL-37
Human T-lymphotropic virus type 1 ( HTLV-1 ) causes leukaemia or chronic inflammatory disease in ∼5% of infected hosts . The level of proviral expression of HTLV-1 differs significantly among infected people , even at the same proviral load ( proportion of infected mononuclear cells in the circulation ) . A high level ...	The human leukaemia virus HTLV-1 causes a lifelong infection that cannot be cleared by the immune system . By integrating into the host's DNA , the virus can lie dormant within the cell . The virus can then be reactivated , by processes that are only partly understood , causing the infected cell to multiply and leading...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/persistence", "and", "latency", "virology/viral", "replication", "and", "gene", "regulation", "virology", "virology/viruses", "and", "cancer", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression" ]	2008	HTLV-1 Integration into Transcriptionally Active Genomic Regions Is Associated with Proviral Expression and with HAM/TSP
Apicomplexans facilitate host cell invasion through formation of a tight-junction interface between parasite and host plasma membranes called the moving junction ( MJ ) . A complex of the rhoptry neck proteins RONs 2/4/5/8 localize to the MJ during invasion where they are believed to provide a stable anchoring point fo...	Toxoplasma and related apicomplexan parasites are obligate intracellular pathogens that actively invade their host cells , creating a specialized vacuole within which the parasite is able to replicate . Invasion involves the establishment of a tight-junction interface between host and parasite membranes called the movi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parastic", "protozoans", "toxoplasma", "gondii", "microbial", "pathogens", "protozoology", "host-pathogen", "interaction", "biology", "microbiology", "molecular", "cell", "biology", "parasitology" ]	2014	RON5 Is Critical for Organization and Function of the Toxoplasma Moving Junction Complex
Viruses interfere with and usurp host machinery and circumvent defense responses to create a suitable cellular environment for successful infection . This is usually achieved through interactions between viral proteins and host factors . Geminiviruses are a group of plant-infecting DNA viruses , of which some contain a...	Viruses pose a serious threat to field crops worldwide; therefore , understanding the mechanisms of viral disease can help crop improvements . Here , we investigate how Cotton leaf curl Multan virus ( CLCuMuV ) interacts with plant to cause viral disease . We found that CLCuMuV uses its sole satellite-encoded protein β...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "plant", "anatomy", "membrane", "staining", "rna", "extraction", "organisms", "plant", "science", "genetically", "modified", "plants", "molecular", "biology", "techniques", "plants", "extraction", "techniques", "genetic", "engineering", "research", "and",...	2016	CLCuMuB βC1 Subverts Ubiquitination by Interacting with NbSKP1s to Enhance Geminivirus Infection in Nicotiana benthamiana
Mastermind-like 1 ( MAML1 ) is a transcriptional co-activator in the Notch signaling pathway . Recently , however , several reports revealed novel and unique roles for MAML1 that are independent of the Notch signaling pathway . We found that MAML1 enhances the transcriptional activity of runt-related transcription fact...	To identify new molecules involved in bone and cartilage development and/or homeostasis , we utilized approximately 10 , 000 arrayed and addressable cDNA clones , which allowed systematic , efficient , and unbiased screening of cDNAs encoding factors that could activate critical bone differentiation activity via activa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2013	MAML1 Enhances the Transcriptional Activity of Runx2 and Plays a Role in Bone Development
Human cytomegalovirus ( HCMV ) can infect many different cell types in vivo . Two gH/gL complexes are used for entry into cells . gH/gL/pUL ( 128 , 130 , 131A ) shows no selectivity for its host cell , whereas formation of a gH/gL/gO complex only restricts the tropism mainly to fibroblasts . Here , we describe that dep...	gH/gL complexes of herpesviruses are supposed to promote fusion of the viral envelope with cellular membranes . The gH/gL core complex associates with additional proteins which define the tropism for certain cell types by promoting binding to specific receptors . Two alternative gH/gL complexes of human cytomegalovirus...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/host", "invasion", "and", "cell", "entry", "virology" ]	2011	HCMV Spread and Cell Tropism are Determined by Distinct Virus Populations
Rasa3 is a GTPase activating protein of the GAP1 family which targets Ras and Rap1 . Ubiquitous Rasa3 catalytic inactivation in mouse results in early embryonic lethality . Here , we show that Rasa3 catalytic inactivation in mouse hematopoietic cells results in a lethal syndrome characterized by severe defects during m...	Megakaryocytes are the bone marrow cellular precursors of circulating blood platelets and give rise to nascent platelets by forming branching filaments called proplatelets . Terminal differentiation of round megakaryocytes into branched proplatelet forming megakaryocytes is a complex cytoskeletal-driven process which i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "cell", "differentiation", "gene", "function", "animal", "models", "developmental", "biology", "integrins", "model", "organisms", "gtpase", "signaling", "molecular", "development", "cellular", "structures", "and", "organelles", "...	2014	Rasa3 Controls Megakaryocyte Rap1 Activation, Integrin Signaling and Differentiation into Proplatelet
In Caenorhabditis elegans and Drosophila melanogaster , removing the germline precursor cells increases lifespan . In worms , and possibly also in flies , this lifespan extension requires the presence of somatic reproductive tissues . How the somatic gonad signals other tissues to increase lifespan is not known . The l...	Reproductive tissues are known to generate important intercellular signals . For example , in mammals , the reproductive tissues produce steroid hormones such as estrogen and testosterone that have profound effects on development and physiology . Studies of the nematode C . elegans and other organisms have shown that t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits" ]	2010	The Somatic Reproductive Tissues of C. elegans Promote Longevity through Steroid Hormone Signaling
The spatiotemporal control of cell polarity is crucial for the development of multicellular organisms and for reliable polarity switches during cell cycle progression in unicellular systems . A tight control of cell polarity is especially important in haploid budding yeast , where the new polarity site ( bud site ) is ...	In budding yeast , cell polarization ( or the asymmetric distribution of subcellular components ) ensures the targeted transport of proteins and membrane material to the sites of cell growth or cell division in late mitosis . Two conserved members of the Rho-GTPase family , Rho1 and Cdc42 , are master regulators of cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "model", "organisms", "molecular", "cell", "biology", "cell", "division", "cell", "biology", "cytokinesis", "yeast", "and", "fungal", "models", "biology", "saccharomyces", "cerevisiae", "microbiology", "cytoskeleton" ]	2013	A Safeguard Mechanism Regulates Rho GTPases to Coordinate Cytokinesis with the Establishment of Cell Polarity
Because of great challenges and workload in deleting genes on a large scale , the functions of most genes in pathogenic fungi are still unclear . In this study , we developed a high-throughput gene knockout system using a novel yeast-Escherichia-Agrobacterium shuttle vector , pKO1B , in the rice blast fungus Magnaporth...	Magnaporthe oryzae is not only the fungus causing the rice blast disease , which leads to 20–30% losses in rice production , but also a primary model pathosystem for understanding host-pathogen interactions . However , there is no high-throughput gene knockout system constructed , and little is known about most of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "medical", "microbiology", "fungal", "genetics", "gene", "expression", "genetics", "microbial", "pathogens", "biology", "and", "life", "sciences", "gene", "disruption", "microbiology", "microbial", "genetics", "fungal", "pathogens", "gene", "function" ]	2014	Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus
Cdk1 kinase phosphorylates budding yeast Srs2 , a member of UvrD protein family , displays both DNA translocation and DNA unwinding activities in vitro . Srs2 prevents homologous recombination by dismantling Rad51 filaments and is also required for double-strand break ( DSB ) repair . Here we examine the biological sig...	Broken DNA molecules can be repaired by copying a homologous DNA sequence located elsewhere in the genome . This process , called homologous recombination , needs to be carefully regulated , because unwanted DNA exchanges can lead to genome rearrangements and cell death . Cdk1 kinase is required for cell cycle progress...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/recombination", "genetics", "and", "genomics/gene", "function", "molecular", "biology/dna", "repair" ]	2010	Cdk1 Targets Srs2 to Complete Synthesis-Dependent Strand Annealing and to Promote Recombinational Repair
Ca2+ contributes to a myriad of important cellular processes in all organisms , including the apicomplexans , Plasmodium and Toxoplasma . Due to its varied and essential roles , free Ca2+ is tightly regulated by complex mechanisms . These mechanisms are therefore of interest as putative drug targets . One pathway in Ca...	Calcium is vital to all living organisms . It is used within cells to regulate many essential processes and , because of this , its cellular concentration is tightly controlled . To change cellular calcium levels , cells use calcium transport proteins . These proteins can alter calcium concentration by moving calcium i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "toxoplasma", "gondii", "microbiology", "plasmodium", "falciparum", "parasitic", "diseases", "parasitology", "parasite", "physiology", "parastic", "protozoans", "calcium", "signaling", "infectious", "diseases", "signaling", "in", "cellular", "processes", "biolog...	2013	The Plasmodium berghei Ca2+/H+ Exchanger, PbCAX, Is Essential for Tolerance to Environmental Ca2+ during Sexual Development
For genome-wide association studies in family-based designs , we propose a new , universally applicable approach . The new test statistic exploits all available information about the association , while , by virtue of its design , it maintains the same robustness against population admixture as traditional family-based...	In genome-wide association studies , the multiple testing problem and confounding due to population stratification have been intractable issues . Family-based designs have considered only the transmission of genotypes from founder to nonfounder to prevent sensitivity to the population stratification , which leads to th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/complex", "traits" ]	2009	On the Analysis of Genome-Wide Association Studies in Family-Based Designs: A Universal, Robust Analysis Approach and an Application to Four Genome-Wide Association Studies
Break-induced replication ( BIR ) is a mechanism to repair double-strand breaks ( DSBs ) that possess only a single end that can find homology in the genome . This situation can result from the collapse of replication forks or telomere erosion . BIR frequently produces various genetic instabilities including mutations ...	Maintaining genomic stability is important to prevent birth defects , genetic disorders and other diseases , including cancer . Double-strand DNA breaks ( DSBs ) , which can result from exposure of living cells to ionizing radiation and various chemicals , threaten genomic integrity , thus making DSB repair essential ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "nucleic", "acids", "dna", "dna", "repair", "biology", "dna", "recombination", "molecular", "genetics", "computational", "biology" ]	2014	Cascades of Genetic Instability Resulting from Compromised Break-Induced Replication
Nipah virus ( NiV ) is a highly pathogenic re-emerging virus that causes outbreaks in South East Asia . Currently , no approved and licensed vaccine or antivirals exist . Here , we investigated the efficacy of ChAdOx1 NiVB , a simian adenovirus-based vaccine encoding NiV glycoprotein ( G ) Bangladesh , in Syrian hamste...	Nipah virus was discovered in 1998 after an outbreak in Malaysia . Since then , several outbreaks have been reported in Bangladesh and India . Although most outbreaks are relatively small , a very high case-fatality rate is reported ( 75% ) . Furthermore , human-to-human transmission has been reported . Currently , no ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "respiratory", "infections", "immunology", "geographical", "locations", "vertebrates", "animals", "mammals", "pulmonology", "vaccines", "preventive", "medicine", "infectious", ...	2019	A single-dose ChAdOx1-vectored vaccine provides complete protection against Nipah Bangladesh and Malaysia in Syrian golden hamsters
Chloroplast genomes in land plants contain approximately 100 genes , the majority of which reside in polycistronic transcription units derived from cyanobacterial operons . The expression of chloroplast genes is integrated into developmental programs underlying the differentiation of photosynthetic cells from non-photo...	Chloroplasts are subcellular organelles in plants and algae that carry out the core reactions of photosynthesis . Chloroplasts originated as cyanobacterial endosymbionts . Subsequent coevolution with their eukaryotic host resulted in a massive transfer of genes to the nuclear genome , the acquisition of new gene expres...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "cell", "biology", "messenger", "rna", "chloroplasts", "dna", "transcription", "plant", "science", "molecular", "biology", "techniques", "photosynthesis", "cellular", "structures", "and", "organelles", "genetic", "footprinting", "research", "and", "analysis", "...	2016	Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize
Prophylactic vaccination is a powerful tool for reducing the burden of infectious diseases , due to a combination of direct protection of vaccinees and indirect protection of others via herd immunity . Computational models play an important role in devising strategies for vaccination by making projections of its impact...	Vaccines are vital tools for safeguarding public health from a variety of infectious disease threats . When decisions are being made about investments in vaccination , computational models provide decision makers with projections of the benefits of vaccination . There are many types of uncertainty that can affect these...	[ "Abstract", "Introduction", "Model", "overview", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "animals", "simulation", "and", "modeling", "vaccines", "preventive", "medicine", "vir...	2019	An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections
We have asked how the common S34F mutation in the splicing factor U2AF1 regulates alternative splicing in lung cancer , and why wild-type U2AF1 is retained in cancers with this mutation . A human lung epithelial cell line was genetically modified so that U2AF1S34F is expressed from one of the two endogenous U2AF1 loci ...	Large-scale genomics studies have identified recurrent mutations in many genes that fall outside the conventional domain of proto-oncogenes . They include genes encoding factors that mediate RNA splicing; mutations affecting four of these genes are present in up to half of proliferative myeloid disorders and in a signi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "adenocarcinoma", "of", "the", "lung", "medicine", "and", "health", "sciences", "messenger", "rna", "carcinomas", "cancers", "and", "neoplasms", "cloning", "alternative", "splicing", "oncology", "mutation", "genome", "analysis", "adenocarcino...	2016	Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival
Kaposi's sarcoma ( KS ) is the most common cancer among HIV-positive patients . Histogenetic origin of KS has long been elusive due to a mixed expression of both blood and lymphatic endothelial markers in KS tumor cells . However , we and others discovered that Kaposi's sarcoma herpes virus ( KSHV ) induces lymphatic r...	Kaposi's sarcoma ( KS ) is the most common cancer in HIV-positive patients and KS-associated herpes virus ( KSHV ) was identified as its causing agent . We and others have discovered that when the virus infects endothelial cells of blood vessels , KSHV reprograms the cell type resembling endothelial cells in lymphatic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "infectious", "diseases/hiv", "infection", "and", "aids", "virology/viruses", "and", "cancer", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "cell", "biology/gene", "expr...	2010	Kaposin-B Enhances the PROX1 mRNA Stability during Lymphatic Reprogramming of Vascular Endothelial Cells by Kaposi's Sarcoma Herpes Virus
Repositioning existing drugs for new therapeutic uses is an efficient approach to drug discovery . We have developed a computational drug repositioning pipeline to perform large-scale molecular docking of small molecule drugs against protein drug targets , in order to map the drug-target interaction space and find nove...	Most drugs are designed to bind to and inhibit the function of a disease target protein . However , drugs are often able to bind to ‘off-target’ proteins due to similarities in the protein binding sites . If an off-target is known to be involved in another disease , then the drug has potential to treat the second disea...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "mechanics", "biochemistry", "small", "molecules", "chemistry", "biology", "computational", "chemistry", "drug", "discovery" ]	2011	A Computational Approach to Finding Novel Targets for Existing Drugs
The influenza virus uses the hemagglutinin ( HA ) and neuraminidase ( NA ) glycoproteins to interact with and infect host cells . While biochemical and microscopic methods allow examination of the early steps in flu infection , the genesis of progeny virions has been more difficult to follow , mainly because of difficu...	Enveloped viruses such as the influenza virus cause significant disease in humans . In order to cause a productive infection , the virus particle must interact with the host cell using the viral proteins encoded within its genome . For many such viruses , it is possible to directly observe the early steps in infection ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biochemistry", "chemical", "biology", "immunology", "biology", "microbiology", "chemistry" ]	2012	Chemoenzymatic Site-Specific Labeling of Influenza Glycoproteins as a Tool to Observe Virus Budding in Real Time
Previous studies have demonstrated the role of volatile organic compounds ( VOCs ) produced by skin microbiota in the attraction of mosquitoes to humans . Recently , behavioral experiments confirmed the importance of VOCs released by skin microbiota in the attraction of Rhodnius prolixus ( Hemiptera: Triatominae ) , a ...	Volatile organic compounds released by bacteria growing on human skin are mediating human-blood-sucking insects interactions . In this study we were interested in those volatile organic compounds produced in vitro by skin bacterial metabolism that are involved in the Rhodnius prolixus interaction with humans . Rhodnius...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "skin", "invertebrates", "medicine", "and", "health", "sciences", "integumentary", "system", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "face", "pathogens", "microbiology", "organic", "compounds", "animals", "animal", "models", "animal", "beh...	2018	Behavioral responses of Rhodnius prolixus to volatile organic compounds released in vitro by bacteria isolated from human facial skin
Plant microRNAs ( miRNA ) guide cleavage of target mRNAs by DICER-like proteins , thereby reducing mRNA abundance . Native precursor miRNAs can be redesigned to target RNAs of interest , and one application of such artificial microRNA ( amiRNA ) technology is to generate plants resistant to pathogenic viruses . Transge...	RNA viruses are well-known for their tremendous capacity to evolve , a characteristic that threatens the development of effective antiviral strategies . A new antiviral strategy was recently proposed to control plant RNA viruses that relied on the expression in plants of artificial microRNAs ( amiRNAs ) targeting short...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virus", "evolution", "and", "symbiosis", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance" ]	2009	Molecular Evolution of a Viral Non-Coding Sequence under the Selective Pressure of amiRNA-Mediated Silencing
In prokaryotic genomes the number of transcriptional regulators is known to be proportional to the square of the total number of protein-coding genes . A toolbox model of evolution was recently proposed to explain this empirical scaling for metabolic enzymes and their regulators . According to its rules , the metabolic...	It has been previously reported that in prokaryotic genomes the number of transcriptional regulators is proportional to the square of the total number of genes . We recently offered a general explanation of this empirical powerlaw scaling in terms of the “toolbox” model in which metabolic and regulatory networks co-evo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "physics/interdisciplinary", "physics", "computational", "biology/transcriptional",...	2011	A Toolbox Model of Evolution of Metabolic Pathways on Networks of Arbitrary Topology
Life has effectively colonized most of our planet and extremophilic organisms require specialized enzymes to survive under harsh conditions . Cold-loving organisms ( psychrophiles ) express heat-labile enzymes that possess a high specific activity and catalytic efficiency at low temperatures . A remarkable universal ch...	Cold-adapted organisms require specialized enzymes to maintain functional integrity at low temperatures , and psychrophiles express heat-labile enzymes that possess a high specific activity and catalytic efficiency at low temperatures . The high catalytic rates are achieved by enzyme adaptations yielding lower activati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physics", "biochemistry", "computer", "and", "information", "sciences", "computer", "modeling", "biocatalysis", "thermodynamics", "catalysis", "free", "energy", "biology", "and", "life", "sciences", "chemistry", "physical", "sciences", "biophysics", "biophysical", "simul...	2014	Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin
Epstein-Barr virus ( EBV ) infection often occurs in early childhood and is asymptomatic . However , if delayed until adolescence , primary infection may manifest as acute infectious mononucleosis ( AIM ) , a febrile illness characterised by global CD8+ T-cell lymphocytosis , much of it reflecting a huge expansion of a...	Primary infection with EBV , a common human herpesvirus , is typically asymptomatic in childhood but , if occurring in adolescence or later , often presents as AIM . This febrile illness is characterised by high virus loads in the blood and an exaggerated EBV-specific CD8+ T-cell response that pushes total CD8+ T-cell ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Early Virological and Immunological Events in Asymptomatic Epstein-Barr Virus Infection in African Children
The group model is a useful tool to understand broad-scale patterns of interaction in a network , but it has previously been limited in use to food webs , which contain only predator-prey interactions . Natural populations interact with each other in a variety of ways and , although most published ecological networks o...	Ecological interactions are highly diverse even when considering a single species: the species might feed on a first , disperse the seeds of a second , and pollinate a third . Here we extend the group model , a method for identifying broad patterns of interaction across a food web , to networks which contain multiple t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	What Can Interaction Webs Tell Us About Species Roles?
The small genome of polyomaviruses encodes a limited number of proteins that are highly dependent on interactions with host cell proteins for efficient viral replication . The SV40 large T antigen ( LT ) contains several discrete functional domains including the LXCXE or RB-binding motif , the DNA binding and helicase ...	Viruses have evolved numerous mechanisms to counteract host cell defenses to facilitate productive infection . Simian Virus 40 ( SV40 ) replication depends on specific interactions between large T antigen ( LT ) and a wide variety of host cell proteins . Although the LT C-terminal region has no evident enzymatic activi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "protein", "interactions", "virulence", "factors", "and", "mechanisms", "proteins", "virology", "biology", "microbiology", "host-pathogen", "interaction" ]	2012	Identification of FAM111A as an SV40 Host Range Restriction and Adenovirus Helper Factor
Trypanosoma cruzi is the etiologic agent of Chagas disease throughout the Americas . Few population-level studies have examined the epidemiology of canine infection and strain types of T . cruzi that infect canines in the USA . We conducted a cross-sectional study of T . cruzi infection in working hound dogs in south c...	The parasite Trypanosoma cruzi can cause Chagas disease in humans and dogs . The parasite is typically spread through the feces of a blood-sucking ‘kissing bug’ insect . Despite many documented cases in dogs across Texas , there are few population-level research studies investigating canine Chagas disease in multi-dog ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "united", "states", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "geographical", "locations", "vector-borne", "diseases", "vertebrates", "parasitic", "diseases", "dogs", "parasitic", "protozoans", "animals", "m...	2017	Epidemiology and Molecular Typing of Trypanosoma cruzi in Naturally-Infected Hound Dogs and Associated Triatomine Vectors in Texas, USA
Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is causally associated with Kaposi’s sarcoma , primary effusion lymphoma ( PEL ) and multicentric Castleman’s disease . The IFIT family of proteins inhibits replication of some viruses , but their effects on KSHV lytic replication was unknown . Here we show that KSHV lyt...	The innate immune response to infections is triggered by recognition of pathogens as foreign or non-self . Recognition of invading pathogens is carried out by various sensors or pattern recognition receptors ( PRRs ) that detect conserved features of pathogens including lipids , nucleic acids and proteins . PRR activat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "drugs", "messenger", "rna", "microbiology", "antimalarials", "viruses", "small", "nuclear", "rna", "dna", "replication", "antibio...	2019	Human IFIT proteins inhibit lytic replication of KSHV: A new feed-forward loop in the innate immune system
In learning from trial and error , animals need to relate behavioral decisions to environmental reinforcement even though it may be difficult to assign credit to a particular decision when outcomes are uncertain or subject to delays . When considering the biophysical basis of learning , the credit-assignment problem is...	The key mechanisms supporting memory and learning in the brain rely on changing the strength of synapses which control the transmission of information between neurons . But how are appropriate changes determined when animals learn from trial and error ? Information on success or failure is likely signaled to synapses b...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "decision", "making", "neural", "networks", "neuroscience", "learning", "and", "memory", "cognitive", "neuroscience", "synaptic", "plasticity", "population", "modeling", "computational", "neuroscience", "population", "biology", "animal", "cognition", "coding", "mechanisms",...	2011	Spatio-Temporal Credit Assignment in Neuronal Population Learning
We developed a model of cardiac sarcomere contraction to study the calcium-tension relationship in cardiac muscle . Calcium mediates cardiac contraction through its interactions with troponin ( Tn ) and subsequently tropomyosin molecules . Experimental studies have shown that a slight increase in intracellular calcium ...	Cardiac contraction is the culmination of multiple subcellular processes beginning with calcium induced activation of the contractile machinery . Interestingly , small increases in intracellular calcium concentrations lead to disproportionately large increases in tension development within the cardiac muscle , a phenom...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "myofibrils", "classical", "mechanics", "muscle", "tissue", "muscle", "contraction", "molecular", "motors", "actin", "motors", "chemical", "equilibrium", "motor", "proteins", "cardiac", "muscles", "research", "and", "analysis", ...	2016	Mechano-chemical Interactions in Cardiac Sarcomere Contraction: A Computational Modeling Study
The obligate intracellular parasite Toxoplasma gondii exploits cells of the immune system to disseminate . Upon T . gondii-infection , γ–aminobutyric acid ( GABA ) /GABAA receptor signaling triggers a hypermigratory phenotype in dendritic cells ( DCs ) by unknown signal transduction pathways . Here , we demonstrate tha...	Dendritic cells are considered the gatekeepers of the immune system but can , paradoxically , also function as ‘Trojan horses’ to mediate dissemination of the common intracellular parasite Toxoplasma gondii . Previous work has shown that Toxoplasma hijacks the migratory machinery of dendritic cells by inducing secretio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "neurochemistry", "immune", "physiology", "body", "fluids", "toxoplasma", "gondii", "spleen", "neuroscience", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "tachyzoites", "...	2017	Voltage-dependent calcium channel signaling mediates GABAA receptor-induced migratory activation of dendritic cells infected by Toxoplasma gondii
The microbes that inhabit particular environments must be able to perform molecular functions that provide them with a competitive advantage to thrive in those environments . As most molecular functions are performed by proteins and are conserved between related proteins , we can expect that organisms successful in a g...	Metagenomics provides a unique opportunity to sample the gene content of microbial communities adapted to specific environments and for the study of the correlations between the presence or absence of gene families that occur in organisms within that environment . Such studies provide detailed information about the ada...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/macromolecular", "sequence", "analysis", "computational", "biology/metagenomics", "computational", "biology/ecosystem", "modeling", "biochemistry/bioinformatics" ]	2010	Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families
Some isolates of Yersinia pseudotuberculosis produce the cytotoxic necrotizing factor ( CNFY ) , but the functional consequences of this toxin for host-pathogen interactions during the infection are unknown . In the present study we show that CNFY has a strong influence on virulence . We demonstrate that the CNFY toxin...	Various toxins and effector proteins of bacterial pathogens have been found to manipulate eukaryotic cell machineries to promote persistence and proliferation within their hosts . Many of these virulence factors target small Rho GTPases , but their role in pathogenesis is often unknown . Here , we addressed the express...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2013	The Cytotoxic Necrotizing Factor of Yersinia pseudotuberculosis (CNFY) Enhances Inflammation and Yop Delivery during Infection by Activation of Rho GTPases
Pathogenic treponemes related to Treponema pallidum are both human ( causing syphilis , yaws , bejel ) and animal pathogens ( infections of primates , venereal spirochetosis in rabbits ) . A set of 11 treponemal genome sequences including those of five Treponema pallidum ssp . pallidum ( TPA ) strains ( Nichols , DAL-1...	In the genus Treponema there are several human and animal pathogens that include the causative agent of syphilis ( Treponema pallidum ssp . pallidum; TPA ) , the causative agent of yaws ( T . p . ssp . pertenue; TPE ) , and the causative agent of endemic syphilis ( T . p . ssp . endemicum; TEN ) . T . paraluisleporidar...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "urology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "membrane", "proteins", "treponematoses", "bacterial", "diseases", "outer", "membrane", "proteins", "sexually", "transmit...	2019	Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution
Analysis of polymorphism and divergence in the non-coding portion of the human genome yields crucial information about factors driving the evolution of gene regulation . Candidate cis-regulatory regions spanning more than 15 , 000 genes in 15 African Americans and 20 European Americans were re-sequenced and aligned to ...	It has been suggested that changes in gene expression may have played a more important role in the evolution of modern humans than changes in protein-coding sequences . In order to identify signatures of natural selection on candidate cis-regulatory regions , we examined single nucleotide polymorphisms obtained from th...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "computational", "biology/population", "genetics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "evolutionary", "biology/human", "evolution", "genetics", ...	2009	Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence
Tick-borne diseases are the most prevalent vector-borne diseases in Europe . Knowledge on the incidence and clinical presentation of other tick-borne diseases than Lyme borreliosis and tick-borne encephalitis is minimal , despite the high human exposure to these pathogens through tick bites . Using molecular detection ...	Two most common tick-borne diseases in Europe are Lyme borreliosis and tick-borne encephalitis . Ticks transmit many more pathogens , causing neglected diseases such as anaplasmosis , babesiosis , rickettsiosis and neoehrlichiosis . These diseases are seldom diagnosed , due to their mild and non-characteristic symptoms...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "borrelia", "infection", "rheumatology", "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "ixodes", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "animals", "parasitic", "protozoans", "parasitol...	2016	Molecular Detection of Tick-Borne Pathogens in Humans with Tick Bites and Erythema Migrans, in the Netherlands
C . canimorsus 5 has the capacity to grow at the expenses of glycan moieties from host cells N-glycoproteins . Here , we show that C . canimorsus 5 also has the capacity to deglycosylate human IgG and we analyze the deglycosylation mechanism . We show that deglycosylation is achieved by a large complex spanning the out...	Capnocytophaga canimorsus are Gram-negative bacteria from the normal oral flora of dogs and cats . They cause rare but severe infections in humans that have been bitten or simply licked by a dog or cat . Fulminant septicemia and peripheral gangrene with a high mortality are the most common symptoms . A surprising featu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gram", "negative", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "pathogenesis" ]	2011	The N-glycan Glycoprotein Deglycosylation Complex (Gpd) from Capnocytophaga canimorsus Deglycosylates Human IgG
Intestinal microfold ( M ) cells possess a high transcytosis capacity and are able to transport a broad range of materials including particulate antigens , soluble macromolecules , and pathogens from the intestinal lumen to inductive sites of the mucosal immune system . M cells are also the primary pathway for delivery...	Secretory IgA ( SIgA ) antibodies are secreted into the gut lumen and are considered to be a first line of defense in protecting the intestinal epithelium from gut pathogens . SIgA patrol the mucus and are usually known to help immune tolerance via entrapping dietary antigens and microorganisms and other mechanisms . S...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Dectin-1 Is Essential for Reverse Transcytosis of Glycosylated SIgA-Antigen Complexes by Intestinal M Cells
Beta-cell apoptosis and failure to induce beta-cell regeneration are hallmarks of type 2-like diabetes in mouse models . Here we show that islets from obese , diabetes-susceptible New Zealand Obese ( NZO ) mice , in contrast to diabetes-resistant C57BL/6J ( B6 ) -ob/ob mice , do not proliferate in response to an in-viv...	Complex genetic determinants contribute to an inherent susceptibility of type 2 diabetes , characterized by insulin resistance , a dysfunction and loss of insulin-producing beta-cells . We compared the islet expression profile and the genome of two obese mouse strains that react differently when receiving a caloric enr...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Identification of Four Mouse Diabetes Candidate Genes Altering β-Cell Proliferation
Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes . The class contains nematode-trapping fungi that form unique infection structures , called traps , to capture and kill free-living nematodes . The traps have evolved differently along several lineages and include adhesive traps ( k...	Nematode-trapping fungi are a group of soil-living fungi found worldwide . They capture and kill nematodes and are used as biocontrol agents against parasitic nematodes . The infection structures differ morphologically . Their traps can be classified into several main groups , including adhesive knobs , adhesive nets ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Genomic Mechanisms Accounting for the Adaptation to Parasitism in Nematode-Trapping Fungi
Epidermal growth factor receptor variant III ( EGFRvIII ) has been associated with glioma stemness , but the direct molecular mechanism linking the two is largely unknown . Here , we show that EGFRvIII induces the expression and secretion of pigment epithelium-derived factor ( PEDF ) via activation of signal transducer...	Malignant gliomas are among the most lethal types of cancer , due in part to the stem-cell-like characteristics and invasive properties of the brain tumor cells . However , little is known about the underlying molecular mechanisms that govern such processes . Here , we identify pigment epithelium-derived factor ( PEDF ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Pigment Epithelium-Derived Factor (PEDF) Expression Induced by EGFRvIII Promotes Self-renewal and Tumor Progression of Glioma Stem Cells
Estrogens act by binding to estrogen receptors alpha and beta ( ERα , ERβ ) , ligand-dependent transcription factors that play crucial roles in sex differentiation , tumor growth and cardiovascular physiology . Estrogens also activate the G protein-coupled estrogen receptor ( GPER ) , however the function of GPER in vi...	Estrogen hormones are important for the formation and function of the nervous , reproductive and cardiovascular systems . Here we report that acute exposure to estrogens increases heart rate , a previously unappreciated function of estrogens . Using zebrafish with mutations in genes that respond to estrogens , we found...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "fish", "nervous", "system", "cardiovascular", "anatomy", "vertebrates", "neuroscience", "animals", "hormones", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "heart", "experimental", "organis...	2017	G protein-coupled estrogen receptor regulates embryonic heart rate in zebrafish
Schistosomiasis has a considerable impact on public health in many tropical and subtropical areas . In the new world , schistosomiasis is caused by the digenetic trematode Schistosoma mansoni . Chemotherapy is the main measure for controlling schistosomiasis , and the current drug of choice for treatment is praziquante...	Schistosomiasis causes severe health problems and economic losses in transmission areas in the Americas , Africa , and Southeast Asia . In regions where treatment is available , such as Brazil , chemotherapy has led to decreased morbidity of the disease . However , parasite resistance to drugs is of general concern . D...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2013	Praziquantel Treatment Decreases Schistosoma mansoni Genetic Diversity in Experimental Infections
Canine malignant melanoma , a significant cause of mortality in domestic dogs , is a powerful comparative model for human melanoma , but little is known about its genetic etiology . We mapped the genomic landscape of canine melanoma through multi-platform analysis of 37 tumors ( 31 mucosal , 3 acral , 2 cutaneous , and...	Melanoma , a cancer arising from transformed melanocytes , commonly occurs in pet dogs . Unlike human melanoma , most often occurring in sun-exposed cutaneous skin , canine melanoma typically arises in sun-shielded oral mucosa . Canine melanoma clinically resembles human melanoma , particularly sun-shielded subtypes . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cancer", "genomics", "dermatology", "medicine", "and", "health", "sciences", "cancers", "and", "neoplasms", "basic", "cancer", "research", "oncology", "skin", "neoplasms", "mutation", "cutaneous", "melanoma", "mammalian", "genomics", "molecular", "genetics", "mapk", ...	2018	Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis
Type I interferons ( including IFNαβ ) are innate cytokines that may contribute to pathogenesis during Mycobacterium tuberculosis ( Mtb ) infection . To induce IFNβ , Mtb must gain access to the host cytosol and trigger stimulator of interferon genes ( STING ) signaling . A recently proposed model suggests that Mtb tri...	Bacterial strains from the Mycobacterium tuberculosis complex ( MTBC ) infect one in three humans , however not all infected individuals progress to active tuberculosis disease . It is unknown why immunocompetent individuals develop tuberculosis , and this presents a significant challenge in preventing the disease . On...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "oxides", "mitochondrial", "dna", "physiological", "processes", "forms", "of", "dna", "mitochondria", "dna", "bioenergetics", "cellular", "structures", "and", "organelles", "bacteria", "proteins", "chemis...	2016	The Mechanism for Type I Interferon Induction by Mycobacterium tuberculosis is Bacterial Strain-Dependent
Among the several new antimalarials discovered over the past decade are at least three clinical candidate drugs , each with a distinct chemical structure , that disrupt Na+ homeostasis resulting in a rapid increase in intracellular Na+ concentration ( [Na+]i ) within the erythrocytic stages of Plasmodium falciparum . A...	Malaria remains a major public health challenge in the world , especially with the realization that parasites causing the disease are becoming resistant to currently used antimalarial drugs . There are new antimalarial drugs under development , and among these are 3 clinical candidate drugs that have the propensity to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "trophozoites", "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "membrane", "proteins", "apicomplexa", "protozoans", "pharmaceutics", "cellular", "structures", "and", "organelle...	2016	Na+ Influx Induced by New Antimalarials Causes Rapid Alterations in the Cholesterol Content and Morphology of Plasmodium falciparum
An enduring theme in pathogenic microbiology is poor understanding of the mechanisms of host specificity . Metarhizium is a cosmopolitan genus of invertebrate pathogens that contains generalist species with broad host ranges such as M . robertsii ( formerly known as M . anisopliae var . anisopliae ) as well as speciali...	Host selectivity and host switching have been widely documented in diverse pathogens , but in most cases the underlying mechanisms are poorly understood . Entomopathogenic fungi in the genus Metarhizium are being used as environmentally friendly alternatives to chemical insecticides in agricultural and human disease-ve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "mycology", "pest", "control", "fungal", "evolution", "microbial", "control", "biology", "microbiology", "host-pathogen", "interaction", "infectious", "disease", "control", "agriculture", "pathogenesis" ]	2011	Insertion of an Esterase Gene into a Specific Locust Pathogen (Metarhizium acridum) Enables It to Infect Caterpillars
Aedes albopictus , the Asian tiger mosquito , is a vector of several arboviruses including dengue and chikungunya , and is also a significant nuisance mosquito . It is one of the most invasive of mosquitoes with a relentlessly increasing geographic distribution . Conventional control methods have so far failed to contr...	The Asian Tiger mosquito , Aedes albopictus , is a highly invasive species which took advantage of human activity to spread from South-East Asia to Africa , North and South America , and Europe in the past forty years . Beyond the annoying biting nuisance , this mosquito is also a significant public health threat , cap...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "entomology", "synthetic", "biology", "biology", "zoology", "molecular", "biology" ]	2012	Female-Specific Flightless (fsRIDL) Phenotype for Control of Aedes albopictus
Schistosomiasis affects nearly 40 million women of reproductive age , and is known to elicit a pro-inflammatory signature in the placenta . We have previously shown that antigens from schistosome eggs can elicit pro-inflammatory cytokine production from trophoblast cells specifically; however , the influence of these a...	Approximately 40 million women of childbearing age suffer from schistosome infection globally at any given time . Multiple studies in rodent models , as well as a few reports in humans , suggest that schistosome infection results in poor pregnancy outcomes . We have previously shown that antigens released from schistos...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "schistosomiasis", "obstetrics", "and", "gynecology", "pregnancy", "global", "health", "neglected", "tropical", "diseases" ]	2013	Schistosoma japonicum Soluble Egg Antigens Attenuate Invasion in a First Trimester Human Placental Trophoblast Model
Emerging evidence indicates that gene products implicated in human cancers often cluster together in “hot spots” in protein-protein interaction ( PPI ) networks . Additionally , small sub-networks within PPI networks that demonstrate synergistic differential expression with respect to tumorigenic phenotypes were recent...	Intensive research on cancer has led to an understanding of many individual genes that may be important for the initiation and progression of tumors . However , since cancer is a progressive disease that results from accumulation of multiple mutations likely acting in concert , individual markers can only provide limit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/systems", "biology", "oncology/gastrointestinal", "cancers", "biotechnology/protein", "chemistry", "and", "proteomics" ]	2010	An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer
Visceral leishmaniasis ( VL ) is a vector-borne disease affecting humans and domestic animals that constitutes a serious public health problem in many countries . Although many antigens have been examined so far as protein- or DNA-based vaccines , none of them conferred complete long-term protection . The use of the li...	Visceral leishmaniasis ( VL ) is the most severe form of leishmaniasis and has emerged as an opportunistic infection in HIV-1 infected patients in many parts of the world . Drug-resistant forms have developed so emergence and increased the need for advanced preventive strategies . Using live avirulent organisms as a va...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology", "veterinary", "science" ]	2013	Development of Novel Prime-Boost Strategies Based on a Tri-Gene Fusion Recombinant L. tarentolae Vaccine against Experimental Murine Visceral Leishmaniasis
Large-scale gene expression datasets are providing an increasing understanding of the location of cis-eQTLs in the human genome and their role in disease . However , little is currently known regarding the extent of regulatory site-sharing between genes . This is despite it having potentially wide-ranging implications ...	Where a gene’s regulatory site is disrupted by a genetic variant , its expression levels will vary between individuals depending on the version of the variant they carry . Such genetic loci , termed eQTLs , have been found to be disproportionately associated with disease and have proven to be a powerful tool for identi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "evolution", "gene", "regulation", "human", "genomics", "mathematics", "epigenetics", "mammalian", "genomics", "chromatin", "discrete", "mathematics", "combinatorics", "chromosome", "biology", "gene", "expression", "molecular", "evolution", "evolutionary", "geneti...	2017	Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy
Chronic obstructive pulmonary disease ( COPD ) is a leading cause of global morbidity and mortality and , whilst smoking remains the single most important risk factor , COPD risk is heritable . Of 26 independent genomic regions showing association with lung function in genome-wide association studies , eleven have been...	Very large genome-wide association studies in general population cohorts have successfully identified at least 26 genes or gene regions associated with lung function and a number of these also show association with chronic obstructive pulmonary disease ( COPD ) . However , these findings explain a small proportion of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "chronic", "obstructive", "pulmonary", "disease", "psychology", "medicine", "and", "health", "sciences", "addiction", "genetic", "association", "studies", "genome", "analysis", "recreational", "drug", "addiction", "genetics", "biol...	2014	Whole Exome Re-Sequencing Implicates CCDC38 and Cilia Structure and Function in Resistance to Smoking Related Airflow Obstruction
Dengue virus ( DENV ) has emerged as major human pathogen . Despite the serious socio-economic impact of DENV-associated diseases , antiviral therapy is missing . DENV replicates in the cytoplasm of infected cells and induces a membranous replication organelle , formed by invaginations of the endoplasmic reticulum memb...	Dengue virus ( DENV ) is one of the most prevalent mosquito-transmitted human pathogens . The only licensed vaccine has limited efficacy and an antiviral therapy is not available . The multifunctional non-structural protein 1 ( NS1 ) of DENV is secreted from infected cells , counteracts antiviral immune response and co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "dengue", "virus", "medicine", "and", "health", "sciences", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "insertion", "mutation", "pathogens", "microbiology", "viruses", "physiological", "processes", "mutation", "rna", "viruses"...	2019	A novel interaction between dengue virus nonstructural protein 1 and the NS4A-2K-4B precursor is required for viral RNA replication but not for formation of the membranous replication organelle
To be able to colonize its host , invading Salmonella enterica serovar Typhimurium must disrupt and severely affect host-microbiome homeostasis . Here we report that S . Typhimurium induces acute infectious colitis by inhibiting peroxisome proliferator-activated receptor gamma ( PPARγ ) expression in intestinal epithel...	Enteric pathogens like S . Typhimurium convert the host intestine into an inflamed environment in which they are well adapted to thrive . However , the precise strategy that this pathogen employs to achieve such favorable conditions for its survival remains unclear . Here , we uncovered a novel mechanism whereby S . Ty...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gastroenterology", "and", "hepatology", "medicine", "biology", "microbiology" ]	2014	Absence of Intestinal PPARγ Aggravates Acute Infectious Colitis in Mice through a Lipocalin-2–Dependent Pathway
The chromosomes of multicellular animals are organized into a series of topologically independent looped domains . This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome . A special set of architectural elements , called boundaries or insulat...	The chromosomes of multicellular animals are organized into a series of topologically independent looped domains . This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome . A special set of architectural elements , called boundaries or insulat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "homologous", "chromosomes", "chromosome", "structure", "and", "function", "developmental", "biology", "insulators", "materials", "science", "epigenetics", "embryos", "chromatin", "embryology", "chromosome", "biology", "gene", "expression", "materials", "by", "attribute", ...	2016	Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans
We reviewed studies that analyzed cysticercosis ( CC ) , neurocysticercosis ( NCC ) and epilepsy across Latin America , Asia and Sub-Saharan Africa , to estimate the odds ratio and etiologic fraction of epilepsy due to CC in tropical regions . We conducted a systematic review of the literature on cysticercosis and epil...	Cysticercosis is a helminthic infection of the central nervous system ( CNS ) and the leading cause of late onset epilepsy in low-and middle-income countries . This neurological disease is a public health problem in Sub-Saharan Africa , Asia and Latin America , affecting impoverished rural and peri-urban populations wh...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "diagnostic", "radiology", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "neuroscience", "mathematics", "statistics", "(mathematics)", "neglected", "tropical", "diseases"...	2017	Systematic review and meta-analysis estimating association of cysticercosis and neurocysticercosis with epilepsy
Halobacterium salinarum is a bioenergetically flexible , halophilic microorganism that can generate energy by respiration , photosynthesis , and the fermentation of arginine . In a previous study , using a genome-scale metabolic model , we have shown that the archaeon unexpectedly degrades essential amino acids under a...	Living cells can produce usable energy through various means . For example , animals derive energy , through respiration , from nutrients that they consume , and plants from light using photosynthesis . The particular microorganism that we study , Halobacterium salinarum , is a model organism for the archaeal domain of...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "physiology", "and", "metabolism", "biochemistry/bioinformatics", "computational", "biology/metabolic", "networks", "computational", "biology/systems", "biology" ]	2009	Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum
One of network epidemiology's central assumptions is that the contact structure over which infectious diseases propagate can be represented as a static network . However , contacts are highly dynamic , changing at many time scales . In this paper , we investigate conceptually simple methods to construct static graphs f...	To understand how diseases spread in a population , it is important to study the network of people in contact . Many methods to model epidemic outbreaks make the assumption that one can treat this network as static . In reality , we know that contact patterns between people change in time , and old contacts are soon ir...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "social", "and", "behavioral", "sciences", "infectious", "disease", "epidemiology", "epidemiology", "social", "networks", "sociology", "population", "biology", "biology", "infectious", "disease", "modeling" ]	2013	Epidemiologically Optimal Static Networks from Temporal Network Data
Studies of social microbes often focus on one fitness component ( reproductive success within the social complex ) , with little information about or attention to other stages of the life cycle or the ecological context . This can lead to paradoxical results . The life cycle of the social amoeba Dictyostelium discoideu...	Fitness in social microbes is often measured in terms of reproductive success in the social stage , with little regard to other stages of the life cycle ( e . g . solitary ) or to the ecological context . This approach can lead to seemingly paradoxical results that point to complex social interactions ( e . g . , socia...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "death", "rates", "cell", "death", "ecology", "and", "environmental", "sciences", "dictyostelium", "fruiting", "body", "demography", "cell", "cycle", "and", "cell", "division", "dictyosteliomycota", "cell", "processes", "microbiology", "dictyostelium", "spore", "cells",...	2016	Lack of Ecological and Life History Context Can Create the Illusion of Social Interactions in Dictyostelium discoideum
Ixodes scapularis is the most medically important tick species and transmits five of the 14 reportable human tick borne disease ( TBD ) agents in the USA . This study describes LC-MS/MS identification of 582 tick- and 83 rabbit proteins in saliva of I . scapularis ticks that fed for 24 , 48 , 72 , 96 , and 120 h , as w...	Ixodes scapularis , the blacklegged tick or the deer tick , is among the most medically important ticks that transmit human tick borne disease agents including the spirochaete Lyme disease agent . To develop new tick control methods , a deeper understanding of how the tick feeds is needed . We collected saliva from rab...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2016	Ixodes scapularis Tick Saliva Proteins Sequentially Secreted Every 24 h during Blood Feeding
North African populations are distinct from sub-Saharan Africans based on cultural , linguistic , and phenotypic attributes; however , the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood . Here , we interrogate the multilayered history of North Africa...	Proposed migrations between North Africa and neighboring regions have included Paleolithic gene flow from the Near East , an Arabic migration across the whole of North Africa 1 , 400 years ago ( ya ) , and trans-Saharan transport of slaves from sub-Saharan Africa . Historical records , archaeology , and mitochondrial a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "evolution", "genome", "scans", "population", "genetics", "gene", "pool", "genome", "analysis", "tools", "effective", "population", "size", "population", "biology", "genetic", "polymorphism", "biology", "evolutionary", "genetics", "genetic", "drift", "haplotyp...	2012	Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Ecological and laboratory studies have demonstrated that temperature modulates West Nile virus ( WNV ) transmission dynamics and spillover infection to humans . Here we explore whether inclusion of temperature forcing in a model depicting WNV transmission improves WNV forecast accuracy relative to a baseline model depi...	West Nile virus ( WNV ) is the leading cause of domestically acquired arthropod-borne viral disease in the United States . Here we show that accurate retrospective forecasts of mosquito infection rates and human WNV cases can be generated for a variety of locations in the U . S . Incorporation of temperature forcing in...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "atmospheric", "science", "pathogens", "microbiology", "vertebrates", "animals", "viruses", "seasons", "mathematics", "rna", "viruses", "forecasting", "statistics", "(m...	2018	Use of temperature to improve West Nile virus forecasts
Understanding how populations of neurons encode sensory information is a major goal of systems neuroscience . Attempts to answer this question have focused on responses measured over several hundred milliseconds , a duration much longer than that frequently used by animals to make decisions about the environment . How ...	How can humans and animals make complex decisions on time scales as short as 100 ms ? The information required for such decisions is coded in neural activity and should be read out on a very brief time scale . Traditional approaches to coding of neural information rely on the number of electrical pulses , or spikes , t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "neuroscience", "biology", "sensory", "systems", "neuroscience" ]	2012	Fast Coding of Orientation in Primary Visual Cortex
Hepatitis E virus ( HEV ) causes acute hepatitis in many parts of the world including Asia , Africa and Latin America . Though self-limiting in normal individuals , it results in ~30% mortality in infected pregnant women . It has also been reported to cause acute and chronic hepatitis in organ transplant patients . Of ...	Hepatitis E virus ( HEV ) is one of the most common causes of acute and sporadic viral hepatitis . It is a small positive strand RNA virus , which is transmitted through the feco-oral route . Owing to lack of sanitation and unavailibility of safe drinking water , populations of developing and resource starved countries...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "nucleic", "acid", "synthesis", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "immunology", "enzymology", "microbiology", "viruses", "immunoprecipitation", "rna", "synthesis", "antibo...	2016	Endoplasmic Reticulum Stress Induced Synthesis of a Novel Viral Factor Mediates Efficient Replication of Genotype-1 Hepatitis E Virus
Highly phagocytic macrophages line the marginal zone ( MZ ) of the spleen and the lymph node subcapsular sinus . Although these macrophages have been attributed with a variety of functions , including the uptake and clearance of blood and lymph-borne pathogens , little is known about the effector mechanisms they employ...	Macrophages are phagocytic cells that play a dual role in infection . They can kill ingested micro-organisms and thus help eliminate the threat from infection , but some pathogens have adapted to survive within macrophages and use the intracellular niche they provide as a means of immune evasion . Although it has long ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immunity", "to", "infections", "microbiology/parasitology", "immunology/innate", "immunity" ]	2010	Innate Killing of Leishmania donovani by Macrophages of the Splenic Marginal Zone Requires IRF-7
Methicillin-resistant Staphylococcus aureus ( MRSA ) is an important human pathogen , which is cross-resistant to virtually all β-lactam antibiotics . MRSA strains are defined by the presence of mecA gene . The transcription of mecA can be regulated by a sensor-inducer ( MecR1 ) and a repressor ( MecI ) , involving a u...	Methicillin-resistance Staphylococcus aureus ( MRSA ) is an important human pathogen , causing a wide range of infections . MRSA strains are resistant to virtually all β-lactam antibiotics and often are also resistant to many other classes of antibiotics , leaving physicians with few therapeutic options . MRSA is defin...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "cellular", "stress", "responses", "mechanisms", "of", "signal", "transduction", "gene", "regulation", "microbiology", "dna", "transcription", "bacterial", "diseases", "methicillin-resistant", "staphylococcus", "aureus", "microbial", "evolution", ...	2012	The Anti-Repressor MecR2 Promotes the Proteolysis of the mecA Repressor and Enables Optimal Expression of β-lactam Resistance in MRSA
An important objective in genome research is to relate genome structure to gene function . Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences of functional significance . Here , we describe a 379-kb region on chromosome 1 of maize that enables us to reconstruct c...	Plant genomes analyzed to date contain 15% or more genes that are arranged in tandem arrays . Tandem duplications are a source for allelic variability since their homologous sequences can serve in recombination events . For example , unequal crossing over between amplified genes can result in contraction and expansion ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology/plant", "genomes", "and", "evolution", "evolutionary", "biology/plant", "genetics", "and", "gene", "expression" ]	2009	Change of Gene Structure and Function by Non-Homologous End-Joining, Homologous Recombination, and Transposition of DNA
The membrane scission event that separates nascent enveloped virions from host cell membranes often requires the ESCRT pathway , which can be engaged through the action of peptide motifs , termed late ( L- ) domains , in viral proteins . Viral PTAP and YPDL-like L-domains bind directly to the ESCRT-I and ALIX component...	The release of an enveloped virus particle from an infected cell requires the separation of the viral and cell membranes . Many enveloped viruses accomplish this by parasitizing a set of cellular proteins , termed the ESCRT pathway , that normally separates cellular membranes from each other . In some cases , viral str...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/membranes", "and", "sorting", "virology/virion", "structure,", "assembly,", "and", "egress" ]	2010	Functional Interchangeability of Late Domains, Late Domain Cofactors and Ubiquitin in Viral Budding
Recent studies have demonstrated that the DNA methylome changes with age . This epigenetic drift may have deep implications for cellular differentiation and disease development . However , it remains unclear how much of this drift is functional or caused by underlying changes in cell subtype composition . Moreover , no...	Two well-known features of aging are the gradual decline of the body’s ability to regenerate tissues , as well as an increased incidence of diseases like cancer and Alzheimers . One of the most recent exciting findings which may underlie the aging process is a gradual modification of DNA , called epigenetic drift , whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusions", "Methods" ]	[]	2015	An Integrative Multi-scale Analysis of the Dynamic DNA Methylation Landscape in Aging
Naturally acquired clinical immunity to Plasmodium falciparum is partly mediated by antibodies directed at parasite-derived antigens expressed on the surface of red blood cells which mediate disease and are extremely diverse . Unlike children , adults recognize a broad range of variant surface antigens ( VSAs ) and are...	Immunity to human malaria parasites never fully protects against infection , even after a lifetime of exposure . By contrast , protection against severe disease occurs early in life in malaria-endemic areas . Both anti-infection and anti-disease immunity depend on antibody responses to proteins expressed by the parasit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "serum", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "parasitic", "diseases", "sequence", "motif", "analysis", "molecular", "biology", "...	2019	Antigenic cartography of immune responses to Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1)
The evolution of heteromorphic sex chromosomes creates a genetic condition favoring the invasion of sex-ratio meiotic drive elements , resulting in the biased transmission of one sex chromosome over the other , in violation of Mendel's first law . The molecular mechanisms of sex-ratio meiotic drive may therefore help u...	Mendel's first law of genetics states that two alleles of a heterozygote are transmitted to the next generation at an equal ratio . The cornerstone of population genetics , this law states that the evolutionary fate of genetic variants is solely governed by their contribution to the good of their carriers . However , m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "evolutionary", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2007	A sex-ratio Meiotic Drive System in Drosophila simulans. II: An X-linked Distorter
Genome-wide association studies using commercially available outbred mice can detect genes involved in phenotypes of biomedical interest . Useful populations need high-frequency alleles to ensure high power to detect quantitative trait loci ( QTLs ) , low linkage disequilibrium between markers to obtain accurate mappin...	We show that commercially available mice are a resource for detecting single genes by genome-wide association . We surveyed 66 populations and identified those with properties conducive to high-resolution mapping . Importantly , we show that the same alleles contribute to variation in different colonies , so that when ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/disease", "models" ]	2010	Commercially Available Outbred Mice for Genome-Wide Association Studies
Movement of the transcription machinery along a template alters DNA topology resulting in the accumulation of supercoils in DNA . The positive supercoils generated ahead of transcribing RNA polymerase ( RNAP ) and the negative supercoils accumulating behind impose severe topological constraints impeding transcription p...	The generation of DNA topological constraint is intrinsic to transcription . Although in vitro studies indicated DNA gyrase and topoisomerase I action in the removal of excess supercoils , ahead and behind the transcribing RNA polymerase , in vivo recruitment and interaction of both topoisomerases with the genome has n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "microbiology", "dna", "transcription", "bacterial", "genetics", "sequence", "motif", "analysis", "dna", "microbial", "genetics", "bacteria", "microbial", "genomics", "research", "and", "analysis", "methods", "sequence", "analysis", "bacterial", "genomics"...	2017	Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Trypanosoma cruzi is the causative agent of Chagas' disease . Novel chemotherapy with the drug K11777 targets the major cysteine protease cruzain and disrupts amastigote intracellular development . Nevertheless , the biological role of the protease in infection and pathogenesis remains unclear as cruzain gene knockout ...	Trypanosoma cruzi ( T . cruzi ) is the unicellular parasite that causes Chagas' disease , a devastating health burden throughout Latin America now also affecting developed countries . Macrophages are the first cells that become infected by T . cruzi and disseminate the infection to other tissues . The parasite then pre...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2011	The Trypanosoma cruzi Protease Cruzain Mediates Immune Evasion
Aβ peptide accumulation is thought to be the primary event in the pathogenesis of Alzheimer's disease ( AD ) , with downstream neurotoxic effects including the hyperphosphorylation of tau protein . Glycogen synthase kinase-3 ( GSK-3 ) is increasingly implicated as playing a pivotal role in this amyloid cascade . We hav...	Alzheimer's disease ( AD ) is the leading cause of dementia in the ageing population . Symptoms include memory loss and decline in understanding and reasoning . Alois Alzheimer , who reported the first case of AD , observed plaques and tangles in the brains of patients . The plaques are made up of amyloid protein , whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "geriatrics/dementia", "genetics", "and", "genomics/animal", "genetics", "neurological", "disorders/alzheimer", "disease" ]	2010	Inhibition of GSK-3 Ameliorates Aβ Pathology in an Adult-Onset Drosophila Model of Alzheimer's Disease
The metabolism of microorganisms is regulated through two main mechanisms: changes of enzyme capacities as a consequence of gene expression modulation ( “hierarchical control” ) and changes of enzyme activities through metabolite-enzyme interactions . An increasing body of evidence indicates that hierarchical control i...	Metabolism is a fundamental biochemical process that enables cells to operate and grow by converting nutrients into ‘building blocks’ and energy . Metabolism happens through the work of enzymes , which are encoded by genes . Thus , genes and their regulation are often thought of controlling metabolism , somewhat at the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "carbohydrate", "metabolism", "chemical", "compounds", "enzymes", "metabolic", "networks", "enzymology", "carbohydrates", "glucose", "metabolism", "organic", "compounds", "glucose", "cell", "metabolism", "network", "analysis", "enzyme", "metabolism", ...	2017	Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli
Mutations are a critical driver of cancer initiation . While extensive studies have focused on exposure-induced mutations , few studies have explored the importance of tissue physiology as a modulator of mutation susceptibility in vivo . Of particular interest is inflammation , a known cancer risk factor relevant to ch...	People with chronic inflammatory conditions have a markedly increased risk for cancer . In addition , many cancers have an inflammatory microenvironment that promotes tumor growth . Here , we show that inflammatory infiltration synergizes with tissue regeneration to induce DNA sequence rearrangements in vivo . Chronica...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Inflammation-Induced Cell Proliferation Potentiates DNA Damage-Induced Mutations In Vivo
Advances in proteomic technologies continue to substantially accelerate capability for generating experimental data on protein levels , states , and activities in biological samples . For example , studies on receptor tyrosine kinase signaling networks can now capture the phosphorylation state of hundreds to thousands ...	Proteomic measurements , especially modification measurements , are greatly expanding the current knowledge of the state of proteins under various conditions . Harnessing these measurements to understand how these modifications are enzymatically regulated and their subsequent function in cellular signaling and physiolo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "bioengineering", "systems", "biology", "biochemistry", "biological", "systems", "engineering", "biology", "computational", "biology", "proteomics", "genetics", "and", "genomics", "engineering" ]	2011	MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets
Dysregulation of sleep and feeding has widespread health consequences . Despite extensive epidemiological evidence for interactions between sleep and metabolic function , little is known about the neural or molecular basis underlying the integration of these processes . D . melanogaster potently suppress sleep in respo...	Neural regulation of sleep and feeding are interconnected and are critical for survival . Many animals reduce their sleep in response to starvation , presumably to forage for food . Here , we find that in the fruit fly Drosophila melanogaster , the neuropeptide leucokinin is required for the modulation of starvation-de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "chemical", "compounds", "statistics", "sleep", "green", "fluorescent", "protein", "carbohydrates", "neuroscience", "animals", "organic", "compounds", "glucose", "animal", "models", "physiolo...	2019	A single pair of leucokinin neurons are modulated by feeding state and regulate sleep–metabolism interactions
After obtaining certification of the absence of transmission of the Trypanosoma cruzi by Triatoma infestans in 2006 , other native species of protozoan vectors have been found in human dwellings within municipalities of the State of Paraná , Southern Brazil . However , the spatial distribution of T . cruzi vectors and ...	Trypanosoma cruzi , the etiologic agent of Chagas' disease ( CD ) , circulates among humans , vectors and domestic and wild reservoirs . Frequent invasion of housing by infected triatomines may present a risk of vector transmission from T . cruzi to humans . The objective of this study was to predict the potential dist...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "atmospheric", "science", "population", "dynamics", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "animals", ...	2018	Spatial prediction of risk areas for vector transmission of Trypanosoma cruzi in the State of Paraná, southern Brazil
The leishmanioses , vector-borne diseases caused by the trypanosomatid protozoan Leishmania , are transmitted to susceptible mammals by infected phlebotomine sand flies that inoculate promastigotes into hemorrhagic pools created in host skin . We assumed that promastigotes are delivered to a blood pool , and analyzed e...	Leishmania infection is transmitted to mammalian hosts by phlebotomine sand flies . During the vector's bloodmeal , promastigotes are inoculated into hemorrhagic spots in the skin or are delivered into the extracellular matrix of the dermis . In the first case , blood is involved in transmission; in the second , it app...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/innate", "immunity" ]	2010	Kinetic Analysis of Ex Vivo Human Blood Infection by Leishmania
The t-tubules of mammalian ventricular myocytes are invaginations of the cell membrane that occur at each Z-line . These invaginations branch within the cell to form a complex network that allows rapid propagation of the electrical signal , and hence synchronous rise of intracellular calcium ( Ca2+ ) . To investigate h...	In cardiac muscle cells , calcium ( Ca2+ ) is best known for its role in contraction activation . A remarkable amount of quantitative data on cardiac cell structure , ion-transporting protein distributions and intracellular Ca2+ dynamics has been accumulated . Various alterations in the protein distributions or cell ul...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cardiovascular", "disorders/arrhythmias,", "electrophysiology,", "and", "pacing", "mathematics", "physiology/cardiovascular", "physiology", "and", "circulation", "biophysics/theory", "and", "simulation", "computational", "biology/systems", "biology" ]	2010	Numerical Analysis of Ca2+ Signaling in Rat Ventricular Myocytes with Realistic Transverse-Axial Tubular Geometry and Inhibited Sarcoplasmic Reticulum
Genome-wide sequence divergence between populations can cause hybrid sterility through the action of the anti-recombination system , which rejects crossover repair of double strand breaks between nonidentical sequences . Because crossovers are necessary to ensure proper segregation of homologous chromosomes during meio...	Different species are kept genetically separated from each other by reproductive isolation , which can result in the production of sterile hybrids . Despite the central role of reproductive isolation in evolutionary biology , the mechanisms underlying hybrid sterility remain controversial . We focus on one potential ca...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion" ]	[ "fungal", "spores", "meiosis", "homologous", "chromosomes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "fungi", "protein", "expression", "model", "organisms", "experimental", "organism", "systems", "molecular", "biology", "techniques", "dna", "fu...	2018	Spore-autonomous fluorescent protein expression identifies meiotic chromosome mis-segregation as the principal cause of hybrid sterility in yeast
Point process generalized linear models ( PP-GLMs ) provide an important statistical framework for modeling spiking activity in single-neurons and neuronal networks . Stochastic stability is essential when sampling from these models , as done in computational neuroscience to analyze statistical properties of neuronal d...	Earthquakes , gene regulatory elements , financial transactions , and action potentials produced by nerve cells are examples of sequences of discrete events in space or time . In many cases , such events do not appear independently of each other . Instead , the occurrence of one event changes the rate of upcoming event...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "optimization", "systems", "science", "mathematics", "computational", "neuroscience", "research", "and", "analysis...	2017	On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs
In many cases , the computation of a neural system can be reduced to a receptive field , or a set of linear filters , and a thresholding function , or gain curve , which determines the firing probability; this is known as a linear/nonlinear model . In some forms of sensory adaptation , these linear filters and gain cur...	Many neurons are known to achieve a wide dynamic range by adaptively changing their computational input/output function according to the input statistics . These adaptive changes can be very rapid , and it has been suggested that a component of this adaptation could be purely input-driven: even a fixed neural system ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/theoretical", "neuroscience", "biophysics/theory", "and", "simulation", "neuroscience/sensory", "systems" ]	2008	Intrinsic Gain Modulation and Adaptive Neural Coding
Yellow skin is an abundant phenotype among domestic chickens and is caused by a recessive allele ( W*Y ) that allows deposition of yellow carotenoids in the skin . Here we show that yellow skin is caused by one or more cis-acting and tissue-specific regulatory mutation ( s ) that inhibit expression of BCDO2 ( beta-caro...	Many bird species possess yellow skin and legs whereas other species have white or black skin color . Yellow or white skin is due to the presence or absence of carotenoids . The genetic basis underlying this diversity is unknown . Domestic chickens with yellow skin are homozygous for a recessive allele , and white skin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/evolutionary", "and", "comparative", "gene...	2008	Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken

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