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Despite the devastating impact of mosquito-borne illnesses on human health , surprisingly little is known about mosquito developmental biology , including development of the olfactory system , a tissue of vector importance . Analysis of mosquito olfactory developmental genetics has been hindered by a lack of means to t...	Although mosquitoes transmit many of the world's deadliest diseases , mosquito developmental biology has been grossly understudied . To address this issue , we have begun to develop the dengue and yellow fever vector Aedes aegypti as an emerging model for understanding mosquito developmental genetics . In this investig...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "developmental", "biology", "developmental", "neuroscience", "infectious", "diseases", "global", "health", "genetics", "sensory", "systems", "biology", "neuroscience", "evolutionary", "developmental", "biology", "gene", "function" ]	2013	Disruption of Aedes aegypti Olfactory System Development through Chitosan/siRNA Nanoparticle Targeting of semaphorin-1a
The development of multicellular organisms relies on interconnected genetic programs that control progression through their life cycle . MicroRNAs ( miRNAs ) and transcription factors ( TFs ) play key roles in such regulatory circuits . Here , we describe how three evolutionary conserved miRNA-TF pairs interact to form...	Development of multicellular organisms relies on properly timed execution of different genetic programs . An example is provided by developmental progression of flowers , which begins with the initiation of individual organs , followed by differentiation , growth , and finally production of the gametes . This article i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "plant", "science", "ecology", "plant", "biology", "genetics", "biology", "genetics", "and", "genomics" ]	2013	Coordination of Flower Maturation by a Regulatory Circuit of Three MicroRNAs
Metastasis remains the primary cause of patient morbidity and mortality in solid tumors and is due to the action of a large number of tumor-autonomous and non-autonomous factors . Here we report the results of a genome-wide integrated strategy to identify novel metastasis susceptibility candidate genes and molecular pa...	Metastasis , the spread and growth of tumor cells from the original tumor to secondary sites throughout the body , is the primary cause of cancer-related death for most solid tumor types . The process of metastasis is very complex , requiring multiple individual steps and the cooperation of different cell types during ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "breast", "tumors", "cancer", "treatment", "cancers", "and", "neoplasms", "basic", "cancer", "research", "oncology", "animal", "models", "model", "organisms", "genome", "analysis", "mammalian", "genomics", "research", "and", ...	2016	An Integrated Genome-Wide Systems Genetics Screen for Breast Cancer Metastasis Susceptibility Genes
Several arboviruses , including dengue virus ( DENV ) , Zika virus ( ZIKV ) and chikungunya virus ( CHIKV ) , transmitted by Aedes mosquitoes , circulate in northeast Brazil . Diseases caused by these viruses are of great public health relevance , however , their epidemiological features in areas where the three viruse...	Infection with Zika ( ZIKV ) and chikungunya ( CHIKV ) viruses can lead to severe symptoms or outcomes . These viruses are transmitted by the same mosquito vectors that transmit dengue virus ( DENV ) and the symptoms of all three diseases are similar , thus , it may be difficult for health professionals to diagnose the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "immunology", "tropical", "diseases", "microbiology", ...	2017	Zika virus displacement by a chikungunya outbreak in Recife, Brazil
Envenomings by snakebites constitute a serious and challenging global health issue . The mainstay in the therapy of snakebite envenomings is the parenteral administration of animal-derived antivenoms . Significantly , antivenoms are only partially effective in the control of local tissue damage . A novel approach to mi...	Snake envenoming affects approximately 2 . 5 million people and causes more than 100 , 000 deaths annually . The WHO includes envenoming as a category A Neglected Tropical Disease . Therapy involves intravenous delivery of animal-derived antivenoms , constituted by IgG from the plasma of mammals immunized with venom . ...	[ "Abstract", "Introduction", "Methods", "and", "materials", "Results", "and", "discussion" ]	[ "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "enzymes", "tropical", "diseases", "enzymology", "vertebrates", "animals", "toxicology", "toxic", "agents", "serine", "proteases", "route...	2018	Engineered nanoparticles bind elapid snake venom toxins and inhibit venom-induced dermonecrosis
In large populations , many beneficial mutations may be simultaneously available and may compete with one another , slowing adaptation . By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population , we find limits to the rate of adaptive substitution , , that depend on ...	In small populations , adaptation may be limited by a lack of beneficial alleles on which selection can act; in such populations , increasing the supply of mutations ( by increasing the population size or the rate of beneficial mutation per individual ) proportionally increases the rate of adaptation . However , when m...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mutation", "effective", "population", "size", "natural", "selection", "population", "genetics", "biology", "evolutionary", "biology", "evolutionary", "genetics", "evolutionary", "theory" ]	2012	Limits to the Rate of Adaptive Substitution in Sexual Populations
The reduced rainfall in southeast Australia has placed this region's urban and rural communities on escalating water restrictions , with anthropogenic climate change forecasts suggesting that this drying trend will continue . To mitigate the stress this may place on domestic water supply , governments have encouraged t...	Current and projected rainfall reduction in southeast Australia has seen the installation of large numbers of government-subsidised and ad hoc domestic water storage containers that could create the possibility of the mosquito Ae . aegypti expanding out of Queensland into southern Australian's urban regions . By assess...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/viral", "infections" ]	2009	Australia's Dengue Risk Driven by Human Adaptation to Climate Change
CpG islands ( CGIs ) are vertebrate genomic landmarks that encompass the promoters of most genes and often lack DNA methylation . Querying their apparent importance , the number of CGIs is reported to vary widely in different species and many do not co-localise with annotated promoters . We set out to quantify the numb...	In the decade since the sequence of the human genome was announced , efforts have been made to annotate all genes with their regulatory sequences . CpG islands are short regions containing the sequence CG at high density that map to regions controlling the expression of most human genes ( known as promoters ) . Using a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "cell", "biology/gene", "expression" ]	2010	Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome
Disease tolerance is a defense strategy against infections that aims at maintaining host health even at high pathogen replication or load . Tolerance mechanisms are currently intensively studied with the long-term goal of exploiting them therapeutically . Because tolerance-based treatment imposes less selective pressur...	Conventional therapies improve patient health by eliminating the pathogen , or , at least , reducing its burden . Recently , alternative therapies that exploit host tolerance mechanisms have received attention from the medical community as a promising strategy . These treatments aim at reducing the level of illness due...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "evolutionary", "ecology", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "pathogens", "microbiology", "mathematical", "models...	2018	Assessing the public health impact of tolerance-based therapies with mathematical models
There is a need for effective methods to control Aedes aegypti and prevent the transmission of dengue , chikungunya , yellow fever and Zika viruses . Insecticide treated screening ( ITS ) is a promising approach , particularly as it targets adult mosquitoes to reduce human-mosquito contact . A cluster-randomised contro...	An ITS based intervention , screened houses with insecticide-treated netting ( long-lasting insecticidal nets permanently fixed with aluminium frames on external doors and windows ) , in Merida city , Mexico . Screened houses had >50% less chance of having Ae . aegypti mosquitoes indoors and importantly , >50% fewer fe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "pathogens", "geographical", "locations", "microbiology", "animals", "alphaviruses", "north", "america", "viruses", "chikungunya", "virus", "rna", "virus...	2018	House screening with insecticide-treated netting provides sustained reductions in domestic populations of Aedes aegypti in Merida, Mexico
Adult schistosomes have a well-developed alimentary tract comprising an oral sucker around the mouth , a short esophagus and a blind ending gut . The esophagus is not simply a muscular tube for conducting blood from the mouth to gut but is divided into compartments , surrounded by anterior and posterior glands , where ...	Schistosomes are parasitic flatworms inhabiting the human bloodstream , surrounded by and feeding on humoral and cellular components of the immune system . They are normally long-lived but the rhesus macaque is able to mount a self-cure response directed against the esophageal secretions of the adult Schistosoma japoni...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusions" ]	[ "sequencing", "techniques", "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "body", "fluids", "helminths", "neuroscience", "animals", "brain", "mapping", "sequence", "motif", "analysis", "molecular", "biology", "technique...	2018	Microexon gene transcriptional profiles and evolution provide insights into blood processing by the Schistosoma japonicum esophagus
Dengue virus ( DENV ) infection is widespread and its disease burden has increased in past decades . However , little is known about the epidemiology of dengue in the Middle East and North Africa ( MENA ) . Following Cochrane Collaboration guidelines and reporting our findings following PRISMA guidelines , we systemati...	Dengue is a mosquito-transmitted flavivirus whose global distribution and disease incidence has increased in recent decades . In the Middle East and North Africa , the epidemiology of dengue remains poorly characterized despite increasing reports of outbreaks and transmission in new areas . In order to understand the e...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusions" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "vector-borne", "diseases", "microbiology", "geographical", "locations", "sudan", "animals", "viruses", "rna", "viruses", ...	2016	Dengue in the Middle East and North Africa: A Systematic Review
In budding yeast , an HO endonuclease-inducible double-strand break ( DSB ) is efficiently repaired by several homologous recombination ( HR ) pathways . In contrast to gene conversion ( GC ) , where both ends of the DSB can recombine with the same template , break-induced replication ( BIR ) occurs when only the centr...	A chromosomal double-strand break ( DSB ) poses a severe threat to genome integrity , and budding yeast cells use several homologous recombination mechanisms to repair the break . In gene conversion ( GC ) , both ends of the DSB share homology to an intact donor locus , and the break is repaired by copying the donor to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/recombination", "molecular", "biology/dna", "repair" ]	2010	Sgs1 and Exo1 Redundantly Inhibit Break-Induced Replication and De Novo Telomere Addition at Broken Chromosome Ends
Thymine DNA glycosylase ( TDG ) functions in base excision repair , a DNA repair pathway that acts in a lesion-specific manner to correct individual damaged or altered bases . TDG preferentially catalyzes the removal of thymine and uracil paired with guanine , and is also active on 5-fluorouracil ( 5-FU ) paired with a...	DNA repair is vital to the survival and propagation of cells . It helps protect DNA from becoming permanently damaged and prevents cells from becoming cancerous . The base excision repair ( BER ) pathway is responsible for the removal of up to 20 , 000 lesions/cell/day . Thymine DNA glycosylase ( TDG ) is one of the DN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "radiobiology" ]	2014	A Germline Polymorphism of Thymine DNA Glycosylase Induces Genomic Instability and Cellular Transformation
The mechanisms underlying the development of disease during arenavirus infection are poorly understood . However , common to all hemorrhagic fever diseases is the involvement of macrophages as primary target cells , suggesting that the immune response in these cells may be of paramount importance during infection . Thu...	It remains unclear how arenavirus infection causes disease; however , for other hemorrhagic fever viruses , infection has been linked to over-production of numerous cytokines by macrophages that can then affect vascular integrity . In order to determine if a similar mechanism might contribute to arenavirus pathogenesis...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immune", "cells", "cytokines", "immune", "activation", "emerging", "viral", "diseases", "immunology", "microbiology", "inflammation", "virulence", "factors", "and", "mechanisms", "biology", "pathogenesis", "immune", "response", "immune", "system", "monocytes", "immunity"...	2011	Tacaribe Virus but Not Junin Virus Infection Induces Cytokine Release from Primary Human Monocytes and Macrophages
The rapid digitization of genealogical and medical records enables the assembly of extremely large pedigree records spanning millions of individuals and trillions of pairs of relatives . Such pedigrees provide the opportunity to investigate the sociological and epidemiological history of human populations in scales muc...	The advent of online genealogy services allows the assembly of population-scale family trees , spanning millions of individuals and centuries of human history . Such datasets enable answering genetic epidemiology questions on unprecedented scales . Here we present Sci-LMM , a pedigree analysis framework that combines t...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "sociology", "social", "sciences", "random", "variables", "covariance", "epistasis", "human", "families", "mathematics", "genetic", "epidemiology", "research", "and", "analysis", "methods", "animal", "studies", "epidemiology", "p...	2019	Estimating variance components in population scale family trees
Tuberculosis , caused by Mycobacterium tuberculosis infection , is a major cause of morbidity and mortality in the world today . M . tuberculosis hijacks the phagosome-lysosome trafficking pathway to escape clearance from infected macrophages . There is increasing evidence that manipulation of autophagy , a regulated c...	Tuberculosis is responsible for approximately 2 million deaths worldwide each year . Current treatment regimens require administration of multiple drugs over several months and resistance to these drugs is on the rise . Mycobacterium tuberculosis , the causative agent of the disease , can proliferate within host cells ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "cells", "small", "molecules", "enzymes", "tor", "signaling", "immunology", "microbiology", "chemical", "biology", "signaling", "in", "cellular", "processes", "enzyme", "classes", "oxidoreductases", "biology", "molecular", "biology", "drug", "discovery", "bioc...	2012	Nitazoxanide Stimulates Autophagy and Inhibits mTORC1 Signaling and Intracellular Proliferation of Mycobacterium tuberculosis
The nonmevalonate pathway is responsible for isoprenoid production in microbes , including H . pylori , M . tuberculosis and P . falciparum , but is nonexistent in humans , thus providing a desirable route for antibacterial and antimalarial drug discovery . We coordinate a structural study of IspH , a [4Fe-4S] protein ...	Drug resistance has recently entered into media conversations through the lens of MRSA ( methicillin-resistant Staphylococcus aureus ) infections , but conventional therapies are also failing to address resistance in cases of malaria and other bacterial infections , such as tuberculosis . To address these problems , we...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs
Co-infections alter the host immune response but how the systemic and local processes at the site of infection interact is still unclear . The majority of studies on co-infections concentrate on one of the infecting species , an immune function or group of cells and often focus on the initial phase of the infection . H...	Infections with different infecting agents can alter the immune response against any one parasite and the relative abundance and persistence of the infections within the host . This is because the immune system is not compartmentalized but acts as a whole to allow the host to maintain control of the infections as well ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "virology", "biology", "microbiology" ]	2012	Network Model of Immune Responses Reveals Key Effectors to Single and Co-infection Dynamics by a Respiratory Bacterium and a Gastrointestinal Helminth
Despite effective control of plasma viremia with the use of combination antiretroviral therapies ( cART ) , minor cognitive and motor disorders ( MCMD ) persist as a significant clinical problem in HIV-infected patients . Non-human primate models are therefore required to study mechanisms of disease progression in the ...	Despite effective control of plasma viremia with the use of combination antiretroviral therapies , neurologic disease resulting from HIV-infection of the central nervous system ( CNS ) persists as a significant clinical problem . Non-human primate models are therefore required to study mechanisms of disease progression...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "nervous", "system", "pathogens", "microbiology", "vertebrates", "cloning", "animals", "mammals", "retroviruses", "primates", "immunodeficiency", "viruses", "viruses",...	2017	A SIV molecular clone that targets the CNS and induces neuroAIDS in rhesus macaques
Soil-transmitted helminth infections are common throughout the tropics and subtropics and they disproportionately affect the poorest of the poor . In view of a growing global commitment to control soil-transmitted helminthiasis , there is a need to elucidate the effect of repeated stool sampling and the use of differen...	Diseases caused by parasitic worms inflict an enormous public health burden in developing countries . There is a growing effort to control worms with drugs . The success of repeated drug administrations can be assessed by measuring the decline in the prevalence and intensity of worm infections . Accurate diagnosis is a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "public", "health", "and", "epidemiology", "pediatrics", "and", "child", "health" ]	2008	Diagnosis of Soil-Transmitted Helminths in the Era of Preventive Chemotherapy: Effect of Multiple Stool Sampling and Use of Different Diagnostic Techniques
The mycobacterial cell envelope has been implicated in the pathogenicity of tuberculosis and therefore has been a prime target for the identification and characterization of surface proteins with potential application in drug and vaccine development . In this study , the genome of Mycobacterium tuberculosis H37Rv was s...	Since the publication of the Mycobacterium tuberculosis genome in 1998 , great expectations have emerged regarding speeding up the process of developing vaccines against tuberculosis . Our group has been focused on identifying molecules localized on the mycobacterial surface that could act as ligands facilitating this ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "biology/bioinformatics", "computational", "biology/comparative", "sequence", "analysis", "microbiology" ]	2010	Computational Prediction and Experimental Assessment of Secreted/Surface Proteins from Mycobacterium tuberculosis H37Rv
A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate . Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells . Developing treatments against biofilms requires an ...	Pseudomonas aeruginosa is one of the most frequently found bacterial pathogens in patients with chronic infections , such as chronic wounds and cystic fibrosis . The persistence of P . aeruginosa in these infections is enabled by its ability to form biofilms . Standard antibiotic treatments , effective against bacteria...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism
Treatment for schistosomiasis , which is responsible for more than 280 , 000 deaths annually , depends exclusively on the use of praziquantel . Millions of people are treated annually with praziquantel and drug resistant parasites are likely to evolve . In order to identify novel drug targets the Schistosoma mansoni se...	Schistosomiasis is a chronic , debilitating disease that affects hundreds of millions of people . The treatment of schistosomiasis relies solely on monotherapy with praziquantel and there is concern that drug-resistant parasites will evolve . Therefore , it is imperative to identify new drugs for schistosomiasis treatm...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "small", "molecules", "enzymes", "parasitic", "diseases", "parasitology", "global", "health", "neglected", "tropical", "diseases", "zoology", "infectious", "diseases", "proteins", "biology", "drug", "discovery", "helminthology", "biochemistry", "schistosomiasis"...	2011	Characterization of the Phytochelatin Synthase of Schistosoma mansoni
Cells are regularly exposed to stress conditions that may lead to protein misfolding . To cope with this challenge , molecular chaperones selectively target structurally perturbed proteins for degradation via the ubiquitin-proteasome pathway . In mammals the co-chaperone BAG-1 plays an important role in this system . B...	The accumulation of misfolded proteins represents a considerable threat to the health of individual cells and has been linked to severe diseases , including cancer and neurodegenerative disorders . To cope with this threat , especially under stress conditions , cells have evolved efficient quality control mechanisms . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cellular", "stress", "responses", "model", "organisms", "proteins", "genetic", "screens", "gene", "identification", "and", "analysis", "chaperone", "proteins", "genetics", "schizosaccharomyces", "pombe", "molecular", "genetics", "yeast", "and", "fungal", ...	2014	A Chaperone-Assisted Degradation Pathway Targets Kinetochore Proteins to Ensure Genome Stability
Type I interferon ( IFN-I ) -dependent orchestrated mobilization of innate cells in inflamed tissues is believed to play a critical role in controlling replication and CNS-invasion of herpes simplex virus ( HSV ) . However , the crucial regulators and cell populations that are affected by IFN-I to establish the early e...	Herpes simplex virus type 1 and 2 ( HSV-1 and HSV-2 ) are the most common cause of genital ulceration in humans worldwide with lifelong latent infection after peripheral replication in mucosal tissues . Furthermore , acquisition of human immunodeficiency virus ( HIV ) is increased in HSV-infected individuals , undersco...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Distinct Upstream Role of Type I IFN Signaling in Hematopoietic Stem Cell-Derived and Epithelial Resident Cells for Concerted Recruitment of Ly-6Chi Monocytes and NK Cells via CCL2-CCL3 Cascade
Resection is an early step in homology-directed recombinational repair ( HDRR ) of DNA double-strand breaks ( DSBs ) . Resection enables strand invasion as well as reannealing following DNA synthesis across a DSB to assure efficient HDRR . While resection of only one end could result in genome instability , it has not ...	DNA double-strand breaks ( DSBs ) can cause genome instability and cancer . While repair can occur through recombination , coincident events at both ends—while assumed—have not been directly addressable at unique or random damage-induced DSBs . Here , we describe pulse-field gel electrophoresis approaches that for the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2013	Coincident Resection at Both Ends of Random, γ–Induced Double-Strand Breaks Requires MRX (MRN), Sae2 (Ctp1), and Mre11-Nuclease
Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae is thought to be important in the adaptation and evolution of this pathogen . While competent pneumococci are able to scavenge DNA added to laboratory cultures , large-scale transfers of multiple kb are rare under these condi...	Bacteria shuffle their genes far less often than humans do and genes or traits are more directly linked with the singular bacterial parent cell rather than the two parents that are involved in sexual reproduction . However , bacteria do occasionally have sex in the form of homologous recombination by taking up external...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biofilms", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pneumococcus", "pathogens", "microbiology", "gene", "transfer", "dna", "filter", "assay", "dna", "molecular", "biology", "techniques", "bacteria", "bacterial", "pathogens...	2018	Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae
The eukaryotic nucleus is both spatially and functionally partitioned . This organization contributes to the maintenance , expression , and transmission of genetic information . Though our ability to probe the physical structure of the genome within the nucleus has improved substantially in recent years , relatively li...	A number of recent studies have debunked the idea that chromosomes exist as a tangled mass of chromatin fibers within the nucleus . In many organisms , including mammals , each chromosome occupies a specific region of the nucleus known as a chromosome territory . This organization has implications for many biological p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chromosome", "structure", "and", "function", "centromeres", "animal", "models", "telomeres", "drosophila", "melanogaster", "model", "organisms", "chromatin", "chromosome", "biology", "biology", "cell", "biology", "genetics", "genomics", "molecular", "cell", "biology", ...	2012	Condensin II Promotes the Formation of Chromosome Territories by Inducing Axial Compaction of Polyploid Interphase Chromosomes
We previously showed that broadly neutralizing anti-HIV-1 antibody 2G12 ( human IgG1 ) naturally forms dimers that are more potent than monomeric 2G12 in in vitro neutralization of various strains of HIV-1 . In this study , we have investigated the protective effects of monomeric versus dimeric 2G12 against HIV-1 infec...	Most successful vaccines function by eliciting antibodies that bind to the surface of pathogens of interest from the host immunologic repertoire . This should also be the case for an HIV-1 vaccine , but broadly neutralizing anti-HIV-1 antibodies have proven hard to elicit with any reagent . Thus , methods to directly a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "immunology/immunity", "to", "infections" ]	2010	Dimeric 2G12 as a Potent Protection against HIV-1
Systems-level genetic studies in humans and model systems increasingly involve both high-resolution genotyping and multi-dimensional quantitative phenotyping . We present a novel method to infer and interpret genetic interactions that exploits the complementary information in multiple phenotypes . We applied this appro...	Parallel advances in genotype and phenotype measurement technologies are yielding large-scale , multidimensional datasets that can potentially decipher the genetic etiology of complex traits . Understanding these data will require methods that combine the experimental power of molecular biology and the quantitative pow...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "epistasis", "systems", "biology", "phenotypes", "heredity", "genetics", "genetic", "suppression", "biology", "computational", "biology", "quantitative", "traits", "gene", "networks", "genetics", "and", "genomics", "complex", "traits" ]	2012	Use of Pleiotropy to Model Genetic Interactions in a Population
The Human Papillomavirus E7 oncoprotein plays an essential role in the development and maintenance of malignancy , which it achieves through targeting a number of critical cell control pathways . An important element in the ability of E7 to contribute towards cell transformation is the presence of a Casein Kinase II ph...	In this study we have used genome editing to mutate the HPV-18 E7 CKII phospho-acceptor site in cells derived from a cervical cancer . We demonstrate that this results in a decrease in cell proliferation and renders the cells particularly susceptible to low nutrient conditions . Furthermore these cells are defective in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "cell", "processes", "microbiology", "viruses", "hpv-18", "physiological", "processes", "dna", "viruses", "human", "papillomavirus"...	2019	The HPV-18 E7 CKII phospho acceptor site is required for maintaining the transformed phenotype of cervical tumour-derived cells
The lineage factor Foxp3 is essential for the development and maintenance of regulatory T cells , but little is known about the mechanisms involved . Here , we demonstrate that an N-terminal proline-rich interaction region is crucial for Foxp3’s function . Subdomains within this key region link Foxp3 to several indepen...	The suppressive activity of regulatory T cells provides the immune system with a mechanism to prevent detrimental immune responses , such as autoimmunity , attack of the beneficial commensal microbiota and rejection of the fetus . Intriguingly , expression of a single lineage factor Foxp3 is sufficient to completely re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding
Duplicate genes emerge as copy-number variations ( CNVs ) at the population level , and remain copy-number polymorphic until they are fixed or lost . The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity , complexity and innovatio...	After a locus is duplicated in a genome , individuals from a population instantaneously differ in the number of copies of this locus producing a copy-number variation ( CNV ) . Over time , the joint effects of selection and other evolutionary forces will act to either eliminate the extra genetic copy or retain it . Dep...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "structural", "genomics", "genomics", "genome", "evolution", "natural", "selection", "genome", "analysis", "genetics", "biology", "and", "life", "sciences", "comparative", "genomics", "molecular", "evolution", "computational", "biology", "evolutionary", "biology", "popula...	2014	Extensive Copy-Number Variation of Young Genes across Stickleback Populations
Natural killer ( NK ) cells serve essential functions in immunity and reproduction . Diversifying these functions within individuals and populations are rapidly-evolving interactions between highly polymorphic major histocompatibility complex ( MHC ) class I ligands and variable NK cell receptors . Specific to simian p...	Natural killer ( NK ) cells are versatile lymphocytes that make essential contributions to immune defense and placental reproduction . Essential to NK cell development , diversification and function are variable families of surface receptors that recognize equally variable determinants of polymorphic major histocompati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "immunology/reproductive", "immunology", "evolutionary", "biology/human", "evolution", "evolutionary", "biology/genomics", "immunology/innate", "immunity", "immunology/genetics", "of", "the", "immune", "system", "infectious",...	2010	Human-Specific Evolution and Adaptation Led to Major Qualitative Differences in the Variable Receptors of Human and Chimpanzee Natural Killer Cells
Foot-and-mouth disease virus ( FMDV ) belongs to the Aphthovirus genus of the Picornaviridae , a family of small , icosahedral , non-enveloped , single-stranded RNA viruses . It is a highly infectious pathogen and is one of the biggest hindrances to the international trade of animals and animal products . FMDV capsids ...	This is the first structure of dissociated pentamers for FMDV , and indeed for any picornavirus . We also present the first visualization of a picornavirus particle assembled from pentamers comprising VP1 , 2 and 3 . The formation of regular assemblies rather than random aggregates has enabled us to solve the structure...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "diseases", "chemical", "compounds", "disaccharides", "foot", "and", "mouth", "disease", "condensed", "matter", "physics", "microbiology", "viral", "structure", "carbohydrates", "organic", "compounds", "electron", "cryo-microscopy", "viruses", "rna", "viruses", ...	2017	Structures of foot and mouth disease virus pentamers: Insight into capsid dissociation and unexpected pentamer reassociation
Plasmodium malariae is widely distributed across the tropics , causing symptomatic malaria in humans with a 72-hour fever periodicity , and may present after latency periods lasting up to many decades . Delayed occurrence of symptoms is observed in humans using chemoprophylaxis , or patients having received therapies t...	Plasmodium malariae is a widely distributed parasite infecting humans across the tropics , and causing symptomatic malaria with a 72-hour fever periodicity . It is rarely studied . This parasite has the notable ability to recur after many decades of apparent absence . Further , people who have received drug treatment f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Delayed Onset of Symptoms and Atovaquone-Proguanil Chemoprophylaxis Breakthrough by Plasmodium malariae in the Absence of Mutation at Codon 268 of pmcytb
Bacterial superantigens ( SAg ) stimulate T-cell hyper-activation resulting in immune modulation and severe systemic illnesses such as Staphylococcus aureus toxic shock syndrome . However , all known S . aureus SAgs are encoded by mobile genetic elements and are made by only a proportion of strains . Here , we report t...	Staphylococcus aureus is a global pathogen , responsible for an array of different illnesses in humans and animals . In particular , community-associated methicillin-resistant S . aureus ( CA-MRSA ) strains of the pandemic USA300 clone have the capacity to cause lethal human necrotizing pneumonia , but the molecular ba...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "staphylococci", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "evolution", "bacterial", "pathogens" ]	2011	A Novel Core Genome-Encoded Superantigen Contributes to Lethality of Community-Associated MRSA Necrotizing Pneumonia
Systemic lupus erythematosus ( SLE ) is an autoimmune disease that causes multiple organ damage . Although recent genome-wide association studies ( GWAS ) have contributed to discovery of SLE susceptibility genes , few studies has been performed in Asian populations . Here , we report a GWAS for SLE examining 891 SLE c...	Although recent genome-wide association study ( GWAS ) approaches have successfully contributed to disease gene discovery , many susceptibility loci are known to be still uncaptured due to strict significance threshold for multiple hypothesis testing . Therefore , prioritization of GWAS results by incorporating additio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "rheumatology", "genome", "analysis", "tools", "genomics", "clinical", "immunology", "genetics", "autoimmune", "diseases", "immunology", "biology", "computational", "biology", "genetics", "and", "genomics", "human", "genetics" ]	2012	A Genome-Wide Association Study Identified AFF1 as a Susceptibility Locus for Systemic Lupus Eyrthematosus in Japanese
The ubiquitous Epstein-Barr virus ( EBV ) is the primary cause of infectious mononucleosis and is etiologically linked to the development of several malignancies and autoimmune diseases . EBV has a multifaceted life cycle that comprises virus lytic replication and latency programs . Considering EBV infection holistical...	Human herpesviruses are tremendously successful pathogens that establish lifelong infection in a substantial proportion of the population . The oncogenic γ-herpesvirus EBV , like other herpesviruses , expresses a plethora of open-reading frames throughout its multifaceted life cycle . We have developed a prophylactic v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "organisms", "viruses", "preventive", "medicine", "dna", ...	2018	Immunogenic particles with a broad antigenic spectrum stimulate cytolytic T cells and offer increased protection against EBV infection ex vivo and in mice
Malaria is an important global public health challenge , and is transmitted by anopheline mosquitoes during blood feeding . Mosquito vector control is one of the most effective methods to control malaria , and population replacement with genetically engineered mosquitoes to block its transmission is expected to become ...	Malaria , transmitted by anopheline mosquitoes , represents an important global public health challenge . The salivary glands of mosquitoes are an attractive target tissue for malaria and vector control . We produced a transgenic strain inducing cell death in the salivary glands with a cell death effector molecule in t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "cell", "death", "medicine", "and", "health", "sciences", "body", "fluids", "cell", "processes", "tropical", "diseases", "parasitic", "diseases", "animals", "parasitic", "protozoans", "protozoans", "infectious", "disease", "control", "insect", "vectors"...	2016	Inhibition of Malaria Infection in Transgenic Anopheline Mosquitoes Lacking Salivary Gland Cells
Nucleosome occupancy controls the accessibility of the transcription machinery to DNA regulatory regions and serves an instructive role for gene expression . Chromatin remodelers , such as the BAF complexes , are responsible for establishing nucleosome occupancy patterns , which are key to epigenetic regulation along w...	DNA is packaged with proteins into higher-order chromatin structures , which makes genes inherently resistant to transcription initiation . The importance of chromatin remodelers in inducing structural changes to chromatin and , therefore , in controlling the expression of genes has recently resurfaced with the realiza...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "expression", "genetics", "epigenetics", "biology", "molecular", "cell", "biology", "chromatin" ]	2013	SNF5 Is an Essential Executor of Epigenetic Regulation during Differentiation
T cell receptor ( TCR ) signaling is required for T-cell activation , proliferation , differentiation , and effector function . Hepatitis C virus ( HCV ) infection is associated with impaired T-cell function leading to persistent viremia , delayed and inconsistent antibody responses , and mild immune dysfunction . Alth...	Globally , approximately 200 million people are persistently infected with Hepatitis C virus ( HCV ) . Mechanisms by which HCV establishes persistent infection are complex , and several host and viral factors appear to contribute to the ability of HCV to evade immune clearance . T cell activation through the T cell rec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Conserved Motifs within Hepatitis C Virus Envelope (E2) RNA and Protein Independently Inhibit T Cell Activation
Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation , metabolism , or immune function . Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying corr...	Adaptation to local environments is one of the most important factors shaping human genetic variation among different geographically distributed populations . Here we develop a statistical framework aimed at identifying signals of genetic adaptation . We correlate the spatial distribution of allele frequencies of a lar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "adaptation", "evolutionary", "biology", "clinical", "immunology", "natural", "selection", "autoimmune", "diseases", "population", "genetics", "biology", "computational", "biology", "microbiology", "host-pathogen", "interaction", "evolutionary", "processes", "immu...	2011	Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution
Visceral leishmaniasis ( VL ) is a zoonosis caused by the protozoan Leishmania infantum and in Brazil is transmitted mainly by the bite of Lutzomuyia longipalpis sand flies . Data about the presence , distribution , natural infection rate , seasonal and monthly dynamics of the vector population are important for optimi...	Visceral leishmaniasis ( VL ) is a parasitic disease transmited by a sand fly vector . VL is an important public health issue in Brazil occurring in all its regions with increasing incidences in big urban centers . In the State of Bahia , VL has spread to new hotspots in the last decade reaching the coastal area to the...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "population", "genetics", "tropical", "diseases", "geographical", "locations", "sand", "flies", "parasitic", "diseases", "parasitic", "protozoans", "gene", "pool", "protozoans", "leishmania", "neglected", "tropical", ...	2019	Natural infection by Leishmania infantum in the Lutzomyia longipalpis population of an endemic coastal area to visceral leishmaniasis in Brazil is not associated with bioclimatic factors
Multiphenotype genome-wide association studies ( GWAS ) may reveal pleiotropic genes , which would remain undetected using single phenotype analyses . Analysis of large pedigrees offers the added advantage of more accurately assessing trait heritability , which can help prioritise genetically influenced phenotypes for ...	While many large genetic association studies have identified genes playing a role in complex disorders , there is still concern over the amount of missing genetic heritability . With this in mind , we have used a data reduction approach alongside pedigree-based association to obtain highly heritable components which ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Phenomic Scan of the Norfolk Island Genetic Isolate Identifies a Major Pleiotropic Effect Locus Associated with Metabolic and Renal Disorder Markers
Prophylaxis with high doses of neutralizing antibody typically offers protection against challenge with viruses producing acute infections . In this study , we have investigated the ability of the neutralizing human monoclonal antibody , KZ52 , to protect against Ebola virus in rhesus macaques . This antibody was previ...	Ebola virus is one of the most feared of human pathogens with a mortality that can approach 90% and an extremely rapid disease course that can lead to death within days of infection . Antibodies able to inhibit viral infection in culture , neutralizing antibodies , can typically prevent viral infection in animals and h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "primates", "viruses", "infectious", "diseases", "virology", "immunology", "animals" ]	2007	Neutralizing Antibody Fails to Impact the Course of Ebola Virus Infection in Monkeys
Loiasis is currently receiving attention as a disease of public health importance because of the possibility of increased risk of developing neurologic serious adverse event following mass ivermectin treatment against onchocerciasis in individual co-infected with Onchocerca volvulus and Loa loa . Rapid assessment proce...	Loiasis recently emerged as a disease of public health importance because of the risk of rare severe adverse events ( SAEs ) associated with the rapid killing of Loa loa microfilariae in heavily parasitized individuals following ivermectin treatment . for onchocerciasis . The possibility of developing these SAEs has be...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Co-endemicity of Loiasis and Onchocerciasis in Rain Forest Communities in Southwestern Nigeria
In India the sand fly , Phlebotomus argentipes , transmitted parasitic disease termed kala-azar is caused by Leishmania donovani ( LD ) in humans . These immune-evading parasites have increasingly developed resistance to the drug sodium antimony gluconate in endemic regions . Lack of early diagnosis methods for the dis...	The disease Kala-azar is caused by Leishmania donovani ( LD ) . The disease is characterized by the depression of cellular immune response . In the Indian subcontinent LD parasites are mostly resistant to commonly used antileishmanial drug , like sodium antimony gluconate ( SAG ) . It is known that infection with penta...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immune", "response", "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "clinical", "immunology", "immunity", "leishmaniasis", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "immunology", ...	2014	Antimony Resistant Leishmania donovani but Not Sensitive Ones Drives Greater Frequency of Potent T-Regulatory Cells upon Interaction with Human PBMCs: Role of IL-10 and TGF-β in Early Immune Response
Aging involves a progressive physiological remodeling that is controlled by both genetic and environmental factors . Many of these factors impact also on white adipose tissue ( WAT ) , which has been shown to be a determinant of lifespan . Interrogating a transcriptional network for predicted causal regulatory interact...	The progression of aging is controlled by both genetic and environmental factors . Many of these factors are present also in adipose tissue , which itself has been shown to determine lifespan . Applying advanced bioinformatics methods on a large mouse gene expression data set , we identified Pparg ( Nr1c3 ) , an import...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "developmental", "biology/aging", "diabetes", "and", "endocrinology/obesity", "computational", "biology/systems", "biology", "diabetes", "and", "endocrinology/type", "2", "diabetes" ]	2009	Pparγ2 Is a Key Driver of Longevity in the Mouse
The role intrinsic statistical fluctuations play in creating avalanches – patterns of complex bursting activity with scale-free properties – is examined in leaky Markovian networks . Using this broad class of models , we develop a probabilistic approach that employs a potential energy landscape perspective coupled with...	Networks of noisy interacting components arise in diverse scientific disciplines . Here , we develop a mathematical framework to study the underlying causes of a bursting phenomenon in network activity known as avalanching . As prototypical examples , we study a model of disease spreading in a population of individuals...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physics", "stochastic", "processes", "veterinary", "epidemiology", "mathematics", "statistical", "mechanics", "population", "modeling", "computational", "neuroscience", "biology", "computational", "biology", "nonlinear", "dynamics", "veterinary", "science", "markov", "model"...	2014	Intrinsic Noise Induces Critical Behavior in Leaky Markovian Networks Leading to Avalanching
Infection with Helicobacter pylori is responsible for gastritis and gastroduodenal ulcers but is also a high risk factor for the development of gastric adenocarcinoma and lymphoma . The most pathogenic H . pylori strains ( i . e . , the so-called type I strains ) associate the CagA virulence protein with an active VacA...	The gram-negative bacterium Helicobacter pylori is the main causative agent of peptic ulcer and gastric cancer in humans . Our work sheds light on a new molecular mechanism by which H . pylori would exert its highly efficient colonization strategy of the human host . In this paper , we show that the H . pylori CagA pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gastroenterology", "and", "hepatology/gastrointestinal", "cancers", "cell", "biology/cellular", "death", "and", "stress", "responses", "cell", "biology/cell", "signaling", "gastroenterology", "and", "hepatology/gastrointestinal", "infections", "cell", "biology/membranes", "and...	2009	Helicobacter pylori Counteracts the Apoptotic Action of Its VacA Toxin by Injecting the CagA Protein into Gastric Epithelial Cells
Chikungunya virus ( CHIKV ) and o’nyong nyong virus ( ONNV ) are mosquito-borne alphaviruses endemic in East Africa that cause acute febrile illness and arthritis . The objectives of this study were to measure the seroprevalence of CHIKV and ONNV in coastal Kenya and link it to demographics and other risk factors . Dem...	Alphaviruses , such as chikungunya and o’nyong nyong viruses , are likely important causes of human disease in endemic regions , but are often misdiagnosed as malaria in the acute care setting . Our objective was to uncover the burden of alphavirus exposure in our study region , rural coastal Kenya . Of 1848 participan...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	High Rates of O’Nyong Nyong and Chikungunya Virus Transmission in Coastal Kenya
Trachomatous trichiasis ( TT ) surgery is provided free or subsidised in most trachoma endemic settings . However , only 18–66% of TT patients attend for surgery . This study analyses barriers to attendance among TT patients in Ethiopia , the country with the highest prevalence of TT in the world . Participants with pr...	Trachoma is the commonest infectious cause of blindness worldwide . It causes trichiasis ( inturning of the eyelashes to touch the eye ) , which can cause visual loss . Trachomatous trichiasis ( TT ) affects over eight million people , of whom 1 . 2 million live in Ethiopia – the most affected country worldwide . Surge...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "behavioral", "and", "social", "aspects", "of", "health", "ophthalmology", "neglected", "tropical", "diseases", "surgery", "trachoma", "public", "health" ]	2012	Why Do People Not Attend for Treatment for Trachomatous Trichiasis in Ethiopia? A Study of Barriers to Surgery
The neuroinvasive property of several alpha-herpesviruses underlies an uncommon infectious process that includes the establishment of life-long latent infections in sensory neurons of the peripheral nervous system . Several herpesvirus proteins are required for replication and dissemination within the nervous system , ...	Subsets of herpesviruses , such as herpes simplex virus and pseudorabies virus , are neuroinvasive pathogens . Upon infection , these viruses efficiently target peripheral nervous system tissue and establish a life-long infection for which there is no cure . Very few pathogens are known that invade the nervous system p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "virology/animal", "models", "of", "infection", "virology", "neuroscience/neuronal", "and", "glial", "cell", "biology", "virology/host", "invasion", "and", "cell", "entry" ]	2009	A Herpesvirus Encoded Deubiquitinase Is a Novel Neuroinvasive Determinant
The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3 . In monocentric chromosomes , the centromere is characterized by a single CenH3-containing ...	During cell division , DNA packed in chromosomes must be perfectly distributed between daughter cells . Centromeres play a crucial role in this process . Current centromere biology maintains that stable chromosomes can be either monocentric , with one functional domain located at a single position , or polycentric , wi...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "retrotransposons", "chromosome", "structure", "and", "function", "centromeres", "cytogenetic", "analysis", "mitosis", "genome", "sequencing", "epigenetics", "molecular", "genetics", "chromatin", "transposons", "chromosome", "biology", "biology", "molecular", "biology", "ce...	2012	Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains
Two specific chromosome-targeting and gene regulatory systems are present in Drosophila melanogaster . The male X chromosome is targeted by the male-specific lethal complex believed to mediate the 2-fold up-regulation of the X-linked genes , and the highly heterochromatic fourth chromosome is specifically targeted by t...	Species where males and females have a different number of sex chromosomes have to equalize the transcriptional output from the genes located on the X chromosome . In Drosophila this mechanism is achieved by a 2-fold up-regulation of the single male X chromosome . Flies also possess an additional chromosome-wide regula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "drosophila", "genetics", "and", "genomics" ]	2007	POF and HP1 Bind Expressed Exons, Suggesting a Balancing Mechanism for Gene Regulation
Eukaryotic genomes are duplicated from multiple replication origins exactly once per cell cycle . In Saccharomyces cerevisiae , a complex molecular network has been identified that governs the assembly of the replication machinery . Here we develop a mathematical model that links the dynamics of this network to its per...	For a cell to divide into two daughter cells , its genetic information must be accurately duplicated . The large genomes in eukaryotic cells are copied from hundreds or thousands of replication origins to achieve the duplication of the entire DNA in a limited time span . Errors that result in incomplete or multiple cop...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "computational", "biology/systems", "biology", "biochemistry/theory", "and", "simulation" ]	2010	Mathematical Modelling of DNA Replication Reveals a Trade-off between Coherence of Origin Activation and Robustness against Rereplication
Although emerging evidence suggests that transposable elements ( TEs ) have contributed novel regulatory elements to the human genome , their global impact on transcriptional networks remains largely uncharacterized . Here we show that TEs have contributed to the human genome nearly half of its active elements . Using ...	Nearly half of the human genome is composed of repetitive sequences , most of which were derived from transposable elements that have replicated in the genome during the evolution of our species . There is growing evidence showing that some of these transposon-derived sequences have been a source of new binding sites f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "retrotransposons", "genome", "evolution", "viral", "classification", "microbiology", "retroviruses", "molecular", "cell", "biology", "transposons", "regulatory", "networks", "comparative", "genomics", "biology", "virology", "genetics", "genomics", ...	2013	The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements
Identifying genomic locations that have experienced selective sweeps is an important first step toward understanding the molecular basis of adaptive evolution . Using statistical methods that account for the confounding effects of population demography , recombination rate variation , and single-nucleotide polymorphism...	A selective sweep is a single realization of adaptive evolution at the molecular level . When a selective sweep occurs , it leaves a characteristic signal in patterns of variation in genomic regions linked to the selected site; therefore , recently released population genomic datasets can be used to search for instance...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "none", "computational", "biology", "evolutionary", "biology", "homo", "(human)", "genetics", "and", "genomics" ]	2007	Localizing Recent Adaptive Evolution in the Human Genome
The Leishmania genus comprises up to 35 species , some with status still under discussion . The multilocus sequence typing ( MLST ) —extensively used for bacteria—has been proposed for pathogenic trypanosomatids . For Leishmania , however , a detailed analysis and revision on the taxonomy is still required . We have pa...	Leishmania is a protozoan genus comprising many species , some associated with a human neglected disease called leishmaniasis . This parasite is found worldwide and is transmitted by sand flies , having numerous domestic and sylvatic animals as reservoirs . Leishmania is genetically and ecologically diverse and it has ...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "parastic", "protozoans", "haplotypes", "genetic", "polymorphism", "leishmania", "protozoology", "biology", "microbiology", "population", "biology", "population", "genetics", "genetics", "and", "genomics" ]	2012	New Insights on Taxonomy, Phylogeny and Population Genetics of Leishmania (Viannia) Parasites Based on Multilocus Sequence Analysis
Bovine spongiform encephalopathy ( BSE ) is a transmissible spongiform encephalopathy ( TSE ) of cattle and was first detected in 1986 in the United Kingdom . It is the most likely cause of variant Creutzfeldt-Jakob disease ( CJD ) in humans . The origin of BSE remains an enigma . Here we report an H-type BSE case asso...	Bovine spongiform encephalopathy ( BSE or Mad Cow Disease ) , a transmissible spongiform encephalopathy ( TSE ) or prion disease of cattle , was first discovered in the United Kingdom in 1986 . BSE is most likely the cause of a human prion disease known as variant Creutzfeldt Jakob Disease ( vCJD ) . In this study , we...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/animal", "genetics", "genetics", "and", "genomics/animal", "genetics", "pathology/neuropathology", "genetics", "and", "genomics/functional", "genomics", "infectious", "diseases/prion", "diseases", "biochemistry/protein", "folding", "microbiology/microbial",...	2008	BSE Case Associated with Prion Protein Gene Mutation
Recent cross-sectional analyses of HIV-1+ plasmas have indicated that broadly cross-reactive neutralizing antibody responses are developed by 10%–30% of HIV-1+ subjects . The timing of the initial development of such anti-viral responses is unknown . It is also unknown whether the emergence of these responses coincides...	A fraction of those infected with HIV develop broadly neutralizing antibodies ( bNAbs ) capable of preventing cell-infection by diverse HIV isolates; the type of antibodies we wish to elicit by vaccination . Identifying factors associated with the natural development of bNabs , and defining the timing of their emergenc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "virology/immunodeficiency", "viruses", "immunology/immunity", "to", "infections", "virology/vaccines" ]	2011	Characteristics of the Earliest Cross-Neutralizing Antibody Response to HIV-1
Daily , circadian rhythms influence essentially all living organisms and affect many physiological processes from sleep and nutrition to immunity . This ability to respond to environmental daily rhythms has been conserved along evolution , and it is found among species from bacteria to mammals . The hematopoietic proce...	Most living organisms are able to sense the time and in particular time of day by their internal clocks . So-called clock proteins control these internal clockworks . BMAL1 and CLK are two important clock proteins , which together form a complex that serves as a transcription factor and controls the production of diurn...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "neurochemistry", "evolutionary", "biology", "genetics", "biology", "comparative", "genomics", "evolutionary", "immunology", "evolutionary", "genetics", "genetics", "and", "genomics", "gene", "function" ]	2013	Astakine 2—the Dark Knight Linking Melatonin to Circadian Regulation in Crustaceans
In addition to the commonly accepted importance of the vampire bat in the maintenance and transmission of the rabies virus ( RABV ) in South America , RABV infection of other species is widely evidenced , challenging their role in the viral cycle . To identify the bioecological drivers of RABV circulation in neotropica...	The vampire bat is known to be the main reservoir of the rabies virus ( RABV ) in South America . Nevertheless , other bat species are implicated in the cycle of the virus . Indeed , seven genus-specific rabies lineages have been described in insectivorous bats in Brazil . In French Guiana , we looked for the presence ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "vertebrates", "animals", "mammals", "animal", "phylogenetics", "viruses"...	2016	Bioecological Drivers of Rabies Virus Circulation in a Neotropical Bat Community
The development of the endomembrane system was a major step in eukaryotic evolution . Membrane coats , which exhibit a unique arrangement of β-propeller and α-helical repeat domains , play key roles in shaping eukaryotic membranes . Such proteins are likely to have been present in the ancestral eukaryote but cannot be ...	Despite decades of research , the origin of eukaryotic cells remains an unsolved issue . The endomembrane system defines the eukaryotic cell , and its origin is linked to that of eukaryotes . A search was conducted within all known sequences for proteins that are characteristic of the eukaryotic endomembrane system , u...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "computational", "biology/protein", "homology", "detection", "evolutionary", "biology/genomics", "computational", "biology/protein", "structure",...	2010	The Compartmentalized Bacteria of the Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum Have Membrane Coat-Like Proteins
Fbh1 , an F-box helicase related to bacterial UvrD , has been proposed to modulate homologous recombination in fission yeast . We provide several lines of evidence for such modulation . Fbh1 , but not the related helicases Srs2 and Rqh1 , suppressed the formation of crossover recombinants from single HO-induced DNA dou...	Homologous recombination is required for repairing DNA double-strand breaks ( DSBs ) , which are induced by exogenous factors such as DNA damaging agents or by endogenous factors such as collapse of DNA replication fork in mitotic cells . If improperly processed , DSBs could lead to chromosome rearrangement , cell deat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "molecular", "genetics" ]	2014	Multiple Regulation of Rad51-Mediated Homologous Recombination by Fission Yeast Fbh1
A fundamental problem in neuroscience is understanding how working memory—the ability to store information at intermediate timescales , like tens of seconds—is implemented in realistic neuronal networks . The most likely candidate mechanism is the attractor network , and a great deal of effort has gone toward investiga...	A critical component of cognition is memory—the ability to store information , and to readily retrieve it on cue . Existing models postulate that recalled items are represented by self-sustained activity; that is , they are represented by activity that can exist in the absence of input . These models , however , are in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "primates", "neuroscience", "mammals" ]	2007	A Balanced Memory Network
Kaposi Sarcoma Herpesvirus ( KSHV ) , a γ2-herpesvirus and class 1 carcinogen , is responsible for at least three human malignancies: Kaposi Sarcoma ( KS ) , Primary Effusion Lymphoma ( PEL ) and Multicentric Castleman’s Disease ( MCD ) . Its major nuclear latency protein , LANA , is indispensable for the maintenance a...	KSHV latency-associated nuclear antigen , LANA , is essential for the replication of latent viral episomes , their segregation to daughter cells and overcoming the p53-dependent cell cycle block induced by an activated DNA damage response . In addition , cytoplasmic forms of LANA have been shown to modulate cGAS-depend...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "gene", "regulation", "pathogens", "immunology", "immunoblotting", "microbiology", "plasmid", "construction", "viruses", "immunoprec...	2017	Kaposi Sarcoma Herpesvirus (KSHV) Latency-Associated Nuclear Antigen (LANA) recruits components of the MRN (Mre11-Rad50-NBS1) repair complex to modulate an innate immune signaling pathway and viral latency
Tubulin genes encode a series of homologous proteins used to construct microtubules which are essential for multiple cellular processes . Neural development is particularly reliant on functional microtubule structures . Tubulin genes comprise a large family of genes with very high sequence similarity between multiple f...	Tubulin proteins are assembled into microtubules to provide essential cellular cytoskeletal elements . Microtubules are especially crucial for neuronal development . Multiple studies demonstrate that human malformations of cortical development are caused by genetic variants in several tubulin genes . Interestingly , mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "methods" ]	[ "medicine", "and", "health", "sciences", "alleles", "amino", "acid", "sequence", "analysis", "animal", "models", "developmental", "biology", "histology", "model", "organisms", "experimental", "organism", "systems", "mammalian", "genomics", "tubulins", "embryos", "resear...	2019	Differential requirements of tubulin genes in mammalian forebrain development
Hepatitis C virus ( HCV ) and human pegivirus ( HPgV ) , formerly GBV-C , are the only known human viruses in the Hepacivirus and Pegivirus genera , respectively , of the family Flaviviridae . We present the discovery of a second pegivirus , provisionally designated human pegivirus 2 ( HPgV-2 ) , by next-generation seq...	To date , only one human hepacivirus ( HCV ) and one human pegivirus ( HPgV-1/GBV-C ) in the family Flaviviridae are known to exist . Using unbiased metagenomic next-generation sequencing , we discovered and assembled the genome of a novel pegivirus from plasma corresponding to an HCV-infected patient who died from unk...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection
Despite the long history of Rift Valley fever ( RVF ) in Tanzania , extent of its suitable habitat in the country remains unclear . In this study we investigated potential effects of temperature , precipitation , elevation , soil type , livestock density , rainfall pattern , proximity to wild animals , protected areas ...	Rift Valley fever is a viral disease that is transmitted to livestock and humans by mosquitoes . Humans get infected mainly through direct contact with blood or aborted materials from infected animals . In Tanzania , a total of 10 RVF epidemics have been reported from 1930 to 2007 . Despite the long history of RVF in T...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "rift", "valley", "fever", "virus", "ecological", "niches", "pathology", "and", "laboratory", "medicine", "atmospheric", "science", "pathogens", "tropical", "diseases", ...	2016	Spatial Heterogeneity of Habitat Suitability for Rift Valley Fever Occurrence in Tanzania: An Ecological Niche Modelling Approach
Protein-DNA recognition is a central biological process that governs the life of cells . A protein will often undergo a conformational transition to form the functional complex with its target DNA . The protein conformational dynamics are expected to contribute to the stability and specificity of DNA recognition and th...	Protein-DNA recognition is crucial for many key biological processes in cells . Protein often undergoes large-scale conformational change during DNA recognition . However , the physical and global understanding of flexible protein-DNA binding is still challenging . Here , we developed a theoretical approach to investig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "dynamics", "dna-binding", "proteins", "computerized", "simulations", "molecular", "mechanics", "simulation", "and", "modeling", "polymerases", "dna", "intrinsically", "disordered", "proteins", "dna", "synthesis", "research", "and", "analysis", "methods", "co...	2014	Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA
Bacterial capsular polysaccharides ( CPS ) are produced by a multi-protein membrane complex , in which a particular type of tyrosine-autokinases named BY-kinases , regulate their polymerization and export . However , our understanding of the role of BY-kinases in these processes remains incomplete . In the human pathog...	Bacteria utilize a multi-protein membrane complex to synthesize and export the polysaccharide capsule that conceals and covers the cell . In bacterial pathogens , the capsule protects the cell form opsonophagocytosis and complement-mediated killing . The mechanisms allowing the bacterial cell to maintain this protectiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Autophosphorylation of the Bacterial Tyrosine-Kinase CpsD Connects Capsule Synthesis with the Cell Cycle in Streptococcus pneumoniae
Living systems are capable of processing multiple sources of information simultaneously . This is true even at the cellular level , where not only coexisting signals stimulate the cell , but also the presence of fluctuating conditions is significant . When information is received by a cell signaling network via one spe...	Far from being silent and static , the habitat of a cell is usually composed by multiple and simultaneous signals . We can consider nutrients , hormones , temperature , light , and other stimuli as elements building a default environment in which cells grow , divide and die . This environment , which has an intrinsical...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "systems", "biology", "biology", "computational", "biology", "signaling", "networks", "genetics", "and", "genomics" ]	2011	Information Routing Driven by Background Chatter in a Signaling Network
Symptoms on virus-infected plants are often very specific to the given virus . The molecular mechanisms involved in viral symptom induction have been extensively studied , but are still poorly understood . Cucumber mosaic virus ( CMV ) Y satellite RNA ( Y-sat ) is a non-coding subviral RNA and modifies the typical symp...	Cucumber mosaic virus ( CMV ) Y satellite RNA ( Y-sat ) is an interesting subviral RNA because it changes the green mosaic induced by CMV into a bright yellow mosaic in Nicotiana tabacum . The molecular basis underlying the induction of symptoms by viruses is not well understood , and this Y-sat-mediated modification o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "virology", "plant", "biology", "biology", "microbiology" ]	2011	A Viral Satellite RNA Induces Yellow Symptoms on Tobacco by Targeting a Gene Involved in Chlorophyll Biosynthesis using the RNA Silencing Machinery
Pathogenic members of the genus Leptospira are the causative agents of leptospirosis , a neglected disease of public and veterinary health concern . Leptospirosis is a systemic disease that in its severest forms leads to renal insufficiency , hepatic dysfunction , and pulmonary failure . Many strains of Leptospira prod...	The spirochete Leptospira causes leptospirosis , a potentially deadly disease of humans and animals . Candidate factors that promote infection include hemolysins encoded by several leptospiral genes . Hemolysins rupture red blood cells in vitro . Some hemolysins are sphingomyelinases , which target sphingomyelin in the...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Role of sph2 Gene Regulation in Hemolytic and Sphingomyelinase Activities Produced by Leptospira interrogans
Entamoeba histolytica ( Eh ) is the causative agent of amebiasis , one of the major causes of dysentery-related morbidity worldwide . Recent studies have underlined the importance of the intercellular junction between Eh and host cells as a determinant in the pathogenesis of amebiasis . Despite the fact that direct con...	The protozoan parasite Entamoeba histolytica can establish an enteric infection in human hosts that leads to symptoms ranging from diarrhea to abscesses in the liver and the brain . Host susceptibility to amebic infection is in part determined by the quality and potency of the host immune response that occurs once the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "viral", "transmission", "and", "infection", "gene", "regulation", "immunology", "microbiology", "physiological", "processes", "integrins", "cellular", "structures", "and", "organelles", "cyto...	2017	The macrophage cytoskeleton acts as a contact sensor upon interaction with Entamoeba histolytica to trigger IL-1β secretion
Typhoid fever , caused by Salmonella enterica serovar Typhi ( S . Typhi ) , is a major health problem especially in developing countries . Vaccines against typhoid are commonly used by travelers but less so by residents of endemic areas . We used single nucleotide polymorphism ( SNP ) typing to investigate the populati...	Typhoid fever is caused by the bacterium Salmonella enterica serovar Typhi ( S . Typhi ) and is a major health problem especially in developing countries . Vaccines against typhoid are commonly used by travelers but less so by residents of endemic areas . We used single nucleotide polymorphism ( SNP ) typing to investi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "vaccination", "clinical", "immunology", "immunity", "immunology", "biology", "microbiology", "bacterial", "pathogens" ]	2012	High-Resolution Genotyping of the Endemic Salmonella Typhi Population during a Vi (Typhoid) Vaccination Trial in Kolkata
During the 2012 cholera outbreak in the Republic of Guinea , the Ministry of Health , supported by Médecins Sans Frontières - Operational Center Geneva , used the oral cholera vaccine Shanchol as a part of the emergency response . The rapid diagnostic test ( RDT ) Crystal VC , widely used during outbreaks , detects lip...	The rapid diagnostic test ( RDT ) Crystal VC detects lipopolysaccharide antigens from V . cholerae O1 and O139 in stool samples , which are also present in the oral cholera vaccine Shanchol . It is important to take into consideration the possibility of a positive result to the RDT due to vaccination and not to cholera...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunizations", "medicine", "infectious", "diseases", "test", "evaluation", "cholera", "diagnostic", "medicine", "neglected", "tropical", "diseases", "public", "health" ]	2013	Use of a Cholera Rapid Diagnostic Test during a Mass Vaccination Campaign in Response to an Epidemic in Guinea, 2012
Human iPS cells have been generated using a diverse range of tissues from a variety of donors using different reprogramming vectors . However , these cell lines are heterogeneous , which presents a limitation for their use in disease modeling and personalized medicine . To explore the basis of this heterogeneity we gen...	Human induced pluripotent stem ( hiPS ) cells are a potentially powerful model system for studying human disease and development , and a resource for personalized medicine . However , it has been reported that hiPS cells exhibit substantial heterogeneity which could limit their use as model systems . Clearly , knowledg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "developmental", "biology", "cell", "biology", "animal", "cells", "stem", "cells", "induced", "pluripotent", "stem", "cells", "genomic", "imprinting", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "cellular", "types", "cell",...	2014	Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells
Tinkering with pre-existing genes has long been known as a major way to create new genes . Recently , however , motherless protein-coding genes have been found to have emerged de novo from ancestral non-coding DNAs . How these genes originated is not well addressed to date . Here we identified 24 hominoid-specific de n...	Ever since the pre-genomic era , people believed that “mother gene”-based mechanisms such as gene duplication were the major means of creating new genes . Recently , we and others reported several “motherless” protein-coding genes in human , challenging the conventional idea in that some protein-coding genes might have...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "genomics", "natural", "selection", "biology", "evolutionary", "biology", "comparative", "genomics", "evolutionary", "processes", "genetics", "and", "genomics", "evolutionary", "theory" ]	2012	Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs
DNA double-strand breaks ( DSBs ) are harmful lesions that arise mainly during replication . The choice of the sister chromatid as the preferential repair template is critical for genome integrity , but the mechanisms that guarantee this choice are unknown . Here we identify new genes with a specific role in assuring t...	Double-strand breaks ( DSBs ) are among the most dangerous DNA lesions and can lead to genomic instability , a process associated with cancer and hereditary diseases . An important source of DSBs is replication , Sister Chromatid Recombination ( SCR ) being the main mechanism for DSB repair in dividing eukaryotic cells...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dna", "metabolism", "cancer", "genetics", "cellular", "stress", "responses", "microbiology", "gene", "function", "histone", "modification", "model", "organisms", "dna", "replication", "epigenetics", "molecular", "genetics", "dna", "dna", "synthesis", "gene", "expressio...	2013	Histone H3K56 Acetylation, Rad52, and Non-DNA Repair Factors Control Double-Strand Break Repair Choice with the Sister Chromatid
During infection Neisseria meningitidis ( Nm ) encounters multiple environments within the host , which makes rapid adaptation a crucial factor for meningococcal survival . Despite the importance of invasion into the bloodstream in the meningococcal disease process , little is known about how Nm adapts to permit surviv...	Neisseria meningitidis ( Nm ) is an exclusively human pathogen and a leading cause of bacterial meningitis and septicemia worldwide . Characterization of the bacterial transcriptome during host-pathogen interactions is a fundamental step for understanding the infectious processes of bacterial pathogens . Despite the se...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "microbial", "pathogens", "biology", "genomics", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics", "pathogenesis" ]	2011	Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival
Chronic alcohol consumption perturbs the normal intestinal microbial communities ( dysbiosis ) . To investigate the relationship between alcohol-mediated dysbiosis and pulmonary host defense we developed a fecal adoptive transfer model , which allows us to investigate the impact of alcohol-induced gut dysbiosis on host...	Alcohol use disorders ( AUD ) are an established risk factor for bacterial pneumonia . Further , alcohol consumption perturbs the normal intestinal microbial communities . Intestinal microbiota dysbiosis has been linked to impaired pulmonary host defense , however the role of alcohol-associated intestinal dysbiosis on ...	[ "Abstract", "Introduction", "Results", "Discussion", "Summary", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "microbiome", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "diet", "bacterial", "diseases", "klebsiella", "infections", "nutrition", "signs", "and",...	2017	Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae
Spontaneous activity is a fundamental characteristic of the developing nervous system . Intriguingly , it often takes the form of multiple structured assemblies of neurons . Such assemblies can form even in the absence of afferent input , for instance in the zebrafish optic tectum after bilateral enucleation early in l...	Even in the absence of sensory stimulation , the developing brain can exhibit highly organised patterns of neural activity . This activity often takes the form of structured assemblies of neurons . Here we draw on calcium imaging experiments in zebrafish larvae to construct a computational model of assembly formation i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fish", "medicine", "and", "health", "sciences", "neural", "networks", "brain", "vertebrates", "neuroscience", "animals", "animal", "models", "osteichthyes", "model", "organisms", "mathematics", "algebra", "network", "analysis", "experimental", "organism", "systems", "n...	2018	Emergence of spontaneous assembly activity in developing neural networks without afferent input
While the human gut microbiota are suspected to produce diffusible small molecules that modulate host signaling pathways , few of these molecules have been identified . Species of Bacteroides and their relatives , which often comprise >50% of the gut community , are unusual among bacteria in that their membrane is rich...	While human gut bacteria are thought to produce diffusible molecules that influence host biology , few of these molecules have been identified . Species of Bacteroides , a Gram-negative bacterial genus whose members often comprise >50% of the gut community , are unusual in that they produce sphingolipids , signaling mo...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "biology", "chemistry", "biology", "microbiology" ]	2013	Production of α-Galactosylceramide by a Prominent Member of the Human Gut Microbiota
The gene composition of present-day genomes has been shaped by a complicated evolutionary history , resulting in diverse distributions of genes across genomes . The pattern of presence and absence of a gene in different genomes is called its phylogenetic profile . It has been shown that proteins whose encoding genes ha...	Every genome of current day species contains a very unique selection of genes . Why a specific genome is composed of exactly those genes is determined by many factors , but often not resolvable . It seems plausible that interacting genes would either occur together or be absent together , because if one of them is alon...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "phyletic", "patterns", "organismal", "evolution", "genome", "complexity", "functional", "genomics", "protein", "interactions", "genome", "evolution", "eukaryotic", "evolution", "comparative", "genomics", "biology", "genomics", "evolutionary", "biology", "genomic", "evoluti...	2013	Shared Protein Complex Subunits Contribute to Explaining Disrupted Co-occurrence
In Brazil , leprosy has been listed among the health priorities since 2006 , in a plan known as the “Pact for life” ( Pacto pela Vida ) . It is the sole country on the American continent that has not reached the global goal of disease elimination . Local health systems face many challenges to achieve this global goal ....	Brazil still has not achieved the goal of leprosy elimination established by World Health Organization . The diagnosis and treatment of leprosy is easy and the country is striving to fully integrate leprosy services into existing general health services . Access to information , diagnosis and treatment with multidrug t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "health", "care", "quality", "health", "promotion", "public", "and", "occupational", "health", "bacterial", "diseases", "infectious", "diseases", "health", "screening", "medicine", "and", "health", "sciences", "plant", "science", "primary", "care", "infectious", "dise...	2014	Patients' Perceptions on the Performance of a Local Health System to Eliminate Leprosy, Paraná State, Brazil
Dietary restriction ( DR ) and reduced insulin growth factor ( IGF ) signaling extend lifespan in Caenorhabditis elegans and other eukaryotic organisms . Autophagy , an evolutionarily conserved lysosomal degradation pathway , has emerged as a central pathway regulated by various longevity signals including DR and IGF s...	Restriction of dietary food without malnutrition robustly extends lifespan in more than twenty species . It was also reported that fruit flies ( Drosophila melanogaster ) deficient in olfactory function live longer and that the longevity induced by food restriction is partially due to decreased olfaction . These observ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "invertebrates", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "neurochemistry", "caenorhabditis", "cell", "processes", "neuroscience", "animals", "hormones", "animal", "models", "physiological", "processes", "developmental", "bi...	2017	The cell non-autonomous function of ATG-18 is essential for neuroendocrine regulation of Caenorhabditis elegans lifespan
The direct fluorescent antibody test ( DFA ) , is performed in all rabies reference laboratories across Latin America and the Caribbean ( LAC ) . Despite DFA being a critical capacity in the control of rabies , there is not a standardized protocol in the region . We describe the results of the first inter-laboratory pr...	The incidence of dog-maintained rabies in Latin America has showed a significant reduction in the last 30 years . Although several countries have achieved its elimination there are still focalized areas in the region where rabies remain endemic . Many factors , including poverty , geographic and environmental features ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "storage", "and", "handling", "pathogens", "tropical", "diseases", "brain", "light", "microscopy", "microbiology", "viruses", "specimen", "storage"...	2017	An inter- laboratory proficiency testing exercise for rabies diagnosis in Latin America and the Caribbean
In Drosophila melanogaster , cis-regulatory modules that are activated by the Notch cell–cell signaling pathway all contain two types of transcription factor binding sites: those for the pathway's transducing factor Suppressor of Hairless [Su ( H ) ] and those for one or more tissue- or cell type–specific factors calle...	Enhancers , or cis-regulatory modules , are the major transcriptional control elements in the genome . Some enhancers are activated by the Notch cell–cell signaling pathway , in many different cellular contexts in the same organism . It is well established that the cell type–specific activity of each such enhancer depe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "genetics", "biology", "genetics", "and", "genomics" ]	2012	Role of Architecture in the Function and Specificity of Two Notch-Regulated Transcriptional Enhancer Modules
Yeasts can form multicellular patterns as they expand on agar plates , a phenotype that requires a functional copy of the FLO11 gene . Although the biochemical and molecular requirements for such patterns have been examined , the mechanisms underlying their formation are not entirely clear . Here we develop quantitativ...	Microbial biofilms are commonly found in nature and are highly relevant to public health . Biofilms can impose high risks to drinking water distribution by stable adherence to the interior of water pipes , and to food industry by contamination of food processing systems . Biofilm adherence to indwelling medical devices...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "fourier", "analysis", "population", "dynamics", "light", "microscopy", "mathematical", "models", "biomechanics", "fungi", "model", "organisms", "microscopy", "population", "modeling", "population", "biology", "research", "and", "analysis", "methods", "saccharomyces", "co...	2014	Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation
The telomerase reverse transcriptase synthesizes new telomeres onto chromosome ends by copying from a short template within its integral RNA component . During telomere synthesis , telomerase adds multiple short DNA repeats successively , a property known as repeat addition processivity . However , the consequences of ...	Mutations in the essential telomerase components cause a spectrum of diseases mediated by short telomeres . Most frequently , these disorders manifest in the lung in an age-related disease: idiopathic pulmonary fibrosis . Telomerase synthesizes telomere repeats using a specialized reverse transcriptase , hTERT , that c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics" ]	2011	Ancestral Mutation in Telomerase Causes Defects in Repeat Addition Processivity and Manifests As Familial Pulmonary Fibrosis
Similar to many diurnal animals , Drosophila melanogaster exhibits a mid-day siesta that is more robust as ambient temperature rises , an adaptive response aimed at minimizing exposure to heat . Mid-day siesta levels are partly regulated by the thermosensitive splicing of a small intron ( termed dmpi8 ) found in the 3’...	In warm climates many animals , including humans , exhibit a mid-day siesta , almost certainly a behavior meant to minimize the harm from prolonged exposure to the hot mid-day sun . But what about animals that adapted to cooler more temperate climates , might they have a less pronounced siesta ? Indeed , we show that i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "3'", "utr", "sleep", "messenger", "rna", "geographical", "locations", "australia", "animals", "genetic", "mapping", "animal", "models", "physiological", "processes", "drosophila", "melanogaster", "model", "organ...	2018	Parallel clinal variation in the mid-day siesta of Drosophila melanogaster implicates continent-specific targets of natural selection
Bacterial pathogens typically infect only a limited range of hosts; however , the genetic mechanisms governing host-specificity are poorly understood . The α-proteobacterial genus Bartonella comprises 21 species that cause host-specific intraerythrocytic bacteremia as hallmark of infection in their respective mammalian...	Pathogens are—as the result of adaptive evolution in their principal host ( s ) —typically limited in the range of hosts that they can infect successfully . However , infrequently such host-restricted pathogens may undergo a spontaneous host switch , which can lead to the evolution of pathogens with altered host specif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "computational", "biology/comparative", "sequence", "analysis", "microbiology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/gene", "function", "infectious", "diseases/bacterial", "in...	2010	The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes
In complex systems with stochastic components , systems laws often emerge that describe higher level behavior regardless of lower level component configurations . In this paper , emergent laws for describing mechanochemical systems are investigated for processive myosin-actin motility systems . On the basis of prior ex...	Complex biological systems consist of many parts that interact in non-obvious ways . In these systems , levels of organization often emerge , as evidenced by cases where cells form tissues , tissues form organs , and organs interact to form complete organisms . We hypothesized that that laws exist that describe system ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity
The cuticle covering plants' aerial surfaces is a unique structure that plays a key role in organ development and protection against diverse stress conditions . A detailed analysis of the tomato colorless-peel y mutant was carried out in the framework of studying the outer surface of reproductive organs . The y mutant ...	A major step in the evolution of land plants was the formation of a cuticular layer on their outer surfaces . Despite the cuticle's key role in organ development and in protecting against a variety of stresses , very little is known about the regulation of the metabolic pathways that generate its building blocks . Flav...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/gene", "expression", "biotechnology/plant", "biotechnology", "plant", "biology", "plant", "biology/plant-environment", "interactions", "genetics", "and", "genomics/gene", "function", "plant", "biolo...	2009	Fruit-Surface Flavonoid Accumulation in Tomato Is Controlled by a SlMYB12-Regulated Transcriptional Network
Hepatitis E virus ( HEV ) , a non-enveloped , positive-stranded RNA virus , is transmitted in a faecal-oral manner , and causes acute liver diseases in humans . The HEV capsid is made up of capsomeres consisting of homodimers of a single structural capsid protein forming the virus shell . These dimers are believed to p...	Infectious viral hepatitis is a major disease in both developing and developed countries . Hepatitis E virus ( HEV ) is one of the major causes of severe inflammation of the liver , which is characterized by jaundice , fever , liver enlargement , and abdominal pain in humans and non-human primates . The hepatitis E vir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/vaccines" ]	2009	Dimerization of Hepatitis E Virus Capsid Protein E2s Domain Is Essential for Virus–Host Interaction
Nuclear factor of activated T cells 5 ( NFAT5 ) /Tonicity enhancer binding protein ( TonEBP ) is a transcription factor induced by hypertonic stress in the kidney . However , the function of NFAT5 in other organs has rarely been studied , even though it is ubiquitously expressed . Indeed , although NFAT5 was reported t...	Coxsackievirus B3 ( CVB3 ) is one of the predominant pathogens of viral myocarditis , which is a major cause of sudden death in children and young adults . CVB3 alters the expression of many proteins in host cells to facilitate its multiplication . Nuclear factor of activated T cells 5 ( NFAT5 ) is known to be involved...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "chemical", "compounds", "hela", "cells", "cardiovascular", "anatomy", "gene", "regulation", "enzymes", "biological", "cultures", "enzymology", "microbiology", "tonicity", "organic", "compounds", "hyperton...	2017	Cleavage of osmosensitive transcriptional factor NFAT5 by Coxsackieviral protease 2A promotes viral replication

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