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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Recent findings indicate that perturbations of the mitochondrial electron transport chain ( METC ) can cause extended longevity in evolutionarily diverse organisms . To uncover the molecular basis of how altered METC increases lifespan in C . elegans , we performed an RNAi screen and revealed that three predicted trans...	Mitochondria have long been associated with aging and age-related diseases . Recent research has shown that a slight dampening of mitochondrial function can dramatically increase the lifespan of a wide range of organisms , suggesting that a similar mechanism likely operates in humans . The molecular basis of this obser...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "anatomy", "and", "physiology", "animal", "models", "physiological", "processes", "caenorhabditis", "elegans", "model", "organisms", "biology", "molecular", "biology", "aging", "signal", "transduction", "genetic", "screens", "physiology", "genetics", "molecular", "cell", ...	2011	The Homeobox Protein CEH-23 Mediates Prolonged Longevity in Response to Impaired Mitochondrial Electron Transport Chain in C. elegans
Gene expression variation within species is relatively common , however , the role of natural selection in the maintenance of this variation is poorly understood . Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species , D . simulans , to determine whether the two specie...	While gene expression variation in natural populations is common , the population genetic processes responsible for the maintenance of this variation remain obscure . Here we study geographic differences in gene expression in recently established low and high latitude populations of two closely related species of Droso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans
The RNA response element TAR plays a critical role in HIV replication by providing a binding site for the recruitment of the viral transactivator protein Tat . Using a structure-guided approach , we have developed a series of conformationally-constrained cyclic peptides that act as structural mimics of the Tat RNA bind...	The HIV-1 transactivator protein ( Tat ) , together with the elongation factor P-TEFb binds to an HIV-1 RNA secondary structure in the 5′-UTRs of nascent viral mRNAs ( TAR ) and promotes transcription elongation . This process has been an attractive target for drug development but previous inhibitors that bind either T...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "hiv", "retrovirology", "and", "hiv", "immunopathogenesis", "viral", "diseases" ]	2011	Inhibition of Both HIV-1 Reverse Transcription and Gene Expression by a Cyclic Peptide that Binds the Tat-Transactivating Response Element (TAR) RNA
Mitosis and meiosis are two distinct cell division programs . During mitosis , sister chromatids separate , whereas during the first meiotic division , homologous chromosomes pair and then segregate from each other . In most organisms , germ cells do both programs sequentially , as they first amplify through mitosis , ...	Meiosis is a special type of cell division occurring in germ cells to produce sexual gametes . Initially , germ cells contain two copies of each chromosome , one from the mother and one from the father , which are called homologs . During meiosis , cells divide twice to produce haploid gametes with only one copy of eac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Synaptonemal Complex Components Promote Centromere Pairing in Pre-meiotic Germ Cells
Preventive chemotherapy ( PC ) with benzimidazole drugs is the backbone of soil-transmitted helminth ( STH ) control programs . Over the past decade , drug coverage has increased and with it , the possibility of developing anthelmintic resistance . It is therefore of utmost importance to monitor drug efficacy . Current...	During the last decade , the scale of deworming programs that aim to eliminate the morbidity caused by intestinal worms has increased to a level that is unprecedented in history . It is therefore of utmost importance to monitor any change in therapeutic efficacy that may arise from emerging drug resistance . Currently ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "hookworms", "geographical", "locations", "parasitic", "diseases", "animals", "ascaris", "ascaris", "lumbricoides", "tanzania", "pharmaceutics", "drug", "administration", "neglect...	2019	Therapeutic efficacy of albendazole against soil-transmitted helminthiasis in children measured by five diagnostic methods
Recent data shows that HIV-1 is characterised by variation in viral virulence factors that is heritable between infections , which suggests that viral virulence can be naturally selected at the population level . A trade-off between transmissibility and duration of infection appears to favour viruses of intermediate vi...	Recent studies have suggested that virulence in HIV-1 is partly a characteristic of the virus which is carried from one infection to the next . An infection with intermediate virulence will produce more transmissions during the infectious lifetime because it optimises the trade-off between rate of transmission and dura...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "organismal", "evolution", "public", "health", "and", "epidemiology", "microbial", "mutation", "viral", "transmission", "and", "infection", "infectious", "disease", "epidemiology", "emerging", "viral", "diseases", "population", "genetics", "evolutionary", "sel...	2011	Transmission Selects for HIV-1 Strains of Intermediate Virulence: A Modelling Approach
The role of the pineal gland is to translate the rhythmic cycles of night and day encoded by the retina into hormonal signals that are transmitted to the rest of the neuronal system in the form of serotonin and melatonin synthesis and release . Here we describe that the production of both melatonin and serotonin by the...	Animals respond to cycles of light and dark with patterns in sleeping , feeding , body temperature alterations , and other biological functions . The pineal gland translates these light signals received from the retina into a language understandable to the rest of the body through the rhythmic synthesis and release of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "molecular", "neuroscience", "cellular", "neuroscience", "neurochemistry", "biology", "neuroscience", "hormones" ]	2012	Circadian-Related Heteromerization of Adrenergic and Dopamine D4 Receptors Modulates Melatonin Synthesis and Release in the Pineal Gland
Whirligig beetles ( Coleoptera , Gyrinidae ) can fly through the air , swiftly swim on the surface of water , and quickly dive across the air-water interface . The propulsive efficiency of the species is believed to be one of the highest measured for a thrust generating apparatus within the animal kingdom . The goals o...	The whirligig beetles belong to the family Gyrinidae , consisting of over 700 species of water beetles . They are characterized by a divided eye , ellipsoidal body , and rapidly swim in circles when alarmed . Perhaps the most interesting characteristic of whirligig beetles is their ability to rapidly swim on the surfac...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "robotics", "physics", "mechanics", "mechanical", "engineering", "classical", "mechanics", "biophysic", "al", "simulations", "dynamics", "(mechanics)", "biology", "computational", "biology", "engineering" ]	2012	Experimental Studies and Dynamics Modeling Analysis of the Swimming and Diving of Whirligig Beetles (Coleoptera: Gyrinidae)
Buruli Ulcer ( BU ) is caused by the environmental microbe Mycobacterium ulcerans . Despite unclear transmission , contact with a BU endemic region is the key known risk factor . In Victoria , Australia , where endemic areas have been carefully mapped , we aimed to estimate the Incubation Period ( IP ) of BU by intervi...	Buruli Ulcer ( BU ) is a necrotizing skin infection caused by the environmental organism Mycobacterium ulcerans . Despite an unknown mode of transmission , contact with a BU endemic region is the known key risk factor . In Victoria , Australia , endemic areas have been carefully mapped and patients are known to report ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	The Incubation Period of Buruli Ulcer (Mycobacterium ulcerans Infection)
During the recent Ebola outbreak in West Africa several international mobile laboratories were deployed to the mainly affected countries Guinea , Sierra Leone and Liberia to provide ebolavirus diagnostic capacity . Additionally , imported cases and small outbreaks in other countries required global preparedness for Ebo...	For the highly infectious and deadly ebolavirus disease ( EVD ) to date neither specific treatment nor vaccines are available . Rapid and adequate isolation of patients is the only option to contain and to combat spreading of the disease . Reliable and sensitive diagnosis that allows efficient identification of infecte...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "rna", "extraction", "microbiology", "viruses", "organisms", "filoviruses", "rna", "viruses", "molecular", "biol...	2017	External quality assessment study for ebolavirus PCR-diagnostic promotes international preparedness during the 2014 – 2016 Ebola outbreak in West Africa
Typhoid persists as a major cause of global morbidity . While several licensed vaccines to prevent typhoid are available , they are of only moderate efficacy and unsuitable for use in children less than two years of age . Development of new efficacious vaccines is complicated by the human host-restriction of Salmonella...	Typhoid fever is a common cause of febrile illness in tropical countries . Although currently available typhoid vaccines are moderately effective , they are not suitable for use in young children . Development of new vaccines is complicated as Salmonella Typhi , the causative bacteria , only infect humans . In this stu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "salmonella", "typhi", "vaccines", "preventive", "medicine", "bacterial", "diseases", "signs", "an...	2016	Using a Human Challenge Model of Infection to Measure Vaccine Efficacy: A Randomised, Controlled Trial Comparing the Typhoid Vaccines M01ZH09 with Placebo and Ty21a
Thyroid hormone is essential for normal metabolism and development , and overt abnormalities in thyroid function lead to common endocrine disorders affecting approximately 10% of individuals over their life span . In addition , even mild alterations in thyroid function are associated with weight changes , atrial fibril...	Levels of thyroid hormones are tightly regulated by TSH produced in the pituitary , and even mild alterations in their concentrations are strong indicators of thyroid pathologies , which are very common worldwide . To identify common genetic variants associated with the highly heritable markers of thyroid function , TS...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "biology", "genetics", "and", "genomics" ]	2013	A Meta-Analysis of Thyroid-Related Traits Reveals Novel Loci and Gender-Specific Differences in the Regulation of Thyroid Function
Ixodes ricinus is the most widespread and abundant tick in Europe , frequently bites humans , and is the vector of several pathogens including those responsible for Lyme disease , Tick-Borne Encephalitis , anaplasmosis , babesiosis and bartonellosis . These tick-borne pathogens are transmitted to vertebrate hosts via t...	I . ricinus is the most common tick species in Europe and the vector for several pathogens , including bacteria from the Bartonella genus . The mechanisms by which ticks modulate their gene expression in response to pathogen infection are poorly understood . In this report , we compared the differential expression of g...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences" ]	2014	IrSPI, a Tick Serine Protease Inhibitor Involved in Tick Feeding and Bartonella henselae Infection
As cell-invading molecular machinery , coronavirus spike proteins pose an evolutionary conundrum due to their high divergence . In this study , we determined the cryo-EM structure of avian infectious bronchitis coronavirus ( IBV ) spike protein from the γ-genus . The trimeric IBV spike ectodomain contains three recepto...	Because of their structural and functional diversity , coronavirus spike proteins represent a model system for studying viral evolution . Their evolutionary relationships and history pose major puzzles in virology . A critical missing piece in understanding the evolution of coronavirus spikes is the unavailability of t...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "flow", "cytometry", "organismal", "evolution", "microbiology", "viral", "structure", "electron", "cryo-microscopy", "microscopy", "microbial", "evolution", "protein", "structure", "research", "and", "analysis", "methods", "protein", "structure", "determination", "proteins"...	2018	Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins
Yeast cells are able to tolerate and adapt to a variety of environmental stresses . An essential aspect of stress adaptation is the regulation of monovalent ion concentrations . Ion regulation determines many fundamental physiological parameters , such as cell volume , membrane potential , and intracellular pH . It is ...	Ion regulation is fundamental to cell physiology . The concentrations of monovalent ions , such as H+ , K+ and Na+ , determine many physiological parameters such as cell volume , plasma membrane potential and intracellular pH . In yeast cells , these parameters are maintained within a narrow range during the adaptation...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "biochemical", "simulations", "regulatory", "networks", "biology", "computational", "biology" ]	2013	An Integrative Model of Ion Regulation in Yeast
Ivermectin has emerged as very promising pediculicide , particularly in cases of resistance to commonly used pediculicides . Recently , however , the first field-evolved ivermectin-resistance in lice was reported . To gain insight into the mechanisms underlying ivermectin-resistance , we both looked for mutations in th...	Through its unique mode of action , ivermectin represents a relatively new and very promising tool to combat multiple helminthic diseases and other infestations in humans and animals . However , ivermectin resistance in the field began to be reported . Therefore , understanding the mechanisms involved is a key step in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "invertebrates", "medicine", "and", "health", "sciences", "chemical", "characterization", "rna", "interference", "animals", "protein", "expression", "body", "lice", "molecular", "biology", "techniques", "epigenetics", "insect", "...	2018	Complexin in ivermectin resistance in body lice
The gold-standard method for quantifying neutralizing antibody responses to many viruses , including dengue virus ( DENV ) , is the plaque reduction neutralization test ( PRNT , also called the immunofocus reduction neutralization test ) . The PRNT conducted on 96-well plates is high-throughput and requires a smaller v...	Although the plaque reduction neutralization test ( PRNT ) is an important assay for measuring neutralizing antibody responses against many viruses , no free , open-source programs specifically designed for virus plaque counting and neutralizing antibody titer estimation are available . We have developed Viridot , a pa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "serum", "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "body", "fluids", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "immunology", "microbi...	2018	Viridot: An automated virus plaque (immunofocus) counter for the measurement of serological neutralizing responses with application to dengue virus
Schistosomiasis is a serious health problem especially in developing countries and affects more than 243 million people . Only few anthelmintic drugs are available up to now . A major obstacle for drug treatment is the different developmental stages and the varying host compartments during worm development . Anthelmint...	Schistosomiasis is one of the major parasitic diseases in developing countries and still causes 200 , 000 deaths per year . Mass drug administration programs with praziquantel , the drug of choice against schistosomiasis , are currently undertaken in Sub-Saharan Africa . Praziquantel , although efficient against adult ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Drug-Induced Exposure of Schistosoma mansoni Antigens SmCD59a and SmKK7
Transposon-insertion sequencing ( TIS ) is a powerful approach for deciphering genetic requirements for bacterial growth in different conditions , as it enables simultaneous genome-wide analysis of the fitness of thousands of mutants . However , current methods for comparative analysis of TIS data do not adjust for sto...	Transposon insertion sequencing ( TIS ) is a powerful method that couples high-density transposon mutagenesis with next-generation sequencing to comprehensively assess the fitness of thousands of transposon mutants across a genome . TIS is an extremely flexible technique that has been used to define genomic loci requir...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "and", "life", "sciences", "microbiology" ]	2014	ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing
Lonomia obliqua venom is nephrotoxic and acute kidney injury ( AKI ) is the main cause of death among envenomed victims . Mechanism underlying L . obliqua-induced AKI involves renal hypoperfusion , inflammation , tubular necrosis and loss of glomerular filtration and tubular reabsorption capacities . In the present stu...	The envenomation by venomous animals is considered a common and serious occupational disease , especially in rural areas of tropical developing countries . Its public health relevance has been largely ignored by medical authorities worldwide . Specifically in regions of southern and southeast Brazil , accidents with th...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "reactive", "oxygen", "species", "neurochemistry", "body", "fluids", "toxins", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "cytokines", "immunology", "neuroscience", "toxic"...	2019	Renal and vascular effects of kallikrein inhibition in a model of Lonomia obliqua venom-induced acute kidney injury
Synaptic connections must be precisely controlled to ensure proper neural circuit formation . In Drosophila melanogaster , bone morphogenetic protein ( BMP ) promotes growth of the neuromuscular junction ( NMJ ) by binding and activating the BMP ligand receptors wishful thinking ( Wit ) and thickveins ( Tkv ) expressed...	Bi-directional signaling between neurons and their target cells is critical for synapse formation , growth , and plasticity , as well as for neuronal survival . Bone morphogenetic protein ( BMP ) acts as a retrograde signal promoting synaptic growth at the Drosophila neuromuscular junction ( NMJ ) , but little is known...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Drosophila S6 Kinase Like Inhibits Neuromuscular Junction Growth by Downregulating the BMP Receptor Thickveins
Interleukin-33 ( IL-33 ) is associated with multiple diseases , including asthma , rheumatoid arthritis , tissue injuries and infections . Although IL-33 has been indicated to be involved in Staphylococcus aureus ( S . aureus ) wound infection , little is known about how IL-33 is regulated as a mechanism to increase ho...	Interleukin-33 ( IL-33 ) is associated with multiple diseases , including asthma , rheumatoid arthritis , tissue injuries and infections . Although IL-33 has been indicated to be involved in wound infections , little is known about how IL-33 is regulated as a mechanism to increase host defense against skin bacterial in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunity", "innate", "immunity", "staphylococci", "immune", "defense", "host-pathogen", "interaction", "biology", "microbiology", "bacterial", "pathogens" ]	2014	Interleukin-33 Increases Antibacterial Defense by Activation of Inducible Nitric Oxide Synthase in Skin
Apicomplexans are obligate intracellular parasites that actively penetrate their host cells to create an intracellular niche for replication . Commitment to invasion is thought to be mediated by the rhoptries , specialized apical secretory organelles that inject a protein complex into the host cell to form a tight-junc...	Apicomplexans possess a highly polarized secretory pathway that is critical for their ability to invade host cells and cause disease . This unique cellular organization enables delivery of protein cargo to specialized secretory organelles called micronemes and rhoptries that drive forward penetration into the host cell...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "parastic", "protozoans", "biochemistry", "model", "organisms", "transmembrane", "proteins", "proteins", "protozoology", "biology", "microbiology", "host-pathogen", "interaction", "protozoan", "models", "parasitology", "pathogenesis" ]	2013	A Toxoplasma Palmitoyl Acyl Transferase and the Palmitoylated Armadillo Repeat Protein TgARO Govern Apical Rhoptry Tethering and Reveal a Critical Role for the Rhoptries in Host Cell Invasion but Not Egress
Lymphatic filariasis ( LF ) is known to be associated with an increased production of IL-10 . The role of the other IL-10 family members in the pathogenesis of infection and/or disease is not known . We examined the expression patterns of IL-10 family members – IL-19 , IL-24 and IL-26 in LF . We demonstrate that both C...	Lymphatic filariasis afflicts over 120 million people worldwide . While the infection is mostly clinically asymptomatic , approximately 40 million people suffer from overt , morbid clinical pathology , characterized by swelling of the scrotal area and lower limbs ( hydrocele and lymphedema ) . Host immunologic factors ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "helminth", "infections", "medicine", "and", "health", "sciences", "filariasis", "clinical", "immunology", "biology", "and", "life", "sciences", "immunology", "parasitic", "diseases", "immunomodulation", "immune", "response" ]	2014	Expansion of Parasite-Specific CD4+ and CD8+ T Cells Expressing IL-10 Superfamily Cytokine Members and Their Regulation in Human Lymphatic Filariasis
RNA silencing is an evolutionarily conserved sequence-specific gene-inactivation system that also functions as an antiviral mechanism in higher plants and insects . To overcome antiviral RNA silencing , viruses express silencing-suppressor proteins . These viral proteins can target one or more key points in the silenci...	RNA silencing is an evolutionarily conserved sequence-specific gene-inactivation system that also functions as a major antiviral mechanism in higher plants and insects . Viral RNAs are processed by Dicer-like proteins into small interfering ( si ) RNAs , which trigger the RNA-induced silencing complex ( RISC ) assembly...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology", "plant", "biology/plant", "genetics", "and", "gene", "expression", "virology/host", "antiviral", "responses" ]	2010	Viral Protein Inhibits RISC Activity by Argonaute Binding through Conserved WG/GW Motifs
Genome-scale metabolic models ( GEMs ) are mathematically structured knowledge bases of metabolism that provide phenotypic predictions from genomic information . GEM-guided predictions of growth phenotypes rely on the accurate definition of a biomass objective function ( BOF ) that is designed to include key cellular b...	The formulation of phenotypic predictions by genome-scale models ( GEMs ) is dependent on the specified objective . The idea of a biomass objective function ( BOF ) is to represent all metabolites necessary for cells to double so that optimizing the BOF is equivalent to optimizing growth . Knowledge of the qualitative ...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion", "Availability", "and", "future", "directions" ]	[ "cell", "physiology", "coenzymes", "metabolic", "networks", "enzymology", "cell", "metabolism", "metabolites", "network", "analysis", "genome", "analysis", "macromolecules", "enzyme", "chemistry", "polymer", "chemistry", "computer", "and", "information", "sciences", "lipi...	2019	BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
Cryptosporidiosis causes gastroenteritis and is transmitted to humans via contaminated water and food , and contact with infected animals and people . We analyse long-term cryptosporidiosis patterns across Australia ( 2001–2012 ) and review published Australian studies and jurisdictional health bulletins to identify hi...	The parasite Cryptosporidium is a common cause of gastroenteritis worldwide . Ineffectively focused interventions are partly why the disease remains a challenge to control . In this study , we describe the geographical , seasonal and demographic characteristics of reported cryptosporidiosis in Australia from 2001–2012 ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Cryptosporidiosis: A Disease of Tropical and Remote Areas in Australia
Acetylcholine receptors are pentameric ligand–gated channels involved in excitatory neuro-transmission in both vertebrates and invertebrates . In nematodes , they represent major targets for cholinergic agonist or antagonist anthelmintic drugs . Despite the large diversity of acetylcholine-receptor subunit genes presen...	The control of parasitic nematode infections in humans , livestock and companion animals is critically dependent on anthelmintic treatment . However , the indiscriminate use of anthelmintic drugs has inevitably led to the selection of resistant parasites . In this respect there is currently an urgent need to increase o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Functional Characterization of a Novel Class of Morantel-Sensitive Acetylcholine Receptors in Nematodes
Benzimidazoles ( BZ ) are essential components of the limited chemotherapeutic arsenal available to control the global burden of parasitic nematodes . The emerging threat of BZ resistance among multiple nematode species necessitates the development of novel strategies to identify genetic and molecular mechanisms underl...	Nematode parasites have a tremendous impact on human health with almost two billion people infected worldwide . The control of nematode infections relies mainly on the efficacy of a limited repertoire of anthelmintic compounds , including the benzimidazoles ( BZ ) . Already a significant problem in veterinary medicine ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "genome-wide", "association", "studies", "invertebrates", "medicine", "and", "health", "sciences", "quantitative", "trait", "loci", "caenorhabditis", "population", "genetics", "parasitic", "diseases", "animals", "nematode", "infections", "animal", "models", "caenorhabditis"...	2018	Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles
The Vi capsular polysaccharide is a virulence-associated factor expressed by Salmonella enterica serotype Typhi but absent from virtually all other Salmonella serotypes . In order to study this determinant in vivo , we characterised a Vi-positive S . Typhimurium ( C5 . 507 Vi+ ) , harbouring the Salmonella pathogenicit...	Pathogens of the genus Salmonella are closely related yet cause distinct diseases and have different host-range . Salmonella Typhi causes a systemic disease called typhoid fever specifically in humans , and is commonly modelled using a surrogate host-pathogen combination , namely Salmonella Typhimurium infection in mic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology", "microbiology", "salmonella", "bacterial", "pathogens", "immune", "response" ]	2011	A Salmonella Typhimurium-Typhi Genomic Chimera: A Model to Study Vi Polysaccharide Capsule Function In Vivo
Bolivia is one of the countries with a high intestinal helminth and protozoan infection rate . Despite the high prevalence of the parasitic infection , nationwide preventive measures for Bolivian children have not yet been implemented . We evaluated the effect of mass stool examination and treatment as a strategy for d...	Intestinal helminth and protozoan ( parasitic ) infections are found mainly in areas with warm , humid climates and in many developing countries . Bolivia currently has high parasite infection rates , including intestinal helminth and protozoan infections . Despite the high prevalence of parasitic infections , nationwi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "digestive", "system", "gastrointestinal", "tract", "invertebrates", "helminth", "infections", "medicine", "and", "health", "sciences", "protozoans", "parasitic", "intestinal", "diseases", "anatomy", "helminths", "biology", "and", "life", "sciences", "pediatric", "infecti...	2016	Effect of Mass Stool Examination and Mass Treatment For Decreasing Intestinal Helminth and Protozoan Infection Rates in Bolivian Children: A Cross-Sectional Study
B cell activating factor receptor ( BAFFR ) -/- mice have a profound reduction in mature B cells , but unlike μMT mice , they have normal numbers of newly formed , immature B cells . Using a West Nile virus ( WNV ) challenge model that requires antibodies ( Abs ) for protection , we found that unlike wild-type ( WT ) m...	Many individuals including infants , the elderly and the immunocompromised do not develop protective immunity after immunization with current vaccines . Thus , new vaccine strategies are needed to overcome underlying immune deficiencies and mediate protection . In this study , we examined whether it was possible to ind...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "blood", "serum", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "enzyme-linked", "immunoassays", "pathogens", "immunology", "cell-mediated", "immunity", "microbiology", "viru...	2017	Protection of mice deficient in mature B cells from West Nile virus infection by passive and active immunization
The HOXB13 gene has been implicated in prostate cancer ( PrCa ) susceptibility . We performed a high resolution fine-mapping analysis to comprehensively evaluate the association between common genetic variation across the HOXB genetic locus at 17q21 and PrCa risk . This involved genotyping 700 SNPs using a custom Illum...	Genome-wide association studies ( GWAS ) have identified numerous low penetrance disease susceptibility variants , yet few causal alleles have been unambiguously identified . The underlying causal variants are expected to be predominantly common; however synthetic associations with rare , higher penetrance variants hav...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "biology", "cancer", "genetics" ]	2014	Fine-Mapping the HOXB Region Detects Common Variants Tagging a Rare Coding Allele: Evidence for Synthetic Association in Prostate Cancer
Human African Trypanosomiasis ( HAT ) or sleeping sickness is a Neglected Tropical Disease . Long regarded as an invariably fatal disease , there is increasing evidence that infection by T . b . gambiense can result in a wide range of clinical outcomes , including latent infections , which are long lasting infections w...	Since it was first identified , human African trypanosomiasis ( HAT ) or sleeping sickness has been described as invariably fatal . Recent data however suggest that infection by T . b . gambiense can result in a wide range of clinical outcomes in its human host including long lasting infections , that can be detected b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2017	Candidate genes-based investigation of susceptibility to Human African Trypanosomiasis in Côte d’Ivoire
The ability of the tubercle bacillus to arrest phagosome maturation is considered one major mechanism that allows its survival within host macrophages . To identify mycobacterial genes involved in this process , we developed a high throughput phenotypic cell-based assay enabling individual sub-cellular analysis of over...	One of the major virulence mechanisms of the tuberculosis bacillus , Mycobacterium tuberculosis , is its ability to resist killing by phagocytic cells of the host immune system , namely the macrophages . Macrophages degrade invading microbes by engulfment inside a vacuole , or phagosome , that progressively acidifies a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases/respiratory", "infections" ]	2010	High Content Phenotypic Cell-Based Visual Screen Identifies Mycobacterium tuberculosis Acyltrehalose-Containing Glycolipids Involved in Phagosome Remodeling
Malaria and dengue are the most prevalent vector-borne diseases worldwide and represent major public health problems . Both are endemic in tropical regions , propitiating co-infection . Only few co-infection cases have been reported around the world , with insufficient data so far to enhance the understanding of the ef...	Malaria and dengue fever are typical diseases in tropical regions of developing countries; such as the Brazilian Amazon . They become serious problems in public health as they mostly affect vulnerable populations . Both diseases are mosquito-borne . These diseases present similar signs and symptoms . Brazil registers m...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "tropical", "diseases", "medicine", "and", "health", "sciences", "epidemiology" ]	2014	P. vivax Malaria and Dengue Fever Co-infection: A Cross-Sectional Study in the Brazilian Amazon
Optimal immune activation of naïve CD8 T cells requires signal 1 mediated by the T cell receptor , signal 2 mediated by co-stimulation and signal 3 provided by pro-inflammatory cytokines . However , the potential for signal 3 cytokines to rescue anti-viral responses in functionally exhausted T cells has not been define...	Persistent viral infections continue to cause major morbidity and mortality; chronic hepatitis B virus infection alone accounts for more than a million deaths annually . Such infections are characterised by a failure of viral control perpetuated by exhaustion of the T cell response . Here we show that the cytokine IL-1...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology" ]	2013	The Third Signal Cytokine IL-12 Rescues the Anti-Viral Function of Exhausted HBV-Specific CD8 T Cells
In order to fully understand protein kinase networks , new methods are needed to identify regulators and substrates of kinases , especially for weakly expressed proteins . Here we have developed a hybrid computational search algorithm that combines machine learning and expert knowledge to identify kinase docking sites ...	Protein kinases are enzymes that regulate key cellular processes by covalently attaching a phosphate group to substrate proteins; they are crucial components of signaling pathways involved in cancer , diabetes , and many other diseases . Identifying the substrates of particular protein kinases is challenging , and many...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "biochemistry", "computational", "biology/genomics", "cell", "biology/cell", "signaling" ]	2010	Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors
The Plasmodium ookinete develops over several hours in the bloodmeal of its mosquito vector where it is exposed to exogenous stresses , including cytotoxic reactive oxygen species ( ROS ) . How the parasite adapts to these challenging conditions is not well understood . We have systematically investigated the expressio...	The malaria parasite Plasmodium is transmitted by Anopheles mosquitoes . Within the midgut of the insect , it is exposed to multiple environmental stresses , including cytotoxic reactive oxygen species ( ROS ) . To avoid destruction , the parasite develops into a motile ookinete capable of leaving the midgut . Yet , oo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "enzymes", "microbiology", "host-pathogen", "interaction", "plasmodium", "falciparum", "parasitology", "parasite", "physiology", "parastic", "protozoans", "anopheles", "enzyme", "classes", "oxidoreductases", "biology", "biochemistry", "cell"...	2013	Expression of Cytosolic Peroxiredoxins in Plasmodium berghei Ookinetes Is Regulated by Environmental Factors in the Mosquito Bloodmeal
Zika virus ( ZIKV; Flaviviridae , Flavivirus ) was declared a public health emergency of international concern by the World Health Organization ( WHO ) in February 2016 , because of the evidence linking infection with ZIKV to neurological complications , such as Guillain-Barre Syndrome in adults and congenital birth de...	Zika virus ( ZIKV ) isolates are genetically diverse , but belong to two recognized lineages , termed “African” and “Asian . ” Asian ZIKV infection during pregnancy causes fetal abnormalities including microcephaly . Developing an effective preventative Zika virus vaccine that protects pregnant women is essential for m...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "mammals", "viruses", "primates", "animal", "models", "vaccines", "preventive", "medicin...	2016	Heterologous Protection against Asian Zika Virus Challenge in Rhesus Macaques
West Nile virus ( WNV ) , an arbovirus maintained in a bird-mosquito enzootic cycle , can infect other vertebrates including humans . WNV was first reported in the US in 1999 where , to date , three genotypes belonging to WNV lineage I have been described ( NY99 , WN02 , SW/WN03 ) . We report here the WNV sequences obt...	West Nile Virus ( WNV ) is a mosquito-borne virus of African origin that is widespread around the world . The WNV life-cycle involves mosquitoes and birds , but humans and other animals can be infected , although they are not considered to be important players in the transmission cycle . Clinically , most WNV infection...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "rna", "viruses", "emerging", "infectious", "diseases", "west", "nile", "fever", "molecular", "epidemiology", "viral", "classification", "virology", "emerging", "viral", "diseases", "epidemiology", "neglected", "tropical", "diseases",...	2013	Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011: Phylogeny, Selection Pressure and Evolutionary Time-Scale Analysis
Trypanosoma brucei gambiense is the main causative agent of Human African Trypanosomiasis ( HAT ) , also known as sleeping sickness . Because of limited alternatives and treatment toxicities , new therapeutic options are urgently needed for patients with HAT . Sterol 14alpha-demethylase ( CYP51 ) is a potential drug ta...	Human African trypanosomiasis ( HAT ) , also known as sleeping sickness , is a parasitic disease exclusively located in sub-Saharan and southern Africa where it is transmitted by infected tsetse flies and is caused by a blood parasite named Trypanosoma brucei . Because of limited alternatives , toxicity and high expens...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "rna", "interference", "african", "trypanosomiasis", "cell", "processes", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "animal", "models", "model", "organisms", "protozoans", "cell", "growth", "negl...	2016	Trypanosoma brucei CYP51: Essentiality and Targeting Therapy in an Experimental Model
Soluble N-ethylmaleimide-sensitive factor attachment receptors ( SNAREs ) play a crucial role in the development and virulence through mediation of membrane fusion and vesicle trafficking in pathogens . Our previous studies reported that the SNARE protein FgVam7 and its binding proteins FgVps39/41 are involved in vesic...	SNARE proteins which mediate fusion of transport vesicles with the correct target membrane , are essential components of vesicle trafficking machinery . Together with the cognate effectors , SNAREs coordinate the dynamics of trafficking pathway and determines the cargo proteins destination . Here , we found that SNARE ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "vacuoles", "cell", "processes", "light", "microscopy", "electrophysiology", "neuroscience", "snare", "proteins", "ion", "channels", "microscopy", "golgi", "apparatus", "plants", "cellular", "structures", "and", "orga...	2019	The t-SNARE protein FgPep12, associated with FgVam7, is essential for ascospore discharge and plant infection by trafficking Ca2+ ATPase FgNeo1 between Golgi and endosome/vacuole in Fusarium graminearum
Nonmembrane-bound organelles that behave like liquid droplets are widespread among eukaryotic cells . Their dysregulation appears to be a critical step in several neurodegenerative conditions . Here , we report that tau protein , the primary constituent of Alzheimer neurofibrillary tangles , can form liquid droplets an...	Tau is a common neuronal protein that , under circumstances and conditions not well understood to date , self-assembles into intracellular aggregates in several neurodegenerative diseases including Alzheimer disease . These aggregates are formed of fibrous polymers . The mechanism by which this critical transition from...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "transfer", "rna", "medicine", "and", "health", "sciences", "deer", "ruminants", "hek", "293", "cells", "drugs", "biological", "cultures", "vertebrates", "neuroscience", "animals", "mammals", "immunoprecipitation", "molecular", "biology", "te...	2017	RNA stores tau reversibly in complex coacervates
Malaria parasites reside inside erythrocytes and the disease manifestations are linked to the growth inside infected erythrocytes ( IE ) . The growth of the parasite is mostly confined to the trophozoite stage during which nuclear division occurs followed by the formation of cell bodies ( schizogony ) . The mechanism a...	Malaria is a serious human health problem and the disease manifestations are caused by erythrocytic stages . The growth of Plasmodium in erythrocytes occurs through the peculiar process of schizogony where the nucleus undergoes several divisions followed by cell body formation . Inside a red blood cell ( RBC ) , how do...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "molecular", "cell", "biology", "tropical", "diseases", "(non-neglected)", "biology", "microbiology", "malaria", "parasitic", "diseases", "parasitology" ]	2012	Arrest of Nuclear Division in Plasmodium through Blockage of Erythrocyte Surface Exposed Ribosomal Protein P2
Poverty has been implicated as a challenge in the control of the current Ebola outbreak in West Africa . Although disparities between affected countries have been appreciated , disparities within West African countries have not been investigated as drivers of Ebola transmission . To quantify the role that poverty plays...	Despite recognition that resource constraints contributed to the difficulty in controlling West Africa’s ongoing Ebola outbreak , no previous study has been conducted to quantify the impact of poverty on transmission . In particular , the extent to which within country heterogeneity in socioeconomic status ( SES ) coul...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Quantifying Poverty as a Driver of Ebola Transmission
A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment . While the log-rank test is widely used for this purpose , nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in m...	The identification of genetic variants associated with survival time is crucial in genomic studies . To this end , a number of methods have been proposed to computing a p-value that summarized the difference in survival time of two or more population . The most widely used method among these is the log-rank test . Wide...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Accurate Computation of Survival Statistics in Genome-Wide Studies
Transcription factors ( TFs ) are fundamental controllers of cellular regulation that function in a complex and combinatorial manner . Accurate identification of a transcription factor's targets is essential to understanding the role that factors play in disease biology . However , due to a high false positive rate , i...	Transcription factors ( TFs ) are crucial to the precise regulation of many cellular processes and thus , are responsible for many human phenotypes and diseases . Now that the ENCODE project has mapped hundreds of TFs to their genomic binding locations , extracting functional biological signals is the next step in unde...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "functional", "genomics", "regulatory", "networks", "biology", "genomics", "computational", "biology", "genomic", "medicine" ]	2014	Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association
Glial cells regulate multiple aspects of synaptogenesis . In the absence of Schwann cells , a peripheral glial cell , motor neurons initially innervate muscle but then degenerate . Here , using a genetic approach , we show that neural activity-regulated negative factors produced by muscle drive neurodegeneration in Sch...	We utilized genetic methods to examine how Schwann cells prevent degeneration of motor neurons ( MNs ) in the spinal cord . Blocking peripheral , neuromuscular activity completely rescued MNs and neuromuscular junctions ( NMJs ) in erbB3 mutant mice lacking Schwann cells , which normally exhibit profound neurodegenerat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "enzymes", "enzymology", "electrophysiology", "neuroscience", "macroglial", "cells", "serine", "proteases", "muscle", "proteins", "respiratory", "system", "schwann", "cells", "nerve", "fibers", "thrombin", "a...	2019	Glial cells maintain synapses by inhibiting an activity-dependent retrograde protease signal
Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , the causative agent of Kaposi’s sarcoma , encodes 25 mature viral miRNAs . MCP-1-induced protein-1 ( MCPIP1 ) , a critical regulator of immune homeostasis , has been shown to suppress miRNA biosynthesis via cleavage of precursor miRNAs through its RNase domain . We dem...	A subset of viruses , including Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , encode microRNAs within their own genomes . We propose that the human host may possess strategies to repress viral microRNA biogenesis as an antiviral strategy by taking advantage of unique temporal features of viral microRNA biogenesis ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "pathology", "and", "laboratory", "medicine", "3'", "utr", "gene", "regulation", "pathogens", "enzymes", "messenger", "rna", "microbiology", "enzymology", "viruses", "micrornas", "untranslated", "regions", "dna", ...	2016	Virus-Mediated Alterations in miRNA Factors and Degradation of Viral miRNAs by MCPIP1
Leptospirosis , caused by spirochetes of the genus Leptospira , is a globally widespread , neglected and emerging zoonotic disease . While whole genome analysis of individual pathogenic , intermediately pathogenic and saprophytic Leptospira species has been reported , comprehensive cross-species genomic comparison of a...	Leptospirosis is an emerging and re-emerging globally important zoonotic infectious disease caused by spirochetes of the genus Leptospira . This genus is complex , with members that cause lethal human disease , yet mechanisms that underlie pathogenesis remain obscure . Leptospira species are divided into those that are...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "bacteriophages", "pathogens", "microbiology", "viruses", "genome", "analysis", "molecular", "biology", "techniques", "bacteria", "bacterial", ...	2016	What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira
Protein kinases play key roles in signaling and response to changes in the external environment . The ability of Candida albicans to quickly sense and respond to changes in its environment is key to its survival in the human host . Our guiding hypothesis was that creating and screening a set of protein kinase mutant st...	Candida albicans is the major fungal commensal and pathogen of humans . Like most microorganisms , C . albicans is surrounded and protected by a cell wall . This cell wall has two purposes: to act as a rigid “exoskeleton” to prevent cells from bursting , and to provide a surface where a cell can interact with the outsi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/fungal", "infections", "genetics", "and", "genomics/gene", "function", "microbiology/microbial", "growth", "and", "development", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics" ]	2010	An Extensive Circuitry for Cell Wall Regulation in Candida albicans
The fungal cell wall is the first point of interaction between an invading fungal pathogen and the host immune system . The outer layer of the cell wall is comprised of GPI anchored proteins , which are post-translationally modified by both N- and O-linked glycans . These glycans are important pathogen associated molec...	Candida albicans is an opportunistic fungal pathogen of humans , which can cause superficial infections of the oral and genital epithelium or fatal systemic disease in immune compromised individuals . The cell wall of C . albicans consists of an inner layer of chitin and β-glucan and an outer fibrillar layer of highly ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "applied", "microbiology", "biochemistry", "pathogenesis", "mycology", "polysaccharides", "fungi", "proteoglycans", "immunity", "medical", "microbiology", "innate", "immunity", "microbial", "pathogens", "host-pathogen", "interaction", "glycoproteins", "biology"...	2013	The Mnn2 Mannosyltransferase Family Modulates Mannoprotein Fibril Length, Immune Recognition and Virulence of Candida albicans
Yap is a transcriptional co-activator that regulates cell proliferation and apoptosis downstream of the Hippo kinase pathway . We investigated Yap function during mouse kidney development using a conditional knockout strategy that specifically inactivated Yap within the nephrogenic lineage . We found that Yap is essent...	The mammalian kidney undergoes reiterative and stereotypical morphogenetic changes to create the elaborately convoluted adult nephron , the functional filtration unit of the kidney . How these sequential morphological events are controlled remains poorly understood . Here we show that the transcriptional activator Yap ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "model", "organisms", "cell", "growth", "signaling", "pathways", "morphogenesis", "pattern", "formation", "gene", "expression", "biology", "mouse", "molecular", "biology", "signal", "transduction", "cell", "biology", "mole...	2013	Yap- and Cdc42-Dependent Nephrogenesis and Morphogenesis during Mouse Kidney Development
Mitochondria are central to many cellular processes including respiration , ion homeostasis , and apoptosis . Using computational predictions combined with traditional quantitative experiments , we have identified 100 proteins whose deficiency alters mitochondrial biogenesis and inheritance in Saccharomyces cerevisiae ...	Mitochondria are the proverbial powerhouses of the cell , running the fundamental biochemical processes that produce energy from nutrients using oxygen . These processes are conserved in all eukaryotes , from humans to model organisms such as baker's yeast . In humans , mitochondrial dysfunction plays a role in a varie...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "cell", "biology/morphogenesis", "and", "cell", "biology", "computational", "biology", "computational", "biology/systems", "biology", "cell", "biology/cytoskeleton" ]	2009	Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis
Accurate methods to assess the pathogenicity of mutations are needed to fully leverage the possibilities of genome sequencing in diagnosis . Current data-driven and bioinformatics approaches are , however , limited by the large number of new variations found in each newly sequenced genome , and often do not provide dir...	The protein quality control system targets misfolded proteins for degradation . So far it has not been possible from sequence or structural data to predict the biological stability of a misfolded protein , or the effect of mutations on intracellular protein levels . Here we demonstrate that in silico saturation mutagen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "genetic", "diseases", "mutation", "hereditary", "nonpolyposis", "colorectal", "cancer", "chaperone", "proteins", "autosomal", "dominant", "diseases", "thermodynam...	2017	Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations
An important step in epithelial organ development is size maturation of the organ lumen to attain correct dimensions . Here we show that the regulated expression of Tenectin ( Tnc ) is critical to shape the Drosophila melanogaster hindgut tube . Tnc is a secreted protein that fills the embryonic hindgut lumen during tu...	Epithelial tubes constitute the functional units of vital organs , and they undergo highly regulated changes in size and shape during development to accommodate the three-dimensional configurations optimal for organ physiology . Through studies of Drosophila melanogaster , we show that epithelial tube diameter can be m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "extracellular", "matrix", "composition", "gene", "function", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "organism", "development", "morphogenesis", "extracellular", "matrix", "organogenesis", "...	2012	A Luminal Glycoprotein Drives Dose-Dependent Diameter Expansion of the Drosophila melanogaster Hindgut Tube
Bloodstream forms of Trypanosoma brucei contain a glycosylphosphatidylinositol-specific phospholipase C ( GPI-PLC ) that cleaves the GPI-anchor of the variable surface glycoprotein ( VSG ) . Its location in trypanosomes has been controversial . Here , using confocal microscopy and surface labelling techniques , we show...	African trypanosomes cause sleeping sickness , for which current therapy is inadequate . The parasite protects its surface from the host immune system by regularly switching its surface coat . The glycosylphosphatidylinositol-PLC only occurs in the bloodstream form , where it removes the surface coat after it enters th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "biochemistry", "infectious", "diseases", "cell", "biology" ]	2009	The Glycosylphosphatidylinositol-PLC in Trypanosoma brucei Forms a Linear Array on the Exterior of the Flagellar Membrane Before and After Activation
Previous studies in Drosophila melanogaster have demonstrated that many tumor suppressor pathways impinge on Rb/E2F to regulate proliferation and survival . Here , we report that Tuberous Sclerosis Complex 1 ( TSC1 ) , a well-established tumor suppressor that regulates cell size , is an important regulator of dE2F1 dur...	Tuberous Sclerosis Complex genes 1 ( TSC1 ) is a downstream component of the Insulin Receptor signaling pathway that is often deregulated in many tumors . In this study , we discovered that the fruit fly homolog of TSC1 regulates E2F transcription factor by controlling protein expression . E2F family proteins are key r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/molecular", "development", "cell", "biology/cell", "growth", "and", "division" ]	2010	Tuberous Sclerosis Complex 1 Regulates dE2F1 Expression during Development and Cooperates with RBF1 to Control Proliferation and Survival
Although single genes underlying several evolutionary adaptations have been identified , the genetic basis of complex , polygenic adaptations has been far more challenging to pinpoint . Here we report that the budding yeast Saccharomyces paradoxus has recently evolved resistance to citrinin , a naturally occurring myco...	Adaptation via natural selection has been a subject of great interest for well over a century , yet we still have little understanding of its molecular basis . What are the genetic changes that are actually being selected ? While single genes underlying several adaptations have been identified , the genetic basis of co...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation
DNA damage checkpoints arrest cell cycle progression to facilitate DNA repair . The ability to survive genotoxic insults depends not only on the initiation of cell cycle checkpoints but also on checkpoint maintenance . While activation of DNA damage checkpoints has been studied extensively , molecular mechanisms involv...	DNA is constantly damaged both by factors outside our bodies ( such as ultraviolet rays from sunlight ) and by factors from within ( such as reactive oxygen species produced during metabolism ) . DNA damage can lead to malfunctioning of genes , and persistent DNA damage can result in developmental disorders or the deve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "cell", "biology/cell", "signaling" ]	2010	A Mitotic Phosphorylation Feedback Network Connects Cdk1, Plk1, 53BP1, and Chk2 to Inactivate the G2/M DNA Damage Checkpoint
Rho family GTPases act as molecular switches regulating actin cytoskeleton dynamics . Attenuation of their signaling capacity is provided by GTPase-activating proteins ( GAPs ) , including p190A , that promote the intrinsic GTPase activity of Rho proteins . In the current study we have performed a small-scale ENU mutag...	Glomerulocystic kidney disease occurs either in isolation or in combination with other cystic diseases . To date , the paucity of mouse models have impeded our progress in understanding the molecular mechanisms leading to glomerular cyst development . Using an ENU mutagenesis approach , we present here a novel mouse mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "immunofluorescence", "staining", "glomeruli", "fibroblasts", "developmental", "biology", "connective", "tissue", "cells", "embryos", "kidneys", "cellular", "structures", "and", "organelles", "cytoskeleton", "research", "and", "ana...	2016	A Point Mutation in p190A RhoGAP Affects Ciliogenesis and Leads to Glomerulocystic Kidney Defects
Epidemiological studies carried out using culture or microscopy in most of the amoebiasis endemic developing countries , yielded confusing results since none of these could differentiate the pathogenic Entamoeba histolytica from the non-pathogenic Entamoeba dispar and Entamoeba moshkovskii . The Northeastern part of In...	Most epidemiologic studies in developing countries carried out for amoebiasis is either based on microscopy alone or culture/ microscopy used as a screening tool , have poor sensitivity and specificity and thus fails to figure out its true magnitude . The purpose of this study was to assess the true prevalence of amoeb...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Molecular Epidemiology of Amoebiasis: A Cross-Sectional Study among North East Indian Population
Syphilis affects approximately 11 million people each year globally , and is the third most prevalent sexually transmitted bacterial infection in the United States . Inability to independently culture and genetically manipulate Treponema pallidum subsp . pallidum , the causative agent of this disease , has hindered our...	Syphilis is one of the most prevalent sexually transmitted infections that affect millions of people around the world . The causative bacterium , Treponema pallidum subsp . pallidum , can be transmitted from mother to fetus during maternal infection , resulting in adverse pregnancy outcomes . Although timely treatment ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "binding", "cell", "physiology", "urology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "biological", "cultures", "tropical", "diseases", "microbiology", "trepon...	2019	Analysis of host cell binding specificity mediated by the Tp0136 adhesin of the syphilis agent Treponema pallidum subsp. pallidum
Multipartite viruses replicate through a puzzling evolutionary strategy . Their genome is segmented into two or more parts , and encapsidated in separate particles that appear to propagate independently . Completing the replication cycle , however , requires the full genome , so that a systemic infection of a host requ...	Viruses typically consist of some genetic material wrapped up in a single particle , the capsid . Multipartite viruses follow another lifestyle . Their genome is made up of several segments , each packed in independent particles . However , since the completion of the viral cycle requires the full genome , these partic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "microbiology", "viral", "structure", "microbial", "evolution", "extinct", "genomes", "microbial", "genomics", "viral", "genomics", "pathogenesis", "viral", ...	2019	Endemicity and prevalence of multipartite viruses under heterogeneous between-host transmission
The allosteric inhibitors of integrase ( termed ALLINIs ) interfere with HIV replication by binding to the viral-encoded integrase ( IN ) protein . Surprisingly , ALLINIs interfere not with DNA integration but with viral particle assembly late during HIV replication . To investigate the ALLINI inhibitory mechanism , we...	A promising new class of antivirals called “ALLINIs” ( allosteric inhibitors of integrase ) potently inhibits HIV replication . Like other drugs , ALLINIs seem to target also the HIV-1 integrase ( IN ) , which is crucial for the replication of this virus , but instead of acting at early phases of HIV replication , they...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dimers", "(chemical", "physics)", "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "condensed", "matter", "physics", "microbiology", "viral", "structure", "retroviruses", "viruses", "immunodeficie...	2016	Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase
Plant stress responses require both protective measures that reduce or restore stress-inflicted damage to cellular structures and mechanisms that efficiently remove damaged and toxic macromolecules , such as misfolded and damaged proteins . We have recently reported that NBR1 , the first identified plant autophagy adap...	Environmental stresses such as heat cause generation of misfolded and damaged proteins , which are highly toxic and must be efficiently removed . In plants , NBR1 , the first isolated autophagy receptor with an ubiquitin-association domain , plays a critical role in plant stress tolerance by targeting ubiquitinated pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology", "agriculture" ]	2014	E3 Ubiquitin Ligase CHIP and NBR1-Mediated Selective Autophagy Protect Additively against Proteotoxicity in Plant Stress Responses
Protein synthesis-dependent , late long-term potentiation ( LTP ) and depression ( LTD ) at glutamatergic hippocampal synapses are well characterized examples of long-term synaptic plasticity . Persistent increased activity of protein kinase M ζ ( PKMζ ) is thought essential for maintaining LTP . Additional spatial and...	A fundamental problem in neurobiology is to understand how memories are maintained for up to years . Long-term potentiation ( LTP ) , an enduring increase in the strength of specific connections ( synapses ) between neurons , is thought to comprise , at least in part , the substrate of learning and memory . What proces...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "nonlinear", "dynamics", "molecular", "neuroscience", "mathematics", "computational", "neuroscience", "signaling", "pathways", "biology", "computational", "biology", "signaling", "networks", "neuroscience", "learning", "and", "memory" ]	2012	Molecular Constraints on Synaptic Tagging and Maintenance of Long-Term Potentiation: A Predictive Model
Hox transcription factors control a number of developmental processes with the help of the PBC class proteins . In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide ( HX ) . This paradigm is at the basis of the vast majority of e...	Hox proteins are key transcriptional regulators of animal development , famously helping to determine identity along the anterior-posterior body axis . Although their evolution and developmental roles are well established , the molecular mechanisms underlying their specific functions remain poorly characterized . The c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Hox Proteins Display a Common and Ancestral Ability to Diversify Their Interaction Mode with the PBC Class Cofactors
Individuals with Cornelia de Lange Syndrome ( CdLS ) display diverse developmental deficits , including slow growth , multiple limb and organ abnormalities , and intellectual disabilities . Severely-affected individuals most often have dominant loss-of-function mutations in the Nipped-B-Like ( NIPBL ) gene , and milder...	Cornelia de Lange Syndrome ( CdLS ) alters many aspects of growth and development . CdLS is caused by mutations in genes encoding proteins that ensure that chromosomes are distributed equally when a cell divides . These include genes that encode components of the cohesin complex , and Nipped-B-Like ( NIPBL ) that puts ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Drosophila Nipped-B Mutants Model Cornelia de Lange Syndrome in Growth and Behavior
The pulmonary collectins , surfactant proteins A and D ( SP-A and SP-D ) have been implicated in the regulation of the innate immune system within the lung . In particular , SP-D appears to have both pro- and anti-inflammatory signaling functions . At present , the molecular mechanisms involved in switching between the...	Cells of the lung lining secrete a microbe-binding molecule called surfactant protein D ( SP-D ) that helps activate the inflammatory system against invading pathogens . In the absence of infection , SP-D is important in limiting inflammation , demonstrated by the fact that mice lacking the SP-D gene have chronic infla...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "physiology", "immunology", "respiratory", "medicine" ]	2008	S-Nitrosylation of Surfactant Protein-D Controls Inflammatory Function
Many of the factors that contribute to CD8+ T cell immunodominance hierarchies during viral infection are known . However , the functional differences that exist between dominant and subdominant epitope-specific CD8+ T cells remain poorly understood . In this study , we characterized the phenotypic and functional diffe...	MHC-restricted CD8+ T cell populations that bind viral proteins are often present at different frequencies . It is thought that those virus-specific CD8+ T cells that are present at the highest frequency are predominantly responsible for eliciting control of viral infections . While the number of virus-specific CD8+ T ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "biomacromolecule-ligand", "interactions", "flow", "cytometry", "immune", "cells", "protein", "interactions", "immunology", "vertebrates", "animals", "mammals", "dna", "transcription", "primates", "animal", "models", "model", "organisms", "immunologic", ...	2014	TCR Affinity Associated with Functional Differences between Dominant and Subdominant SIV Epitope-Specific CD8+ T Cells in Mamu-A*01+ Rhesus Monkeys
The Flavivirus genus includes a large number of medically relevant pathogens that cycle between humans and arthropods . This host alternation imposes a selective pressure on the viral population . Here , we found that dengue virus , the most important viral human pathogen transmitted by insects , evolved a mechanism to...	Flaviviruses constitute the most important and diverse group of arthropod-transmitted viruses , including relevant human pathogens such as dengue , Zika , yellow fever , and West Nile viruses . The natural alternation of these viruses between vertebrate and invertebrate hosts imposes a selective pressure on the viral p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dengue", "virus", "microbial", "mutation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "rna", "extraction", "microbiology", "viral", "structure", "viruses", "mutation", "rna", "viruses", "extraction", "techniques"...	2017	Dengue virus genomic variation associated with mosquito adaptation defines the pattern of viral non-coding RNAs and fitness in human cells
Systemic lupus erythematosus ( SLE ) is a complex autoimmune disease with a strong genetic predisposition , characterized by an upregulated type I interferon pathway . MicroRNAs are important regulators of immune homeostasis , and aberrant microRNA expression has been demonstrated in patients with autoimmune diseases ....	Genome-wide association studies have identified quite a number of susceptibility loci associated with complex diseases such as systemic lupus erythematosus ( SLE ) . However , for most of them , the intrinsic link between genetic variation and disease mechanism is not fully understood . SLE is characterized by a signif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "rheumatology", "gene", "networks", "rna", "interference", "gene", "regulation", "immunology", "dna", "transcription", "genetics", "of", "disease", "molecular", "genetics", "immunomodulation", "systemic", "lupus", "erythematosus", "lupus", "erythematosus", "ge...	2011	A Functional Variant in MicroRNA-146a Promoter Modulates Its Expression and Confers Disease Risk for Systemic Lupus Erythematosus
To make good judgments people gather information . An important problem an agent needs to solve is when to continue sampling data and when to stop gathering evidence . We examine whether and how the desire to hold a certain belief influences the amount of information participants require to form that belief . Participa...	People tend to gather information before making judgments . As information is often unlimited a decision has to be made as to when the data is sufficient to reach a conclusion . Here , we show that the decision to stop gathering data is influenced by whether the data points towards the desired conclusion . Importantly ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "recreation", "learning", "engineering", "and", "technology", "reaction", "time", "social", "sciences", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "cognitive", "neuroscience", "cognitive", "psychology", "mathematics", "probability", "dis...	2019	Evidence accumulation is biased by motivation: A computational account
Most animal species are cold-blooded , and their neuronal circuits must maintain function despite environmental temperature fluctuations . The central pattern generating circuits that produce rhythmic motor patterns depend on the orderly activation of circuit neurons . We describe the effects of temperature on the pylo...	The neural circuits that produce behaviors such as walking , chewing , and swimming must be both robust and flexible to changing internal and environmental demands . How then do cold-blooded animals cope with temperature fluctuations when the underlying processes that give rise to circuit performance are themselves tem...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/theoretical", "neuroscience", "physiology/neural", "homeostasis", "neuroscience/motor", "systems", "marine", "and", "aquatic", "sciences/evolutionary", "biology", "biophysics/experimental", "biophysical", "methods", "neuroscience/neural", "homeostasis", "physiology", ...	2010	Precise Temperature Compensation of Phase in a Rhythmic Motor Pattern
In the study of metabolic networks , optimization techniques are often used to predict flux distributions , and hence , metabolic phenotype . Flux balance analysis in particular has been successful in predicting metabolic phenotypes . However , an inherent limitation of a stoichiometric approach such as flux balance an...	Being able to predict the metabolic fluxes and growth rate of a microorganism is an important topic in microbial systems biology . One approach , constraint-based modeling , uses a reconstructed metabolic network and optimization techniques to make such predictions . Although widely used , the success of this approach ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "microbiology/microbial", "physiology", "and", "metabolism", "biotechnology/applied", "microbiology", "microbiology/microbial", "evolution", "and", "genomics", "computational", "biology/metabolic", "networks", "...	2009	Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation
RNase E , which is the central component of the multienzyme RNA degradosome , serves as a scaffold for interaction with other enzymes involved in mRNA degradation including the DEAD-box RNA helicase RhlB . Epifluorescence microscopy under live cell conditions shows that RNase E and RhlB are membrane associated , but ne...	Recent discoveries that two ribonucleases with major roles in mRNA degradation , RNase E of Escherichia coli and RNase Y of Bacillus subtilis , are localized to the inner cytoplasmic membrane suggest that spatial separation of transcription and mRNA degradation are general features of the bacterial cell . Here we show ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Membrane Recognition and Dynamics of the RNA Degradosome
The FrzCD chemoreceptor from the gliding bacterium Myxococcus xanthus forms cytoplasmic clusters that occupy a large central region of the cell body also occupied by the nucleoid . In this work , we show that FrzCD directly binds to the nucleoid with its N-terminal positively charged tail and recruits active signaling ...	In this work , we show that the cytoplasmic chemoreceptor of the Frz chemosensory system , FrzCD , does not bind the cytoplasmic membrane like most MCPs but bind the bacterial nucleoid directly , thus forming distributed protein clusters also containing the FrzE kinase . In vitro and in vivo experiments show that DNA-b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "chemical", "characterization", "nuclear", "staining", "electrophoretic", "mobility", "shift", "assay", "cell", "polarity", "membrane", "receptor", "signaling", "molecular", "biology", "techniques", "gel", "electrophoresis", "research", "and", "analy...	2017	The nucleoid as a scaffold for the assembly of bacterial signaling complexes
The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers . Some studies suggest that linker DNA lengths preferentially occur at certain quantized values , differing one from another by integral multiples of the DNA helical repeat ...	Eukaryotic genomic DNA exists as chromatin , with the DNA wrapped locally into a repeating array of protein–DNA complexes ( “nucleosomes” ) separated by short stretches of unwrapped “linker” DNA . Nucleosome arrays further compact into ∼30-nm-wide higher-order chromatin structures . Despite decades of work , there rema...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics/statistics", "computational", "biology" ]	2008	Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae
Tomato yellow leaf curl virus ( TYLCV ) and its related begomoviruses cause fast-spreading diseases in tomato worldwide . How this virus induces diseases remains largely unclear . Here we report a noncoding RNA-mediated model to elucidate the molecular mechanisms of TYLCV-tomato interaction and disease development . Th...	Tomato yellow leaf curl virus ( TYLCV ) is an important threat to tomato production worldwide . Six resistance/tolerance genes ( Ty ) have been introgressed from wild tomato species for breeding against the virus and some of them confer tolerance to TYLCV by enhancing gene silencing . Here , we propose a novel model fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "gene", "regulation", "rna", "extraction", "microbiology", "long", "non-coding", "rnas", "virus", "effects", "on", "host", "gene", "expression", "plant", "science", "plants", "flowering", "plants", "extraction", "techniques", "research", "and", "...	2019	Tomato yellow leaf curl virus intergenic siRNAs target a host long noncoding RNA to modulate disease symptoms
There is a body of literature that describes the geometry and the physics of filopodia using either stochastic models or partial differential equations and elasticity and coarse-grained theory . Comparatively , there is a paucity of models focusing on the regulation of the network of proteins that control the formation...	Cells move and interact with the environment by forming migratory structures composed of self organized polymers of actin . These protrusions can be flat and short surfaces , the lamellipodia , or adopt an elongated , finger-like shape called filopodia . In this article , we analyze the ‘computation’ performed by cells...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "molecular", "cell", "biology", "cell", "biology", "regulatory", "networks", "biology", "computational", "biology", "cytoskeleton" ]	2011	The Eps8/IRSp53/VASP Network Differentially Controls Actin Capping and Bundling in Filopodia Formation
Many antimicrobial and anti-tumour drugs elicit hormetic responses characterised by low-dose stimulation and high-dose inhibition . While this can have profound consequences for human health , with low drug concentrations actually stimulating pathogen or tumour growth , the mechanistic understanding behind such respons...	Hormesis is a highly controversial and poorly understood phenomenon . It describes the idea that an inhibitor molecule , like an anti-cancer or anti-microbial drug , can inadvertently stimulate cell growth instead of suppressing it . This can have a profound effect on human health leading to failures in clinical treatm...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "dose", "prediction", "methods", "enzymology", "mathematical", "models", "pharmaceutics", "pharmacology", "enzyme", "inhibitors", "mapk", "signaling", "cascades", "adjustment", "of", "dosage", "at", "steady", "...	2016	Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle
Two genes linked to early onset Parkinson's disease , PINK1 and Parkin , encode a protein kinase and a ubiquitin-ligase , respectively . Both enzymes have been suggested to support mitochondrial quality control . We have reported that Parkin is phosphorylated at Ser65 within the ubiquitin-like domain by PINK1 in mammal...	Parkinson's disease is a neurodegenerative disorder caused by degeneration of the midbrain dopaminergic system in addition to other nervous systems . PINK1 and parkin , which encode protein kinase and ubiquitin-ligase , respectively , were identified as the genes responsible for the autosomal recessive form of juvenile...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "neurobiology", "of", "disease", "and", "regeneration", "medicine", "and", "health", "sciences", "neurodegenerative", "diseases", "neuroscience", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "drosophila", "research", ...	2014	PINK1-Mediated Phosphorylation of Parkin Boosts Parkin Activity in Drosophila
Bronchodilators are a standard medicine for treating airway obstructive diseases , and β2 adrenergic receptor agonists have been the most commonly used bronchodilators since their discovery . Strikingly , activation of G-protein-coupled bitter taste receptors ( TAS2Rs ) in airway smooth muscle ( ASM ) causes a stronger...	Bitter taste receptors ( TAS2Rs ) , a G-protein-coupled receptor family long thought to be solely expressed in taste buds on the tongue , have recently been detected in airways . Bitter substances can activate TAS2Rs in airway smooth muscle to cause greater bronchodilation than β2 adrenergic receptor agonists , the mos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology", "veterinary", "science" ]	2013	The Cellular and Molecular Basis of Bitter Tastant-Induced Bronchodilation
The causative agent of Chagas disease , Trypanosoma cruzi , is divided into 6 Discrete Typing Units ( DTU ) : Tc I , IIa , IIb , IIc , IId and IIe . In order to assess the relative pathogenicities of different DTUs , blood samples from three different clinical groups of chronic Chagas disease patients ( indeterminate ,...	Around 30–50% of Trypanosoma cruzi infections in Latin America cause chronic Chagas disease 10–30 years after the primary infection due to lack of effective treatment . The major clinical complications associated with chronic Chagas disease are cardiac myositis ( leading to cardiac failure ) , and autonomous neuroplexu...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "cardiovascular", "disorders/myopathies", "infectious", "diseases/neglected", "tropical", "diseases", "cardiovascular", "disorders/heart", "failure", "immunology/autoimmunity", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	Lineage Analysis of Circulating Trypanosoma cruzi Parasites and Their Association with Clinical Forms of Chagas Disease in Bolivia
Melioidosis is caused by Burkholderia pseudomallei , a Gram-negative bacillus , primarily found in soils in Southeast Asia and northern Australia . A recent case of melioidosis in non-endemic Arizona was determined to be the result of locally acquired infection , as the patient had no travel history to endemic regions ...	Melioidosis is a bacterial disease caused by percutaneous inoculation , aspiration or ingestion of the soil bacteria Burkholderia pseudomallei . Melioidosis is primarily found in Southeast Asia and Northern Australia , and , to a lesser degree , nearby regions . A recent case of melioidosis in Southwestern United State...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "population", "genetics", "microbiology", "sequence", "assembly", "tools", "genome", "sequencing", "mutation", "genome", "analysis", "tools", "bacterial", "pathogens", "applied", "microbiology", "sequence", "analysis", "genetic", "polymorphism", "microbial"...	2011	Molecular Investigations of a Locally Acquired Case of Melioidosis in Southern AZ, USA
The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear . One key component of this machinery are aminoacyl tRNA synthetases ( aaRS ) , which ligate tRNAs to amino acids while consuming ATP . Sequence analyses revealed that these enzymes can be divided into two complementary cla...	Aminoacyl tRNA synthetases ( aaRS ) are primordial enzymes essential for interpretation and transfer of genetic information . Understanding the origin of the peculiarities observed with aaRS can explain what constituted the earliest life forms and how the genetic code was established . The increasing amount of experime...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "bonding", "glycosylamines", "chemical", "compounds", "phosphates", "split-decomposition", "method", "organic", "compounds", "multiple", "alignment", "calculation", "basic", "amino", "acids", "amino", "acids", "sequence", "motif", "analysis", "protein", "struc...	2018	Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases
In harsh conditions , Caenorhabditis elegans arrests development to enter a non-aging , resistant diapause state called the dauer larva . Olfactory sensation modulates the TGF-β and insulin signaling pathways to control this developmental decision . Four mutant alleles of daf-25 ( abnormal DAuer Formation ) were isolat...	C . elegans mutants that either fail to form or arrest development as dauer larvae , a stress-resistant lifestage , usually have defects in genes involved in evolutionarily conserved signaling pathways . In this study , we identified the gene mutated in daf-25 mutant strains , which inappropriately arrest as dauer larv...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "developmental", "biology", "neuroscience/sensory", "systems", "cell", "biology/neuronal", "signaling", "mechanisms", "genetics", "and", "genomics/gene", "function" ]	2010	Localization of a Guanylyl Cyclase to Chemosensory Cilia Requires the Novel Ciliary MYND Domain Protein DAF-25
Recognition of viral RNA by the retinoic acid-inducible gene-I ( RIG-I ) -like receptors ( RLRs ) , including RIG-I and MDA5 , initiates innate antiviral responses . Although regulation of RLR-mediated signal transduction has been extensively investigated , how the recognition of viral RNA by RLRs is regulated remains ...	Infection by virus , such as the RNA virus Sendai virus , induces the host cells to express proteins that mediate antiviral immune responses . Upon infections , the retinoic acid-inducible gene-I ( RIG-I ) -like receptors ( RLRs ) detects the intracellular viral RNA and initiates innate immune responses . Although the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicular", "stomatitis", "virus", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "pathogens", "immunology", "immunoblotting", "microbiology", "dna", "transcription", "viruses", "rna", "viruses",...	2019	The heterogeneous nuclear ribonucleoprotein hnRNPM inhibits RNA virus-triggered innate immunity by antagonizing RNA sensing of RIG-I-like receptors
The ability to assay genome-scale methylation patterns using high-throughput sequencing makes it possible to carry out association studies to determine the relationship between epigenetic variation and phenotype . While bisulfite sequencing can determine a methylome at high resolution , cost inhibits its use in compara...	In the vertebrates , methylation of cytosine residues in DNA regulates gene activity in concert with proteins that associate with DNA . Large-scale genomewide comparative studies that seek to link specific methylation patterns to disease will require hundreds or thousands of samples , and thus economical methods that a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "computer", "science", "computational", "biology/molecular", "genetics", "computational", "biology/genomics", "mathematics/statistics", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/bioinformatics" ]	2010	MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations
Recently , the nuclear protein known as Poly ( ADP-ribose ) Polymerase1 ( PARP1 ) was shown to play a key role in regulating transcription of a number of genes and controlling the nuclear sub-organelle nucleolus . PARP1 enzyme is known to catalyze the transfer of ADP-ribose to a variety of nuclear proteins . At present...	Previous studies revealed vital roles for the Poly ( ADP-ribose ) Polymerase ( PARP ) protein in developmental program regulation , as well as in chromatin loosening and transcriptional activation . The main gap in our understanding of PARP protein roles during development involves integrating the biological activities...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/nuclear", "structure", "and", "function", "cell", "biology/nuclear", "structure", "and", "function" ]	2009	Poly (ADP-Ribose) Polymerase 1 Is Required for Protein Localization to Cajal Body
The processing of a visual stimulus can be subdivided into a number of stages . Upon stimulus presentation there is an early phase of feedforward processing where the visual information is propagated from lower to higher visual areas for the extraction of basic and complex stimulus features . This is followed by a late...	Our experience with the visual world allows us to group image elements that belong to the same perceptual object and to segregate them from other objects and the background . If subjects learn to group contour elements , this experience influences neuronal activity in early visual cortical areas , including the primary...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[]	2015	Reinforcement Learning of Linking and Tracing Contours in Recurrent Neural Networks
Trichomonas vaginalis ( Tv ) is an extracellular protozoan parasite that causes the most common non-viral sexually transmitted infection: trichomoniasis . While acute symptoms in women may include vaginitis , infections are often asymptomatic , but can persist and are associated with medical complications including inc...	The unicellular parasite Trichomonas vaginalis ( Tv ) causes the most common non-viral sexually transmitted infection worldwide , with approximately one quarter of a billion people infected annually . Tv infections are linked to pre-term and low-weight infant birth , increased susceptibility to and transmission of HIV ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "immunology", "developmental", "biology", "signs", "and", "symptoms", "molecu...	2016	Leukocyte Lysis and Cytokine Induction by the Human Sexually Transmitted Parasite Trichomonas vaginalis
Histone acetyltransferase 1 is an evolutionarily conserved type B histone acetyltransferase that is thought to be responsible for the diacetylation of newly synthesized histone H4 on lysines 5 and 12 during chromatin assembly . To understand the function of this enzyme in a complex organism , we have constructed a cond...	The packaging of genomic DNA during replication is a highly orchestrated process . An important aspect of chromatin assembly is the processing of newly synthesized histones prior to their incorporation into chromatin . The transient acetylation of histone H3 and H4 NH2-terminal tails is a hallmark of this processing wi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Histone Acetyl Transferase 1 Is Essential for Mammalian Development, Genome Stability, and the Processing of Newly Synthesized Histones H3 and H4
Treatment of chronic bacterial infections , such as tuberculosis ( TB ) , requires a remarkably long course of therapy , despite the availability of drugs that are rapidly bacteriocidal in vitro . This observation has long been attributed to the presence of bacterial populations in the host that are “drug-tolerant” bec...	Despite the availability of antibiotics that rapidly kill bacteria in vitro , the treatment of chronic bacterial infections , such as tuberculosis , requires long-term drug therapy . The reasons for this are unclear , but many have hypothesized that the slow replication and concomitantly low metabolic rate of bacteria ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "global", "health", "genetics", "biology", "genomics", "microbiology", "genetics", "and", "genomics" ]	2011	Metabolic Regulation of Mycobacterial Growth and Antibiotic Sensitivity
Reversible epithelial-to-mesenchymal transition ( EMT ) is central to tissue development , epithelial stemness , and cancer metastasis . While many regulatory elements have been identified to induce EMT , the complex process underlying such cellular plasticity remains poorly understood . Utilizing a systems biology app...	Cumulative evidence reveals remarkable lineage plasticity of somatic cells . Epithelial-to-mesenchymal transition ( EMT ) represents a prime example of such plasticity where an epithelial cell is converted into a mesenchymal cell . This process is used in normal development to generate crucial cell types , and is hijac...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States
Decision making between several alternatives is thought to involve the gradual accumulation of evidence in favor of each available choice . This process is profoundly variable even for nominally identical stimuli , yet the neuro-cognitive substrates that determine the magnitude of this variability are poorly understood...	Variability is a hallmark of how we make decisions between different alternatives: Even when we are presented with identical repetitions of a stimulus , the timing and accuracy of our associated decisions vary dramatically . Representations of variability or ‘noise’ have necessarily been a prominent feature of how cogn...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cognitive", "neuroscience", "behavioral", "neuroscience", "cognitive", "psychology", "cognition", "decision", "making", "reaction", "time", "psychophysics", "biology", "and", "life", "sciences", "sensory", "perception", "vigilance", "(psychology)", "cognitive", "science", ...	2014	Pupil-Linked Arousal Determines Variability in Perceptual Decision Making
Young children are infected by a diverse variety of enteric pathogens in low-income , high-burden countries . Little is known about which conditions pose the greatest risk for enteric pathogen exposure and infection . Young children frequently play in residential public areas around their household , including areas co...	The enteric infections that cause diarrheal disease remain a leading cause of morbidity and mortality in young children in low-income settings where sanitation infrastructure is limited . The role of different exposure pathways in transmission of enteric pathogens to young children is unknown , but accurate information...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "surface", "water", "pathology", "and", "laboratory", "medicine", "pathogens", "neighborhoods", "microbiology", "social", "sciences", "viruses", "age", "groups", "physiological", "processes", "families", "human", "geo...	2019	The landscape of enteric pathogen exposure of young children in public domains of low-income, urban Kenya: The influence of exposure pathway and spatial range of play on multi-pathogen exposure risks
Transcription of HIV provirus is a key step of the viral cycle , and depends on the recruitment of the cellular positive transcription elongation factor b ( P-TEFb ) to the HIV promoter . The viral transactivator Tat can displace P-TEFb from the 7SK small nuclear ribonucleoprotein , where it is bound and inactivated by...	HIV remains a major health issue , with still no vaccine or cure available , and lifelong antiretroviral treatment required for the always-increasing number of people living with the virus . Combination antiretroviral therapy inhibits HIV replication , but the persistence of latently infected cells remains a challenge ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "hiv", "infections", "medicine", "and", "health", "sciences", "hiv", "prevention", "immune", "cells", "pathology", "and", "laboratory", "medicine", "293t", "cells", "pathogens", "biological", "cultures", "immunology", "microbiology", "retroviruses", ...	2018	HEXIM1-Tat chimera inhibits HIV-1 replication

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