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Gene regulatory networks show robustness to perturbations . Previous works identified robustness as an emergent property of gene network evolution but the underlying molecular mechanisms are poorly understood . We used a multi-tier modeling approach that integrates molecular sequence and structure information with netw...	Development from egg to embryo depends to a large extent on regulatory networks of genes called transcription factors . Previous research has shown these gene regulatory networks to be robust to perturbations at the level of the connections between transcription factors . Here , we investigate the mechanisms underlying...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "theoretical", "biology", "biology", "computational", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2013	The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks
Resistance against all available antimalarial drugs calls for novel compounds that hit unexploited targets in the parasite . Here , we show that the recently discovered Plasmodium falciparum lactate/proton symporter , PfFNT , is a valid druggable target , and describe a new class of fluoroalkyl vinylogous acids that po...	The fight against malaria , i . e . one of the three major infectious diseases and transmitted by mosquitos , is conducted at three levels: i . transmission control ( by attacking the mosquito vector or biological processes of vector infection ) , ii . vaccination ( by stimulating the immune system to produce antibodie...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "chemical", "compounds", "plasmodium", "drugs", "tropical", "diseases", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "antimalarials", "parasitology", "fungi", "apicomplexa", "protozoans", ...	2017	Substrate-analogous inhibitors exert antimalarial action by targeting the Plasmodium lactate transporter PfFNT at nanomolar scale
The hypothesis that developmental estrogenic exposure induces a constellation of male reproductive tract abnormalities is supported by experimental and human evidence . Experimental data also suggest that some induced effects persist in descendants of exposed males . These multi- and transgenerational effects are assum...	Developmental exposure to manmade chemicals that interfere with endogenous hormones ( endocrine disrupting chemicals ) has been reported to adversely affect male reproductive health , increasing the incidence of reproductive tract abnormalities and reducing sperm production . Experimental evidence suggests that some ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "spermatocytes", "hormones", "germ", "cells", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "dna", "epigenetics", "estrogens", "estradiol", "sperm", "homologous", "reco...	2017	Germline and reproductive tract effects intensify in male mice with successive generations of estrogenic exposure
Autophagy is the mechanism by which cytoplasmic components and organelles are degraded by the lysosomal machinery in response to diverse stimuli including nutrient deprivation , intracellular pathogens , and multiple forms of cellular stress . Here , we show that the membrane-associated E3 ligase RNF5 regulates basal l...	Autophagy is an intracellular catabolic process by which a cell's own components are degraded through the lysosomal machinery . Autophagy is implicated in various cellular processes such as growth and development , cancer , and inflammation . Using biochemistry , cell biology , and genetic models , we identify a ubiqui...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "subcellular", "organelles", "cellular", "stress", "responses", "streptococci", "enzymes", "regulatory", "proteins", "microbiology", "host-pathogen", "interaction", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "ligases", "...	2012	Regulation of ATG4B Stability by RNF5 Limits Basal Levels of Autophagy and Influences Susceptibility to Bacterial Infection
Although the central coast of the Ecuador is considered endemic for Chagas disease , few studies have focused on determining the risk of transmission in this region . In this study we describe the triatomine household infestation in Manabí province ( Central Coast region ) , determine the rate of Trypanosoma cruzi infe...	Chagas disease is an important public health problem in most of Latin America , including Ecuador . It is caused by the parasite Trypanosoma cruzi , which in endemic areas is transmitted mainly by the feces of insects called triatomines . Control efforts in the region have reduced the number of new cases of Chagas dise...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "ecuador", "forest", "ecology", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "protozoans", "neglected", "tropical", "disease...	2017	Distribution of triatomine species in domestic and peridomestic environments in central coastal Ecuador
Biochemical pathways are often genetically encoded as simple transcription regulation networks , where one transcription factor regulates the expression of multiple genes in a pathway . The relative timing of each promoter’s activation and shut-off within the network can impact physiology . In the DNA damage repair pat...	As the precise timing of gene expression is critical for cells to respond and adapt to new environments , it is important to understand the underlying mechanisms which control this timing . In this report , we studied the timing of transcription for genes in the bacterial DNA damage repair pathway ( known as the SOS re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "gene", "regulation", "regulatory", "proteins", "condensed", "matter", "physics", "dna-binding", "proteins", "anisotropy", "dna", "transcription", "dna", "damage", "chemical", "equilibrium", "materials", "science", "transcription", "factors", "dna", "chemical", "dissociat...	2018	Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network
Dengue virus , a mosquito-borne flavivirus , is a causative agent for dengue infection , which manifests with symptoms ranging from mild fever to fatal dengue shock syndrome . The presence of four serotypes , against which immune cross-protection is short-lived and serotype cross-reactive antibodies that might enhance ...	Dengue virus is a human pathogen that causes dengue fever , which can either resolve after mild fever or lead to severe dengue hemorrhagic fever/dengue shock syndrome . The role of dengue virus levels in the blood and the kinetics of infection and immune response that results in severe dengue disease in humans is not w...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "dengue", "virus", "innate", "immune", "system", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology...	2016	Immune Response to Dengue Virus Infection in Pediatric Patients in New Delhi, India—Association of Viremia, Inflammatory Mediators and Monocytes with Disease Severity
Allosteric regulation involves conformational transitions or fluctuations between a few closely related states , caused by the binding of effector molecules . We introduce a quantity called binding leverage that measures the ability of a binding site to couple to the intrinsic motions of a protein . We use Monte Carlo ...	Allosteric protein regulation is the mechanism by which binding of a molecule to one site in a protein affects the activity at another site . Although the two classical phenomenological models , Monod-Wyman-Changeux ( MWC ) and Koshland-Némethy-Filmer ( KNF ) , span from the case of hemoglobin to membrane receptors , t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "theoretical", "biology", "biology", "computational", "biology", "biophysics" ]	2011	Binding Leverage as a Molecular Basis for Allosteric Regulation
DNA methylation is an important epigenetic mechanism for phenotypic diversification in all forms of life . We previously described remarkable cell-to-cell heterogeneity in epigenetic pattern within a clonal population of Streptococcus pneumoniae , a leading human pathogen . We here report that the epigenetic diversity ...	DNA methylation is a well-known epigenetic mechanism for phenotypic diversification in all forms of life . This study reports our discovery that the Spn556II type-I RM locus in human pathogen Streptococcus pneumoniae undergoes extensive DNA inversions among three homologous DNA methyltransferase genes . These site-spec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "enzymes", "enzymology", "alleles", "sequence", "motif", "analysis", "epigenetics", "dna", "molecular", "biology", "techniques", "dna", "methylation", "chromatin", "research", "and", "analysis", "methods", "sequence", "analysis", "artificial", ...	2016	Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae
Carbonic anhydrase-8 ( CA8 ) is an intracellular protein that functions as an allosteric inhibitor of inositol trisphosphate receptor-1 ( ITPR1 ) critical to intracellular Ca++ release , synaptic functions and neuronal excitability . We showed previously that murine nociception and analgesic responses are regulated by ...	Carbonic anhydrase-8 ( CA8 ) inhibits IP3 binding to the inositol trisphosphate receptor-1 ( ITPR1 ) , which regulates intracellular calcium signaling critical to neuronal functions . Recessive CA8-null mutants are associated with spinocerebellar ataxia and neurodegenerative disorders . We have previously demonstrated ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "drugs", "immunology", "alternative", "splicing", "signs", "and", "symptoms", "analgesics", "molecular", "biology", "techniques", "pharmacology", "calcium", "signaling",...	2019	Profound analgesia is associated with a truncated peptide resulting from tissue specific alternative splicing of DRG CA8-204 regulated by an exon-level cis-eQTL
Chemical genomic screens have recently emerged as a systematic approach to drug discovery on a genome-wide scale . Drug target identification and elucidation of the mechanism of action ( MoA ) of hits from these noisy high-throughput screens remain difficult . Here , we present GIT ( Genetic Interaction Network-Assiste...	Chemical genomic screens have been developed to systematically explore compound-gene interactions with the goal of identifying new drugs and drug targets . Haploinsufficiency profiling and homozygous profiling screens measure the drug-induced growth sensitivities of deletion strains that are grown in the presence of a ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "caffeine", "medicine", "and", "health", "sciences", "genetic", "networks", "alkaloids", "chemical", "compounds", "protein", "interaction", "networks", "network", "analysis", "genome", "analysis", "pharmacology", "genetic", "interactions", "research", "and", "analysis", ...	2017	Network-assisted target identification for haploinsufficiency and homozygous profiling screens
Paracoccidioidomycosis , a primary fungal infection restricted to Latin America , is acquired by inhalation of fungal particles . The immunoregulatory mechanisms that control the severe and mild forms of paracoccidioidomycosis are still unclear . Indoleamine 2 , 3-dioxygenase ( IDO ) , an IFN-γ induced enzyme that cata...	Immunoprotection to paracoccidiodomycosis , a systemic mycosis endemic in Latin America , is mediated by T cell immunity whereas immunosuppression characterizes the severe forms of the disease . Indoleamine 2 , 3-dioxygenase ( IDO ) , an enzyme mainly induced by IFN-γ , catabolizes tryptophan along the kynurenines path...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunopathology", "animal", "models", "of", "infection", "infectious", "disease", "immunology", "mycology", "clinical", "immunology", "medical", "microbiology", "microbial", "pathogens", "paracoccidioides", "brasiliensis", "biology", "and", "life", "sciences", "immunology"...	2014	Indoleamine 2,3-Dioxygenase Controls Fungal Loads and Immunity in Paracoccidioidomicosis but is More Important to Susceptible than Resistant Hosts
Rasa3 is a GTPase activating protein of the GAP1 family which targets R-Ras and Rap1 . Although catalytic inactivation or deletion of Rasa3 in mice leads to severe hemorrhages and embryonic lethality , the biological function and cellular location of Rasa3 underlying these defects remains unknown . Here , using a combi...	Because it delivers oxygen and nutriments to every tissue in the body , the vascular system is essential to vertebrate life . Blood vessels consist of a layer of interconnected endothelial cells delineating a luminal space through which blood flows . Formation of vascular lumens is a critical step in vascular developme...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "endothelial", "cells", "enzymes", "ocular", "anatomy", "enzymology", "epithelial", "cells", "bone", "marrow", "cells", "developmental", "biology", "integrins", ...	2018	Rasa3 controls turnover of endothelial cell adhesion and vascular lumen integrity by a Rap1-dependent mechanism
The control of mosquito populations with insecticide treated bed nets and indoor residual sprays remains the cornerstone of malaria reduction and elimination programs . In light of widespread insecticide resistance in mosquitoes , however , alternative strategies for reducing transmission by the mosquito vector are urg...	Mosquito control is the only intervention that can reduce malaria transmission from very high levels to close to zero . However , current mosquito control methods are severely threatened by the rapid spread of insecticide resistance in anopheline mosquito populations that transmit the malaria-causing Plasmodium parasit...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "plasmodium", "demography", "tropical", "diseases", "parasitic", "diseases", "animals", "parasitic", "protozoans", "parasitology", "hormones", "apicomplexa"...	2016	Disrupting Mosquito Reproduction and Parasite Development for Malaria Control
Extrachromosomal hereditary elements such as organelles , viruses , and plasmids are important for the cell fitness and survival . Their transcription is dependent on host cellular RNA polymerase ( RNAP ) or intrinsic RNAP encoded by these elements . The yeast Kluyveromyces lactis contains linear cytoplasmic DNA virus-...	Yeast cytoplasmic double-stranded DNA virus-like elements ( VLEs , also known as linear plasmids ) were widely investigated in the past but the topic was almost entirely abandoned , partly due to an inability to express VLE-encoded proteins using conventional expression systems . In this study , we re-opened investigat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "messenger", "rna", "dna", "transcription", "phylogenetics", "data", "management", "model", "organisms", "fungi", "phylogenetic", "analysis", "experimental", "organism", "systems", "sequence", "motif", "analysis", "research", "and", "analysis", "methods", "s...	2018	Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin
Microhomology ( MH ) flanking a DNA double-strand break ( DSB ) drives chromosomal rearrangements but its role in mutagenesis has not yet been analyzed . Here we determined the mutation frequency of a URA3 reporter gene placed at multiple locations distal to a DSB , which is flanked by different sizes ( 15- , 18- , or ...	Recurrent chromosome translocations juxtapose chromosomal fragments and alter expression of tumor suppressors or oncogenes at or near breakpoint junctions to develop distinct types of leukemias and childhood sarcomas . The prevalence of 2–20 bp of imperfect overlapping sequences ( a . k . a . microhomology [MH] ) at th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "insertion", "mutation", "carbohydrates", "galactose", "organic", "compounds", "microhomology-mediated", "end", "joining", "surgical", "and", "invasive", "medical", "procedures", "mutation", "dna", "translo...	2017	Microhomology-mediated end joining induces hypermutagenesis at breakpoint junctions
Mutations are a major driving force of evolution and genetic disease . In eukaryotes , mutations are produced in the chromatin environment , but the impact of chromatin on mutagenesis is poorly understood . Previous studies have determined that in yeast Saccharomyces cerevisiae , Rtt109-dependent acetylation of histone...	Mutations strongly predispose humans to cancer and many other diseases . Despite significant progress , we still do not fully understand the molecular mechanisms that protect us from mutations . Human DNA is part of a highly organized complex called chromatin . Chromatin regulates our development , metabolism , and beh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Reversible Histone H3 Acetylation Cooperates with Mismatch Repair and Replicative Polymerases in Maintaining Genome Stability
Sexual reproduction in fungi is governed by a specialized genomic region called the mating-type locus ( MAT ) . The human fungal pathogenic and basidiomycetous yeast Cryptococcus neoformans has evolved a bipolar mating system ( a , α ) in which the MAT locus is unusually large ( >100 kb ) and encodes >20 genes includin...	Fungal gene clusters mediate sex determination , natural product synthesis , and metabolic functions . Eukaryotic organisms share features of gene cluster formation including translocations , inversions , gene conversion , and suppressed recombination . The C . neoformans/C . gattii mating-type ( MAT ) locus spans a si...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "biology", "microbiology", "evolutionary", "biology" ]	2012	Discovery of a Modified Tetrapolar Sexual Cycle in Cryptococcus amylolentus and the Evolution of MAT in the Cryptococcus Species Complex
The Polo-Like Kinase 1 ( PLK1 ) acts as a central regulator of mitosis and is over-expressed in a wide range of human tumours where high levels of expression correlate with a poor prognosis . PLK1 comprises two structural elements , a kinase domain and a polo-box domain ( PBD ) . The PBD binds phosphorylated substrates...	Cell division is a key biological process and imperfections in the process can lead to diseases like cancer . Polo-Like Kinase 1 ( PLK1 ) is a protein kinase enzyme that controls cell division by interacting with many other proteins . Malfunction of PLK1 has been implicated in cancer . To understand how PLK1 interacts ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "oncology", "biochemistry/experimental", "biophysical", "methods", "biochemistry/biomacromolecule-ligand", "interactions", "biochemistry/macromolecular", "assemblies", "and", "machines", "biochemistry/theory", "and", "simulation", "computational", "biology/molecular", "dynamics", "bi...	2010	Computational Analysis of Phosphopeptide Binding to the Polo-Box Domain of the Mitotic Kinase PLK1 Using Molecular Dynamics Simulation
Many aspects of human motor behavior can be understood using optimality principles such as optimal feedback control . However , these proposed optimal control models are risk-neutral; that is , they are indifferent to the variability of the movement cost . Here , we propose the use of a risk-sensitive optimal controlle...	In economic decision-making it is well-known that when decision-makers have several options , each associated with uncertain outcomes , their decision is not purely determined by the average payoff , but also takes into account the risk ( that is , variability of the payoff ) associated with each option . Some actions ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/motor", "systems", "neuroscience/psychology", "computer", "science/systems", "and", "control", "theory", "neuroscience/theoretical", "neuroscience" ]	2010	Risk-Sensitive Optimal Feedback Control Accounts for Sensorimotor Behavior under Uncertainty
Mutational correlation patterns found in population-level sequence data for the Human Immunodeficiency Virus ( HIV ) and the Hepatitis C Virus ( HCV ) have been demonstrated to be informative of viral fitness . Such patterns can be seen as footprints of the intrinsic functional constraints placed on viral evolution und...	HIV and HCV cause devastating infectious diseases for which no functional vaccine exists . A key problem is that while individual mutations in viral epitopes under immune pressure may substantially compromise viral fitness , immune escape is typically facilitated by other “compensatory” mutations that restore fitness ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "statistical", "noise", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "protein", "interaction", "networks", "split-decomposition", "method", "condensed", "matter", "physics", "microbiology", "vi...	2018	Co-evolution networks of HIV/HCV are modular with direct association to structure and function
ClinicalTrials . gov ( NCT01261130 for the Brazil trial and NCT01385189 for the US trial ) Over 400 million people are infected with hookworm , predominantly in resource-limited tropical regions of the world [1] . Hookworm is a soil-transmitted nematode helminth that is primarily acquired after skin contact with infect...	Hookworm infection caused by Necator americanus is a major neglected tropical disease with significant associated morbidity . New tools , such as vaccines , are needed due to the inadequacy of current control strategies . Glutathione-S-Transferase-1 of N . americanus ( Na-GST-1 ) is one of the lead hookworm vaccine can...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "helminths", "immunology", "geographical", "locations", "hookworms", "animals", "liver", "diseases", "vaccines", "preventive", "medicine", "infectious", "hepat...	2017	Safety and immunogenicity of the Na-GST-1 hookworm vaccine in Brazilian and American adults
The Lyme disease spirochete Borrelia burgdorferi must differentially express genes and proteins in order to survive in and transit between its tick vector and vertebrate reservoir . The putative DEAH-box RNA helicase , HrpA , has been recently identified as an addition to the spirochete's global regulatory machinery; u...	The bacterium causing Lyme disease , Borrelia burgdorferi , must differentially express genes and proteins in order to survive in and transit between its tick vector and animals that it infects . RNA helicases , enzymes that unwind double-stranded RNA , have recently emerged as major players in all types of processes i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	HrpA, an RNA Helicase Involved in RNA Processing, Is Required for Mouse Infectivity and Tick Transmission of the Lyme Disease Spirochete
Leprosy is the most frequent treatable neuromuscular disease . Yet , every year , thousands of patients develop permanent peripheral nerve damage as a result of leprosy . Since early detection and treatment of neuropathy in leprosy has strong preventive potential , we conducted a cohort study to determine which test de...	Leprosy is the most frequent treatable disease of the peripheral nerves . Yet , every year , thousands of patients develop nerve damage as a result of leprosy . If this is detected and treated early , the prognosis is good . We conducted the largest prospective study on this topic to date to determine which test would ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neurological", "disorders/neuromuscular", "diseases", "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "infectious", "diseases/neglected", "tropical", "diseases", "neurological", "disorders/peripheral", "neuropathies", "public", "health", "and...	2008	Early Diagnosis of Neuropathy in Leprosy—Comparing Diagnostic Tests in a Large Prospective Study (the INFIR Cohort Study)
HLA class I polymorphism has a major influence on adult HIV disease progression . An important mechanism mediating this effect is the impact on viral replicative capacity ( VRC ) of the escape mutations selected in response to HLA-restricted CD8+ T-cell responses . Factors that contribute to slow progression in pediatr...	HLA plays a central role in determining disease outcome in adult HIV infection . A principal mechanism by which this HLA effect is mediated is via viral replicative capacity ( VRC ) , protective HLA alleles such as HLA-B*57 driving the selection of viral escape mutants that reduce VRC . The factors contributing to the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Discordant Impact of HLA on Viral Replicative Capacity and Disease Progression in Pediatric and Adult HIV Infection
Most plant and animal microRNAs ( miRNAs ) are transcribed by RNA polymerase II . We previously discovered miRNA–like small RNAs ( milRNAs ) in the filamentous fungus Neurospora crassa and uncovered at least four different pathways for milRNA production . To understand the evolutionary origin of milRNAs , we determined...	microRNAs ( miRNAs ) are small RNAs that are used by many organisms to regulate a wide variety of molecular , developmental , and physiological activities . In higher eukaryotes , such as animals and plants , the majority of the independent transcribed miRNAs are produced by RNA polymerase II ( Pol II ) , an enzyme tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Transcription of the Major Neurospora crassa microRNA–Like Small RNAs Relies on RNA Polymerase III
Gene expression in eukaryotes is controlled by DNA sequences at promoter and enhancer regions , whose accessibility for binding by regulatory proteins dictates their specific patterns of activity . Here , we identify the protein Zbtb7a as a factor required for inducible changes in accessibility driven by transcription ...	Gene activation is driven by the binding of regulatory proteins to the specific DNA sequences that control each gene . However , these sequences are not always accessible for binding in every type of cell , and so differences in their accessibility can underlie the range of cell types in which particular genes can be a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "gene", "regulation", "immunology", "fibroblasts", "dna", "transcription", "developmental", "biology", "clinical", "medicine", "connective", "tissue", "cells", "m...	2018	Zbtb7a is a transducer for the control of promoter accessibility by NF-kappa B and multiple other transcription factors
The t-haplotype , a variant form of the t-complex region on mouse chromosome 17 , acts as selfish genetic element and is transmitted at high frequencies ( >95% ) from heterozygous ( t/+ ) males to their offspring . This phenotype is termed transmission ratio distortion ( TRD ) and is caused by the interaction of the t-...	Selfish genetic elements , which promote their own propagation and thereby violate Mendel's laws , have attracted much attention within the scientific community and by the public . The molecular principles underlying their exceptional behaviour are , in general , not well understood . A notable exception is the t-haplo...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "signal", "transduction", "signaling", "in", "cellular", "processes", "molecular", "cell", "biology", "heredity", "genetics", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2012	The Nucleoside Diphosphate Kinase Gene Nme3 Acts as Quantitative Trait Locus Promoting Non-Mendelian Inheritance
Nucleic acid sensor elements are proving increasingly useful in biotechnology and biomedical applications . A number of ligand-sensing , conformational-switching ribozymes ( also known as allosteric ribozymes or aptazymes ) have been generated by some combination of directed evolution or rational design . Such sensor e...	Aptamers are nucleic acids that bind their cognate ligands ( ranging from metal ions to small molecules to proteins ) specifically and tightly . Through rational design and/or directed evolution , aptamers can be engineered into allosteric nucleic acids whose conformations can be regulated by their ligands . Aptamer be...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/synthetic", "biology", "biotechnology/bioengineering", "biochemistry/theory", "and", "simulation", "biochemistry/transcription", "and", "translation", "chemical", "biology/directed", "molecular", "evolution" ]	2009	Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes
Metformin is a biguanide widely prescribed to treat Type II diabetes that has gained interest as an antineoplastic agent . Recent work suggests that metformin directly antagonizes cancer cell growth through its actions on complex I of the mitochondrial electron transport chain ( ETC ) . However , the mechanisms by whic...	Cancer is a disease characterized by unregulated proliferation of transformed cells . To meet the increased biosynthetic demands of proliferation , biosynthetic building blocks required for cellular growth must be generated in large quantities . As cancer cells increase their anabolic metabolism to promote cell growth ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Metformin Antagonizes Cancer Cell Proliferation by Suppressing Mitochondrial-Dependent Biosynthesis
The biosynthesis of membrane lipids is an essential pathway for virtually all bacteria . Despite its potential importance for the development of novel antibiotics , little is known about the underlying signaling mechanisms that allow bacteria to control their membrane lipid composition within narrow limits . Recent stu...	An opportunistic Gram-positive pathogen , Staphylococcus aureus is a major threat to humans and animals , being responsible for a variety of infections ranging from mild superficial to severe infections such as infective endocarditis , septic arthritis , osteomyelitis and sepsis . The increasing resistance of S . aureu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Structural Basis for Feed-Forward Transcriptional Regulation of Membrane Lipid Homeostasis in Staphylococcus aureus
Bardet-Biedl syndrome ( BBS ) is a well-known ciliopathy with mutations reported in 18 different genes . Most of the protein products of the BBS genes localize at or near the primary cilium and the centrosome . Near the centrosome , BBS proteins interact with centriolar satellite proteins , and the BBSome ( a complex o...	Bardet-Biedl syndrome ( BBS ) is a genetically heterogeneous autosomal recessive ciliopathy with 18 causative genes reported to date . The syndrome is characterized by obesity , polydactyly , renal defects , hypogenitalism and retinal degeneration . Previous work has illustrated a role for BBS proteins in the trafficki...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cellular", "structures", "subcellular", "organelles", "protein", "interactions", "genetics", "molecular", "genetics", "biology", "proteomics", "molecular", "cell", "biology", "genetics", "of", "disease", "gene", "function" ]	2014	The Centriolar Satellite Protein AZI1 Interacts with BBS4 and Regulates Ciliary Trafficking of the BBSome
In China alone , an estimated 30 million people are at risk of schistosomiasis , caused by the Schistosoma japonicum parasite . Disease has re-emerged in several regions that had previously attained transmission control , reinforcing the need for active surveillance . The environmental stage of the parasite is known to...	Schistosomiasis ranks second only to malaria among parasitic diseases with regard to the number of people infected and those at risk . Schistosoma japonicum is the species that causes human and animal disease in China , the Philippines , and to a lesser extent , Indonesia . Recent evidence of schistosomiasis re-emergen...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/infectious", "diseases", "public", "health", "and", "epidemiology/environmental", "health" ]	2008	Quantitative Detection of Schistosoma japonicum Cercariae in Water by Real-Time PCR
Saccharomyces cerevisiae is one of the best-studied model organisms , yet the three-dimensional structure and molecular function of many yeast proteins remain unknown . Yeast proteins were parsed into 14 , 934 domains , and those lacking sequence similarity to proteins of known structure were folded using the Rosetta d...	The three-dimensional structure of a protein can reveal much about that protein's evolutionary relationships and functions . Such information about all the proteins in an organism—the proteome—would offer a more global view of these relationships , but solving each structure individually would be a formidable task . In...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "yeast", "and", "fungi", "computational", "biology", "genetics", "and", "genomics", "saccharomyces" ]	2007	Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology
The Sterol Regulatory Element Binding Proteins ( SREBPs ) are basic-helix-loop-helix transcription regulators that control the expression of sterol biosynthesis genes in higher eukaryotes and some fungi . Surprisingly , SREBPs do not regulate sterol biosynthesis in the ascomycete yeasts ( Saccharomycotina ) as this rol...	Transcription regulation is the primary step by which most cells control the expression of their genes . At its core , this process is mediated by proteins ( transcription regulators ) that bind to short DNA regulatory elements in a sequence-specific manner . Recent research in multiple model organisms ranging from ver...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "dna-binding", "proteins", "microbiology", "fungi", "regulator", "genes", "experimental", "organism", "systems", "gene...	2018	Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi
The recent 2009 pandemic H1N1 virus infection in humans has resulted in nearly 5 , 000 deaths worldwide . Early epidemiological findings indicated a low level of infection in the older population ( >65 years ) with the pandemic virus , and a greater susceptibility in people younger than 35 years of age , a phenomenon c...	Influenza A viruses generally infect individuals of all ages and cause severe respiratory disease in very young children and elderly people ( >65 years ) . However , the 2009 pandemic H1N1 virus infection is predominantly seen in children and adults ( <35 years of age ) , but rarely in people older than 65 years of age...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/vaccines", "virology/animal", "models", "of", "infection", "virology" ]	2010	Protection of Mice against Lethal Challenge with 2009 H1N1 Influenza A Virus by 1918-Like and Classical Swine H1N1 Based Vaccines
Calpains constitute a superfamily of Ca2+-dependent cysteine proteases , indispensable for various cellular processes . Among the 15 mammalian calpains , calpain 8/nCL-2 and calpain 9/nCL-4 are predominantly expressed in the gastrointestinal tract and are restricted to the gastric surface mucus ( pit ) cells in the sto...	The continuous or improper ingestion of irritants , including alcohol , nonsteroidal anti-inflammatory drugs ( NSAIDs ) , and Helicobacter pylori , often leads to serious gastropathies , affecting a wide range of people . A complex gastric defense system helps protect against these threats , for example by secreting mu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/protein", "chemistry", "genetics", "and", "genomics/genetics", "of", "disease", "gastroenterology", "and", "hepatology/stomach", "and", "duodenum" ]	2010	Calpain 8/nCL-2 and Calpain 9/nCL-4 Constitute an Active Protease Complex, G-Calpain, Involved in Gastric Mucosal Defense
Magnesium , potassium , and sodium , cations commonly measured in serum , are involved in many physiological processes including energy metabolism , nerve and muscle function , signal transduction , and fluid and blood pressure regulation . To evaluate the contribution of common genetic variation to normal physiologic ...	Magnesium , potassium , and sodium are involved in important physiological processes . To better understand how common genetic variation may contribute to inter-individual differences in serum concentrations of these electrolytes , we evaluated single nucleotide polymorphisms ( SNPs ) across the genome in association w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "public", "health", "and", "epidemiology", "physiology/genomics", "physiology/renal,", "fluid,", "and", "electrolyte", "physiology", "cardiovascular", "disorders" ]	2010	Genome-Wide Association Studies of Serum Magnesium, Potassium, and Sodium Concentrations Identify Six Loci Influencing Serum Magnesium Levels
Cells respond to defects in mitochondrial function by activating signaling pathways that restore homeostasis . The mitochondrial peptide exporter HAF-1 and the bZip transcription factor ATFS-1 represent one stress response pathway that regulates the transcription of mitochondrial chaperone genes during mitochondrial dy...	Defects in mitochondrial function are associated with numerous age-related diseases including cancer and Parkinson's . Mitochondrial function relies upon maintenance of the mitochondrial proteome , which is comprised of nuclear and mitochondrial-encoded proteins . Nuclear-encoded polypeptides are translated in the cyto...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Protective Coupling of Mitochondrial Function and Protein Synthesis via the eIF2α Kinase GCN-2
Dengue viruses ( DENVs ) are emerging , mosquito-borne flaviviruses which cause dengue fever and dengue hemorrhagic fever . The DENV complex consists of 4 serotypes designated DENV1-DENV4 . Following natural infection with DENV , individuals develop serotype specific , neutralizing antibody responses . Monoclonal antib...	Dengue viruses are mosquito-borne flaviviruses and the agents of dengue fever and dengue hemorrhagic fever . It has been widely assumed that antibodies that neutralize dengue bind to regions on the viral envelope ( E ) protein that are conserved within each serotype . However , few studies have explored how natural var...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/vaccines", "virology/virion", "structure,", "assembly,", "and", "egress", "virology/emerging", "viral", "diseases", "virology", "virology/immune", "evasion", "virology/host", "antiviral", "responses" ]	2010	Natural Strain Variation and Antibody Neutralization of Dengue Serotype 3 Viruses
Viral fusogenic envelope proteins are important targets for the development of inhibitors of viral entry . We report an approach for the computational design of peptide inhibitors of the dengue 2 virus ( DENV-2 ) envelope ( E ) protein using high-resolution structural data from a pre-entry dimeric form of the protein ....	Virus surface proteins mediate interactions with target cells during the initial events in the process of infection . Inhibiting these proteins is therefore a major target for the development of antiviral drugs . However , there are a very large number of different viruses , each with their own distinct surface protein...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "computational", "biology/protein", "structure", "prediction", "computational", "biology/macromolecular", "structure", "analysis" ]	2010	Structural Optimization and De Novo Design of Dengue Virus Entry Inhibitory Peptides
Over evolutionary time , members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches . At the sequence level , such divergence appears as correlations that arise from residue patterns distinct to each subgroup . Such a superfamily may be view...	Protein sequence data , when gathered in great quantity , contain important but implicit biological information manifest as statistical correlations . Here we describe an approach to access this information by comprehensively modeling and characterizing the distribution of sequences belonging to a major protein superfa...	[ "Abstract", "Introduction", "Results", "Application", "Discussion", "Methods" ]	[ "chemical", "compounds", "markov", "models", "split-decomposition", "method", "organic", "compounds", "multiple", "alignment", "calculation", "mathematics", "basic", "amino", "acids", "protein", "structure", "amino", "acids", "research", "and", "analysis", "methods", "s...	2016	Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
In a sample of 3 , 187 twins and 3 , 294 of their parents , we sought to investigate association of both individual variants and a genotype-based height score involving 176 of the 180 common genetic variants with adult height identified recently by the GIANT consortium . First , longitudinal observations on height span...	We evaluated the developmental specificity of 176 SNPs known to affect adult height based on meta-analysis from the GIANT consortium . First , longitudinal observations on height spanning pre-adolescence through adulthood in a twin sample allowed us to investigate the individual effects of the previously identified SNP...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "aging", "genome-wide", "association", "studies", "developmental", "biology", "organism", "development", "heredity", "genetic", "association", "studies", "genetics", "biology", "quantitative", "traits", "genetics", "and", "genomics", "complex", "traits", "human", "genetic...	2011	An Assessment of the Individual and Collective Effects of Variants on Height Using Twins and a Developmentally Informative Study Design
Parvoviruses halt cell cycle progression following initiation of their replication during S-phase and continue to replicate their genomes for extended periods of time in arrested cells . The parvovirus minute virus of mice ( MVM ) induces a DNA damage response that is required for viral replication and induction of the...	DNA viruses induce cellular DNA damage responses that can present a block to infection that must be overcome , or alternatively , can be utilized to viral advantage . Parvoviruses , the only known viruses of vertebrates that contain single-stranded linear DNA genomes , induce a robust DNA damage response ( DDR ) that f...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "Methods" ]	[ "host", "cells", "viral", "transmission", "and", "infection", "virology", "biology", "microbiology", "molecular", "cell", "biology", "viral", "replication" ]	2014	Parvovirus-Induced Depletion of Cyclin B1 Prevents Mitotic Entry of Infected Cells
The incidence of dengue has grown dramatically in recent decades worldwide , especially in Southeast Asia and the Americas with substantial transmission in 2014–2015 . Yet the mechanisms underlying the spatio-temporal circulation of dengue virus ( DENV ) serotypes at large geographical scales remain elusive . Here we i...	In the past half century the incidence of dengue fever worldwide has increased 30-fold , with an estimated ~390 million infections per year . The years 2014 and 2015 were characterized by large dengue outbreaks worldwide , which are a threat to public health , especially in Asian countries . Here we use a phylogeograph...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biogeography", "dengue", "virus", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "transportation", "china", "pathogens", "population", "genetics", ...	2017	Increasing airline travel may facilitate co-circulation of multiple dengue virus serotypes in Asia
Mycobacterial pathogens are the causative agents of chronic infectious diseases like tuberculosis and leprosy . Autophagy has recently emerged as an innate mechanism for defense against these intracellular pathogens . In vitro studies have shown that mycobacteria escaping from phagosomes into the cytosol are ubiquitina...	Tuberculosis is a serious infectious disease that claims over a million lives annually . Vaccination provides insufficient protection and the causative bacterial pathogen , Mycobacterium tuberculosis , is becoming increasingly resistant to antibiotic therapy . Therefore , there is an urgent need for novel therapeutic s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "autophagic", "cell", "death", "fish", "medicine", "and", "health", "sciences", "cell", "processes", "tropical", "diseases", "vertebrates", "animals", "animal", "models", "osteichthyes", "bacterial", "diseases", "developmental", "biology", "model", "o...	2019	The selective autophagy receptors Optineurin and p62 are both required for zebrafish host resistance to mycobacterial infection
Once the genome sequence of an organism is obtained , attention turns from identifying genes to understanding their function , their organization and control of metabolic pathways and networks that determine its physiology . Recent technical advances in acquiring genome-wide data have led to substantial progress in ide...	Phenotypic description has long been used to discriminate between bacteria and , with the publication of Bergey's Manual of Determinative Bacteriology in 1923 , microbiologists began to systematically describe and define bacterial species based on lists of phenotypes . Because growth phenotypes are directly and indirec...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/comparative", "genomics", "microbiology/medical", "microbiology", "genetics", "and", "genomics/functional", "genomics", "computational", "biology/metabolic", "networks", "computational", "biology/genomics", "inf...	2010	Global Genotype-Phenotype Correlations in Pseudomonas aeruginosa
Chronic Obstructive Pulmonary Disease ( COPD ) is an inflammatory process of the lung inducing persistent airflow limitation . Extensive systemic effects , such as skeletal muscle dysfunction , often characterize these patients and severely limit life expectancy . Despite considerable research efforts , the molecular b...	Chronic Obstructive Pulmonary Disease ( COPD ) is a major life threatening disease of the lungs , characterized by airflow limitation and chronic inflammation . Progressive reduction of the body muscle mass is a condition linked to COPD that significantly decreases quality of life and survival . Physical exercise has b...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "medicine", "chronic", "obstructive", "pulmonary", "diseases", "genetics", "and", "genomics", "biology", "genomics", "respiratory", "medicine", "pulmonology" ]	2011	A Systems Biology Approach Identifies Molecular Networks Defining Skeletal Muscle Abnormalities in Chronic Obstructive Pulmonary Disease
This paper is concerned with the potential multistability of protein concentrations in the cell . That is , situations where one , or a family of , proteins may sit at one of two or more different steady state concentrations in otherwise identical cells , and in spite of them being in the same environment . For models ...	Models of multisite protein phosphorylation have been of great interest to the systems biology community , largely due to their ability to exhibit multistable behaviour . In the presence of excess substrate it has been shown that the number of stable steady states achieved can increase linearly with the number of phosp...	[ "Abstract", "Introduction", "Models", "Results/Discussion" ]	[ "phosphorylation", "enzymes", "applied", "mathematics", "enzymology", "phosphatases", "simulation", "and", "modeling", "algorithms", "probability", "distribution", "mathematics", "systems", "science", "algebra", "polynomials", "research", "and", "analysis", "methods", "comp...	2018	Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains
In nature , microbes often need to "decide" which of several available nutrients to utilize , a choice that depends on a cell’s inherent preference and external nutrient levels . While natural environments can have mixtures of different nutrients , phenotypic variation in microbes’ decisions of which nutrient to utiliz...	In nature , microbes often need to decide which of many potential nutrients to consume . This decision making process is complex , involving both intracellular constraints and the organism’s perception of the environment . To begin to mimic the complexity of natural environments , we grew cells in mixtures of two sugar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "compounds", "population", "genetics", "galactose", "carbohydrates", "organic", "compounds", "glucose", "alleles", "genetic", "mapping", "fungi", "model", "organisms", "experimental", "organism", "systems", "population", "biology", "saccharomyces", "research", ...	2017	Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes
Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator ( CFTR ) gene affect CFTR protein biogenesis or its function as a chloride channel , resulting in dysregulation of epithelial fluid transport in the lung , pancreas and other organs in cystic fibrosis ( CF ) . Development of pharmaceutical strategies ...	Cystic Fibrosis is a severe genetic disorder caused by mutations in the gene coding for CFTR . This defect induces protein misfolding and channel dysfunction , resulting in the disruption of hydration of epithelial surfaces in different organs . Restoring channel activity in the mutant protein requires a greater unders...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "bonding", "ion", "channel", "gating", "medicine", "and", "health", "sciences", "single", "channel", "recording", "molecular", "dynamics", "chemical", "compounds", "computational", "biology", "electrophysiology", "neuroscience", "organic", "compounds", "electr...	2017	Transmembrane helical interactions in the CFTR channel pore
Fat represents a calorically potent food source that yields approximately twice the amount of energy as carbohydrates or proteins per unit of mass . The highly palatable taste of free fatty acids ( FAs ) , one of the building blocks of fat , promotes food consumption , activates reward circuitry , and is thought to con...	Fat represents a calorically potent food source that yields approximately twice the amount of energy as carbohydrates or proteins per unit of mass . Dietary lipids are comprised of both triacylglycerides and FAs , and growing evidence suggests that it is the free FAs that are detected by the gustatory system . The high...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "alkaloids", "medicine", "and", "health", "sciences", "chemical", "compounds", "disaccharides", "gustatory", "system", "oleic", "acid", "social", "sciences", "carbohydrates", "neuroscience", "organic", "compounds", "animals", "animal", "models", "drosophi...	2017	A subset of sweet-sensing neurons identified by IR56d are necessary and sufficient for fatty acid taste
ATP-dependent chromatin remodelers control DNA access for transcription , recombination , and other processes . Acf1 ( also known as BAZ1A in mammals ) is a defining subunit of the conserved ISWI-family chromatin remodelers ACF and CHRAC , first purified over 15 years ago from Drosophila melanogaster embryos . Much is ...	The eukaryotic genome is packaged into a periodic nucleoprotein complex known as chromatin . Wrapping of DNA around nucleosomes , the basic repeat unit of chromatin , enables packing of long stretches of DNA into a compact nucleus but also impedes access by protein factors involved in essential cellular processes such ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Mouse BAZ1A (ACF1) Is Dispensable for Double-Strand Break Repair but Is Essential for Averting Improper Gene Expression during Spermatogenesis
Metalloproteins form a major class of enzymes in the living system that are involved in crucial biological functions such as catalysis , redox reactions and as ‘switches’ in signal transductions . Iron dependent repressor ( IdeR ) is a metal-sensing transcription factor that regulates free iron concentration in Mycobac...	The importance of iron for tuberculosis infection and criticality of IdeR as an iron regulator in Mycobacterium tuberculosis have now been well-established . Although crystal structures of the protein in different forms are available , its dynamical properties have not been explored before . Macromolecules possess an i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study
It is well known that , under suitable conditions , microRNAs are able to fine tune the relative concentration of their targets to any desired value . We show that this function is particularly effective when one of the targets is a Transcription Factor ( TF ) which regulates the other targets . This combination define...	Gene expression is controlled by a complex network of regulatory interactions which may be organized in two complementary subnetworks: the transcriptional one , mediated by Transcription Factors ( TF ) , and the post-transcriptional one , in which a central role is played by microRNAs . In this paper we add a further s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "biology", "computational", "biology" ]	2014	A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes
A major problem for the effective diagnosis and management of prion diseases is the lack of rapid high-throughput assays to measure low levels of prions . Such measurements have typically required prolonged bioassays in animals . Highly sensitive , but generally non-quantitative , prion detection methods have been deve...	Prion diseases are deadly infectious neurodegenerative disorders of mammals which involve the misfolding of host prion protein . To better manage these diseases , we need to be able to detect and quantify the infectious particles , or prions , in biological samples . However , current tests lack the sensitivity , speed...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "infectious", "diseases", "infectious", "diseases/prion", "diseases", "biochemistry/protein", "chemistry", "neurological", "disorders/prion", "diseases" ]	2010	Rapid End-Point Quantitation of Prion Seeding Activity with Sensitivity Comparable to Bioassays
Somitogenesis , the formation of the body's primary segmental structure common to all vertebrate development , requires coordination between biological mechanisms at several scales . Explaining how these mechanisms interact across scales and how events are coordinated in space and time is necessary for a complete under...	Recent decades have seen a revolution in experimental techniques that has shifted the focus of experimental biology from behaviors at the micron ( cell ) scale to those at the nanometer ( molecular ) scale . An ever-increasing number of studies detail subcellular behaviors , genetic pathways and protein interactions th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "segmentation", "signaling", "networks", "cell", "differentiation", "developmental", "biology", "body", "plan", "organization", "morphogenesis", "biophysics", "simulations", "pattern", "formation", "embryology", "regulatory", "networks", "biology", "biophysics", "biophysic", ...	2011	A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation
For females , menarche is a most significant physiological event . Age at menarche ( AAM ) is a trait with high genetic determination and is associated with major complex diseases in women . However , specific genes for AAM variation are largely unknown . To identify genetic factors underlying AAM variation , a genome-...	Menarche is a physical milestone in a woman's life . Age at menarche ( AAM ) is related to many common female health problems . AAM is mainly determined by genetic factors . However , the specific genes and the associated mechanisms underlying AAM are largely unknown . Here , taking advantage of the most recent technol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics" ]	2009	Genome-Wide Association Analyses Identify SPOCK as a Key Novel Gene Underlying Age at Menarche
The faithful inheritance of chromosomes during cell division requires their precise replication and segregation . Numerous mechanisms ensure that each of these fundamental cell cycle events is performed with a high degree of fidelity . The fidelity of chromosomal replication is maintained in part by re-replication cont...	The stable inheritance of genetic information requires an elaborate mitotic machinery that acts on the centromeres of chromosomes to ensure their precise segregation . Errors in this segregation can lead to aneuploidy , an unbalanced chromosomal state in which some chromosomes have different copy number than others . B...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Re-replication of a Centromere Induces Chromosomal Instability and Aneuploidy
In Africa , onchocerciasis and lymphatic filariasis ( LF ) are co-endemic in many areas . Current efforts to eliminate both diseases are through ivermectin-based mass drug administration ( MDA ) . Years of ivermectin distribution for onchocerciasis may have interrupted LF transmission in certain areas . The Kédougou re...	Onchocerciasis and lymphatic filariasis ( LF ) are neglected tropical diseases caused by infection with filarial parasites , Onchocerca volvulus and Wuchereria bancrofti or Brugia species respectively . Efforts to eliminate both diseases are through ivermectin-based mass drug administration ( MDA ) for onchocerciasis a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "onchocerca", "volvulus", "rivers", "helminths", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "onchocerca", "filariasis", "...	2016	Evaluation of Lymphatic Filariasis and Onchocerciasis in Three Senegalese Districts Treated for Onchocerciasis with Ivermectin
Rare individuals with inactivating mutations in the Huntington’s disease gene ( HTT ) exhibit variable abnormalities that imply essential HTT roles during organ development . Here we report phenotypes produced when increasingly severe hypomorphic mutations in the murine HTT orthologue Htt , ( HdhneoQ20 , HdhneoQ50 , Hd...	The HTT gene mutated in Huntington’s Disease ( HD ) has essential roles during normal development . However , still not fully understood are the functional consequences of its partial inactivation . Our genetic study provides a comprehensive description of the effects of progressively more severe decreases in expressio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "natural", "antisense", "transcripts", "gene", "regulation", "ears", "alleles", "cell", "differentiation", "physiological", "processes", "developmental", "biology", "mutation", "micrornas", "embryos", "embryology", "gene", "express...	2019	Hypomorphic mutation of the mouse Huntington’s disease gene orthologue
Climate change is increasingly being implicated in species' range shifts throughout the world , including those of important vector and reservoir species for infectious diseases . In North America ( México , United States , and Canada ) , leishmaniasis is a vector-borne disease that is autochthonous in México and Texas...	We explored the consequences of climate change for the spread of leishmaniasis in North America . We modeled the distribution of two sand fly vector and four rodent reservoir species found in northern México and the southern United States . Models were based on occurrence data and environmental and topographic layers ....	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology/global", "change", "ecology", "public", "health", "and", "epidemiology", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/infectious", "diseases", "compu...	2010	Climate Change and Risk of Leishmaniasis in North America: Predictions from Ecological Niche Models of Vector and Reservoir Species
Community associated methicillin-resistant Staphylococcus aureus ( CA-MRSA ) has become a major cause of skin and soft tissue infections ( SSTIs ) in the US . We developed an age-structured compartmental model to study the spread of CA-MRSA at the population level and assess the effect of control intervention strategie...	Community associated methicillin-resistant Staphylococcus aureus ( CA-MRSA ) is a bacteria that causes skin infections in the US . We developed a mathematical model of CA-MRSA transmission among different age groups at the population level . We parameterized the model using monthly time series data on number of SSTIs i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	A Data-Driven Mathematical Model of CA-MRSA Transmission among Age Groups: Evaluating the Effect of Control Interventions
Many host-adapted bacterial pathogens contain DNA methyltransferases ( mod genes ) that are subject to phase-variable expression ( high-frequency reversible ON/OFF switching of gene expression ) . In Haemophilus influenzae , the random switching of the modA gene controls expression of a phase-variable regulon of genes ...	The pathogenic Neisseria are bacterial pathogens that cause meningitis and gonorrhoea . They have adapted to life exclusively in humans and have developed unique strategies to colonize the host and to evade the immune response . Central among these strategies are genetic switches that randomly turn genes on and off . I...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "molecular", "biology/dna", "methylation", "genetics", "and", "genomics/gene", "expression" ]	2009	Phasevarions Mediate Random Switching of Gene Expression in Pathogenic Neisseria
The observation that disease associated proteins often interact with each other has fueled the development of network-based approaches to elucidate the molecular mechanisms of human disease . Such approaches build on the assumption that protein interaction networks can be viewed as maps in which diseases can be identif...	Diseases are rarely the result of an abnormality in a single gene , but involve a whole cascade of interactions between several cellular processes . To disentangle these complex interactions it is necessary to study genotype-phenotype relationships in the context of protein-protein interaction networks . Our analysis o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome
The Ion Torrent Personal Genome Machine ( PGM ) is a new sequencing platform that substantially differs from other sequencing technologies by measuring pH rather than light to detect polymerisation events . Using re-sequencing datasets , we comprehensively characterise the biases and errors introduced by the PGM at bot...	DNA sequencing is used routinely within biology to reveal the genetic information of living organisms . In recent years , technological advances have led to the availability of high-throughput , low-cost DNA sequencing machines ( ‘sequencers’ ) . In 2011 , Life Sciences released a new sequencer , the Ion Torrent Person...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genomics", "biology", "computational", "biology" ]	2013	Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data
Distinct prion strains often exhibit different incubation periods and patterns of neuropathological lesions . Strain characteristics are generally retained upon intraspecies transmission , but may change on transmission to another species . We investigated the inactivation of two related prions strains: BSE prions from...	“Mad cow” disease , formally known as bovine spongiform encephalopathy ( BSE ) , belongs to a family of diseases affecting humans and a number of commercially important animal species . These diseases are not spread by bacteria or viruses , but by infectious proteins , termed “prions . ” Prions are known to be very dif...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/prion", "diseases" ]	2008	Resistance of Bovine Spongiform Encephalopathy (BSE) Prions to Inactivation
Leptospirosis is a highly endemic bacterial zoonosis in French Polynesia ( FP ) . Nevertheless , data on the epidemiology of leptospirosis in FP are scarce . We conducted molecular studies on Leptospira isolated from humans and the potential main animal reservoirs in order to identify the most likely sources for human ...	Leptospirosis , a zoonosis caused by Leptospira spp . bacteria , is an important but neglected disease in the Pacific region . The bacteria can lead to human infections , either through direct contact with infected animals or through water and soil contaminated with urine . Although animals play a key role in the trans...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "vertebrates", "animals", "mammals", "dogs", "bacterial", "diseases", "neglected", "tropical", "diseases", "kidneys", ...	2017	Leptospira diversity in animals and humans in Tahiti, French Polynesia
Despite their importance in animal and human health , the epidemiology of species of the Leishmania enriettii complex remains poorly understood , including the identity of their biological vectors . Biting midges of the genus Forcipomyia ( Lasiohelea ) have been implicated in the transmission of a member of the L . enr...	This study investigates the laboratory infection of two species of Culicoides biting midges ( Diptera: Ceratopogonidae ) and one species of sand fly ( Diptera: Psychodidae ) with two species of Leishmania . These members of the L . enriettii complex were demonstrated to colonize the stomodeal valve of Culicoides sonore...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	The Biting Midge Culicoides sonorensis (Diptera: Ceratopogonidae) Is Capable of Developing Late Stage Infections of Leishmania enriettii
Chlamydia trachomatis is an obligate intracellular bacterium that replicates within a vacuole termed an inclusion . At the end of their intracellular developmental cycle , chlamydiae are released either by lysis of the host cell or extrusion of the intact inclusion . The inclusion membrane is extensively modified by th...	At the end of their intracellular developmental cycle , chlamydiae exit host cells by one of two mechanisms; lysis of the host cell or extrusion of a membrane bound vesicle containing viable chlamydiae . Sequestration of infectious organisms within a vesicle is believed to aid in dissemination of the bacteria from site...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "hela", "cells", "enzymes", "chlamydia", "trachomatis", "pathogens", "cell", "processes", "biological", "cultures", "microbiology", "enzymology", "phosphatases", "membrane", "proteins",...	2018	Chlamydia trachomatis inclusion membrane protein MrcA interacts with the inositol 1,4,5-trisphosphate receptor type 3 (ITPR3) to regulate extrusion formation
Alternative transcript isoforms are common in tumors and act as potential drivers of cancer . Mechanisms determining altered isoform expression include somatic mutations in splice regulatory sites or altered splicing factors . However , since DNA methylation is known to regulate transcriptional isoform activity in norm...	In eukaryotes , one gene can be transcribed into multiple RNA sequences ( or isoforms ) that are subsequently translated into proteins with different functions in response to specific cellular needs . Recent studies showed that cancer cells can obtain abnormal functions via expressing different isoforms . In normal cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "squamous", "cell", "lung", "carcinoma", "cancer", "risk", "factors", "carcinomas", "cancers", "and", "neoplasms", "endometrial", "carcinoma", "dna", "transcription", "oncology", "adenocarcinomas", "head", "and", "neck", "tumor...	2019	Aberrant DNA methylation defines isoform usage in cancer, with functional implications
The natural history of ocular Chlamydia trachomatis infections in endemic communities has not been well characterised and is an important determinant of the effectiveness of different mass treatment strategies to prevent blindness due to trachoma . A multistate hidden Markov model was fitted to data on infection and ac...	Trachoma is an infectious disease of the eye that causes blindness in many of the poorest parts of the world . In this paper , we use a novel statistical approach to estimate the characteristics of this disease among people living in The Gambia who were examined every 2 weeks over a 6-month period . We found that the t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/bacterial", "infections", "infectious", "diseases/epidemiology", "and", ...	2008	The Natural History of Trachoma Infection and Disease in a Gambian Cohort with Frequent Follow-Up
The spatial organization of the genome in the nucleus plays a role in the regulation of gene expression . Whether co-regulated genes are subject to coordinated repositioning to a shared nuclear space is a matter of considerable interest and debate . We investigated the nuclear organization of estrogen receptor alpha ( ...	Whether co-regulated genes relocalize in a coordinated fashion to a shared nuclear space is a matter of considerable interest and debate . We investigated the spatial organization of estrogen receptor alpha ( ERα ) target genes in three human breast epithelial cell lines , human epithelial cells ( HMEC ) , the MCF10A n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "oncology/breast", "cancer", "cell", "biology/nuclear", "structure", "and", "function", "genetics", "and", "genomics/nuclear", "structure", "and", "function", "cell", "biology", "genetics",...	2010	Activation of Estrogen-Responsive Genes Does Not Require Their Nuclear Co-Localization
Cryptosporidiosis and giardiasis are recognized as significant enteric diseases due to their long-term health effects in humans and their economic impact in agriculture and medical care . Molecular analysis is essential to identify species and genotypes causing these infectious diseases and provides a potential tool fo...	Infectious diseases threaten the health and well-being of wildlife , livestock and human populations and contribute to significant economic impact in agriculture and medical care . Cryptosporidium and Giardia are enteric protozoan pathogens that cause diarrhea and nutritional disorders on a global level . Using molecul...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biogeography", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "giardia", "pathogens", "population", "dynamics", "population", "genetics", "geographical", "locations", "microbiology", "...	2017	Local and global genetic diversity of protozoan parasites: Spatial distribution of Cryptosporidium and Giardia genotypes
Recursive splicing ( RS ) is an evolutionarily conserved process of removing long introns via multiple steps of splicing . It was first discovered in Drosophila and recently proven to occur also in humans . The detailed mechanism of recursive splicing is not well understood , in particular , whether it is kinetically c...	Nascent precursor RNAs newly transcribed from a DNA template are processed into mature RNAs by splicing out introns and ligating exons . Recursive splicing ( RS ) is a special kind of splicing whereby long introns are removed piecewise in multiple consecutive steps . Only nine human introns are known to undergo recursi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "neuroscience", "dna", "transcription", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "rna", "sequencing", "research", "and", "analysis", "methods", "sequence", "analysis", "exon", "mapping", "genome", "complexity", "...	2018	The temporal landscape of recursive splicing during Pol II transcription elongation in human cells
Complex spatial patterning , common in the brain as well as in other biological systems , can emerge as a result of dynamic interactions that occur locally within developing structures . In the rodent somatosensory cortex , groups of neurons called “barrels” correspond to individual whiskers on the contralateral face ....	Complex spatial patterning , common in the brain as well as in other biological systems , can emerge as a result of dynamic interactions that occur locally within developing structures . In rodent somatosensory cortex , groups of neurons called “barrels” correspond to individual whiskers on the contralateral face . Bar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "neuroscience/neurodevelopment", "neuroscience/theoretical", "neuroscience" ]	2009	Subbarrel Patterns in Somatosensory Cortical Barrels Can Emerge from Local Dynamic Instabilities
Human echinococcosis is a neglected zoonosis caused by parasites of the genus Echinococcus . The most frequent clinical forms of echinococcosis , cystic echinococcosis ( CE ) and alveolar echinococcosis ( AE ) , are responsible for a substantial health and economic burden , particularly to low-income societies . Quanti...	Echinococcosis is considered a neglected zoonotic disease caused by the larval form of Echinococcus spp . tapeworms . Humans become infected through the accidental intake of parasitic eggs excreted by the faeces of definitive hosts ( dogs , foxes and other canids ) . Infection involves the development of cysts , primar...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Discussion" ]	[ "public", "health", "medicine", "echinococcosis", "infectious", "diseases", "veterinary", "epidemiology", "neglected", "tropical", "diseases", "parasitic", "diseases", "veterinary", "science" ]	2013	A Systematic Review of the Epidemiology of Echinococcosis in Domestic and Wild Animals
Triatoma infestans-mediated transmission of Tripanosoma cruzi , the causative agent of Chagas disease , remains as a major health issue in southern South America . Key factors of T . infestans prevalence in specific areas of the geographic Gran Chaco region—which extends through northern Argentina , Bolivia , and Parag...	Chagas disease , also known as American Trypanosomiasis , is the most relevant parasitic disease in Latin America , being a major burden that affects mostly poor human populations living in rural areas . The kissing-bugs of the Triatominae family transmit the parasite Trypanosoma cruzi by infectious blood-sucking; Tria...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "biochemistry", "microbiology/applied", "microbiology" ]	2009	Control of Pyrethroid-Resistant Chagas Disease Vectors with Entomopathogenic Fungi
It is generally thought that mucosal fluids protect underlying epithelial surfaces against opportunistic infection via their antimicrobial activity . However , our published data show that human tear fluid can protect against the major opportunistic pathogen Pseudomonas aeruginosa independently of bacteriostatic activi...	Pseudomonas aeruginosa is an opportunistic pathogen that causes life-threatening infections . P . aeruginosa disease is increasing in prevalence while bacteria continue to evolve antibiotic resistance . It is not clear how mucosal fluids usually protect against opportunistic pathogens . Knowing the key ingredients woul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "ocular", "anatomy", "microbiology", "saliva", "pili", "and", "fimbriae", "epithelial", "cells", "pseudomonas", "aeruginosa", "analysis", "of", "varia...	2017	Mucosal fluid glycoprotein DMBT1 suppresses twitching motility and virulence of the opportunistic pathogen Pseudomonas aeruginosa
Control operations targeting Animal African Trypanosomiasis and its primary vector , the tsetse , were covering approximately 128 , 000 km2 of Africa in 2001 , which is a mere 1 . 3% of the tsetse infested area . Although extensive trypanosomiasis and tsetse ( T&T ) control operations have been running since the beginn...	Despite decades of control efforts targeting Animal African Trypanosomiasis , its distribution has hardly receded and the situation in sub-Saharan Africa has recently been described as “serious and deteriorating” . This disease of livestock affects farmers’ livelihood and welfare , food security and poses a threat to p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "livestock", "medicine", "and", "health", "sciences", "ruminants", "african", "trypanosomiasis", "geographical", "locations", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "mammals", "neglected", "tropical", "diseases", "infectious", "disease", ...	2016	Past and Ongoing Tsetse and Animal Trypanosomiasis Control Operations in Five African Countries: A Systematic Review
Information transmission in the human brain is a fundamentally dynamic network process . In partial epilepsy , this process is perturbed and highly synchronous seizures originate in a local network , the so-called epileptogenic zone ( EZ ) , before recruiting other close or distant brain regions . We studied patient-sp...	Epilepsy is characterized by perturbed dynamics that originate in a local network before spreading to other brain regions . We studied patient-specific brain network models of epilepsy patients , comprising 88 nodes equipped with region specific neural mass models capable of demonstrating epileptiform discharges . Appl...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "neural", "networks", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "mathematics", "signs", "and", "symptoms", "algebra", "network", "analysis", "epilepsy", ...	2019	Controlling seizure propagation in large-scale brain networks
Knowledge of the structural basis of protein-protein interactions ( PPI ) is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI . Allosteric modulators play an important role in regulating such interactions by bin...	Protein-protein interactions ( PPI ) play an essential role in virtually all physiological processes . Knowledge of the principles governing PPI is of fundamental importance for understanding the organization and functioning of biological systems . Furthermore , a number of human diseases intractable to conventional th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "applications", "biomacromolecule-ligand", "interactions", "protein", "interactions", "molecular", "dynamics", "small", "molecules", "macromolecular", "assemblies", "regulatory", "proteins", "computer-aided", "design", "chemical", "biology", "molecular", "mechanics"...	2013	Surface Dynamics in Allosteric Regulation of Protein-Protein Interactions: Modulation of Calmodulin Functions by Ca2+
The Latency-Associated Nuclear Antigen ( LANA ) , encoded by ORF73 , is a conserved gene among the γ2-herpesviruses ( rhadinoviruses ) . The Kaposi's Sarcoma-Associated Herpesvirus ( KSHV ) LANA is consistently expressed in KSHV-associated malignancies . In the case of the rodent γ2-herpesvirus , murine gammaherpesviru...	The human gammaherpesviruses Epstein-Barr virus ( EBV ) and Kaposi's sarcoma-associated herpesvirus ( KSHV ) are tightly associated with a number of different cancers . Unfortunately , due to their very narrow host tropism , characterizing the pathogenesis of these viruses has been difficult . Infection of laboratory m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "persistence", "and", "latency", "virology", "biology", "microbiology" ]	2012	Unbiased Mutagenesis of MHV68 LANA Reveals a DNA-Binding Domain Required for LANA Function In Vitro and In Vivo
Understanding how epidemics spread in a system is a crucial step to prevent and control outbreaks , with broad implications on the system’s functioning , health , and associated costs . This can be achieved by identifying the elements at higher risk of infection and implementing targeted surveillance and control measur...	Following the emergence of a transmissible disease epidemic , interventions and resources need to be prioritized to efficiently control its spread . While the knowledge of the pattern of disease-transmission contacts among hosts would be ideal for this task , the continuously changing nature of such pattern makes its u...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Conclusions", "Methods" ]	[]	2015	Predicting Epidemic Risk from Past Temporal Contact Data
The switch between latency and the lytic cycle of Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is controlled by the expression of virally encoded ORF50 protein . Thus far , the regulatory mechanism underlying the protein stability of ORF50 is unknown . Our earlier studies have demonstrated that a protein abundance ...	The switch of Kaposi’s sarcoma-associated herpesvirus ( KSHV ) from latency to lytic replication is an essential process for controlling viral dissemination and the pathogenesis of KSHV-associated diseases . The virally encoded ORF50 protein is known as the master controller of viral reactivation . We previously report...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "compounds", "molecular", "probe", "techniques", "293t", "cells", "enzymes", "biological", "cultures", "immunoblotting", "enzymology", "protein", "abundance", "organic", "compounds", "immunoprecipitation", "basic", "amino", "acids", "amino", "acids", "molecula...	2016	Regulation of the Abundance of Kaposi’s Sarcoma-Associated Herpesvirus ORF50 Protein by Oncoprotein MDM2
Canine rabies is endemic in urban India . A questionnaire was administered to 204 residents of the urbanised municipality of Panchkula in north India to assess the influence of gender , age , family size , social status and dog ownership , over the knowledge , attitudes and practices ( KAP ) towards rabies control and ...	An enhanced level of awareness regarding rabies and management of dog-bite wounds is usually expected of urban residents owing to improved health care facilities and superior avenues for information dissemination . This perception can be misleading as gaps were found in the knowledge of residents of the Municipal Corpo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "health", "education", "and", "awareness", "pathology", "and", "laboratory", "medicine", "statistics", "pathogens", "tropical", "diseases", "geographical", "locations", "vertebrates", "india", "microbiology", "...	2019	Knowledge, attitudes and practices (KAP) towards rabies and free roaming dogs (FRD) in Panchkula district of north India: A cross-sectional study of urban residents
A key process in the lifecycle of the malaria parasite Plasmodium falciparum is the fast invasion of human erythrocytes . Entry into the host cell requires the apical membrane antigen 1 ( AMA-1 ) , a type I transmembrane protein located in the micronemes of the merozoite . Although AMA-1 is evolving into the leading bl...	Malaria is one of the most lethal parasitic diseases worldwide , causing more than 1 million fatalities per annum . Drug resistance is widespread , and a vaccine is not available . One of the leading blood stage vaccine candidates is the apical membrane antigen 1 ( AMA-1 ) , which is well-conserved among apicomplexan p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "cell", "biology/cell", "adhesion", "microbiology/parasitology" ]	2009	Functional Analysis of the Leading Malaria Vaccine Candidate AMA-1 Reveals an Essential Role for the Cytoplasmic Domain in the Invasion Process
Increases in fruit weight of cultivated vegetables and fruits accompanied the domestication of these crops . Here we report on the positional cloning of a quantitative trait locus ( QTL ) controlling fruit weight in tomato . The derived allele of Cell Size Regulator ( CSR-D ) increases fruit weight predominantly throug...	Starting about 10 , 000 years ago , during the Neolithic period , human societies began the transformation from a hunting and gathering-dependent lifestyle to an agrarian lifestyle . This transformation was accompanied by plant and animal domestication . Tomato shows a huge increase in fruit weight that has arisen as a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "methods" ]	[ "biotechnology", "plant", "anatomy", "population", "genetics", "ploidy", "brassica", "plant", "science", "model", "organisms", "genetically", "modified", "plants", "experimental", "organism", "systems", "sequence", "motif", "analysis", "population", "biology", "plants", ...	2017	Fruit weight is controlled by Cell Size Regulator encoding a novel protein that is expressed in maturing tomato fruits
Current chemotherapy for Chagas disease is unsatisfactory due to its limited efficacy , particularly in the chronic phase , with frequent side effects that can lead to treatment discontinuation . Combined therapy is envisioned as an ideal approach since it may improve treatment efficacy whilst decreasing toxicity and t...	In this study , we investigated the efficacy of posaconazole in combination with benznidazole against Trypanosoma cruzi acute infections in mice , to support the potential clinical evaluation of such combination therapy for Chagas disease . The curative action of benznidazole/posaconazole combinations was explored in a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "medicine", "trypanosoma", "drug", "research", "and", "development", "drugs", "and", "devices", "protozoology", "biology", "microbiology" ]	2013	Benznidazole and Posaconazole in Experimental Chagas Disease: Positive Interaction in Concomitant and Sequential Treatments
Ebola Zaire virus is highly pathogenic for humans , with case fatality rates approaching 90% in large outbreaks in Africa . The virus replicates in macrophages and dendritic cells ( DCs ) , suppressing production of type I interferons ( IFNs ) while inducing the release of large quantities of proinflammatory cytokines ...	Ebola Zaire virus causes severe hemorrhagic fever in humans that is fatal in almost 90% of cases . The rapid spread of the virus to macrophages and dendritic cells results in the release of high levels of inflammatory cytokines , causing shock and bleeding . The ability of Ebola virus to overwhelm host defenses is beli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "virology/host", "antiviral", "responses", "immunology/innate", "immunity" ]	2009	Ebola Zaire Virus Blocks Type I Interferon Production by Exploiting the Host SUMO Modification Machinery
Human Neutrophil Peptide 1 ( HNP1 ) produced by neutrophils , is a well-known antimicrobial peptide which plays a role both in innate as well as in adaptive immunity and is under intensive investigation as a potential therapeutic agent . Previous in vitro experiments have indicated the leishmaniacidal effect of recombi...	The outbreak level of cutaneous leishmaniasis is approximated between one and 1 . 5 million individuals per year . Owning to several disadvantages of current therapies , special attention to expand novel and efficient therapies has been demanded . Among Anti-Microbial Peptides ( AMPs ) , Human Neutrophil Peptide 1 ( HN...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "neurochemistry", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "parasite", "replication", "immunology", "tropical", "diseases", "microbiology", "parasitic", "disea...	2017	Human Neutrophil Peptide 1 as immunotherapeutic agent against Leishmania infected BALB/c mice
Discovery of lineage-specific somatic copy number variation ( CNV ) in mammals has led to debate over whether CNVs are mutations that propagate disease or whether they are a normal , and even essential , aspect of cell biology . We show that 1 , 000N polyploid trophoblast giant cells ( TGCs ) of the mouse placenta cont...	Generally , every mammalian cell has the same complement of each part of its genome . However , copy number variation ( CNV ) can occur , where , compared to the rest of its genome , a cell has either more or less of a specific genomic region . It is unknown whether CNVs cause disease , or whether they are a normal asp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "structural", "genomics", "cell", "biology", "chromosome", "biology", "chromosome", "structure", "and", "function", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "epigenetics", "genomics", "chromatin", "cell", "diffe...	2014	Copy Number Variation Is a Fundamental Aspect of the Placental Genome
Zika virus ( ZIKV ) recently caused a pandemic complicated by Guillain-Barre syndrome ( GBS ) and birth defects . ZIKV is structurally similar to the dengue viruses ( DENV ) and in vitro studies suggest antibody dependent enhancement occurs in ZIKV infections preceded by DENV; however , the clinical significance of thi...	Zika virus ( ZIKV ) is a mosquito borne virus that recently caused a large epidemic with some cases complicated by ascending paralysis ( Guillain-Barre syndrome ) and birth defects . One major concern is that such complications may be more common in those who have had previous infection with the closely related mosquit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "statistics", "pathogens", "metaanalysis", "immunolo...	2019	Does prior dengue virus exposure worsen clinical outcomes of Zika virus infection? A systematic review, pooled analysis and lessons learned
Meningococcal invasive isolates of the ST-11 clonal complex are most frequently associated with disease and rarely found in carriers . Unlike carriage isolates , invasive isolates induce apoptosis in epithelial cells through the TNF-α signaling pathway . While invasive and non-invasive isolates are both able to trigger...	Strains of Neisseria meningitidis isolated from patients induce apoptotic cell death through the TNF-α pathway , whereas strains isolated from healthy carriage isolates do not . Part of the difference has been shown to arise from differential shedding of the type 1 TNF-α receptor ( TNFR1 ) from the surface of the cells...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "microbiology", "molecular", "cell", "biology" ]	2011	Late Repression of NF-κB Activity by Invasive but Not Non-Invasive Meningococcal Isolates Is Required to Display Apoptosis of Epithelial Cells
The detection of the activities of pathogen-encoded virulence factors by the innate immune system has emerged as a new paradigm of pathogen recognition . Much remains to be determined with regard to the molecular and cellular components contributing to this defense mechanism in mammals and importance during infection ....	The pathogenic potentials of most microbes depend on a repertoire of virulence factors . Despite major progress in the understanding of the molecular mechanisms underlying the activities of bacterial effectors , little is known about how they cooperate during infection to overcome host immune defenses and promote micro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Escherichia coli α-Hemolysin Counteracts the Anti-Virulence Innate Immune Response Triggered by the Rho GTPase Activating Toxin CNF1 during Bacteremia
Cellular functions are shaped by reaction networks whose dynamics are determined by the concentrations of underlying components . However , cellular mechanisms ensuring that a component’s concentration resides in a given range remain elusive . We present network properties which suffice to identify components whose con...	We present a computational approach for inferring concentration ranges from genome-scale metabolic models . The approach specifies a determinant and molecular mechanism underling facile control of concentration ranges for components in large-scale cellular networks . Most importantly , the predictions about concentrati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "cell", "physiology", "medicine", "and", "health", "sciences", "enzymes", "metabolic", "networks", "enzymology", "microbiology", "cell", "metabolism", "metabolites", "network", "analysis", "enzyme", "metabolism", "bacterial", "genetics", "pharmacology", "m...	2019	Cellular determinants of metabolite concentration ranges
Southeast Asia is an epicenter of multidrug-resistant Plasmodium falciparum strains . Selective pressures on the subcontinent have recurrently produced several allelic variants of parasite drug resistance genes , including the P . falciparum chloroquine resistance transporter ( pfcrt ) . Despite significant reductions ...	Point mutations in the Plasmodium falciparum chloroquine resistance transporter ( PfCRT ) earlier thwarted the clinical efficacy of chloroquine , the former gold standard , and constitute a major determinant of parasite susceptibility to antimalarial drugs . Recently , we reported that the highly mutated Cambodian PfCR...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "heme", "medicine", "and", "health", "sciences", "parasite", "groups", "plasmodium", "drugs", "population", "genetics", "microbiology", "parasitology", "antimalarials", "apicomplexa", "metabolites", "pharmacology", "population", "biology", "drug", "metabolism", "antimicrobi...	2016	Evolution of Fitness Cost-Neutral Mutant PfCRT Conferring P. falciparum 4-Aminoquinoline Drug Resistance Is Accompanied by Altered Parasite Metabolism and Digestive Vacuole Physiology
The worldwide distribution of dengue is expanding , in part due to globalized traffic and trade . Aedes albopictus is a competent vector for dengue viruses ( DENV ) and is now established in numerous regions of Europe . Viremic travellers arriving in Europe from dengue-affected areas of the world can become catalysts o...	The global disease burden of dengue is staggering . Continuous expansion and vaccine failures illustrate the limitations of current dengue control efforts . Novel approaches and additional tools are required to combat and contain the disease . In Europe , dengue infections are rare and the last outbreak of dengue occur...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "plant", "science", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "epidemiology", "disease", "dynamics", "disease", "surveillance", "plant", "pathology", "biology", "and", "life", "sciences", "spatial", "epidemiology", "disease", "vec...	2014	International Dispersal of Dengue through Air Travel: Importation Risk for Europe
The simian immunodeficiency virus ( SIV ) challenge model of lentiviral infection is often used as a model to human immunodeficiency virus type 1 ( HIV-1 ) for studying vaccine mediated and immune correlates of protection . However , knowledge of the structure of the SIV envelope ( Env ) glycoprotein is limited , as is...	An antibody-based approach targeting human immunodeficiency virus ( HIV ) envelope ( Env ) protein may eventually prove to be effective in treating or preventing HIV infection . However , before any candidate HIV treatment or vaccine can be tested in humans , it must first be evaluated in nonhuman primates ( NHPs ) –th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "cell", "binding", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "cloning", "animals", ...	2016	Targeted Isolation of Antibodies Directed against Major Sites of SIV Env Vulnerability
The clinicopathological features of the hamster model of visceral leishmaniasis ( VL ) closely mimic active human disease . Studies in humans and hamsters indicate that the inability to control parasite replication in VL could be related to ineffective classical macrophage activation . Therefore , we hypothesized that ...	Visceral leishmaniasis ( VL ) , caused by the intracellular protozoan Leishmania donovani , is a progressive , potentially fatal infection found in many resource-poor regions of the world . We initiated these studies of an experimental model of VL to better understand the molecular and cellular determinants underlying ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "microbiology", "protozoology" ]	2012	Progressive Visceral Leishmaniasis Is Driven by Dominant Parasite-induced STAT6 Activation and STAT6-dependent Host Arginase 1 Expression

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