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article stringlengths 4.36k 149k | summary stringlengths 32 3.35k | section_headings listlengths 1 91 | keywords listlengths 0 141 | year stringclasses 13
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China used to be among the countries with a high prevalence of trachoma . At the launch of The Global Elimination of Trachoma ( GET ) 2020 campaign by the World Health Organization ( WHO ) in 1996 , China was placed on the list of countries endemic for trachoma based on historical data . However , empirical observation... | China used to a country with a high burden of trachoma , but recent empirical observation and routinely collected eye care data were suggesting that elimination of trachoma had been achieved in China . In order to verify that and reach the target set in the WHA 51 . 11 Resolution , we have assessed current situation us... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"standardized",
"tests",
"medicine",
"and",
"health",
"sciences",
"education",
"china",
"sociology",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"bacterial",
"diseases",
"eye",
"diseases",
"global",
"health",
"neglected",
"tropical",
"dise... | 2019 | Assessment of trachoma in suspected endemic areas within 16 provinces in mainland China |
Pseudomonas aeruginosa , an important opportunistic pathogen of man , exploits numerous factors for initial attachment to the host , an event required to establish bacterial infection . In this paper , we rigorously explore the role of two major bacterial adhesins , type IV pili ( Tfp ) and flagella , in bacterial adhe... | Pseudomonas aeruginosa is one of the most virulent nosocomial opportunistic pathogens that is associated with a broad spectrum of life-threatening infections . Antibiotic resistance is widespread and attributable mortality remains near 50% . Complex binding to epithelial cells is a key first step for this potent pathog... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biochemistry",
"infectious",
"diseases",
"genetics",
"biology",
"microbiology",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Pseudomonas aeruginosa Pili and Flagella Mediate Distinct Binding and Signaling Events at the Apical and Basolateral Surface of Airway Epithelium |
Pore-forming toxins ( PFTs ) are by far the most abundant bacterial protein toxins and are important for the virulence of many important pathogens . As such , cellular responses to PFTs critically modulate host-pathogen interactions . Although many cellular responses to PFTs have been recorded , little is understood ab... | Bacteria make many different protein toxins to attack our cells and immune system in order to infect . Amongst them , pore-forming toxins ( PFTs ) , which punch holes in the protective plasma membrane that surrounds cells , are by far the most abundant and constitute important virulence factors . Since the integrity of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"infectious",
"diseases",
"cell",
"biology/cellular",
"death",
"and",
"stress",
"responses",
"cell",
"biology/cell",
"signaling",
"genetics",
"and",
"genomics/genetics",
"of",
"the",
"immune",
"system",
"immunology/immune"... | 2009 | Hypoxia and the Hypoxic Response Pathway Protect against Pore-Forming Toxins in C. elegans |
Japanese encephalitis ( JE ) is a mosquito-borne disease that is associated with considerable morbidity and mortality in many Asian countries . The objective of this study was to describe the impact of the JE immunization program using SA 14-14-2 JE vaccine implemented in Nepal during 2006 through 2011 . A previous ass... | In 2006 , the Ministry of Health and Population in Nepal commenced a Japanese encephalitis ( JE ) immunization program using SA 14-14-2 JE vaccine , with mass campaigns conducted in selected districts , followed by introduction of JE vaccine into the routine childhood immunization program . JE and acute encephalitis sy... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"medicine",
"and",
"health",
"sciences",
"demography",
"immunology",
"geographical",
"locations",
"tropical",
"diseases",
"encephalitis",
"vaccines",
"preventive",
"medicine",
"age",
"groups",
"neglected",
"tropical",
"diseases",
"infectious",
"disease",... | 2017 | Updated estimation of the impact of a Japanese encephalitis immunization program with live, attenuated SA 14-14-2 vaccine in Nepal |
A PCR-enzyme-linked immunosorbent assay ( PCR-ELISA ) was developed to overcome the need for sensitive techniques for the efficient diagnosis of Schistosoma infection in endemic settings with low parasitic burden . This system amplifies a 121-base pair tandem repeat DNA sequence , immobilizes the resultant 5′ biotinyla... | Schistosomiasis is a neglected disease caused by worms of the genus Schistosoma . The transmission cycle requires contamination of bodies of water by parasite eggs present in excreta , specific snails as intermediate hosts and human contact with water . Fortunately , relatively safe and easily administrable drugs are a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology"
] | 2010 | Development and Evaluation of a Sensitive PCR-ELISA System for Detection of Schistosoma Infection in Feces |
The genus Bartonella comprises facultative intracellular bacteria adapted to mammals , including previously recognized and emerging human pathogens . We report the 2 , 341 , 328 bp genome sequence of Bartonella grahamii , one of the most prevalent Bartonella species in wild rodents . Comparative genomics revealed that ... | Emerging infectious diseases represent an increasing human health problem with many examples of disease outbreaks caused by transmissions from animals to humans , such as , most recently , the bird flu virus . Genes involved in virulence and antibiotic resistance are often carried by mobile elements like plasmids and v... | [
"Abstract",
"Introduction",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/microbial",
"evolution",
"and",
"genomics",
"genetics",
"and",
"genomics/comparative",
"genomics",
"evolutionary",
"biology/genomics"
] | 2009 | Run-Off Replication of Host-Adaptability Genes Is Associated with Gene Transfer Agents in the Genome of Mouse-Infecting Bartonella grahamii |
Identifying enhancers regulating gene expression remains an important and challenging task . While recent sequencing-based methods provide epigenomic characteristics that correlate well with enhancer activity , it remains onerous to comprehensively identify all enhancers across development . Here we introduce a computa... | Enhancers are distal gene regulatory elements that can activate tissue- and time-point specific gene expression . Identification of active enhancers is challenging , and is the subject of intense investigation . We developed an automated computational framework to predict transcription factors ( TFs ) and enhancers tha... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"functional",
"genomics",
"biology",
"computational",
"biology"
] | 2014 | Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data |
Zika virus ( ZIKV ) has emerged since 2013 as a significant global human health threat following outbreaks in the Pacific Islands and rapid spread throughout South and Central America . Severe congenital and neurological sequelae have been linked to ZIKV infections . Assessing the ability of common mosquito species to ... | Assessing the ability of common mosquito species to transmit Zika virus ( ZIKV ) and characterizing variation in mosquito transmission of different ZIKV strains is important for estimating regional outbreak potential and for prioritizing local mosquito control strategies for Aedes and Culex species . In this study , we... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"vero",
"cells",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"biological",
"cultures",
"microbiology",
"saliva",
"animals",
"viruses",
"rna",
"viruses",
"mammalian",
"genomics",
... | 2018 | Vector competence of Aedes aegypti, Culex tarsalis, and Culex quinquefasciatus from California for Zika virus |
Expansion or shrinkage of existing tandem repeats ( TRs ) associated with various biological processes has been actively studied in both prokaryotic and eukaryotic genomes , while their origin and biological implications remain mostly unknown . Here we describe various duplications ( de novo TRs ) that occurred in the ... | β-lactamases can adapt to new antibiotics by mutations in their genes . The original and the extended substrate spectrums of β-lactamases define two phases of catalytic activity , and the conversion by point mutations is unidirectional from the initial to the new spectrum . We describe duplication mutations that enable... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"antimicrobials",
"organismal",
"evolution",
"microbial",
"mutation",
"medicine",
"and",
"health",
"sciences",
"burkholderia",
"infection",
"microbiology",
"bacterial",
"diseases",
"antibiotics",
"microbial",
"evolution",
"molecular",
"genetics",
"bacterial",
... | 2014 | The Tandem Repeats Enabling Reversible Switching between the Two Phases of β-Lactamase Substrate Spectrum |
Dynamics and functions of G-protein coupled receptors ( GPCRs ) are accurately regulated by the type of ligands that bind to the orthosteric or allosteric binding sites . To glean the structural and dynamical origin of ligand-dependent modulation of GPCR activity , we performed total ~ 5 μsec molecular dynamics simulat... | As the key signal transmitters of a number of physiological processes , G-protein coupled receptors ( GPCRs ) are arguably one of the most important therapeutic targets . Orchestration of the intra-molecular signaling across transmembrane domain is key for the function of GPCRs . To investigate the microscopic underpin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Communication over the Network of Binary Switches Regulates the Activation of A2A Adenosine Receptor |
We used an individual-based molecular multisource approach to assess the epidemiological importance of Triatoma brasiliensis collected in distinct sites and ecotopes in Rio Grande do Norte State , Brazil . In the semi-arid zones of Brazil , this blood sucking bug is the most important vector of Trypanosoma cruzi—the pa... | Blood-sucking bugs are vectors of the parasite Trypanosoma cruzi , which causes Chagas disease . Triatoma brasiliensis is the main Chagas disease vector in the Caatinga eco-region of northeastern Brazil . We showed that T . brasiliensis exhibits gene flow between sylvatic and anthropic ( domiciliary and peridomiciliary... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"population",
"genetics",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"animals",
"organisms",
"protozoans",
"neglected",
"tropical",
"diseases",
"population",
"biology",
"infectious",
... | 2016 | Molecular Individual-Based Approach on Triatoma brasiliensis: Inferences on Triatomine Foci, Trypanosoma cruzi Natural Infection Prevalence, Parasite Diversity and Feeding Sources |
The peritrophic matrix ( PM ) plays a key role in compartmentalization of the blood meal and as barrier to pathogens in many disease vectors . To establish an infection in sand flies , Leishmania must escape from the endoperitrophic space to prevent excretion with remnants of the blood meal digestion . In spite of the ... | For a successful development within the midgut of the sand fly vector , Leishmania must overcome several barriers imposed by the vector that include the digestive proteases secreted within the midgut following a blood meal by the insect , the need to escape from the endoperitrophic space , and attachment to the midgut ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"functional",
"genomics",
"molecular",
"cell",
"biology",
"biology",
"genomics",
"microbiology",
"genetics",
"and",
"genomics"
] | 2013 | Characterization of Phlebotomus papatasi Peritrophins, and the Role of PpPer1 in Leishmania major Survival in its Natural Vector |
Essential genes code for fundamental cellular functions required for the viability of an organism . For this reason , essential genes are often highly conserved across organisms . However , this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organism... | In any given organism , a fraction of all genes in the genome are required for viability; if they are experimentally deleted , the organism dies . Interestingly , the set of essential genes is usually not identical even for closely related organisms . Genes that are essential in one organism are sometimes nonessential ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"biology",
"microbiology",
"evolutionary",
"biology"
] | 2012 | Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability |
Local excitatory connections in mouse primary visual cortex ( V1 ) are stronger and more prevalent between neurons that share similar functional response features . However , the details of how functional rules for local connectivity shape neuronal responses in V1 remain unknown . We hypothesised that complex responses... | The brain is a highly complex structure , with abundant connectivity between nearby neurons in the neocortex , the outermost and evolutionarily most recent part of the brain . Although the network architecture of the neocortex can appear disordered , connections between neurons seem to follow certain rules . These rule... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"nervous",
"system",
"brain",
"social",
"sciences",
"electrophysiology",
"neuroscience",
"computational",
"neuroscience",
"vision",
"neuroimaging",
"neuronal",
"tuning",
"research",
"and",
"analysis",
"methods... | 2017 | Specific excitatory connectivity for feature integration in mouse primary visual cortex |
We study the structure and dynamics of spherical high density lipoprotein ( HDL ) particles through coarse-grained multi-microsecond molecular dynamics simulations . We simulate both a lipid droplet without the apolipoprotein A-I ( apoA-I ) and the full HDL particle including two apoA-I molecules surrounding the lipid ... | Cardiovascular diseases are the primary cause of death in western countries . One of the main causes is lipid accumulation and plaque formation on arterial walls , called atherosclerosis . The risk of being exposed to this condition is reduced by high levels of high density lipoprotein ( HDL ) . The functionality of HD... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/molecular",
"dynamics",
"biophysics/macromolecular",
"assemblies",
"and",
"machines",
"biochemistry/macromolecular",
"assemblies",
"and",
"machines",
"biophysics/theory",
"and",
"simulation"
] | 2010 | Role of Lipids in Spheroidal High Density Lipoproteins |
Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise . In addition , some regulatory polymorphisms may become apparent only in specific tissues . We derived human induced pluripotent stem ( iPS ) cells from adult skin primary fibroblasts and attempted ... | Most complex traits likely result from a combination of genetic polymorphisms . The normal variation in gene expression is thought to be an important contributor . In order to examine a wide range of personalized tissue types from a given individual , we developed a robust method for detecting regulatory variants genom... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/gene",
"expression",
"genetics",
"and",
"genomics/functional",
"genomics"
] | 2009 | A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells |
Activation of NLRP3 inflammasome is important for effective host defense against invading pathogen . Together with apoptosis-associated speck-like protein containing CARD domain ( ASC ) , NLRP3 induces the cleavage of caspase-1 to facilitate the maturation of interleukin-1beta ( IL-1β ) , an important pro-inflammatory ... | The immune system protects the infected host and clears the invading pathogens . An important part of the innate immune response is the activation of NLRP3 inflammasome , which is induced upon exposure to pathogens . Activated inflammasome subsequently regulates the maturation of IL-1β that plays an important role in i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"enzyme-linked",
"immunoassays",
"molecular",
"probe",
"techniques",
"immunology",
"immunoblotting",
"physiological",
"processes",
"inflammasomes",
"molecular",
"biology",
"techniques",
"immunolog... | 2017 | EV71 3D Protein Binds with NLRP3 and Enhances the Assembly of Inflammasome Complex |
Most previous genetic epidemiology studies within the field of osteoporosis have focused on the genetics of the complex trait areal bone mineral density ( aBMD ) , not being able to differentiate genetic determinants of cortical volumetric BMD ( vBMD ) , trabecular vBMD , and bone microstructural traits . The objective... | Osteoporosis is a common highly heritable skeletal disease characterized by reduced bone mineral density ( BMD ) and deteriorated bone microstructure , resulting in an increased risk of fracture . Most previous genetic epidemiology studies have focused on the genetics of the complex trait BMD , not being able to separa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"epidemiology",
"endocrinology",
"diabetes",
"and",
"endocrinology",
"genetics",
"and",
"genomics",
"clinical",
"genetics"
] | 2013 | Genetic Determinants of Trabecular and Cortical Volumetric Bone Mineral Densities and Bone Microstructure |
Heterozygous germline mutations and deletions in PHOX2B , a key regulator of autonomic neuron development , predispose to neuroblastoma , a tumor of the peripheral sympathetic nervous system . To gain insight into the oncogenic mechanisms engaged by these changes , we used zebrafish models to study the functional conse... | Neuroblastoma , a tumor of the peripheral sympathetic nervous system , is the most common cancer diagnosed in infancy . Although most cases arise sporadically , familial predisposition also occurs in association with mutations in a single copy of the PHOX2B gene , a “master regulator” of sympathetic neuronal developmen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"oncology",
"medicine",
"neurological",
"tumors",
"developmental",
"biology",
"developmental",
"neuroscience",
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"cancer",
"genetics",
"pediatric",
"oncology",
"genetics",
"biology",
"cancers",
"and",
"neoplasms",
"gen... | 2013 | Distinct Neuroblastoma-associated Alterations of PHOX2B Impair Sympathetic Neuronal Differentiation in Zebrafish Models |
Apicomplexa are obligate intracellular pathogens that have fine-tuned their proliferative strategies to match a large variety of host cells . A critical aspect of this adaptation is a flexible cell cycle that remains poorly understood at the mechanistic level . Here we describe a forward genetic dissection of the apico... | Parasites of the phylum Apicomplexa cause numerous important diseases , including malaria , toxoplasmosis , and cryptosporidiosis . The ability to modify the genome of these parasites by transfection has been the technological key to unlock the biology of parasitic diseases at a molecular level . In this study we furth... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"apicomplexa",
"toxoplasma",
"toxoplasma",
"gondii",
"eukaryotes",
"microbiology"
] | 2008 | Forward Genetic Analysis of the Apicomplexan Cell Division Cycle in Toxoplasma gondii |
Plasmodium vivax can cause severe malaria , however its pathogenesis is poorly understood . In contrast to P . falciparum , circulating vivax parasitemia is low , with minimal apparent sequestration in endothelium-lined microvasculature , and pathogenesis thought unrelated to parasite biomass . However , the relationsh... | How vivax parasites cause severe malaria is not known . In contrast to falciparum parasites , the number of vivax parasites circulating in peripheral blood is low , and there is thought to be little sequestration of parasitized red cells within endothelium-lined small blood vessels in vital organs . Total parasite burd... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"plasmodium",
"vivax",
"protozoans",
"malarial",
"parasites",
"biology",
"and",
"life",
"sciences",
"malaria",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"organisms"
] | 2015 | Parasite Biomass-Related Inflammation, Endothelial Activation, Microvascular Dysfunction and Disease Severity in Vivax Malaria |
The recent development of novel Polymerase Chain Reaction ( PCR ) technologies that confer theoretical advantages over quantitative PCR has considerable potential in the diagnosis of low load infections , such as Trypanosoma cruzi in the chronic phase of Chagas disease . We evaluated the utility of the digital droplet ... | Chagas disease is a complex pathology caused by the parasite Trypanosoma cruzi . This disease affects more than 8 million people in Latin America and is considered a serious public health problem . The diagnosis of the disease is challenging due to the natural course of infection and therefore molecular tools such as q... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"tropical",
"diseases",
"microbiology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoan",
"life",
"cycles",
"organisms",
"developmental",
"biology",
"trypomastigotes",
"protozoans",
"neglected",
"tropical",
"diseases",... | 2018 | Evaluation of the analytical and diagnostic performance of a digital droplet polymerase chain reaction (ddPCR) assay to detect Trypanosoma cruzi DNA in blood samples |
Anatomically based procedures to ablate atrial fibrillation ( AF ) are often successful in terminating paroxysmal AF . However , the ability to terminate persistent AF remains disappointing . New mechanistic approaches use multiple-electrode basket catheter mapping to localize and target AF drivers in the form of rotor... | In computer simulations we determined the accuracy of using multiple-electrode basket catheters to detect atrial fibrillation sources ( rotors ) during an ablation procedure . We used a realistic 3D atrial model and a virtual multiple-electrode basket catheter placed in three different positions inside the right atrium... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results"
] | [
"biotechnology",
"medicine",
"and",
"health",
"sciences",
"engineering",
"and",
"technology",
"cardiovascular",
"anatomy",
"catheters",
"membrane",
"potential",
"electrophysiology",
"endocardium",
"veins",
"interpolation",
"mathematics",
"cardiology",
"cardiac",
"atria",
"a... | 2018 | Factors affecting basket catheter detection of real and phantom rotors in the atria: A computational study |
Legionella pneumophila , the etiological agent of Legionnaires’ disease , replicates intracellularly in protozoan and human hosts . Successful colonization and replication of this pathogen in host cells requires the Dot/Icm type IVB secretion system , which translocates approximately 300 effector proteins into the host... | Actin is a core component of the actin cytoskeleton , which plays a crucial role in diverse cellular processes including cell migration , cytokinesis , endocytosis and vesicle trafficking . Therefore , it is not surprising that many pathogens target actin and/or proteins involved in the regulation of actin activity for... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"intracellular",
"pathogens",
"viral",
"transmission",
"and",
"infection",
"molecular",
"probe",
"techniques",
"pathogens",
"cell",
"processes",
"microbiology",
"immunoblotting",
"fungi... | 2017 | A Legionella Effector Disrupts Host Cytoskeletal Structure by Cleaving Actin |
Biomphalaria glabrata snails that display either resistant or susceptible phenotypes to the parasitic trematode , Schistosoma mansoni provide an invaluable resource towards elucidating the molecular basis of the snail-host/schistosome relationship . Previously , we showed that induction of stress genes either after hea... | Biomphalaria glabrata snails that are either resistant or susceptible to the parasite , Schistosoma mansoni , have been an invaluable resource in studies aimed at understanding the molecular basis of the snail/schistosome interaction . Schistosomes cause the chronic debilitating disease schistosomiasis . Thus , it is h... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"systems",
"biology",
"genetics",
"immunology",
"biology",
"zoology",
"genetics",
"and",
"genomics"
] | 2012 | Reversing the Resistance Phenotype of the Biomphalaria glabrata Snail Host Schistosoma mansoni Infection by Temperature Modulation |
Early studies have shown that moderate levels of calcium overload can cause lower oxidative phosphorylation rates . However , the mechanistic interpretations of these findings were inadequate . And while the effect of excessive calcium overload on mitochondrial function is well appreciated , there has been little to no... | Mitochondrial calcium handling has been studied for nearly half a century . As we understand it today , low concentrations ( 1–10 nmol/mg mitochondria ) of calcium exert beneficial effects on energy transduction . And high concentrations ( >500 nmol/mg mitochondria ) lead to respiratory uncoupling and membrane damage .... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"protons",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"phosphates",
"metabolic",
"processes",
"membrane",
"potential",
"permeability",
"electrophysiology",
"simulation",
"and",
"modeling",
"oxidative",
"phosphorylation",
"materials",
"science",
"mitoc... | 2019 | Calcium phosphate precipitation inhibits mitochondrial energy metabolism |
Hendra and Nipah viruses ( genus Henipavirus , family Paramyxoviridae ) are highly pathogenic bat-borne viruses . The need for high biocontainment when studying henipaviruses has hindered the development of therapeutics and knowledge of the viral infection cycle . We have performed a genome-wide siRNA screen at biosafe... | The henipaviruses Hendra and Nipah are bat-borne paramyxoviruses that are highly pathogenic in humans . The need for high biocontainment when studying Hendra and Nipah virus biology has hindered the development of therapeutics and knowledge of the viral infection cycle . This study describes a genome-wide functional ge... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"transfection",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"respiratory",
"infections",
"hela",
"cells",
"gene",
"regulation",
"henipavirus",
"pathogens",
"biological",
"cultures",
"microbiology",
"pulmonology",
"viruses",
"rna"... | 2016 | Genome-wide siRNA Screening at Biosafety Level 4 Reveals a Crucial Role for Fibrillarin in Henipavirus Infection |
Expression of ABO and Lewis histo-blood group antigens by the gastrointestinal epithelium is governed by an α-1 , 2-fucosyltransferase enzyme encoded by the Fut2 gene . Alterations in mucin glycosylation have been associated with susceptibility to various bacterial and viral infections . Salmonella enterica serovar Typ... | The intestinal epithelium is a crucial biological interface , interacting with both commensal and pathogenic microorganisms . It’s lined with heavily glycosylated proteins and glycolipids which can act as both attachment sites and energy sources for intestinal bacteria . Fut2 , the enzyme governing epithelial α1 , 2-fu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"pili",
"and",
"fimbriae",
"salmonellosis",
"epithelial",
"cells",
"bacterial",
"diseases",
"signs",
"and",
"symptoms",
"enterobacteriaceae",
... | 2019 | Std fimbriae-fucose interaction increases Salmonella-induced intestinal inflammation and prolongs colonization |
A spatially-explicit , stochastic model is developed for Bahia bark scaling , a threat to citrus production in north-eastern Brazil , and is used to assess epidemiological principles underlying the cost-effectiveness of disease control strategies . The model is fitted via Markov chain Monte Carlo with data augmentation... | We consider how mathematical models can be used to inform the control of plant disease , even when the identity and biology of the pathogen are not well understood . This is often the case: control of emerging epidemics is most likely to have a significant effect when epidemics remain small , but little may then be kno... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"population",
"modeling",
"biology",
"and",
"life",
"sciences",
"population",
"biology",
"infectious",
"disease",
"modeling",
"computational",
"biology",
"infectious",
"disease",
"control"
] | 2014 | Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus |
Dissection of the genetic architecture of complex traits persists as a major challenge in biology; despite considerable efforts , much remains unclear including the role and importance of genetic interactions . This study provides empirical evidence for a strong and persistent contribution of both second- and third-ord... | This study provides evidence for a strong and persistent contribution of epistatic interactions to the selection response in two chicken lines subjected to 50 generations of divergent selection for 8-week body weight . We show that the genetic architecture of the trait involves genetic interactions of both second- and ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"genetics",
"genetic",
"networks",
"genome",
"evolution",
"genome",
"scans",
"chicken",
"statistics",
"quantitative",
"traits",
"epistasis",
"animal",
"models",
"genome",
"analysis",
"tools",
"model",
"organisms",
"mathematics",
"trait",
"locus",
"analysis",
... | 2011 | Replication and Explorations of High-Order Epistasis Using a Large Advanced Intercross Line Pedigree |
Frataxin ( Yfh1 in yeast ) is a conserved protein and deficiency leads to the neurodegenerative disease Friedreich’s ataxia . Frataxin is a critical protein for Fe-S cluster assembly in mitochondria , interacting with other components of the Fe-S cluster machinery , including cysteine desulfurase Nfs1 , Isd11 and the I... | Frataxin was discovered because mutations in the corresponding gene cause the neurodegenerative disease Friedreich’s ataxia . The finding that frataxin protein physically associates with scaffold proteins Isu1/IscU places it squarely in the pathway of Fe-S cluster assembly . Fe-S clusters are essential cofactors for ma... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Turning Saccharomyces cerevisiae into a Frataxin-Independent Organism |
Gamma-herpesviruses persist in lymphocytes and cause disease by driving their proliferation . Lymphocyte infection is therefore a key pathogenetic event . Murid Herpesvirus-4 ( MuHV-4 ) is a rhadinovirus that like the related Kaposi's Sarcoma-associated Herpesvirus persists in B cells in vivo yet infects them poorly in... | Rhadinoviruses cause lymphocytic cancers . Their infection of lymphocytes is therefore an important therapeutic target . How this occurs is unclear . One prevalent hypothesis has been that virions directly infect lymphocytes when they enter new hosts . Here we show that host entry by Murid Herpesvirus-4 , a close relat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"of",
"infection",
"viral",
"entry",
"host",
"cells",
"viral",
"persistence",
"and",
"latency",
"viral",
"transmission",
"and",
"infection",
"virology",
"biology",
"microbiology",
"host-pathogen",
"interaction"
] | 2012 | Myeloid Infection Links Epithelial and B Cell Tropisms of Murid Herpesvirus-4 |
The dopamine D2 and D3 receptors ( D2R and D3R ) are important targets for antipsychotics and for the treatment of drug abuse . SB269652 , a bitopic ligand that simultaneously binds both the orthosteric binding site ( OBS ) and a secondary binding pocket ( SBP ) in both D2R and D3R , was found to be a negative alloster... | G protein-coupled receptors ( GPCRs ) are targets of more than 25% of prescription drugs on the market . Due to their critical roles in human physiology , competitive modulation of these receptors has been found to be associated with many undesired side effects . Allosteric modulation holds the promise of retaining nor... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"chemical",
"characterization",
"crystal",
"structure",
"chemical",
"compounds",
"markov",
"models",
"molecular",
"dynamics",
"condensed",
"matter",
"physics",
"neuroscience",
"organic",
"compounds",
"hormones",
"... | 2018 | The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors |
Many individuals tested for inherited cancer susceptibility at the BRCA1 gene locus are discovered to have variants of unknown clinical significance ( UCVs ) . Most UCVs cause a single amino acid residue ( missense ) change in the BRCA1 protein . They can be biochemically assayed , but such evaluations are time-consumi... | A significant number of breast and ovarian cancers are due to inherited mutations in the BRCA1 and BRCA2 genes . Many women who receive genetic testing for these mutations are found to have variants of the genes that result in changed amino acids in the BRCA1 or BRCA2 proteins . The effect of these variants on cancer r... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Supporting",
"Information"
] | [
"oncology",
"in",
"vitro",
"homo",
"(human)",
"computational",
"biology"
] | 2007 | Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning |
The characterization of protein interactions is essential for understanding biological systems . While genome-scale methods are available for identifying interacting proteins , they do not pinpoint the interacting motifs ( e . g . , a domain , sequence segments , a binding site , or a set of residues ) . Here , we deve... | Recent advances in experimental methods have produced a deluge of protein–protein interactions data . However , these methods do not supply information on which specific protein regions are physically in contact during the interactions . Identifying these regions ( interfaces ) is fundamental for scientific disciplines... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"saccharomyces",
"computational",
"biology"
] | 2007 | Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions |
We exploit flow propagation on the directed neuronal network of the nematode C . elegans to reveal dynamically relevant features of its connectome . We find flow-based groupings of neurons at different levels of granularity , which we relate to functional and anatomical constituents of its nervous system . A systematic... | One of the goals of systems neuroscience is to elucidate the relationship between the structure of neuronal networks and the functional dynamics that they implement . An ideal model organism to study such interactions is the roundworm C . elegans , which not only has a fully mapped connectome , but has also been the ob... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infographics",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"nervous",
"system",
"caenorhabditis",
"electrophysiology",
"neuroscience",
"animals",
"motor",
"neurons",
"animal",
"models",
"caenorhabditis",
"elegans",
"model",
"organisms",
... | 2016 | Flow-Based Network Analysis of the Caenorhabditis elegans Connectome |
Overexpression or mutation of α-Synuclein is associated with protein aggregation and interferes with a number of cellular processes , including mitochondrial integrity and function . We used a whole-genome screen in the fruit fly Drosophila melanogaster to search for novel genetic modifiers of human [A53T]α-Synuclein–i... | Parkinson's disease ( PD ) is a progressive neurodegenerative disorder , pathologically characterized by loss of dopaminergic neurons in the substantia nigra pars compacta brain region . Mutations in α-Synuclein or gene duplication or triplication result in autosomal-dominant inherited PD . Indeed , aggregated and inso... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"animal",
"models",
"model",
"organisms",
"genetics",
"biology",
"neuroscience",
"genetics",
"and",
"genomics"
] | 2012 | The Mitochondrial Chaperone Protein TRAP1 Mitigates α-Synuclein Toxicity |
While circadian dysfunction and neurodegeneration are correlated , the mechanism for this is not understood . It is not known if age-dependent circadian dysfunction leads to neurodegeneration or vice-versa , and the proteins that mediate the effect remain unidentified . Here , we show that the knock-down of a regulator... | Alzheimer’s disease is the most common cause of dementia in the aging population . It is a progressive neurodegenerative disorder that attacks the brain neurons , resulting in loss of memory , thinking and behavioral changes . One pathological hallmark is aggregation of the microtubule-associated protein Tau . A growin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Drosophila Spaghetti and Doubletime Link the Circadian Clock and Light to Caspases, Apoptosis and Tauopathy |
Pilocytic astrocytoma ( PA ) is the most common brain tumor in children . This tumor is usually benign and has a good prognosis . Total resection is the treatment of choice and will cure the majority of patients . However , often only partial resection is possible due to the location of the tumor . In that case , spont... | The most common brain tumor in children and young adults is pilocytic astrocytoma ( PA ) . This tumor is usually benign and often follows an indolent course . The treatment of choice is resection and the prognosis is very favorable if total excision can be achieved . However , due to the location of the tumor , only pa... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Model-Based Evaluation of Spontaneous Tumor Regression in Pilocytic Astrocytoma |
In bacteria , transformation and restriction-modification ( R-M ) systems play potentially antagonistic roles . While the former , proposed as a form of sexuality , relies on internalized foreign DNA to create genetic diversity , the latter degrade foreign DNA to protect from bacteriophage attack . The human pathogen S... | Natural genetic transformation can compensate for the absence of sexual reproduction in bacteria , allowing genetic diversification by recombination . It proceeds through the internalization of single stranded ( ss ) DNA fragments created from an exogenous double stranded ( ds ) DNA substrate , which are incorporated i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology"
] | 2013 | Programmed Protection of Foreign DNA from Restriction Allows Pathogenicity Island Exchange during Pneumococcal Transformation |
Here we investigated the role of the Nod/Rip2 pathway in host responses to Chlamydophila pneumoniae–induced pneumonia in mice . Rip2−/− mice infected with C . pneumoniae exhibited impaired iNOS expression and NO production , and delayed neutrophil recruitment to the lungs . Levels of IL-6 and IFN-γ levels as well as KC... | Chlamydophila pneumoniae ( C . pneumoniae ) is a common intracellular parasite that causes lung infections and contributes to several diseases characterized by chronic inflammation . Toll-like receptors expressed on the cell surface detect C . pneumoniae and mount a vigorous defense , but it is not known how the cell d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"microbiology/immunity",
"to",
"infections",
"microbiology/innate",
"immunity",
"immunology/innate",
"immunity",
"pathology/immunology",
"infectious",
"diseases/respiratory",
"infections",
"infectious",
"diseases/bacterial... | 2009 | The NOD/RIP2 Pathway Is Essential for Host Defenses Against Chlamydophila pneumoniae Lung Infection |
Changes in the spatial positioning of genes within the mammalian nucleus have been associated with transcriptional differences and thus have been hypothesized as a mode of regulation . In particular , the localization of genes to the nuclear and nucleolar peripheries is associated with transcriptional repression . Howe... | Eukaryotic genomes are compartmentalized within nuclei such that physiological events , including transcription and DNA replication , can efficiently occur . The mechanisms that regulate this organization represent an exciting , and equally enigmatic , subject of research . In mammals , the identification of elements t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"cell",
"biology",
"cell",
"biology",
"chromosome",
"biology",
"gene",
"expression",
"genetics",
"epigenetics",
"biology",
"molecular",
"genetics",
"genetics",
"and",
"genomics"
] | 2012 | Nucleolar Association and Transcriptional Inhibition through 5S rDNA in Mammals |
Dengue virus ( DENV ) transmission is spatially heterogeneous . Hence , to stratify dengue prevalence in space may be an efficacious strategy to target surveillance and control efforts in a cost-effective manner particularly in Venezuela where dengue is hyperendemic and public health resources are scarce . Here , we de... | Dengue is a mosquito-borne viral disease of global impact . In Venezuela , dengue is endemic with the co-circulation of the 4 viral serotypes and has become one of the most important public health problems of urban areas . During 2010 and 2011 , a baseline cross-sectional study was carried out as part of a dengue prosp... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"water",
"resources",
"venezuela",
"geographical",
"locations",
"vector-borne",
"diseases",
"animals",
"geoinformatics",
"infectious",
"disease",
"control",
"insect",
... | 2017 | Spatial Analysis of Dengue Seroprevalence and Modeling of Transmission Risk Factors in a Dengue Hyperendemic City of Venezuela |
A major challenge of eco-epidemiology is to determine which factors promote the transmission of infectious diseases and to establish risk maps that can be used by public health authorities . The geographic predictions resulting from ecological niche modelling have been widely used for modelling the future dispersion of... | Cutaneous leishmaniasis is a vector-borne zoonotic disease with a complex transmission cycle that includes many parasite , vector and host species . This disease continues to pose public health problems worldwide despite the measures put in place . In recent years , methodological tools commonly used in ecology , calle... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"forest",
"ecology",
"tropical",
"diseases",
"vertebrates",
"parasitic",
"diseases",
"animals",
"mammals",
"neglected",
"tropical",
"diseases",
"population",
"biology",
"ecological",
... | 2019 | Ecological niche modelling for predicting the risk of cutaneous leishmaniasis in the Neotropical moist forest biome |
Cells in the wing blade of Drosophila melanogaster exhibit an in-plane polarization causing distal orientation of hairs . Establishment of the Planar Cell Polarity ( PCP ) involves intercellular interactions as well as a global orienting signal . Many of the genetic and molecular components underlying this process have... | Epithelial tissues are often polarized in a preferred direction which determines , for example , the direction of hair growth on mammalian skin , the orientation of scales in fish , the alignment of ommatidia in the fly eye and of sensory hair cells in the vertebrate cochlea . This in-plane polarization , known as plan... | [
"Abstract",
"Introduction",
"Results"
] | [
"physics",
"developmental",
"biology/morphogenesis",
"and",
"cell",
"biology",
"cell",
"biology/morphogenesis",
"and",
"cell",
"biology",
"biophysics/theory",
"and",
"simulation",
"cell",
"biology/developmental",
"molecular",
"mechanisms",
"computational",
"biology/systems",
... | 2009 | Order and Stochastic Dynamics in Drosophila Planar Cell Polarity |
Homeotic genes code for key transcription factors ( HOX-TFs ) that pattern the animal body plan . During embryonic development , Hox genes are expressed in overlapping patterns and function in a partially redundant manner . In vitro biochemical screens probing the HOX-TF sequence specificity revealed largely overlappin... | Hox genes encode transcription factors that determine the vertebrate body plan and pattern structures and organs in the developing embryo . Despite decades of effort and research on Hox genes , little is known about the HOX-DNA binding properties in vivo . This lack of knowledge is mainly due to the absence of appropri... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Bioinformatic",
"Analyses"
] | [
"livestock",
"chemical",
"characterization",
"gene",
"regulation",
"regulatory",
"proteins",
"enzymology",
"vertebrates",
"dna-binding",
"proteins",
"animals",
"transcription",
"factors",
"sequence",
"motif",
"analysis",
"enzyme",
"chemistry",
"research",
"and",
"analysis",... | 2017 | Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF |
Telomere shortening is associated with aging and age-associated diseases . Additionally , telomere dysfunction resulting from telomerase gene mutation can lead to premature aging , such as apparent skin atrophy and hair loss . However , the molecular signaling linking telomere dysfunction to skin atrophy remains elusiv... | Patients with mutations in the telomerase component ( eg , Dyskerin , TERT , TERC ) are frequently accompanied by symptoms of abnormal epidermis , such as hyperpigmentation , premature skin degradation , hair follicle shedding , skin atrophy , and dry skin . Mice with mutations in telomere-associated proteins or telome... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"skin",
"medicine",
"and",
"health",
"sciences",
"integumentary",
"system",
"chromosome",
"structure",
"and",
"function",
"cell",
"differentiation",
"telomeres",
"developmental",
"biology",
"stem",
"cells",
"epidermis",
"epigenetics",
"dna",
"chromatin",
"dna",
"methyla... | 2019 | Telomere dysfunction impairs epidermal stem cell specification and differentiation by disrupting BMP/pSmad/P63 signaling |
Systematic , genome-wide RNA interference ( RNAi ) analysis is a powerful approach to identify gene functions that support or modulate selected biological processes . An emerging challenge shared with some other genome-wide approaches is that independent RNAi studies often show limited agreement in their lists of impli... | Genome-wide RNA interference assays of gene functions offer the potential for systematic , global analysis of biological processes . A pressing challenge is to develop meta-analysis methods that effectively combine information from multiple studies . One puzzle is that implicated gene lists from independent studies of ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors |
Zoonotic visceral leishmaniasis ( VL ) is a severe infectious disease caused by protozoan parasites of the genus Leishmania and the domestic dogs are the main urban parasite reservoir hosts . In Brazil , indirect fluorescence antibody tests ( IFAT ) and indirect enzyme linked immunosorbent assay ( ELISA ) using promast... | Visceral leishmaniasis is endemic in many areas of tropical and subtropical America where it constitutes a significant public health problem . It is usually diagnosed by enzyme-linked immunosorbent assays ( ELISA ) using crude Leishmania antigens , but a variety of other immunological methods may also be applied . Alth... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"biology",
"veterinary",
"science"
] | 2012 | Improved Canine and Human Visceral Leishmaniasis Immunodiagnosis Using Combinations of Synthetic Peptides in Enzyme-Linked Immunosorbent Assay |
Listeria monocytogenes is an opportunistic Gram-positive bacterial pathogen responsible for listeriosis , a human foodborne disease . Its cell wall is densely decorated with wall teichoic acids ( WTAs ) , a class of anionic glycopolymers that play key roles in bacterial physiology , including protection against the act... | Listeria monocytogenes is a foodborne bacterial pathogen that preferentially infects immunocompromised hosts , eliciting a severe and often lethal disease . In humans , clinical manifestations range from asymptomatic intestinal carriage and gastroenteritis to harsher systemic states of the disease such as sepsis , meni... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | L-Rhamnosylation of Listeria monocytogenes Wall Teichoic Acids Promotes Resistance to Antimicrobial Peptides by Delaying Interaction with the Membrane |
Insulin is a major regulator of metabolism in metazoans , including the fruit fly Drosophila melanogaster . Genome-wide association studies ( GWAS ) suggest a genetic basis for reductions of both insulin sensitivity and insulin secretion , phenotypes commonly observed in humans with type 2 diabetes mellitus ( T2DM ) . ... | Genome-wide association studies in patients with type 2 diabetes mellitus have identified more than 65 loci , encoding up to 500 candidate susceptibility genes . Thus , investigators are fundamentally challenged to ( i ) screen and identify relevant candidates in vivo , ( ii ) determine if loss- or gain-of-function und... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"of",
"disease",
"genetics",
"biology",
"and",
"life",
"sciences"
] | 2014 | A Genetic Strategy to Measure Circulating Drosophila Insulin Reveals Genes Regulating Insulin Production and Secretion |
The modular organization of networks of individual neurons interwoven through synapses has not been fully explored due to the incredible complexity of the connectivity architecture . Here we use the modularity-based community detection method for directed , weighted networks to examine hierarchically organized modules ... | Caenorhabditis elegans ( C . elegans ) is a tiny worm whose neuronal network is fully revealed . Since the modular organization in a network of individual neurons interwoven through synapses is not yet fully explored owing to incredibly complex connectivity architecture , this study is designed to investigate hierarchi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"neuroscience/behavioral",
"neuroscience"
] | 2011 | Topological Cluster Analysis Reveals the Systemic Organization of the Caenorhabditis elegans Connectome |
Using a DNA polymerase to record intracellular calcium levels has been proposed as a novel neural recording technique , promising massive-scale , single-cell resolution monitoring of large portions of the brain . This technique relies on local storage of neural activity in strands of DNA , followed by offline analysis ... | This work demonstrates a necessary computational tool for the development and implementation of molecular recorders , a promising potential technique for massive-scale neuroscience . Molecular recorders use proteins to encode levels of a substance we want to measure ( e . g . calcium in neural applications ) as detecta... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular",
"neuroscience",
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"applied",
"mathematics",
"membrane",
"potential",
"experimental",
"design",
"electrophysiology",
"neuroscience",
"simulation",
"and",
"modeling",
"algorithms",
"research",
"design... | 2017 | Nucleotide-time alignment for molecular recorders |
Pseudomonas aeruginosa ( P . aeruginosa ) is a major opportunistic human pathogen , causing serious nosocomial infections among immunocompromised patients by multi-determinant virulence and high antibiotic resistance . The CzcR-CzcS signal transduction system in P . aeruginosa is primarily involved in metal detoxificat... | P . aeruginosa inhabits diverse environments and is one of the most prevalent opportunistic human pathogens of immunocompromised patients . The high antibiotic resistance is a major cause of therapeutic failure in the treatment of P . aeruginosa infections . The opportunistic pathogen P . aeruginosa co-regulates cross-... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"antimicrobials",
"dimers",
"(chemical",
"physics)",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"pathogens",
"drugs",
"microbiology",
"organic",
"compounds",
"toxicology",
"pseudomonas",
"aeruginosa",
"a... | 2017 | Structural basis of Zn(II) induced metal detoxification and antibiotic resistance by histidine kinase CzcS in Pseudomonas aeruginosa |
In motor tasks with redundancy neuromotor noise can lead to variations in execution while achieving relative invariance in the result . The present study examined whether humans find solutions that are tolerant to intrinsic noise . Using a throwing task in a virtual set-up where an infinite set of angle and velocity co... | It is widely recognized that variability or noise is present at all levels of the sensorimotor system . How the central nervous system generates functional behavior with a sufficient degree of accuracy in the face of this noise remains an open question . This is specifically relevant when the motor task is redundant , ... | [
"Abstract",
"Introduction",
"Methods",
"Discussion"
] | [
"medicine",
"social",
"and",
"behavioral",
"sciences",
"biology",
"engineering"
] | 2011 | Neuromotor Noise, Error Tolerance and Velocity-Dependent Costs in Skilled Performance |
Leptospirosis is an important re-emerging infectious disease that affects humans worldwide . Infection occurs from indirect environment-mediated exposure to pathogenic leptospires through contaminated watered environments . The ability of pathogenic leptospires to persist in the aqueous environment is a key factor in t... | Leptospirosis is an emerging zoonotic disease caused by infection with pathogenic strains of Leptospira . Most human infections arise from environmental exposure to contaminated freshwater environments or watered soils where pathogenic Leptospira are considered as able to survive for prolonged periods . Therefore , a g... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"surface",
"water",
"leptospira",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"tropical",
"diseases",
"microbiology",
"bacterial",
"diseases",
"neglected",
"tropical",
"diseases",
"bacteria",
"bacterial",
"pathogens"... | 2017 | Seeking the environmental source of Leptospirosis reveals durable bacterial viability in river soils |
Molecular mechanisms for the establishment of transcriptional memory are poorly understood . 5 , 6-dichloro-1-D-ribofuranosyl-benzimidazole ( DRB ) is a P-TEFb kinase inhibitor that artificially induces the poised RNA polymerase II ( RNAPII ) , thereby manifesting intermediate steps for the establishment of transcripti... | Transcriptional mechanisms in eukaryotes are composed of numerous consecutive steps , including chromatin modification and remodeling . Recent reports using yeast genetics have revealed that Lys36 methylation of histone H3 , a hallmark of the active gene , is a consequence of transcriptional elongation . Similarly , a ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Ash1l Methylates Lys36 of Histone H3 Independently of Transcriptional Elongation to Counteract Polycomb Silencing |
The intestine is a common site for invasion by intracellular pathogens , but little is known about how pathogens restructure and exit intestinal cells in vivo . The natural microsporidian parasite N . parisii invades intestinal cells of the nematode C . elegans , progresses through its life cycle , and then exits cells... | The intestine is a common site for invasion by pathogens , but little is known about how pathogens exit out of live intestinal cells in order to spread and propagate . One group of parasites that often invades the intestine is the microsporidia , which comprise a phylum of over 1200 fungal-like species that can cause d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"microbiology",
"host-pathogen",
"interaction"
] | 2011 | Non-Lytic, Actin-Based Exit of Intracellular Parasites from C. elegans Intestinal Cells |
Transposable elements ( TEs ) have been active in the mammalian genome for millions of years and the silencing of these elements in the germline is important for the survival of the host . Mice carrying reporter transgenes can be used to model transcriptional silencing . A mutagenesis screen for modifiers of epigenetic... | Almost half of the genomes of humans and mice are made up of transposable elements . During host evolution , subsets of these elements have periods of transpositional activity during which they spread throughout the genome . This is dependent on the transcriptional activity of these elements in the cells that contribut... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome |
Quorum sensing ( QS ) is a mechanism of chemical communication that bacteria use to monitor cell-population density and coordinate group behaviors . QS relies on the production , detection , and group-wide response to extracellular signal molecules called autoinducers . Vibrio cholerae employs parallel QS circuits that... | Bacteria communicate , count their numbers , and act as collectives using a process called quorum sensing . Quorum sensing relies on the production , release and group-wide detection of small molecules called autoinducers . Curiously , quorum-sensing bacteria often employ multiple autoinducers that funnel information i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"enzymes",
"pathogens",
"vibrio",
"gene",
"regulation",
"regulatory",
"proteins",
"microbiology",
"enzymology",
"dna-binding",
"proteins",
"operons",
"electromagnetic",... | 2017 | Asymmetric regulation of quorum-sensing receptors drives autoinducer-specific gene expression programs in Vibrio cholerae |
Stochastic expression of genes produces heterogeneity in clonal populations of bacteria under identical conditions . We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions . Ou... | Expressing genes in a bacterial cell is noisy and random . A colony of bacteria grown from a single cell can show remarkable differences in the copy number per cell of a given protein after only a few generations . In this work we use computer simulations to study the variation in how individual cells in a population e... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"physics",
"cellular",
"structures",
"stochastic",
"processes",
"mathematics",
"theoretical",
"biology",
"cell",
"biology",
"chemical",
"physics",
"gene",
"expression",
"biology",
"computational",
"biology",
"molecular",
"cell",
"biology",
"biophysics",
"molecular",
"biol... | 2011 | Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study |
Sphingolipids , lipids with a common sphingoid base ( also termed long chain base ) backbone , play essential cellular structural and signaling functions . Alterations of sphingolipid levels have been implicated in many diseases , including neurodegenerative disorders . However , it remains largely unclear whether sphi... | Lipids play many essential cellular roles as structural components of biological membranes or signaling molecules . Alterations of lipids have been observed in the brains of patients with neurodegenerative diseases . However , whether these changes can cause neurodegeneration or otherwise influence the pathology of the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"lipids",
"animal",
"genetics",
"sphingolipids",
"genetics",
"biology",
"neuroscience",
"genetics",
"and",
"genomics"
] | 2011 | A Deficiency of Ceramide Biosynthesis Causes Cerebellar Purkinje Cell Neurodegeneration and Lipofuscin Accumulation |
Low- and middle-income countries are facing a dual disease burden with infectious diseases ( e . g . , gastrointestinal tract infections ) and non-communicable diseases ( e . g . , diabetes ) being common . For instance , chronic parasite infections lead to altered immune regulatory networks , anemia , malnutrition , a... | Parasitic worms ( e . g . , pinworm , roundworm , and whipworm ) , intestinal protozoa ( e . g . , Cryptosporidium parvum and Giardia intestinalis ) , and the bacterium Helicobacter pylori persist at high rates in the gastrointestinal tract of people from low- and middle-income countries . These infectious agents are i... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"education",
"pathogens",
"sociology",
"microbiology",
"social",
"sciences",
"parasitic",
"diseases",
"nematode",
"infections",
"diabetes",
"mellitus",
"hba1c",
"endocrine",
"disorders"... | 2018 | Association between gastrointestinal tract infections and glycated hemoglobin in school children of poor neighborhoods in Port Elizabeth, South Africa |
Chandipura virus ( CHAV ) , a member of the vesiculovirus genus , is an emerging human pathogen . As for other rhabdoviruses , CHAV entry into susceptible cells is mediated by its single envelope glycoprotein G which is both involved in receptor recognition and fusion of viral and cellular membranes . Here , we have ch... | Chandipura virus ( CHAV , belonging to vesiculovirus genus ) , is an emerging pathogen associated with deadly encephalitis , principally among children , in India . CHAV single envelope glycoprotein G is involved in two successive steps of virus entry: receptor recognition that allows endocytosis of the virion and fusi... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Structure of the Low pH Conformation of Chandipura Virus G Reveals Important Features in the Evolution of the Vesiculovirus Glycoprotein |
Cytomegaloviruses ( CMV ) are highly species-specific due to millennia of co-evolution and adaptation to their host , with no successful experimental cross-species infection in primates reported to date . Accordingly , full genome phylogenetic analysis of multiple new CMV field isolates derived from two closely related... | Nonhuman primates are excellent models of HCMV infection and immunity , and their CMVs closely resemble HCMV in genomic organization and coding potential . Here , we expand the existing models by isolating new full-length , non-human primate CMV strains that more closely resemble primary HCMV isolates . In addition , w... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"body",
"fluids",
"immunology",
"vertebrates",
"animals",
"fibroblasts",
"mammals",
"primates",
"urine",
"connective",
"tissue",
"cells",
"genome",
"analysis",
"cytotoxic",
"t",
"cells",
"... | 2016 | Cross-Species Rhesus Cytomegalovirus Infection of Cynomolgus Macaques |
Anti-TNF agents have been in the first line of treatment of various inflammatory diseases such as Rheumatoid Arthritis and Crohn’s Disease , with a number of different biologics being currently in use . A detailed analysis of their effect at transcriptome level has nevertheless been lacking . We herein present a concis... | A number of anti-TNF drugs are being used in the treatment of inflammatory autoimmune diseases , such as Rheumatoid Arthritis and Crohn’s Disease . Despite their wide use there has been , to date , no detailed analysis of their effect on the affected tissues at a transcriptome level . In this work we applied four diffe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [] | 2019 | An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis |
Pathogens have evolved sophisticated mechanisms to evade detection and destruction by the host immune system . Large DNA viruses encode homologues of chemokines and their receptors , as well as chemokine-binding proteins ( CKBPs ) to modulate the chemokine network in host response . The SECRET domain ( smallpox virus-e... | Chemokines are a family of small proteins that help the immune system fight against invading pathogens by inducing the white blood cells to the areas of infection and inflammation . Due to the important roles of chemokines in immune response , the pathogens evolve diverse mechanisms to neutralize their activities . One... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry",
"viral",
"immune",
"evasion",
"proteins",
"virology",
"protein",
"structure",
"biology",
"microbiology"
] | 2011 | Structural Basis of Chemokine Sequestration by CrmD, a Poxvirus-Encoded Tumor Necrosis Factor Receptor |
The budding yeast spindle pole body ( SPB ) is anchored in the nuclear envelope so that it can simultaneously nucleate both nuclear and cytoplasmic microtubules . During SPB duplication , the newly formed SPB is inserted into the nuclear membrane . The mechanism of SPB insertion is poorly understood but likely involves... | Accurate segregation of chromosomes during mitosis is essential to prevent genetic instability and aneuploidy that lead to cancer and other diseases . Centrosomes and spindle pole bodies mediate the assembly of a microtubule-based structure known as the mitotic spindle , which physically separates chromosomes during mi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology",
"chemical",
"biology",
"mitosis",
"histology",
"model",
"organisms",
"cell",
"growth",
"molecular",
"genetics",
"chromosome",
"biology",
"membranes",
"and",
"sorting",
"chemistry",
"biology",
"cell",
"biology",
"genetic",
"screens",
"genetics",
"yeast",
... | 2011 | The SUN Protein Mps3 Is Required for Spindle Pole Body Insertion into the Nuclear Membrane and Nuclear Envelope Homeostasis |
In insects , products of the male reproductive tract are essential for initiating and maintaining the female post-mating response ( PMR ) . The PMR includes changes in egg laying , receptivity to courting males , and sperm storage . In Drosophila , previous studies have determined that the main cells of the male access... | Similar to the prostate gland and seminal vesicle in mammals , the Drosophila male accessory gland produces seminal fluid proteins that are critical for individual male reproductive success . In Drosophila , many of these proteins function to induce a suite of long-lasting physiological changes in mated females , like ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"genetic",
"mutation",
"fertilization",
"gene",
"expression",
"genetics",
"molecular",
"genetics",
"biology",
"pattern",
"formation",
"genetics",
"and",
"genomics",
"cell",
"differentiation",
"evolutionary",
"developmental",
"biology",
"gene",
... | 2013 | A Novel Function for the Hox Gene Abd-B in the Male Accessory Gland Regulates the Long-Term Female Post-Mating Response in Drosophila |
The phosphorylation of a substrate at multiple sites is a common protein modification that can give rise to important structural and electrostatic changes . Scaffold proteins can enhance protein phosphorylation by facilitating an interaction between a protein kinase enzyme and its target substrate . In this work we con... | The modification of a protein at multiple sites can result in a number of interesting behaviors at the cellular level , such as all-or-none responses to an external input , or two different stable cellular states in otherwise identical environments . Such behaviors can aid in many different forms of cellular decision-m... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"mathematics",
"biology",
"computational",
"biology",
"nonlinear",
"dynamics",
"genetics",
"and",
"genomics"
] | 2012 | Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems |
Several important human pathogens are represented in the Corynebacterineae suborder , including Mycobacterium tuberculosis and Corynebacterium diphtheriae . These bacteria are surrounded by a multilayered cell envelope composed of a cytoplasmic membrane , a peptidoglycan ( PG ) cell wall , a second polysaccharide layer... | The pathways involved in bacterial surface assembly are critical for cell morphogenesis and serve as attractive targets for antibiotic development . Bacteria in the suborder Corynebacterineae , which includes important pathogens like Mycobacterium tuberculosis , possess a unique multilayered surface structure . In addi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"walls",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"light",
"microscopy",
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"genetic",
"elements",
"cellular",
"structures",
"and",
"organelles",
"bacteria",
"research",
"and",
"analysis",
"methods",
"fluore... | 2019 | Identification of new components of the RipC-FtsEX cell separation pathway of Corynebacterineae |
Hepatitis B virus ( HBV ) is a common cause of liver diseases , including chronic hepatitis , steatosis , fibrosis , cirrhosis , and hepatocellular carcinoma ( HCC ) . HBV chronically infects about 240 million people worldwide , posing a major global health problem . The current standard antiviral therapy effectively i... | Little is known about the importance of host factors in HBV infection , assembly , and release due to the lack of robust cell culture models of HBV infection and propagation . The discovery of sodium taurocholate cotransporting polypeptide ( NTCP ) as the HBV receptor has made it possible to determine the roles of cell... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
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"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"biological",
"cultures",
"immunology",
"microbiology",
"viral",
"structure",
"hepatitis",
"b",
"virus",
"viruses",
"cell",
... | 2019 | Human apolipoprotein E promotes hepatitis B virus infection and production |
Nerve cells produce electrical impulses ( “spikes” ) through the coordinated opening and closing of ion channels . Markov processes with voltage-dependent transition rates capture the stochasticity of spike generation at the cost of complex , time-consuming simulations . Schmandt and Galán introduced a novel method , b... | Discrete state , continuous time Markov processes occur throughout cell biology , neuroscience , and ecology , representing the random dynamics of processes transitioning among multiple locations or states . Complexity reduction for such models aims to capture the essential dynamics and stochastic properties via a simp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"electrophysiology",
"random",
"variables",
"neuroscience",
"covariance",
"simulation",
"and",
"modeling",
"ion",
"channels",
"mathematics",
"statistics",
"(mathematics)",
"algebra",
"research",
"and",
"analysis",
"methods",
"nicot... | 2018 | Stochastic shielding and edge importance for Markov chains with timescale separation |
3% of the population develops saccular intracranial aneurysms ( sIAs ) , a complex trait , with a sporadic and a familial form . Subarachnoid hemorrhage from sIA ( sIA-SAH ) is a devastating form of stroke . Certain rare genetic variants are enriched in the Finns , a population isolate with a small founder population a... | Genome-wide association studies ( GWAS ) have been extensively used to identify common genetic variants associated with complex diseases . As common genetic variants have explained only a small fraction of the heritability of most complex diseases , there is a growing interest in the role of how low frequency and rare ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"genome-wide",
"association",
"studies",
"stroke",
"genetics",
"biology",
"human",
"genetics",
"cardiovascular"
] | 2014 | High Risk Population Isolate Reveals Low Frequency Variants Predisposing to Intracranial Aneurysms |
Blood donor screening leads to large numbers of new diagnoses of Trypanosoma cruzi infection , with most donors in the asymptomatic chronic indeterminate form . Information on electrocardiogram ( ECG ) findings in infected blood donors is lacking and may help in counseling and recognizing those with more severe disease... | Chagas disease ( ChD ) , caused by the protozoa Trypanosoma cruzi , is endemic in most Latin America countries and may be transmitted via blood transfusions . Cardiac disease is a major feature of chronically infected patients and may be lethal . Universal blood bank screening for ChD has been established in most Latin... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"chagas",
"disease",
"neglected",
"tropical",
"diseases"
] | 2013 | Electrocardiographic Abnormalities in Trypanosoma cruzi Seropositive and Seronegative Former Blood Donors |
Aedes aegypti is a primary vector of dengue , chikungunya , Zika , and urban yellow fever viruses . Indoor , ultra low volume ( ULV ) space spraying with pyrethroid insecticides is the main approach used for Ae . aegypti emergency control in many countries . Given the widespread use of this method , the lack of large-s... | Aedes aegypti is a primary vector for medically important viruses that typically resides within houses . Indoor , ultra low volume ( ULV ) adulticide space spraying is considered to be more effective in controlling Ae . aegypti populations than outdoor spraying , and is widely used in tropical cities . Given the widesp... | [
"Abstract",
"Introduction",
"Methods",
"and",
"materials",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"animals",
"research",
"design",
"surveys",
"population",
"biology",
"infectious",
"disease",
"control",
"insect",
"vectors",
"zoology",
"research",
"and",
"analysis",
"methods",
"public",
"and",
"occupational",
... | 2018 | Efficacy of Aedes aegypti control by indoor Ultra Low Volume (ULV) insecticide spraying in Iquitos, Peru |
The association of anaemia with intestinal schistosomiasis and hookworm infections are poorly explored in populations that are not limited to children or pregnant women . We sampled 1 , 832 individuals aged 5–90 years from 30 communities in Mayuge District , Uganda . Demographic , village , and parasitological data wer... | Anaemia remains an intractable public health problem in sub-Saharan Africa ( SSA ) , owing largely to its complex and multifactorial causes . The absolute number of anaemia cases has increased by 50% in SSA from the year 1990 to 2010 . To administer the appropriate treatment , identification of anaemia attributable to ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Influence of Schistosoma mansoni and Hookworm Infection Intensities on Anaemia in Ugandan Villages |
Forward genetics screens with N-ethyl-N-nitrosourea ( ENU ) provide a powerful way to illuminate gene function and generate mouse models of human disease; however , the identification of causative mutations remains a limiting step . Current strategies depend on conventional mapping , so the propagation of affected mice... | Damaging mutations in single genes are an important source of information about the causes of disease , including more complex genetic disease; but these single gene disorders are typically rare in humans . An important strategy for identifying new disease mechanisms is to introduce multiple random mutations in mice an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"genetics",
"genetic",
"mutation",
"population",
"genetics",
"immunology",
"gene",
"function",
"animal",
"models",
"mutation",
"model",
"organisms",
"linkage",
"(genetics)",
"sequence",
"analysis",
"genetic",
"polymorphism",
"biology",
"mouse",
"genotypes",
"m... | 2013 | Unlocking the Bottleneck in Forward Genetics Using Whole-Genome Sequencing and Identity by Descent to Isolate Causative Mutations |
Primary Ciliary Dyskinesia is a heterogeneous genetic disease that is characterized by cilia dysfunction of the epithelial cells lining the respiratory tracts , resulting in recurrent respiratory tract infections . Despite lifelong physiological therapy and antibiotics , the lungs of affected patients are progressively... | This manuscript reports on a successful gene therapy attempt on human airway epithelial cells of a patient suffering from Primary Ciliary Dyskinesia . In this autosomal recessive disease , cilia of the epithelial cells that border the upper and lower respiratory tracks are not functioning . As a result , patients suffe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"respiratory",
"medicine/respiratory",
"infections",
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"and",
"genomics/gene",
"therapy",
"respiratory",
"medicine",
"genetics",
"and",
"genomics/medical",
"genetics"
] | 2009 | Ciliary Beating Recovery in Deficient Human Airway Epithelial Cells after Lentivirus Ex Vivo Gene Therapy |
Snakebites have been recognized as a neglected public health problem in several tropical and subtropical countries . Bothrops snakebites frequently complicate with acute kidney injury ( AKI ) with relevant morbidity and mortality . To date , the only treatment available for Bothrops envenomation is the intravenous admi... | Snakebites have been recognized as a neglected public health problem in several tropical and subtropical countries . Snakes from the genus Bothrops are the most common snakes found in Latin America . Bothrops snakebites frequently complicate with kidney impairment with increased risk of death . The only treatment curre... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"toxins",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"oxidative",
"stress",
"tropical",
"diseases",
"vertebrates",
"animals",
"toxic",
"agents",
"toxicology",
"reptiles",
"vasoconstriction",
"neglected",
"tro... | 2017 | Allopurinol attenuates acute kidney injury following Bothrops jararaca envenomation |
The construction of a large dendritic arbor requires robust growth and the precise delivery of membrane and protein cargoes to specific subcellular regions of the developing dendrite . How the microtubule-based vesicular trafficking and sorting systems are regulated to distribute these dendritic development factors thr... | Building a complex dendritic arbor requires tremendous cellular growth , and how membrane and protein components are transported to support a rapidly growing , polarized dendrite remains unclear . We have identified the small GTPase RAB-10 as a key regulator of this process , providing insight into both dendritic devel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | RAB-10 Regulates Dendritic Branching by Balancing Dendritic Transport |
High throughput sequencing has facilitated a precipitous drop in the cost of genomic sequencing , prompting predictions of a revolution in medicine via genetic personalization of diagnostic and therapeutic strategies . There are significant barriers to realizing this goal that are related to the difficult task of inter... | Technological advances have dramatically reduced the cost of sequencing the human genome . Tools for analyzing such data across families including annotation of clinically important variants and aggregation of variants for personalizing drug prescriptions have been developed but few are publically available . Here we d... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data |
The best measure to limit spread of contagious diseases caused by influenza A viruses ( IAVs ) is annual vaccination . The growing global demand for low-cost vaccines requires the establishment of high-yield production processes . One possible option to address this challenge is the engineering of novel vaccine produce... | Influenza viruses depend on cellular functions at every step of their life cycle and a comprehensive picture of virus-host cell interactions is the key to understand influenza disease and establish antiviral therapies . Over the past decade , this was supported by numerous screening approaches , which identified cellul... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2019 | Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth |
Membrane fusion is essential to both cellular vesicle trafficking and infection by enveloped viruses . While the fusion protein assemblies that catalyze fusion are readily identifiable , the specific activities of the proteins involved and nature of the membrane changes they induce remain unknown . Here , we use many a... | Membrane fusion is a common underlying process critical to neurotransmitter release , cellular trafficking , and infection by many viruses . Proteins have been identified that catalyze fusion , and mutations to these proteins have yielded important information on how fusion occurs . However , the precise mechanism by w... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"virology/host",
"invasion",
"and",
"cell",
"entry",
"computational",
"biology/molecular",
"dynamics",
"biophysics/theory",
"and",
"simulation",
"biophysics/membrane",
"proteins",
"and",
"energy",
"transduction"
] | 2010 | Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails |
Gene transcription mediated by RNA polymerase II ( pol-II ) is a key step in gene expression . The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression . In this work , we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time ... | Cells express proteins in response to changes in their environment so as to maintain normal function . An initial step in the expression of proteins is transcription , which is mediated by RNA polymerase II ( pol-II ) . To understand changes in transcription arising due to stimuli it is useful to model the dynamics of ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"and",
"life",
"sciences",
"computer",
"and",
"information",
"sciences"
] | 2014 | Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data |
The species of the Rickettsia genus are separated into four groups: the ancestral group , typhus group , transitional group and spotted fever group . Rickettsia parkeri , a spotted fever group Rickettsia , has been reported across the American continents as infecting several tick species and is associated with a relati... | Rickettsia is a bacterial genus that contains distinct species that are transmitted by arthropods . Many of these agents produce infection and disease in humans . The illness can range from very severe , such as Rocky Mountain spotted fever caused by Rickettsia rickettsii to mild human disease characterized by eschar f... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"bacteriology",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"ixodes",
"pathology",
"and",
"laboratory",
"medicine",
"animal",
"models",
"of",
"disease",
"pathogens",
"microbiology",
"rickettsia",
"animals",
"animal",
"models",
"model",
"organisms",
"experi... | 2019 | A biosafety level-2 dose-dependent lethal mouse model of spotted fever rickettsiosis: Rickettsia parkeri Atlantic Rainforest strain |
Many genes can play a role in multiple biological processes or molecular functions . Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular functioning , thereby leading to a better understanding of the funct... | Almost every aspect of cellular function depends on protein activity . In spite of being fine-tuned to carry out highly specific functions , proteins can also multitask . Experimental studies have identified genes and proteins endowed with more than one molecular function , or participating in very different biological... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Genome-Wide Detection and Analysis of Multifunctional Genes |
Protein–protein interactions , a key to almost any biological process , are mediated by molecular mechanisms that are not entirely clear . The study of these mechanisms often focuses on all residues at protein–protein interfaces . However , only a small subset of all interface residues is actually essential for recogni... | Interactions between proteins underlie all biological processes . Hence , to fully understand or to control biological processes we need to unravel the principles of protein interactions . The quest for these principles has focused predominantly on the entire interfaces between two interacting proteins . However , it h... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biotechnology",
"biochemistry",
"none",
"eukaryotes",
"biophysics"
] | 2007 | Protein–Protein Interaction Hotspots Carved into Sequences |
The modular architecture of protein-protein interaction ( PPI ) networks is evident in diverse species with a wide range of complexity . However , the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified . Here , we show that weak domain-linear motif interaction... | Modular architecture is important for the evolution of cellular systems . Modular rearrangements facilitate functional innovations and modular insulations provide robustness to perturbations . However , molecular-level understanding of the mechanisms underlying modular network evolution is currently not well understood... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"protein-protein",
"interactions",
"protein",
"interactions",
"proteins",
"protein",
"structure",
"protein",
"domains",
"biology",
"and",
"life",
"sciences",
"molecular",
"evolution",
"evolutionary",
"biology",
"molecular",
"biology",
"macromolecular",
"stru... | 2014 | Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks |
The survival of a bacterial pathogen within a host depends upon its ability to outmaneuver the host immune response . Thus , mutant pathogens provide a useful tool for dissecting host-pathogen relationships , as the strategies the microbe has evolved to counteract immunity reveal a host's immune mechanisms . In this st... | To infect a host and survive attacks from the host immune system , bacteria express genes that allow them to counteract immune responses . By identifying these genes we can learn how hosts fight infections and how bacteria resist immune attacks . We identified Francisella novicida genes that interact with the fruit fly... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"microbiology/innate",
"immunity"
] | 2010 | Reciprocal Analysis of Francisella novicida Infections of a Drosophila melanogaster Model Reveal Host-Pathogen Conflicts Mediated by Reactive Oxygen and imd-Regulated Innate Immune Response |
Environmental transmission of the zoonotic parasite Toxoplasma gondii , which is shed only by felids , poses risks to human and animal health in temperate and tropical ecosystems . Atypical T . gondii genotypes have been linked to severe disease in people and the threatened population of California sea otters . To inve... | Toxoplasma gondii , a global parasite shed by domestic and wild felids , can cause severe disease in people and animals . In coastal California , USA , many sea otters have died due to T . gondii . Because T . gondii is shed by felids on land , otter infection suggests that this extremely hardy parasite is transported ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonoses",
"veterinary",
"epidemiology",
"veterinary",
"parasitology",
"medicine",
"and",
"health",
"sciences",
"epidemiology",
"parasitology",
"biology",
"and",
"life",
"sciences",
"spatial",
"epidemiology",
"protozoan",... | 2014 | Using Molecular Epidemiology to Track Toxoplasma gondii from Terrestrial Carnivores to Marine Hosts: Implications for Public Health and Conservation |
Elimination of onchocerciasis ( river blindness ) through mass administration of ivermectin in the six countries in Latin America where it is endemic is considered feasible due to the relatively small size and geographic isolation of endemic foci . We evaluated whether transmission of onchocerciasis has been interrupte... | Brought to the Americas from Africa by the slave trade , onchocerciasis is present in six countries in Latin America . The disease is caused by a round worm and is transmitted to humans by the bite of an infected black fly . Once in a human , the adult worms produce larvae that circulate through the body , causing itch... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"public",
"health",
"and",
"epidemiology/global",
"health",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases"
] | 2009 | Successful Interruption of Transmission of Onchocerca volvulus in the Escuintla-Guatemala Focus, Guatemala |
Snakebite envenoming is a major public health burden in tropical parts of the developing world . In sub-Saharan Africa , neglect has led to a scarcity of antivenoms threatening the lives and limbs of snakebite victims . Technological advances within antivenom are warranted , but should be evaluated not only on their po... | Given the medical importance of snakebite envenoming and the current shortage of antivenoms in sub-Saharan Africa , technological advances in antivenom development and production are needed . One of the avenues that could be taken involves the use of recombinant antivenoms based on oligoclonal mixtures of human IgG ant... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"discussion",
"Conclusions"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"toxins",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"tropical",
"diseases",
"biological",
"cultures",
"vertebrates",
"animals",
"toxicology",
"toxic",
"agents",
"reptiles",
"neglected",
"... | 2017 | Recombinant snakebite antivenoms: A cost-competitive solution to a neglected tropical disease? |
Skeletal muscle morphogenesis transforms short muscle precursor cells into long , multinucleate myotubes that anchor to tendons via the myotendinous junction ( MTJ ) . In vertebrates , a great deal is known about muscle specification as well as how somitic cells , as a cohort , generate the early myotome . However , th... | Despite the importance of muscle fiber development and tendon attachment , this process is incompletely understood in vertebrates . One critical step is muscle fiber elongation; muscle precursor cells are short and subsequent elongation/fusion generates long , multinucleate muscle fibers . Using a vertebrate model orga... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"developmental",
"biology/embryology",
"developmental",
"biology/morphogenesis",
"and",
"cell",
"biology",
"cell",
"biology/morphogenesis",
"and",
"cell",
"biology",
"cell",
"biology/developmental",
"molecular",
"mechanisms",
"genetics",
"and",
"genomics/gene",
"function",
"m... | 2008 | Time-Lapse Analysis and Mathematical Characterization Elucidate Novel Mechanisms Underlying Muscle Morphogenesis |
Prevention is most effective in reducing dengue infection risk , especially in endemic countries like Pakistan . Evaluation of public awareness and health beliefs regarding dengue fever ( DF ) is important for devising disease control strategies . This study assessed dengue knowledge , health beliefs , and preventive p... | Dengue is a massive health threat worldwide . Dengue prevention is the most effective way to reduce the risk of dengue infection , especially in endemic countries like Pakistan . Evaluation of public awareness and health beliefs regarding dengue fever plays an important role in developing strategies for disease control... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"demography",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"neuroscience",
"health",
"care",
"regression",
"analysis",
"age",
"groups",
"academic",
"skills",
"cognitive",
"psychology",
"mathematics",
... | 2016 | Use of the Health Belief Model for the Assessment of Public Knowledge and Household Preventive Practices in Karachi, Pakistan, a Dengue-Endemic City |
Understanding the factors that promote , disrupt , or shape the nature of cooperation is one of the main tasks of evolutionary biology . Here , we focus on attitudes and beliefs supportive of in-group favoritism and strict adherence to moral consensus , collectively known as ideological rigidity , that have been linked... | Attitudes , beliefs , and resulting value systems may represent important motivational and decision-making factors that have strong impact on cooperation in a society . Accordingly , understanding the social function of value systems is a topic of great interest in evolutionary biology , but one where progress is made ... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Methods"
] | [
"social",
"systems",
"social",
"sciences",
"evolutionary",
"modeling",
"biology",
"and",
"life",
"sciences",
"sociology",
"computational",
"sociology",
"evolutionary",
"theory",
"evolutionary",
"biology",
"social",
"research",
"computational",
"biology"
] | 2014 | Barriers to Cooperation Aid Ideological Rigidity and Threaten Societal Collapse |
The current evidence-base for recommendations on the treatment of cutaneous leishmaniasis ( CL ) is generally weak . Systematic reviews have pointed to a general lack of standardization of methods for the conduct and analysis of clinical trials of CL , compounded with poor overall quality of several trials . For CL , t... | Solid evidence is needed to decide how to treat conditions . In the case of cutaneous leishmaniasis , the diversity of clinical conditions , combined with the heterogeneity and weaknesses of the methodologies used in clinical trials , make it difficult to derive robust conclusions as to which treatments should be used ... | [
"Abstract",
"Introduction",
"Defining",
"trial",
"participants",
"Endpoint",
"-",
"outcome",
"measures",
"and",
"therapeutic",
"assessment",
"Study",
"registration",
"and",
"reporting",
"Complying",
"with",
"regulations",
"Disclaimer"
] | [
"medicine",
"infectious",
"diseases",
"leishmaniasis",
"neglected",
"tropical",
"diseases"
] | 2013 | Methodology of Clinical Trials Aimed at Assessing Interventions for Cutaneous Leishmaniasis |
One of the hallmarks of viral immune evasion is the capacity to disrupt major histocompatibility complex class I ( MHCI ) antigen presentation to evade T-cell detection . Cowpox virus encoded protein CPXV203 blocks MHCI surface expression by exploiting the KDEL-receptor recycling pathway , and here we show that CPXV203... | Viruses encode a wide array of proteins whose principle function is to disable the surveillance and effector functions of the immune system . A common viral target is the MHC class I antigen processing and presentation pathway , which is a potent mechanism used by the host for the detection and killing of virally infec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"major",
"histocompatibility",
"complex",
"antigen",
"processing",
"and",
"recognition",
"viral",
"immune",
"evasion",
"virology",
"immunology",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"biophysics"
] | 2012 | Structural Mechanism of ER Retrieval of MHC Class I by Cowpox |
We have identified from the mutualistic grass endophyte Epichloë festucae a non-ribosomal peptide synthetase gene ( sidN ) encoding a siderophore synthetase . The enzymatic product of SidN is shown to be a novel extracellular siderophore designated as epichloënin A , related to ferrirubin from the ferrichrome family . ... | Perennial ryegrass is a cool-season grass that is agriculturally important as forage , especially in Australasia . Essential to the longevity and maintenance of healthy pastures are epichloae fungi , such as Epichloë/Neotyphodium spp . that live inside these grasses in a symbiotic manner . These fungi produce bioactive... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetically",
"modified",
"organisms",
"gene",
"identification",
"and",
"analysis",
"genetics",
"molecular",
"genetics",
"biology",
"agricultural",
"biotechnology",
"agriculture",
"gene",
"function"
] | 2013 | An Extracellular Siderophore Is Required to Maintain the Mutualistic Interaction of Epichloë festucae with Lolium perenne |
Variation in the TGF-β signaling pathway is emerging as an important mechanism by which gonadal sex determination is controlled in teleosts . Here we show that amhy , a Y-specific duplicate of the anti-Müllerian hormone ( amh ) gene , induces male sex determination in Nile tilapia . amhy is a tandem duplicate located i... | Unlike mammals , the identity of the master sex-determining gene varies among fish species , and it is not yet clear if there is a common molecular pathway regulating gonadal sex determination across teleosts . Here we show that a Y-linked duplicate of the anti-Mullerian hormone ( amhy ) is essential for male sex deter... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | A Tandem Duplicate of Anti-Müllerian Hormone with a Missense SNP on the Y Chromosome Is Essential for Male Sex Determination in Nile Tilapia, Oreochromis niloticus |
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