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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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Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data . It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple ind... | Bayesian phylogenetic inference methods have undergone considerable development in recent years , and joint modelling of rich evolutionary data , including genomes , phenotypes and fossil occurrences is increasingly common . Advanced computational software packages that allow robust development of compatible ( sub- ) m... | [
"Abstract",
"Introduction",
"New",
"BEAST",
"functionality",
"Beyond",
"time",
"trees:",
"Extended",
"phylogenetic",
"structures",
"New",
"models",
"Model",
"selection",
"and",
"model",
"adequacy",
"New",
"simulation",
"tools",
"Validation,",
"testing",
"and",
"qualit... | [] | 2019 | BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis |
Discovery of efficient anti-cancer drug combinations is a major challenge , since experimental testing of all possible combinations is clearly impossible . Recent efforts to computationally predict drug combination responses retain this experimental search space , as model definitions typically rely on extensive drug p... | Fighting cancer with combinations of drugs increases success of treatment . However , due to the large number of drugs and tumor variants , it remains a tremendous challenge to identify efficient combinations . To illustrate this , a set of 150 drugs corresponds to more than 10 . 000 possible pairwise drug combinations... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling |
Dengue and chikungunya are global re-emerging mosquito-borne diseases . In Singapore , sustained vector control coupled with household improvements reduced domestic mosquito populations for the past 45 years , particularly the primary vector Aedes aegypti . However , while disease incidence was low for the first 30 yea... | Dengue and chikungunya are mosquito-borne diseases and re-emerging as a global burden of the 21st century . Because of the absence of cure and limitations of the current vaccine , vector control remains the sole efficient intervention to mitigate epidemics . The highly-populated city of Singapore represents an example ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"togaviruses",
"chikungunya",
"infection",
"pathogens",
"tropical",
"diseases",
"microbiology",
"geographical",
"locations",
"animals",
"alphaviruses",
"reproductive",
"p... | 2017 | Peridomestic Aedes malayensis and Aedes albopictus are capable vectors of arboviruses in cities |
Cell populations display heterogeneous and dynamic phenotypic states at multiple scales . Similar to molecular features commonly used to explore cell heterogeneity , cell behavior is a rich phenotypic space that may allow for identification of relevant cell states . Inference of cell state from cell behavior across a t... | Cells in a population are not all alike . The differences between cells impact how each cell responds to stimuli , with implications for development and disease . How do cells change between these functionally important states over time ? This question is difficult to answer using molecular biology , because these meth... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"motility",
"classical",
"mechanics",
"mathematical",
"models",
"multivariate",
"analysis",
"developmental",
"biology",
"systems",
"science",
"mathematics",
"stem",
"cells",
"statistics",
"(mathematics)",
"morphogenesis",
"research",
"and",
"analysis",
"methods",
... | 2018 | Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance |
Interleukin-1 receptor-associated kinases ( IRAKs ) are crucial mediators of the IL-1R/TLR signaling pathways that regulate the immune and inflammation response in mammals . Recent studies also suggest a critical role of IRAKs in tumor development , though the underlying mechanism remains elusive . Pelle is the sole Dr... | In the present study we report a Toll pathway independent function of Pll in modulating apoptotic cell death . Our major findings include: 1 ) loss of pll generates Toll pathway-independent wing phenotypes , which are caused by a reduction in cell number but not cell size; 2 ) depletion of pll up-regulates the transcri... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Pelle Modulates dFoxO-Mediated Cell Death in Drosophila |
Australian bat lyssavirus ( ABLV ) belongs to the genus Lyssavirus which also includes classic rabies virus and the European lyssaviruses . To date , the only three known human ABLV cases , all fatal , have been reported from Queensland , Australia . ABLV is widely distributed in Australian bats , and any bite or scrat... | Australian bat lyssavirus ( ABLV ) , closely related to classic rabies virus , is widely distributed in bats in Australia . So far , the only three known human ABLV cases , all fatal , have been reported in Queensland , Australia . Any Australian bat-related injury ( bite or scratch ) , or contact of bat saliva/neural ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"post-exposure",
"prophylaxis",
"membrane",
"potential",
"tropical",
"diseases",
"immunology",
"vertebrates",
"electrophysiology",
"animals",
"mammals",
"vaccines",
"preventive",
"medicine",
"rabies",
"neglected",
"tropical",
"diseas... | 2016 | Potential Exposures to Australian Bat Lyssavirus Notified in Queensland, Australia, 2009−2014 |
Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals . To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide , we generated temporal DNA occupancy profiles by RNA polymerase II ( Po... | In mammalian organs such as the liver , many metabolic and physiological processes occur preferentially at specific times during the 24-hour daily cycle . The timing of these rhythmic functions depends on a complex interplay between the endogenous circadian clock and environmental timing cues relayed through the master... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biochemistry",
"biology",
"computational",
"biology",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles |
Drosophila body pigmentation has emerged as a major Evo-Devo model . Using two Drosophila melanogaster lines , Dark and Pale , selected from a natural population , we analyse here the interaction between genetic variation and environmental factors to produce this complex trait . Indeed , pigmentation varies with genoty... | Complex traits such as size or disease susceptibility are typically modulated by both genetic variation and environmental conditions . Model organisms such as fruit flies ( Drosophila ) are particularly appropriate to analyse the interactions between genetic variation and environmental factors during the development of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"skin",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"integumentary",
"system",
"gene",
"regulation",
"population",
"genetics",
"animals",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"pupae",
"experiment... | 2018 | bric à brac (bab), a central player in the gene regulatory network that mediates thermal plasticity of pigmentation in Drosophila melanogaster |
Dendritic morphology has been shown to have a dramatic impact on neuronal function . However , population features such as the inherent variability in dendritic morphology between cells belonging to the same neuronal type are often overlooked when studying computation in neural networks . While detailed models for morp... | Computational models of neurons and neural networks provide a valuable avenue to test our understanding of brain regions and to make predictions to guide future experimentation . Each neuron has a unique dendritic tree , features of which can vary depending on the location of the neuron within the particular brain regi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroanatomy",
"anatomy",
"computational",
"neuroscience",
"nervous",
"system",
"single",
"neuron",
"function",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"neuroscience",
"artificial",
"neural",
"networks"
] | 2014 | Linking Macroscopic with Microscopic Neuroanatomy Using Synthetic Neuronal Populations |
We developed a new statistical framework to find genetic variants associated with extreme longevity . The method , informed GWAS ( iGWAS ) , takes advantage of knowledge from large studies of age-related disease in order to narrow the search for SNPs associated with longevity . To gain support for our approach , we fir... | Longevity is a complex phenotype , and few genetic variants that affect lifespan have been identified . However , aging and disease are closely related , and a great deal is known about the genetic basis of disease risk . Here , we show using genome-wide association studies ( GWAS ) of longevity and disease that there ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Genome-Wide Scan Informed by Age-Related Disease Identifies Loci for Exceptional Human Longevity |
Proteins with long , pathogenic polyglutamine ( polyQ ) sequences have an enhanced propensity to spontaneously misfold and self-assemble into insoluble protein aggregates . Here , we have identified 21 human proteins that influence polyQ-induced ataxin-1 misfolding and proteotoxicity in cell model systems . By analyzin... | Spinocerebellar ataxias ( SCAs ) are a group of inherited neurodegenerative diseases with around 30 subtypes , which are characterized by a progressive loss of cerebellar neurons . Neuronal death has been linked to the aggregation of mutated disease-causing proteins , such as ataxin-1 ( ATXN1 ) . Pathogenic ATXN1 conta... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"protein",
"interactions",
"neurodegenerative",
"diseases",
"amyotrophic",
"lateral",
"sclerosis",
"molecular",
"genetics",
"motor",
"neuron",
"diseases",
"proteins",
"gene",
"expression",
"biology",
"proteomics",
"systems",
"biology",
"biochemistry",
"neurologi... | 2012 | Identification of Human Proteins That Modify Misfolding and Proteotoxicity of Pathogenic Ataxin-1 |
Overexpression of the histone methyltransferase MMSET in t ( 4;14 ) + multiple myeloma patients is believed to be the driving factor in the pathogenesis of this subtype of myeloma . MMSET catalyzes dimethylation of lysine 36 on histone H3 ( H3K36me2 ) , and its overexpression causes a global increase in H3K36me2 , redi... | Precise spatial and temporal gene expression is required for normal development , and aberrant regulation of gene expression is a common factor in many diseases , including cancer . Histone modifications contribute to the control of gene expression by altering chromatin structure and affecting the recruitment of transc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology",
"chromosome",
"biology",
"genetics",
"biology",
"and",
"life",
"sciences",
"epigenetics",
"chromatin",
"histone",
"modification"
] | 2014 | Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation |
Infection with Trypanosoma cruzi causes Chagas disease , a major public health problem throughout Latin America . There is no vaccine and the only drugs have severe side effects . Efforts to generate new therapies are hampered by limitations in our understanding of parasite biology and disease pathogenesis . Studies ar... | 5–8 million people in Latin America are infected with the single-cell parasite Trypanosoma cruzi , the causative agent of Chagas disease . Of these , approximately one-third will develop chronic disease pathology , leading to disability and premature death . Only two drugs are available , both of which can have severe ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"transfection",
"fluorescence",
"imaging",
"medicine",
"and",
"health",
"sciences",
"luciferase",
"enzymes",
"enzymology",
"green",
"fluorescent",
"protein",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"luminescent",
"proteins",
"protozoans",
"molecular",
"biology",... | 2018 | Expanding the toolbox for Trypanosoma cruzi: A parasite line incorporating a bioluminescence-fluorescence dual reporter and streamlined CRISPR/Cas9 functionality for rapid in vivo localisation and phenotyping |
Digestive organ expansion factor ( Def ) is a nucleolar protein that plays dual functions: it serves as a component of the ribosomal small subunit processome for the biogenesis of ribosomes and also mediates p53 degradation through the cysteine proteinase calpain-3 ( CAPN3 ) . However , nothing is known about the exact... | The nucleolus is primarily known as the subcellular organelle for the biogenesis of the ribosomal small and large subunits in eukaryotic cells . However , it is also increasingly evident that many nucleolar proteins also play essential roles in other biological processes . Here , we show that Digestive organ expansion ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"liver",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"vertebrates",
"animals",
"animal",
"models",
"osteichthyes",
"developmental",
"biology",
"mutation",
"substitution",
"mutation",
"model... | 2016 | Phosphorylation of Def Regulates Nucleolar p53 Turnover and Cell Cycle Progression through Def Recruitment of Calpain3 |
Since the 1990s , paratyphoid fever caused by Salmonella Paratyphi A has emerged in Southeast Asia and China . In 2010 , a large-scale outbreak involving 601 cases of paratyphoid fever occurred in the whole of Yuanjiang county in China . Epidemiological and laboratory investigations were conducted to determine the etio... | Typhoid and paratyphoid fever remain public health concerns for developing countries . From May 2010 to June 2011 , a large-scale outbreak involving 601 cases of paratyphoid fever occurred in China . Epidemiological and laboratory investigations were conducted to determine the etiology , source and transmission factors... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | A Large-Scale Community-Based Outbreak of Paratyphoid Fever Caused by Hospital-Derived Transmission in Southern China |
Dengue virus infection ( DVI ) among children is a leading cause of hospitalization in endemic areas . Hospitalized patients are at risk of receiving unnecessary antibiotics . A retrospective medical review analysis study was conducted to evaluate the prevalence , indication , and choice of antibiotics given to hospita... | DVI among children is a leading cause of hospitalization in endemic areas . In developing or underdeveloped countries , the antibiotics stewardship policy has not been well implemented yet . Thus , the risk of unnecessary antibiotics used in hospitalized patients becomes higher . Changing the way medical doctors use an... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"antimicrobials",
"urology",
"children",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"drugs",
"tropical",
"diseases",
"microbiology",
"pediatrics",
"bacterial",
"diseases",
"age",
"groups",
"signs",
"and",
"symptoms",
"antibiot... | 2019 | The inappropriate use of antibiotics in hospitalized dengue virus-infected children with presumed concurrent bacterial infection in teaching and private hospitals in Bandung, Indonesia |
Sperm and egg proteins constitute a remarkable paradigm in evolutionary biology: despite their fundamental role in mediating fertilization ( suggesting stasis ) , some of these molecules are among the most rapidly evolving ones known , and their divergence can lead to reproductive isolation . Because of strong selectio... | Interacting sperm and egg proteins must co-evolve to maintain compatibility at fertilization , so their divergence among species should be correlated—lineages with rapidly evolving sperm proteins should have rapidly evolving egg proteins . We use this expectation to target biochemical studies of fertilization in a mode... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"evolutionary",
"biology"
] | 2013 | Duplicate Abalone Egg Coat Proteins Bind Sperm Lysin Similarly, but Evolve Oppositely, Consistent with Molecular Mimicry at Fertilization |
Ascaris spp . infection affects 800 million people worldwide , and half of the world population is currently at risk of infection . Recurrent reinfection in humans is mostly due to the simplicity of the parasite life cycle , but the impact of multiple exposures to the biology of the infection and the consequences to th... | Human ascariasis caused by the helminths Ascaris lumbricoides and Ascaris suum , is the most prevalent neglected tropical disease in the world , affecting more than 800 million people and mainly school-aged children . The parasite life cycle may be divided in two distinct phases after the initial infection: ( i ) migra... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"respiratory",
"infections",
"immunology",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"pulmonology",
"developmenta... | 2016 | Multiple Exposures to Ascaris suum Induce Tissue Injury and Mixed Th2/Th17 Immune Response in Mice |
What governs the concentrations of metabolites within living cells ? Beyond specific metabolic and enzymatic considerations , are there global trends that affect their values ? We hypothesize that the physico-chemical properties of metabolites considerably affect their in-vivo concentrations . The recently achieved exp... | What governs the identity and concentrations of metabolites within living cells ? The first part of this question has received much attention . Organisms were found to qualitatively prefer hydrophilic and charged metabolites , a phenomenon that was explained to be a result of constraints imposed by contemporary as well... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"microbial",
"metabolism",
"theoretical",
"biology",
"biology",
"computational",
"biology",
"metabolic",
"networks",
"microbiology",
"genetics",
"and",
"genomics"
] | 2011 | Hydrophobicity and Charge Shape Cellular Metabolite Concentrations |
The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs , respectively . Although whipworms in human and non-human primates historically have been referred to as T . trichiura , recent reports suggest that several Trichuris spp . are found in primates . We sequenced and annot... | Trichuris trichiura and Trichuris suis are whipworms found in humans and pigs , respectively , causing morbidity in humans and being associated with production losses in pigs . Although Trichuris from non-human primates is attributed to T . trichiura , hence considered the same species as the one infecting humans , sev... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Mitochondrial Genome Analyses Suggest Multiple Trichuris Species in Humans, Baboons, and Pigs from Different Geographical Regions |
The contact structure between hosts shapes disease spread . Most network-based models used in epidemiology tend to ignore heterogeneity in the weighting of contacts between two individuals . However , this assumption is known to be at odds with the data for many networks ( e . g . sexual contact networks ) and to have ... | Understanding how infectious diseases spread has public health and ecological implications . The contact structure between hosts strongly affects this spread . However , most studies assume that all types of contacts are identical , when in reality some individuals interact more strongly than others . This is particula... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"network",
"analysis",
"(management)",
"social",
"and",
"behavioral",
"sciences",
"theoretical",
"biology",
"management",
"engineering",
"epidemiology",
"social",
"networks",
"sociology",
"management",
"planning",
"and",
"control",
"biology",
"spatial",
"epide... | 2013 | Epidemic Spread on Weighted Networks |
Small noncoding RNAs ( sRNAs ) are ubiquitous posttranscriptional regulators of gene expression . Using the model plant-pathogenic bacterium Xanthomonas campestris pv . vesicatoria ( Xcv ) , we investigated the highly expressed and conserved sRNA sX13 in detail . Deletion of sX13 impinged on Xcv virulence and the expre... | Since the discovery of the first regulatory RNA in 1981 , hundreds of small RNAs ( sRNAs ) have been identified in bacteria . Although sRNA-mediated control of virulence was demonstrated for numerous animal- and human-pathogenic bacteria , sRNAs and their functions in plant-pathogenic bacteria have been enigmatic . We ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"expression",
"analysis",
"gene",
"regulation",
"host-pathogen",
"interaction",
"microbiology",
"rna",
"stability",
"developmental",
"biology",
"genome",
"analysis",
"tools",
"plant",
"science",
"molecular",
"cell",
"biology",
"molecular",
"development",
"plant"... | 2013 | Small RNA sX13: A Multifaceted Regulator of Virulence in the Plant Pathogen Xanthomonas |
Infectious prions propagate from peripheral entry sites into the central nervous system ( CNS ) , where they cause progressive neurodegeneration that ultimately leads to death . Yet the pathogenesis of prion disease can vary dramatically depending on the strain , or conformational variant of the aberrantly folded and a... | Prion diseases are fatal neurodegenerative disorders that are also infectious . Prions are composed of a misfolded , aggregated form of a normal cellular protein that is highly expressed in neurons . Prion- infected individuals show variability in the clinical signs and brain regions that selectively accumulate prions ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"neurological",
"disorders",
"neurology",
"chemistry",
"chemical",
"biology"
] | 2012 | Biochemical Properties of Highly Neuroinvasive Prion Strains |
Toxocarosis is a widespread zoonosis caused by the ascarid nematodes Toxocara canis and Toxocara cati , which primarily infect dogs and cats , respectively . Most human infections with Toxocara are asymptomatic; however , some infected individuals may develop a serious illness and even death . Nevertheless , epidemiolo... | Toxocarosis , a typical neglected and underestimated human health problem , is caused by the ascarid nematodes Toxocara canis and Toxocara cati , which primarily infect dogs and cats , respectively . Previous studies have reported an increased risk for Toxocara infection in humans worldwide , especially in children and... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"veterinary",
"diseases",
"zoonoses",
"parasitic",
"intestinal",
"diseases",
"biology",
"and",
"life",
"sciences",
"tropical",
"diseases",
"parasitic",
"diseases",
"veterinary",
"science",
"nematode",
"i... | 2014 | Toxocara Seroprevalence among Clinically Healthy Individuals, Pregnant Women and Psychiatric Patients and Associated Risk Factors in Shandong Province, Eastern China |
This article presents the first attempt to formalize the optimization of experimental design with the aim of comparing models of brain function based on neuroimaging data . We demonstrate our approach in the context of Dynamic Causal Modelling ( DCM ) , which relates experimental manipulations to observed network dynam... | During the past two decades , brain mapping research has undergone a paradigm switch . In addition to localizing brain regions that encode specific sensory , motor or cognitive processes , neuroimaging data is nowadays further exploited to ask questions about how information is transmitted through brain networks . The ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"experimental",
"psychology",
"psychology",
"social",
"and",
"behavioral",
"sciences",
"mathematics",
"statistics",
"biology",
"computational",
"biology",
"neuroscience",
"probability",
"theory"
] | 2011 | Optimizing Experimental Design for Comparing Models of Brain Function |
Computational prediction of cancer associated SNPs from the large pool of SNP dataset is now being used as a tool for detecting the probable oncogenes , which are further examined in the wet lab experiments . The lack in prediction accuracy has been a major hurdle in relying on the computational results obtained by imp... | The genetic mutations in human were shown by single nucleotide polymorphisms ( SNPs ) , and several of them were supposed to cause deleterious and disease associated phenotypic effects . The ability to differentiate between pathogenic and neutral nsSNPs ( non-synonymous Single Nucleotide Polymorphisms ) using computati... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results/Discussion"
] | [
"biochemistry",
"cancer",
"genetics",
"proteins",
"protein",
"folding",
"protein",
"structure",
"genetics",
"biology",
"and",
"life",
"sciences",
"biophysics"
] | 2014 | Use of Long Term Molecular Dynamics Simulation in Predicting Cancer Associated SNPs |
Resection of DNA double-strand break ( DSB ) ends is generally considered a critical determinant in pathways of DSB repair and genome stability . Unlike for enzymatically induced site-specific DSBs , little is known about processing of random “dirty-ended” DSBs created by DNA damaging agents such as ionizing radiation ... | Double-strand breaks ( DSBs ) in chromosomal DNA are common sources of genomic change that may be beneficial or deleterious to an organism , from yeast to humans . While they can arise through programmed cellular events , DSBs are frequently associated with defective chromosomal replication , and they are induced by va... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/environmental",
"microbiology",
"molecular",
"biology/recombination",
"genetics",
"and",
"genomics/chromosome",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics",
"molecular",
"biology/dna",
"repair"
] | 2009 | RAD50 Is Required for Efficient Initiation of Resection and Recombinational Repair at Random, γ-Induced Double-Strand Break Ends |
We present a computational framework , called DISCERN ( DIfferential SparsE Regulatory Network ) , to identify informative topological changes in gene-regulator dependence networks inferred on the basis of mRNA expression datasets within distinct biological states . DISCERN takes two expression datasets as input: an ex... | Certain genes can regulate other genes’ expression and activity levels to perform key biological processes in a cell . Understanding how genes affect expression levels among one another is a fundamental goal in molecular biology . New statistical techniques that analyze genome-wide mRNA expression data obtained from di... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"acute",
"myeloid",
"leukemia",
"leukemias",
"medicine",
"and",
"health",
"sciences",
"genetic",
"networks",
"breast",
"tumors",
"myeloid",
"leukemia",
"gene",
"regulation",
"regulatory",
"proteins",
"cancers",
"and",
"neoplasms",
"dna-binding",
"proteins",
"oncology",
... | 2016 | Identifying Network Perturbation in Cancer |
Photoperiod dependent flowering is one of several mechanisms used by plants to initiate the developmental transition from vegetative growth to reproductive growth . The NUCLEAR FACTOR Y ( NF-Y ) transcription factors are heterotrimeric complexes composed of NF-YA and histone-fold domain ( HFD ) containing NF-YB/NF-YC ,... | For plants to have reproductive success , they must time their flowering with the most beneficial biotic and abiotic environmental conditions—after all , reproductive success would likely be low if flowers developed when pollinators were not present or freezing temperatures were on the horizon . Proper timing mechanism... | [
"Abstract",
"Introduction",
"Results"
] | [
"biotechnology",
"plant",
"anatomy",
"gene",
"regulation",
"brassica",
"dna-binding",
"proteins",
"regulator",
"genes",
"plant",
"science",
"model",
"organisms",
"genetically",
"modified",
"plants",
"gene",
"types",
"molecular",
"biology",
"techniques",
"plants",
"flowe... | 2016 | NUCLEAR FACTOR Y, Subunit A (NF-YA) Proteins Positively Regulate Flowering and Act Through FLOWERING LOCUS T |
The large size of metabolic networks entails an overwhelming multiplicity in the possible steady-state flux distributions that are compatible with stoichiometric constraints . This space of possibilities is largest in the frequent situation where the nutrients available to the cells are unknown . These two factors: net... | Metabolic fluxes are steady-state rates of metabolite interconversion within living cells . They determine the rates of growth and product formation , and are of biotechnological and medical importance . An important and pressing question is how to identify the actual distribution of fluxes in living cells among the ma... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"biotechnology",
"bioengineering",
"biochemistry",
"biological",
"systems",
"engineering",
"biomedical",
"engineering",
"systems",
"biology",
"metabolic",
"pathways",
"biology",
"computational",
"biology",
"metabolic",
"networks",
"metabolism",
"genetics",
"and",
"genomics",
... | 2013 | Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements |
The innate immune system pattern recognition receptors ( PRR ) are the first line of host defenses recognizing the various pathogen- or danger-associated molecular patterns and eliciting defenses by regulating the production of pro-inflammatory cytokines such as IL-1β , IL-18 or interferon β ( IFN-β ) . NOD-like recept... | Invasion of a host cell by pathogens , including viruses , is sensed by pattern-recognition receptors resulting in the elicitation of the host innate defenses such as the formation of multi-protein inflammasome complexes , inflammatory IL-1β and IL-18 cytokine production and interferon-β production via the cytoplasmic ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | BRCA1 Regulates IFI16 Mediated Nuclear Innate Sensing of Herpes Viral DNA and Subsequent Induction of the Innate Inflammasome and Interferon-β Responses |
In ecology , “disease tolerance” is defined as an evolutionary strategy of hosts against pathogens , characterized by reduced or absent pathogenesis despite high pathogen load . To our knowledge , tolerance has to date not been quantified and disentangled from host resistance to disease in any clinically relevant human... | When confronted with pathogens , hosts can either evolve to fight them or learn to live with them . The first of these two strategies is called “resistance” and the second “tolerance” . In the context of HIV , many genes conferring resistance have been identified , but no tolerance genes are known . Using statistical t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases",
"hiv",
"infections",
"evolutionary",
"ecology",
"medicine",
"and",
"health",
"sciences",
"major",
"histocompatibility",
"complex",
"ecology",
"clinical",
"immunology",
"population",
"modeling",
"aids",
"biology",
"and",
"life",
"sciences",
"imm... | 2014 | Disentangling Human Tolerance and Resistance Against HIV |
Point mutations in peripherin-2 ( PRPH2 ) are associated with severe retinal degenerative disorders affecting rod and/or cone photoreceptors . Various disease-causing mutations have been identified , but the exact contribution of a given mutation to the clinical phenotype remains unclear . Exonic point mutations are us... | Photoreceptors are the light sensing cells of the retina and consist of dim light and night vision mediating rods and daylight and color vision mediating cones . PRPH2 is crucial for the structural and functional integrity of photoreceptors . Some point mutations in PRPH2 lead to degeneration of rods , whereas others o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | In Vivo Analysis of Disease-Associated Point Mutations Unveils Profound Differences in mRNA Splicing of Peripherin-2 in Rod and Cone Photoreceptors |
Neurocysticercosis is a disease caused by the oral ingestion of eggs from the human parasitic worm Taenia solium . Although drugs are available they are controversial because of the side effects and poor efficiency . An expressed sequence tag ( EST ) library is a method used to describe the gene expression profile and ... | A method used to describe expressed genes at a specific stage in an organism is an EST library . In this method mRNA from a specific organism is isolated , transcribed into cDNA and sequenced . The sequence will derive from the 5′-end of the cDNA . The library will not have sequences from all genes , especially if they... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"molecular",
"biology/bioinformatics",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"microbiology/parasitology"
] | 2010 | Analyses of an Expressed Sequence Tag Library from Taenia solium, Cysticerca |
To assess the efficacy of HIV vaccine candidates or preventive treatment , many research groups have started to challenge monkeys repeatedly with low doses of the virus . Such challenge data provide a unique opportunity to assess the importance of exposure history for the acquisition of the infection . I developed stoc... | Individuals are exposed to Human Immunodeficiency Virus ( HIV ) many times before they contract the virus . It is not known what an instance of exposure , which does not result in infection , does to the host . Frequent exposures to the virus are hypothesized to immunize an individual , and result in resistance to infe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"immunology",
"biology",
"computational",
"biology"
] | 2012 | The Role of Exposure History on HIV Acquisition: Insights from Repeated Low-dose Challenge Studies |
An important challenge in the analysis of mechanochemical coupling in molecular motors is to identify residues that dictate the tight coupling between the chemical site and distant structural rearrangements . In this work , a systematic attempt is made to tackle this issue for the conventional myosin . By judiciously c... | Molecular motors are inherently allosteric in nature because the small structural changes associated with the chemistry in the active site are propagated over a long distance and amplified into much larger conformational transitions . A fundamental challenge for understanding such processes concerns the identification ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"in",
"vitro",
"none",
"molecular",
"biology",
"computational",
"biology"
] | 2007 | Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues |
Active screening by mobile teams is considered the most effective method for detecting gambiense-type human African trypanosomiasis ( HAT ) but constrained funding in many post-conflict countries limits this approach . Non-specialist health care workers ( HCWs ) in peripheral health facilities could be trained to ident... | Human African trypanosomiasis ( HAT or sleeping sickness ) is a fatal but treatable disease affecting poor people in sub-Saharan Africa . Most HAT diagnostic equipment , infrastructure and expertise is located in hospitals . The expense of expanding testing services to remote areas using mobile teams severely restricts... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"conflict",
"epidemiology",
"public",
"health",
"medicine",
"infectious",
"diseases",
"health",
"screening",
"social",
"and",
"behavioral",
"sciences",
"primary",
"care",
"mental",
"health",
"behavioral",
"and",
"social",
"aspects",
"of",
"health",
"epidemiology",
"af... | 2014 | A Mixed Methods Study of a Health Worker Training Intervention to Increase Syndromic Referral for Gambiense Human African Trypanosomiasis in South Sudan |
Phospoenolpyruvate carboxylase ( PEPC ) is absent from humans but encoded in the Plasmodium falciparum genome , suggesting that PEPC has a parasite-specific function . To investigate its importance in P . falciparum , we generated a pepc null mutant ( D10Δpepc ) , which was only achievable when malate , a reduction pro... | The genome of the human malaria parasite Plasmodium falciparum encodes a protein called phosphoenolpyruvate carboxylase ( PEPC ) absent from the human host . PEPC is known to fix CO2 to generate metabolites used for energy metabolism in plants and bacteria , but its function in malaria parasites remained an enigma . Ou... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"parastic",
"protozoans",
"systems",
"biology",
"biochemistry",
"protozoology",
"biology",
"microbiology",
"plasmodium",
"falciparum",
"parasitology",
"parasite",
"physiology",
"pathogenesis"
] | 2014 | Phosphoenolpyruvate Carboxylase Identified as a Key Enzyme in Erythrocytic Plasmodium falciparum Carbon Metabolism |
Estimation of division and death rates of lymphocytes in different conditions is vital for quantitative understanding of the immune system . Deuterium , in the form of deuterated glucose or heavy water , can be used to measure rates of proliferation and death of lymphocytes in vivo . Inferring these rates from labeling... | Understanding of cellular processes is impossible without quantitative estimates of how quickly cells in an organism divide and die . The most widely used approach to measure rates of cell turnover in humans is by labeling dividing cells with deuterium given in the form of deuterated glucose or heavy water . Surprising... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"mathematics/statistics",
"immunology/immune",
"response",
"computational",
"biology"
] | 2010 | Explicit Kinetic Heterogeneity: Mathematical Models for Interpretation of Deuterium Labeling of Heterogeneous Cell Populations |
Mycobacterium tuberculosis ( Mtb ) remains a major public health problem , with an effective vaccine continuing to prove elusive . Progress in vaccination strategies has been hampered by a lack of appreciation of the bacterium's response to dynamic changes in the host immune environment . Here , we utilize reporter Mtb... | Mycobacterium tuberculosis ( Mtb ) remains a serious challenge to global health , a situation that is exacerbated by emerging drug resistance , the paucity of new antibiotics , and the absence of an effective vaccine . Whilst there is no doubt that an anti-tuberculosis vaccine would have an extraordinary impact on the ... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"biology",
"and",
"life",
"sciences",
"immunology",
"microbiology"
] | 2014 | Exploitation of Mycobacterium tuberculosis Reporter Strains to Probe the Impact of Vaccination at Sites of Infection |
Schistosomiasis is the most widespread water-based disease in sub-Saharan Africa . Transmission is governed by the spatial distribution of specific freshwater snails that act as intermediate hosts and human water contact patterns . Remote sensing data have been utilized for spatially explicit risk profiling of schistos... | Schistosomiasis is a parasitic worm infection that is widespread in sub-Saharan Africa where people get in contact with open freshwater bodies . For many years , the strategy to control schistosomiasis was to prevent morbidity through deworming of school-aged children . Recently , transmission control has gained intere... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Modeling and Validation of Environmental Suitability for Schistosomiasis Transmission Using Remote Sensing |
Two different strategies for stabilizing proteins are ( i ) positive design in which the native state is stabilized and ( ii ) negative design in which competing non-native conformations are destabilized . Here , the circumstances under which one strategy might be favored over the other are explored in the case of latt... | Most proteins are functional only in their native states . The stability of the native state of proteins is , therefore , of paramount importance both in vivo and for many biotechnological applications in vitro . Protein stability is determined by the difference between the free energies of the native and non-native st... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"computational",
"biology/macromolecular",
"sequence",
"analysis",
"biophysics/theory",
"and",
"simulation"
] | 2009 | Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins |
The abundance and identity of functional variation segregating in natural populations is paramount to dissecting the molecular basis of quantitative traits as well as human genetic diseases . Genome sequencing of multiple organisms of the same species provides an efficient means of cataloging rearrangements , insertion... | DNA sequence variation makes an important contribution to most traits that vary in natural populations . However , mapping mutations that underlie a trait of interest is a significant challenge . Genome sequencing of multiple organisms provides a complete list of DNA sequence differences responsible for any trait that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/genome",
"projects",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2008 | A Catalog of Neutral and Deleterious Polymorphism in Yeast |
Herpes simplex virus type 1 ( HSV-1 ) infection results in lifelong chronic infection of trigeminal ganglion ( TG ) neurons , also referred to as neuronal HSV-1 latency , with periodic reactivation leading to recrudescent herpetic disease in some persons . HSV-1 proteins are expressed in a temporally coordinated fashio... | HSV-1 is an endemic human herpesvirus worldwide that establishes a lifelong latent infection of neurons in the trigeminal ganglion ( TG ) , allowing intermittent reactivation resulting in recurrent disease in some persons . Studies in HSV-1 models suggest a central role of TG-infiltrating virus-specific CD8 T-cells to ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"flow",
"cytometry",
"medicine",
"immune",
"cells",
"cytokines",
"herpes",
"simplex",
"immunologic",
"subspecialties",
"immunity",
"to",
"infections",
"immunology",
"host-pathogen",
"interaction",
"microbiology",
"anatomy",
"and",
"physiology",
"adaptive",
"immunity",
"im... | 2013 | Local CD4 and CD8 T-Cell Reactivity to HSV-1 Antigens Documents Broad Viral Protein Expression and Immune Competence in Latently Infected Human Trigeminal Ganglia |
The highly pathogenic avian influenza ( HPAI ) H5N1 virus lineage has undergone extensive genetic reassortment with viruses from different sources to produce numerous H5N1 genotypes , and also developed into multiple genetically distinct sublineages in China . From there , the virus has spread to over 60 countries . Th... | H5N1 influenza virus has been responsible for poultry outbreaks over the last 12 years—the longest recorded example of highly pathogenic avian influenza ( HPAI ) circulation in poultry . The ecological success of this virus in diverse species of both poultry and wild birds with sporadic introduction to humans suggests ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/population",
"genetics",
"virology/emerging",
"viral",
"diseases",
"computational",
"biology/evolutionary",
"modeling",
"evolutionary",
"biology",
"computational",
"biology/molecular",
"dynamics",
"infectious",
"diseases/epidemiology",
"and",
"control",
... | 2008 | Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses |
Trichomonas vaginalis is an extracellular eukaryotic parasite that causes the most common , non-viral sexually transmitted infection worldwide . Although disease burden is high , molecular mechanisms underlying T . vaginalis pathogenesis are poorly understood . Here , we identify a family of putative T . vaginalis rhom... | Trichomonas vaginalis , a common pathogen with a worldwide distribution , causes a sexually transmitted infection and exacerbates other diseases . Estimated to infect over a million people annually in the United States alone , the Center for Disease Control and Prevention categorized trichomoniasis as one of five negle... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | A Trichomonas vaginalis Rhomboid Protease and Its Substrate Modulate Parasite Attachment and Cytolysis of Host Cells |
Local supra-linear summation of excitatory inputs occurring in pyramidal cell dendrites , the so-called dendritic spikes , results in independent spiking dendritic sub-units , which turn pyramidal neurons into two-layer neural networks capable of computing linearly non-separable functions , such as the exclusive OR . O... | Classical views on single neuron computation treat dendrites as mere collectors of inputs , that is forwarded to the soma for linear summation and causes a spike output if it is sufficiently large . Such a single neuron model can only compute linearly separable input-output functions , representing a small fraction of ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"neuroscience",
"single",
"neuron",
"function",
"biology",
"neuroscience"
] | 2013 | Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions |
Primary visual cortex is often viewed as a “cyclopean retina” , performing the initial encoding of binocular disparities between left and right images . Because the eyes are set apart horizontally in the head , binocular disparities are predominantly horizontal . Yet , especially in the visual periphery , a range of no... | Because our eyes are set apart horizontally in our head , the images they see are mainly offset horizontally . However , small vertical disparities also occur , and can have a measurable effect on perception , showing that they must be detected by the visual system . The trouble is that encoding a two-dimensional quant... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"neuroscience/natural",
"and",
"synthetic",
"vision",
"neuroscience/theoretical",
"neuroscience",
"neuroscience/sensory",
"systems"
] | 2010 | Vertical Binocular Disparity is Encoded Implicitly within a Model Neuronal Population Tuned to Horizontal Disparity and Orientation |
Mosquitoes feed on plant-derived fluids such as nectar and sap and are exposed to bioactive molecules found in this dietary source . However , the role of such molecules on mosquito vectorial capacity is unknown . Weather has been recognized as a major determinant of the spread of dengue , and plants under abiotic stre... | The dramatic climate changes currently occurring on our planet may likely influence the biology and the distribution of mosquitoes . Aedes aegypti is a major vector of arboviruses . However , females feed on plants for a few days before feeding on blood for the first time . Plants are sessile and cannot move to search ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"cell",
"death",
"fluorescence",
"imaging",
"medicine",
"and",
"health",
"sciences",
"autophagic",
"cell",
"death",
"microbiome",
"cell",
"processes",
"microbiology",
"diet",
"light",
"microscopy",
"animals",
"nutrition",
"microscopy",
"insect",
"vector... | 2016 | Polyphenol-Rich Diets Exacerbate AMPK-Mediated Autophagy, Decreasing Proliferation of Mosquito Midgut Microbiota, and Extending Vector Lifespan |
Bacteria are often attached to surfaces in natural ecosystems . A surface-associated lifestyle can have advantages , but shifts in the physiochemical state of the environment may result in conditions in which attachment has a negative fitness impact . Therefore , bacteria employ numerous mechanisms to control the trans... | Living on a surface within a community of cells confers a number of advantages to a bacterium . However , the transition from a free-living , planktonic state to a surface-attached lifestyle should be tightly regulated to ensure that cells avoid adhering to toxic or resource-limited niches . Many bacteria build adhesiv... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"caulobacter",
"gene",
"regulation",
"drugs",
"regulatory",
"proteins",
"microbiology",
"dna-binding",
"proteins",
"organic",
"compounds",
"prokaryotic",
"models",
"regulator",
"genes",
"a... | 2019 | Regulation of bacterial surface attachment by a network of sensory transduction proteins |
Necrosis and ethylene-inducing peptide 1 ( Nep1 ) -like proteins ( NLPs ) are secreted by several phytopathogenic microorganisms . They trigger necrosis in various eudicot plants upon binding to plant sphingolipid glycosylinositol phosphorylceramides ( GIPC ) . Interestingly , HaNLP3 from the obligate biotroph oomycete... | The rhizosphere and phyllosphere of terrestrial plants are home to a number of microorganisms , many of which are potentially pathogenic at certain stages during their associations with plants . The pathogens use diverse routes to penetrate physical barriers and colonize host plants with different lifestyles . Necrosis... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"plant",
"anatomy",
"medicine",
"and",
"health",
"sciences",
"vesicles",
"crystal",
"structure",
"molecular",
"dynamics",
"pathology",
"and",
"laboratory",
"medicine",
"condensed",
"matter",
"physics",
"toxicology",
"membrane",
"proteins",
"toxicity",
"plant",
"science"... | 2019 | Molecular basis for functional diversity among microbial Nep1-like proteins |
Wolbachia are intracellular bacterial symbionts that are able to protect various insect hosts from viral infections . This tripartite interaction was initially described in Drosophila melanogaster carrying wMel , its natural Wolbachia strain . wMel has been shown to be genetically polymorphic and there has been a recen... | Wolbachia are bacterial symbionts that infect many arthropods and can protect insects from viral infection . Here we show that different variants of Wolbachia from Drosophila melanogaster ( wMel ) are phenotypically heterogeneous: they differ in the level of protection they confer and the titres they reach in their hos... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Wolbachia Variants Induce Differential Protection to Viruses in Drosophila melanogaster: A Phenotypic and Phylogenomic Analysis |
In order to study the ability of coupled neural oscillators to synchronize in the presence of intrinsic as opposed to synaptic noise , we constructed hybrid circuits consisting of one biological and one computational model neuron with reciprocal synaptic inhibition using the dynamic clamp . Uncoupled , both neurons fir... | Many biological phenomena exhibit synchronized oscillations in the presence of noise and heterogeneity . These include brain rhythms that underlie cognition and spinal rhythms that underlie rhythmic motor activity like breathing and locomotion . A two oscillator system was constructed in which most of the circuit was i... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"and",
"life",
"sciences"
] | 2014 | Slow Noise in the Period of a Biological Oscillator Underlies Gradual Trends and Abrupt Transitions in Phasic Relationships in Hybrid Neural Networks |
Circular DNA elements are involved in genome plasticity , particularly of tandem repeats . However , amplifications of DNA segments in Saccharomyces cerevisiae reported so far involve pre-existing repetitive sequences such as ribosomal DNA , Ty elements and Long Terminal Repeats ( LTRs ) . Here , we report the generati... | Xylose is an important component of lignocellulose hydrolysates used for the production of bioethanol , but the yeast Saccharomyces cerevisiae is unable to utilize xylose . Insertion of a bacterial xylose isomerase gene and improvement of growth on xylose by evolutionary adaptation resulted in amplification of this gen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Rapid Evolution of Recombinant Saccharomyces cerevisiae for Xylose Fermentation through Formation of Extra-chromosomal Circular DNA |
Computational biology is an interdisciplinary field , and many computational biology research projects involve distributed teams of scientists . To accomplish their work , these teams must overcome both disciplinary and geographic barriers . Introducing new training paradigms is one way to facilitate research progress ... | Computational biology research is frequently conducted by virtual teams: groups of scientists in different locations that use shared resources and online communication tools to collaborate on a problem . It is imperative that the next generation of computational biologists can easily work in these interdisciplinary , d... | [
"Abstract",
"Introduction",
"Student",
"recruitment",
"and",
"selection",
"Structure",
"of",
"the",
"research",
"experience",
"Results",
"Discussion"
] | [
"learning",
"employment",
"education",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"careers",
"research",
"design",
"scientists",
"cognitive",
"psychology",
"undergraduates",
"educational",
"status",
"science",
"and",
"technology",
"workforce",
"res... | 2017 | A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design |
The West African Ebola epidemic of 2013–2016 was by far the largest outbreak of the disease on record . Sierra Leone suffered nearly half of the 28 , 646 reported cases . This paper presents a set of culturally contextualized Ebola messages that are based on the findings of qualitative interviews and focus group discus... | The work on which the paper is based was conducted in two Ebola ‘hotspots’ in Sierra Leone ( urban Freetown and rural Bombali district ) between January and April 2015 . Numerous misperceptions about Ebola had developed in the community over the course of 2014 , and it was becoming increasingly clear that the largely t... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"learning",
"medicine",
"and",
"health",
"sciences",
"engineering",
"and",
"technology",
"transportation",
"sociology",
"geographical",
"locations",
"tropical",
"diseases",
"social",
"sciences",
"ebola",
"hemorrhagic",
"fever",
"neuroscience",
"learning",
"and",
"memory",... | 2017 | Development of a set of community-informed Ebola messages for Sierra Leone |
Plague is still a public health problem in the world and is re-emerging , but no efficient vaccine is available . We previously reported that oral inoculation of a live attenuated Yersinia pseudotuberculosis , the recent ancestor of Yersinia pestis , provided protection against bubonic plague . However , the strain poo... | Plague , among the most deadly infections of mankind's history , is present in Africa , Asia and America , and is currently re-emerging , recently causing cases in areas from where it had disappeared for decades . Pneumonic plague , its most deadly and contagious form , is responsible for human-to-human spreading of th... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"bacterial",
"diseases",
"infectious",
"diseases",
"immunity",
"immunology",
"biology",
"microbiology",
"bacterial",
"pathogens"
] | 2012 | An Encapsulated Yersinia pseudotuberculosis Is a Highly Efficient Vaccine against Pneumonic Plague |
Models of the hexagonally arrayed spatial activity pattern of grid cell firing in the literature generally fall into two main categories: continuous attractor models or oscillatory interference models . Burak and Fiete ( 2009 , PLoS Comput Biol ) recently examined noise in two continuous attractor models , but did not ... | For many animals , including rats , accurate spatial memory over relatively large areas is important in order to find food and shelter . Just as unique points in time can be efficiently represented by combinations of repeating elements like hours , days , and months , points in space can be represented as combinations ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"mathematics",
"neuroscience",
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience"
] | 2009 | Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators |
Enteric bacterial pathogens such as enterohemorrhagic E . coli ( EHEC ) and Salmonella Typhimurium target the intestinal epithelial cells ( IEC ) lining the mammalian gastrointestinal tract . Despite expressing innate Toll-like receptors ( TLRs ) , IEC are innately hypo-responsive to most bacterial products . This is t... | Despite being in close contact with billions of commensal bacteria , the epithelial cells that line the intestine develop very weak innate inflammatory responses to bacterial products . The goal of this study was to explore why these cells respond so poorly , and how increasing their innate responsiveness would impact ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"bacterial",
"and",
"foodborne",
"illness",
"immunity",
"gastroenterology",
"and",
"hepatology",
"innate",
"immunity",
"immune",
"defense",
"immunology",
"immune",
"tolerance",
"biology",
"immunity",
"to",
"infections",
"immunoregulation",
"inflammatory",
"bow... | 2013 | SIGIRR, a Negative Regulator of TLR/IL-1R Signalling Promotes Microbiota Dependent Resistance to Colonization by Enteric Bacterial Pathogens |
Studies of evolutionary responses to novel environments typically consider single species or perhaps pairs of interacting species . However , all organisms co-occur with many other species , resulting in evolutionary dynamics that might not match those predicted using single species approaches . Recent theories predict... | Understanding how species adapt to new environments is important both for evolutionary theory and for predicting and managing ecosystem responses to changing environments . However , most research into adaptation to new environments has considered species in isolation . Whether results from these systems apply to more ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"community",
"ecology",
"evolutionary",
"ecology",
"adaptation",
"coevolution",
"ecology",
"ecosystems",
"evolutionary",
"biology",
"ecosystem",
"functioning",
"biology",
"species",
"interactions",
"evolutionary",
"processes"
] | 2012 | Species Interactions Alter Evolutionary Responses to a Novel Environment |
To facilitate whole-genome association studies ( WGAS ) , several high-density SNP genotyping arrays have been developed . Genetic coverage and statistical power are the primary benchmark metrics in evaluating the performance of SNP arrays . Ideally , such evaluations would be done on a SNP set and a cohort of individu... | Advances in SNP genotyping array technologies have made whole-genome association studies ( WGAS ) a readily available approach . Genetic coverage and the statistical power are two key properties to evaluate on the arrays . In this study , 359 newly sampled individuals were genotyped using Affymetrix 500K and Illumina 6... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"and",
"genomics",
"computational",
"biology/genomics",
"computational",
"biology/transcriptional",
"regulation"
] | 2008 | Calibrating the Performance of SNP Arrays for Whole-Genome Association Studies |
The mechanism of intra-protein communication and allosteric coupling is key to understanding the structure-property relationship of protein function . For subtilisin Carlsberg , the Ca2+-binding loop is distal to substrate-binding and active sites , yet the serine protease function depends on Ca2+ binding . The atomic ... | A hallmark of protein molecules is their machine-like behaviors while carrying out biological functions . At the molecular level , molecular signals such as binding a metal ion at an action site can cause long-range effects and alter protein function . Such phenomena are often referred to as intra-protein communication... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"protein",
"chemistry",
"genomics",
"computational",
"chemistry",
"molecular",
"dynamics",
"biophysic",
"al",
"simulations",
"chemical",
"physics",
"gaussian",
"fluctuations",
"chemistry",
"biology",
"computational",
"biology",
"biophysics",
"simulations",
"biophysics",
"ph... | 2011 | “Fluctuograms” Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution |
The in vivo activity of CA1 pyramidal neurons alternates between regular spiking and bursting , but how these changes affect information processing remains unclear . Using a detailed CA1 pyramidal neuron model , we investigate how timing and spatial arrangement variations in synaptic inputs to the distal and proximal d... | Pyramidal neurons in the hippocampus are crucially involved in learning and memory functions , but the ways in which they contribute to the processing of sensory inputs and their internal representation remain mostly unclear . The principal neurons of the CA1 region of the hippocampus are surrounded by at least 21 diff... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"biology/neuronal",
"and",
"glial",
"cell",
"biology",
"neuroscience",
"neuroscience/sensory",
"systems",
"cell",
"biology/cell",
"signaling",
"biophysics/experimental",
"biophysical",
"methods",
"biophysics/theory",
"and",
"simulation",
"cell",
"biology",
"cell",
"... | 2010 | Encoding of Spatio-Temporal Input Characteristics by a CA1 Pyramidal Neuron Model |
IbNAC1 is known to activate the defense system by reprogramming a genetic network against herbivory in sweet potato . This regulatory activity elevates plant defense potential but relatively weakens plants by IbNAC1-mediated JA response . The mechanism controlling IbNAC1 expression to balance plant vitality and surviva... | Plants develop sophisticated defense systems against insect attack . IbNAC1 is a transcriptional activator , which up-regulates sporamin expression against herbivory in sweet potato . However , it simultaneously injures the plant by IbNAC1-induced JA response . Thus , dynamic regulatory networks to coordinate the expre... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"anatomy",
"ecology",
"and",
"environmental",
"sciences",
"gene",
"regulation",
"regulatory",
"proteins",
"brassica",
"dna-binding",
"proteins",
"plant",
"physiology",
"sweet",
"potato",
"plant",
"science",
"model",
"organisms",
"herbivory",
"transcription",
"f... | 2016 | The Sweet Potato NAC-Domain Transcription Factor IbNAC1 Is Dynamically Coordinated by the Activator IbbHLH3 and the Repressor IbbHLH4 to Reprogram the Defense Mechanism against Wounding |
In multicellular organisms , development , growth and reproduction require coordinated expression of numerous functional and regulatory genes . Insects , in addition to being the most speciose animal group with enormous biological and economical significance , represent outstanding model organisms for studying regulati... | In addition to being vectors of devastating human diseases , mosquitoes represent outstanding model organisms for studying regulatory mechanisms of differential gene expression due to their rapid reproductive cycles . About 7500 transcripts are differentially expressed in four sequential waves during the 72-h reproduct... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Regulation of Gene Expression Patterns in Mosquito Reproduction |
Parental imprinting is a mammalian-specific form of epigenetic regulation in which one allele of a gene is silenced depending on its parental origin . Parentally imprinted genes have been shown to play a role in growth , metabolism , cancer , and behavior . Although the molecular mechanisms underlying parental imprinti... | Parental genomic imprinting is a mammalian-specific form of epigenetic control that regulates genes differently depending upon whether they are paternally or maternally inherited . The selective advantage of genomic imprinting is poorly understood and has been the subject of numerous theories . In the last several deca... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"milk",
"body",
"fluids",
"vertebrates",
"mice",
"neuroscience",
"animals",
"mammals",
"hormones",
"animal",
"models",
"model",
"organisms",
"probability",
"distribution",
"animal",
"behavior",
"mathematics",
"z... | 2016 | A Novel Mutant Allele of Pw1/Peg3 Does Not Affect Maternal Behavior or Nursing Behavior |
In regenerative tissues , one of the strategies to protect stem cells from genetic aberrations , potentially caused by frequent cell division , is to transiently expand the stem cell daughters before further differentiation . However , failure to exit the transit amplification may lead to overgrowth , and the molecular... | In regenerative tissues , the successive differentiation of stem cell lineage is well controlled and coordinated with proper cell proliferation at each differentiation stage . Disruption of the control mechanism can lead to tumor growth or tissue degeneration . The germline stem cell lineage of Drosophila spermatogenes... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"gene",
"function",
"developmental",
"biology",
"stem",
"cells",
"animal",
"cells",
"cell",
"biology",
"genetics",
"biology",
"and",
"life",
"sciences",
"cellular",
"types",
"cell",
"differentiation",
"adult",
"stem",
"cells"
] | 2014 | Three RNA Binding Proteins Form a Complex to Promote Differentiation of Germline Stem Cell Lineage in Drosophila |
A challenge in structural genomics is prediction of the function of uncharacterized proteins . When proteins cannot be related to other proteins of known activity , identification of function based on sequence or structural homology is impossible and in such cases it would be useful to assess structurally conserved bin... | For a substantial proportion of proteins , their functions are not known since these proteins are not related in sequence to any other known proteins . Binding sites are evolutionarily conserved across very distant protein families , and finding similar binding sites between known and unknown proteins can provide clues... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison |
Downstream of gene expression , effectors such as the actomyosin contractile machinery drive embryo morphogenesis . During Drosophila embryonic axis extension , actomyosin has a specific planar-polarised organisation , which is responsible for oriented cell intercalation . In addition to these cell rearrangements , cel... | The morphogenesis of living organisms is a facinating process during which a genetic programme controls a sequence of molecular changes which will cause the original embryo to acquire a new shape . While we have a growing knowledge of the timing and spatial distribution of key molecules downstream of genetic programmes... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"invertebrates",
"classical",
"mechanics",
"fluid",
"mechanics",
"condensed",
"matter",
"physics",
"anisotropy",
"animals",
"simulation",
"and",
"modeling",
"animal",
"models",
"developmental",
"biology",
"viscosity",
"drosophila",
"melanogaster",
"model",
"organisms",
"m... | 2017 | Geometry can provide long-range mechanical guidance for embryogenesis |
Phagocytosis plays a key role in nutrient uptake and virulence of the protist parasite Entamoeba histolytica . Phagosomes have been characterized by proteomics , and their maturation in the cells has been studied . However , there is so far not much understanding about initiation of phagocytosis and formation of phagos... | Entamoeba histolytica is one of the major causes of morbidity and mortality in developing countries . Phagocytosis plays an important role in both survival and virulence , and has been used as one of the virulence markers . E . histolytica displays a high rate of phagocytosis and offers a unique system to understand th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"cell",
"biology",
"biology",
"and",
"life",
"sciences",
"microbiology",
"molecular",
"biology",
"parasitology"
] | 2014 | A Novel Alpha Kinase EhAK1 Phosphorylates Actin and Regulates Phagocytosis in Entamoeba histolytica |
It has recently been demonstrated that the nucleobase-density profiles of mRNA coding sequences are related in a complementary manner to the nucleobase-affinity profiles of their cognate protein sequences . Based on this , it has been proposed that cognate mRNA/protein pairs may bind in a co-aligned manner , especially... | Messenger RNAs and proteins , two essential types of biopolymers , have recently been shown to exhibit closely related , complementary physicochemical properties . Specifically , density profiles of certain groups in messenger RNA sequences directly match the affinity profiles for precisely those groups in protein sequ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"protein",
"interactions",
"nucleobases",
"messenger",
"rna",
"nucleotides",
"amino",
"acid",
"sequence",
"analysis",
"mathematics",
"statistics",
"(mathematics)",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"rna",
"structure",
"bioinformatics",
"pro... | 2017 | mRNA/protein sequence complementarity and its determinants: The impact of affinity scales |
Venezuelan equine encephalitis virus ( VEEV ) is an arbovirus endemic to the Americas that is responsible for severe , sometimes fatal , disease in humans and horses . We previously described an IRES-based VEE vaccine candidate based up the IE serotype that offers complete protection against a lethal subtype IE VEEV ch... | Venezuelan equine encephalitis virus ( VEEV ) is a mosquito-borne arbovirus endemic to the Americas that affects a wide range of equids and humans . Vaccination has been one of the strategies to combat spread of disease in areas with high rates incidence of VEEV , although existing vaccines have proven less than effect... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | IRES-Containing VEEV Vaccine Protects Cynomolgus Macaques from IE Venezuelan Equine Encephalitis Virus Aerosol Challenge |
Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages . They are found in many species including most clinical strains of the human pathogens , Staphylococcus aureus and Salmonella enterica serovar Typhimurium . Previously , temperate phages were considered ... | Viruses ( phages ) that only attack bacteria are highly common . Some of these phages naturally reside within the bacterial chromosome for extended periods of time . Upon release and propagation on phage susceptible cells , new phage particles are made but occasionally bacterial rather than phage DNA is packaged into p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"bacteriology",
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"bacteriophages",
"pathogens",
"drugs",
"microbiology",
"staphylococcus",
"aureus",
"viruses",
"antibiotic",
"resistance",
"lysogeny",
"antibiotics",
"ba... | 2019 | Bacteriophages benefit from generalized transduction |
Streptococcus equi subspecies equi ( S . equi ) is a clonal , equine host-adapted pathogen of global importance that causes a suppurative lymphodendopathy of the head and neck , more commonly known as Strangles . The disease is highly prevalent , can be severe and is highly contagious . Antibiotic treatment is usually ... | Numerous research groups have vaccinated , using recombinant antigens , against streptococcal infections in mouse model systems and shown protection . We have here demonstrated efficient protective vaccination of the natural host , the horse , using recombinant antigens . Streptococcus equi subspecies equi ( S . equi )... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/immunity",
"to",
"infections",
"immunology/immune",
"response",
"microbiology/innate",
"immunity",
"pathology/histopathology",
"molecular",
"biology/bioinformatics",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"infectious",
"diseases/respiratory",
... | 2009 | Getting to Grips with Strangles: An Effective Multi-Component Recombinant Vaccine for the Protection of Horses from Streptococcus equi Infection |
Misfolded proteins ( MP ) are a key component in aging and associated neurodegenerative disorders . For example , misfolded Amyloid-ß ( Aß ) and tau proteins are two neuropathogenic hallmarks of Alzheimer's disease . Mechanisms underlying intra-brain MP propagation/deposition remain essentially uncharacterized . Here ,... | Misfolded proteins ( MP ) mechanisms are a characteristic pathogenic feature of most prevalent human neurodegenerative diseases , such as Alzheimer's disease ( AD ) . Characterizing the mechanisms underlying intra-brain MP propagation and deposition still constitutes a major challenge . Here , we hypothesize that these... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"connectomics",
"medicine",
"and",
"health",
"sciences",
"dementia",
"neuroanatomy",
"anatomy",
"mental",
"health",
"and",
"psychiatry",
"computational",
"neuroscience",
"nervous",
"system",
"neurology",
"neurodegenerative",
"diseases",
"biology",
"and",
"life",
"sciences... | 2014 | Epidemic Spreading Model to Characterize Misfolded Proteins Propagation in Aging and Associated Neurodegenerative Disorders |
A high level of robustness against gene deletion is observed in many organisms . However , it is still not clear which biochemical features underline this robustness and how these are acquired during evolution . One hypothesis , specific to metabolic networks , is that robustness emerges as a byproduct of selection for... | One of the most surprising recent biological findings is the high level of tolerance organisms show towards loss of single genes . This observation suggests that there are certain features of biological systems that give them a high tolerance ( i . e . robustness ) towards gene loss . We still lack an exact understandi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"biology/microbial",
"physiology",
"and",
"metabolism",
"biochemistry/molecular",
"evolution",
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"mathematics",
"computational",
... | 2010 | Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks |
T cells orchestrate the adaptive immune response , making them targets for immunotherapy . Although immunosuppressive therapies prevent disease progression , they also leave patients susceptible to opportunistic infections . To identify novel drug targets , we established a logical model describing T-cell receptor ( TC... | The cells of the mammalian immune system do not exist in isolation , but rather form an integrated network that is constantly scanning the body for signs of ‘foreign’ invasion . Working together , these cells possess the ability to repel invaders and thereby establish protective immunity . One central population in thi... | [
"Abstract",
"Introduction",
"Methods",
"Results/Discussion"
] | [
"biochemistry",
"signal",
"transduction",
"molecular",
"cell",
"biology",
"immune",
"cells",
"proteins",
"t",
"cells",
"immunology",
"biology",
"computational",
"biology",
"signaling",
"networks",
"molecular",
"biology",
"t-cell",
"receptors"
] | 2011 | Integrating Signals from the T-Cell Receptor and the Interleukin-2 Receptor |
Latent toxoplasmosis , a lifelong infection with the protozoan Toxoplasma gondii , has cumulative effects on the behaviour of hosts , including humans . The most impressive effect of toxoplasmosis is the “fatal attraction phenomenon , ” the conversion of innate fear of cat odour into attraction to cat odour in infected... | Latent toxoplasmosis , a lifelong infection with the protozoan Toxoplasma gondii , has cumulative effects on the behaviour of hosts , including humans . The most impressive effect of toxoplasmosis is the so-called “fatal attraction phenomenon , ” the conversion of innate fear of odour of the definitive host , the cat ,... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"evolutionary",
"ecology",
"behavioral",
"neuroscience",
"animal",
"behavior",
"ecology",
"parasitology",
"biology",
"sensory",
"perception",
"zoology",
"neuroscience",
"animal",
"cognition",
"behavioral",
"ecology"
] | 2011 | Fatal Attraction Phenomenon in Humans – Cat Odour Attractiveness Increased for Toxoplasma-Infected Men While Decreased for Infected Women |
Endogenous small molecule metabolites that regulate animal longevity are emerging as a novel means to influence health and life span . In C . elegans , bile acid-like steroids called the dafachronic acids ( DAs ) regulate developmental timing and longevity through the conserved nuclear hormone receptor DAF-12 , a homol... | Although well known for their role in the absorption of dietary fat , bile acids have emerged as important metabolic signaling molecules that regulate cholesterol , fat , and glucose metabolism . Bile acids work through nuclear receptors , a class of transcription factors that bind to fat soluble hormones to directly c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"biochemistry",
"developmental",
"biology",
"lipids",
"signal",
"transduction",
"model",
"organisms",
"molecular",
"cell",
"biology",
"organism",
"development",
"molecular",
"development",
"biology",
"metabolism",
"molecular",
"biology"
] | 2012 | A Novel 3-Hydroxysteroid Dehydrogenase That Regulates Reproductive Development and Longevity |
The nucleolus is a multifunctional structure within the nucleus of eukaryotic cells and is the primary site of ribosome biogenesis . Almost all viruses target and disrupt the nucleolus—a feature exclusive to this pathogen group . Here , using a combination of bio-imaging , genetic and biochemical analyses , we demonstr... | Many of the world's most important diseases are caused by bacterial pathogens that deliver effector proteins into the cells of their host . Effector proteins are collectively responsible for causing disease and an important area of research is to define the functions of these proteins and identify how they are regulate... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"virology/virulence",
"factors",
"and",
"mechanisms",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis",
"cell",
"biology/nuclear",
"structure",
"and",
"function"
] | 2010 | The Enteropathogenic E. coli Effector EspF Targets and Disrupts the Nucleolus by a Process Regulated by Mitochondrial Dysfunction |
Genome-wide dynamic changes in DNA methylation are indispensable for germline development and genomic imprinting in mammals . Here , we report single-base resolution DNA methylome and transcriptome maps of mouse germ cells , generated using whole-genome shotgun bisulfite sequencing and cDNA sequencing ( mRNA-seq ) . Oo... | In mammals , germ-cell–specific methylation patterns and genomic imprints are established throughout large-scale de novo DNA methylation in oogenesis and spermatogenesis . These steps are required for normal germline differentiation and embryonic development; however , current DNA methylation analyses only provide us a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"developmental",
"biology",
"genetics",
"biology",
"genomics",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks |
Polycomb Group ( PcG ) proteins are epigenetic repressors that control metazoan development and cell differentiation . In Drosophila , PcG proteins form five distinct complexes targeted to genes by Polycomb Response Elements ( PREs ) . Of all PcG complexes PhoRC is the only one that contains a sequence-specific DNA bin... | Polycomb Group ( PcG ) proteins are epigenetic repressors essential for development and cell differentiation . PcG proteins form five complexes targeted to specific genes by Polycomb Response Elements ( PREs ) . How PcG complexes are recruited to PREs is poorly understood . Here we investigate the recruitment of PhoRC ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"developmental",
"biology",
"model",
"organisms",
"genetics",
"biology",
"and",
"life",
"sciences",
"genomics",
"research",
"and",
"analysis",
"methods"
] | 2014 | Combinatorial Interactions Are Required for the Efficient Recruitment of Pho Repressive Complex (PhoRC) to Polycomb Response Elements |
The carbohydrate larval antigen , CarLA , is present on the exposed surface of all strongylid nematode infective L3 larvae tested , and antibodies against CarLA can promote rapid immune rejection of incoming Trichostrongylus colubriformis larvae in sheep . A library of ovine recombinant single chain Fv ( scFv ) antibod... | Strongylid nematode worm parasites currently infect hundreds of millions of people , and most farmed animals , causing enormous morbidity and economic loss . These parasites commonly produce chronic gastrointestinal infections that are highly refractory to immune clearance mechanisms . Mucosal antibodies against a carb... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"immunology/immunity",
"to",
"infections",
"immunology/immune",
"response",
"infectious",
"diseases/gastrointestinal",
"infections"
] | 2009 | Intraspecific Epitopic Variation in a Carbohydrate Antigen Exposed on the Surface of Trichostrongylus colubriformis Infective L3 Larvae |
Dengue virus ( DENV ) is an enveloped RNA virus that causes the most common arthropod-borne infection worldwide . The mechanism by which DENV infects the host cell remains unclear . In this work , we used live-cell imaging and single-virus tracking to investigate the cell entry , endocytic trafficking , and fusion beha... | Dengue virus ( DENV ) is the most common arthropod-borne infection worldwide with 50–100 million cases annually . Despite its high clinical impact , little is known about the infectious cell entry pathway of the virus . Previous studies have shown conflicting evidence about whether the virus fuses directly with the cel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/host",
"invasion",
"and",
"cell",
"entry"
] | 2008 | Dissecting the Cell Entry Pathway of Dengue Virus by Single-Particle Tracking in Living Cells |
Many protein-protein interactions ( PPIs ) are compelling targets for drug discovery , and in a number of cases can be disrupted by small molecules . The main goal of this study is to examine the mechanism of binding site formation in the interface region of proteins that are PPI targets by comparing ligand-free and li... | Many protein-protein interfaces ( PPIs ) are biologically compelling drug targets . Disrupting the interaction between two large proteins by a small inhibitor requires forming a high affinity binding site in the interface that generally can bind both peptides and drug-like compounds . Here we investigate whether such s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"biochemistry",
"molecular",
"complexes",
"biophysics",
"theory",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"biophysics",
"molecular",
"biology",
"biophysical",
"simulations"
] | 2014 | Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces |
Several studies have shown Dengue Virus ( DENV ) nucleic acids and/or antibodies present in Neotropical wildlife including bats , suggesting that some bat species may be susceptible to DENV infection . Here we aim to elucidate the role of house-roosting bats in the DENV transmission cycle . Bats were sampled in househo... | Dengue is the most important human vector-borne disease . Several studies have shown DENV presence in mammalian wildlife such as bats , thus considering them putative reservoirs or hosts . We aimed to elucidate if bats that cohabit in houses in close proximity with humans may be involved in a dengue transmission cycle ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"taxonomy",
"invertebrates",
"dengue",
"virus",
"animal",
"types",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"vertebrates",
"animals",
"mamm... | 2017 | Neotropical bats that co-habit with humans function as dead-end hosts for dengue virus |
Interleukin-6 is a pleiotropic , pro-inflammatory cytokine that can promote both innate and adaptive immune responses . In humans with respiratory virus infections , such as Respiratory Syncytial Virus ( RSV ) , elevated concentrations of IL-6 are associated with more severe disease . In contrast the polymorphisms in t... | In clearing a respiratory virus , the host must strike a careful balance between the need to clear the infection and the potential of the immune response to damage the delicate structure of the lungs . Here we show that Interleukin-6 , a soluble mediator commonly associated with inflammation and seen in humans with sev... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"respiratory",
"infections",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"orthom... | 2017 | Early IL-6 signalling promotes IL-27 dependent maturation of regulatory T cells in the lungs and resolution of viral immunopathology |
The recent emergence of a novel H7N9 influenza A virus ( IAV ) causing severe human infections in China raises concerns about a possible pandemic . The lack of pre-existing neutralizing antibodies in the broader population highlights the potential protective role of IAV-specific CD8+ cytotoxic T lymphocyte ( CTL ) memo... | The emergence of human infections with a novel strain of avian-origin H7N9 virus in China raises a pandemic concern . The introduction of a new subtype in humans makes people at all ages susceptible due to the lack of population-wide neutralizing antibodies . However , cross-subtype protection from existing host immuni... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Diverse Heterologous Primary Infections Radically Alter Immunodominance Hierarchies and Clinical Outcomes Following H7N9 Influenza Challenge in Mice |
Viral invasion into a host is initially recognized by the innate immune system , mainly through activation of the intracellular cytosolic signaling pathway and coordinated activation of interferon regulatory factor 3 ( IRF3 ) and nuclear factor kappa B ( NF-κB ) transcription factors that promote type I interferon gene... | The innate immune system has evolved to detect and neutralize viral invasion . Triggering of this defense mechanism relies on the production and secretion of soluble factors that stimulate an intracellular antiviral defense mechanism . The protein Optineurin was shown to negatively regulate this process . Importantly ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Optineurin Regulates the Interferon Response in a Cell Cycle-Dependent Manner |
Isolated influenza A virus nucleoprotein exists in an equilibrium between monomers and trimers . Samples containing only monomers or only trimers can be stabilized by respectively low and high salt . The trimers bind RNA with high affinity but remain trimmers , whereas the monomers polymerise onto RNA forming nucleopro... | The RNAs of negative strand RNA viruses are encapsidated by their specific viral nucleoproteins , forming helical nucleoprotein-RNA structures that are the template for transcription and replication . All these nucleoproteins have two activities in common: RNA binding and self-polymerisation , and it is likely that the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"rna",
"rna",
"viruses",
"nucleic",
"acids",
"virology",
"viral",
"classification",
"biology",
"microbiology"
] | 2013 | Monomeric Nucleoprotein of Influenza A Virus |
The current unprecedented expansion of infrastructure promises to enhance human wellbeing but risks causing substantial harm to natural ecosystems and the benefits they provide for people . A framework for systematically and proactively identifying the likely benefits and costs of such developments is badly needed . He... | Proposals for new infrastructure in developing countries are typically muted on its environmental impacts , while environmentalists typically say little about its potential benefits for people . This study explores a more conciliatory approach by trying to identify where beneficial infrastructure might be expanded at l... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"ecology",
"and",
"environmental",
"sciences",
"engineering",
"and",
"technology",
"transportation",
"geographical",
"locations",
"vertebrates",
"biodiversity",
"animals",
"transportation",
"infrastructure",
"roads",
"habitats",
"civil",
"engineering",
"birds",
"ecosystems",
... | 2016 | Getting Road Expansion on the Right Track: A Framework for Smart Infrastructure Planning in the Mekong |
Preventing germline stem cell proliferation extends lifespan in nematodes and flies . So far , studies on germline-longevity signaling have focused on daf-16/FOXO and daf-12/VDR . Here , we report on NHR-80/HNF4 , a nuclear receptor that specifically mediates longevity induced by depletion of the germ line through a me... | Reproduction and aging are two processes that seem to be closely intertwined . Experiments in Caenorhabditis elegans and Drosophila have shown that depletion of the germ line increases lifespan and that this process depends on insulin and lipophilic-hormone signaling . Recently , it was demonstrated that when germline ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/aging"
] | 2011 | Fatty Acid Desaturation Links Germ Cell Loss to Longevity Through NHR-80/HNF4 in C. elegans |
Abnormal accumulation of the microtubule-interacting protein tau is associated with neurodegenerative diseases including Alzheimer’s disease ( AD ) . β-amyloid ( Aβ ) lies upstream of abnormal tau behavior , including detachment from microtubules , phosphorylation at several disease-specific sites , and self-aggregatio... | Alzheimer’s disease ( AD ) is the most common cause of dementia resulting from progressive neuron loss . Two proteins , β-amyloid ( Aβ ) and tau , accumulate in AD brains and are involved in AD pathogenesis . In healthy neurons , tau binds to microtubules to regulate its stability; in AD brains , however , tau is detac... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"rna",
"interference",
"microtubules",
"pathology",
"and",
"laboratory",
"medicine",
"neurodegenerative",
"diseases",
"toxicology",
"toxicity",
"epigenetics",
"tubulins",
"alzheimer",
"disease",
"cellular",
"struct... | 2016 | Stabilization of Microtubule-Unbound Tau via Tau Phosphorylation at Ser262/356 by Par-1/MARK Contributes to Augmentation of AD-Related Phosphorylation and Aβ42-Induced Tau Toxicity |
Reproduction in fishes and other vertebrates represents the timely coordination of many endocrine factors that culminate in the production of mature , viable gametes . In recent years there has been rapid growth in understanding fish reproductive biology , which has been motivated in part by recognition of the potentia... | Reproduction in fishes and other vertebrates represents the timely coordination of many endocrine factors that culminate in the production of mature , viable gametes . Improving the ability to estimate reproductive performance in fish is important , due to the growth of the aquaculture industry and the need to maintain... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"body",
"fluids",
"nervous",
"system",
"vertebrates",
"neuroscience",
"animals",
"reproductive",
"physiology",
"endocrine",
"physiology",
"germ",
"cells",
"osteichthyes",
"oocytes",
"gnrh",
"stimulation",
... | 2016 | A Computational Model of the Rainbow Trout Hypothalamus-Pituitary-Ovary-Liver Axis |
Development and function of tissues and organs are powered by the activity of mitochondria . In humans , inherited genetic mutations that lead to progressive mitochondrial pathology often manifest during infancy and can lead to death , reflecting the indispensable nature of mitochondrial biogenesis and function . Here ... | Mitochondrial pathologies which result from mutations in the nuclear DNA remain incurable and often lead to death . As mitochondria play various roles in cellular and tissue-specific contexts , the symptoms of mitochondrial pathologies can differ between patients . Thus , diagnosis and treatment of mitochondrial disord... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"fish",
"medicine",
"and",
"health",
"sciences",
"skeletal",
"muscles",
"computational",
"biology",
"vertebrates",
"animals",
"animal",
"models",
"osteichthyes",
"developmental",
"biology",
"fungi",
"model",
"organisms",
"experimental",
"organism",
"systems",
"genome",
... | 2018 | Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish |
Severe leptospirosis features bleeding and multi-organ failure , leading to shock and death . Currently it is assumed that both exaggerated inflammation and immune suppression contribute to mortality in sepsis . Indeed , several proinflammatory cytokines are reported to be induced during leptospirosis . Toll-like recep... | Leptospirosis is a bacterial disease that is mainly spread by rodents and other small mammals . Transmission frequently occurs in ( sub- ) tropical countries , where environmental circumstances are most favourable . Severe leptospirosis can cause bleeding and vital organ dysfunction . An exaggerated immune response is ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"immunology/immune",
"response",
"immunology/innate",
"immunity",
"critical",
"care",
"and",
"emergency",
"medicine/sepsis",
"and",
"multiple",
"organ",
"failure",
"immunology",
"infectious"... | 2009 | Soluble ST2 Levels Are Associated with Bleeding in Patients with Severe Leptospirosis |
T cells are known to contribute to immune protection against scrub typhus , a potentially fatal infection caused by the obligate intracellular bacterium Orientia ( O . ) tsutsugamushi . However , the contribution of CD8+ T cells to protection and pathogenesis during O . tsutsugamushi infection is still unknown . Using ... | Orientia ( O . ) tsutsugamushi is the causative agent of scrub typhus , a potentially fatal disease that is endemic in South East Asia . This bacterium replicates in the cytoplasm of its host cells . The obligate intracytoplasmic lifestyle resembles that of many viruses , but among pathogenic bacteria it is unique to O... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"spleen",
"pathogens",
"animal",
"models",
"of",
"disease",
"immunology",
"microbiology",
"animal",
"models",
"bacterial... | 2016 | Protective and Pathogenic Roles of CD8+ T Lymphocytes in Murine Orientia tsutsugamushi Infection |
This paper presents a new agent-based model ( ABM ) for investigating T . b . rhodesiense human African trypanosomiasis ( rHAT ) disease dynamics , produced to aid a greater understanding of disease transmission , and essential for development of appropriate mitigation strategies . The ABM was developed to model rHAT i... | African trypanosomiasis is a parasitic disease which affects humans and other animals in 36 sub-Saharan African countries . The disease is transmitted by the tsetse fly , and the human form of the diseases is known as sleeping sickness . Infectious disease transmission has traditionally been modelled using techniques t... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion",
"Conclusion"
] | [
"death",
"rates",
"invertebrates",
"livestock",
"animal",
"types",
"medicine",
"and",
"health",
"sciences",
"ruminants",
"demography",
"african",
"trypanosomiasis",
"tropical",
"diseases",
"vertebrates",
"parasitic",
"diseases",
"animals",
"mammals",
"glossina",
"simulati... | 2016 | A Multi-Host Agent-Based Model for a Zoonotic, Vector-Borne Disease. A Case Study on Trypanosomiasis in Eastern Province, Zambia |
Associating genetic variation with quantitative measures of gene regulation offers a way to bridge the gap between genotype and complex phenotypes . In order to identify quantitative trait loci ( QTLs ) that influence the binding of a transcription factor in humans , we measured binding of the multifunctional transcrip... | We have systematically measured the effect of normal genetic variation present in a human population on the binding of a specific chromatin protein ( CTCF ) to DNA by measuring its binding in 51 human cell lines . We observed a large number of changes in protein binding that we can confidently attribute to genetic effe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetic",
"association",
"studies",
"genome",
"analysis",
"trait",
"locus",
"analysis",
"genetics",
"biology",
"and",
"life",
"sciences",
"epigenomics",
"computational",
"biology",
"human",
"genetics"
] | 2014 | Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association |
We present a study investigating the role of mitochondrial variability in generating noise in eukaryotic cells . Noise in cellular physiology plays an important role in many fundamental cellular processes , including transcription , translation , stem cell differentiation and response to medication , but the specific r... | Cellular variability has been found to play a major role in diverse and important phenomena , including stem cell differentiation and drug resistance , but the sources of this variability have yet to be satisfactorily explained . We propose a mechanism , supported by a substantial number of recent and new experiments ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"cellular",
"structures",
"theoretical",
"biology",
"cell",
"biology",
"biology",
"computational",
"biology",
"molecular",
"cell",
"biology",
"biophysics",
"genetics",
"and",
"genomics"
] | 2012 | Mitochondrial Variability as a Source of Extrinsic Cellular Noise |
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