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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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|---|---|---|---|---|---|
The p53 family activates many of the same genes in response to DNA damage . Because p63 and p73 have structural differences from p53 and play distinct biological functions in development and metastasis , it is likely that they activate a unique transcriptional network . Therefore , we performed a genome-wide analysis u... | p63 and p73 have been identified as important suppressors of tumorigenesis and metastasis . Although they are structurally similar to p53 , they have many functions that are unique including roles in development and metastasis . Here we show , using a genome-wide analysis of cells lacking p63 and p73 individually and i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"genetics",
"and",
"genomics/cancer",
"genetics",
"genetics",
"and",
"genomics/bioinformatics"
] | 2009 | p63 and p73 Transcriptionally Regulate Genes Involved in DNA Repair |
Accurate chromosome segregation during meiosis requires that homologous chromosomes pair and become physically connected so that they can orient properly on the meiosis I spindle . These connections are formed by homologous recombination closely integrated with the development of meiosis-specific , higher-order chromos... | Meiosis is the specialized cell division that gives rise to reproductive cells such as sperm and eggs . During meiosis in most organisms , genetic information is exchanged between homologous maternal and paternal chromosomes through the process of homologous recombination . This recombination forms connections between ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/germ",
"cells",
"genetics",
"and",
"genomics/nuclear",
"structure",
"and",
"function",
"genetics",
"and",
"genomics/chromosome",
"biology",
"biochemistry/replication",
"and",
"repair",
"genetics",
"and",
"genomics/gene",
"function"
] | 2010 | Mouse TRIP13/PCH2 Is Required for Recombination and Normal Higher-Order Chromosome Structure during Meiosis |
The parameters that modulate the functional capacity of secondary Th1 effector cells are poorly understood . In this study , we employ a serial adoptive transfer model system to show that the functional differentiation and secondary memory potential of secondary CD4+ effector T cells are dependent on the inflammatory e... | A key to the development of strategies for manipulating immune responses is the identification of the factors that regulate the generation of memory T cells . Many vaccination strategies rely on multiple injections to boost memory cell numbers , yet the factors that regulate the function and survival of memory T cells ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"activation",
"immunity",
"to",
"infections",
"immunology",
"vaccination",
"and",
"immunization",
"white",
"blood",
"cells",
"inflammation",
"animal",
"cells",
"t",
"cells",
"imm... | 2014 | Dynamic Functional Modulation of CD4+ T Cell Recall Responses Is Dependent on the Inflammatory Environment of the Secondary Stimulus |
BICD2 is one of the two mammalian homologues of the Drosophila Bicaudal D , an evolutionarily conserved adaptor between microtubule motors and their cargo that was previously shown to link vesicles and mRNP complexes to the dynein motor . Here , we identified a G2-specific role for BICD2 in the relative positioning of ... | Bidirectional microtubule-based transport is responsible for the positioning of a large variety of cellular organelles , but the molecular mechanisms underlying the recruitment of microtubule-based motors to their cargoes and their activation remain poorly understood . In particular , the molecular players involved in ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/cell",
"growth",
"and",
"division",
"cell",
"biology",
"cell",
"biology/cytoskeleton"
] | 2010 | Bicaudal D2, Dynein, and Kinesin-1 Associate with Nuclear Pore Complexes and Regulate Centrosome and Nuclear Positioning during Mitotic Entry |
A diverse subset of pattern recognition receptors ( PRRs ) detects pathogen-associated nucleic acids to initiate crucial innate immune responses in host organisms . Reflecting their importance for host defense , pathogens encode various countermeasures to evade or inhibit these immune effectors . PRRs directly engaged ... | A pathogen’s ability to infect new individuals within and across species is largely driven by its capacity to hijack cellular machinery and overcome the immune system . Pathogens have evolved multiple means to evade and shut down host immunity . Typically , mechanisms of inactivation involve direct interactions between... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods",
"and",
"Materials"
] | [] | 2015 | Overlapping Patterns of Rapid Evolution in the Nucleic Acid Sensors cGAS and OAS1 Suggest a Common Mechanism of Pathogen Antagonism and Escape |
Yaws and trachoma are targeted for eradication and elimination as public health problems . In trachoma-endemic populations mass administration of azithromycin can simultaneously treat yaws . We conducted a population-based prevalence survey in the five northernmost provinces of Vanuatu , where trachoma and yaws are sus... | Yaws and trachoma are infectious diseases targeted by the World Health Organization ( WHO ) for eradication and elimination as a public health problem , respectively . Both diseases are found in the rural , isolated and underserved communities of the world’s poorest countries . The WHO strategy for trachoma elimination... | [
"Abstract",
"Introduction",
"Methods",
"Household",
"Risk",
"factors",
"Survey",
"Statistical",
"Analysis",
"Ethical",
"Considerations",
"Results",
"Clinical",
"Yaws",
"Treponemal",
"RDT",
"Results",
"Risk",
"Factors",
"Associated",
"with",
"TF",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"chlamydia",
"trachomatis",
"pathogens",
"immunology",
"tropical",
"diseases",
"geographical",
"locations",
"vanuatu",
"microbiology",
"health",
"care",
"treponematoses",
"bacterial",
"... | 2017 | Integrated Mapping of Yaws and Trachoma in the Five Northern-Most Provinces of Vanuatu |
Snake bite is a major neglected public health issue within poor communities living in the rural areas of several countries throughout the world . An estimated 2 . 5 million people are bitten by snakes each year and the cost and lack of efficacy of current anti-venom therapy , together with the lack of detailed knowledg... | Snake bite is a major neglected public health issue causing an estimated 125 , 000 deaths each year , predominantly within poor communities living in rural areas of countries in South East Asia and Africa . Current treatments for snake bites are costly and have limited effectiveness , thus there is a need to develop no... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"public",
"health",
"and",
"epidemiology",
"chemical",
"biology/biocatalysis",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"biochemistry/protein",
"chemistry",
"biochemistry/macromolecular",
"chemistry",
"molecular",
"biology/bioinformatics",
"comput... | 2010 | Purification and Functional Characterisation of Rhiminopeptidase A, a Novel Aminopeptidase from the Venom of Bitis gabonica rhinoceros |
Nervous systems are information processing networks that evolved by natural selection , whereas very large scale integrated ( VLSI ) computer circuits have evolved by commercially driven technology development . Here we follow historic intuition that all physical information processing systems will share key organizati... | Brains are often compared to computers but , apart from the trivial fact that both process information using a complex physical pattern of connections , it has been unclear whether this is more than just a metaphor . In our work , we rigorously uncover novel quantitative organizational principles that underlie the netw... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"physics/interdisciplinary",
"physics",
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience"
] | 2010 | Efficient Physical Embedding of Topologically Complex Information Processing Networks in Brains and Computer Circuits |
RNA silencing , mediated by small RNAs including microRNAs ( miRNAs ) and small interfering RNAs ( siRNAs ) , is a potent antiviral or antibacterial mechanism , besides regulating normal cellular gene expression critical for development and physiology . To gain insights into host small RNA metabolism under infections b... | Small RNA-mediated RNA silencing is a widespread antiviral or antibacterial mechanism in different organisms . Although the host and pathogen factors involved in this mode of host defense and pathogen counter-defense have been extensively investigated , much less is known about how a pathogen alters the small RNA metab... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mechanisms",
"of",
"resistance",
"and",
"susceptibility",
"plant",
"science",
"virology",
"plant",
"pathogens",
"plant",
"biology",
"plant",
"pathology",
"biology",
"microbiology"
] | 2011 | Viral Infection Induces Expression of Novel Phased MicroRNAs from Conserved Cellular MicroRNA Precursors |
Quantitative models of cis-regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation . However , the few models available today have been based on simplistic assumptions about the sequences being modeled , or heuristic approximations of the underlying regulatory mecha... | The development of complex multicellular organisms requires genes to be expressed at specific stages and in specific tissues . Regulatory DNA sequences , often called cis-regulatory modules , drive the desired gene expression patterns by integrating information about the environment in the form of the activities of tra... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"and",
"genomics/gene",
"expression",
"computational",
"biology/transcriptional",
"regulation",
"biophysics/theory",
"and",
"simulation",
"computational",
"biology/macromolecular",
"sequence",
"analysis",
"biophysics/transcription",
"and",
"translation"
] | 2010 | Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression |
The N-methyl-D-aspartate receptor ( NMDAR ) , a major excitatory ligand-gated ion channel in the central nervous system ( CNS ) , is a principal mediator of synaptic plasticity . Here we report that neuropilin tolloid-like 1 ( Neto1 ) , a complement C1r/C1s , Uegf , Bmp1 ( CUB ) domain-containing transmembrane protein ... | The fundamental unit for information processing in the brain is the synapse , a highly specialized site of communication between the brain's multitude of individual neurons . The strength of the communication at each synapse changes in response to neuronal activity—a process called synaptic plasticity—allowing networks... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neurological",
"disorders",
"neuroscience",
"genetics",
"and",
"genomics"
] | 2009 | Neto1 Is a Novel CUB-Domain NMDA Receptor–Interacting Protein Required for Synaptic Plasticity and Learning |
The dose response curve is the gold standard for measuring the effect of a drug treatment , but is rarely used in genomic scale transcriptional profiling due to perceived obstacles of cost and analysis . One barrier to examining transcriptional dose responses is that existing methods for microarray data analysis can id... | Transcriptional profiling is arguably the most powerful hypothesis-free method for investigating biological effects of drugs—so why do the experiments typically use outmoded single-dose designs ? Such single-dose experiments will co-mingle effects that can occur with different potency ( e . g . , effects on the known t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry/drug",
"discovery",
"genetics",
"and",
"genomics/gene",
"expression",
"biotechnology/chemical",
"biology",
"of",
"the",
"cell",
"pharmacology/drug",
"development",
"molecular",
"biology/bioinformatics",
"computational",
"biology/systems",
"biology"
] | 2009 | Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities |
The epithelium efficiently attracts immune cells upon infection despite the low number of pathogenic microbes and moderate levels of secreted chemokines per cell . Here we examined whether horizontal intercellular communication between cells may contribute to a coordinated response of the epithelium . Listeria monocyto... | All body surfaces are covered by a single layer of epithelial cells . Epithelial cells form a physical barrier to separate the underlying sterile tissue from the environment . In addition , epithelial cells actively sense bacterial and viral infection . The recognition of pathogenic microorganisms results in cell stimu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"immunology/innate",
"immunity"
] | 2010 | Potentiation of Epithelial Innate Host Responses by Intercellular Communication |
Temporal lobe epilepsy strongly affects hippocampal dentate gyrus granule cells morphology . These cells exhibit seizure-induced anatomical alterations including mossy fiber sprouting , changes in the apical and basal dendritic tree and suffer substantial dendritic spine loss . The effect of some of these changes on th... | Neurogenesis is currently a well known phenomenon in the adult brain , in special in some areas such as the subventricular zone and the dentate gyrus in the hippocampus , in which different endogenous and exogenous factors provoke cell proliferation . In the specific case of the dentate gyrus , granule cells proliferat... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"circuit",
"models",
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"medicine",
"and",
"health",
"sciences",
"computational",
"neuroscience",
"neurology",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"neuroscience"
] | 2014 | Combined Role of Seizure-Induced Dendritic Morphology Alterations and Spine Loss in Newborn Granule Cells with Mossy Fiber Sprouting on the Hyperexcitability of a Computer Model of the Dentate Gyrus |
Plant infection by pathogenic fungi involves the differentiation of appressoria , specialized infection structures , initiated by fungal sensing and responding to plant surface signals . How plant fungal pathogens control infection-related morphogenesis in response to plant-derived signals has been unclear . Here we sh... | Phytopathogenic fungi cause many of the most serious crop diseases . Many fungal pathogens form specialized infection structures , called appressoria in response to plant surface signals . Networks of protein kinase-based signaling pathways regulate a wide variety of key morphological processes including appressorium d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"plant",
"anatomy",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"plant",
"growth",
"and",
"development",
"enzymes",
"distillation",
"plant",
"embryo",
"anatomy",
"enzymology",
"fungal",
"structure",
"developmental",
"biology",
... | 2017 | The morphogenesis-related NDR kinase pathway of Colletotrichum orbiculare is required for translating plant surface signals into infection-related morphogenesis and pathogenesis |
Biogenesis of ribosomes is an essential cellular process conserved across all eukaryotes and is known to require >170 genes for the assembly , modification , and trafficking of ribosome components through multiple cellular compartments . Despite intensive study , this pathway likely involves many additional genes . Her... | Ribosomes are the extremely complex cellular machines responsible for constructing new proteins . In eukaryotic cells , such as yeast , each ribosome contains more than 80 protein or RNA components . These complex machines must themselves be assembled by an even more complex machinery spanning multiple cellular compart... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/rna-protein",
"interactions",
"genetics",
"and",
"genomics/functional",
"genomics",
"molecular",
"biology/nucleolus",
"and",
"nuclear",
"bodies",
"molecular",
"biology/translation",
"mechanisms",
"computational",
"biology/molecular",
"genetics",
"genetics",
... | 2009 | Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics |
In host and cancer tissues , drug metabolism and susceptibility to drugs vary in a circadian ( 24 h ) manner . In particular , the efficacy of a cell cycle specific ( CCS ) cytotoxic agent is affected by the daily modulation of cell cycle activity in the target tissues . Anti-cancer chronotherapy , in which treatments ... | Chronotherapy of cancers aims at exploiting daily physiological rhythms to improve anti-cancer efficacy and tolerance to drugs by administering treatments at a specific time of the day . Recent clinical trials have shown that chronotherapy can be beneficial in improving quality of life and median life span in patients ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"mathematics/statistics",
"cell",
"biology/cell",
"growth",
"and",
"division",
"computational",
"biology/systems",
"biology",
"oncology/gastrointestinal",
"cancers"
] | 2010 | Tumor Growth Rate Determines the Timing of Optimal Chronomodulated Treatment Schedules |
Mosquito-borne diseases are increasingly being recognized as global threats , with increased air travel accelerating their occurrence in travelers and their spread to new locations . Since the early days of aviation , concern over the possible transportation of infected mosquitoes has led to recommendations to disinsec... | Vector-borne diseases such as malaria , dengue , yellow fever , and Zika are global challenges to public health . International policies , such as the International Health Regulations , call for controlling mosquitoes on aircraft to prevent the introduction of mosquito-borne pathogens and invasive mosquito species . Th... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"dengue",
"virus",
"medicine",
"and",
"health",
"sciences",
"parasite",
"groups",
"pathology",
"and",
"laboratory",
"medicine",
"plasmodium",
"engineering",
"and",
"technology",
"transportation",
"pathogens",
"vector-borne",
"diseases",
"microbiology",
"t... | 2017 | Mosquitoes on a plane: Disinsection will not stop the spread of vector-borne pathogens, a simulation study |
The main objective of the study was to determine the degree of sensitization to Anisakis spp . antigens in healthy coastal population of Dalmatia given the high thermally unprocessed fish intake rate present in this area , suggested as a significant risk factor for anisakiasis . We performed a monocenter , cross-sectio... | Anisakiasis is a zoonosis induced by infection with the Anisakis third-stage larvae , contracted through consumption of thermally unprocessed or lightly processed seafood . Its diagnosis is difficult to suspect in countries where the illness was not previously reported , where it is infrequent , or in the cases of subc... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"veterinary",
"diseases",
"clinical",
"immunology",
"zoonotic",
"diseases",
"allergy",
"and",
"hypersensitivity",
"parasitic",
"diseases",
"veterinary",
"science",
"helminth",
"infection",
"foodborne",
"diseases"
] | 2014 | Anti-Anisakis IgE Seroprevalence in the Healthy Croatian Coastal Population and Associated Risk Factors |
Robustness of organisms is widely observed although difficult to precisely characterize . Performance can remain nearly constant within some neighborhood of the normal operating regime , leading to homeostasis , but then abruptly break down with pathological consequences beyond this neighborhood . Currently , there is ... | The ability of organisms to survive under a multitude of conditions is readily apparent . This robustness in performance is difficult to precisely characterize and quantify . At a biochemical level , it leads to physiological behavior when the parameters of the system remain within some neighborhood of their normal val... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"hematology/disorders",
"of",
"red",
"cell",
"metabolism",
"mathematics",
"computational",
"biology/metabolic",
"networks",
"biochemistry/theory",
"and",
"simulation",
"computational",
"biology/systems",
"biology"
] | 2009 | Quantifying Global Tolerance of Biochemical Systems: Design Implications for Moiety-Transfer Cycles |
The cable equation is a proper framework for modeling electrical neural signalling that takes place at a timescale at which the ionic concentrations vary little . However , in neural tissue there are also key dynamic processes that occur at longer timescales . For example , endured periods of intense neural signaling m... | When neurons generate electrical signals they release potassium ions ( K+ ) into the extracellular space . During periods of intense neural activity , the local extracellular K+ may increase drastically . If it becomes too high , it can lead to neural dysfunction . Astrocytes ( a kind of glial cells ) are involved in p... | [
"Abstract",
"Introduction",
"Model",
"Results",
"Discussion"
] | [] | 2013 | Electrodiffusive Model for Astrocytic and Neuronal Ion Concentration Dynamics |
Schistosomiasis ( or bilharzia ) , a major parasitic disease , affects more than 260 million people worldwide . In chronic cases of intestinal schistosomiasis caused by trematodes of the Schistosoma genus , hepatic fibrosis develops as a host immune response to the helminth eggs , followed by potentially lethal portal ... | Schistosomiasis ( or bilharzia ) , a major helminth disease , affects more than 260 million people worldwide . While the adult worms survive for years within veins of the gastrointestinal system , symptoms are due to inflammatory reactions to their eggs in several organs . Hepatic fibrosis may develop in chronic cases ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | In Vivo MRI Assessment of Hepatic and Splenic Disease in a Murine Model of Schistosmiasis |
Cerebellar Purkinje cells display complex intrinsic dynamics . They fire spontaneously , exhibit bistability , and via mutual network interactions are involved in the generation of high frequency oscillations and travelling waves of activity . To probe the dynamical properties of Purkinje cells we measured their phase ... | By observing how brief current pulses injected at different times between spikes change the phase of spiking of a neuron ( and thus obtaining the so-called phase response curve ) , it should be possible to predict a full spike train in response to more complex stimulation patterns . When we applied this traditional pro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience/neuronal",
"signaling",
"mechanisms",
"neuroscience/theoretical",
"neuroscience"
] | 2010 | A New Approach for Determining Phase Response Curves Reveals that Purkinje Cells Can Act as Perfect Integrators |
A significant current challenge in human genetics is the identification of interacting genetic loci mediating complex polygenic disorders . One of the best characterized polygenic diseases is Down syndrome ( DS ) , which results from an extra copy of part or all of chromosome 21 . A short interval near the distal tip o... | A large fraction of human genes may contribute to polygenic disorders , yet few experimental methods for identifying such genes are currently available . For example , with regard to congenital heart defects ( CHD ) caused by extra copies of genes on chromosome 21 in Down syndrome patients , it is not known which genes... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"genome",
"expression",
"analysis",
"cardiovascular",
"animal",
"models",
"model",
"organisms",
"chromosomal",
"disorders",
"biology",
"down",
"syndrome",
"congenital",
"heart",
"disease",
"clinical",
"genetics",
"genetic",
"screens",
"genetics",
"genomics",
... | 2011 | Over-Expression of DSCAM and COL6A2 Cooperatively Generates Congenital Heart Defects |
Infectious disease treatments , both pharmaceutical and vaccine , face three universal challenges: the difficulty of targeting treatments to high-risk ‘superspreader’ populations who drive the great majority of disease spread , behavioral barriers in the host population ( such as poor compliance and risk disinhibition ... | We introduce a proposed intervention against infectious diseases that extends and optimizes the recognized benefit of ‘transmissible immunization’ that occurs with live-attenuated vaccines such as Oral Polio Vaccine ( OPV ) , the vaccine chosen for the worldwide polio eradication campaign . The intervention proposed he... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"immunodeficiency",
"viruses",
"viruslike",
"particles",
"population",
"modeling",
"evolutionary",
"modeling",
"virology",
"synthetic",
"biology",
"biology",
"computational",
"biology",
"infectious",
"disease",
"modeling",
"microbiology",
"molecular",
"biology"
] | 2011 | Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies |
The Sonic hedgehog ( Shh ) signaling pathway is crucial for pattern formation in early central nervous system development . By systematically analyzing high-throughput in situ hybridization data of E11 . 5 mouse brain , we found that Shh and its receptor Ptch1 define two adjacent mutually exclusive gene expression doma... | Recent large-scale projects of high-throughput in situ hybridization ( ISH ) have generated a wealth of spatiotemporal information on gene expression patterns in the early mouse brain . We have developed a computational approach that combines publicly available high-throughput ISH data with our own experimental data to... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"developmental",
"biology",
"biology",
"and",
"life",
"sciences",
"gene",
"regulatory",
"networks",
"computational",
"biology"
] | 2014 | Reconstruction of the Gene Regulatory Network Involved in the Sonic Hedgehog Pathway with a Potential Role in Early Development of the Mouse Brain |
During mismatch repair ( MMR ) MSH proteins bind to mismatches that form as the result of DNA replication errors and recruit MLH factors such as Mlh1-Pms1 to initiate excision and repair steps . Previously , we identified a negative epistatic interaction involving naturally occurring polymorphisms in the MLH1 and PMS1 ... | In nature , bacterial populations with high mutation rates can adapt faster to new environments by acquiring beneficial mutations . However , such populations also accumulate harmful mutations that reduce their fitness . We show that the model eukaryote baker’s yeast can use a similar mutator strategy to adapt to new e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | A Genetic Incompatibility Accelerates Adaptation in Yeast |
Studies on the Bin-Amphiphysin-Rvs ( BAR ) domain have advanced a fundamental understanding of how proteins deform membrane . We previously showed that a BAR domain in tandem with a Pleckstrin Homology ( PH domain ) underlies the assembly of ACAP1 ( Arfgap with Coil-coil , Ankryin repeat , and PH domain I ) into an unu... | Membrane remodeling is needed for a wide range of cellular events . Our current understanding of how proteins bend membrane to achieve such remodeling has come , in large part , from studies on proteins that contain the BAR domain . These studies have elucidated that the BAR domain dimerize to form a crescent-shaped st... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"vesicles",
"classical",
"mechanics",
"protein",
"interactions",
"membrane",
"proteins",
"materials",
"science",
"damage",
"mechanics",
"protein",
"structure",
"oligomers",
"cellular",
"structures",
"and",
"organelles",
"polymer",
"chemistry",
"proteins",
"deformation",
"... | 2019 | ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages |
Random Item Generation tasks ( RIG ) are commonly used to assess high cognitive abilities such as inhibition or sustained attention . They also draw upon our approximate sense of complexity . A detrimental effect of aging on pseudo-random productions has been demonstrated for some tasks , but little is as yet known abo... | It has been unclear how this ability evolves over a person’s lifetime and it had not been possible to be assessed with previous classical tools for statistical randomness . To better understand how age impacts behavior , we have assessed more than 3 , 400 people aged 4 to 91 years old . Each participant performed a ser... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"discussion"
] | [
"computer",
"applications",
"education",
"decision",
"making",
"sociology",
"social",
"sciences",
"neuroscience",
"age",
"groups",
"adults",
"cognitive",
"psychology",
"cognition",
"computer",
"and",
"information",
"sciences",
"behavior",
"educational",
"attainment",
"peo... | 2017 | Human behavioral complexity peaks at age 25 |
Transposon mutagenesis , in combination with parallel sequencing , is becoming a powerful tool for en-masse mutant analysis . A probability generating function was used to explain observed miniHimar transposon insertion patterns , and gene essentiality calls were made by transposon insertion frequency analysis ( TIFA )... | Metabolic modeling techniques play a central role in rational design of industrial strains , personalized medicine , and automated network reconstruction . However , due to the large size of models , very few have been comprehensively tested using single gene knockout mutants for every gene in the model . Such a geneti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biology",
"and",
"life",
"sciences",
"microbiology",
"computational",
"biology"
] | 2014 | Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis |
Dengue has emerged as a significant public health problem in Sri Lanka . Historically surveillance was passive , with mandatory dengue notifications based on clinical diagnosis with only limited laboratory confirmation . To obtain more accurate data on the disease burden of dengue , we set up a laboratory-based enhance... | The dramatic spread of epidemic dengue underscores the urgent need for better surveillance and control of this disease . The main purpose of surveillance is to provide timely and more accurate information to institute preventive or control measures for epidemic dengue . Dengue has emerged as a major public health probl... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"clinical",
"laboratory",
"sciences",
"geographical",
"locations",
"tropical",
"diseases",
"neglected",
"tropical",
"diseases",
"infectious",
"disease",
"control",
"research",
"facilities",
"research",
"and",
"analysis",
"methods",... | 2016 | Laboratory-Enhanced Dengue Sentinel Surveillance in Colombo District, Sri Lanka: 2012-2014 |
The female Aedes aegypti salivary gland plays a pivotal role in bloodmeal acquisition and reproduction , and thereby dengue virus ( DENV ) transmission . It produces numerous immune factors , as well as immune-modulatory , vasodilatory , and anti-coagulant molecules that facilitate blood-feeding . To assess the impact ... | Dengue virus ( DENV ) is transmitted between humans through the bite of infected Aedes aegypti mosquitoes . Since the virus is inoculated in saliva , infection of the mosquito salivary gland is an essential requirement for transmission . In addition , the gland also produces numerous biologically active compounds that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunity",
"virology",
"biology",
"microbiology"
] | 2012 | Dengue Virus Infection of the Aedes aegypti Salivary Gland and Chemosensory Apparatus Induces Genes that Modulate Infection and Blood-Feeding Behavior |
Enterocytozoon bieneusi is a widespread parasite with high genetic diversity among hosts . Its natural reservoir remains elusive and data on population structure are available only in isolates from primates . Here we describe a population genetic study of 101 E . bieneusi isolates from pigs using sequence analysis of t... | This study explored the genetic characteristics of the ITS and four mini- and microsatellite markers and assessed the population structure and substructures in 101 E . bieneusi isolates from pigs in China . The measures of LD and recombination events supported the occurrence of clonal evolution among the isolates from ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biogeography",
"livestock",
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"population",
"genetics",
"vertebrates",
"animals",
"mammals",
"primates",
"population",
"biology",
"infectio... | 2016 | Clonal Evolution of Enterocytozoon bieneusi Populations in Swine and Genetic Differentiation in Subpopulations between Isolates from Swine and Humans |
Recent advances in sleep neurobiology have allowed development of physiologically based mathematical models of sleep regulation that account for the neuronal dynamics responsible for the regulation of sleep-wake cycles and allow detailed examination of the underlying mechanisms . Neuronal systems in general , and those... | All biological systems are inherently noisy and heterogeneous . Disorder is mostly expected to disturb proper functioning of a system , like it can be the case with noise in a radio signal . However , it has been demonstrated by numerous studies that noise can actually improve signal encoding – the so-called stochastic... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"physics",
"computational",
"neuroscience",
"interdisciplinary",
"physics",
"biology",
"biophysics",
"neuroscience"
] | 2012 | Diversity and Noise Effects in a Model of Homeostatic Regulation of the Sleep-Wake Cycle |
Movement interactions and the underlying social structure in groups have relevance across many social-living species . Collective motion of groups could be based on an “egalitarian” decision system , but in practice it is often influenced by underlying social network structures and by individual characteristics . We in... | How does a group of family dogs decide the direction of their collective movements ? Is there a leader , or is decision-making based on an egalitarian system ? Is leadership related to social dominance status ? We collected GPS trajectory data from an owner and her six dogs during several walks . We found that dogs adj... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mathematics",
"animal",
"behavior",
"statistics",
"biology",
"biostatistics",
"zoology"
] | 2014 | Leadership and Path Characteristics during Walks Are Linked to Dominance Order and Individual Traits in Dogs |
Functional characterization of causal variants present on risk haplotypes identified through genome-wide association studies ( GWAS ) is a primary objective of human genetics . In this report , we evaluate the function of a pair of tandem polymorphic dinucleotides , 42 kb downstream of the promoter of TNFAIP3 , ( rs148... | A key objective of human genetics is the identification and characterization of variants responsible for association with complex diseases . A pair of single nucleotide polymorphisms ( rs148314165 , rs200820567 ) 42 kb downstream from the promoter of TNFAIP3 , have been proposed as the variants responsible for associat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | An Enhancer Element Harboring Variants Associated with Systemic Lupus Erythematosus Engages the TNFAIP3 Promoter to Influence A20 Expression |
Leprosy is characterized by polar clinical , histologic and immunological presentations . Previous immunologic studies of leprosy polarity were limited by the repertoire of cytokines known at the time . We used a candidate gene approach to measure mRNA levels in skin biopsies from leprosy lesions . mRNA from 24 chemoki... | Leprosy presents with a polarized spectrum , with lepromatous leprosy having high bacillary numbers and TH2 dermal cytokines , versus tuberculoid leprosy showing very few bacilli and TH1 cytokines . The mechanism underlying this polarized presentation is largely unknown . In the following study , we isolated mRNA from ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"bacterial",
"diseases",
"infectious",
"diseases",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immunity",
"neglected",
"tropical",
"diseases",
"biology",
"and",
"life",
"sciences",
"immunology",
"microbiology",
"tropical",
"diseases",
"lepros... | 2014 | Differential Dermal Expression of CCL17 and CCL18 in Tuberculoid and Lepromatous Leprosy |
In oocytes , where centrosomes are absent , the chromosomes direct the assembly of a bipolar spindle . Interactions between chromosomes and microtubules are essential for both spindle formation and chromosome segregation , but the nature and function of these interactions is not clear . We have examined oocytes lacking... | In acentrosomal oocytes , spindle assembly depends on the chromosomes . The nature of the chromosome-microtubule interactions in oocytes that organize spindle bipolarity and orientation of the homologs has been unclear . We have found that several types of functional chromosome-microtubule interactions exist in oocytes... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Lateral and End-On Kinetochore Attachments Are Coordinated to Achieve Bi-orientation in Drosophila Oocytes |
Many algorithms for sequence analysis rely on word matching or word statistics . Often , these approaches can be improved if binary patterns representing match and don’t-care positions are used as a filter , such that only those positions of words are considered that correspond to the match positions of the patterns . ... | We propose a fast algorithm to generate spaced seeds for database searching , read mapping and alignment-free sequence comparison . Spaced seeds—i . e . patterns of match and don’t-care positions—are used by many algorithms for sequence analysis; designing optimal seeds is therefore an active field of research . In seq... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing",
"techniques",
"taxonomy",
"applied",
"mathematics",
"split-decomposition",
"method",
"database",
"searching",
"simulation",
"and",
"modeling",
"algorithms",
"multiple",
"alignment",
"calculation",
"optimization",
"phylogenetics",
"data",
"management",
"mathemati... | 2016 | rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison |
Bacillus anthracis produces a binary toxin composed of protective antigen ( PA ) and one of two subunits , lethal factor ( LF ) or edema factor ( EF ) . Most studies have concentrated on induction of toxin-specific antibodies as the correlate of protective immunity , in contrast to which understanding of cellular immun... | Anthrax is of concern with respect to human exposure in endemic regions , concerns about bioterrorism and the considerable global burden of livestock infections . The immunology of this disease remains poorly understood . Vaccination has been based on B . anthracis filtrates or attenuated spore-based vaccines , with mo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences",
"medicine",
"and",
"health",
"sciences"
] | 2014 | Anthrax Lethal Factor as an Immune Target in Humans and Transgenic Mice and the Impact of HLA Polymorphism on CD4+ T Cell Immunity |
Zoonotic pathogens such as Ebola and rabies pose a major health risk to humans . One proven approach to minimizing the impact of a pathogen relies on reducing its prevalence within animal reservoir populations using mass vaccination . However , two major challenges remain for vaccination programs that target free-rangi... | Zoonotic pathogens pose a significant health risk to humans . Mass vaccination programs have shown promise for controlling zoonoses in reservoir populations and , in turn , lessening the health burden posed to neighboring human populations . Despite some significant successes , major logistical challenges remain for pr... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"animal",
"types",
"medicine",
"and",
"health",
"sciences",
"zoonotic",
"pathogens",
"animal",
"pathogens",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"tropical",
"diseases",
"microbiology",
"vertebrates",
"animals",
"mammals",
"vaccines",
... | 2019 | A little goes a long way: Weak vaccine transmission facilitates oral vaccination campaigns against zoonotic pathogens |
During development , signaling networks control the formation of multicellular patterns . To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear . Here , we describe a computational approach to predict and analyze the phenotypic diversity that is accessible... | The diversity of metazoan life forms that we experience today arose as multicellular systems continually sampled new phenotypes that withstood ever changing selective pressures . This phenotypic diversification is driven by variations in the underlying regulatory network that instructs cells to form multicellular patte... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/developmental",
"evolution",
"computational",
"biology/signaling",
"networks",
"computational",
"biology/systems",
"biology"
] | 2009 | Predicting Phenotypic Diversity and the Underlying Quantitative
Molecular Transitions |
Toxoplasma gondii is found worldwide , but distribution of its genotypes as well as clinical expression of human toxoplasmosis varies across the continents . Several studies in Europe , North America and South America argued for a role of genotypes in the clinical expression of human toxoplasmosis . Genetic data concer... | Prevalence of human toxoplasmosis in tropical African countries usually exceeds 50% . Its role as a major opportunistic infection of AIDS patients is regularly described . Due to the lack of investigation , congenital infection is certainly underestimated in Africa . Incidence of Toxoplasma ocular disease is higher in ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"microbiology/parasitology",
"infectious",
"diseases/protozoal",
"infections",
"ecology/population",
"ecology",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2010 | Additional Haplogroups of Toxoplasma gondii out of Africa: Population Structure and Mouse-Virulence of Strains from Gabon |
Respiratory syncytial virus ( RSV ) is the major cause of viral lower respiratory tract illness in children . In contrast to the RSV prototypic strain A2 , clinical isolate RSV 2–20 induces airway mucin expression in mice , a clinically relevant phenotype dependent on the fusion ( F ) protein of the RSV strain . Epider... | Respiratory syncytial virus ( RSV ) is responsible for severe lower respiratory disease in infants and young children . Overabundant airway mucus contributes to airway obstruction in RSV bronchiolitis , and a better understanding of RSV pathogenesis may contribute to needed therapies and vaccines . We reported previous... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"flow",
"cytometry",
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"respiratory",
"infections",
"293t",
"cells",
"biological",
"cultures",
"egfr",
"signaling",
"pulmonology",
"epithelial",
"cells",
"animal",
"models",
"model",
"organisms",
"research",
... | 2016 | EGFR Interacts with the Fusion Protein of Respiratory Syncytial Virus Strain 2-20 and Mediates Infection and Mucin Expression |
Beetle horns are attractive models for studying the evolution of novel traits , as they display diverse shapes , sizes , and numbers among closely related species within the family Scarabaeidae . Horns radiated prolifically and independently in two distant subfamilies of scarabs , the dung beetles ( Scarabaeinae ) , an... | Goliath and Hercules beetles include some of the largest insects known , and the horns they wield are spectacular . These ‘rhinoceros’ beetles form a subfamily within the Scarabaeidae , a clade containing ~35 , 000 primarily hornless species . The other subfamily of horned scarabs , dung beetles , is distantly related ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"rna",
"interference",
"animals",
"dung",
"beetles",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"experimental",
"organism",
"systems",
"epigenetics",
"drosop... | 2018 | Rhinoceros beetle horn development reveals deep parallels with dung beetles |
Most tissues in multicellular organisms are maintained by continuous cell renewal processes . However , high turnover of many cells implies a large number of error-prone cell divisions . Hierarchical organized tissue structures with stem cell driven cell differentiation provide one way to prevent the accumulation of mu... | We investigate the average stem cell driven dynamics of cell counts in an abstract multi compartment model . Within this framework one can represent different tissue structures , as for example hematopoiesis , the skin or the colonic crypt . Our analysis is based on an individual cell model in which cells can different... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"theoretical",
"biology",
"disease",
"dynamics",
"population",
"dynamics",
"biology",
"population",
"biology"
] | 2011 | Dynamics of Mutant Cells in Hierarchical Organized Tissues |
Salmonella enterica subspecies can establish persistent , systemic infections in mammals , including human typhoid fever . Persistent S . enterica disease is characterized by an initial acute infection that develops into an asymptomatic chronic infection . During both the acute and persistent stages , the bacteria gene... | Microbes that establish persistent infections present serious problems for world health but are not well understood . The bacteria Salmonella enterica cause asymptomatic chronic infection in humans . Carriers shed the bacteria into the environment , leading to periodic acute typhoid fever epidemics . Antibiotics are ef... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"infectious",
"diseases",
"microbiology",
"mus",
"(mouse)",
"homo",
"(human)",
"eubacteria"
] | 2007 | Hemophagocytic Macrophages Harbor Salmonella enterica during Persistent Infection |
Viruses diversify over time within hosts , often undercutting the effectiveness of host defenses and therapeutic interventions . To design successful vaccines and therapeutics , it is critical to better understand viral diversification , including comprehensively characterizing the genetic variants in viral intra-host ... | New sequencing technologies provide unprecedented resolution to study pathogen populations , such as the single stranded RNA viruses HIV , dengue ( DENV ) , and West Nile ( WNV ) , and how they evolve within infected individuals in response to immune , therapeutic , and vaccine pressures . While these new technologies ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"evolutionary",
"biology",
"population",
"modeling",
"population",
"genetics",
"biology",
"computational",
"biology",
"microbiology",
"genetics",
"and",
"genomics"
] | 2012 | Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data |
Evolutionary outcomes depend not only on the selective forces acting upon a species , but also on the genetic background . However , large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species . Experimental evolution is one tool t... | Both comparative genomics and experimental evolution are powerful tools that can be used to make inferences about evolutionary processes . Together , these approaches provide the opportunity to observe evolutionary adaptation over millions of years where selective history is largely unknown , and over short timescales ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"genome",
"evolution",
"chemical",
"compounds",
"salts",
"fungi",
"model",
"organisms",
"fungal",
"evolution",
"experimental",
"organism",
"systems",
"saccharomyces",
"research",
"and",
"analysis",
"methods",
"mycology",
"sulfates",
"molecular",
"evolution",
"chemistry",
... | 2017 | Differential paralog divergence modulates genome evolution across yeast species |
Factor H binding protein ( fHbp ) is an important antigen for vaccines against meningococcal serogroup B disease . The protein binds human factor H ( fH ) , which enables the bacteria to resist serum bactericidal activity . Little is known about the vaccine-potential of fHbp for control of meningococcal epidemics in Af... | Epidemics of meningococcal meningitis are common in sub-Saharan Africa . Most are caused by encapsulated serogroup A strains , which rarely cause disease in industrialized countries . A serogroup A polysaccharide protein conjugate vaccine recently was introduced in some countries in sub-Saharan Africa . The antibodies ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"vaccines",
"medicine",
"vaccination",
"clinical",
"immunology",
"immunity",
"vaccine",
"development",
"biology",
"microbiology",
"immunology",
"bacterial",
"pathogens"
] | 2011 | Meningococcal Factor H Binding Proteins in Epidemic Strains from Africa: Implications for Vaccine Development |
Trinucleotide hereditary diseases such as Huntington disease and Friedreich ataxia are cureless diseases associated with inheriting an abnormally large number of DNA trinucleotide repeats in a gene . The genes associated with different diseases are unrelated and harbor a trinucleotide repeat in different functional reg... | Trinucleotide diseases are a broad family of hereditary diseases characterized genetically by an expanded DNA region consisting of a repeated three-letter code . Patients inheriting such an abnormal DNA region experience sudden disease onset at an age that inversely depends on the size of the expanded region , followed... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"homo",
"(human)",
"genetics",
"and",
"genomics",
"computational",
"biology"
] | 2007 | A Universal Mechanism Ties Genotype to Phenotype in Trinucleotide Diseases |
Early malacological literature suggests that the outbreak of schistosomiasis , a parasitic disease transmitted by aquatic snails , in the Senegal River basin occurred due to ecological changes resulting from the construction of the Diama dam . The common treatment , the drug praziquantel , does not protect from the hig... | Schistosomiasis is a chronic parasitic disease that infects millions of people , especially in Africa . Schistosomes are transmitted by direct contact with water sources infested by freshwater snails , which are intermediate hosts for the parasite . The cure in humans is a drug , praziquantel , that kills the mature pa... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"developmental",
"biology",
"fisheries",
"science",
"ecology",
"agriculture",
"ecosystems",
"coastal",
"ecosystems",
"aquaculture",
"life",
"cycles",
"biology",
"and",
"life",
"sciences",
"intestinal",
"parasites",
"freshwater",
"ecology",
"marine",
"biol... | 2014 | The Prawn Macrobrachium vollenhovenii in the Senegal River Basin: Towards Sustainable Restocking of All-Male Populations for Biological Control of Schistosomiasis |
MITA ( also called STING ) is a central adaptor protein in innate immune response to cytosolic DNA . Cellular trafficking of MITA from the ER to perinuclear microsomes after DNA virus infection is critical for MITA activation and onset of innate antiviral response . Here we found that SNX8 is a component of DNA-trigger... | Infection by virus , such as the DNA virus herpes simplex virus 1 , induces the host cells to express proteins that mediate antiviral immune response . The protein called MITA plays an essential role in the process of antiviral immune response . After viral infection , MITA traffics from the endoplasmic reticulum ( ER ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"luciferase",
"assay",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"hela",
"cells",
"molecular",
"probe",
"techniques",
"biological",
"cultures",
"immunology",
"biochemical",
"analysis",
"developmental",
"b... | 2018 | SNX8 modulates innate immune response to DNA virus by mediating trafficking and activation of MITA |
The obligate intracellular pathogen Chlamydia trachomatis replicates within a membrane-bound inclusion that acquires host sphingomyelin ( SM ) , a process that is essential for replication as well as inclusion biogenesis . Previous studies demonstrate that SM is acquired by a Brefeldin A ( BFA ) -sensitive vesicular tr... | C . trachomatis is the leading cause of non-congenital blindness in developing countries and is the number one cause of sexually transmitted disease and non-congenital infertility in Western countries . The capacity of Chlamydia infections to lead to infertility and blindness , their association with chronic diseases ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"women's",
"health",
"biology",
"microbiology",
"molecular",
"cell",
"biology"
] | 2011 | Chlamydia trachomatis Co-opts GBF1 and CERT to Acquire Host Sphingomyelin for Distinct Roles during Intracellular Development |
Cytokinins and gibberellins ( GAs ) play antagonistic roles in regulating reproductive meristem activity . Cytokinins have positive effects on meristem activity and maintenance . During inflorescence meristem development , cytokinin biosynthesis is activated via a KNOX-mediated pathway . Increased cytokinin activity le... | Grain number per panicle , a valuable agronomic trait for rice yield improvement , is profoundly affected by reproductive meristem activity . This activity , in turn , is controlled by transcriptional and plant hormone regulators , especially KNOX proteins and cytokinins . However , little is known about the roles of G... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"anatomy",
"panicles",
"floral",
"meristem",
"plant",
"physiology",
"hormones",
"cereal",
"crops",
"plant",
"science",
"rice",
"model",
"organisms",
"plant",
"hormones",
"crops",
"inflorescences",
"plants",
"research",
"and",
"analysis",
"methods",
"cytokinin... | 2016 | The QTL GNP1 Encodes GA20ox1, Which Increases Grain Number and Yield by Increasing Cytokinin Activity in Rice Panicle Meristems |
Visceral leishmaniasis ( VL ) is the most severe form of leishmaniasis and is potentially fatal if not diagnosed and treated . Accurate and timely diagnosis is considered one of the pillars needed for the reduction in disease-related lethality . Brazil is currently one of the three eco-epidemiological hotspots for this... | Visceral leishmaniasis ( VL ) is a tropical disease distributed worldwide . In the Americas , Brazil reports about 96% of VL cases , which has been highlighted by the increase in lethality in last years . Accurate VL diagnosis is of utmost importance . Despite this , the performance of some commercial tests currently a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"enzyme-linked",
"immunoassays",
"pathology",
"and",
"laboratory",
"medicine",
"tropical",
"diseases",
"geographical",
"locations",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoans",
"leishmania",
"neglected",
"tropica... | 2019 | Performance of serological tests available in Brazil for the diagnosis of human visceral leishmaniasis |
Ciliopathies represent a broad class of disorders that affect multiple organ systems . The craniofacial complex is among those most severely affected when primary cilia are not functional . We previously reported that loss of primary cilia on cranial neural crest cells , via a conditional knockout of the intraflagellar... | Primary cilia are ubiquitous organelles that serve to transduce molecular signals within a cell . Loss of functional primary cilia results in a disease class called ciliopathies . Ciliopathies have a broad range of phenotypes; however , severe facial anomalies are commonly associated with this disease class . The facia... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"safranin",
"staining",
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"cytoplasmic",
"staining",
"developmental",
"biology",
"transcription",
"factors",
"embryos",
"cellular",
"structures",
"and",
"organelles",
"research",
"and",
"analysis",
"... | 2016 | Craniofacial Ciliopathies Reveal Specific Requirements for GLI Proteins during Development of the Facial Midline |
Cellular and viral S-adenosylmethionine-dependent methyltransferases are involved in many regulated processes such as metabolism , detoxification , signal transduction , chromatin remodeling , nucleic acid processing , and mRNA capping . The Severe Acute Respiratory Syndrome coronavirus nsp16 protein is a S-adenosylmet... | A novel coronavirus emerged in 2003 and was identified as the etiological agent of the deadly disease called Severe Acute Respiratory Syndrome . This coronavirus replicates and transcribes its giant genome using sixteen non-structural proteins ( nsp1-16 ) . Viral RNAs are capped to ensure stability , efficient translat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"biochemistry",
"antivirals",
"proteins",
"virology",
"enzymes",
"protein",
"structure",
"emerging",
"viral",
"diseases",
"viral",
"enzymes",
"biology",
"microbiology"
] | 2011 | Crystal Structure and Functional Analysis of the SARS-Coronavirus RNA Cap 2′-O-Methyltransferase nsp10/nsp16 Complex |
Mammalian genomes harbor millions of retrotransposon copies , some of which are transpositionally active . In mouse prospermatogonia , PIWI-interacting small RNAs ( piRNAs ) combat retrotransposon activity to maintain the genomic integrity . The piRNA system destroys retrotransposon-derived RNAs and guides de novo DNA ... | Retrotransposons are a class of transposable elements , of which mobility has mutagenic potential . Therefore , it is important to regulate the expression of retrotransposons for maintaining the genomic integrity . In male germ cells , DNA methylation and the piRNA system are thought to play roles in retrotransposon si... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"sequencing",
"techniques",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"spermatocytes",
"retrotransposons",
"spermatogonia",
"germ",
"cells",
"genetic",
"elements",
"epigenetics",
"dna",
"molecular",
"biology",
"techniques",
"rna",
"sequencing",
"d... | 2017 | Switching of dominant retrotransposon silencing strategies from posttranscriptional to transcriptional mechanisms during male germ-cell development in mice |
DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development , X-chromosome inactivation , genomic imprinting and susceptibility to complex disease . However , the dynamics of DNA methylation changes between humans and their closest relatives are still p... | Differences in protein coding sequences between humans and their closest relatives are too small to account for their phenotypic differences . It has been hypothesized that these differences may be explained by alterations of gene regulation rather than primary genome sequence . DNA methylation is an important epigenet... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Dynamics of DNA Methylation in Recent Human and Great Ape Evolution |
The rate of germline mutation varies widely between species but little is known about the extent of variation in the germline mutation rate between individuals of the same species . Here we demonstrate that an allele that increases the rate of germline mutation can result in a distinctive signature in the genomic regio... | Each time a genome is replicated there is the possibility of error resulting in the incorporation of an incorrect base or bases in the genome sequence . When these errors occur in cells that lead to the production of gametes they can be incorporated into the germline . Such germline mutations are the basis of evolution... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"mutation",
"deletion",
"mutation",
"haplotypes",
"nucleic",
"acids",
"heredity",
"germline",
"mutation",
"gene",
"identification",
"and",
"analysis",
"genetics",
"mutation",
"detection",
"biology",
"and",
"life",
"sciences",
"dna",
"dna",
"repair",
"a... | 2017 | Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data |
We performed a Phenome-wide association study ( PheWAS ) utilizing diverse genotypic and phenotypic data existing across multiple populations in the National Health and Nutrition Examination Surveys ( NHANES ) , conducted by the Centers for Disease Control and Prevention ( CDC ) , and accessed by the Epidemiological Ar... | The Epidemiological Architecture for Genes Linked to Environment ( EAGLE ) study performed a Phenome-Wide Association Study ( PheWAS ) to investigate comprehensive associations between a wide range of phenotypes and single-nucleotide polymorphisms using the diverse genotypic and phenotypic data that exists across multi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"statistical",
"analysis",
"of",
"genetic",
"association",
"genetic",
"networks",
"genomics",
"genome",
"analysis",
"trait",
"locus",
"analysis",
"genetics",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"geno... | 2014 | Detection of Pleiotropy through a Phenome-Wide Association Study (PheWAS) of Epidemiologic Data as Part of the Environmental Architecture for Genes Linked to Environment (EAGLE) Study |
Paracoccidioides spp . , a dimorphic pathogenic fungus , is the etiologic agent of paracoccidioidomycosis ( PCM ) . PCM is an endemic disease that affects at least 10 million people in Latin America , causing severe public health problems . The drugs used against pathogenic fungi have various side effects and limited e... | Paracoccidioidomycosis ( PCM ) is a neglected human systemic mycosis caused by Paracoccidioides spp . fungus that invades the host’s lungs and can disseminate to many other organs . Treatment usually involves amphotericin B , sulfadiazine , trimethoprim-sulfamethoxazole , itraconazole , ketoconazole or fluconazole for ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2016 | Effects of Argentilactone on the Transcriptional Profile, Cell Wall and Oxidative Stress of Paracoccidioides spp. |
The brain exhibits temporally complex patterns of activity with features similar to those of chaotic systems . Theoretical studies over the last twenty years have described various computational advantages for such regimes in neuronal systems . Nevertheless , it still remains unclear whether chaos requires specific cel... | Cortical circuits exhibit complex temporal patterns of spiking and are exquisitely sensitive to small perturbations in their ongoing activity . These features are all suggestive of an underlying chaotic dynamics . Theoretical works have indicated that a rich dynamical reservoir can endow neuronal circuits with remarkab... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Models",
"Dynamical",
"Mean-Field",
"Theory",
"of",
"the",
"Single",
"Inhibitory",
"Population",
"Two-population",
"networks",
"Numerical",
"simulations"
] | [] | 2015 | Asynchronous Rate Chaos in Spiking Neuronal Circuits |
Sex determination in mammals is controlled by the presence or absence of the Y-linked gene SRY . In the developing male ( XY ) gonad , sex-determining region of the Y ( SRY ) protein acts to up-regulate expression of the related gene , SOX9 , a transcriptional regulator that in turn initiates a downstream pathway of te... | In mammals , whether an individual develops as a male or female depends on its sex chromosome constitution: those with a Y chromosome become males because of the development of the embryonic gonad into a testis . The Y-linked sex determining gene SRY regulates this process by initiating a pathway of gene and protein ex... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/germ",
"cells",
"developmental",
"biology/embryology",
"genetics",
"and",
"genomics/animal",
"genetics",
"developmental",
"biology",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"a... | 2009 | Loss of Mitogen-Activated Protein Kinase Kinase Kinase 4 (MAP3K4) Reveals a Requirement for MAPK Signalling in Mouse Sex Determination |
The treatment of Buruli ulcer ( BU ) that is caused by Mycobacterium ulcerans , is currently based on a daily administration of rifampin and streptomycin ( RIF-STR ) . A fully oral intermittent regimen would greatly simplify its treatment on the field . The objective of this study was to assess the bactericidal and ste... | Buruli ulcer , caused by Mycobacterium ulcerans , is the third most frequent disease due to a bacteria of the mycobacteria family , after tuberculosis and leprosy . The disease consists of a cutaneous infection leading to skin ulcerations that can cause severe and debilitating scars . It occurs mostly in Africa where a... | [
"Abstract",
"Introduction",
"Material",
"and",
"methods",
"Results",
"Discussion"
] | [
"antimicrobials",
"body",
"weight",
"medicine",
"and",
"health",
"sciences",
"animal",
"models",
"of",
"disease",
"drugs",
"tropical",
"diseases",
"microbiology",
"animal",
"models",
"bacterial",
"diseases",
"model",
"organisms",
"physiological",
"parameters",
"pharmace... | 2016 | Sterilizing Activity of Fully Oral Intermittent Regimens against Mycobacterium Ulcerans Infection in Mice |
Riboviruses ( RNA viruses without DNA replication intermediates ) are the most abundant pathogens infecting animals and plants . Only a few riboviral infections can be controlled with antiviral drugs , mainly because of the rapid appearance of resistance mutations . Little reliable information is available concerning i... | Viral disease is a subject of major concern in public health . Diseases produced by riboviruses ( RNA viruses sensu stricto ) represent a special urgency , because these viruses display an exceptional capability to generate resistance mutations against antiviral drugs . Unfortunately , little is known about the rate an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"model",
"organisms",
"genetics",
"biology",
"microbiology",
"genetics",
"and",
"genomics"
] | 2012 | The Three Faces of Riboviral Spontaneous Mutation: Spectrum, Mode of Genome Replication, and Mutation Rate |
β-defensin peptides are a family of antimicrobial peptides present at mucosal surfaces , with the main site of expression under normal conditions in the male reproductive tract . Although they kill microbes in vitro and interact with immune cells , the precise role of these genes in vivo remains uncertain . We show her... | β-defensins are small molecules , considered primarily to be antimicrobials and important in the first defence response to invading organisms . They are predominantly produced at surfaces in contact with the outside environment and these include skin , airway and reproductive tract . We show here that when we delete fr... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Partial Deletion of Chromosome 8 β-defensin Cluster Confers Sperm Dysfunction and Infertility in Male Mice |
A community-based longitudinal study was performed in the Eastern Province of Zambia , in which repeated serological samplings were done to determine the incidence of human cysticercosis . Three sampling rounds were carried out at six months intervals . A total of 867 participants presented for all three samplings . Al... | Human neurocysticercosis is an infection of the central nervous system caused by the larval stage of the pork tapeworm ( Taenia solium ) . The infection occurs mainly in developing countries and is associated with poverty , poor sanitation and free-range pig management . It is estimated to be responsible for 30% of cas... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"taeniasis",
"medicine",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"zoonoses",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"cysticercosis",
"neglected",
"tropical",
"diseases",
"parasitic",
"diseases"
] | 2013 | The Incidence of Human Cysticercosis in a Rural Community of Eastern Zambia |
The p12 protein is a cleavage product of the Gag precursor of the murine leukemia virus ( MLV ) . Specific mutations in p12 have been described that affect early stages of infection , rendering the virus replication-defective . Such mutants showed normal generation of genomic DNA but no formation of circular forms , wh... | All retroviruses reverse transcribe their RNA genome to a DNA copy in the cytoplasm of the infected cell . To be expressed , the viral genomic DNA has to travel to the cell nucleus and to integrate into the cellular chromosomes . This trafficking is governed by cellular and viral proteins that associate with the viral ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/virion",
"structure,",
"assembly,",
"and",
"egress",
"virology/effects",
"of",
"virus",
"infection",
"on",
"host",
"gene",
"expression",
"virology/immunodeficiency",
"viruses",
"virology/viral",
"replication",
"and",
"gene",
"regulation"
] | 2010 | The Gag Cleavage Product, p12, is a Functional Constituent of the Murine Leukemia Virus Pre-Integration Complex |
Following envelope mediated fusion , the HIV-1 core is released into the cytoplasm of the target cell and undergoes a series of trafficking and replicative steps that result in the nuclear import of the viral genome , which ultimately leads to the integration of the proviral DNA into the host cell genome . Previous stu... | Fusion of viral and target cell membranes releases the HIV-1 viral capsid , which houses the viral RNA and proteins necessary for viral reverse transcription and integration , into the cytoplasm of target cells . To complete infection , the viral capsid must ultimately traffic to the nucleus and undergo a process known... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"nuclear",
"import",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"hela",
"cells",
"gene",
"regulation",
"pathogens",
"biological",
"cultures",
"cell",
"processes",
"microbiology",
"viral",
"structure",
"retroviruses",
"viruses"... | 2016 | KIF5B and Nup358 Cooperatively Mediate the Nuclear Import of HIV-1 during Infection |
Protozoan pathogens of the genus Leishmania have evolved unique signaling mechanisms that can sense changes in the host environment and trigger adaptive stage differentiation essential for host cell infection . The signaling mechanisms underlying parasite development remain largely elusive even though Leishmania mitoge... | Leishmaniasis is an important human disease caused by Leishmania parasites . A crucial aspect of Leishmania infectivity is its capacity to sense different environments and adapt for survival inside insect vector and vertebrate host by stage differentiation . This process is triggered by environmental changes encountere... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mutagenesis",
"signal",
"transduction",
"kinetoplastids",
"cell",
"biology",
"molecular",
"biology",
"genetics",
"biology",
"and",
"life",
"sciences",
"molecular",
"genetics",
"microbiology",
"protozoology",
"microbial",
"genetics",
"cell",
"signaling",
"mapk",
"signalin... | 2014 | Transgenic Analysis of the Leishmania MAP Kinase MPK10 Reveals an Auto-inhibitory Mechanism Crucial for Stage-Regulated Activity and Parasite Viability |
Aedes albopictus is a very invasive and aggressive insect vector that causes outbreaks of dengue fever , chikungunya disease , and yellow fever in many countries . Vector ecology and disease epidemiology are strongly affected by environmental changes . Urbanization is a worldwide trend and is one of the most ecological... | Aedes albopictus has expanded its ecological habitat range throughout the world . Although Ae . albopictus was previously considered a rural vector , this species has adapted well to suburban and urban environments , and it has become the most important and sometimes the sole vector of dengue virus transmission in urba... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"ecology",
"epidemiology",
"vector",
"biology",
"dengue",
"fever",
"neglected",
"tropical",
"diseases",
"biology",
"and",
"life",
"sciences",
"vector-borne",
"diseases",
"viral",
"diseases",
"tropical",
... | 2014 | Urbanization Increases Aedes albopictus Larval Habitats and Accelerates Mosquito Development and Survivorship |
Plasma insulin oscillations are known to have physiological importance in the regulation of blood glucose . In insulin-secreting β-cells of pancreatic islets , K ( ATP ) channels play a key role in regulating glucose-dependent insulin secretion . In addition , they convey oscillations in cellular metabolism to the memb... | Pulsatile insulin secretion is important for the proper regulation of blood glucose , and disruption of this pulsatility is a hallmark of type II diabetes . An ion channel was discovered more than three decades ago that conveys the metabolic state of insulin-secreting β-cells to the plasma membrane because it is blocke... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"body",
"fluids",
"chemical",
"compounds",
"diabetic",
"endocrinology",
"membrane",
"potential",
"electrophysiology",
"carbohydrates",
"neuroscience",
"organic",
"compounds",
"glucose",
"hormones",
"ion",
"c... | 2017 | Upregulation of an inward rectifying K+ channel can rescue slow Ca2+ oscillations in K(ATP) channel deficient pancreatic islets |
Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment . Endocytosis and the late secretory route are mediated by clathrin-coated vesicles , while the COat Protein I and II ( COPI and COPII ) routes stand for the bidi... | Vesicle trafficking systems are fundamental among cellular transport mechanisms; various cargo molecules are transported via different coated vesicles to their specific destinations in every eukaryotic cell . Clathrin-coated vesicles mediate endocytosis and the late secretory route , while the COat Protein I and II ( C... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"proteins",
"macromolecular",
"assemblies",
"biology",
"computational",
"biology",
"molecular",
"cell",
"biology"
] | 2013 | Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways |
HIV-1 is transmitted primarily across mucosal surfaces and rapidly spreads within the intestinal mucosa during acute infection . The type I interferons ( IFNs ) likely serve as a first line of defense , but the relative expression and antiviral properties of the 12 IFNα subtypes against HIV-1 infection of mucosal tissu... | The therapeutic potential of recombinant IFNα against HIV-1 infection has been explored for 25 years , but its effectiveness was inconsistent . However , these clinical trials administered IFNα2 , which is only one member of a 12-protein family of IFNα subtypes . More recently , IFNα was found to activate ‘restriction ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Interferon-α Subtypes in an Ex Vivo Model of Acute HIV-1 Infection: Expression, Potency and Effector Mechanisms |
There is a growing interest in developing novel brain stimulation methods to control disease-related aberrant neural activity and to address basic neuroscience questions . Conventional methods for manipulating brain activity rely on open-loop approaches that usually lead to excessive stimulation and , crucially , do no... | Brain stimulation is being used to ease symptoms in several neurological disorders in cases where pharmacological treatment is not effective ( anymore ) . The most common way for stimulation so far has been to apply a fixed , predetermined stimulus irrespective of the actual state of the brain or the condition of the p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"population",
"dynamics",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"systems",
"science",
"mathematics",
"algebra",
"computational",
"neuroscience",
"population",
"bio... | 2016 | Recovery of Dynamics and Function in Spiking Neural Networks with Closed-Loop Control |
Biological sensory systems react to changes in their surroundings . They are characterized by fast response and slow adaptation to varying environmental cues . Insofar as sensory adaptive systems map environmental changes to changes of their internal degrees of freedom , they can be regarded as computational devices ma... | The ability to process information is a ubiquitous feature of living organisms . Indeed , in order to survive , every living being , from the smallest bacterium to the biggest mammal , has to gather and process information about its surrounding environment . In the same way as our everyday computers need power to funct... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"physics",
"thermodynamics",
"biophysics",
"theory",
"biology",
"and",
"life",
"sciences",
"physical",
"sciences",
"biophysics"
] | 2014 | Thermodynamic Costs of Information Processing in Sensory Adaptation |
Yra1 is an essential nuclear factor of the evolutionarily conserved family of hnRNP-like export factors that when overexpressed impairs mRNA export and cell growth . To investigate further the relevance of proper Yra1 stoichiometry in the cell , we overexpressed Yra1 by transforming yeast cells with YRA1 intron-less co... | Yra1 is an essential nuclear RNA-binding protein that plays a role in mRNA export in Saccharomyces cerevisiae . The cellular levels of Yra1 are tightly auto-regulated by splicing of an unusual intron in its pre-mRNA , removal of which causes Yra1 overexpression that results in a dominant-negative growth defect and mRNA... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetic",
"networks",
"chromosome",
"structure",
"and",
"function",
"messenger",
"rna",
"telomeres",
"dna",
"replication",
"network",
"analysis",
"genome",
"analysis",
"protein",
"structure",
"dna",
"molecular",
"biology",
"techniques",
"research",
"and",
"analysis",
... | 2016 | Excess of Yra1 RNA-Binding Factor Causes Transcription-Dependent Genome Instability, Replication Impairment and Telomere Shortening |
Echinoderms , which are phylogenetically related to vertebrates and produce large numbers of transparent embryos that can be experimentally manipulated , offer many advantages for the analysis of the gene regulatory networks ( GRN ) regulating germ layer formation . During development of the sea urchin embryo , the ect... | Echinoderms ( sea urchins , starfish , etc . ) are marine invertebrates that share a close ancestry with vertebrates . Their embryos offer many advantages for the analysis of transcriptional circuits that control developmental programs . During early development of the common sea urchin Paracentrotus lividus , a signal... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/morphogenesis",
"and",
"cell",
"biology",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/gene",
"expression",
"developmental",
"biology/developmental",
"evolution",
"developmental",
"biology/pattern",
"formation",
"g... | 2010 | Ancestral Regulatory Circuits Governing Ectoderm Patterning Downstream of Nodal and BMP2/4 Revealed by Gene Regulatory Network Analysis in an Echinoderm |
Access to nutrients is a key factor governing development , reproduction and ultimately fitness . Within social groups , contest-competition can fundamentally affect nutrient access , potentially leading to reproductive asymmetry among individuals . Previously , agent-based models have been combined with the Geometric ... | Getting enough nutrients and at the right balance is among the primary challenges that an animal has to overcome . Animals that live in groups have the added complexity of competition among individuals over foods . We used an evolutionary simulation to explore how the intensity of such competition interacts with the co... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [] | 2015 | Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model |
Homologous recombination ( HR ) is initiated by DNA double-strand breaks ( DSB ) . However , it remains unclear whether single-strand lesions also initiate HR in genomic DNA . Chicken B lymphocytes diversify their Immunoglobulin ( Ig ) V genes through HR ( Ig gene conversion ) and non-templated hypermutation . Both typ... | An important class of chemotherapeutic drugs used in the treatment of cancer induces DNA damage that interferes with DNA replication . The resulting block to replication results in the formation of single-strand gaps in DNA . These gaps can be filled by specialized DNA polymerases , a process associated with the introd... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"oncology",
"immunology",
"molecular",
"biology/dna",
"repair"
] | 2009 | Genetic Evidence for Single-Strand Lesions Initiating Nbs1-Dependent Homologous Recombination in Diversification of Ig V in Chicken B Lymphocytes |
Transient Receptor Potential ( TRP ) channels serve as temperature receptors in a wide variety of animals and must have played crucial roles in thermal adaptation . The TRP vanilloid ( TRPV ) subfamily contains several temperature receptors with different temperature sensitivities . The TRPV3 channel is known to be hig... | Evolution of temperature perception is crucial for adaptation to thermal environments; however , this process is poorly understood . Here we investigated the evolution of the vertebrate TRPV subfamily which contains several mammalian temperature receptors . We identified several novel TRPV genes that have not been foun... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"signal",
"transduction",
"molecular",
"cell",
"biology",
"molecular",
"biology",
"genetics",
"genetics",
"and",
"genomics",
"biology",
"evolutionary",
"biology",
"comparative",
"genomics",
"neuroscience",
"evolutionary",
"processes",
"sensory",
"perception",
"gene",
"fun... | 2011 | Evolution of Vertebrate Transient Receptor Potential Vanilloid 3 Channels: Opposite Temperature Sensitivity between Mammals and Western Clawed Frogs |
Affinity maturation and class switching of antibodies requires activation-induced cytidine deaminase ( AID ) -dependent hypermutation of Ig V ( D ) J rearrangements and Ig S regions , respectively , in activated B cells . AID deaminates deoxycytidine bases in Ig genes , converting them into deoxyuridines . In V ( D ) J... | To generate highly specific antibodies in response to an immune challenge , the antibody genes in activated B cells mutate at a very high rate over a period of several days . The enzyme that initiates antibody gene mutation is activation-induced cytidine deaminase ( AID ) , the first protein recognized to directly edit... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"in",
"vitro",
"immunology",
"molecular",
"biology"
] | 2007 | DNA-Dependent Protein Kinase Inhibits AID-Induced Antibody Gene Conversion |
The soil-dwelling saprophyte bacterium Burkholderia pseudomallei is the cause of melioidosis , a severe disease of humans and animals in southeast Asia and northern Australia . Despite the detection of B . pseudomallei in various soil and water samples from endemic areas , the environmental habitat of B . pseudomallei ... | Melioidosis is a severe disease affecting humans and animals in the tropics . It is caused by the bacterium Burkholderia pseudomallei , which lives in tropical soil and especially occurs in southeast Asia and northern Australia . Despite the recognition that melioidosis is an emerging infectious disease , little is kno... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/bacterial",
"infections",
"ecology/environmental",
"microbiology",
"microbiology/medical",
"microbiology",
"infectious",
"diseases/tropical",
"and",
"travel-associated",
"diseases"
] | 2009 | Landscape Changes Influence the Occurrence of the Melioidosis Bacterium Burkholderia pseudomallei in Soil in Northern Australia |
The JAK/STAT pathway is a key signaling pathway in the regulation of development and immunity in metazoans . In contrast to the multiple combinatorial JAK/STAT pathways in mammals , only one canonical JAK/STAT pathway exists in Drosophila . It is activated by three secreted proteins of the Unpaired family ( Upd ) : Upd... | Innate immunity acts as the primary line of defense to overcome invading organisms . This response starts through sensing of microbe-specific molecules such as lipopolysaccharide and peptidoglycan by host receptors . Metazoans can also recognize signals that are associated with tissue damage and wounding , to then acti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"animals",
"animal",
"models",
"c-jun",
"n-terminal",
"kinase",
"signaling",
"cascade",
"bacterial",
"diseases",
"drosophila",
"melanogaste... | 2016 | Remote Control of Intestinal Stem Cell Activity by Haemocytes in Drosophila |
In human cells and in Saccharomyces cerevisiae , BLAP75/Rmi1 acts together with BLM/Sgs1 and TopoIIIα/Top3 to maintain genome stability by limiting crossover ( CO ) formation in favour of NCO events , probably through the dissolution of double Holliday junction intermediates ( dHJ ) . So far , very limited data is avai... | Recombination is a process by which cells can repair DNA damage . Such repair can either be crossovers ( CO ) , in which DNA molecules are submitted to major exchanges , or non-crossover ( NCO ) events . Eukaryotic cells have developed several mechanisms to maintain genome stability during vegetative development by lim... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/recombination",
"molecular",
"biology/chromosome",
"structure",
"genetics",
"and",
"genomics/chromosome",
"biology",
"cell",
"biology/plant",
"genetics",
"and",
"gene",
"expression",
"molecular",
"biology/dna",
"repair"
] | 2008 | The Arabidopsis BLAP75/Rmi1 Homologue Plays Crucial Roles in Meiotic Double-Strand Break Repair |
Lepidopterans ( butterflies and moths ) are a rich and diverse order of insects , which , despite their economic impact and unusual biological properties , are relatively underrepresented in terms of genomic resources . The genome of the silkworm Bombyx mori has been fully sequenced , but comparative lepidopteran genom... | Butterflies and moths ( called the Lepidoptera ) are a large and diverse group of insects that has long captured the attention of biologists and laymen . The colorful patterns on the wings of butterflies , in particular , offer an ideal system to investigate which genes and developmental mechanisms contribute to evolut... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/gene",
"discovery",
"genetics",
"and",
"genomics/comparative",
"genomics",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics",
"evolutionary",
"biology/genomics",
"evolutionary",
"biology/developmental",
"evolution"
] | 2009 | A Gene-Based Linkage Map for Bicyclus anynana Butterflies Allows for a Comprehensive Analysis of Synteny with the Lepidopteran Reference Genome |
It is an assumption of large , population-based datasets that samples are annotated accurately whether they correspond to known relationships or unrelated individuals . These annotations are key for a broad range of genetics applications . While many methods are available to assess relatedness that involve estimates of... | High-density microarrays measuring single nucleotide polymorphisms ( SNPs ) provide information about the genotypes across many loci . SNP genotypes observed for any two individuals can be compared in terms of identity-by-state ( IBS ) , in which two individuals are observed to have 0 , 1 , or 2 alleles in common at a ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"haplotypes",
"chromosomal",
"inheritance",
"heredity",
"genetics",
"population",
"genetics",
"biology",
"human",
"genetics",
"genetics",
"and",
"genomics"
] | 2011 | Inference of Relationships in Population Data Using Identity-by-Descent and Identity-by-State |
The fungal pathogen Candida glabrata has risen from an innocuous commensal to a major human pathogen that causes life-threatening infections with an associated mortality rate of up to 50% . The dramatic rise in the number of immunocompromised individuals from HIV infection , tuberculosis , and as a result of immunosupp... | Candida glabrata is a major human pathogen due to its low susceptibility to conventional antifungal drugs and the dramatic increase in the number of immunocompromised individuals suffering from HIV AIDS , cancer , and diabetes . Iron overload is one of the most common genetically inherited diseases and reports suggest ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/nosocomial",
"and",
"healthcare-associated",
"infections",
"microbiology/immunity",
"to",
"infections",
"infectious",
"diseases/fungal",
"infections",
"microbiology/innate",
"immunity",
"cell",
"biology/microbial",
"growth",
"and",
"development",
"microbio... | 2011 | Host Iron Withholding Demands Siderophore Utilization for Candida glabrata to Survive Macrophage Killing |
Pulmonary infections are a major global cause of morbidity , exacerbated by an increasing threat from antibiotic-resistant pathogens . In this context , therapeutic interventions aimed at protectively modulating host responses , to enhance defence against infection , take on ever greater significance . Pseudomonas aeru... | Lung infections are a common cause of death worldwide . As the threat of antibiotic-resistance becomes realised , new approaches are needed to treat disease-causing bacteria , such as multidrug-resistant Pseudomonas aeruginosa . Treatments that could enhance the body’s most effective natural defences can overcome antib... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2019 | Cathelicidin is a “fire alarm”, generating protective NLRP3-dependent airway epithelial cell inflammatory responses during infection with Pseudomonas aeruginosa |
Repurposing existing proteins for new cellular functions is recognized as a main mechanism of evolutionary innovation , but its role in organelle evolution is unclear . Here , we explore the mechanisms that led to the evolution of the centrosome , an ancestral eukaryotic organelle that expanded its functional repertoir... | The centrosome helps cells to divide , and is important for the development of animals . It has its evolutionary origins in the basal body , which was present in the last common ancestor of all eukaryotes . Here , we study how the evolution of novel proteins helped the formation of the centrosome . Coiled-coil proteins... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"sequence",
"analysis",
"biochemistry",
"organismal",
"evolution",
"evolutionary",
"modeling",
"animal",
"evolution",
"biology",
"and",
"life",
"sciences",
"molecular",
"biology",
"techniques",
"proteomics",
"computational",
"biology",
"evolution... | 2014 | Coiled-Coil Proteins Facilitated the Functional Expansion of the Centrosome |
Cationic amino acid transporters ( CAT ) are important regulators of NOS2 and ARG1 activity because they regulate L-arginine availability . However , their role in the development of Th1/Th2 effector functions following infection has not been investigated . Here we dissect the function of CAT2 by studying two infectiou... | Recent studies conducted with amino transporter Slc7a2-deficient mice ( CAT2 ) demonstrated that NOS2 activity in macrophages is regulated by CAT2 . NOS2 , which synthesizes nitric oxide , regulates numerous important activities , including resistance to infectious organisms , tumor development , and autoimmune disease... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"gastroenterology",
"and",
"hepatology/hepatology",
"immunology/immune",
"response",
"infectious",
"diseases/helminth",
"infections",
"infectious",
"diseases/pr... | 2008 | Cationic Amino Acid Transporter-2 Regulates Immunity by Modulating Arginase Activity |
FAS-associated factor-1 ( FAF1 ) is a component of the death-inducing signaling complex involved in Fas-mediated apoptosis . It regulates NF-κB activity , ubiquitination , and proteasomal degradation . Here , we found that FAF1 positively regulates the type I interferon pathway . FAF1gt/gt mice , which deficient in FAF... | Type I interferon-mediated antiviral response is critical for controlling virus infections . However , interferon-mediated immune responses need to be tightly regulated to maintain host immune homeostasis . Recently , molecules involved in regulating interferon-mediated innate immune response are the subject of much re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"enzyme-linked",
"immunoassays",
"immune",
"physiology",
"cytokines",
"antiviral",
"immune",
"response",
"immunology",
"microbiology",
"light",
"microscopy",
"viruses",
"developmental",
"biology",
"rna... | 2017 | FAS-associated factor-1 positively regulates type I interferon response to RNA virus infection by targeting NLRX1 |
Mucociliary clearance is one of the major lines of defense of the human respiratory system . The mucus layer coating the airways is constantly moved along and out of the lung by the activity of motile cilia , expelling at the same time particles trapped in it . The efficiency of the cilia motion can experimentally be a... | Mucociliary clearance is the first line of defense mechanisms of the human airways . The mucus transporting debris , particles , microorganisms and pollutants is carried away by the coordinated motion of cilia beating at the surface of the airway epithelium . We present here a mathematical and numerical model aiming at... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"velocity",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"classical",
"mechanics",
"fluid",
"mechanics",
"mechanical",
"stress",
"cellular",
"structures",
"and",
"organelles",
"mucus",
"flow",
"field",
"fluid",
"dynamics",
"continuum",
"mechanics",
"flui... | 2017 | A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part II, modeling |
Trypanosoma cruzi infection is associated with severe T cell unresponsiveness to antigens and mitogens and is characterized by decreased IL-2 synthesis . In addition , the acquisition of the anergic phenotype is correlated with upregulation of “gene related to anergy in lymphocytes” ( GRAIL ) protein in CD4 T cells . W... | Chagas disease is caused by the protozoan parasite Trypanosoma cruzi and is endemic in Central and South America , where it affects about 10 million people . In addition , migration has led to the disease being established in non-endemic countries . Infection involves an acute stage that evolves to a chronic stage wher... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"t",
"helper",
"cells",
"flow",
"cytometry",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"spleen",
"immunology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoans",
"anergy",
"research",
"and",
... | 2017 | GRAIL and Otubain-1 are Related to T Cell Hyporesponsiveness during Trypanosoma cruzi Infection |
There is a global need for cost-effective and environmentally friendly tools for control of mosquitoes and mosquito-borne diseases . One potential way to achieve this is to combine already available tools to gain synergistic effects to reduce vector mosquito populations . Another possible way to improve mosquito contro... | Traditionally , a key intervention in mosquito control is the use of insecticides against the adult stage . However , various factors limit the long-term use of these control methods , including the development of insecticide resistance , changes in mosquito biting behaviour , and concerns regarding potential negative ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"larvicides",
"invertebrates",
"emulsions",
"medicine",
"and",
"health",
"sciences",
"demography",
"colloids",
"animals",
"reproductive",
"physiology",
"developmental",
"biology",
"waxes",
"materials",
"science",
"pest",
"control",
"population",
"biology... | 2016 | Combining Attractants and Larvicides in Biodegradable Matrices for Sustainable Mosquito Vector Control |
Histamine is an important chemical messenger that regulates multiple physiological processes in both vertebrate and invertebrate animals . Even so , how glial cells and neurons recycle histamine remains to be elucidated . Drosophila photoreceptor neurons use histamine as a neurotransmitter , and the released histamine ... | Neurotransmitter transporters that remove neurotransmitters and recycle them after their release have particular importance at visual synapses , which must signal at high frequencies and therefore required rapid clearance of neurotransmitters from the synaptic cleft . In this study , we identified a SLC22 family transp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Histamine Recycling Is Mediated by CarT, a Carcinine Transporter in Drosophila Photoreceptors |
The countries of West Africa are largely portrayed as cholera endemic , although the dynamics of outbreaks in this region of Africa remain largely unclear . To understand the dynamics of cholera in a major portion of West Africa , we analyzed cholera epidemics from 2009 to 2015 from Benin to Mauritania . We conducted a... | We analyzed cholera epidemics from Benin to Mauritania , during 2009 to 2015 , and performed a series of field visits as well as molecular epidemiology analyses of V . cholerae isolates from most recent epidemics throughout West Africa . We found that at least 54% of cases concerned populations living in the three urba... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"guinea",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"vibrio",
"tropical",
"diseases",
"geographical",
"locations",
"microbiology",
"bacterial",
"diseases",
"vibrio",
"cholerae",
"benin",
"neglected",
"tropical",
... | 2018 | Dynamics of cholera epidemics from Benin to Mauritania |
Forecasting the emergence and spread of influenza viruses is an important public health challenge . Timely and accurate estimates of influenza prevalence , particularly of severe cases requiring hospitalization , can improve control measures to reduce transmission and mortality . Here , we extend a previously published... | In the United States , seasonal influenza causes thousands of deaths and hundreds of thousands of hospitalizations . The annual timing and burden of the flu season vary considerably with the severity of the circulating viruses . Epidemic forecasting can inform early and effective countermeasures to limit the human toll... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"influenza",
"sociology",
"social",
"sciences",
"social",
"media",
"mathematics",
"forecasting",
"statistics",
"(mathematics)",
"internet",
"network",
"analysis",
"social",
"networks",
"distribution",
"curves",
"social",
"communica... | 2018 | Optimal multi-source forecasting of seasonal influenza |
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