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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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Within the genomes of metazoans , nucleosomes are highly organised adjacent to the binding sites for a subset of transcription factors . Here we have sought to investigate which chromatin remodelling enzymes are responsible for this . We find that the ATP-dependent chromatin remodelling enzyme SNF2H plays a major role ... | CTCF is a transcriptional regulator acting as an insulator element interfering with enhancer function and as a boundary between chromatin domains . CTCF has been shown to organise an exquisite array of phased nucleosomes flanking its binding sites . Here we identified SNF2H as the enzyme primarily responsible for organ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"nucleosome",
"mapping",
"transcription",
"factors",
"epigenetics",
"molecular",
"biology",
"techniques",
"chromatin",
"research",
"and",
"analysis",
"methods",
"small",
"interfering",
"rnas",
"gen... | 2016 | The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors |
Key steps in a viral life-cycle , such as self-assembly of a protective protein container or in some cases also subsequent maturation events , are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales . These salient aspects of a viral life cycle are hence well described... | The genetic material of viruses is packaged inside capsids constituted from a few tens to thousands of proteins . The latter can organize in multimers that serve as fundamental blocks for the viral shell assembly or that control the capsid conformational transitions and response to mechanical stress . In this work , we... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [] | 2013 | Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition |
HIV-1 is subject to immune pressure exerted by the host , giving variants that escape the immune response an advantage . Virus released from activated latent cells competes against variants that have continually evolved and adapted to host immune pressure . Nevertheless , there is increasing evidence that virus display... | Increasing evidence suggests that HIV-1 released from activated latent cells survives in productively infected cells in patient plasma despite competition against better adapted virus variants that have evolved in response to the host immune pressure . Long-term survival requires that latent virus forms adapt to the ho... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [] | 2015 | Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population |
The burden of malaria in Vietnam has drastically reduced , prompting the National Malaria Control Program to officially engage in elimination efforts . Plasmodium vivax is becoming increasingly prevalent , remaining a major problem in the country's central and southern provinces . A better understanding of P . vivax ge... | In Vietnam , Plasmodium vivax ( P . vivax ) is the second most frequent human malaria parasite and a major obstacle to countrywide malaria elimination . Knowing the local parasite structure is useful for elimination efforts . Therefore , we analyzed , with a panel of 14 microsatellite markers , 234 P . vivax mono infec... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"parasite",
"groups",
"ecology",
"and",
"environmental",
"sciences",
"rivers",
"plasmodium",
"population",
"genetics",
"tropical",
"diseases",
"geographical",
"locations",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"parasi... | 2016 | Population Genetics of Plasmodium vivax in Four Rural Communities in Central Vietnam |
Although ICP4 is the only essential transcription activator of herpes simplex virus 1 ( HSV-1 ) , its mechanisms of action are still only partially understood . We and others propose a model in which HSV-1 genomes are chromatinized as a cellular defense to inhibit HSV-1 transcription . To counteract silencing , HSV-1 w... | The nuclear-replicating DNA viruses of the family herpesviridae cause a variety of diseases . Eight herpesviruses infect humans . Three of them , including herpes simplex virus 1 ( HSV-1 ) , belong to the alpha-herpesvirus sub-family . Viruses in this family have the fastest replication cycles of all herpesviruses , pr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"herpes",
"simplex",
"virus",
"vero",
"cells",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"biological",
"cultures",
"dna-binding",
"proteins",
"microbiology",
"dna",
"transcription",
"viruses",
"dna",
"replication... | 2016 | An Essential Viral Transcription Activator Modulates Chromatin Dynamics |
Synchronized oscillation is very commonly observed in many neuronal systems and might play an important role in the response properties of the system . We have studied how the spontaneous oscillatory activity affects the responsiveness of a neuronal network , using a neural network model of the visual cortex built from... | In the nervous system , information is delivered and processed digitally via voltage spikes transmitted between cells . A neural system is characterized by its input/output spike signal patterns . Generally , a network of neurons shows a very different response pattern than that of a single neuron . In some cases , a n... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/systems",
"biology",
"biophysics/theory",
"and",
"simulation",
"neuroscience/theoretical",
"neuroscience"
] | 2009 | Spontaneous Local Gamma Oscillation Selectively Enhances Neural
Network Responsiveness |
The Mitogen-Activated Protein Kinase ( MAPK ) network consists of tightly interconnected signalling pathways involved in diverse cellular processes , such as cell cycle , survival , apoptosis and differentiation . Although several studies reported the involvement of these signalling cascades in cancer deregulations , t... | Depending on environmental conditions , strongly intertwined cellular signalling pathways are activated , involving activation/inactivation of proteins and genes in response to external and/or internal stimuli . Alterations of some components of these pathways can lead to wrong cell behaviours . For instance , cancer-r... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision |
During meiotic prophase , a structure called the synaptonemal complex ( SC ) assembles at the interface between aligned pairs of homologous chromosomes , and crossover recombination events occur between their DNA molecules . Here we investigate the inter-relationships between these two hallmark features of the meiotic ... | Reliable chromosome inheritance during sexual reproduction depends on the formation of temporary connections between homologous chromosomes that enable them to segregate toward opposite spindle poles at the meiosis I division . These connections are established during an extended meiotic prophase characterized by two p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"fluorescence",
"imaging",
"invertebrates",
"meiosis",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"gonads",
"caenorhabditis",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"light",
"microscopy",
"animals",
"animal",
"models",
... | 2017 | Meiotic recombination modulates the structure and dynamics of the synaptonemal complex during C. elegans meiosis |
Combinatorial regulation of gene expression is ubiquitous in eukaryotes with multiple inputs converging on regulatory control elements . The dynamic properties of these elements determine the functionality of genetic networks regulating differentiation and development . Here we propose a method to quantitatively charac... | Hematopoiesis—blood cell development—has long served as a model for study of cellular differentiation and its control by underlying gene regulatory networks . The Scl-Gata2-Fli1 triad is a network module essential for the development of hematopoietic stem cells but its mechanistic role is not well understood . The tran... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"hematology/hematopoiesis",
"developmental",
"biology/stem",
"cells",
"computational",
"biology/transcriptional",
"regulation"
] | 2010 | Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate |
The intracellular pathogen Legionella pneumophila hijacks the endoplasmic reticulum ( ER ) -derived vesicles to create an organelle designated Legionella-containing vacuole ( LCV ) required for bacterial replication . Maturation of the LCV involved acquisition of Rab1 , which is mediated by the bacterial effector prote... | Legionella pneumophila delivers 275 validated substrates into the host cytosol by its Dot/Icm type IV secretion system . Several substrates including SidM/DrrA and LidA directly interact with the host Rab GTPases and interfere with the vesicle secretion pathway . SidM/DrrA is necessary for Rab1 recruitment , function a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"proteins",
"biology",
"microbiology",
"biophysics",
"bacterial",
"pathogens"
] | 2012 | Structural Insights into a Unique Legionella pneumophila Effector LidA Recognizing Both GDP and GTP Bound Rab1 in Their Active State |
We investigated the spatiotemporal dynamics of HSV genome transport during the initiation of infection using viruses containing bioorthogonal traceable precursors incorporated into their genomes ( HSVEdC ) . In vitro assays revealed a structural alteration in the capsid induced upon HSVEdC binding to solid supports tha... | Virtually all DNA virus classes as well as many RNA viruses must deposit their genomes within the nucleus for transcription , genome replication and subsequent capsid assembly . While infecting capsids have been studied by various methods and biochemical approaches have been used to investigate the bulk genome populati... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"microbiology",
"viral",
"structure",
"dna",
"replication",
"dna",
"immunologic",
"techniques",
"microbial",
"genomics",
"research",
"and",
"analysis",
"methods",
"viral",
"genomics",
"genomic",
"signal",
"processing",
"immunoassays",
"comparative",
"genomics",
"viral",
... | 2017 | Spatiotemporal dynamics of HSV genome nuclear entry and compaction state transitions using bioorthogonal chemistry and super-resolution microscopy |
Using a computational model , we simulated mitochondrial deoxynucleotide metabolism and mitochondrial DNA replication . Our results indicate that the output from the mitochondrial salvage enzymes alone is inadequate to support a mitochondrial DNA replication duration of as long as 10 hours . We find that an external so... | The powerhouses of human cells , mitochondria , contain DNA that is distinct from the primary genome , the DNA in the nucleus of cells . The mitochondrial genome needs to be replicated often to ensure continued generation of ATP ( adenosine triphosphate ) which is the energy currency of the cell . Problems with mainten... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"enzymes",
"metabolic",
"networks",
"nucleotides",
"bioenergetics",
"enzyme",
"kinetics",
"mitochondrial",
"diseases",
"theoretical",
"biology",
"biochemistry",
"simulations",
"metabolic",
"pathways",
"biology",
"biochemistry",
"biochemical",
"simulations",
"nucleic",
"acids"... | 2011 | Enzyme Kinetics of the Mitochondrial Deoxyribonucleoside Salvage Pathway Are Not Sufficient to Support Rapid mtDNA Replication |
The zebrafish Danio rerio is a powerful model system to study the genetics of development and disease . However , maintenance of zebrafish husbandry records is both time intensive and laborious , and a standardized way to manage and track the large amount of unique lines in a given laboratory or centralized facility ha... | FishNET facilitates remote tracking of individual zebrafish lines and links associated biological resources to enable robust and efficient colony management and storage of laboratory information related to zebrafish . | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"fish",
"ecology",
"and",
"environmental",
"sciences",
"methods",
"and",
"resources",
"relational",
"databases",
"vertebrates",
"computer",
"hardware",
"computers",
"animals",
"animal",
"models",
"osteichthyes",
"developmental",
"biology",
"model",
"organisms",
"experimen... | 2019 | FishNET: An automated relational database for zebrafish colony management |
Globally , vaccine-preventable diseases remain a significant cause of early childhood mortality despite concerted efforts to improve vaccine coverage . One reason for impaired protection may be the influence of prenatal exposure to parasitic antigens on the developing immune system . Prior research had shown a decrease... | This mother-baby cohort study continued our investigations into the potential impact of a mother’s parasitic infection ( s ) during pregnancy on a baby’s ability to respond to early life vaccinations . In a rural Kenyan setting where malaria and helminth infections are common , we tested infants’ anti-vaccine antibody ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"children",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"maternal",
"health",
"obstetrics",
"and",
"gynecology",
"immunology",
"tropical",
"diseases",
"parasitic",
"diseases",
"vaccines",
"preventive",
"medicine",
"age",
"groups",
"women's",
"health... | 2019 | Parasitic infections during pregnancy need not affect infant antibody responses to early vaccination against Streptococcus pneumoniae, diphtheria, or Haemophilus influenzae type B |
Conjugative transfer of the integrative and conjugative element ICEclc in the bacterium Pseudomonas knackmussii is the consequence of a bistable decision taken in some 3% of cells in a population during stationary phase . Here we study the possible control exerted by the stationary phase sigma factor RpoS on the bistab... | Horizontal gene transfer is one of the amazing phenomena in the prokaryotic world , by which DNA can be moved between species with means of a variety of specialized “elements” and/or specific host cell mechanisms . In particular the molecular decisions that have to be made in order to transfer DNA from one cell to anot... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbial",
"evolution",
"biology",
"microbiology"
] | 2012 | Cellular Variability of RpoS Expression Underlies Subpopulation Activation of an Integrative and Conjugative Element |
Exposure to ultraviolet ( UV ) radiation from sunlight accounts for 90% of the symptoms of premature skin aging and skin cancer . The tumor suppressor serine-threonine kinase LKB1 is mutated in Peutz-Jeghers syndrome and in a spectrum of epithelial cancers whose etiology suggests a cooperation with environmental insult... | Environmental insults are directly involved in cancer development . In particular , Ultraviolet ( UV ) radiation has been associated to the acquisition of different types skin cancer and premature skin aging . UV radiation causes modifications in the genetic material of cells ( DNA ) that if not repaired properly will ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"dna",
"damage",
"biochemistry",
"dermatology",
"skin",
"neoplasms",
"medicine",
"and",
"health",
"sciences",
"skin",
"tumors",
"biology",
"and",
"life",
"sciences",
"dna",
"repair",
"dna",
"biochemical",
"activity"
] | 2014 | A Mouse Model Uncovers LKB1 as an UVB-Induced DNA Damage Sensor Mediating CDKN1A (p21WAF1/CIP1) Degradation |
Focal adhesions are protein complexes that anchor cells to the extracellular matrix . During migration , the growth and disassembly of these structures are spatiotemporally regulated , with new adhesions forming at the leading edge of the cell and mature adhesions disassembling at the rear . Signalling proteins and str... | Cellular migration is crucial in both physiological and pathological functions . Maintenance of proper migration and development of aberrant migration are effectuated by cellular machinery involving protein complexes , called adhesions , that anchor the cell to its environment . Over time , these adhesions assemble at ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell",
"binding",
"phosphorylation",
"cell",
"physiology",
"cell",
"motility",
"ecology",
"and",
"environmental",
"sciences",
"chemical",
"compounds",
"atmospheric",
"science",
"enzymes",
"enzymology",
"organic",
"compounds",
"fluorophotometry",
"developmental",
"biology",... | 2018 | Paxillin phosphorylation at serine 273 and its effects on Rac, Rho and adhesion dynamics |
Active and repressed ribosomal RNA ( rRNA ) genes are characterised by specific epigenetic marks and differentially positioned nucleosomes at their promoters . Repression of the rRNA genes requires a non-coding RNA ( pRNA ) and the presence of the nucleolar remodeling complex ( NoRC ) . ATP-dependent chromatin remodeli... | Tumour cells overexpress ribosomal RNA ( rRNA ) , which is required for ribosome assembly and cell growth . rRNA gene repression is mediated by the chromatin remodeling complex ( NoRC ) and a non-coding RNA that binds to this enzyme . This study addresses the mechanism of nucleosome positioning by NoRC and the function... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"biochemistry",
"nucleic",
"acids",
"proteins",
"enzymes",
"genetics",
"gene",
"expression",
"biology",
"biophysics",
"gene",
"function"
] | 2014 | Chromatin Targeting Signals, Nucleosome Positioning Mechanism and Non-Coding RNA-Mediated Regulation of the Chromatin Remodeling Complex NoRC |
It has been proposed that switching from annual to biannual ( twice yearly ) mass community-directed treatment with ivermectin ( CDTI ) might improve the chances of onchocerciasis elimination in some African foci . However , historically , relatively few communities have received biannual treatments in Africa , and the... | The African Programme for Onchocerciasis Control ( APOC ) has recently been extended until 2025 , with renewed commitment towards onchocerciasis elimination . This aim is aligned with the goals stated by the World Health Organization and the London Declaration on Neglected Tropical Diseases in January 2012 . Switching ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | The Cost of Annual versus Biannual Community-Directed Treatment of Onchocerciasis with Ivermectin: Ghana as a Case Study |
The modulation of fitness by single mutational substitutions during environmental change is the most fundamental consequence of natural selection . The antagonistic tradeoffs of pleiotropic mutations that can be selected under changing environments therefore lie at the foundation of evolutionary biology . However , the... | The most fundamental mechanism of natural selection in a changing environment is the modulation of fitness by mutations . It is the tradeoffs offered by these mutations that drive evolution . However , fitness tradeoffs are rarely understood at the molecular level , in terms of how the selected mutations affect protein... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"organismal",
"evolution",
"microbial",
"mutation",
"enzymes",
"macromolecular",
"assemblies",
"population",
"genetics",
"evolutionary",
"selection",
"microbiology",
"mutation",
"mechanisms",
"of",
"resistance",
"and",
"susceptibility"... | 2012 | Selective Pressure Causes an RNA Virus to Trade Reproductive Fitness for Increased Structural and Thermal Stability of a Viral Enzyme |
Arabidopsis thaliana high-affinity potassium transporter 1 ( AtHKT1 ) limits the root-to-shoot sodium transportation and is believed to be essential for salt tolerance in A . thaliana . Nevertheless , natural accessions with ‘weak allele’ of AtHKT1 , e . g . Tsu-1 , are mainly distributed in saline areas and are more t... | Identifying the genetic variation driving plant adaptation to salinity is critical for understanding natural selection and evolutionary mechanisms . In this study , we have revealed that the gene AtHKT1 drives natural variation in the adaptation of A . thaliana to salinity . Our evidences directly show that the AtHKT1 ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"&",
"methods"
] | [
"plant",
"anatomy",
"ecology",
"and",
"environmental",
"sciences",
"brassica",
"plant",
"physiology",
"plant",
"science",
"model",
"organisms",
"experimental",
"organism",
"systems",
"plant",
"pathology",
"evolutionary",
"adaptation",
"plant",
"ecology",
"plants",
"flow... | 2017 | AtHKT1 drives adaptation of Arabidopsis thaliana to salinity by reducing floral sodium content |
Social insects make elaborate use of simple mechanisms to achieve seemingly complex behavior and may thus provide a unique resource to discover the basic cognitive elements required for culture , i . e . , group-specific behaviors that spread from “innovators” to others in the group via social learning . We first explo... | Social insects make use of simple mechanisms to achieve many seemingly complex behaviors and thus may be able to provide a unique resource for uncovering the basic cognitive elements required for culture . Here , we first show that bumblebees can be trained to pull a string to access a reward , but most could not learn... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"learning",
"invertebrates",
"plant",
"anatomy",
"medicine",
"and",
"health",
"sciences",
"legs",
"sociology",
"social",
"sciences",
"limbs",
"(anatomy)",
"neuroscience",
"learning",
"and",
"memory",
"animals",
"plant",
"science",
"cognitive",
"psychology",
"animal",
... | 2016 | Associative Mechanisms Allow for Social Learning and Cultural Transmission of String Pulling in an Insect |
In interocular suppression , a suprathreshold monocular target can be rendered invisible by a salient competitor stimulus presented in the other eye . Despite decades of research on interocular suppression and related phenomena ( e . g . , binocular rivalry , flash suppression , continuous flash suppression ) , the neu... | In interocular suppression , a visible target presented in one eye can be rendered invisible by a competing image ( the competitor ) presented in the other eye . This phenomenon is a striking demonstration of the discrepancy between physical inputs to the visual system and perception , and it also allows neuroscientist... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Deconstructing Interocular Suppression: Attention and Divisive Normalization |
Over the past 30 years , benzimidazoles have increasingly been used to treat cystic echinococcosis ( CE ) . The efficacy of benzimidazoles , however , remains unclear . We systematically searched MEDLINE , EMBASE , SIGLE , and CCTR to identify studies on benzimidazole treatment outcome . A large heterogeneity of method... | Cystic echinococcosis ( CE ) is a parasitic infection of worldwide occurrence transmitted to humans by dogs . After infection cysts develop , mainly in the liver and lung . Ultrasound-based staging of cysts into active , transitional , and inactive has opened new venues for treatment and follow-up . Currently four trea... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections"
] | 2009 | Treatment Response of Cystic Echinococcosis to Benzimidazoles: A Systematic Review |
Cytomegalovirus ( CMV ) is a ubiquitous β-herpesvirus that establishes life-long latent infection in a high percentage of the population worldwide . CMV induces the strongest and most durable CD8+ T cell response known in human clinical medicine . Due to its unique properties , the virus represents a promising candidat... | Vaccines against influenza typically induce immune responses based on antibodies , small molecules that recognize the virus particles outside of cells and neutralize them before they infect a cell . However , influenza rapidly evolves , escaping immune recognition , and the fastest evolution is seen in the part of the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"cell",
"motility",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"spleen",
"pathogens",
"immunology",
"microbiology",
"orthomyxoviruses",
"viruses... | 2019 | Mucosal CD8+ T cell responses induced by an MCMV based vaccine vector confer protection against influenza challenge |
With the rapidly increasing abundance and accessibility of genomic data , there is a growing interest in using population genetic approaches to characterize fine-scale dispersal of organisms , providing insight into biological processes across a broad range of fields including ecology , evolution and epidemiology . For... | The spatiotemporal dispersal of organisms can inform efforts to conserve endangered species , to contain the spread of drug resistance , and to eliminate disease . As genomic data become increasingly more affordable and accessible via public depositories , the demand for methods capable of extracting fine-scale populat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"parasite",
"groups",
"plasmodium",
"population",
"genetics",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"parasitology",
"ethnicities",
"apicomplexa",
"protozoans",
"mathematics",
"dna",
"population",... | 2017 | Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent |
Diverse clinical features have been reported in human African trypanosomiasis ( HAT ) foci caused by Trypanosoma brucei rhodesiense ( T . b . rhodesiense ) giving rise to the hypothesis that HAT manifests as a chronic disease in South-East African countries and increased in virulence towards the North . Such variation ... | T . b . gambiense and T . b . rhodesiense cause human African trypanosomiasis ( HAT ) . These parasite subspecies differ in their rate of progression to central nervous system ( CNS ) infection , and consequently to coma and death . Variation in disease progression and severity has also been documented between northern... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/protozoal",
"infections",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/epidemiology",
"and",
"control",
"of",
"infectious",
"diseases"
] | 2010 | Focus–Specific Clinical Profiles in Human African Trypanosomiasis Caused by Trypanosoma brucei rhodesiense |
Bovine tuberculosis is a zoonotic disease with largely unknown impact in Africa , with risk factors such as HIV and direct contact with animals or consumption of Mycobacterium bovis infected animal products . In order to understand and quantify this risk and design intervention strategies , good epidemiological studies... | Bovine tuberculosis is a rather neglected zoonotic disease caused by Mycobacterium bovis that is of global concern owing to the persistence of the bacillus in reservoirs that can spread bovine tuberculosis between animals and humans . Africa remains understudied regarding this pathogen , and should be an area of concer... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biogeography",
"animal",
"types",
"ecology",
"and",
"environmental",
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"milk",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"ruminants",
"population",
"genetics",
"geographical",
"locations",
"vertebrates",
"diet",
"animals",
"mammals",
"nutriti... | 2018 | Genetic diversity and potential routes of transmission of Mycobacterium bovis in Mozambique |
Software produced for research , published and otherwise , suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer’s computer . We present ten simple rules to make such software robust enough to be run by anyone , anywhere ,... | Many researchers have found out the hard way that there’s a world of difference between “works for me on my machine” and “works for other people on theirs . ” Many common challenges can be avoided by following a few simple rules; doing so not only improves reproducibility but can accelerate research . | [
"Abstract",
"Introduction",
"Rule",
"1:",
"Use",
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"Rule",
"2:",
"Document",
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"3:",
"Make",
"common",
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"easy",
"to",
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"4:",
"Version",
"your",
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"Rule",
"5:",
... | [
"sequence",
"analysis",
"operating",
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"sequence",
"alignment",
"bioinformatics",
"engineering",
"and",
"technology",
"research",
"assessment",
"computer",
"software",
"database",
"and",
"informatics",
"methods",
"sof... | 2017 | Ten simple rules for making research software more robust |
Rift Valley fever virus ( RVFV ) is a mosquito-borne virus in the family Bunyaviridiae that has spread throughout continental Africa to Madagascar and the Arabian Peninsula . The establishment of RVFV in North America would have serious consequences for human and animal health in addition to a significant economic impa... | In anticipation of continued pathogen emergence in the U . S . due to globalization climate change , and other factors , the development of proactive management plans and interventions to predict and then intervene is going to be more efficient and effective than retrospective plans developed after pathogen emergence .... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"animals",
"population",
"modeling",
"veterinary",
"science",
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonoses",
"epidemiology",
"infectious",
"disease",
... | 2014 | Predicting the Mosquito Species and Vertebrate Species Involved in the Theoretical Transmission of Rift Valley Fever Virus in the United States |
There is growing evidence that gene expression profiling of peripheral blood cells is a valuable tool for assessing gene signatures related to exposure , drug-response , or disease . However , the true promise of this approach can not be estimated until the scientific community has robust baseline data describing varia... | As a major defence and transport system , blood cells are capable of adjusting gene expression in response to various clinical , biochemical , and pathological conditions . Here , we expand our understanding about the nature and extent of variation in gene expression from blood among healthy individuals . Using a large... | [
"Abstract",
"Introduction",
"Discussion",
"Methods"
] | [
"genetics",
"and",
"genomics/genomics",
"public",
"health",
"and",
"epidemiology/epidemiology",
"genetics",
"and",
"genomics/physiogenomics",
"genetics",
"and",
"genomics/gene",
"expression"
] | 2010 | Deciphering Normal Blood Gene Expression Variation—The NOWAC Postgenome Study |
Plants produce large amounts of secondary metabolites in their shoots and roots and store them in specialized secretory structures . Although secondary metabolites and their secretory structures are commonly assumed to have a defensive function , evidence that they benefit plant fitness under herbivore attack is scarce... | Plant roots produce diverse and abundant blends of bioactive metabolites . One potential function of these compounds is to protect roots against the devastating effects of below ground herbivore attack . However , examples demonstrating such a protective function in native plant-herbivore systems are lacking . Here , w... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | A Latex Metabolite Benefits Plant Fitness under Root Herbivore Attack |
The cochlea not only transduces sound-induced vibration into neural spikes , it also amplifies weak sound to boost its detection . Actuators of this active process are sensory outer hair cells in the organ of Corti , whereas the inner hair cells transduce the resulting motion into electric signals that propagate via th... | Outer hair cells are highly specialized force producers inside the inner ear: they can change length when stimulated electrically . However , how exactly this electromotile effect contributes to the astonishing sensitivity and frequency selectivity of the inner ear has remained unclear . Here we show for the first time... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"classical",
"mechanics",
"engineering",
"and",
"technology",
"vibration",
"ears",
"signal",
"processing",
"neuroscience",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"labyrinth",
"supporting",
"cells",
"epithelial",
... | 2018 | Static length changes of cochlear outer hair cells can tune low-frequency hearing |
Probability matching is a classic theory of decision making that was first developed in models of cognition . Posterior probability matching , a variant in which observers match their response probabilities to the posterior probability of each response being correct , is being used increasingly often in models of perce... | Decision making is partly random: a person can make different decisions at different times based on the same information . The theory of probability matching says that one reason for this randomness is that people usually choose the response that they think is most likely to be correct , but they sometimes intentionall... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [] | 2015 | Posterior Probability Matching and Human Perceptual Decision Making |
Computational protein design has been successful in modeling fixed backbone proteins in a single conformation . However , when modeling large ensembles of flexible proteins , current methods in protein design have been insufficient . Large barriers in the energy landscape are difficult to traverse while redesigning a p... | In this article , we report a new approach for protein design , which combines traditional structural modeling with machine learning and integer programming . Using this method , we are able to design antibodies that are predicted to bind large panels of antigenically diverse HIV variants . The combination of methods f... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biotechnology",
"sequencing",
"techniques",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"engineering",
"and",
"technology",
"pathogens",
"synthetic",
"biology",
"immunology",
"microbiology",
"synthetic",
... | 2018 | Integrating linear optimization with structural modeling to increase HIV neutralization breadth |
Neural progenitors produce neurons whose identities can vary as a function of the time that specification occurs . Here , we describe the heterochronic specification of two photoreceptor ( PhR ) subtypes in the zebrafish pineal gland . We find that accelerating PhR specification by impairing Notch signaling favors the ... | A major goal in the field of developmental neurobiology is to identify the mechanisms that underly the diversification of the subtypes of neurons that are needed for the function of the nervous system . When investigating these mechanisms , time is an often-overlooked variable . Here , we show that in the zebrafish pin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pineal",
"gland",
"in",
"situ",
"hybridization",
"molecular",
"probe",
"techniques",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"social",
"sciences",
"neuroscience",
"notch",
"signaling",
"developmental",... | 2019 | A Notch-mediated, temporal asymmetry in BMP pathway activation promotes photoreceptor subtype diversification |
Homologous recombination ( HR ) is the principal mechanism of DNA repair acting during meiosis and is fundamental for the segregation of chromosomes and the increase of genetic diversity . Nevertheless , non-homologous end joining ( NHEJ ) mechanisms can also act during meiosis , mainly in response to exogenously-induc... | DNA repair is critical for both somatic and meiotic cells . During meiosis , hundreds of DNA double strand breaks ( DSBs ) are introduced endogenously . To repair this damage , meiotic cells use a specialized version of the homologous recombination ( HR ) pathway that uses specific meiotic recombinases , such as DMC1 ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"meiosis",
"homologous",
"chromosomes",
"spermatocytes",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"germ",
"cells",
"dna",
"damage",
"dna",
"sperm",
"sex",
"chromosomes",
"animal",
"cells",
"chromosome",
"biology",
"autosomes",
"biochemistry",
... | 2019 | Transition from a meiotic to a somatic-like DNA damage response during the pachytene stage in mouse meiosis |
Plasmodium knowlesi is now recognised as a leading cause of malaria in Malaysia . As humans come into increasing contact with the reservoir host ( long-tailed macaques ) as a consequence of deforestation , assessing the potential for a shift from zoonotic to sustained P . knowlesi transmission between humans is critica... | Plasmodium knowlesi is a malaria of macaques which is now recognised as a leading cause of human malaria in Malaysia . Although current human infections are a result of human-macaque contact , there is a potential for P . knowlesi to be transmitted solely among humans . The authors developed a multi-host , multi-site t... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonoses",
"medicine",
"and",
"health",
"sciences",
"population",
"modeling",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"biology",
"and",
"life",
"sciences",
"population",
"biology",
"infectious",
"diseas... | 2014 | Transmission and Control of Plasmodium knowlesi: A Mathematical Modelling Study |
Neither genetic nor environmental factors fully account for variability in individual longevity: genetically identical invertebrates in homogenous environments often experience no less variability in lifespan than outbred human populations . Such variability is often assumed to result from stochasticity in damage accum... | Why do some individuals live longer than others ? Unexpectedly , genetic differences contribute surprisingly little to lifespan variation in humans . The situation is thrown into relief in studies of C . elegans , in which genetically identical siblings reared in identical environments usually experience different life... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"aging",
"physiological",
"processes",
"developmental",
"biology",
"organism",
"development",
"physiology",
"genetics",
"epigenetics",
"biology",
"anatomy",
"and",
"physiology",
"genetics",
"and",
"genomics"
] | 2011 | MicroRNA Predictors of Longevity in Caenorhabditis elegans |
Filamentous fungi are of great importance in ecology , agriculture , medicine , and biotechnology . Thus , it is not surprising that genomes for more than 100 filamentous fungi have been sequenced , most of them by Sanger sequencing . While next-generation sequencing techniques have revolutionized genome resequencing ,... | Fungi have immense impacts on ecosystems and affect many aspects of society . They are used as convenient organisms for fundamental research because their typically haploid genetics enable straightforward phenotyping of mutations and because most fungal cells can differentiate the entire organism . Fungi have compact g... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/genomics",
"microbiology"
] | 2010 | De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis |
Class 1 integrons are widespread genetic elements that allow bacteria to capture and express gene cassettes that are usually promoterless . These integrons play a major role in the dissemination of antibiotic resistance among Gram-negative bacteria . They typically consist of a gene ( intI ) encoding an integrase ( tha... | Integrons are widespread bacterial genetic elements able to capture and express gene cassettes that often encode antibiotic resistance determinants . Gene cassettes are usually promoterless and are transcribed from a common promoter , Pc . Pc is located within the coding sequence of the integron integrase , IntI , whic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/microbial",
"evolution",
"and",
"genomics",
"microbiology/medical",
"microbiology",
"infectious",
"diseases/antimicrobials",
"and",
"drug",
"resistance"
] | 2010 | Inverse Correlation between Promoter Strength and Excision Activity in Class 1 Integrons |
Dengue is a major public health problem worldwide and continues to increase in incidence . Dengue virus ( DENV ) infection leads to a range of outcomes , including subclinical infection , undifferentiated febrile illness , Dengue Fever ( DF ) , life-threatening syndromes with fluid loss and hypotensive shock , or other... | Dengue is a mosquito-transmitted viral disease that is a major public health problem worldwide . Dengue virus ( DENV ) infection leads to Dengue Fever ( DF ) and a spectrum of life-threatening syndromes with fluid loss and hypotensive shock or other severe manifestations . Recently , the traditional World Health Organi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"virology",
"dengue",
"fever",
"neglected",
"tropical",
"diseases",
"dengue",
"biology",
"microbiology",
"viral",
"diseases",
"viral",
"disease",
"diagnosis"
] | 2011 | Evaluation of the Traditional and Revised WHO Classifications of Dengue Disease Severity |
When confronted with poor oxygenation , cells adapt by activating survival signaling pathways , including the oxygen-sensitive transcriptional regulators called hypoxia-inducible factor alphas ( HIF-αs ) . We report here that HIF-1α also regulates the life cycle of Epstein-Barr virus ( EBV ) . Incubation of EBV-positiv... | Most adults throughout the world are infected with Epstein-Barr virus ( EBV ) , a human herpesvirus frequently associated in a latent state with some cancers of epithelial and B-cell origin such as nasopharyngeal carcinoma and Burkitt lymphoma , respectively . To develop an oncolytic therapy for treating patients with ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"cardiovascular",
"anatomy",
"293t",
"cells",
"pathogens",
"immunology",
"biological",
"cultures",
"microbiology",
"cell",
"differentiation",
"dna... | 2017 | Hypoxia-inducible factor-1α plays roles in Epstein-Barr virus’s natural life cycle and tumorigenesis by inducing lytic infection through direct binding to the immediate-early BZLF1 gene promoter |
Allosteric regulation has traditionally been described by mathematically-complex allosteric rate laws in the form of ratios of polynomials derived from the application of simplifying kinetic assumptions . Alternatively , an approach that explicitly describes all known ligand-binding events requires no simplifying assum... | Enzymatic rate laws have historically been used to simulate the dynamics of complex metabolic networks with regulated reactions represented by allosteric rate laws . Here , we use detailed elementary reaction descriptions of regulatory enzymes that allow for the explicit computation of the fraction of the enzymes that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"allosteric",
"regulation",
"medicine",
"and",
"health",
"sciences",
"enzymes",
"metabolic",
"processes",
"metabolic",
"networks",
"enzymology",
"glycolysis",
"physiological",
"processes",
"homeostasis",
"network",
"analysis",
"enzyme",
"metabolism",
"enzyme",
"kinetics",
... | 2018 | Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials |
The neurotrophin-3 ( NT-3 ) receptor tropomyosin receptor kinase C ( TrkC/NTRK3 ) has been described as a dependence receptor and , as such , triggers apoptosis in the absence of its ligand NT-3 . This proapoptotic activity has been proposed to confer a tumor suppressor activity to this classic tyrosine kinase receptor... | Tropomyosin receptor kinase C ( TrkC ) is a transmembrane receptor at the cell surface and has been described to work paradoxically both as an oncogene and as a tumor suppressor . We partly solved this paradox in a previous study , demonstrating that TrkC is a double-facet receptor: Upon interaction with its ligand neu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"death",
"nuclear",
"staining",
"gene",
"regulation",
"cell",
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"green",
"fluorescent",
"protein",
"cloning",
"luminescent",
"proteins",
"immunoprecipitation",
"mitochondria",
"molecular",
"biology",
"techniques",
"bioenergetics",
"cellular",
"structures"... | 2018 | Hey1- and p53-dependent TrkC proapoptotic activity controls neuroblastoma growth |
Protein translation is the most expensive operation in dividing cells from bacteria to humans . Therefore , managing the speed and allocation of resources is subject to tight control . From bacteria to humans , clusters of relatively rare tRNA codons at the N′-terminal of mRNAs have been implicated in attenuating the p... | Measurements of translation by ribosomal profiling and additional large-scale methods support the notion that the elongation speed and ribosomal occupancy are tightly regulated . We revisited the proteomes of a number of organisms , from yeast to human , and focused on the appearance of codons' clusters that impact the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2014 | Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective |
Species abundance distributions ( SAD ) are probably ecology’s most well-known empirical pattern , and over the last decades many models have been proposed to explain their shape . There is no consensus over which model is correct , because the degree to which different processes can be discerned from SAD patterns has ... | In order to predict and mitigate the response of ecological communities to global change , we need to understand the processes that allow multiple species to coexist in close proximity . A classic idea in Ecology is that species coexist because they occupy different “niches” . However , random processes such as dispers... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | When Can Species Abundance Data Reveal Non-neutrality? |
Mammalian Peptidoglycan Recognition Proteins ( PGRPs ) are a family of evolutionary conserved bactericidal innate immunity proteins , but the mechanism through which they kill bacteria is unclear . We previously proposed that PGRPs are bactericidal due to induction of reactive oxygen species ( ROS ) , a mechanism of ki... | Bacterial infections are still a major cause of morbidity and mortality because of increasing antibiotic resistance . New targets for developing new approaches to antibacterial therapy are needed , because discovering new or improving current antibiotics have become increasingly difficult . One such approach is develop... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"innate",
"immune",
"system",
"medical",
"microbiology",
"microbial",
"pathogens",
"biology",
"and",
"life",
"sciences",
"immunology",
"microbiology",
"bacterial",
"biochemistry",
"bacterial",
"pathogens",
"immune",
"system"
] | 2014 | Peptidoglycan Recognition Proteins Kill Bacteria by Inducing Oxidative, Thiol, and Metal Stress |
Heterologous transinfection with the endosymbiotic bacterium Wolbachia has been shown previously to induce pathogen interference phenotypes in mosquito hosts . Here we examine an artificially infected strain of Aedes polynesiensis , the primary vector of Wuchereria bancrofti , which is the causative agent of Lymphatic ... | Lymphatic filariasis ( LF ) , the leading cause of morbidity in South Pacific regions , is caused by a filarial worm , Wuchereria bancrofti . Elimination of LF in the South Pacific requires an approach integrating both mass drug administration and strategies targeting the primary mosquito vector , Aedes polynesiensis .... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"applied",
"microbiology",
"medicine",
"veterinary",
"diseases",
"zoonotic",
"diseases",
"immunology",
"biology",
"veterinary",
"science",
"immune",
"response"
] | 2012 | Reactive Oxygen Species Production and Brugia pahangi Survivorship in Aedes polynesiensis with Artificial Wolbachia Infection Types |
Inflammatory bowel disease ( IBD ) is a chronic condition driven by loss of homeostasis between the mucosal immune system , the commensal gut microbiota , and the intestinal epithelium . Our goal is to understand how these components of the intestinal ecosystem cooperate to control homeostasis . By combining quantitati... | Chronic inflammation of the gastrointestinal track is the common defect shared by inflammatory bowel diseases ( IBDs ) , such as Crohn’s disease and ulcerative colitis , which affect many people around the world . However , the genetic and physiologic complexities of IBDs have made it difficult to identify therapeutica... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"motility",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"organoids",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"biological",
"cultures",
"cell",
"differentiation",
"colitis",
"deve... | 2018 | The colonic epithelium plays an active role in promoting colitis by shaping the tissue cytokine profile |
Many protein interactions are conserved among organisms despite changes in the amino acid sequences that comprise their contact sites , a property that has been used to infer the location of these sites from protein homology . In an inter-species complementation experiment , a sequence present in a homologue is substit... | The interactions of proteins with each other are essential for almost all biological processes . Many of the sites of protein contact have evolved to maintain these interactions , but use different sets of amino acid residues . As a result , the residues at a contact site in a protein from one species might not allow a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Combining Natural Sequence Variation with High Throughput Mutational Data to Reveal Protein Interaction Sites |
Tsetse flies of the Palpalis group are the main vectors of sleeping sickness in Africa . Insecticide impregnated targets are one of the most effective tools for control . However , the cost of these devices still represents a constraint to their wider use . The objective was therefore to improve the cost effectiveness ... | Tsetse flies transmit trypanosomes causing sleeping sickness and nagana . Controlling tsetse prevents transmission of these diseases . Insecticide impregnated targets are highly effective but are too costly . This study aims to improve the cost effectiveness of targets . Experiments were performed on three tsetse speci... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"african",
"trypanosomiasis",
"neglected",
"tropical",
"diseases"
] | 2011 | Towards an Optimal Design of Target for Tsetse Control: Comparisons of Novel Targets for the Control of Palpalis Group Tsetse in West Africa |
Fragment-based drug discovery using NMR and x-ray crystallographic methods has proven utility but also non-trivial time , materials , and labor costs . Current computational fragment-based approaches circumvent these issues but suffer from limited representations of protein flexibility and solvation effects , leading t... | Fragment-based drug discovery is based on a simple yet powerful principle: instead of trying to screen through the vast number of possible drug-like compounds during the drug discovery process , screen representative drug-like fragments , which are far fewer in number . Once a suitable fragment is discovered , it can t... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"computational",
"biology/molecular",
"dynamics",
"biochemistry/biomacromolecule-ligand",
"interactions",
"biochemistry/theory",
"and",
"simulation",
"biophysics/theory",
"and",
"simulation"
] | 2009 | Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation |
p38 has long been known as a central mediator of protein kinase A ( PKA ) signaling in brown adipocytes , which positively regulate the transcription of uncoupling protein 1 ( UCP-1 ) . However , the physiological role of p38 in adipose tissues , especially the white adipose tissue ( WAT ) , is largely unknown . Here ,... | The functional brown adipose tissue ( BAT ) identified in human adults consists of not only classic brown adipocytes but also brown-like adipocytes ( beige adipocytes ) , both of which are important for energy homeostasis . Due to the same ability to convert fat into heat as brown adipocytes , beige adipocytes have bee... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"group-specific",
"staining",
"body",
"weight",
"medicine",
"and",
"health",
"sciences",
"hematoxylin",
"staining",
"brown",
"adipose",
"tissue",
"animal",
"models",
"model",
"organisms",
"adipocytes",
"physiological",
"parameters",
"connective",
"tissue",
"cells",
"obe... | 2018 | Metabolic benefits of inhibition of p38α in white adipose tissue in obesity |
The surface of polyomavirus virions is composed of pentameric knobs of the major capsid protein , VP1 . In previously studied polyomavirus species , such as SV40 , two interior capsid proteins , VP2 and VP3 , emerge from the virion to play important roles during the infectious entry process . Translation of the VP3 pro... | Merkel cell polyomavirus ( MCV or MCPyV ) is a recently discovered member of the viral family Polyomaviridae . The virus plays a causal role in Merkel cell carcinoma , a highly lethal form of skin cancer . MCV encodes a major capsid protein , VP1 , which forms the non-enveloped surface of the virion . Other polyomaviru... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"viral",
"entry",
"viral",
"transmission",
"and",
"infection",
"virology",
"biology",
"microbiology",
"viral",
"structure",
"viral",
"evolution"
] | 2013 | The Merkel Cell Polyomavirus Minor Capsid Protein |
Genetic prion diseases are late onset fatal neurodegenerative disorders linked to pathogenic mutations in the prion protein-encoding gene , PRNP . The most prevalent of these is the substitution of Glutamate for Lysine at codon 200 ( E200K ) , causing genetic Creutzfeldt-Jakob disease ( gCJD ) in several clusters , inc... | Inherited prion diseases , such as genetic CJD , are dominant disorders linked to mutations in the gene encoding the prion protein , PrP . Since therapeutic intervention in all types of human prion diseases has failed , we propose that therapeutic efforts should be directed mostly to the development of preventive treat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biology"
] | 2011 | Fatal Prion Disease in a Mouse Model of Genetic E200K Creutzfeldt-Jakob Disease |
Peptide-protein interactions contribute a significant fraction of the protein-protein interactome . Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces . To address this challenge we developed a... | Peptide-protein interactions are crucial components of various important biological processes in living cells . High-resolution structural information of such interactions provides insight about the underlying biophysical principles governing the interactions , and a starting point for their targeted manipulations . Ac... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"protein",
"interactions",
"applied",
"mathematics",
"simulation",
"and",
"modeling",
"algorithms",
"receptor",
"physiology",
"mathematics",
"protein",
"structure",
"prediction",
"protein",
"structure",
"sequence",
"motif",
"analysis",
"protein",
"st... | 2017 | High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock |
To characterize intracellular energy transfer in the heart , two organ-level methods have frequently been employed: inversion and saturation transfer , and dynamic labeling . Creatine kinase ( CK ) fluxes obtained by following oxygen labeling have been considerably smaller than the fluxes determined by saturation trans... | In heart , the movement of energy metabolites between force-producing myosin , other ATPases , and mitochondria is vital for its function and closely related to heart pathologies . In addition to diffusion , transport of ATP , ADP , Pi , and phosphocreatine occurs along parallel pathways such as the adenylate kinase an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"animal",
"models",
"medicine",
"applied",
"chemistry",
"nuclear",
"magnetic",
"resonance",
"model",
"organisms",
"chemistry",
"biology",
"computational",
"biology",
"metabolic",
"networks",
"biophysics",
"rat",
"cardiovascular",
"chemical",
"properties"
] | 2012 | Sensitivity Analysis of Flux Determination in Heart by H218O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways |
The transferrin receptor of bloodstream form Trypanosoma brucei is a heterodimer encoded by expression site associated genes 6 and 7 . This low-abundance glycoprotein with a single glycosylphosphatidylinositol membrane anchor and eight potential N-glycosylation sites is located in the flagellar pocket . The receptor is... | The tsetse fly transmitted parasite that causes human African trypanosomiasis , or sleeping sickness , scavenges iron from the bloodstream of the infected individual so that it can live , multiply and ultimately cause disease . To do this , it places a glycoprotein ( a protein with carbohydrate chains attached ) called... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"analytical",
"chemistry",
"chemistry",
"biology"
] | 2012 | Modeling of the N-Glycosylated Transferrin Receptor Suggests How Transferrin Binding Can Occur within the Surface Coat of Trypanosoma brucei |
The identification of cell cycle–related genes is still a difficult task , even for organisms with relatively few genes such as the fission yeast . Several gene expression studies have been published on S . pombe showing similarities but also discrepancies in their results . We introduce a network in which the weight o... | Because of the diversity in technological and analytical approaches , published microarray studies on a given organism show similarities as well as differences . While a great amount of data is now available , there is a general need for comprehensive methodologies that would allow us to analyze and compare all these d... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell",
"biology",
"genetics",
"and",
"genomics",
"eukaryotes",
"computational",
"biology"
] | 2007 | Bottleneck Genes and Community Structure in the Cell Cycle Network of S. pombe |
In the Cameroon , previous efforts to identify Buruli ulcer ( BU ) through the mobilization of community health workers ( CHWs ) yielded poor results . In this paper , we describe the successful creation of a BU community of practice ( BUCOP ) in Bankim , Cameroon composed of hospital staff , former patients , CHWs , a... | Buruli ulcer ( BU ) is a neglected tropical disease primarily found in West Africa largely effecting the rural poor . BU has a known cause and cure , but an unknown route of transmission and a poorly understood incubation period . If not treated early and in a timely manner , BU often progresses to an advanced state re... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"health",
"services",
"research",
"sociology",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"health",
"care",
"bacterial",
"diseases",
"research",
"desig... | 2018 | Developing a Buruli ulcer community of practice in Bankim, Cameroon: A model for Buruli ulcer outreach in Africa |
Polyamines are known to play important roles in the proliferation and differentiation of many types of cells . Although considerable amounts of polyamines are synthesized and stored in the testes , their roles remain unknown . Ornithine decarboxylase antizymes ( OAZs ) control the intracellular concentration of polyami... | Polyamines are essential for cell proliferation and differentiation , but their role in these processes is unknown . Ornithine decarboxylase antizymes ( OAZs ) are enzymes that control the concentration of polyamines in cells . To elucidate the role of one of these enzymes , OAZ-t , in the regulation of polyamine conce... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/germ",
"cells"
] | 2009 | OAZ-t/OAZ3 Is Essential for Rigid Connection of Sperm Tails to Heads in Mouse |
Mosquito biting frequency and how bites are distributed among different people can have significant epidemiologic effects . An improved understanding of mosquito vector-human interactions would refine knowledge of the entomological processes supporting pathogen transmission and could reveal targets for minimizing risk ... | Dengue , a potentially lethal infection impacting hundreds of millions of human lives annually , is caused by viruses transmitted during mosquito blood feeding . With no vaccine or treatment commercially available , understanding the underlying factors linked to virus exposure is critical for developing more effective ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"and",
"life",
"sciences",
"medicine",
"and",
"health",
"sciences"
] | 2014 | Heterogeneous Feeding Patterns of the Dengue Vector, Aedes aegypti, on Individual Human Hosts in Rural Thailand |
Exotic invasive species can influence the behavior and ecology of native and resident species , but these changes are often overlooked . Here we hypothesize that the ghost ant , Tapinoma melanocephalum , living in areas that have been invaded by the red imported fire ant , Solenopsis invicta , displays behavioral diffe... | Insects display a wide range of dependence on symbiotic bacteria for basic functions . Responses by resident species to selective pressures imposed by invasive species , as well as specific underlying mechanisms that give rise to these responses are still poorly understood . Here we investigate the role of the symbioti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"b",
"vitamins",
"invertebrates",
"species",
"colonization",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"invasive",
"species",
"sociology",
"social",
"sciences",
"diet",
"animals",
"wolbachia",
"organ... | 2019 | Symbiotic microbiota may reflect host adaptation by resident to invasive ant species |
Cholera remains an important public health problem . Yet there are few reliable population-based estimates of laboratory-confirmed cholera incidence in endemic areas around the world . We established treatment facility–based cholera surveillance in three sites in Jakarta ( Indonesia ) , Kolkata ( India ) , and Beira ( ... | Cholera is an often forgotten disease affecting the world's forgotten people . When a large cholera outbreak occurs , the disease appears briefly on the radar of public attention . Some unfortunate populations around the world suffer recurrent episodes of cholera but their plight goes unnoticed . We established cholera... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology",
"pediatrics",
"and",
"child",
"health"
] | 2008 | The High Burden of Cholera in Children: Comparison of Incidence from Endemic Areas in Asia and Africa |
Loop-mediated isothermal amplification ( LAMP ) of DNA is a novel technique that rapidly amplifies target DNA under isothermal conditions . In the present study , a LAMP test was designed from the serum resistance-associated ( SRA ) gene of Trypanosoma brucei rhodesiense , the cause of the acute form of African sleepin... | Control of human African trypanosomiasis ( HAT ) or sleeping sickness relies on diagnosis and treatment of infected patients . However , the diagnostic tests in routine use have limited sensitivity , due to a characteristically low parasitaemia in infected individuals . Differentiation of infections by Trypanosoma bruc... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"molecular",
"biology"
] | 2008 | Loop-Mediated Isothermal Amplification (LAMP) Method for Rapid Detection of Trypanosoma brucei rhodesiense |
Anthrax lethal toxin ( LT ) is a bipartite protease-containing toxin and a key virulence determinant of Bacillus anthracis . In mice , LT causes the rapid lysis of macrophages isolated from certain inbred strains , but the correlation between murine macrophage sensitivity and mouse strain susceptibility to toxin challe... | Inflammasomes are multiprotein cytoplasmic complexes that respond to a variety of danger signals by activating the host innate immune response . The sensor components of these complexes are NLR ( NOD-like receptor ) proteins . In this report , a recombinant inbred rat strain collection was used to genetically map anthr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"microbiology/innate",
"immunity",
"immunology/innate",
"immunity",
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"infectious",
"diseases/bacterial",
"infections",
"microbiology/cellular",
"microbiology",
"and",
"path... | 2010 | Susceptibility to Anthrax Lethal Toxin-Induced Rat Death Is Controlled by a Single Chromosome 10 Locus That Includes rNlrp1 |
Embryonic stem cells exhibit pluripotency: they can differentiate into all types of somatic cells . Pluripotent genes such as Oct4 and Nanog are activated in the pluripotent state , and their expression decreases during cell differentiation . Inversely , expression of differentiation genes such as Gata6 and Gata4 is pr... | Characterization of pluripotent states , in which cells can both self-renew and differentiate , and the irreversible loss of pluripotency are important research areas in developmental biology . In particular , an understanding of these processes is essential to the reprogramming of cells for biomedical applications , i... | [
"Abstract",
"Introduction",
"Construction",
"of",
"GRN",
"model",
"Results",
"Discussion",
"Models"
] | [] | 2015 | Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation |
Plants have a profound capacity to regenerate organs from differentiated somatic tissues , based on which propagating plants in vitro was made possible . Beside its use in biotechnology , in vitro shoot regeneration is also an important system to study de novo organogenesis . Phytohormones and transcription factor WUSC... | Plants have a strong ability to generate organs from differentiated somatic tissues . Due to this feature , shoot regeneration in vitro has been used as an important way for producing whole plants in agriculture and biotechnology . Phytohormones and the transcription factor WUSCHEL ( WUS ) are essential for reprogrammi... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"developmental",
"biology",
"genetic",
"mutation",
"gene",
"expression",
"genetics",
"epigenetics",
"biology",
"dna",
"modification",
"genetics",
"and",
"genomics",
"cell",
"differentiation",
"dna",
"transcription",
"histone",
"mod... | 2011 | DNA Methylation and Histone Modifications Regulate De Novo Shoot Regeneration in Arabidopsis by Modulating WUSCHEL Expression and Auxin Signaling |
Biological systems evolved to be functionally robust in uncertain environments , but also highly adaptable . Such robustness is partly achieved by genetic redundancy , where the failure of a specific component through mutation or environmental challenge can be compensated by duplicate components capable of performing ,... | Bacteria have found many niches in which to live , and one of them is inside eukaryotic cells . These intracellular bacteria include endosymbionts like Buchnera aphidicola , which provides its host , an aphid , with essential amino acids , as well as many pathogenic bacteria such as Mycobacterium leprae and Rickettsia ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"computational",
"biology/systems",
"biology",
"computational",
"biology/genomics"
] | 2011 | Loss of Genetic Redundancy in Reductive Genome Evolution |
Homology modeling predicts the 3D structure of a query protein based on the sequence alignment with one or more template proteins of known structure . Its great importance for biological research is owed to its speed , simplicity , reliability and wide applicability , covering more than half of the residues in protein ... | Since a protein’s function is largely determined by its structure , predicting a protein’s structure from its amino acid sequence can be very useful to understand its molecular functions and its role in biological pathways . By far the most widely used computational approach for protein structure prediction relies on d... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling |
Antigen B ( AgB ) is the major protein secreted by the Echinococcus granulosus metacestode and is involved in key host-parasite interactions during infection . The full comprehension of AgB functions depends on the elucidation of several structural aspects that remain unknown , such as its subunit composition and oligo... | Antigen B ( AgB ) is the major secretory protein of the Echinococcus granulosus hydatid cyst , the causative agent of cystic hydatid disease . Structurally , AgB is a multisubunit protein formed by 8-kDa subunits , but it is not known which subunits are secreted by a single parasite ( cyst ) and how they interact in th... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"biochemistry",
"infectious",
"diseases",
"veterinary",
"diseases",
"proteins",
"zoonotic",
"diseases",
"genetics",
"biology",
"parasitic",
"diseases",
"zoology",
"biophysics",
"genetics",
"and",
"genomics",
"veterinary",
"science"
] | 2012 | Echinococcus granulosus Antigen B Structure: Subunit Composition and Oligomeric States |
Four related cows showed hairless streaks on various parts of the body with no correlation to the pigmentation pattern . The stripes occurred in a consistent pattern resembling the lines of Blaschko . The non-syndromic hairlessness phenotype observed occurred across three generations of a single family and was compatib... | The identification of causal mutations of rare monogenic disorders provides an insight into the function of single genes . We herein report an example which demonstrates that the bovine species presents an excellent system for identifying these inherited phenotypes . The individual health status of modern dairy cows is... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Hairless Streaks in Cattle Implicate TSR2 in Early Hair Follicle Formation |
Large genome-wide association studies ( GWAS ) have identified many genetic loci associated with risk for myocardial infarction ( MI ) and coronary artery disease ( CAD ) . Concurrently , efforts such as the National Institutes of Health ( NIH ) Roadmap Epigenomics Project and the Encyclopedia of DNA Elements ( ENCODE ... | Coronary artery disease ( CAD ) and its subcomponent , myocardial infarction ( MI ) , are the leading causes of infirmity and death worldwide . Large-scale genetic association studies have identified many genetic markers associated with CAD and MI . However , it has been difficult to determine the precise functional ef... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Disproportionate Contributions of Select Genomic Compartments and Cell Types to Genetic Risk for Coronary Artery Disease |
Human adenoviruses have been studied extensively in cell culture and have been a model for studies in molecular , cellular , and medical biology . However , much less is known about adenovirus replication and pathogenesis in vivo in a permissive host because of the lack of an adequate animal model . Presently , the mos... | The biology of human adenoviruses has been studied extensively; however , much less is known about the replication and pathogenesis of the virus in a permissive host . Our laboratory pioneered the use of Syrian hamsters to study the pathogenesis of human adenoviruses . Syrian hamsters are permissive for species C human... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | STAT2 Knockout Syrian Hamsters Support Enhanced Replication and Pathogenicity of Human Adenovirus, Revealing an Important Role of Type I Interferon Response in Viral Control |
Clonally derived bacterial populations exhibit significant genotypic and phenotypic diversity that contribute to fitness in rapidly changing environments . Here , we show that serial passage of Salmonella enterica serovar Typhimurium LT2 ( StLT2 ) in broth , or within a mouse host , results in selection of an evolved p... | Salmonella Typhimurium is a bacterium that causes intestinal diseases in a number of animals including humans . In mice , this pathogen invades tissues , causing symptoms similar to typhoid fever . In an effort to understand the evolution of this pathogen , we grew S . Typhimurium in either liquid broth or in mice for ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"cell",
"death",
"organismal",
"evolution",
"microbial",
"mutation",
"genome",
"evolution",
"cell",
"processes",
"population",
"genetics",
"microbiology",
"developmental",
"biology",
"mutation",
"molecular",
"cell",
"biology",
"cell",
"growth",
"microbial"... | 2014 | Selection of Orphan Rhs Toxin Expression in Evolved Salmonella enterica Serovar Typhimurium |
Communication between cells is a ubiquitous feature of cell populations and is frequently realized by secretion and detection of signaling molecules . Direct visualization of the resulting complex gradients between secreting and receiving cells is often impossible due to the small size of diffusing molecules and becaus... | Haploid budding yeast cells cannot actively move to find a mating partner , like some flagellated bacteria do . Instead they must grow a so-called shmoo – a mating projection – precisely into the direction of a potential partner . They communicate with each other by releasing pheromones into their environment , which a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"fungi",
"mycology",
"microbial",
"physiology",
"biology",
"and",
"life",
"sciences",
"microbiology",
"biophysics",
"organisms",
"yeast"
] | 2014 | Yeast Mating and Image-Based Quantification of Spatial Pattern Formation |
Varicella-zoster virus ( VZV ) is a human alphaherpesvirus that causes varicella ( chickenpox ) and herpes zoster ( shingles ) . Like all herpesviruses , the VZV DNA genome is replicated in the nucleus and packaged into nucleocapsids that must egress across the nuclear membrane for incorporation into virus particles in... | Varicella-zoster virus ( VZV ) , the cause of varicella and zoster , is a human herpesvirus that replicates in the host cell nucleus where viral genomes are packaged into virion nucleocapsids . We have recently identified antiviral PML ( promyelocytic leukemia ) nuclear cages that sequester VZV nucleocapsids and inhibi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology",
"biology",
"microbiology",
"host-pathogen",
"interaction"
] | 2012 | 3D Reconstruction of VZV Infected Cell Nuclei and PML Nuclear Cages by Serial Section Array Scanning Electron Microscopy and Electron Tomography |
Organogenesis relies on the spatiotemporal balancing of differentiation and proliferation driven by an expanding pool of progenitor cells . In the mouse pancreas , lineage tracing at the population level has shown that the expanding pancreas progenitors can initially give rise to all endocrine , ductal , and acinar cel... | In order to form organs of the right size and cell composition , progenitor cells must balance their proliferation and their differentiation into functional cell types . Here we study how individual progenitor cells in the developing pancreas execute their choices to either expand their pool or differentiate into hormo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Cell Cycle–Dependent Differentiation Dynamics Balances Growth and Endocrine Differentiation in the Pancreas |
There are two main classes of natural killer ( NK ) cell receptors in mammals , the killer cell immunoglobulin-like receptors ( KIR ) and the structurally unrelated killer cell lectin-like receptors ( KLR ) . While KIR represent the most diverse group of NK receptors in all primates studied to date , including humans ,... | Most receptors of natural killer ( NK ) cells interact with highly polymorphic major histocompatibility complex ( MHC ) class I molecules and thereby regulate the activity of NK cells against infected or malignant target cells . Whereas humans , apes , and Old and New World monkeys use the family of killer cell immunog... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/comparative",
"genomics",
"genetics",
"and",
"genomics/genetics",
"of",
"the",
"immune",
"system"
] | 2009 | A Novel System of Polymorphic and Diverse NK Cell Receptors in Primates |
Gammaherpesviruses such as KSHV and EBV establish lifelong persistent infections through latency in lymphocytes . These viruses have evolved several strategies to counteract the various components of the innate and adaptive immune systems . We conducted an unbiased screen using the genetically and biologically related ... | Human gammaherpesviruses , Kaposi's sarcoma-associated herpesvirus and Epstein-Barr virus , are the cause of several malignancies , especially in patients immunocompromised due to HIV infection . The study of these human gammaherpesviruses is difficult due to their inability to replicate in cell culture and the lack of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"viral",
"latency",
"genetic",
"mutation",
"cytokines",
"viruses",
"and",
"cancer",
"immune",
"activation",
"viral",
"enzymes",
"immunology",
"microbiology",
"host-pathogen",
"interaction",
"membrane",
"receptor",
"signaling",
"immunologic",
"techniques",
"animal",
"model... | 2011 | The Anti-interferon Activity of Conserved Viral dUTPase ORF54 is Essential for an Effective MHV-68 Infection |
Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation . Rearrangements are especially common following interspecific hybridization , and some of these could be expected to have strong selective value . To test this expectation we created de novo interspecif... | Interspecific hybridization occurs when two different species mate and produce viable offspring . While hybrid offspring are usually sterile , like the mule , which results from a horse–donkey mating , sometimes they are fertile , creating new species . Indeed , many plant and animal species have arisen via this mechan... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbial",
"mutation",
"genetic",
"mutation",
"genome",
"evolution",
"chromosome",
"structure",
"and",
"function",
"population",
"genetics",
"microbiology",
"genome",
"sequencing",
"model",
"organisms",
"mutation",
"types",
"microbial",
"evolution",
"forms",
"of",
"ev... | 2013 | Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression |
Helminthic infections are highly endemic in Mozambique , due to limited access to healthcare and resources for disease prevention . Data on the subclinical prevalence of these diseases are scarce due to the fact that an immunological and imaging diagnosis is not often available in endemic areas . We conducted a cross-s... | In Mozambique many parasitic diseases persist as a result of low living standards and environmental contamination from human and animal fecal waste . Parasites undermine the health of Mozambique's poorest inhabitants and will be difficult to eradicate without a considerable improvement in the sanitary conditions . Many... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences"
] | 2014 | A Cross-sectional Serological Study of Cysticercosis, Schistosomiasis, Toxocariasis and Echinococcosis in HIV-1 Infected People in Beira, Mozambique |
Lethal acrodermatitis ( LAD ) is a genodermatosis with monogenic autosomal recessive inheritance in Bull Terriers and Miniature Bull Terriers . The LAD phenotype is characterized by poor growth , immune deficiency , and skin lesions , especially at the paws . Utilizing a combination of genome wide association study and... | Lethal acrodermatitis ( LAD ) is an autosomal recessive hereditary disease in dogs . It is characterized by poor growth , immune deficiency and characteristic skin lesions of the paws and of the face . We mapped the LAD locus to a ~1 . 11 Mb segment on canine chromosome 14 . Whole genome sequence data of an LAD affecte... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"genome-wide",
"association",
"studies",
"animal",
"types",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"variant",
"genotypes",
"vertebrates",
"pets",
"and",
"companion",
"animals",
"dogs",
"animals",
"mammals",
"genetic",
"m... | 2018 | MKLN1 splicing defect in dogs with lethal acrodermatitis |
Learning the reliability of different sources of rewards is critical for making optimal choices . However , despite the existence of detailed theory describing how the expected reward is learned in the basal ganglia , it is not known how reward uncertainty is estimated in these circuits . This paper presents a class of... | To maximize their chances for survival , animals need to base their decisions not only on the average consequences of chosen actions , but also on the variability of the rewards resulting from these actions . For example , when an animal’s food reserves are depleted , it should prefer to forage in an area where food is... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"learning",
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"decision",
"making",
"nervous",
"system",
"dopaminergics",
"social",
"sciences",
"electrophysiology",
"neuroscience",
"learning",
"and",
"memory",
"simulation",
"and",
"modeling",
"synaptic",
"plastic... | 2016 | Learning Reward Uncertainty in the Basal Ganglia |
P10 is a small , abundant baculovirus protein that accumulates to high levels in the very late stages of the infection cycle . It is associated with a number of intracellular structures and implicated in diverse processes from occlusion body maturation to nuclear stability and lysis . However , studies have also shown ... | High-resolution 3D electron microscopy has revealed the complexity of structures formed by P10 , a small 10kDa protein that accumulates to very high levels in baculovirus-infected cells . We demonstrate the formation and presence of two distinct , possibly unique , P10 structures that account for the diverse roles asso... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"plant",
"anatomy",
"microtubules",
"biological",
"cultures",
"microbiology",
"light",
"microscopy",
"viral",
"structure",
"plant",
"science",
"microscopy",
"cell",
"cultures",
"protein",
"structure",
"confocal",
"microscopy",
"cellular",
"structures",
"and",
"organelles"... | 2019 | In cultured cells the baculovirus P10 protein forms two independent intracellular structures that play separate roles in occlusion body maturation and their release by nuclear disintegration |
Is it possible to extract tethering forces applied on chromatin from the statistics of a single locus trajectories imaged in vivo ? Chromatin fragments interact with many partners such as the nuclear membrane , other chromosomes or nuclear bodies , but the resulting forces cannot be directly measured in vivo . However ... | Is it possible to recover the local environment , the external and internal forces acting on a polymer from a single locus trajectories ? To study this question , we resolve this reverse cell biology problem by developing a method that uses in vivo live single locus trajectories to extract physical forces applied on ch... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions |
Ochollo is a village in southern Ethiopia burdened with cutaneous leishmaniasis ( CL ) , where Phlebotomus pedifer is the only vector for Leishmania aethiopica and hyraxes are confirmed reservoir hosts . A detailed description of the different players of transmission , and the ecology and seasonality of the vector need... | Zoonotic cutaneous leishmaniasis poses a considerable health problem in Ethiopia . Efficient disease control can only be accomplished when all players of transmission are well understood and taken into account . The aim of our study was to investigate in a village in the south , called Ochollo , whether rodents also ha... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"geomorphology",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"landforms",
"hyraxes",
"topography",
"vertebrates",
"sand",
"flies",
"parasitic",
"diseases",
"animals",
"mammals",
"parasitic",
"protozoans",
"diptera",
"protozoans",
"leishmania",
"insect",
"vec... | 2019 | Ecology and seasonality of sandflies and potential reservoirs of cutaneous leishmaniasis in Ochollo, a hotspot in southern Ethiopia |
Functional brain networks detected in task-free ( “resting-state” ) functional magnetic resonance imaging ( fMRI ) have a small-world architecture that reflects a robust functional organization of the brain . Here , we examined whether this functional organization is disrupted in Alzheimer's disease ( AD ) . Task-free ... | Alzheimer's disease ( AD ) is a brain disorder characterized by progressive impairment of episodic memory and other cognitive domains resulting in dementia and , ultimately , death . Functional neuroimaging studies have identified brain regions that show abnormal brain function in AD . Although there is converging evid... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neurological",
"disorders/alzheimer",
"disease",
"mathematics/statistics",
"computer",
"science/systems",
"and",
"control",
"theory",
"radiology",
"and",
"medical",
"imaging/magnetic",
"resonance",
"imaging"
] | 2008 | Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease |
Beriberi occurs in Vientiane , Lao PDR , among breastfed infants . Clinical disease may be the tip of an iceberg with subclinical thiamin deficiency contributing to other illnesses . Thiamin treatment could improve outcome . A cohort of 778 sick infants admitted during one year without clinical evidence of beriberi wer... | Infantile beriberi , or clinical thiamin ( vitamin B1 ) deficiency in infants , is a forgotten disease in Asia , where 100 years ago it was a major public health problem . Infants with this deficiency , commonly aged ∼ 2–3 months , present in cardiac failure but usually rapidly improve if given thiamin injections . It ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"pediatrics",
"and",
"child",
"health"
] | 2011 | Clinically Unapparent Infantile Thiamin Deficiency in Vientiane, Laos |
In microbiome studies , an important goal is to detect differential abundance of microbes across clinical conditions and treatment options . However , the microbiome compositional data ( quantified by relative abundance ) are highly skewed , bounded in [0 , 1 ) , and often have many zeros . A two-part model is commonly... | Semi-continuous compositional data are typically analyzed using two-part models which separately describe the probability of zero values and the distribution of positive values . The second part of the model provides a conditional interpretation of covariate effects on the positive response . However , it is of great i... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"sequencing",
"techniques",
"microbiome",
"microbiology",
"simulation",
"and",
"modeling",
"next-generation",
"sequencing",
"metagenomics",
"probability",
"distribution",
"mathematics",
"genome",
"analysis",
"molecular",
"biology",
"techniques",
"skewness",
"microbial",
"geno... | 2018 | A marginalized two-part Beta regression model for microbiome compositional data |
Mitochondrial DNA ( mtDNA ) mutations cause severe maternally inherited syndromes and the accumulation of somatic mtDNA mutations is implicated in aging and common diseases . However , the mechanisms that influence the frequency and pathogenicity of mtDNA mutations are poorly understood . To address this matter , we cr... | The energy needs of an animal cell are supplied by tiny organelles known as mitochondria . Each of the many mitochondria in a cell has a set of blueprints for making more mitochondria , known as mitochondrial DNA ( mtDNA ) . As animals age , their mtDNA acquires irreversible defects called mutations , which accumulate ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"deletion",
"mutation",
"mitochondrial",
"dna",
"animals",
"invertebrate",
"genomics",
"animal",
"models",
"mutation",
"substitution",
"mutation",
"drosophila",
"melanogaster",
"model",
"organisms",
"experimental",
"organism",
"systems",
"forms",
"of",
"d... | 2018 | Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ |
Schistosoma mansoni and S . haematobium are co-endemic in many areas in Africa . Yet , little is known about the micro-geographical distribution of these two infections or associated disease within such foci . Such knowledge could give important insights into the drivers of infection and disease and as such better tail... | In the developing world , over 230 million people are infected with parasitic Schistosoma worms . Schistosoma mansoni and S . haematobium are the most abundant species in Africa , affecting the liver and urinary tract , respectively . Both parasites are spread through infested freshwater . Although it is known that the... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Micro-Geographical Heterogeneity in Schistosoma mansoni and S. haematobium Infection and Morbidity in a Co-Endemic Community in Northern Senegal |
Viral persistence is associated with hierarchical antiviral CD8 T cell exhaustion with increased programmed death-1 ( PD-1 ) expression . In HCV persistence , HCV-specific CD8 T cells from the liver ( the site of viral replication ) display increased PD-1 expression and a profound functional impairment that is not reve... | Hepatitis C virus ( HCV ) is an important human pathogen with a high rate of persistence associated with chronic liver disease that can progress to cirrhosis and hepatocellular carcinoma . Chronic HCV infection occurs in the setting of impaired antiviral T cells that over-express an inhibitory receptor PD-1 ( programme... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/persistence",
"and",
"latency",
"gastroenterology",
"and",
"hepatology/hepatology",
"virology/new",
"therapies,",
"including",
"antivirals",
"and",
"immunotherapy",
"virology/immune",
"evasion",
"immunology/immunity",
"to",
"infections"
] | 2009 | Synergistic Reversal of Intrahepatic HCV-Specific CD8 T Cell Exhaustion by Combined PD-1/CTLA-4 Blockade |
Bracoviruses are symbiotic viruses associated with tens of thousands of species of parasitic wasps that develop within the body of lepidopteran hosts and that collectively parasitize caterpillars of virtually every lepidopteran species . Viral particles are produced in the wasp ovaries and injected into host larvae wit... | Eukaryotes are generally thought to evolve mainly through the modification of existing genetic information . However , evidence of horizontal gene transfer ( HGT ) in eukaryotes-the accidental acquisition of a novel gene from another species , allowing acquisition of novel traits—is now recognized as an important facto... | [
"Abstract",
"Introduction",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses |
INDETERMINATE DOMAIN ( IDD ) / BIRD proteins are a highly conserved plant-specific family of transcription factors which play multiple roles in plant development and physiology . Here , we show that mutation in IDD4/IMPERIAL EAGLE increases resistance to the hemi-biotrophic pathogen Pseudomonas syringae , indicating th... | This work illustrates the involvement of the IDD family member 4 in the regulation of defense responses against hemibiotrophic pathogens and in processes governing plant growth . IDD4 is embedded in widely-ramified regulatory pathways and exerts transcriptional control of key factors that shape and balance growth with ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"gene",
"regulation",
"immunology",
"brassica",
"dna",
"transcription",
"model",
"organisms",
"experimental",
"organism",
"systems",
"genome",
"analysis",
"sequence",
"motif",
"analysis",
"plants",
"arabidopsis",... | 2019 | INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana |
The respiratory syncytial virus ( RSV ) fusion ( F ) glycoprotein is a major target of neutralizing antibodies arising from natural infection , and antibodies that specifically bind to the prefusion conformation of RSV F generally demonstrate the greatest neutralization potency . Prefusion-stabilized RSV F variants hav... | Respiratory syncytial virus ( RSV ) is a pervasive pathogen that causes severe lower respiratory tract infections , leading to ~100 , 000 deaths globally each year and hundreds of millions of dollars in healthcare costs . However , despite its prevalence , there is no vaccine for RSV and the only available therapy is l... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"chemical",
"bonding",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"crystal",
"structure",
"chemical",
"compounds",
"immunology",
"condensed",
"matter",
"physics",
"microbiology",
"viral",
"structure",
"organic",
"compounds",
"crystals",
"materials",
... | 2019 | Alternative conformations of a major antigenic site on RSV F |
Eosinophilia is a typical finding of the acute/juvenile form of paracoccidioidomycosis ( PCM ) , a systemic mycosis endemic in Latin America . This clinical form is characterized by depressed cellular immune response and production of Th2 cytokines . Moreover , it has been shown that the increased number of eosinophils... | Paracoccidioidomycosis ( PCM ) is a fungal disease endemic of some Latin America countries . The acute clinical form of the disease , which affects children and young adults , is the most severe form of PCM . It is characterized by a depressed T cell immunity and increased number of blood eosinophils that decreases aft... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"cell",
"motility",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"tropical",
"diseases",
"lymph",
"nodes",
"signs",
"and",
"symptoms",
"lymphatic",
"system... | 2017 | Functional and phenotypic evaluation of eosinophils from patients with the acute form of paracoccidioidomycosis |
Accumulating experimental evidence suggests that the gene regulatory networks of living organisms operate in the critical phase , namely , at the transition between ordered and chaotic dynamics . Such critical dynamics of the network permits the coexistence of robustness and flexibility which are necessary to ensure ho... | Dynamically critical systems are those which operate at the border of a phase transition between two behavioral regimes often present in complex systems: order and disorder . Critical systems exhibit remarkable properties such as fast information processing , collective response to perturbations or the ability to integ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"evolutionary",
"modeling",
"genetics",
"regulatory",
"networks",
"biology",
"computational",
"biology",
"gene",
"networks",
"genetics",
"and",
"genomics"
] | 2012 | Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability |
Non-structural protein 1 ( NS1 ) is one of the most enigmatic proteins of the Dengue virus ( DENV ) , playing distinct functions in immune evasion , pathogenesis and viral replication . The recently reported crystal structure of DENV NS1 revealed its peculiar three-dimensional fold; however , detailed information on NS... | Dengue virus ( DENV ) is a major arthropod-borne human pathogen , infecting more than 400 million individuals annually worldwide; however , neither a therapeutic drug nor a prophylactic vaccine is currently available . Amongst the DENV proteins , non-structural protein 1 ( NS1 ) is one of the most enigmatic , being req... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Dengue Virus Non-structural Protein 1 Modulates Infectious Particle Production via Interaction with the Structural Proteins |
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