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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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In 2007 , a novel bunyavirus was found in Henan Province , China and named fever , thrombocytopenia and leukocytopenia syndrome virus ( FTLSV ) ; since then , FTLSV has been found in ticks and animals in many Chinese provinces . Human-to-human transmission has been documented , indicating that FTLSV should be considere... | FTLSV is novel bunyavirus belonging to genus Phlebovirus and was first found in Huaiyangshan area . The epidemiology and pathogenesis of FTLSV remain poorly understood . This lack of information underscores the importance of analyzing the movement and genetic history of FTLSV in China . Recent advances in Bayesian coal... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"and",
"life",
"sciences",
"microbiology",
"virology"
] | 2014 | The Evolutionary History and Spatiotemporal Dynamics of the Fever, Thrombocytopenia and Leukocytopenia Syndrome Virus (FTLSV) in China |
Vertebrate skin is characterized by its patterned array of appendages , whether feathers , hairs , or scales . In avian skin the distribution of feathers occurs on two distinct spatial levels . Grouping of feathers within discrete tracts , with bare skin lying between the tracts , is termed the macropattern , while the... | The distribution of hairs or feathers across the body is not homogeneous , and many animals have characteristic regions of their skin with either profuse or reduced coverage . These features , such as manes , crests , or bald patches , are seen in diverse species , suggesting that they can be selectively advantageous a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"developmental",
"biology",
"mathematics",
"theoretical",
"biology",
"genetics",
"biology",
"evolutionary",
"biology",
"nonlinear",
"dynamics",
"genetics",
"and",
"genomics"
] | 2011 | Cryptic Patterning of Avian Skin Confers a Developmental Facility for Loss of Neck Feathering |
Magnetoencephalography and electroencephalography ( MEG , EEG ) are essential techniques for studying distributed signal dynamics in the human brain . In particular , the functional role of neural oscillations remains to be clarified . For that reason , imaging methods need to identify distinct brain regions that concu... | The oscillatory activity of the brain produces a repertoire of signal dynamics that is rich and complex . Noninvasive recording techniques such as scalp magnetoencephalography and electroencephalography ( MEG , EEG ) are key methods to advance our comprehension of the role played by neural oscillations in brain functio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"acoustics",
"engineering",
"and",
"technology",
"signal",
"processing",
"random",
"variables",
"neuroscience",
"covariance",
"signal",
"filtering",
"mathematics",
"brain",
"mapping",
"discrete",
"mathematics",
"neuroimaging",
"combinatorics",
"research",
"and",
"analysis",... | 2018 | Imaging of neural oscillations with embedded inferential and group prevalence statistics |
Urinary schistosomiasis , the result of infection by Schistosoma haematobium ( Sh ) , remains a major global health concern . A schistosome vaccine could represent a breakthrough in schistosomiasis control strategies , which are presently based on treatment with praziquantel ( PZQ ) . We report the safety and efficacy ... | Vaccines represent an attractive tool in the fight against schistosomiasis . Pre-clinical immunization studies with the schistosome enzyme 28 kDa glutathione S-transferase ( 28GST ) have shown a significant reduction of schistosome egg production and subsequent pathology . The objective of the present phase 3 trial was... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"body",
"fluids",
"helminths",
"immunology",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"vaccines",
"preventive",
"medicine",
"urine",
"neglected",
"tropical"... | 2018 | Safety and efficacy of the rSh28GST urinary schistosomiasis vaccine: A phase 3 randomized, controlled trial in Senegalese children |
Heterotrimeric G proteins act as the physical nexus between numerous receptors that respond to extracellular signals and proteins that drive the cytoplasmic response . The Gα subunit of the G protein , in particular , is highly constrained due to its many interactions with proteins that control or react to its conforma... | Proteins evolve new protein-protein interactions through changes to their residues . Many residue changes are harmful because they disrupt important existing interactions and functions . The more interactions a protein participates in , the more difficult it is to make changes that are not harmful to the protein . And ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry/molecular",
"evolution",
"computational",
"biology/macromolecular",
"structure",
"analysis",
"computational",
"biology/comparative",
"sequence",
"analysis",
"biochemistry/protein",
"chemistry",
"biochemistry/macromolecular",
"chemistry"
] | 2010 | Evolution of a Signaling Nexus Constrained by Protein Interfaces and Conformational States |
The occurrence of outbreaks of human rabies transmitted by Desmodus rotundus in Brazil in 2004 and 2005 reinforced the need for further research into this zoonosis . Studies of knowledge and practices related to the disease will help to define strategies for the avoidance of new cases , through the identification of ga... | In 2004 and 2005 , the occurrence of outbreaks of human rabies caused by the hematophagous bat , Desmodus rotundus in the Brazilian Amazon , highlighted the role of this bat in the transmission of the disease and the importance of further research on this zoonosis in this region . In the present study , we investigated... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"animal",
"types",
"medicine",
"and",
"health",
"sciences",
"education",
"immunology",
"tropical",
"diseases",
"sociology",
"vertebrates",
"social",
"sciences",
"domestic",
"animals",
"animals",
"mammals",
"preventive",
"medicine",
"rabies",
"neglected",
"tropical",
"di... | 2016 | Rabies: Knowledge and Practices Regarding Rabies in Rural Communities of the Brazilian Amazon Basin |
Lymphatic filariasis ( LF ) , a neglected tropical disease ( NTD ) preventable through mass drug administration ( MDA ) , is one of six diseases deemed possibly eradicable . Previously we developed one LF elimination scenario , which assumes MDA scale-up to continue in all countries that have previously undertaken MDA ... | Lymphatic filariasis ( LF ) is a neglected tropical disease ( NTD ) that is targeted for elimination and is thought to be potentially eradicable through once yearly mass drug administration ( MDA ) using drugs that are currently donated to LF endemic countries by the pharmaceutical companies that manufacture them . MDA... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"tropical",
"diseases",
"social",
"sciences",
"parasitic",
"diseases",
"animals",
"data",
"management",
"filariasis",
"pharmaceutics",
"drug",
"administration",
"neglected",
"tropical",
"diseases",
"lymphatic",
"fi... | 2017 | How much will it cost to eradicate lymphatic filariasis? An analysis of the financial and economic costs of intensified efforts against lymphatic filariasis |
Ever since we developed mitochondria to generate ATP , eukaryotes required intimate mito-nuclear communication . In addition , since reactive oxygen species are a cost of mitochondrial oxidative phosphorylation , this demands safeguards as protection from these harmful byproducts . Here we identified a critical transcr... | Energy homeostasis is a vital prerequisite for optimal nutrient utilization and prolonged survival in an environment with fluctuating and frequently scarce food resources . Numerous studies have elucidated the important roles of mitochondrial energy in fasting status but less is known about the role of mitochondria in ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | CAPER Is Vital for Energy and Redox Homeostasis by Integrating Glucose-Induced Mitochondrial Functions via ERR-α-Gabpa and Stress-Induced Adaptive Responses via NF-κB-cMYC |
Dengue is a major global public health problem with increasing incidence and geographic spread . The epidemiology is complex with long inter-epidemic intervals and endemic with seasonal fluctuations . This study was initiated to investigate dengue transmission dynamics in Binh Thuan province , southern Vietnam . Wavele... | Dengue has become a major international public health problem due to increasing geographic distribution and a transition from epidemic transmission with long inter-epidemic intervals to endemic transmission with seasonal fluctuation . Seasonal and multi-annual cycles in dengue incidence vary over time and space . We pe... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/epidemiology",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"infectious",
"diseases/viral",
"infections"
] | 2010 | Dengue Dynamics in Binh Thuan Province, Southern Vietnam: Periodicity, Synchronicity and Climate Variability |
How duplicate genes provide genetic robustness remains an unresolved question . We have examined the duplicated histone deacetylases Sir2p and Hst1p in Saccharomyces cerevisiae and find that these paralogs with non-overlapping functions can provide genetic robustness against null mutations through a substitution mechan... | Gene duplication is an important force in evolution , as it provides a source of new genetic material . However , the mechanisms by which duplicated genes are retained and diverge are understudied at the experimental level . We have examined a pair of duplicated histone deacetylases Hst1p and Sir2p from baker's yeast ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"hst1p/sir2p",
"genetic",
"robustness",
"duplication",
"deacetylase",
"repression",
"molecular",
"biology"
] | 2007 | Substitution as a Mechanism for Genetic Robustness: The Duplicated Deacetylases Hst1p and Sir2p in Saccharomyces cerevisiae |
This study aimed to assess the impact of the Zika epidemic on the registration of birth defects in Brazil . We used an interrupted time series analysis design to identify changes in the trends in the registration of congenital anomalies . We obtained monthly data from Brazilian Live Birth Information System and used tw... | Zika can be characterized as one of the most significant emerging arboviruses . The Zika epidemic in Brazil and the subsequent increase in the number of serious brain anomalies , such as microcephaly , has demonstrated the importance of analysing the impact of Zika infection on the rate of congenital anomalies in an af... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"microcephaly",
"pathology",
"and",
"laboratory",
"medicine",
"congenital",
"anomalies",
"statistics",
"pathogens",
"geographical",
"locations",
"microbiology",
"time",
"series",
"analysis",
"viruses",
"developmental",
"biology",
"... | 2019 | Impact evaluation of Zika epidemic on congenital anomalies registration in Brazil: An interrupted time series analysis |
More than 260 million people live with schistosomiasis and regular mass-treatment should be implemented to prevent morbidity . Praziquantel , dosed at 40 milligrams per kilogram bodyweight , is the drug of choice . During the last decades the WHO Tablet Pole–which estimates tablet need by height as representing weight–... | Schistosomiasis is an acute and chronic parasitic disease caused by Schistosoma worms , contributing to morbidity and mortality in 261 million people , mainly in poor , rural communities . In an effort to control schistosomiasis , the World Health Organization advocates for regular mass treatment to at-risk populations... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"children",
"body",
"weight",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"education",
"sociology",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"parasitic",
"diseases",
"health",
"care",
"urine",
"age",
"groups",
"south",
... | 2016 | The Accuracy of Praziquantel Dose Poles for Mass Treatment of Schistosomiasis in School Girls in KwaZulu-Natal, South Africa |
Gene duplication is a major mechanism facilitating adaptation to changing environments . From recent genomic analyses , the acquisition of zinc hypertolerance and hyperaccumulation characters discriminating Arabidopsis halleri from its zinc sensitive/non-accumulator closest relatives Arabidopsis lyrata and Arabidopsis ... | Arabidopsis halleri has developed the characters of zinc hypertolerance and hyperaccumulation as compared to its close relatives Arabidopsis thaliana and Arabidopsis lyrata . Different candidate genes were proposed to account for the appearance of these characters in A . halleri . One of them is MTP1 ( Metal Tolerance ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/comparative",
"genomics",
"genetics",
"and",
"genomics/functional",
"genomics",
"plant",
"biology/plant-environment",
"interactions",
"genetics",
"and",
"genomics/plant",
"genomes",
"and",
"evolution",
"plant",
"biology/plant",
"biochemistry",
"an... | 2010 | The Five AhMTP1 Zinc Transporters Undergo Different Evolutionary Fates towards Adaptive Evolution to Zinc Tolerance in Arabidopsis halleri |
The ability of influenza A viruses ( IAVs ) to cross species barriers and evade host immunity is a major public health concern . Studies on the phylodynamics of IAVs across different scales – from the individual to the population – are essential for devising effective measures to predict , prevent or contain influenza ... | Influenza A viruses ( IAVs ) are major pathogens of humans and animals . Understanding how IAVs spread and evolve at different scales ( individual , regional , global ) in natural conditions is critical for preventing or managing influenza epidemics . A vast body of knowledge has been generated on the evolution of IAVs... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"emergence",
"viral",
"transmission",
"and",
"infection",
"virology",
"emerging",
"viral",
"diseases",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"biology",
"evolutionary",
"biology",
"microbiology",
"ev... | 2012 | Transmission of Equine Influenza Virus during an Outbreak Is Characterized by Frequent Mixed Infections and Loose Transmission Bottlenecks |
N6-Methyladenosine ( m6A ) accounts for approximately 0 . 2% to 0 . 6% of all adenosine in mammalian mRNA , representing the most abundant internal mRNA modifications . m6A RNA immunoprecipitation followed by high-throughput sequencing ( MeRIP-seq ) is a powerful technique to map the m6A location transcriptome-wide . H... | N6-Methyladenosine ( m6A ) is one of the most abundant and conserved mRNA modifications . It has been reported to influence multiple steps of RNA life cycle and play an important role in the initiation and progression of human cancers . m6A RNA immunoprecipitation followed by high-throughput sequencing ( MeRIP-seq ) is... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cdna",
"libraries",
"sequencing",
"techniques",
"medicine",
"and",
"health",
"sciences",
"methods",
"and",
"resources",
"gene",
"regulation",
"messenger",
"rna",
"cancers",
"and",
"neoplasms",
"oncology",
"immunoprecipitation",
"forms",
"of",
"dna",
"dna",
"libraries... | 2018 | Refined RIP-seq protocol for epitranscriptome analysis with low input materials |
Protozoa and bacteria infect various types of phagocytic cells including macrophages , monocytes , dendritic cells and eosinophils . However , it is not clear which of these cells process and present microbial antigens in vivo and in which cellular compartments parasite peptides are loaded onto Major Histocompatibility... | Phagocytosis is a cellular process that allows the engulfment of solid particles such as bacteria or parasites by the cell membrane and leads to the formation of an intracytoplasmic vesicle , the phagosome . Cell types that are capable of phagocytosis are called phagocytes and include monocytes , macrophages , dendriti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/antigen",
"processing",
"and",
"recognition",
"microbiology/immunity",
"to",
"infections",
"microbiology/parasitology",
"infectious",
"diseases/protozoal",
"infections",
"immunology/immunity",
"to",
"infections"
] | 2010 | Direct Visualization of Peptide/MHC Complexes at the Surface and in the Intracellular Compartments of Cells Infected In Vivo by Leishmania major |
Hepatitis C virus ( HCV ) p7 is a membrane-associated ion channel protein crucial for virus production . To analyze how p7 contributes to this process , we dissected HCV morphogenesis into sub-steps including recruitment of HCV core to lipid droplets ( LD ) , virus capsid assembly , unloading of core protein from LDs a... | Viroporins are small hydrophobic viral membrane proteins which oligomerize and modulate membrane properties to facilitate virus propagation . Within their membrane environment these proteins can form membrane pores or channels which change the permeability of membranes for ions . These properties are known to contribut... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"cell",
"biology",
"virology",
"viral",
"packaging",
"biology",
"microbiology",
"viral",
"replication"
] | 2013 | Hepatitis C Virus p7 is Critical for Capsid Assembly and Envelopment |
Activity regulated neurotransmission shapes the computational properties of a neuron and involves the concerted action of many proteins . Classical , intuitive working models often assign specific proteins to specific steps in such complex cellular processes , whereas modern systems theories emphasize more integrated f... | Synapses , which are small structures where information is transmitted between neurons , are the functional units of computation in the brain implicated in information processing , learning and memory . In the last few years several genes that are expressed in synapses have been linked to brain disorders such as autism... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"algorithms",
"systems",
"biology",
"computer",
"science",
"genomics",
"computer",
"modeling",
"biology",
"computational",
"biology",
"neuroscience",
"genetics",
"and",
"genomics"
] | 2012 | Molecular Machines in the Synapse: Overlapping Protein Sets Control Distinct Steps in Neurosecretion |
Rapid and reliable diagnostic assays for enteric ( typhoid and paratyphoid ) fever are urgently needed . We report the characterization of novel approach utilizing lymphocyte secretions , for diagnosing patients with enteric fever by the TPTest procedure . TPTest detects Salmonella-specific IgA responses in lymphocyte ... | Salmonella enterica serotype Typhi and Paratyphi A are responsible for typhoid and paratyphoid fever respectively and the disease caused is known generally as enteric fever . Appropriate and early diagnosis of the disease is important for initiation of treatment of the patient with a suitable antibiotic . The performan... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"immunology",
"immune",
"response",
"biology"
] | 2013 | Evaluation of a Typhoid/Paratyphoid Diagnostic Assay (TPTest) Detecting Anti-Salmonella IgA in Secretions of Peripheral Blood Lymphocytes in Patients in Dhaka, Bangladesh |
Type VI secretion systems ( T6SS ) are macromolecular machines of the cell envelope of Gram-negative bacteria responsible for bacterial killing and/or virulence towards different host cells . Here , we characterized the regulatory mechanism underlying expression of the enteroagregative Escherichia coli sci1 T6SS gene c... | DNA methylation plays an important role in the regulation of genes involved in assembly of cell surface adhesins or appendages . Methylation at a GATC motif by the Dam methylase influences binding of transcriptional regulators , leading to variation in the gene expression pattern . In several cases , this may lead to d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"macromolecular",
"assemblies",
"microbiology",
"host-pathogen",
"interaction",
"dna",
"transcription",
"escherichia",
"coli",
"epigenetics",
"bacterial",
"pathogens",
"gene",
"expression",
"microbial",
"pathogens",
"biology",
"dna",
"modification",
"biochemis... | 2011 | An Epigenetic Switch Involving Overlapping Fur and DNA Methylation Optimizes Expression of a Type VI Secretion Gene Cluster |
The 3’end genomic region encodes a wide range of regulatory process including mRNA stability , 3’ end processing and translation . Here , we systematically investigate the sequence determinants of 3’ end mediated expression control by measuring the effect of 13 , 000 designed 3’ end sequence variants on constitutive ex... | We present a large-scale experimental investigation into sequence determinants of 3’ end mediated gene expression regulation , by measuring 13 , 000 designed 3’ end sequences . While 3’ end sequences contribute to expression differences through a variety of mechanisms including mRNA stability and regulation of translat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control |
The complex three-dimensional shapes of tree-like structures in biology are constrained by optimization principles , but the actual costs being minimized can be difficult to discern . We show that despite quite variable morphologies and functions , bifurcations in the scleractinian coral Madracis and in many different ... | Morphology is constrained by function and vice-versa . Often , intricate morphology can be explained by optimization of a cost . However , in biology , the exact form of the cost function is seldom clear . Previously , for many different natural trees authors have reported that most bifurcations are planar and we confi... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"medicine",
"plant",
"biology",
"cardiovascular",
"anatomy",
"trees",
"anatomy",
"and",
"physiology",
"geometry",
"neuroscience",
"marine",
"biology",
"plant",
"science",
"mathematics",
"computational",
"neuroscience",
"plants",
"corals",
"theoretical",
"biology",
"marine... | 2012 | Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat |
Alternative splicing ( AS ) provides a potent mechanism for increasing protein diversity and modulating gene expression levels . How alternate splice sites are selected by the splicing machinery and how AS is integrated into gene regulation networks remain important questions of eukaryotic biology . Here we report that... | Mammalian gene expression is extensively controlled at the post-transcriptional level and understanding of the underlying mechanisms can provide important biomedical insights . Here we identified a number of novel alternate splicing ( AS ) events where the choice between competing splice sites ( ss ) is regulated by po... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"alternative",
"splicing",
"biochemistry",
"rna",
"developmental",
"biology",
"rna",
"processing",
"cell",
"biology",
"gene",
"regulatory",
"networks",
"gene",
"expression",
"genetics",
"gene",
"regulation",
"biology",
"and",
"life",
"sciences",
"cell",
"differentiation... | 2014 | Regulation of mRNA Abundance by Polypyrimidine Tract-Binding Protein-Controlled Alternate 5′ Splice Site Choice |
Acquired resistance is one of the major barriers to successful cancer therapy . The development of resistance is commonly attributed to genetic heterogeneity . However , heterogeneity of drug penetration of the tumor microenvironment both on the microscopic level within solid tumors as well as on the macroscopic level ... | Failure of cancer therapy is commonly attributed to the outgrowth of pre-existing resistant mutants already present prior to treatment , yet there is increasing evidence that the tumor microenvironment influences cell sensitivity to drugs and thus mediates the evolution of resistance during treatment . Here , we take i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy |
Uncontrolled immune responses to intracellular DNA have been shown to induce autoimmune diseases . Homeostasis regulation of immune responses to cytosolic DNA is critical for limiting the risk of autoimmunity and survival of the host . Here , we report that the E3 ubiquitin ligase tripartite motif protein 30α ( TRIM30α... | Negative-feedback regulation is a broad and pivotal biological event to maintain the homeostasis of the host . Viral DNA species derived from DNA viruses or retroviruses can activate STING signaling to produce pro-inflammatory cytokines and type I interferon , which further recruit immune cells or induce interferon sti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | TRIM30α Is a Negative-Feedback Regulator of the Intracellular DNA and DNA Virus-Triggered Response by Targeting STING |
Selective and/or neutral processes may govern variation in DNA content and , ultimately , genome size . The observation in several organisms of a negative correlation between recombination rate and intron size could be compatible with a neutral model in which recombination is mutagenic for length changes . We used whol... | One major implication from genetic work done several decades ago is that the genome contains a lot of sequences that do not constitute genes or other functional elements . The total amount of DNA—the genome size—is thus not necessarily an indicator of DNA complexity or organismal complexity , an observation often refer... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genomics",
"genetic",
"mutation",
"genome",
"evolution",
"genomic",
"evolution",
"genetics",
"biology",
"evolutionary",
"biology",
"comparative",
"genomics",
"evolutionary",
"genetics",
"genetics",
"and",
"genomics"
] | 2012 | Recombination Drives Vertebrate Genome Contraction |
The fruit fly Drosophila melanogaster is a powerful model system for the study of innate immunity in vector insects as well as mammals . For vector insects , it is particularly important to understand all aspects of their antiviral immune defenses , which could eventually be harnessed to control the transmission of hum... | Mosquitoes and other biting insects transmit many harmful pathogens to humans , including parasites and viruses . In order to better protect humans from these diseases , we must gain a more complete understanding of how insects successfully—or unsuccessfully—combat these infections . While we know a great deal regardin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"rna",
"interference",
"viral",
"transmission",
"and",
"infection",
"microbiology",
"animals",
"salmonellosis",
"animal",
"models",
"bacterial",
"diseases",
"drosophila",
"melanogaster",
"model",
"organisms",
"expe... | 2018 | p38b and JAK-STAT signaling protect against Invertebrate iridescent virus 6 infection in Drosophila |
RNA polymerase II ( RNAPII ) contains a unique C-terminal domain that is composed of heptapeptide repeats and which plays important regulatory roles during gene expression . RNAPII is responsible for the transcription of most protein-coding genes , a subset of non-coding genes , and retrotransposons . Retrotransposon t... | RNA Polymerase II ( RNAPII ) is the enzyme responsible for the transcription of all protein-coding genes , many non-coding genes and retrotransposons . RNAPII has a unique C-terminal domain ( CTD ) that is composed of repeats of a seven amino acid sequence and is conserved across species . The CTD functions as a recrui... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The RNAPII-CTD Maintains Genome Integrity through Inhibition of Retrotransposon Gene Expression and Transposition |
Homolog pairing , which plays a critical role in meiosis , poses a potential risk if it occurs in inappropriate tissues or between nonallelic sites , as it can lead to changes in gene expression , chromosome entanglements , and loss-of-heterozygosity due to mitotic recombination . This is particularly true in Drosophil... | Meiosis is a specialized cell division that permits the transmission of genetic material to following generations . A pivotal step for this process is the pairing and recombination between homologous chromosomes . In the case of Drosophila , which supports organismal-wide homolog pairing throughout development , it has... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Germline Progenitors Escape the Widespread Phenomenon of Homolog Pairing during Drosophila Development |
The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants , but also more recently to assist in the interpretation and elucidation of disease signals . To date , many studies have looked in specific tissues and population-based samples , but the... | Variation among individuals in the degree to which genes are expressed ( i . e . turned on or off ) is a characteristic exhibited by all species , and studies have identified regions of the genome harboring genetic variation affecting gene expression levels . To assess the degree of human inter-population variability i... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genomics",
"gene",
"expression",
"genetics",
"population",
"genetics",
"biology",
"human",
"genetics",
"genetics",
"and",
"genomics"
] | 2012 | Patterns of Cis Regulatory Variation in Diverse Human Populations |
All living organisms exist in a precarious state of homeostasis that requires constant maintenance . A wide variety of stresses , including hypoxia , heat , and infection by pathogens perpetually threaten to imbalance this state . Organisms use a battery of defenses to mitigate damage and restore normal function . Prev... | It is increasingly clear that living organisms surveil their cellular structures and physiology to gain early warning about the presence and activity of pathogens or abiotic threats ( like hypoxia , hyper- or hypothermia , oxidative damage , etc . ) . Upon recognizing dysfunction , host defense networks are engaged to ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
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"rna",
"interference",
"pathology",
"and",
"laboratory",
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"caenorhabditis",
"gene",
"regulation",
"pathogens",
"regulatory",
"proteins",
"immunology",
"microbiology",
"dna-binding",
"proteins",
"animals",
... | 2017 | A conserved mitochondrial surveillance pathway is required for defense against Pseudomonas aeruginosa |
As emerging and re-emerging infectious arboviruses like dengue , chikungunya , and Zika threaten new populations worldwide , officials scramble to assess local severity and transmissibility , with little to no epidemiological history to draw upon . Indirect estimates of risk from vector habitat suitability maps are pro... | When novel infectious diseases like chikungunya or Zika emerge and threaten global spread , public health officials worldwide must assess the risk for local introductions and outbreaks . These assessments are made in anticipation of local case data , and officials must draw upon historic evidence from similar diseases ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"united",
"states",
"dengue",
"virus",
"medicine",
"and",
"health",
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"pathology",
"and",
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"infectious",
"disease",
"epidemiology",
"pathogens",
"geographical",
"locations",
"microbiology",
"north",
"america",
"viruses",
"texas",
"prob... | 2019 | Downgrading disease transmission risk estimates using terminal importations |
Although scabies is estimated to be one of the most common skin conditions globally , prevalence data is not available in most settings . Disease mapping is required to develop and monitor successful control programs . Non-expert health workers are likely to play an important role in scabies mapping activities in endem... | Scabies is a parasitic infection that leads to significant morbidity worldwide . Mapping of scabies prevalence would improve the understanding of the true burden of disease and the need for control programs in specific countries and regions . The diagnosis of scabies in low resource settings , where the disease is most... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
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"sociology",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"parasitic",
"diseases",
... | 2019 | The diagnosis of scabies by non-expert examiners: A study of diagnostic accuracy |
Mutation of DNA damage checkpoint signaling kinases ataxia telangiectasia-mutated ( ATM ) or ATM- and Rad3-related ( ATR ) results in genomic instability disorders . However , it is not well understood how the instability observed in these syndromes relates to DNA replication/repair defects and failed checkpoint contro... | All cells have evolved pathways to maintain the integrity of the genetic information stored in their chromosomes . Endogenous and exogenous agents induce mutations and other damage in DNA , most frequently during DNA replication . Such DNA damage is under surveillance by a complex network of proteins that interact with... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"viral",
"replication",
"dna",
"replication",
"nucleic",
"acids",
"virology",
"viral",
"nucleic",
"acid",
"viruses",
"and",
"cancer",
"dna",
"biology",
"dna",
"recombination",
"dna",
"repair",
"microbiology"
] | 2013 | ATM and ATR Activities Maintain Replication Fork Integrity during SV40 Chromatin Replication |
The identity of plant host genetic factors controlling the composition of the plant microbiota and the extent to which plant genes affect associated microbial populations is currently unknown . Here , we use a candidate gene approach to investigate host effects on the phyllosphere community composition and abundance . ... | The leaves of plants are inhabited by a diverse community of microorganisms . These leaf inhabitants influence their hosts with respect to growth and resistance to abiotic and biotic stresses . Recent studies revealed that the bacterial communities associated with leaves undergo selection , resulting in conserved micro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"prokaryotic",
"models",
"plant",
"science",
"model",
"organisms",
"plant",
"and",
"algal",
"models",
"plant",
"microbiology",
"genetic",
"screens",
"gene",
"identification",
"and",
"analysis",
"genetics",
"synthetic",
"biology",
"biology",
"and",
"life",
"sciences",
... | 2014 | A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota |
Hepatitis C virus ( HCV ) entry , translation , replication , and assembly occur with defined kinetics in distinct subcellular compartments . It is unclear how HCV spatially and temporally regulates these events within the host cell to coordinate its infection . We have developed a single molecule RNA detection assay t... | The stages of the viral life cycle are spatially and temporally regulated to coordinate the infectious process in a way that maximizes successful replication and spread . In this study , we used RNA in situ hybridization ( ISH ) to simultaneously detect HCV ( + ) and ( − ) RNAs and analyze the kinetics of HCV infection... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Spatiotemporal Analysis of Hepatitis C Virus Infection |
While women are generally underrepresented in STEM fields , there are noticeable differences between fields . For instance , the gender ratio in biology is more balanced than in computer science . We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology... | There are fewer women than men working in Science , Technology , Engineering and Mathematics ( STEM ) . However , some fields within STEM are more gender-balanced than others . For instance , biology has a relatively high proportion of women , whereas there are few women in computer science . But what about computation... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"engineering",
"and",
"technology",
"bibliometrics",
"sexual",
"and",
"gender",
"issues",
"sociology",
"social",
"sciences",
"social",
"media",
"scientists",
"network",
"analysis",
"social",
"networks",
"social",
"communication",
"science",
"and",
"technology",
"workfor... | 2017 | Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology |
Bithynia siamensis goniomphalos is a freshwater snail that serves as the first intermediate host of the human liver fluke Opisthorchis viverrini . This parasite is a major public health problem in different countries throughout the Greater Mekong sub-region ( Thailand , southern Vietnam , Lao PDR and Cambodia ) . Chron... | The control of snails involved in transmission of trematodes plays a key role in the fight against these parasitic diseases . While some snails have been studied thoroughly , only few genomic and proteomic studies have focused on Bithynia siamensis goniomphalos , the snail intermediate host for Opisthorchis viverrini ,... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
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"parasitic",
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"animals",
"protein",
"expression",
"gastropods",
"peptide",
"libraries",
"molecular",
"biology",
"techniques",
"snails",
"research",
"a... | 2016 | Differential Protein Expression in the Hemolymph of Bithynia siamensis goniomphalos Infected with Opisthorchis viverrini |
We propose a novel statistical framework for integrating the result from molecular quantitative trait loci ( QTL ) mapping into genome-wide genetic association analysis of complex traits , with the primary objectives of quantitatively assessing the enrichment of the molecular QTLs in complex trait-associated genetic va... | Genome-wide association studies ( GWAS ) have been tremendously successful in identifying genetic variants that impact complex diseases . However , the roles of such studies in disease etiology remain poorly understood , primarily because a large proportion of the GWAS findings are located in the non-coding region of t... | [
"Abstract",
"Introduction",
"Method",
"Results",
"Discussion"
] | [
"genome-wide",
"association",
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"and",
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"mathematics",
"simulation",
"and",
"modeling",
"algorithms",
"mathematics",
"genome",
"analysis",
"lipid",
"analysis",
"resea... | 2017 | Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization |
Correctly identifying nearest “neighbors” of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment . Microbial classification based on similarity of physiological and genetic organism traits ( polyphasic similarity ) is experimentally difficult and ... | Taxonomic classification of microorganisms according to similarity is important for industrial and clinical applications where close relationships imply similar uses and/or treatments . Current microbial taxonomy is phylogeny-guided , i . e . , the organisms are grouped based on their evolutionary relationships , defin... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Methods"
] | [] | 2015 | Functional Basis of Microorganism Classification |
Chronic hepatitis C virus ( HCV ) infection is a leading cause of liver disease . Liver inflammation underlies infection-induced fibrosis , cirrhosis and liver cancer but the processes that promote hepatic inflammation by HCV are not defined . We provide a systems biology analysis with multiple lines of evidence to ind... | Hepatitis C virus ( HCV ) causes chronic infection of the liver and is a leading cause of liver inflammation , cirrhosis and liver cancer in nearly 200 million people worldwide . Importantly , hepatic inflammation during chronic HCV infection is considered to be the primary catalyst for progressive liver disease and de... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"immune",
"cells",
"cytokines",
"immunology",
"microbiology",
"hepatitis",
"hepatitis",
"c",
"infectious",
"diseases",
"inflammation",
"viral",
"immune",
"evasion",
"biology",
"pathogenesis",
"immune",
"response",
"immune",
"system",
"immunopathology",
"monocy... | 2013 | IL-1β Production through the NLRP3 Inflammasome by Hepatic Macrophages Links Hepatitis C Virus Infection with Liver Inflammation and Disease |
Misfolded proteins challenge the ability of cells to maintain protein homeostasis and can accumulate into toxic protein aggregates . As a consequence , cells have adopted a number of protein quality control pathways to prevent protein aggregation , promote protein folding , and target terminally misfolded proteins for ... | Most polypeptides by necessity must fold into three-dimensional structures in order to become functional proteins . Misfolding , either during or subsequent to initial folding , can result in toxic protein aggregation . As a consequence , cells have adopted a number of protein quality control pathways to prevent protei... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"flow",
"cytometry",
"engineering",
"and",
"technology",
"enzymes",
"enzymology",
"light",
"microscopy",
"mutation",
"microscopy",
"materials",
"science",
"industrial",
"engineering",
"quality",
"control",
"chaperone",
"proteins",
"ligases",
"research",
"and",
"analysis",... | 2016 | Prefoldin Promotes Proteasomal Degradation of Cytosolic Proteins with Missense Mutations by Maintaining Substrate Solubility |
Strigolactones ( SLs ) are well known for their role in repressing shoot branching . In pea , increased transcript levels of SL biosynthesis genes are observed in stems of highly branched SL deficient ( ramosus1 ( rms1 ) and rms5 ) and SL response ( rms3 and rms4 ) mutants indicative of negative feedback control . In c... | Plant shoot branching results from the precise regulation of bud growth versus dormancy . Positive and negative feedback mechanisms are likely involved in the dynamic control of this highly plastic trait . Strigolactones , the most recently discovered class of plant hormones , play a key role in controlling shoot branc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"plant",
"anatomy",
"stem",
"anatomy",
"internodes",
"brassica",
"hormones",
"plant",
"science",
"model",
"organisms",
"rice",
"plant",
"hormones",
"membrane",
"receptor",
"signaling",
"experimental",
"organism",
"systems",
"hormone",
"receptor",
"signaling",
"plants",
... | 2017 | The pea branching RMS2 gene encodes the PsAFB4/5 auxin receptor and is involved in an auxin-strigolactone regulation loop |
Bacteria have developed various motility mechanisms to adapt to a variety of solid surfaces . A rhizosphere isolate , Paenibacillus sp . NAIST15-1 , exhibited unusual motility behavior . When spotted onto 1 . 5% agar media , Paenibacillus sp . formed many colonies , each of which moved around actively at a speed of 3 .... | Motility is crucial as it enables bacteria to seek out and colonize suitable environments . Here , a new isolate from the rhizosphere , Paenibacillus sp . , exhibited unusual motility behavior . When spotted on low wet , hard agar media , the bacterium formed many colonies , each of which moved around actively like an ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"bacteriology",
"cell",
"motility",
"medicine",
"and",
"health",
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"and",
"laboratory",
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"pathogens",
"bacillus",
"microbiology",
"light",
"microscopy",
"flagellar",
"motility",
"biomechanics",
"biological",
"locomotion",
"prokaryotic",
"... | 2016 | Genetic Analysis of Collective Motility of Paenibacillus sp. NAIST15-1 |
It is estimated that almost a half of all of people living in developing countries today are infected with roundworms , hookworms , or whipworms or combinations of these types of intestinal nematode worms . They can all be treated using safe , effective , and inexpensive single-dose generic drugs costing as little as U... | Almost one in every two people in the developing world is infected with one or more types of intestinal nematode worms . When fewer than 50% of people are infected , most carry only a few worms; but when more than 50% are infected , the number carrying moderate to heavy numbers increases markedly , as does the risk of ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/infectious",
"diseases"
] | 2009 | The Costs and Cost-Effectiveness of Mass Treatment for Intestinal Nematode Worm Infections Using Different Treatment Thresholds |
Tetherin ( BST-2/CD317/HM1 . 24 ) is an IFN induced transmembrane protein that restricts release of a broad range of enveloped viruses . Important features required for Tetherin activity and regulation reside within the cytoplasmic domain . Here we demonstrate that two isoforms , derived by alternative translation init... | Regulation of innate immunity is critical to maintain a balance between control of a perceived threat and immunopathology . The interferon induced cellular factor Tetherin has been shown to restrict budding of a broad range of enveloped viruses including the human immunodeficiency virus . Though Tetherin appears to be ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"biology",
"microbiology"
] | 2012 | Identification of Alternatively Translated Tetherin Isoforms with Differing Antiviral and Signaling Activities |
Between 1998 and 2010 , S . Typhi was an uncommon cause of bloodstream infection ( BSI ) in Blantyre , Malawi and it was usually susceptible to first-line antimicrobial therapy . In 2011 an increase in a multidrug resistant ( MDR ) strain was detected through routine bacteriological surveillance conducted at Queen Eliz... | Typhoid fever is a major cause of disease and death around the world , particularly in resource limited settings , although reports suggest that until recently it has been much less prominent in sub-Saharan Africa ( SSA ) than Asia . Estimates of the precise burden of this disease are , however , difficult , as diagnos... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Rapid Emergence of Multidrug Resistant, H58-Lineage Salmonella Typhi in Blantyre, Malawi |
Metabolomics is a powerful approach for discovering biomarkers and for characterizing the biochemical consequences of genetic variation . While untargeted metabolite profiling can measure thousands of signals in a single experiment , many biologically meaningful signals cannot be readily identified as known metabolites... | Untargeted metabolomics can systematically profile thousands of metabolite signals in biological samples and is an increasingly popular approach for discovering biomarkers and predictors for human traits and diseases . However , currently , a significant portion of the measured signals cannot be identified as known met... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"statistics",
"metaanalysis",
"metabolomics",
"mathematics",
"metabolites",
"genome",
"analysis",
"molecular",
"biology",
"techniques",
"information",
"technology",
"data",
"processing",
"discrete",
"mathematics",
"combinatorics",
"res... | 2019 | PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data |
Barrett’s esophagus ( BE ) patients are routinely screened for high grade dysplasia ( HGD ) and esophageal adenocarcinoma ( EAC ) through endoscopic screening , during which multiple esophageal tissue samples are removed for histological analysis . We propose a computational method called the multistage clonal expansio... | Endoscopic screening for detecting cancer and cancer precursors in Barrett’s esophagus ( BE ) is currently informed by repeated systematic biopsying of the metaplastic BE tissue . Here we present a comprehensive multiscale model of the natural history of esophageal adenocarcinoma ( EAC ) , which describes the entire mu... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | A Multiscale Model Evaluates Screening for Neoplasia in Barrett’s Esophagus |
Stage-specific transcription is a fundamental biological process in the life cycle of the Plasmodium parasite . Proteins containing the AP2 DNA-binding domain are responsible for stage-specific transcriptional regulation and belong to the only known family of transcription factors in Plasmodium parasites . Comprehensiv... | Although malarial parasites have a complex life cycle , they harbor only 30 transcription factors in their genome . The majority of these transcription factors belong to a single family referred to as the AP2 family . Our previous study suggested that stage-specific AP2 family transcription factors have critical roles ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Genome-Wide Identification of the Target Genes of AP2-O, a Plasmodium AP2-Family Transcription Factor |
Having multiple domains in proteins can lead to partial folding and increased aggregation . Folding cooperativity , the all or nothing folding of a protein , can reduce this aggregation propensity . In agreement with bulk experiments , a coarse-grained structure-based model of the three-domain protein , E . coli Adenyl... | Most individual protein domains fold in an all or nothing fashion . This cooperative folding is important because it reduces the existence of partially folded proteins which can stick to each other and create disease causing aggregates . However , numerous proteins have multiple domains , independent units of folding ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"allosteric",
"regulation",
"biochemistry",
"computational",
"chemistry",
"molecular",
"dynamics",
"proteins",
"protein",
"folding",
"enzyme",
"regulation",
"protein",
"structure",
"protein",
"domains",
"biology",
"and",
"life",
"sciences",
"chemistry",
"enzymology",
"com... | 2014 | In the Multi-domain Protein Adenylate Kinase, Domain Insertion Facilitates Cooperative Folding while Accommodating Function at Domain Interfaces |
Several intracellular Leishmania antigens have been identified in order to find a potential vaccine capable of conferring long lasting protection against Leishmania infection . Histones and Acid Ribosomal proteins are already known to induce an effective immune response and have successfully been tested in the cutaneou... | Visceral leishmaniasis caused by Leishmania infantum is the most severe form of leishmaniasis . The disease is fatal if not treated and there is no vaccine available for human use . In the search for potential antigens , the protective ability of conserved parasite protein families such as L . infantum histones ( HIS )... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Vaccination with Leishmania infantum Acidic Ribosomal P0 but Not with Nucleosomal Histones Proteins Controls Leishmania infantum Infection in Hamsters |
Lymphatic filariasis ( LF ) , onchocerciasis , schistosomiasis , soil-transmitted helminths ( STH ) and trachoma represent the five most prevalent neglected tropical diseases ( NTDs ) . They can be controlled or eliminated by means of safe and cost-effective interventions delivered through programs of Mass Drug Adminis... | The five most prevalent neglected tropical diseases ( NTDs ) are lymphatic filariasis ( LF ) , onchocerciasis , schistosomiasis , soil-transmitted helminths ( STH ) and trachoma . They can be controlled or eliminated by means of safe and cost-effective interventions delivered through programs of Mass Drug Administratio... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"tropical",
"diseases",
"social",
"sciences",
"parasitic",
"diseases",
"anemia",
"health",
"care",
"bacterial",
"diseases",
"eye",
"diseases",
"neglected",
"tropical",
"diseases",
"onchocerciasis",
"public",
"and",
"occupational"... | 2017 | The Socioeconomic Benefit to Individuals of Achieving the 2020 Targets for Five Preventive Chemotherapy Neglected Tropical Diseases |
The behaviour of insect vectors has an important bearing on the epidemiology of the diseases they transmit , and on the opportunities for vector control . Two sorts of electrocuting device have been particularly useful for studying the behaviour of tsetse flies ( Glossina spp ) , the vectors of the trypanosomes that ca... | With a view to refining studies of tsetse fly behaviour , we used a catch method , in the field in Zimbabwe , to assess and improve the efficiency of 0 . 5m2 electrocuting grids commonly used to sample tsetse that collide with netting while in flight or which alight on cloth . We found that the efficiency of both sorts... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Efficacy of Electrocuting Devices to Catch Tsetse Flies (Glossinidae) and Other Diptera |
Phages shape the structure of natural bacterial communities and can be effective therapeutic agents . Bacterial resistance to phage infection , however , limits the usefulness of phage therapies and could destabilise community structures , especially if individual resistance mutations provide cross-resistance against m... | Phage therapy is a promising alternative to antibiotics for treating bacterial infections . Yet as with antibiotics , bacteria readily evolve resistance to phage attack , including cross-resistance that protects against multiple phages at once and so limits the usefulness of phage cocktails . Here we show , using labor... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"bacteriology",
"organismal",
"evolution",
"microbial",
"mutation",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"bacteriophages",
"pathogens",
"microbiology",
"pili",
"and",
"fimbriae",
"pseudomonas",
"aeruginosa",
"viruses",
"de... | 2018 | Cross-resistance is modular in bacteria–phage interactions |
Keratocytes are fast-moving cells in which adhesion dynamics are tightly coupled to the actin polymerization motor that drives migration , resulting in highly coordinated cell movement . We have found that modifying the adhesive properties of the underlying substrate has a dramatic effect on keratocyte morphology . Cel... | Cell migration is important for many biological processes: white blood cells chase down and kill bacteria to guard against infection , epithelial cells crawl across open wounds to promote healing , and embryonic cells move collectively to form organs and tissues during embryogenesis . In all of these cases , migration ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"cell",
"motility",
"molecular",
"cell",
"biology",
"biology",
"biophysics",
"genetics",
"and",
"genomics"
] | 2011 | An Adhesion-Dependent Switch between Mechanisms That Determine Motile Cell Shape |
Phosphorothioate ( PT ) modifications of the DNA backbone , widespread in prokaryotes , are first identified in bacterial enteropathogens Escherichia coli B7A more than a decade ago . However , methods for high resolution mapping of PT modification level are still lacking . Here , we developed the PT-IC-seq technique ,... | Phosphorothioate ( PT ) modification is a novel DNA modification , previous studies showed that PT modifications in E . coli occure at GpsAAC/GpsTTC motifs , but the modification frequency at each site are not known . In this study , we introduced two methods: PT-IC-seq , which could quantitatively characterize the gen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"bacteriology",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"organisms",
"bacterial",
"diseases",
"enterobacteriaceae",
"genome",
"analysis",
"bacterial",
"genetics",
"sequence",
"motif",
"analysis",
... | 2019 | Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency |
One of the central questions of developmental biology is how cells of equivalent potential—an equivalence group—come to adopt specific cellular fates . In this study we have used a combination of live imaging , single cell lineage analyses , and perturbation of specific signaling pathways to dissect the specification o... | How specific genes and signals act on initially identical cells to generate the different tissues of the body remains one of the central questions of developmental genetics . Zebrafish are a useful model system to tackle this question as the optically clear embryo allows direct imaging of forming tissues , tracking ind... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"embryology",
"animal",
"genetics",
"genetics",
"molecular",
"genetics",
"biology",
"morphogenesis",
"pattern",
"formation",
"genetics",
"and",
"genomics",
"cell",
"fate",
"determination",
"gene",
"function"
] | 2012 | Morphogenesis and Cell Fate Determination within the Adaxial Cell Equivalence Group of the Zebrafish Myotome |
Rabies virus ( RABV ) invades the central nervous system and nearly always causes fatal disease in humans . How RABV interacts with host neuron membrane receptors to become internalized and cause rabid symptoms is not yet fully understood . Here , we identified a novel receptor of RABV , which RABV uses to infect neuro... | Rabies virus ( RABV ) invades the central nervous system and nearly always causes fatal disease in humans . How RABV interacts with host neuron membrane receptors to become internalized and cause rabid symptoms is not yet fully understood . Here , we identified metabotropic glutamate receptor subtype 2 ( mGluR2 ) as a ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"vesicular",
"stomatitis",
"virus",
"pathology",
"and",
"laboratory",
"medicine",
"vesicles",
"nervous",
"system",
"gene",
"regulation",
"pathogens",
"immunology",
"microbiology",
"neuroscience",
"viruses",
... | 2018 | Metabotropic glutamate receptor subtype 2 is a cellular receptor for rabies virus |
During postnatal life the cerebral cortex passes through critical periods of plasticity allowing its physiological adaptation to the environment . In the visual cortex , critical period onset and closure are influenced by the non-cell autonomous activity of the Otx2 homeoprotein transcription factor , which regulates t... | Classically , cell signaling is based on the secretion of molecules that bind cell surface receptors . Lipophilic agents can do without cell-surface receptors due to their ability to diffuse through the plasma membrane , but this is normally not the case for proteins , which cannot pass the membrane barrier . However ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"nervous",
"system",
"gene",
"regulation",
"regulatory",
"proteins",
"brain",
"dna-binding",
"proteins",
"social",
"sciences",
"neuroscience",
"visual",
"acuity",
"physiological",
"processes",
"transcription",
"... | 2016 | A Mouse Model for Conditional Secretion of Specific Single-Chain Antibodies Provides Genetic Evidence for Regulation of Cortical Plasticity by a Non-cell Autonomous Homeoprotein Transcription Factor |
Participants in mass gathering events are at risk of acquiring imported and locally endemic infectious diseases . The 2014 dengue outbreak in Tokyo gathered attention since it was the first time in 70 years for Japan to experience an autochthonous transmission . Preparation for emerging infectious threats is essential ... | Dengue is a mosquito-borne disease that is most prevalent among the emerging arboviruses . Most patients recover from dengue without complications , but a small portion of cases may progress to severe dengue which carries a high mortality rate if left untreated . In 2014 , a dengue outbreak unexpectedly occurred in Tok... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"physicians",
"medical",
"doctors",
"medical",
"personnel",
"japan",
"sociology",
"geographical",
"locations",
"tropical",
"diseases",
"social",
"sciences",
"vector-borne",
"diseases",
"health",
"care",
"health",
"care",
"provide... | 2018 | Health preparedness plan for dengue detection during the 2020 summer Olympic and Paralympic games in Tokyo |
Studies of learning mechanisms critically depend on the ability to accurately assess learning outcomes . This assessment can be impeded by the often complex , multidimensional nature of behavior . We present a novel , automated approach to evaluating imitative learning . Conceptually , our approach estimates how much o... | Measuring learning outcomes is a critical objective of research into the mechanisms that support learning . Demonstration that a given manipulation results in better or worse learning outcomes requires an accurate and consistent measurement of learning quality . However , many behaviors ( e . g . speaking , walking , a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"syllables",
"learning",
"ornithology",
"linguistics",
"vocalization",
"vertebrates",
"social",
"sciences",
"neuroscience",
"animals",
"learning",
"and",
"memory",
"animal",
"signaling",
"and",
"communication",
"cognitive",
"psychology",
"animal",
"behavior",
"mathematics",... | 2018 | An automated approach to the quantitation of vocalizations and vocal learning in the songbird |
Pathogenic uncultivable treponemes comprise human and animal pathogens including agents of syphilis , yaws , bejel , pinta , and venereal spirochetosis in rabbits and hares . A set of 10 treponemal genome sequences including those of 4 Treponema pallidum ssp . pallidum ( TPA ) strains ( Nichols , DAL-1 , Mexico A , SS1... | The genus Treponema comprises several uncultivable human and animal pathogens including Treponema pallidum ssp . pallidum ( TPA ) , the causative agent of syphilis , T . p . ssp . pertenue ( TPE , the causative agent of yaws ) , and T . p . ssp . endemicum ( TEN , the causative agent of bejel ) . Simian TPE strain Frib... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | A Retrospective Study on Genetic Heterogeneity within Treponema Strains: Subpopulations Are Genetically Distinct in a Limited Number of Positions |
The major histocompatibility complex ( MHC ) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism . The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection . However , introgression from related species was re... | The major histocompatibility complex ( MHC ) , a crucial component of the defense against pathogens , contains the most polymorphic functional genes in vertebrate genomes . The extraordinary genetic variation is generally considered to be ancient . We investigated whether a previously neglected mechanism , introgressio... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"haplotypes",
"major",
"histocompatibility",
"complex",
"genetic",
"polymorphism",
"genome",
"evolution",
"clinical",
"immunology",
"natural",
"selection",
"genetics",
"introgression",
"biology",
"and",
"life",
"sciences",
"population",
"genetics",
"gene",
"flow",
"comput... | 2014 | Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex |
The importance of microRNAs in the regulation of various aspects of biology and disease is well recognized . However , what remains largely unappreciated is that a significant number of miRNAs are embedded within and are often co-expressed with protein-coding host genes . Such a configuration raises the possibility of ... | Animal genomes encode hundreds of microRNA genes that impact all areas of biology by limiting the expression of their targets . What remains largely unappreciated is that a significant proportion of microRNA genes are embedded within protein-coding genes , and are often co-expressed with their hosts , which raises the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"death",
"invertebrates",
"animal",
"genetics",
"gene",
"regulation",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"animals",
"gene",
"function",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"molecular",
"genetics... | 2014 | An Intronic microRNA Links Rb/E2F and EGFR Signaling |
Yaws is a neglected tropical disease , caused by Treponema pallidum subsp . pertenue . The disease causes chronic lesions , primarily in young children living in remote villages in tropical climates . As part of a global yaws eradication campaign initiated by the World Health Organization , we sought to develop and eva... | Yaws is a neglected treponemal infection that is often transmitted among children in developing countries . Eradication programs in the 1940–50’s significantly reduced the incidence of yaws , but the disease has resurged . The World Health Organization has proposed to eliminate yaws by 2020 , and mass treatment trials ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"geomorphology",
"taxonomy",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"landforms",
"pathogens",
"topography",
"tropical",
"diseases",
"microbiology",
"treponematoses",
"bacterial",
"diseases",
"phylogenetics",
"data",
"managemen... | 2017 | Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea |
Neuronal representation and extraction of spatial information are essential for behavioral control . For flying insects , a plausible way to gain spatial information is to exploit distance-dependent optic flow that is generated during translational self-motion . Optic flow is computed by arrays of local motion detector... | Insects , with their limited brain resources and high performance in a wide behavioral repertoire , are exquisite model systems for studying parsimonious signal processing . They extract spatial information by actively shaping their self-motion ( e . g . when performing peering movements or during flight segments with ... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"velocity",
"medicine",
"and",
"health",
"sciences",
"classical",
"mechanics",
"engineering",
"and",
"technology",
"motion",
"detectors",
"social",
"sciences",
"neuroscience",
"insect",
"flight",
"biological",
"locomotion",
"flight",
"(biology)",
"vision",
"sensory",
"p... | 2017 | Local motion adaptation enhances the representation of spatial structure at EMD arrays |
The role of IL-1β and IL-18 during lung infection with the gram-negative bacterium Francisella tularensis LVS has not been characterized in detail . Here , using a mouse model of pneumonic tularemia , we show that both cytokines are protective , but through different mechanisms . Il-18-/- mice quickly succumb to the in... | Francisella tularensis is a Gram-negative bacterium that infects macrophages and other cell types causing tularemia . F . tularensis is considered a potential bioterrorism agent and is a prime model intracellular bacterium to study the interaction of pathogens with the host immune system . The role of the proinflammato... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Production of Anti-LPS IgM by B1a B Cells Depends on IL-1β and Is Protective against Lung Infection with Francisella tularensis LVS |
How tightly packed chromatin is thoroughly inspected for DNA damage is one of the fundamental unanswered questions in biology . In particular , the effective excision of carcinogenic lesions caused by the ultraviolet ( UV ) radiation of sunlight depends on UV-damaged DNA-binding protein ( UV-DDB ) , but the mechanism b... | Like all molecules in living organisms , DNA undergoes spontaneous decay and is constantly under attack by endogenous and environmental agents . Unlike other molecules , however , DNA—the blueprint of heredity—cannot be re-created de novo; it can only be copied . The original blueprint must therefore remain pristine . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"oncology",
"medicine",
"dermatology",
"public",
"health",
"and",
"epidemiology",
"biology",
"geriatrics",
"molecular",
"cell",
"biology",
"public",
"health"
] | 2011 | Regulation of Nucleotide Excision Repair by UV-DDB: Prioritization of Damage Recognition to Internucleosomal DNA |
Breast cancer , the second leading cause of cancer death of women worldwide , is a heterogenous disease with multiple different subtypes . These subtypes carry important implications for prognosis and therapy . Interestingly , it is known that these different subtypes not only have different biological behaviors , but ... | Breast cancer , the second leading cause of cancer death of women worldwide , is a heterogenous disease . Different subtypes of breast cancer display very different expression programs , and these expression programs are associated with different patient outcomes and with different treatment protocols . However , littl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"breast",
"tumors",
"gene",
"regulation",
"cancers",
"and",
"neoplasms",
"oncology",
"alternative",
"splicing",
"genome",
"analysis",
"bioassays",
"and",
"physiological",
"analysis",
"research",
"and",
"analysis",
"methods",
"s... | 2017 | Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression |
Whole-genome sequencing is a powerful technique for obtaining the reference sequence information of multiple organisms . Its use can be dramatically expanded to rapidly identify genomic variations , which can be linked with phenotypes to obtain biological insights . We explored these potential applications using the em... | In this manuscript , we describe novel applications of the newly developed Solexa sequencing technology . We aim to provide insights into the following questions: ( 1 ) Can whole-genome sequencing , while rapidly surveying mega-bases of genome information , also reliably identify variations at the base-pair resolution ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/genomics",
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"microbiology/microbial",
"physiology",
"and",
"metabolism"
] | 2008 | High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies |
Pools of mutants of minimal complexity but maximal coverage of genes of interest facilitate screening for genes under selection in a particular environment . We constructed individual deletion mutants in 1 , 023 Salmonella enterica serovar Typhimurium genes , including almost all genes found in Salmonella but not in re... | One strategy to define bacterial genes with a role during infection involves the screening of a pool of random transposon insertion mutants , where each mutant is identifiable by a specific motif or unique transcript . Changes in the survival of each mutant indicate a role of the mutated region during infection . To en... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"genetics",
"and",
"genomics/functional",
"genomics",
"cell",
"biology/microbial",
"growth",
"and",
"development",
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"and",
"genomics/gene",
"function",
"genetics",
"and",
"genomics/genetics",
"of",... | 2009 | Analysis of Pools of Targeted Salmonella Deletion Mutants Identifies Novel Genes Affecting Fitness during Competitive Infection in Mice |
Resting CD4+ T-cells harboring inducible HIV proviruses are a critical reservoir in antiretroviral therapy ( ART ) -treated subjects . These cells express little to no viral protein , and thus neither die by viral cytopathic effects , nor are efficiently cleared by immune effectors . Elimination of this reservoir is th... | Although modern therapies have greatly improved the lives of HIV-positive people with access to care , a cure remains elusive . This leaves these individuals burdened by a lifelong commitment to medication , and fails to fully restore health . Curing infection would likely require therapies that combine the ability to ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"hiv",
"infections",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"enzyme-linked",
"immunoassays",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"cloning",
"retroviruses",
"... | 2016 | A Subset of Latency-Reversing Agents Expose HIV-Infected Resting CD4+ T-Cells to Recognition by Cytotoxic T-Lymphocytes |
Apoptotic cell death is an important response to genotoxic stress that prevents oncogenesis . It is known that tissues can differ in their apoptotic response , but molecular mechanisms are little understood . Here , we show that Drosophila polyploid endocycling cells ( G/S cycle ) repress the apoptotic response to DNA ... | In order to maintain genome integrity , eukaryotic cells have evolved multiple ways to respond to DNA damage stress . One of the major cellular responses is apoptosis , during which the cell undergoes programmed cell death in order to prevent the propagation of the damaged genome to daughter cells . Although clinical o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences"
] | 2014 | Low Levels of p53 Protein and Chromatin Silencing of p53 Target Genes Repress Apoptosis in Drosophila Endocycling Cells |
Microbial infections usually lead to host innate immune responses and inflammation . These responses most often limit pathogen replication although they can also result in host-tissue damage . The enteropathogenic bacteria Salmonella Typhimurium utilizes a type III secretion system to induce intestinal inflammation by ... | The inflammatory response to microbial pathogens usually limits their replication but it can also cause tissue damage . The enteropathogenic bacteria Salmonella Typhimurium stimulate host signal transduction pathways that result in inflammation . We show here that a family of related Salmonella Typhimurium effector pro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"transfection",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"regulatory",
"proteins",
"immunology",
"microbiology",
"dna-bindin... | 2016 | A Family of Salmonella Type III Secretion Effector Proteins Selectively Targets the NF-κB Signaling Pathway to Preserve Host Homeostasis |
African trypanosomosis , primarily transmitted by tsetse flies , remains a serious public health and economic challenge in sub-Saharan Africa . Interventions employing natural repellents from non-preferred hosts of tsetse flies represent a promising management approach . Although zebras have been identified as non-pref... | The use of repellents from non-preferred hosts represents an innovative approach to control animal African trypanosomosis by limiting contact between tsetse flies and livestock . Although zebras are non-preferred hosts , the possible chemical basis of their avoidance by tsetse flies is unknown . We hypothesized that ce... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"chemical",
"compounds",
"ketones",
"vertebrates",
"animals",
"mammals",
"parasitic",
"protozoans",
"organic",
"compounds",
"glossina",
"parasitology",
"urine",
"protozoans",
"tsetse",
"fly",
"i... | 2019 | Zebra skin odor repels the savannah tsetse fly, Glossina pallidipes (Diptera: Glossinidae) |
A close relative of poliovirus , enterovirus 71 ( EV71 ) is regarded as an important neurotropic virus of serious public health concern . EV71 causes Hand , Foot and Mouth Disease and has been associated with neurological complications in young children . Our limited understanding of the mechanisms involved in its neur... | A close relative of poliovirus , Enterovirus 71 ( EV71 ) causes Hand , Foot and Mouth Disease and has been associated with neurological complications in young children . The lack of effective therapeutics is largely due to our limited understanding of the mechanisms involved in EV71 neuropathogenesis . Here , using a p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"transfection",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"nervous",
"system",
"gene",
"regulation",
"immunology",
"microbiology",
"neuroscience",
"immunoprecipitation",
"mitochondria",
"co-immunoprecipitation",
"bioenergetics",
"molecular",
"biology",
... | 2018 | Prohibitin plays a critical role in Enterovirus 71 neuropathogenesis |
Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis , a health-threatening human systemic mycosis endemic to Latin America . Infection by Paracoccidioides , a dimorphic fungus in the order Onygenales , is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a ... | Paracoccidioides sp . are fungal pathogens that cause paracoccidioidomycosis in humans . They are part of a larger group of dimorphic fungi causing pulmonary infections in immunocompetent people , whereas many other fungi cause opportunistic infections . We sequenced the genomes of two strains of Paracoccidioides brasi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"evolution",
"microbiology",
"fungal",
"physiology",
"genome",
"sequencing",
"fungal",
"evolution",
"microbial",
"evolution",
"genome",
"complexity",
"mycology",
"microbial",
"pathogens",
"comparative",
"genomics",
"biology",
"pathogenesis",
"genomics",
"computati... | 2011 | Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis |
Microbial infection during various stages of human development produces widely different clinical outcomes , yet the links between age-related changes in the immune compartment and functional immunity remain unclear . The ability of the immune system to respond to specific antigens and mediate protection in early life ... | Newborns typically have a heightened sensitivity to infectious diseases , the reasons for which are not yet well understood . One contributing factor is the limited diversity of lymphocyte receptors early in life to recognize antigen and control infection . We have previously shown that antigen-specific CD8+ T cell rep... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"of",
"infection",
"viral",
"vaccines",
"adaptive",
"immunity",
"immunity",
"virology",
"biology",
"microbiology"
] | 2013 | Acute Neonatal Infections ‘Lock-In’ a Suboptimal CD8+ T Cell Repertoire with Impaired Recall Responses |
Small oligomers formed early in the process of amyloid fibril formation may be the major toxic species in Alzheimer's disease . We investigate the early stages of amyloid aggregation for the tau fragment AcPHF6 ( Ac-VQIVYK-NH2 ) using an implicit solvent all-atom model and extensive Monte Carlo simulations of 12 , 24 ,... | It is believed that the self association of certain protein molecules into aggregated structures , known as amyloid fibrils , plays an important role in a variety of human diseases , such as Alzheimer's disease and Parkinson's disease . Although the ability to form such amyloid fibrils is a common property for proteins... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biophysics/theory",
"and",
"simulation"
] | 2008 | Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment |
Preventive chemotherapy has long been practiced against nematode parasites of livestock , leading to widespread drug resistance , and is increasingly being adopted for eradication of human parasitic nematodes even though it is similarly likely to lead to drug resistance . Given that the genetic architecture of resistan... | Teladorsagia circumcincta is an economically significant nematode ( roundworm ) pathogen affecting sheep and goats in temperate regions of the world . The widespread use of prophylactic treatment has resulted in rapid selection for anthelmintic ( anti-worm drug ) resistance in this and other species of livestock parasi... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"ruminants",
"population",
"genetics",
"vertebrates",
"animals",
"mammals",
"invertebrate",
"genomics",
"genetic",
"mapping",
"molecular",
"biology",
"techniques",
"population",
"biology",
"research",
"and",
"analysis",
"methods",
"gene",
"mapping",
"introgression",
"mole... | 2017 | Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta |
G-protein–coupled receptors ( GPCRs ) are generally thought to signal to second messengers like cyclic AMP ( cAMP ) from the cell surface and to become internalized upon repeated or prolonged stimulation . Once internalized , they are supposed to stop signaling to second messengers but may trigger nonclassical signals ... | Cells respond to many environmental cues through the activity of cell surface receptor proteins , which sense these cues and convey that information to signaling molecules inside the cell . G-protein–coupled receptors ( GPCRs ) form the largest eukaryotic family of plasma membrane receptors . They convert the informati... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"diabetes",
"and",
"endocrinology/thyroid",
"cell",
"biology/cell",
"signaling"
] | 2009 | Persistent cAMP-Signals Triggered by Internalized G-Protein–Coupled Receptors |
Recent increased activity of the mosquito-borne Murray Valley encephalitis virus ( MVEV ) in Australia has renewed concerns regarding its potential to spread and cause disease . To better understand the genetic relationships between earlier and more recent circulating strains , patterns of virus movement , as well as t... | Murray Valley encephalitis virus is the most significant cause of mosquito-borne encephalitis in humans in Australia , and can also cause neurological disease in horses . This study reports an expanded phylogenetic study of this virus and the first molecular evolutionary analysis . Of the four recognized genotypes of M... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | The Molecular Epidemiology and Evolution of Murray Valley Encephalitis Virus: Recent Emergence of Distinct Sub-lineages of the Dominant Genotype 1 |
The maintenance of chromosome integrity is crucial for genetic stability . However , programmed chromosome fragmentations are known to occur in many organisms , and in the ciliate Tetrahymena the five germline chromosomes are fragmented into hundreds of minichromosomes during somatic nuclear differentiation . Here , we... | Chromatin diminution was first discovered in the parasite Parascaris univalens by T . Boveri more than one century ago . This process eliminates a large proportion of the genome accompanying germline-soma differentiation during development . Ciliates also carry out DNA elimination that have been studied in depth . Duri... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"sequencing",
"techniques",
"chromosome",
"structure",
"and",
"function",
"genomic",
"databases",
"telomeres",
"model",
"organisms",
"protozoans",
"genome",
"analysis",
"tetrahymena",
"thermophila",
"sequence",
"motif",
"analysis",
"ciliate",
"protozoans",
"molecular",
"b... | 2016 | Programmed Minichromosome Elimination as a Mechanism for Somatic Genome Reduction in Tetrahymena thermophila |
Cell migration in 3D microenvironments is fundamental to development , homeostasis and the pathobiology of diseases such as cancer . Rab-coupling protein ( RCP ) dependent co-trafficking of α5β1 and EGFR1 promotes cancer cell invasion into fibronectin ( FN ) containing extracellular matrix ( ECM ) , by potentiating EGF... | The majority of cancer-related fatalities are caused by the movement of cancer cells away from the primary site to form metastases , making understanding the signalling mechanisms which underpin cell migration and invasion through their local environment of paramount importance . Much has been discovered about key even... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"motility",
"cancer",
"cell",
"migration",
"gene",
"regulation",
"enzymes",
"enzymology",
"signaling",
"networks",
"fluorophotometry",
"developmental",
"biology",
"gtpase",
"signaling",
"network",
"analysis",
"research",
"and",
"analysis",
"methods",
"small",
"i... | 2016 | A MAPK-Driven Feedback Loop Suppresses Rac Activity to Promote RhoA-Driven Cancer Cell Invasion |
Forward genetic screens in model organisms are an attractive means to identify those genes involved in any complex biological process , including neural circuit assembly . Although mutagenesis screens are readily performed to saturation , gene identification rarely is , being limited by the considerable effort generall... | In the nervous system , every neuronal process should know where to grow and when to establish contacts to the next-order neurons . During development , it is known that neural circuit formation is primarily determined by the genes . To identify these genes , we focused on the Drosophila visual circuitry as a model sys... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/gene",
"function",
"developmental",
"biology/neurodevelopment",
"genetics",
"and",
"genomics/gene",
"discovery",
"neuroscience/neurodevelopment"
] | 2008 | Systematic Identification of Genes that Regulate Neuronal Wiring in the Drosophila Visual System |
Biogenesis of mammalian mitochondrial ribosomes requires a concerted maturation of both the small ( SSU ) and large subunit ( LSU ) . We demonstrate here that the m5C methyltransferase NSUN4 , which forms a complex with MTERF4 , is essential in mitochondrial ribosomal biogenesis as mitochondrial translation is abolishe... | Mitochondria perform a number of essential functions in the cell , including synthesis of ATP via the oxidative phosphorylation ( OXPHOS ) system . Normal mitochondrial function requires coordinated expression of two genomes: mitochondria's own genome ( mtDNA ) , which encodes 13 respiratory chain subunits with essenti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry",
"rna",
"rna",
"processing",
"nucleic",
"acids",
"proteins",
"protein",
"translation",
"gene",
"expression",
"genetics",
"biology"
] | 2014 | NSUN4 Is a Dual Function Mitochondrial Protein Required for Both Methylation of 12S rRNA and Coordination of Mitoribosomal Assembly |
Relative to normal tissues , tumor microcirculation exhibits high structural and functional heterogeneity leading to hypoxic regions and impairing treatment efficacy . Here , computational simulations of blood vessel structural adaptation are used to explore the hypothesis that abnormal adaptive responses to local hemo... | Blood vessels of tumors have abnormal structures , being irregular and tortuous . Oxygen supply to tumors is heterogeneous , with regions of low oxygen that resist radiation treatment and some types of chemotherapy . Blood vessels undergo continual structural change ( adaptation ) in response to blood flow and metaboli... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"physiology/cardiovascular",
"physiology",
"and",
"circulation",
"oncology/oncology",
"agents",
"computational",
"biology/systems",
"biology"
] | 2009 | Structural Adaptation and Heterogeneity of Normal and Tumor Microvascular Networks |
Chagas disease is caused by the parasitic infection of Trypanosoma cruzi ( T . cruzi ) . The STOP CHAGAS clinical trial was initiated in 2011 to evaluate posaconazole in treating Chagas disease , with treatment success defined as negative qualitative PCR results of detecting the parasites in blood specimens collected p... | Chagas disease is caused by the infection of the protozoan parasite Trypanosoma cruzi ( T . cruzi ) and carries a significant tropical disease burden in the Western Hemisphere . The STOP CHAGAS study was a global clinical trial evaluating therapies for Chagas disease . PAXgene blood DNA tubes used by the study simplifi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"organisms",
"protozoans",
"dna",
"replication",
"neglected",
"tropical",
"diseases",
"molecular",
"biology",
"techniques",
"dna",
"cel... | 2016 | Development of a PCR Assay to Detect Low Level Trypanosoma cruzi in Blood Specimens Collected with PAXgene Blood DNA Tubes for Clinical Trials Treating Chagas Disease |
HIV reservoirs and production of viral antigens are not eliminated in chronically infected participants treated with combination antiretroviral therapy ( cART ) . Novel therapeutic strategies aiming at viral reservoir elimination are needed to address chronic immune dysfunction and non-AIDS morbidities that exist despi... | Current HIV therapies prevent AIDS by dramatically reducing , but not eliminating , HIV infection . A reservoir of HIV-infected cells persists during long-term antiviral therapy , and individuals are at increased risk to develop non-AIDS illnesses , e . g . , accelerated heart , bone , or kidney disease . Novel strateg... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Targeting HIV Reservoir in Infected CD4 T Cells by Dual-Affinity Re-targeting Molecules (DARTs) that Bind HIV Envelope and Recruit Cytotoxic T Cells |
Reduced DNA methylation has been reported in DICER1-deficient mouse ES cells . Reductions seen at pericentric satellite repeats have suggested that siRNAs are required for the proper assembly of heterochromatin . More recent studies have postulated that the reduced methylation is an indirect effect: the loss of Mir290 ... | In mammalian cells , DNA methylation is required for the maintenance of genome stability . Recent studies have shown that the genome-wide levels of DNA methylation can be reduced in DICER1-deficient mouse embryonic stem ( ES ) cells , suggesting that the activity of DNA methylating enzymes ( DNMTs ) may be regulated by... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"developmental",
"biology",
"genetics",
"biology",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Normal DNA Methylation Dynamics in DICER1-Deficient Mouse Embryonic Stem Cells |
Faithful chromosome segregation during meiosis I depends on the establishment of a crossover between homologous chromosomes . This requires induction of DNA double-strand breaks ( DSBs ) , alignment of homologs , homolog association by synapsis , and repair of DSBs via homologous recombination . The success of these ev... | During meiosis , one round of replication is followed by two divisions to produce haploid gametes . During the first meiotic division , faithful segregation is facilitated by the formation between the parental homologs of a physical tether called crossover . Crossovers require the introduction of DNA double-strand brea... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology"
] | 2013 | Matefin/SUN-1 Phosphorylation Is Part of a Surveillance Mechanism to Coordinate Chromosome Synapsis and Recombination with Meiotic Progression and Chromosome Movement |
Timely , and sometimes rapid , metabolic adaptation to changes in food supply is critical for survival as an organism moves from the fasted to the fed state , and vice versa . These transitions necessitate major metabolic changes to maintain energy homeostasis as the source of blood glucose moves away from ingested car... | Homeostasis of blood glucose concentrations during circadian shifts in survival-related activities , sleep and food availability is crucial for the survival of mammals . This process depends upon glucose intake , short-term storage as glycogen , and gluconeogenesis . The integration of hepatic glycogen anabolic and cat... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"mathematics",
"applied",
"mathematics",
"biology",
"computational",
"biology",
"nonlinear",
"dynamics"
] | 2011 | A Whole-Body Model for Glycogen Regulation Reveals a Critical Role for Substrate Cycling in Maintaining Blood Glucose Homeostasis |
Sinorhizobium meliloti differentiates into persisting , nitrogen-fixing bacteroids within root nodules of the legume Medicago truncatula . Nodule-specific cysteine-rich antimicrobial peptides ( NCR AMPs ) and the bacterial BacA protein are essential for bacteroid development . However , the bacterial factors central to... | Certain bacterial species have the unique capacity to enter into eukaryotic host cells and establish prolonged infections , which can be beneficial ( e . g . bacterial-legume symbiosis ) or detrimental ( e . g . chronic disease ) for the host . However , the mechanisms by which bacteria persist in host cells are poorly... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"plant",
"science",
"plant",
"microbiology",
"plant",
"biology",
"microbial",
"pathogens",
"plant",
"cell",
"biology",
"biology",
"microbial",
"growth",
"and",
"development",
"microbiology",
"host-pathogen",
"interaction",
"bacterial",
"pathoge... | 2011 | Protection of Sinorhizobium against Host Cysteine-Rich Antimicrobial Peptides Is Critical for Symbiosis |
Dose response in micro-parasite infections is usually shallower than predicted by the independent action model , which assumes that each infectious unit has a probability of infection that is independent of the presence of other infectious units . Moreover , the prevalence of mixed-genotype infections was greater than ... | What elements are indispensable in the description of the most basic host-pathogen interactions ? The simplest models of infection generally fail to predict how many host plants or animals will become infected , and which virus genotypes will be present in these infected hosts . These simple models of infection are the... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"population",
"ecology",
"ecology",
"population",
"modeling",
"virology",
"biology",
"computational",
"biology",
"microbiology",
"host-pathogen",
"interaction"
] | 2011 | Heterogeneous Host Susceptibility Enhances Prevalence of Mixed-Genotype Micro-Parasite Infections |
The hierarchical relationships between stem cells and progenitors that guide mammary gland morphogenesis are still poorly defined . While multipotent basal stem cells have been found within the myoepithelial compartment , the in vivo lineage potential of luminal progenitors is unclear . Here we used the expression of t... | Tissue-specific stem cells are believed to be multipotent , thus able to generate all cell types of their tissue of origin . In the mammary gland epithelium , however , the existence of multipotent versus unipotent adult stem cells is currently under debate . In this study , we have identified and characterized a popul... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Luminal Progenitors Restrict Their Lineage Potential during Mammary Gland Development |
Despite of a high disease burden , mainly in Latin America , Chagas disease ( CD ) is underdiagnosed and undertreated . Rapid diagnostic tests ( RDTs ) might improve the access to diagnosis . The aim of this study is to review the accuracy of commercially available RDTs used in field conditions for the diagnosis of chr... | Chagas disease ( CD ) is a parasitic disease that can affect seriously the health status of affected individuals . People with CD , mainly living in remote areas of Latin America , often face major barriers to the disease recognition , diagnosis and treatment . The World Health Organization recommends the combined use ... | [
"Abstract",
"Introduction",
"Methods",
"Inclusion",
"criteria",
"Results",
"Discussion"
] | [
"recombination-based",
"assay",
"medicine",
"and",
"health",
"sciences",
"enzyme-linked",
"immunoassays",
"pathology",
"and",
"laboratory",
"medicine",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"biochemical",
"analysis",
"enzyme",
"assays",... | 2019 | Rapid immunochromatographic tests for the diagnosis of chronic Chagas disease in at-risk populations: A systematic review and meta-analysis |
Mitochondrial antiviral-signaling protein ( MAVS ) transmits signals from RIG-I-like receptors after RNA virus infections . However , the mechanism by which MAVS activates downstream components , such as TBK1 and IKKα/β , is unclear , although previous work suggests the involvement of NEMO or TBK1-binding proteins TANK... | Innate immunity is the first line of defense against virus infection . RIG-I-like receptors ( RLRs ) recognize various viral RNA from RNA viruses and initiate host antiviral responses to produce type I interferons ( IFNs ) and other cytokines . RLRs sense distinct types of viruses by sharing a common adaptor protein ca... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"reverse",
"transcriptase-polymerase",
"chain",
"reaction",
"phosphorylation",
"precipitates",
"enzyme-linked",
"immunoassays",
"hela",
"cells",
"293t",
"cells",
"enzymes",
"biological",
"cultures",
"enzymology",
"immunoprecipitation",
"cell",
"cultures",
"molecular",
"biolog... | 2017 | MAVS activates TBK1 and IKKε through TRAFs in NEMO dependent and independent manner |
Molecular recognition is determined by the structure and dynamics of both a protein and its ligand , but it is difficult to directly assess the role of each of these players . In this study , we use Markov State Models ( MSMs ) built from atomistic simulations to elucidate the mechanism by which the Lysine- , Arginine-... | Protein-ligand interactions are crucial to chemistry , biology and medicine . Many studies have been conducted to probe the mechanism of protein-ligand binding , leading to the development of the induced fit and conformational selection models . Unfortunately , experimentally probing the atomistic details of protein-li... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"physics",
"biochemistry",
"protein",
"chemistry",
"protein",
"interactions",
"proteins",
"protein",
"structure",
"biology",
"biophysics",
"drug",
"discovery"
] | 2011 | A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein |
Kinetically stable proteins , those whose stability is derived from their slow unfolding kinetics and not thermodynamics , are examples of evolution's best attempts at suppressing unfolding . Especially in highly proteolytic environments , both partially and fully unfolded proteins face potential inactivation through d... | Proteins , synthesized as linear polymers of amino acids , fold up into compact native states , burying their hydrophobic amino acids into their interiors . Protein folding minimizes the non-specific interactions that unfolded protein chains can make , which include aggregation with other proteins and degradation by pr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biophysics/protein",
"folding",
"biochemistry/protein",
"folding",
"biophysics/theory",
"and",
"simulation",
"biochemistry/theory",
"and",
"simulation",
"computational",
"biology/molecular",
"dynamics"
] | 2010 | Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease |
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