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article stringlengths 4.36k 149k | summary stringlengths 32 3.35k | section_headings listlengths 1 91 | keywords listlengths 0 141 | year stringclasses 13
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|---|---|---|---|---|---|
The Neotropics contains half of remaining rainforests and Earth's largest reservoir of amphibian biodiversity . However , determinants of Neotropical biodiversity ( i . e . , vicariance , dispersals , extinctions , and radiations ) earlier than the Quaternary are largely unstudied . Using a novel method of ancestral ar... | The Neotropics , which includes South and Central America , contains half of remaining rainforests and the largest reservoir of amphibian diversity . Why there are so many species in certain areas and how such diversity arose before the Quaternary ( i . e . , more that 1 . 8 million years ago [MYA] ) are largely unstud... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"ecology",
"computational",
"biology",
"evolutionary",
"biology"
] | 2009 | Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages |
Cystic echinococcosis is a worldwide distributed helminth zoonosis caused by the larval stage of Echinococcus granulosus . Human secondary cystic echinococcosis is caused by dissemination of protoscoleces after accidental rupture of fertile cysts and is due to protoscoleces ability to develop into new metacestodes . In... | Cystic echinococcosis is a zoonotic disease caused by the larval stage of the cestode Echinococcus granulosus and shows a cosmopolitan distribution with a worldwide prevalence of roughly 6 million infected people . Human cystic echinococcosis can develop in two types of infection . Primary infection occurs by ingestion... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"humoral",
"immunity",
"medicine",
"immune",
"cells",
"cytokines",
"immunity",
"to",
"infections",
"immunology",
"microbiology",
"host-pathogen",
"interaction",
"parasitic",
"diseases",
"helminth",
"infection",
"animal",
"models",
"adaptive",
"immunity",
"model",
"organis... | 2011 | Early Peritoneal Immune Response during Echinococcus granulosus Establishment Displays a Biphasic Behavior |
Ribosome queuing is a fundamental phenomenon suggested to be related to topics such as genome evolution , synthetic biology , gene expression regulation , intracellular biophysics , and more . However , this phenomenon hasn't been quantified yet at a genomic level . Nevertheless , methodologies for studying translation... | During translation , multiple ribosomes may translate the same mRNA . The density of ribosomal traffic across the transcript poses several open questions , such as how often a ribosome’s path is blocked by a second ribosome , do queues of multiple ribosomes typically form on mRNAs and what is their effect on the overal... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"messenger",
"rna",
"simulation",
"and",
"modeling",
"genome",
"analysis",
"molecular",
"biology",
"techniques",
"cellular",
"structures",
"and",
"organelles",
"genetic",
"footprinting",
"research",
"and",
"analysis",
"methods",
"genomics",
"gene",
"expression",
"molecu... | 2018 | The extent of ribosome queuing in budding yeast |
In various fields , statistical models of interest are analytically intractable and inference is usually performed using a simulation-based method . However elegant these methods are , they are often painstakingly slow and convergence is difficult to assess . As a result , statistical inference is greatly hampered by c... | Interesting nonlinear models are often analytically intractable . As a result , statistical inference has to rely on massive , time-intensive , simulations . The main idea of our method is to avoid the redundancy of similar computations that typically occur when different researchers independently fit the same model to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"ellipses",
"statistics",
"random",
"variables",
"geometry",
"covariance",
"simulation",
"and",
"modeling",
"interpolation",
"regression",
"analysis",
"mathematics",
"artificial",
"intelligence",
"research",
"and",
"analysis",
"methods",
"statistical",
"distributions",
"com... | 2019 | Prepaid parameter estimation without likelihoods |
Over a century since Ronald Ross discovered that malaria is caused by the bite of an infectious mosquito it is still unclear how the number of parasites injected influences disease transmission . Currently it is assumed that all mosquitoes with salivary gland sporozoites are equally infectious irrespective of the numbe... | Malaria is transmitted to humans by the bite of an infectious mosquito though it is unclear whether a mosquito with a high number of parasites is more infectious than one with only a few . Here we show that the greater the number of parasites within the salivary gland of the mosquito following blood-feeding the more li... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"parasite",
"groups",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"parasitic",
"protozoans",
"parasitology",
"vaccines",
"preventive",
"me... | 2017 | Probability of Transmission of Malaria from Mosquito to Human Is Regulated by Mosquito Parasite Density in Naïve and Vaccinated Hosts |
Place cells in the hippocampus of higher mammals are critical for spatial navigation . Recent modeling clarifies how this may be achieved by how grid cells in the medial entorhinal cortex ( MEC ) input to place cells . Grid cells exhibit hexagonal grid firing patterns across space in multiple spatial scales along the M... | Spatial navigation is a critical competence of all higher mammals , and place cells in the hippocampus represent the large spaces in which they navigate . Recent modeling clarifies how this may occur via interactions between grid cells in the medial entorhinal cortex ( MEC ) and place cells . Grid cells exhibit hexagon... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"computer",
"science",
"social",
"and",
"behavioral",
"sciences",
"mathematics",
"chemistry",
"biology",
"engineering"
] | 2012 | How Entorhinal Grid Cells May Learn Multiple Spatial Scales from a Dorsoventral Gradient of Cell Response Rates in a Self-organizing Map |
As a consequence of the accumulation of insertion events over evolutionary time , mobile elements now comprise nearly half of the human genome . The Alu , L1 , and SVA mobile element families are still duplicating , generating variation between individual genomes . Mobile element insertions ( MEI ) have been identified... | We embarked on this study to explore the 1000 Genomes Project ( 1000GP ) pilot dataset as a substrate for Mobile Element Insertion ( MEI ) discovery and analysis . MEI is already well known as a significant component of genetic variation in the human population . However the full extent and effects of MEI can only be a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"functional",
"genomics",
"genetic",
"mutation",
"genome",
"evolution",
"genome",
"scans",
"neutral",
"theory",
"population",
"genetics",
"genome",
"sequencing",
"mutation",
"genome",
"analysis",
"tools",
"genome",
"databases",
"mutation",
"types",
"mutation",
"database... | 2011 | A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans |
U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1 , 700 publications over four decades . In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing , we have generated greater than 30× genomic sequence coverage... | Glioblastoma has a particularly dismal prognosis with median survival time of less than fifteen months . Here , we describe the broad genome sequencing of U87MG , a commonly used and thus well-studied glioblastoma cell line . One of the major features of the U87MG genome is the large number of chromosomal abnormalities... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/literature",
"analysis",
"genetics",
"and",
"genomics/genomics",
"oncology",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/genome",
"projects",
"computational",
"biology/genomics",
"genetics",
"and",
"genomics",
"... | 2010 | U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line |
One root cause of the neglect of rabies is the lack of adequate diagnostic tests in the context of low income countries . A rapid , performance friendly and low cost method to detect rabies virus ( RABV ) in brain samples will contribute positively to surveillance and consequently to accurate data reporting , which is ... | The high fatality and burden of rabies stands in contrast to the very low performance of laboratory-based surveillance in resource-challenged countries . The absence of reliable human and animal rabies incidence data ultimately result in neglect of disease prevention and control and the perpetuation of RABV transmissio... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"tropical",
"diseases",
"rna",
"extraction",
"microbiology",
"vertebrates",
"animals",
"mammals",
"dogs",
"viruses",
"rabies",
"rna",
"viruses",
"neglected",
"tropical",
... | 2016 | Validation of a Rapid Rabies Diagnostic Tool for Field Surveillance in Developing Countries |
Nuclear landmarks and biochemical factors play important roles in the organization of the yeast genome . The interaction pattern of budding yeast as measured from genome-wide 3C studies are largely recapitulated by model polymer genomes subject to landmark constraints . However , the origin of inter-chromosomal interac... | The architecture of the cell nucleus and the spatial organization of the genome are important in determining nuclear functions . Single-cell imaging techniques and chromosome conformation capture ( 3C ) based methods have provided a wealth of information on the spatial organization of chromosomes . Here we describe a m... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"transfer",
"rna",
"chromosome",
"structure",
"and",
"function",
"centromeres",
"telomeres",
"fungi",
"model",
"organisms",
"non-coding",
"rna",
"materials",
"science",
"experimental",
"organism",
"systems",
"epigenetics",
"macromolecules",
"structural",
"genomics",
"chro... | 2017 | Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model |
The ability to effectively modify behaviours is increasingly relevant to attain and maintain a good health status . Current behaviour-change models and theories present two main approaches for ( healthier ) decision-making: one analytical/logical , and one experiential/emotional/intuitive . Therefore , to achieve an in... | Since there is no vaccine or treatment available for dengue fever , its prevention relies on community participation . Residents are asked to remove from their houses and gardens all receptacles where mosquitoes can breed . Exploring the public perception regarding dengue prevention is crucial for detecting obstacles t... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Impact of a Dengue Outbreak Experience in the Preventive Perceptions of the Community from a Temperate Region: Madeira Island, Portugal |
Leishmania is transmitted by female sand flies and deposited together with saliva , which contains a vast repertoire of pharmacologically active molecules that contribute to the establishment of the infection . The exposure to vector saliva induces an immune response against its components that can be used as a marker ... | During the blood meal , female sand flies ( insects that transmit the parasite Leishmania ) inject saliva containing a large variety of molecules with different pharmacological activities that facilitate the acquisition of blood . These molecules can induce the production of anti-saliva antibodies , which can then be u... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases"
] | 2010 | Using Recombinant Proteins from Lutzomyia longipalpis Saliva to Estimate Human Vector Exposure in Visceral Leishmaniasis Endemic Areas |
Understanding the cellular mechanisms that ensure an appropriate innate immune response against viral pathogens is an important challenge of biomedical research . In vitro studies have shown that natural killer ( NK ) cells purified from healthy donors can kill heterologous cell lines or autologous CD4+ T cell blasts e... | Natural killer ( NK ) cells represent an important line of defense against viral infections . In vitro studies with exogenously infected CD4+ T cell blasts from healthy donors have demonstrated that NK cells can kill autologous HIV-1-infected target cells . However , the ability of NK cells from HIV-1-infected viremic ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/hiv",
"infection",
"and",
"aids",
"immunology/immunity",
"to",
"infections",
"immunology/innate",
"immunity"
] | 2008 | Lysis of Endogenously Infected CD4+ T Cell Blasts by rIL-2 Activated Autologous Natural Killer Cells from HIV-Infected Viremic Individuals |
Trypanosoma brucei gambiense causes 97% of all cases of African sleeping sickness , a fatal disease of sub-Saharan Africa . Most species of trypanosome , such as T . b . brucei , are unable to infect humans due to the trypanolytic serum protein apolipoprotein-L1 ( APOL1 ) delivered via two trypanosome lytic factors ( T... | Trypanosoma brucei gambiense causes 97% of all cases of African sleeping sickness , a fatal disease of sub-Saharan Africa . Most species of trypanosome , such as T . b . brucei , are unable to infect humans due to trypanolytic factors in human serum . Understanding how T . b . gambiense overcomes these factors and infe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | The TgsGP Gene Is Essential for Resistance to Human Serum in Trypanosoma brucei gambiense |
Plasmodesma ( PD ) is a channel structure that spans the cell wall and provides symplastic connection between adjacent cells . Various macromolecules are known to be transported through PD in a highly regulated manner , and plant viruses utilize their movement proteins ( MPs ) to gate the PD to spread cell-to-cell . Th... | During infection , plant viruses utilize their cell-to-cell movement proteins ( MPs ) to gate plant intercellular connections , the plasmodesmata ( PD ) , and spread between the host cells . The mechanism by which MPs facilitate their cell-to-cell translocation remains elusive . We have identified a tobacco ankyrin rep... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"plant",
"biology/plant-biotic",
"interactions",
"plant",
"biology/plant",
"cell",
"biology",
"virology/host",
"invasion",
"and",
"cell",
"entry"
] | 2010 | ANK, a Host Cytoplasmic Receptor for the Tobacco mosaic virus Cell-to-Cell Movement Protein, Facilitates Intercellular Transport through Plasmodesmata |
Dengue virus ( DV ) infection is one of the most common mosquito-borne viral diseases in the world . The innate immune system is important for the early detection of virus and for mounting a cascade of defense measures which include the production of type 1 interferon ( IFN ) . Hence , a thorough understanding of the i... | Dengue fever , dengue haemmorhagic fever and dengue shock syndrome , which are caused by dengue virus infection , are a major public health problem in many parts of the world , especially South East Asia . The investigation of host cell transcriptional changes in response to virus infection using DNA microarray technol... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"immunology/immune",
"response",
"immunology/immunity",
"to",
"infections",
"immunology/innate",
"immunity",
"microbiology/innate",
"immunity",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis"
] | 2011 | RIG-I, MDA5 and TLR3 Synergistically Play an Important Role in Restriction of Dengue Virus Infection |
Model simulations indicate that the response of growing cell populations on mechanical stress follows the same functional relationship and is predictable over different cell lines and growth conditions despite experimental response curves look largely different . We develop a hybrid model strategy in which cells are re... | The effect of mechanical resistance on the growth of tumor cells remains today largely unquantified . We studied data from two different experimental setups that monitor the growth of tumor cells under mechanical compression . The existing data in the first experiment examined growing CT26 cells in an elastic permeable... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Models"
] | [
"cellular",
"stress",
"responses",
"classical",
"mechanics",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"biological",
"cultures",
"radii",
"mechanical",
"stress",
"geometry",
"simulation",
"and",
"modeling",
"mathematics",
"research",
"and",
"ana... | 2019 | Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids over various growth conditions and cell lines |
The extracellular matrix ( ECM ) provides physical scaffolding for cellular constituents and initiates biochemical and biomechanical cues that are required for physiological activity of living tissues . The ECM enzyme ADAMTS5 , a member of the ADAMTS ( A Disintegrin-like and Metalloproteinase with Thrombospondin-1 moti... | Movement of immune cells is critical for effective clearance of pathogens . The response to influenza virus infection requires immune cell trafficking between the lung , mediastinal lymph node and other peripheral lymphoid organs such as the spleen . We set out to assess the contribution of a specific extracellular mat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"cell",
"motility",
"medicine",
"and",
"health",
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"immune",
"cells",
"immune",
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"laboratory",
"medicine",
"spleen",
"pathogens",
"immunology",
"cell-mediated",
"immunity",
"microbiology",
"orthomyxoviruses",
... | 2016 | ADAMTS5 Is a Critical Regulator of Virus-Specific T Cell Immunity |
The sea lamprey ( Petromyzon marinus ) represents one of the few vertebrate species known to undergo large-scale programmatic elimination of genomic DNA over the course of its normal development . Programmed genome rearrangements ( PGRs ) result in the reproducible loss of ~20% of the genome from somatic cell lineages ... | Lampreys possess a fascinating genome biology wherein large portions of the genome , including large numbers of genes , are programmatically deleted during development . The lamprey therefore represents a uniquely informative system with respect to several broad areas of biology , including genome stability/rearrangeme... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"anaphase",
"micronuclei",
"molecular",
"probe",
"techniques",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"microbiology",
"vertebrates",
"animals",
"lampreys",
"developmental",
"biology",
"epigenetics",
"molecular",
"biology",
"techniques",
"embryos"... | 2016 | Cellular and Molecular Features of Developmentally Programmed Genome Rearrangement in a Vertebrate (Sea Lamprey: Petromyzon marinus) |
Mimulus guttatus and M . nasutus are an evolutionary and ecological model sister species pair differentiated by ecology , mating system , and partial reproductive isolation . Despite extensive research on this system , the history of divergence and differentiation in this sister pair is unclear . We present and analyze... | While speciation is often depicted as a simple population split , in many cases it is likely more complex . Recently , whole genome sequencing and computational methods to interpret patterns of genomic variation have facilitated the inference of complex speciation histories . We present and analyze genomic data to infe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology",
"genetics",
"biology",
"and",
"life",
"sciences",
"genomics"
] | 2014 | Speciation and Introgression between Mimulus nasutus and Mimulus guttatus |
Recent attempts to examine the biological processes responsible for the general characteristics of mutualistic networks focus on two types of explanations: nonmatching biological attributes of species that prevent the occurrence of certain interactions ( “forbidden links” ) , arising from trait complementarity in mutua... | Whether they are antagonistic—as between predator and prey—or beneficial—as between pollinator and flower , interactions among all the key species in an ecosystem follow regular patterns . Connectivity ( the proportion of possible interactions that are actually realised ) , for instance , decreases with network size . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"ecology",
"evolutionary",
"biology",
"plants",
"insects"
] | 2007 | Linkage Rules for Plant–Pollinator Networks: Trait Complementarity or Exploitation Barriers? |
The accepted model of eukaryotic translation initiation begins with the scanning of the transcript by the pre-initiation complex from the 5′end until an ATG codon with a specific nucleotide ( nt ) context surrounding it is recognized ( Kozak rule ) . According to this model , ATG codons upstream to the beginning of the... | Gene translation is an important step of the intra-cellular protein synthesis , which is a central process in all living organisms . Thus , understanding how translation efficiency is encoded in transcripts has ramifications to every biomedical discipline . The aim of the current study is to decipher the way translatio... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"systems",
"biology",
"molecular",
"genetics",
"biology",
"genomics",
"evolutionary",
"biology",
"computational",
"biology"
] | 2013 | New Universal Rules of Eukaryotic Translation Initiation Fidelity |
Visceral Leishmaniasis is a deadly disease caused by Leishmania infantum , endemic in more than 98 countries across the globe . Although the most common means of transmission is via a sand fly vector , there is growing evidence that vertical transmission may be critical for maintaining L . infantum infection within the... | Canine leishmaniosis ( CanL ) is a deadly disease caused by Leishmania infantum parasite , it is found in animal populations , including people , in more than 98 countries across the globe . CanL was first identified within the US in hunting dogs 1980 and then again in 1999 when a large outbreak in a kennel in New York... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"maternal",
"health",
"obstetrics",
"and",
"gynecology",
"tropical",
"diseases",
"vertebrates",
"parasitic",
"diseases",
"dogs",
"parasitic",
"protozoans",
"animals",
"mammals",
"protozoans",
"veterinary",
"diagnostics",
"leishmani... | 2019 | Maternal Leishmania infantum infection status has significant impact on leishmaniasis in offspring |
Plant cells grown in culture exhibit genetic and epigenetic instability . Using a combination of chromatin immunoprecipitation and DNA methylation profiling on tiling microarrays , we have mapped the location and abundance of histone and DNA modifications in a continuously proliferating , dedifferentiated cell suspensi... | Cultured plant cells are genetically and epigenetically unstable . We investigated the epigenomic consequences of long-term plant cell culture and found that some genes show an increase in DNA methylation , reminiscent of immortalized animal cell lines and cancer cells . By contrast , in the heterochromatic portion of ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics"
] | 2008 | Epigenomic Consequences of Immortalized Plant Cell Suspension Culture |
Use of cholera vaccines in response to epidemics ( reactive vaccination ) may provide an effective supplement to traditional control measures . In Haiti , reactive vaccination was considered but , until recently , rejected in part due to limited global supply of vaccine . Using Bissau City , Guinea-Bissau as a case stu... | Cholera remains a major public health threat , causing 3–5 million cases and 100 , 000–120 , 000 deaths each year . In 2010 , data on vaccine performance and the changing epidemiology of cholera prompted the WHO's Strategic Advisory Group to recommend that reactive vaccination be considered in specific areas . We built... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"bacterial",
"diseases",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"cholera",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"neglected",
"tropical",
"diseases",
"spatial",
"epidemiology",
"infectious",
"disease",
"control",
... | 2012 | Urban Cholera Transmission Hotspots and Their Implications for Reactive Vaccination: Evidence from Bissau City, Guinea Bissau |
Viruses have evolved mechanisms of MHCI inhibition in order to evade recognition by cytotoxic CD8+ T cells ( CTLs ) , which is well-illustrated by our prior studies on cowpox virus ( CPXV ) that encodes potent MHCI inhibitors . Deletion of CPXV viral MHCI inhibitors markedly attenuated in vivo infection due to effects ... | The use of vaccinia virus ( VACV ) to eradicate smallpox is the arguably the most successful demonstration of vaccination . The VACV vaccine also provides cross-protection against related zoonotic orthopoxviruses , including monkey poxvirus ( MXPV ) and CPXV , which circulate between various animal hosts and humans . I... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"spleen",
"antigen-presenting",
"cells",
"immunology",
"cytotoxic",
"t",
"cells",
"antibodies",
"research",
"and",
"analysis",
"methods",
"specimen",
"preparation",
"... | 2018 | Cross-priming induces immunodomination in the presence of viral MHC class I inhibition |
HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population , thereby compromising host antiviral immunity as the epidemic progresses . To assess the extent and phenotypic impact of this phenomenon in an immunogenetically diverse population , we gen... | Upon HIV transmission , many – though not all – immune escape mutations selected in the previous host will revert to the consensus residue . The persistence of certain escape mutations following transmission has led to concerns that these could gradually accumulate in circulating HIV sequences over time , thereby under... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"sequencing",
"techniques",
"organismal",
"evolution",
"viral",
"vaccines",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"population",
"genetics",
"immunology",
"microbiology",
"immunodeficiency",
"viruses",
"mic... | 2014 | Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic |
MicroRNAs and Argonaute form the microRNA induced silencing complex or miRISC that recruits GW182 , causing mRNA degradation and/or translational repression . Despite the clear conservation and molecular significance , it is unknown if miRISC-GW182 interaction is essential for gene silencing during animal development .... | Animal cells possess different small RNA species capable of precisely controlling the gene expression . Among them , microRNAs form a silencing complex with an Argonaute protein ( known as miRISC ) that abrogates protein production by targeting specific messenger RNAs . While there is a consensus that miRISCs are effec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"invertebrates",
"protein",
"interactions",
"caenorhabditis",
"gene",
"regulation",
"animals",
"animal",
"models",
"developmental",
"biology",
"caenorhabditis",
"elegans",
"micrornas",
"model",
"organisms",
"immunoprecipitation",
"genetic",
"engineering",
"re... | 2016 | GW182-Free microRNA Silencing Complex Controls Post-transcriptional Gene Expression during Caenorhabditis elegans Embryogenesis |
Across metazoans , cell cycle progression is regulated by E2F family transcription factors that can function as either transcriptional activators or repressors . For decades , the Drosophila E2F family has been viewed as a streamlined RB/E2F network , consisting of one activator ( dE2F1 ) and one repressor ( dE2F2 ) . ... | The Drosophila E2F1 ( dE2F1 ) protein has been studied as one of the principal regulators of cell cycle control in both mitotic cells and cells undergoing a variant cell cycle called the endocycle . dE2F1 is the sole “activator” E2F of the highly streamlined Drosophila RB/E2F network . However , there has been evidence... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"animals",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"experimental",
"organism",
"systems... | 2018 | An alternatively spliced form affecting the Marked Box domain of Drosophila E2F1 is required for proper cell cycle regulation |
The tumor suppressor P53 is a critical mediator of the apoptotic response to DNA double-strand breaks through the transcriptional activation of pro-apoptotic genes . This mechanism is evolutionarily conserved from mammals to lower invertebrates , including Drosophila melanogaster . P53 also transcriptionally induces it... | Organisms have exquisitely sensitive mechanisms to detect and respond to DNA damage . If DNA damage in a cell can be repaired , then that cell may resume its normal function . In multi-cellular organisms , if a cell cannot repair DNA damage it usually undergoes programmed cell death . This prevents the proliferation of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Corp Regulates P53 in Drosophila melanogaster via a Negative Feedback Loop |
Mitochondrial DNA ( mtDNA ) is believed to be highly vulnerable to age-associated damage and mutagenesis by reactive oxygen species ( ROS ) . However , somatic mtDNA mutations have historically been difficult to study because of technical limitations in accurately quantifying rare mtDNA mutations . We have applied the ... | Owing to their evolutionary history , mitochondria harbor independently replicating genomes . Failure to faithfully transmit the genetic information of mtDNA during replication can lead to the production of dysfunctional electron transport proteins and a subsequent decline in energy production . Cellularly-derived reac... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Ultra-Sensitive Sequencing Reveals an Age-Related Increase in Somatic Mitochondrial Mutations That Are Inconsistent with Oxidative Damage |
Differentiation of the fish-borne trematodes belonging to the Opisthorchiidae , Heterophyidae and Lecithodendriidae is important from a clinical and epidemiological perspective , yet it is impossible to do using conventional coprological techniques , as the eggs are morphologically similar . Epidemiological investigati... | It is estimated that approximately 17 million people are currently infected with fish-borne flukes worldwide . The fish-borne liver flukes Opisthrochis viverrini and Clonorchis sinensis cause hepatic and biliary disease in humans . The minute intestinal flukes are widely distributed in southeast Asia and are increasing... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"microbiology/parasitology",
"infectious",
"diseases/neglected",
"tropical",
"diseases"
] | 2009 | A New PCR-Based Approach Indicates the Range of Clonorchis sinensis Now Extends to Central Thailand |
The spatial responses of many of the cells recorded in layer II of rodent medial entorhinal cortex ( MEC ) show a triangular grid pattern , which appears to provide an accurate population code for animal spatial position . In layer III , V and VI of the rat MEC , grid cells are also selective to head-direction and are ... | How do animals self-localize when they explore the environments with variable velocities ? One mechanism is dead reckoning or path-integration . Recent experiments on rodents show that such computation may be performed by grid cells in medial entorhinal cortex . Each grid cell fires strongly when the animal enters loca... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computer",
"and",
"information",
"sciences",
"cognition",
"neural",
"networks",
"computational",
"neuroscience",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"cognitive",
"science",
"neuroscience",
"learning",
"and",
"memory",
"animal",
"cognition"
] | 2014 | Continuous Attractor Network Model for Conjunctive Position-by-Velocity Tuning of Grid Cells |
Homologous recombination between the circular chromosomes of bacteria can generate chromosome dimers . They are resolved by a recombination event at a specific site in the replication terminus of chromosomes , dif , by dedicated tyrosine recombinases . The reaction is under the control of a cell division protein , FtsK... | DNA synthesis , chromosome segregation and cell division must be coordinated to ensure the stable inheritance of the genetic material during proliferation . In eukaryotes , this is achieved by their temporal separation and the existence of checkpoint mechanisms that delay certain steps until others are completed . In c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"dimers",
"(chemical",
"physics)",
"fluorescence",
"imaging",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"cell",
"cycle",
"and",
"cell",
"division",
"pathogens",
"cell",
"processes",
"vibrio",
"microbiology",
"vibrio",
"chol... | 2017 | Fast growth conditions uncouple the final stages of chromosome segregation and cell division in Escherichia coli |
During active behaviours like running , swimming , whisking or sniffing , motor actions shape sensory input and sensory percepts guide future motor commands . Ongoing cycles of sensory and motor processing constitute a closed-loop feedback system which is central to motor control and , it has been argued , for perceptu... | Animals actively exploring or interacting with their surroundings must process a cyclical flow of information from the environment through sensory receptors , the central nervous system , the musculoskeletal system and back to the environment . This closed-loop sensorimotor system is essential for an animal's ability t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"control",
"theory",
"medicine",
"and",
"health",
"sciences",
"fish",
"swimming",
"engineering",
"and",
"technology",
"membrane",
"potential",
"vertebrates",
"electrophysiology",
"social",
"sciences",
"neuroscience",
"animals",
"biological",
"locomotion",
"motor",
"neuron... | 2018 | A theory of how active behavior stabilises neural activity: Neural gain modulation by closed-loop environmental feedback |
Regulatory regions maintain nucleosome-depleted , open chromatin status but simultaneously require the presence of nucleosomes for specific histone modifications . It remains unclear how these can be achieved for proper regulatory function . Here we demonstrate that nucleosomes positioned within accessible chromatin re... | Open chromatin formation and regulation are intimately coupled with nucleosome remodelling and modification . Regulatory regions such as promoters and enhancers maintain nucleosome-free , open chromatin states whilst at the same time the presence of nucleosomes is required for specific histone modifications . In this w... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [] | 2013 | Regulation of the Boundaries of Accessible Chromatin |
Cruzain , the major cysteine protease of Trypanosoma cruzi , is an essential enzyme for the parasite life cycle and has been validated as a viable target to treat Chagas' disease . As a proof-of-concept , K11777 , a potent inhibitor of cruzain , was found to effectively eliminate T . cruzi infection and is currently a ... | Current drugs for Chagas' disease , caused by Trypanosoma cruzi infection , are limited in efficacy and are severely toxic . Hence the development of novel chemotherapeutic agents targeting T . cruzi infections is an important undertaking . In recent years , there has been considerable interest in cruzain , the major p... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"chemistry/organic",
"chemistry",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"pharmacology/drug",
"development",
"biochemistry/biomacromolecule-ligand",
"interactions",
"infectious",
"diseases/protozoal",
"infections",
"biochemistry/small",
"molecule",
"chemistry",
"... | 2010 | In Vitro and In Vivo Studies of the Trypanocidal Properties of WRR-483 against Trypanosoma cruzi |
The mechanisms by which the gain of the neuronal input-output function may be modulated have been the subject of much investigation . However , little is known of the role of dendrites in neuronal gain control . New optogenetic experimental paradigms based on spatial profiles or patterns of light stimulation offer the ... | New experimental techniques based on optogenetics allow neuronal activity to be manipulated with a high degree of spatial and temporal precision . This opens up new prospects for testing computational models of neuronal function , including questions such as the role of dendrites in neuronal gain control . However , co... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"optogenetics",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"ganglion",
"cells",
"brain",
"mapping",
"bioassays",
"and",
"physiological",
"analysis",
"neuronal",
"dendrites",
"research",
"a... | 2018 | Neuronal gain modulability is determined by dendritic morphology: A computational optogenetic study |
In West Africa , Trypanosoma brucei gambiense , causing human African trypanosomiasis ( HAT ) , is associated with a great diversity of infection outcomes . In addition to patients who can be diagnosed in the early hemolymphatic phase ( stage 1 ) or meningoencephalitic phase ( stage 2 ) , a number of individuals can mo... | Whereas immunological mechanisms involved in the control of trypanosome infections have been extensively studied in animal models , knowledge of how Trypanosoma brucei gambiense interacts with its human hosts lags far behind . In this study we measured cytokine levels in sleeping sickness patients and individuals who w... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"parasitology",
"biology",
"and",
"life",
"sciences",
"immunology"
] | 2014 | Unravelling Human Trypanotolerance: IL8 is Associated with Infection Control whereas IL10 and TNFα Are Associated with Subsequent Disease Development |
Switchgrass ( Panicum virgatum L . ) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America . To facilitate accelerated breeding programs of switchgrass , we developed both an association panel and linkage populations for genome-wide association study ( GWAS )... | Recent advances in sequencing technologies have enabled large-scale surveys of genetic diversity in model species with a wholly or partly sequenced reference genome . However , thousands of key species , which are essential for food , health , energy , and ecology , do not have reference genomes . To accelerate their b... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"genome",
"evolution",
"plant",
"biology",
"population",
"genetics",
"ploidy",
"crop",
"genetics",
"genetic",
"maps",
"algorithms",
"genome",
"sequencing",
"genome",
"analysis",
"tools",
"plant",
"science",
"linkage",
"maps",
"plant",
"genomics",
"seq... | 2013 | Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol |
High-dose chemotherapy has long been advocated as a means of controlling drug resistance in infectious diseases but recent empirical studies have begun to challenge this view . We develop a very general framework for modeling and understanding resistance emergence based on principles from evolutionary biology . We use ... | The evolution of antimicrobial resistant pathogens threatens much of modern medicine . For over one hundred years , the advice has been to ‘hit hard’ , in the belief that high doses of antimicrobials best contain resistance evolution . We argue that nothing in evolutionary theory supports this as a good rule of thumb i... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2016 | Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance? |
Understanding the relationship between brain structure and function is a fundamental problem in network neuroscience . This work deals with the general method of structure-function mapping at the whole-brain level . We formulate the problem as a topological mapping of structure-function connectivity via matrix function... | One of the major challenges in neuroscience is to understand how brain structure is related to function . In this work , we present a whole-brain method to quantify the structure-function relationship . Our data-driven approach allows the inferred functional connectivity matrix to be represented as a weighted sum of th... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"diagnostic",
"radiology",
"functional",
"magnetic",
"resonance",
"imaging",
"neural",
"networks",
"signaling",
"networks",
"neuroscience",
"magnetic",
"resonance",
"imaging",
"brain",
"morphometry",
"cognitive",
"neuroscience",
"b... | 2017 | Structure-Function Network Mapping and Its Assessment via Persistent Homology |
Trypanosome lytic factor ( TLF ) is a high-density lipoprotein ( HDL ) subclass providing innate protection to humans against infection by the protozoan parasite Trypanosoma brucei brucei . Two primate-specific plasma proteins , haptoglobin-related protein ( Hpr ) and apolipoprotein L-1 ( ApoL-1 ) , have been proposed ... | African trypanosomes are parasites that can infect a wide range of mammals , including domestic animals and humans . Several hundred thousand humans are infected with African sleeping sickness , but this number would be much higher if not for a natural defense molecule found in human blood . The trypanosome lytic facto... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"infectious",
"diseases",
"in",
"vitro",
"immunology",
"eukaryotes",
"molecular",
"biology"
] | 2007 | Hemoglobin Is a Co-Factor of Human Trypanosome Lytic Factor |
The soil-dwelling bacillus Burkholderia pseudomallei is the etiological-agent of the neglected and life-threatening emerging infection melioidosis . The distribution of B . pseudomallei in West Africa is unknown . In the present study we aimed to determine whether B . pseudomallei and B . thailandensis are present in t... | The environmental bacterium Burkholderia pseudomallei is the cause of melioidosis , an often-fatal but neglected infection prevalent across tropical areas . B . thailandensis is a member of the B . pseudomallei complex , rarely causes disease in humans and is considered a-virulent . Modelling studies have estimated a h... | [
"Abstract",
"Introduction",
"Methods",
"Results/Discussion"
] | [
"taxonomy",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"burkholderia",
"pseudomallei",
"pathogens",
"melioidosis",
"burkholderia",
"infection",
"geographical",
"locations",
"microbiology",
"bacterial",
"diseases",
"phylogenetics",
... | 2019 | Identification of Burkholderia thailandensis with novel genotypes in the soil of central Sierra Leone |
Many picornaviruses cause important diseases in humans and other animals including poliovirus , rhinoviruses ( causing the common cold ) and foot-and-mouth disease virus ( FMDV ) . These small , non-enveloped viruses comprise a positive-stranded RNA genome ( ca . 7–9 kb ) enclosed within a protein shell composed of 60 ... | The picornavirus family includes clinically important human and animal pathogens , for example: poliovirus , rhinovirus ( causing the common cold ) and foot-and-mouth disease virus ( FMDV ) that infects cloven-hoofed animals . Picornaviruses contain a positive-sense RNA genome surrounded by a protein shell , also calle... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"serum",
"animal",
"diseases",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"foot",
"and",
"mouth",
"disease",
"microbiology",
"precursor",
"cells",
"vertebrates",
"animals",
"mammals",
"viruses",
"animal",
"models",
"rna",
"viruses",
"experim... | 2019 | Identification of a short, highly conserved, motif required for picornavirus capsid precursor processing at distal sites |
Onchocerciasis in Yemen is one of the most neglected diseases , where baseline estimates of onchocerciasis and monitoring of the impact of ivermectin regularly administered to the affected individuals on its transmission are lacking . Therefore , this study aimed to determine the anti-Ov16 IgG4 seroprevalence among loc... | Onchocerciasis is endemic in certain foci in the western governorates of Yemen . Monitoring the impact of the regular ivermectin administration to affected individuals on the transmission status and providing baseline onchocerciasis estimates in endemic areas are crucial for planning effective elimination strategies . ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"children",
"medicine",
"and",
"health",
"sciences",
"pruritus",
"onchocerca",
"volvulus",
"pathology",
"and",
"laboratory",
"medicine",
"helminths",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"parasitic",
"diseases",
"anim... | 2018 | Onchocerca volvulus infection in Tihama region - west of Yemen: Continuing transmission in ivermectin-targeted endemic foci and unveiled endemicity in districts with previously unknown status |
The brain contains a complex network of axons rapidly communicating information between billions of synaptically connected neurons . The morphology of individual axons , therefore , defines the course of information flow within the brain . More than a century ago , Ramón y Cajal proposed that conservation laws to save ... | Within the grey matter of cerebral cortex is a complex network formed by a dense tangle of individual branching axons mostly of cortical origin . Yet remarkably when presented with a barrage of complex , noisy sensory stimuli this convoluted network architecture computes accurately and rapidly . How does such a highly ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience/cognitive",
"neuroscience",
"neuroscience/theoretical",
"neuroscience",
"neuroscience/sensory",
"systems",
"physiology/sensory",
"systems",
"computational",
"biology/computational",
"neuroscience",
"physiology/morphogenesis",
"and",
"cell",
"biology",
"computational",
"... | 2010 | Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation |
Identifying microbial pathogens with zoonotic potential in wild-living primates can be important to human health , as evidenced by human immunodeficiency viruses types 1 and 2 ( HIV-1 and HIV-2 ) and Ebola virus . Simian foamy viruses ( SFVs ) are ancient retroviruses that infect Old and New World monkeys and apes . Al... | Cross-species transmissions of infectious agents from primates to humans have led to major disease outbreaks , with AIDS representing a particularly serious example . It has recently been shown that humans who hunt primates frequently acquire simian foamy virus ( SFV ) infections . Thus , these viruses have been propos... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious",
"diseases/hiv",
"infection",
"and",
"aids",
"microbiology/microbial",
"evolution",
"and",
"genomics",
"ecology/evolutionary",
"ecology"
] | 2008 | Molecular Ecology and Natural History of Simian Foamy Virus Infection in Wild-Living Chimpanzees |
Although immunopathology dictates clinical outcome in leprosy , the dynamics of early and chronic infection are poorly defined . In the tuberculoid region of the spectrum , Mycobacterium leprae growth is restricted yet a severe granulomatous lesion can occur . The evolution and maintenance of chronic inflammatory proce... | Despite effective antimicrobial therapy , 30–50% of leprosy patients develop immunological complications called leprosy reactions before , during or even years after being cured . Leprosy reactions are a major risk for neuritis that leads to peripheral nerve damage , disfigurement and disability . Unfortunately , why a... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"intracellular",
"pathogens",
"pathogens",
"tropical",
"diseases",
"microbiology",
"bacterial",
"diseases",
"population",
"modeling",
"neglected",
"tropical",
"diseases",
"bacterial",
"... | 2014 | IL-10 and NOS2 Modulate Antigen-Specific Reactivity and Nerve Infiltration by T Cells in Experimental Leprosy |
Scabies and skin infections are endemic in many Australian Aboriginal communities . There is limited evidence for effective models of scabies treatment in high prevalence settings . We aimed to assess the level of treatment uptake amongst clinically diagnosed scabies cases and amongst their household contacts . In addi... | Like many impoverished areas around the world , Aboriginal communities in Australia experience an unacceptably high burden of scabies , skin infections , and secondary complications . Young children are most at risk . Our study investigated scabies in a remote setting with very high rates of skin disease , a high level... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"pediatrics",
"and",
"child",
"health",
"public",
"health",
"and",
"epidemiology/global",
"health",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"infectious",
"diseases/skin",
"infections"
] | 2009 | Community Management of Endemic Scabies in Remote Aboriginal Communities of Northern Australia: Low Treatment Uptake and High Ongoing Acquisition |
The AraC family transcription factor MarA activates ∼40 genes ( the marA/soxS/rob regulon ) of the Escherichia coli chromosome resulting in different levels of resistance to a wide array of antibiotics and to superoxides . Activation of marA/soxS/rob regulon promoters occurs in a well-defined order with respect to the ... | When environmental conditions change , cell survival can depend on sudden production of proteins that are normally in low demand . Protein production is controlled by transcription factors which bind to DNA near genes and either increase or decrease RNA production . Many puzzles remain concerning the ways transcription... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biophysics/transcription",
"and",
"translation",
"molecular",
"biology/transcription",
"initiation",
"and",
"activation",
"computational",
"biology/transcriptional",
"regulation"
] | 2009 | Model of Transcriptional Activation by MarA in Escherichia coli |
The xanthophyll cycle is involved in dissipating excess light energy to protect the photosynthetic apparatus in a process commonly assessed from non-photochemical quenching ( NPQ ) of chlorophyll fluorescence . Here , it is shown that the xanthophyll cycle is modulated by the necrotrophic pathogen Sclerotinia sclerotio... | In recent years , the role of the chloroplast in the defense against microbes has been intensively investigated and is of high interest to both plant-microbe interaction and photosynthesis research . The xanthophyll cycle is well known to be involved in dissipating excess light energy to protect the photosynthetic appa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Manipulation of the Xanthophyll Cycle Increases Plant Susceptibility to Sclerotinia sclerotiorum |
No efficient vaccine against plague is currently available . We previously showed that a genetically attenuated Yersinia pseudotuberculosis producing the Yersinia pestis F1 antigen was an efficient live oral vaccine against pneumonic plague . This candidate vaccine however failed to confer full protection against bubon... | Yersinia pestis , the agent of plague , is among the deadliest infectious agents affecting humans . Injected in the skin by infected fleas , Y . pestis causes bubonic plague , which occasionally evolves into the very lethal and contagious pneumonic plague . Y . pestis is also a dangerous potential bioweapon but no plag... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Complete Protection against Pneumonic and Bubonic Plague after a Single Oral Vaccination |
The rich dynamical nature of neurons poses major conceptual and technical challenges for unraveling their nonlinear membrane properties . Traditionally , various current waveforms have been injected at the soma to probe neuron dynamics , but the rationale for selecting specific stimuli has never been rigorously justifi... | Neurons perform complicated non-linear transformations on their input before producing their output - a train of action potentials . This input-output transformation is shaped by the specific composition of ion channels , out of the many possible types , that are embedded in the neuron's membrane . Experimentally , cha... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cellular",
"neuroscience",
"computational",
"neuroscience",
"single",
"neuron",
"function",
"biology",
"neuroscience"
] | 2011 | Effective Stimuli for Constructing Reliable Neuron Models |
Many of the lipids found on the cuticles of insects function as pheromones and communicate information about age , sex , and reproductive status . In Drosophila , the composition of the information-rich lipid profile is dynamic and changes over the lifetime of an individual . However , the molecular basis of this chang... | Pheromones are used by many animals to control social behaviors such as mate choice and kin recognition . The pheromone profile of insects is dynamic and can change depending on environmental , physiological , and social conditions . While many genes responsible for the biosynthesis of insect pheromones have been ident... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"chemical",
"compounds",
"organic",
"compounds",
"age",
"groups",
"developmental",
"biology",
"adults",
"steroids",
"lipid",
"signaling",
"lipids",
"chemistry",
"people",
"and",
"places",
"biochemistry",
"signal",
"transduction",
"organic",
"chemistry",
"cell",
"biology... | 2016 | Steroid Hormone Signaling Is Essential for Pheromone Production and Oenocyte Survival |
Mass drug administration ( MDA ) of ivermectin has become the main intervention to control onchocerciasis or “river blindness” . In Togo , after many years of MDA , Onchocerca volvulus infection has declined dramatically , and elimination appears achievable , but in certain river basins the current situation remains un... | Mass drug administration ( MDA ) with ivermectin has become the main tool in the efforts to control and eliminate onchocerciasis ( “river blindness” ) . In some areas , and after many years of MDA , levels of Onchocerca volvulus infection ( the causative parasite ) have declined greatly , and elimination appears achiev... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"onchocerca",
"volvulus",
"rivers",
"helminths",
"keratitis",
"tropical",
"diseases",
"geographical",
"locations",
"parasitic",
"diseases",
"animals",
"onchocerca",
"a... | 2018 | Onchocerca volvulus infection and serological prevalence, ocular onchocerciasis and parasite transmission in northern and central Togo after decades of Simulium damnosum s.l. vector control and mass drug administration of ivermectin |
Stimulator of interferon genes ( STING , also known as MITA , ERIS or MPYS ) induces the activation of TBK1 kinase and IRF3 transcription factor , upon sensing of microbial DNAs . How IRF3 is recruited onto the STING signalosome remains unknown . We report here that silencing of the ER adaptor SCAP markedly impairs the... | The stimulator of interferon genes ( STING/MITA/ERIS/MPYS ) is characterized as the converging point of the cytosolic DNAs-triggered innate immune signaling , and its function has been well documented in mediating the production of type I interferon and other pro-inflammatory cytokines . It remains intriguing to addres... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"transfection",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"microbiology",
"light",
"microscopy",
"immunoprecipitation",
"microscopy",
"signalosomes",
"confocal",
"microscopy",
"molecular",
"biol... | 2016 | ER Adaptor SCAP Translocates and Recruits IRF3 to Perinuclear Microsome Induced by Cytosolic Microbial DNAs |
Deneddylases remove the ubiquitin-like protein Nedd8 from modified proteins . An increased deneddylase activity has been associated with various human cancers . In contrast , we show here that a mutant strain of the model fungus Aspergillus nidulans deficient in two deneddylases is viable but can only grow as a filamen... | The family of small ubiquitin-like ( Ubl ) proteins plays a major role in the control of stability , activity , or localization of modified target proteins in a eukaryotic cell . Lysine side chains are modified by covalent Ubl attachment , and this process can be reversed by specific proteases . Nedd8 is the closest re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cellular",
"stress",
"responses",
"genetic",
"mutation",
"microbiology",
"gene",
"function",
"aspergillus",
"nidulans",
"eukaryotic",
"cells",
"model",
"organisms",
"cell",
"growth",
"molecular",
"genetics",
"gene",
"expression",
"biology",
"systems",
"biology",
"bioch... | 2013 | Control of Multicellular Development by the Physically Interacting Deneddylases DEN1/DenA and COP9 Signalosome |
Severe influenza A virus infection causes high mortality and morbidity worldwide due to delayed antiviral treatment and inducing overwhelming immune responses , which contribute to immunopathological lung injury . Sirolimus , an inhibitor of mammalian target of rapamycin ( mTOR ) , was effective in improving clinical o... | The severity and lethality of influenza A virus infection are frequently aggravated by virus-induced tissue destruction and overwhelming immune responses . Combined therapy with antiviral medications and immunomodulators , which not only inhibit viral replication , but also reduce the damaging consequences of host immu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"respiratory",
"infections",
"influenza",
"immunology",
"pulmonology",
"animal",
"models",
"developmental",
"biology",... | 2018 | Delayed oseltamivir plus sirolimus treatment attenuates H1N1 virus-induced severe lung injury correlated with repressed NLRP3 inflammasome activation and inflammatory cell infiltration |
Cryptococcus neoformans is a ubiquitous human fungal pathogen that causes meningoencephalitis in predominantly immunocompromised hosts . The fungus is typically haploid , and sexual reproduction involves two individuals with opposite mating types/sexes , α and a . However , the overwhelming predominance of mating type ... | Cryptococcus neoformans is a major cause of fungal meningitis , predominantly in immunocompromised individuals . This fungus has two mating types/sexes , a and α , and mating typically requires two individuals with opposite mating types . It is mysterious why the α mating type is overwhelmingly predominant in nature an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"developmental",
"biology",
"infectious",
"diseases",
"cell",
"biology",
"yeast",
"and",
"fungi",
"microbiology",
"evolutionary",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2007 | αADα Hybrids of Cryptococcus neoformans: Evidence of Same-Sex Mating in Nature and Hybrid Fitness |
Information processing in neural networks depends on the connectivity among excitatory and inhibitory neurons . The presence of parallel , distinctly controlled local circuits within a cortical network may ensure an effective and dynamic regulation of microcircuit function . By applying a combination of optogenetics , ... | The perisomatic region of neurons refers collectively to the membrane surface of the cell body or soma , proximal dendrites , and axon initial segment . This is a unique functional domain in which the activity of a neuron can be controlled in the most effective manner . In the cerebral cortex , the perisomatic region o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"nervous",
"system",
"membrane",
"potential",
"brain",
"electrophysiology",
"light",
"neuroscience",
"electromagnetic",
"radiation",
"nerve",
"fibers",
"interneurons",
"neuronal",
"dendrites",
"animal",
"cel... | 2017 | Differential excitatory control of 2 parallel basket cell networks in amygdala microcircuits |
The robust computational design of functional proteins has the potential to deeply impact translational research and broaden our understanding of the determinants of protein function and stability . The low success rates of computational design protocols and the extensive in vitro optimization often required , highligh... | The ability to use computational tools to manipulate the structure and function of proteins has the potential to impact many facets of fundamental and translational science . Due to our limited understanding of the principles that govern protein function and structure , the computational design of functional proteins r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods",
"Availability"
] | [
"crystal",
"structure",
"markov",
"models",
"engineering",
"and",
"technology",
"synthetic",
"biology",
"condensed",
"matter",
"physics",
"synthetic",
"bioengineering",
"mathematics",
"protein",
"structure",
"sequence",
"motif",
"analysis",
"macromolecular",
"design",
"cr... | 2018 | Rosetta FunFolDes – A general framework for the computational design of functional proteins |
Differences in gene expression between individual cells can be mediated by epigenetic regulation; thus , methods that enable detailed analyses of single cells are crucial to understanding this phenomenon . In this study , genomic silencing regions of Saccharomyces cerevisiae that are subject to epigenetic regulation , ... | Although eukaryotic gene repression usually acts on individual genes , cells can also repress larger chromosomal regions via the establishment of a high order chromatin structure called heterochromatin . Once initiated , heterochromatin spreads until halted by a boundary , and in this study we focus on how this boundar... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"gene",
"expression",
"genetics",
"epigenetics",
"biology",
"chromatin",
"histone",
"modification"
] | 2013 | Single Cell Visualization of Yeast Gene Expression Shows Correlation of Epigenetic Switching between Multiple Heterochromatic Regions through Multiple Generations |
Schistosomiasis is a water-related neglected tropical disease . In many endemic low- and middle-income countries , insufficient surveillance and reporting lead to poor characterization of the demographic and geographic distribution of schistosomiasis cases . Hence , modeling is relied upon to predict areas of high tran... | Schistosomiasis is a water-related neglected tropical disease that disproportionately affects school-aged children in poor communities of low- and middle-income countries . Schistosomiasis transmission risk is affected by environmental , socioeconomic , and behavioral factors , including water , sanitation , and hygien... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"surface",
"water",
"education",
"helminths",
"sociology",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"parasitic",
"diseases",
"animals",
"health",
"care",
"data",
"... | 2018 | Improving spatial prediction of Schistosoma haematobium prevalence in southern Ghana through new remote sensors and local water access profiles |
Prokaryotic transcription factors ( TFs ) that bind small xenobiotic molecules ( e . g . , TFs that drive genes that respond to environmental pollutants ) often display a promiscuous effector profile for analogs of the bona fide chemical signals . XylR , the master TF for expression of the m-xylene biodegradation opero... | It is generally taken for granted that promoters regulated by transcriptional factors ( TFs ) that respond to small molecules control their specificity to given effectors by tightening or relaxing the intrinsic dual interaction between the TF and the particular inducer . One such promoter is Pu , which drives expressio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"systems",
"biology",
"environmental",
"biotechnology",
"microbial",
"evolution",
"gene",
"expression",
"genetics",
"synthetic",
"biology",
"biology",
"microbiology",
"gene",
"networks",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Increasing Signal Specificity of the TOL Network of Pseudomonas putida mt-2 by Rewiring the Connectivity of the Master Regulator XylR |
Salicylic acid ( SA ) -induced defense responses are important factors during effector triggered immunity and microbe-associated molecular pattern ( MAMP ) -induced immunity in plants . This article presents evidence that a member of the Arabidopsis CBP60 gene family , CBP60g , contributes to MAMP-triggered SA accumula... | Plants respond to attack by microbial pathogens through activation of a battery of defense responses . This activation is controlled by a complex signaling network . Disease resistance depends on rapid activation of plant defense responses . Improved understanding of the signaling network may lead to development of cro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/gene",
"function",
"genetics",
"and",
"genomics/plant",
"genetics",
"and",
"gene",
"expression",
"genetics",
"and",
"genomics/gene",
"expression"
] | 2009 | Arabidopsis CaM Binding Protein CBP60g Contributes to MAMP-Induced SA Accumulation and Is Involved in Disease Resistance against Pseudomonas syringae |
Proteins are involved in almost all functions in a living cell , and functions of proteins are realized by their tertiary structures . Obtaining a global perspective of the variety and distribution of protein structures lays a foundation for our understanding of the building principle of protein structures . In light o... | Proteins are the major molecules involved in almost all cellular processes . In this work , we present a novel mapping of protein shapes that represents the variety and the similarities of 3D shapes of proteins and their assemblies . This mapping provides various novel insights into protein shapes including determinant... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2019 | A global map of the protein shape universe |
Neural progenitor cells ( NPCs ) , which are apicobasally elongated and densely packed in the developing brain , systematically move their nuclei/somata in a cell cycle–dependent manner , called interkinetic nuclear migration ( IKNM ) : apical during G2 and basal during G1 . Although intracellular molecular mechanisms ... | The development of large brain structures , such as the mammalian cerebral cortex , depends on the continuous and efficient production of cells by neural progenitor cells . Neural progenitor cells are elongated and span the developing brain wall . The nuclei and bodies of these cells move cyclically between the apical ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"g1",
"phase",
"classical",
"mechanics",
"engineering",
"and",
"technology",
"cell",
"cycle",
"and",
"cell",
"division",
"lasers",
"cell",
"processes",
"g2",
"phase",
"mechanical",
"energy",
"molecular",
"motors",
"actin",
"motors",
"stem",
"cells",
"microscopy",
... | 2018 | Elasticity-based boosting of neuroepithelial nucleokinesis via indirect energy transfer from mother to daughter |
Ethylene is the main regulator of climacteric fruit ripening , by contrast the putative role of other phytohormones in this process remains poorly understood . The present study brings auxin signaling components into the mechanism regulating tomato fruit ripening through the functional characterization of Auxin Respons... | The plant hormone ethylene is regarded as the major regulator of fruit ripening but the putative role of other hormones remains elusive . Auxin Response Factors ( ARFs ) are transcriptional regulators modulating the expression of auxin-response genes shown recently to play a primary role in regulating fruit set in toma... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato |
Cutaneous leishmaniasis ( CL ) is caused by Leishmania infection of dermal macrophages and is associated with chronic inflammation of the skin . L . aethiopica infection displays two clinical manifestations , firstly ulcerative disease , correlated to a relatively low parasite load in the skin , and secondly non-ulcera... | Cutaneous leishmaniases are associated with parasite-induced inflammatory lesions of the skin . The degree of clinical pathology is not associated with parasitic burden; on the contrary , ulcerative lesions are associated with low infectious load , and non-ulcerative lesions are associated with an abundant parasite inf... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"and",
"Discussion"
] | [
"immunology/immunomodulation",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"dermatology/skin",
"infections",
"infectious",
"diseases/skin",
"infections",
"microbiology/parasitology",
"infectious",
"diseases/protozoal",
"infections"
] | 2010 | Systemic FasL and TRAIL Neutralisation Reduce Leishmaniasis Induced Skin Ulceration |
Amphiphysin 2 , encoded by BIN1 , is a key factor for membrane sensing and remodelling in different cell types . Homozygous BIN1 mutations in ubiquitously expressed exons are associated with autosomal recessive centronuclear myopathy ( CNM ) , a mildly progressive muscle disorder typically showing abnormal nuclear cent... | The intracellular organization of muscle fibers relies on a complex membrane system important for muscle structural organization , maintenance , contraction , and resistance to stress . Amphiphysin 2 , encoded by BIN1 , plays a central role in membrane sensing and remodelling and is involved in intracellular membrane t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"types",
"animal",
"genetics",
"genetic",
"mutation",
"gene",
"function",
"animal",
"models",
"histology",
"model",
"organisms",
"molecular",
"genetics",
"veterinary",
"science",
"gene",
"splicing",
"membranes",
"and",
"sorting",
"biology",
"veterinary",
"pa... | 2013 | Altered Splicing of the BIN1 Muscle-Specific Exon in Humans and Dogs with Highly Progressive Centronuclear Myopathy |
Existing theories of movement planning suggest that it takes time to select and prepare the actions required to achieve a given goal . These theories often appeal to circumstances where planning apparently goes awry . For instance , if reaction times are forced to be very low , movement trajectories are often directed ... | Two critical processes need to occur before a movement can be made: identification of the goal of the movement and selection and preparation of the motor commands that will be sent to muscles to generate the movement—in other words , what movement to make , and how to make it . It has long been thought that preparing m... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision |
Immunocompromised individuals tend to suffer from influenza longer with more serious complications than otherwise healthy patients . Little is known about the impact of prolonged infection and the efficacy of antiviral therapy in these patients . Among all 189 influenza A virus infected immunocompromised patients admit... | Immunocompromised patients , such as transplant recipients on immune suppressive therapy , are a substantial and gradually expanding patient group . Upon influenza virus infection , these patients clear the virus less efficiently and are more likely to develop severe pneumonia than immunocompetent individuals . Existin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"influenza",
"medicine",
"infectious",
"diseases",
"viral",
"diseases"
] | 2013 | Prolonged Influenza Virus Shedding and Emergence of Antiviral Resistance in Immunocompromised Patients and Ferrets |
Mutations in or dys-regulation of the TDP-43 gene have been associated with TDP-43 proteinopathy , a spectrum of neurodegenerative diseases including Frontotemporal Lobar Degeneration ( FTLD ) and Amyotrophic Lateral Sclerosis ( ALS ) . The underlying molecular and cellular defects , however , remain unclear . Here , w... | TDP-43 proteinopathy is a group of fatal neurological diseases . Here , we report a systematic examination of the role of mitochondrial damage in TDP-43 proteinopathy using patient brain tissues , as well as cellular and animal models . Our data show that TDP-43 induces severe mitochondrial damage , accompanied by acti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"brain",
"damage",
"enzymes",
"enzymology",
"toxicology",
"animal",
"models",
"microscopy",
"experimental",
"organism",
"systems",
"mitochondria",
"bioenergetics",
"cellular",
"structur... | 2019 | TDP-43 induces mitochondrial damage and activates the mitochondrial unfolded protein response |
NK cells are important antiviral effectors , highly enriched in the liver , with the potential to regulate immunopathogenesis in persistent viral infections . Here we examined whether changes in the NK pool are induced when patients with eAg-positive CHB are ‘primed’ with PegIFNα and importantly , whether these changes... | Current therapies for CHB are limited in achieving HBsAg decline and loss leading to a cure . Although PegIFNα may be used , the majority of patients progress to NUC therapy due to treatment failure . PegIFNα and NUCs used in isolation act differentially on the immune response; PegIFNα induces NK cell activation and NU... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"antiviral",
"therapy",
"immunology",
"liver",
"diseases",
"preventive",
"medicine",
"infectious",
"hepatitis",
"hepatitis",
"gastroenterology",
"and",
"hepatology",
"cytotoxic",
"t",
"cells",... | 2016 | Interferon Alpha Induces Sustained Changes in NK Cell Responsiveness to Hepatitis B Viral Load Suppression In Vivo |
Osteogenesis Imperfecta ( OI ) is a human syndrome characterized by exquisitely fragile bones due to osteoporosis . The majority of autosomal dominant OI cases result from point or splice site mutations in the type I collagen genes , which are thought to lead to aberrant osteoid within developing bones . OI also occurs... | Osteogenesis Imperfecta ( OI ) , also known as “brittle bone disease , ” is an inherited condition with multiple defects in collagen-containing structures , including the bones , skin , and other connective tissues . Patients with OI suffer from short stature , scoliosis , thin skin , hearing loss , and , most notably ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"diabetes",
"and",
"endocrinology/bone",
"and",
"mineral",
"metabolism",
"cell",
"biology/extra-cellular",
"matrix",
"biochemistry/protein",
"folding",
"cell",
"biology/developmental",
"molecular",
"mechanisms"
] | 2009 | Severe Osteogenesis Imperfecta in Cyclophilin B–Deficient Mice |
Most Cryptococccus neoformans genes are interrupted by introns , and alternative splicing occurs very often . In this study , we examined the influence of introns on C . neoformans gene expression . For most tested genes , elimination of introns greatly reduces mRNA accumulation . Strikingly , the number and the positi... | Cryptococcus neoformans is a major human pathogen responsible for deadly infection in immunocompromised patients . The analysis of its genome previously revealed that most of its genes are interrupted by introns . Here , we demonstrate that introns modulate gene expression in a cumulative manner . We also demonstrate t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mycology",
"fungi",
"rna",
"processing",
"genetic",
"screens",
"medical",
"microbiology",
"gene",
"identification",
"and",
"analysis",
"gene",
"expression",
"genetics",
"gene",
"regulation",
"molecular",
"genetics",
"gene",
"splicing",
"biology",
"microbiology",
"micro... | 2013 | Introns Regulate Gene Expression in Cryptococcus neoformans in a Pab2p Dependent Pathway |
Cell signaling underlies transcription/epigenetic control of a vast majority of cell-fate decisions . A key goal in cell signaling studies is to identify the set of kinases that underlie key signaling events . In a typical phosphoproteomics study , phosphorylation sites ( substrates ) of active kinases are quantified p... | A key goal in cell signaling studies is to identify the set of kinases that underlie key signaling events . Mass spectrometry-based technologies have emerged as a powerful tool to profile proteome-wide phosphorylation events in vivo at a single amino acid resolution with high precision . However , development of algori... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data |
Meiosis halves the chromosome number because its two divisions follow a single round of DNA replication . This process involves two cell transitions , the transition from prophase to the first meiotic division ( meiosis I ) and the unique meiosis I to meiosis II transition . We show here that the A-type cyclin CYCA1;2/... | In the life cycle of sexual organisms , a specialized cell division—meiosis—reduces the number of chromosomes from two sets ( 2n , diploid ) to one set ( n , haploid ) , while fertilization restores the original chromosome number . Meiosis reduces ploidy because it consists of two divisions following a single DNA repli... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/gene",
"discovery",
"biotechnology/plant",
"biotechnology",
"cell",
"biology/cell",
"growth",
"and",
"division",
"genetics",
"and",
"genomics/gene",
"function",
"genetics",
"and",
"genomics/plant",
"genomes",
"and",
"evolution"
] | 2010 | The CYCLIN-A CYCA1;2/TAM Is Required for the Meiosis I to Meiosis II Transition and Cooperates with OSD1 for the Prophase to First Meiotic Division Transition |
Variability in motor performance results from the interplay of error correction and neuromotor noise . This study examined whether visual amplification of error , previously shown to improve performance , affects not only error correction , but also neuromotor noise , typically regarded as inaccessible to intervention ... | It is widely recognized that neuromotor noise limits human motor performance , generating errors and variability even in highly skilled performers . Arising from many spatiotemporal scales within the physiological system , the intrinsic noise component is commonly assumed to be invariant by most computational models of... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"learning",
"medicine",
"and",
"health",
"sciences",
"engineering",
"and",
"technology",
"signal",
"processing",
"limbs",
"(anatomy)",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"noise",
"reduction",
"regression",
"analysis",
"cognitive",
"psycho... | 2016 | Neuromotor Noise Is Malleable by Amplifying Perceived Errors |
We have previously shown that the Mycobacterium tuberculosis universal stress protein Rv2623 regulates mycobacterial growth and may be required for the establishment of tuberculous persistence . Here , yeast two-hybrid and affinity chromatography experiments have demonstrated that Rv2623 interacts with one of the two f... | Mycobacterium tuberculosis remains a significant public health burden worldwide . The tubercle bacillus can establish a clinically silent latent infection in the host , which can subsequently reactivate to cause diseases , resulting in transmission of the pathogen . We have previously shown that the M . tuberculosis un... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"yeast",
"two-hybrid",
"assays",
"protein",
"interactions",
"chemical",
"compounds",
"threonine",
"organic",
"compounds",
"protein",
"interaction",
"assays",
"amino",
"acids",
"molecular",
"biology",
"techniques",
"gel",
"electrophoresis",
"bacteria",
"... | 2017 | Mycobacterium tuberculosis universal stress protein Rv2623 interacts with the putative ATP binding cassette (ABC) transporter Rv1747 to regulate mycobacterial growth |
The Bacillus subtilis recH342 strain , which decreases interspecies recombination without significantly affecting the frequency of transformation with homogamic DNA , carried a point mutation in the putative recX ( yfhG ) gene , and the mutation was renamed as recX342 . We show that RecX ( 264 residues long ) , which s... | This study describes mechanisms employed by the bacterium Bacillus subtilis to survive DNA damages by recombinational repair ( RR ) and to provide genetic variation via genetic recombination ( GR ) . At the center of homologous recombination ( HR ) is the recombinase RecA , which forms RecA·ssDNA filaments to mediate S... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"molecular",
"cell",
"biology",
"nucleic",
"acids",
"genetics",
"dna",
"biology",
"dna",
"repair",
"molecular",
"genetics",
"population",
"genetics",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | RecX Facilitates Homologous Recombination by Modulating RecA Activities |
Progress in mapping loci associated with common complex diseases or quantitative inherited traits has been expedited by large-scale meta-analyses combining information across multiple studies , assembled through collaborative networks of researchers . Participating studies will usually have been independently designed ... | Meta-analysis of genome-wide association studies ( GWAS ) is a valuable tool for the discovery of genes that protect or predispose individuals to common complex diseases . It can though be hampered by excessive heterogeneity among its participating studies . To date , the impact of heterogeneity is assessed locally on ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"sociology",
"social",
"sciences",
"epidemiological",
"methods",
"and",
"statistics",
"coronary",
"heart",
"disease",
"mathematics",
"statistics",
"(mathematics)",
"genome",
"analysis",
"res... | 2017 | Identifying systematic heterogeneity patterns in genetic association meta-analysis studies |
Intracellular pathogens have evolved diverse strategies to invade and survive within host cells . Among the most studied facultative intracellular pathogens , Listeria monocytogenes is known to express two invasins-InlA and InlB-that induce bacterial internalization into nonphagocytic cells . The pore-forming toxin lis... | Listeria monocytogenes is responsible for the severe foodborne disease listeriosis . During pathogenesis , invasion of nonphagocytic cells by L . monocytogenes is crucial for crossing the host epithelial barriers and colonization of multiple organs including the liver . In this study , we investigated the role of the p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"microbiology",
"molecular",
"cell",
"biology"
] | 2011 | The Pore-Forming Toxin Listeriolysin O Mediates a Novel Entry Pathway of L. monocytogenes into Human Hepatocytes |
RNA interference ( RNAi ) is a powerful tool for post-transcriptional gene silencing . However , the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA ( miRNA ) silencing . To better understand these off-target effects , we inve... | Small interfering RNAs ( siRNAs ) are double stranded RNA molecules designed to perfectly match the sequence of a target gene and silence its expression . The function is exerted through the RNA interference ( RNAi ) pathway and has revolutionised biological research due to its ease-of-use and high potency . While siRN... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects |
The deregulation of metabolism is a hallmark of aging . As such , changes in the expression of metabolic genes and the profiles of amino acid levels are features associated with aging animals . We previously reported that the levels of most amino acids decline with age in Caenorhabditis elegans ( C . elegans ) . Glycin... | There is a growing number of studies showing that amino acids function as signal metabolites that influence aging and health . Although contemporary -OMICs studies have uncovered various associations between metabolite levels and aging , in many cases the directionality of the relationships is unclear . In a recent met... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"rna",
"interference",
"chemical",
"compounds",
"aliphatic",
"amino",
"acids",
"caenorhabditis",
"organic",
"compounds",
"animals",
"animal",
"models",
"caenorhabditis",
"elegans",
"model",
"organisms",
"serine",
"experimental",
"organism",
"systems",
"am... | 2019 | Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion |
In neurogenesis , neural cell fate specification is generally triggered by proneural transcription factors . Whilst the role of proneural factors in fate specification is well studied , the link between neural specification and the cellular pathways that ultimately must be activated to construct specialised neurons is ... | Early during development , cells differentiate and take on specialized forms and functions . This requires the activation of specific genes for different cellular pathways . Our study addresses how this activation is regulated in the developing Drosophila nervous system . In this model , it is well known that proneural... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/cell",
"differentiation",
"neuroscience/neurodevelopment",
"developmental",
"biology/neurodevelopment",
"developmental",
"biology/developmental",
"molecular",
"mechanisms",
"cell",
"biology/gene",
"expression"
] | 2011 | The Gene Regulatory Cascade Linking Proneural Specification with Differentiation in Drosophila Sensory Neurons |
Viruses rely on the metabolic network of the host cell to provide energy and macromolecular precursors to fuel viral replication . Here we used mass spectrometry to examine the impact of two related herpesviruses , human cytomegalovirus ( HCMV ) and herpes simplex virus type-1 ( HSV-1 ) , on the metabolism of fibroblas... | Enveloped viruses draw on cellular machinery and materials to generate copies of their genome , structural proteins , and membrane . These biosynthetic processes use the host metabolic network to provide energy and small-molecule precursors . We have investigated how two important enveloped viruses , human cytomegalovi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"virology",
"biology",
"microbiology",
"metabolism"
] | 2011 | Divergent Effects of Human Cytomegalovirus and Herpes Simplex Virus-1 on Cellular Metabolism |
The World Health Organization ( WHO ) advises treatment of Mycobacterium ulcerans disease , also called “Buruli ulcer” ( BU ) , with a combination of the antibiotics rifampicin and streptomycin ( R+S ) , whether followed by surgery or not . In endemic areas , a clinical case definition is recommended . We evaluated the... | Buruli ulcer ( BU ) disease , a neglected devastating infection caused by Mycobacterium ulcerans , has a huge impact because of the massive necrotizing , disfiguring ulcers that may result if not treated . Therapeutic options are surgery , antibiotics or combinations of both . Since 2004 , the World Health Organization... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases"
] | 2010 | Response to Treatment in a Prospective Cohort of Patients with Large Ulcerated Lesions Suspected to Be Buruli Ulcer (Mycobacterium ulcerans Disease) |
Amyotrophic lateral sclerosis ( ALS ) and frontotemporal lobar degeneration ( FTLD ) are two incurable neurodegenerative disorders that exist on a symptomological spectrum and share both genetic underpinnings and pathophysiological hallmarks . Functional abnormality of TAR DNA-binding protein 43 ( TDP-43 ) , an aggrega... | Functional abnormality of TAR DNA-binding protein 43 ( TDP-43 ) , an aggregation-prone RNA and DNA binding protein , is observed in the vast majority of both familial and sporadic ALS cases and in ~40% of FTLD cases , and mutations in TDP-43 are causal in a subset of familial ALS cases . Although cytoplasmic inclusions... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"cell",
"processes",
"neuroscience",
"animals",
"invertebrate",
"genomics",
"toxicology",
"animal",
"models",
"dna",
"damage",
... | 2017 | Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS |
Lentiviral Envelope ( Env ) antigenic variation and related immune evasion present major hurdles to effective vaccine development . Centralized Env immunogens that minimize the genetic distance between vaccine proteins and circulating viral isolates are an area of increasing study in HIV vaccinology . To date , the eff... | Our best effort for containment of the global HIV epidemic is the development of a broadly protective vaccine . Current research has focused on vaccines that can generate a protective immune response against numerous strains of the virus . For this reason , vaccines with centralized HIV genes as immunogens , which merg... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"viral",
"vaccines",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"retroviruses",
"vaccines",
"viruses",
"vaccination",
"and",
"immunization",
"medical",
"microbiology",
"microbial",
"pat... | 2015 | Protective Efficacy of Centralized and Polyvalent Envelope Immunogens in an Attenuated Equine Lentivirus Vaccine |
The differences in demographic and life-history processes between organisms living in the same population have important consequences for ecological and evolutionary dynamics . Modern statistical and computational methods allow the investigation of individual and shared ( among homogeneous groups ) determinants of the ... | Somatic growth is a crucial determinant of ecological and evolutionary dynamics , since larger organisms often have higher survival and reproductive success . Size may be the result of intrinsic ( i . e . genetic ) , environmental ( temperature , food ) , and social ( competition with conspecifics ) factors and interac... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"ecology",
"and",
"environmental",
"sciences",
"theoretical",
"biology",
"ecology",
"theoretical",
"ecology",
"biology",
"and",
"life",
"sciences"
] | 2014 | Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method |
Mammary epithelial progenitors are the normal cell-of-origin of breast cancer . We previously defined a population of p27+ quiescent hormone-responsive progenitor cells in the normal human breast whose frequency associates with breast cancer risk . Here , we describe that deletion of the Cdkn1b gene encoding the p27 cy... | The frequency and proliferation of tissue-specific stem and progenitor cells is associated with the risk of malignancy . Thus , regulators of the pool size and proliferation of progenitor cells determine cancer risk . p27 is a key regulator of cellular proliferation and is required for the terminal differentiation of a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"breast",
"tumors",
"reproductive",
"system",
"maternal",
"health",
"obstetrics",
"and",
"gynecology",
"cancers",
"and",
"neoplasms",
"cell",
"differentiation",
"hormones",
"epithelial",
"cells",
"oncology",
"developmental",
"bio... | 2019 | Deletion of Cdkn1b in ACI rats leads to increased proliferation and pregnancy-associated changes in the mammary gland due to perturbed systemic endocrine environment |
Whole genome tiling arrays provide a high resolution platform for profiling of genetic , epigenetic , and gene expression polymorphisms . In this study we surveyed natural genomic variation in cytosine methylation among Arabidopsis thaliana wild accessions Columbia ( Col ) and Vancouver ( Van ) by comparing hybridizati... | The functional expression of DNA sequence depends on the chromatin status . Epigenetic marks at specific loci could affect local chromatin accessibility , thus affect the gene activity of that loci . We applied an enzyme methylome approach to globally detect one type of epigenetic mark , cytosine methylation at CCGG re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/epigenetics",
"genetics",
"and",
"genomics/plant",
"genetics",
"and",
"gene",
"expression"
] | 2008 | Global Analysis of Genetic, Epigenetic and Transcriptional Polymorphisms in Arabidopsis thaliana Using Whole Genome Tiling Arrays |
Predicting the three-dimensional structure of proteins from their amino acid sequences remains a challenging problem in molecular biology . While the current structural coverage of proteins is almost exclusively provided by template-based techniques , the modeling of the rest of the protein sequences increasingly requi... | Each protein folds into a unique three-dimensional structure that enables it to carry out its biological function . Knowledge of the atomic details of protein structures is therefore a key to understanding their function . Advances in high throughput experimental technologies have lead to an exponential increase in the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures |
The capacity of tumour cells to maintain continual overgrowth potential has been linked to the commandeering of normal self-renewal pathways . Using an epithelial cancer model in Drosophila melanogaster , we carried out an overexpression screen for oncogenes capable of cooperating with the loss of the epithelial apico-... | Cancer is a multigenic process , involving cooperative interactions between oncogenes or tumour suppressors . In this study , in a genetic screen in the vinegar fly , Drosophila melanogaster , for genes that cooperate with a mutation in the cell polarity ( shape ) regulator , scribbled ( scrib ) , we identify a novel c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biology"
] | 2013 | The BTB-zinc Finger Transcription Factor Abrupt Acts as an Epithelial Oncogene in Drosophila melanogaster through Maintaining a Progenitor-like Cell State |
Network medicine approaches have been largely successful at increasing our knowledge of molecularly characterized diseases . Given a set of disease genes associated with a disease , neighbourhood-based methods and random walkers exploit the interactome allowing the prediction of further genes for that disease . In gene... | The elucidation of the genetic causes of diseases is central to understanding the mechanisms of action of a pathology and the development of treatments . Disease gene prediction methods streamline the discovery of the molecular basis for a disease by prioritizing genes for experimental validation . Although some method... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"interaction",
"networks",
"genetic",
"networks",
"protein",
"interactions",
"statistics",
"applied",
"mathematics",
"protein",
"interaction",
"networks",
"simulation",
"and",
"modeling",
"algorithms",
"mathematics",
"forecasting",
"network",
"analysis",
"genome",
"analysis... | 2019 | Disease gene prediction for molecularly uncharacterized diseases |
Age-related changes in DNA methylation have been implicated in cellular senescence and longevity , yet the causes and functional consequences of these variants remain unclear . To elucidate the role of age-related epigenetic changes in healthy ageing and potential longevity , we tested for association between whole-blo... | Epigenetic patterns vary during healthy ageing and development . Age-related DNA methylation changes have been implicated in cellular senescence and longevity , yet the causes and functional consequences of these variants remain unclear . To understand the biological mechanisms involved in potential longevity and rate ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"genetics",
"epigenetics",
"biology",
"human",
"genetics",
"genetics",
"and",
"genomics"
] | 2012 | Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population |
Leptospira ( L . ) interrogans are bacteria responsible for a worldwide reemerging zoonosis . Rodents carry L . interrogans asymptomatically in their kidneys and excrete bacteria in the urine , contaminating the environment . Humans get infected through skin contact and develop a mild or severe leptospirosis that may l... | Leptospirosis is a bacterial disease transmitted by asymptomatic rodents to humans . The symptoms may be mild , or severe with kidney failure . Renal fibrosis , occurring during inflammatory situations , is characterized by the pathological accumulation of extra-cellular matrix components and can compromise the kidney ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"veterinary",
"science",
"biology"
] | 2014 | Leptospira Interrogans Induces Fibrosis in the Mouse Kidney through Inos-Dependent, TLR- and NLR-Independent Signaling Pathways |
The development of effective diagnostic tools will be essential in the continuing fight to reduce schistosome infection; however , the diagnostic tests available to date are generally laborious and difficult to implement in current parasite control strategies . We generated a series of single-chain antibody Fv domain (... | Mass drug administration using the highly effective drug praziquantel ( PZQ ) is currently the method of choice to combat schistosomiasis . However , this treatment regime has limitations; in particular , it does not prevent re-infection and sporadic parasite resistance against PZQ is a continuing threat . The path to ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Generation of a Novel Bacteriophage Library Displaying scFv Antibody Fragments from the Natural Buffalo Host to Identify Antigens from Adult Schistosoma japonicum for Diagnostic Development |
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