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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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Phenotypic switching allows for rapid transitions between alternative cell states and is important in pathogenic fungi for colonization and infection of different host niches . In Candida albicans , the white-opaque phenotypic switch plays a central role in regulating the program of sexual mating as well as interaction... | The white-opaque phenotypic switch has been extensively characterized in the human fungal pathogen Candida albicans , where it plays a central role in regulating entry into sexual reproduction . This epigenetic switch is strictly regulated by the MTL locus so that only a or α cell types can switch to the opaque state ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"expression",
"analysis",
"gene",
"regulation",
"microbiology",
"host-pathogen",
"interaction",
"emerging",
"infectious",
"diseases",
"fungal",
"evolution",
"molecular",
"genetics",
"fungal",
"reproduction",
"mycology",
"gene",
"expression",
"biology",
"pathogenes... | 2013 | MTL–Independent Phenotypic Switching in Candida tropicalis and a Dual Role for Wor1 in Regulating Switching and Filamentation |
Several studies have shown that cytotoxic T lymphocytes ( CTLs ) play an important role in controlling HIV/SIV infection . Notably , the observation of escape mutants suggests a selective pressure induced by the CTL response . However , it remains difficult to assess the definite role of the cellular immune response . ... | As a result of their high mutation rate , HIV and its counterpart SIV in non-human primates can evade recognition by the host immune response through the generation of viral variants , the so-called escape mutants . This avoidance of cytotoxic T lymphocyte ( CTL ) mediated killing seems to be one of the major reasons w... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious",
"diseases/hiv",
"infection",
"and",
"aids",
"immunology/immune",
"response",
"computational",
"biology"
] | 2008 | Dynamics of Immune Escape during HIV/SIV Infection |
Myxoma virus ( MYXV ) -encoded protein M029 is a member of the poxvirus E3 family of dsRNA-binding proteins that antagonize the cellular interferon signaling pathways . In order to investigate additional functions of M029 , we have constructed a series of targeted M029-minus ( vMyx-M029KO and vMyx-M029ID ) and V5-tagge... | Poxviruses exploit diverse strategies to modulate host anti-viral responses in order to achieve broad cellular tropism and replication . Here we report the findings that Myxoma virus ( MYXV ) , a rabbit-specific poxvirus , expresses a viral protein M029 that possesses dual immunomodulatory functions . M029 binds and in... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"veterinary",
"diseases",
"virulence",
"factors",
"and",
"mechanisms",
"viral",
"immune",
"evasion",
"immunity",
"veterinary",
"virology",
"virology",
"innate",
"immunity",
"viruses",
"and",
"cancer",
"veterinary",
"microbiology",
"immunology",
"host-pathogen"... | 2013 | Myxoma Virus Protein M029 Is a Dual Function Immunomodulator that Inhibits PKR and Also Conscripts RHA/DHX9 to Promote Expanded Host Tropism and Viral Replication |
α- ( 1 , 3 ) -Glucan is a major component of the cell wall of Aspergillus fumigatus , an opportunistic human fungal pathogen . There are three genes ( AGS1 , AGS2 and AGS3 ) controlling the biosynthesis of α- ( 1 , 3 ) -glucan in this fungal species . Deletion of all the three AGS genes resulted in a triple mutant that... | Aspergillus fumigatus is the predominant mold pathogen of humans , responsible for life-threatening systemic infections in patients with depressed immunity . Because of its external localization and specific composition , the fungal cell wall represents a target for recognition by and interaction with the host immune c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Deletion of the α-(1,3)-Glucan Synthase Genes Induces a Restructuring of the Conidial Cell Wall Responsible for the Avirulence of Aspergillus fumigatus |
During nervous system development , gradients of Sonic Hedgehog ( Shh ) and Netrin-1 attract growth cones of commissural axons toward the floor plate of the embryonic spinal cord . Mice defective for either Shh or Netrin-1 signaling have commissural axon guidance defects , suggesting that both Shh and Netrin-1 are requ... | During development of the nervous system , axons are propelled by the growth cone , a motile structure that is specialized to detect the direction of concentration gradients of guidance cues . Although it is known that commissural axons—those that cross the midline from one side of the nervous system to the other—of th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Integration of Shallow Gradients of Shh and Netrin-1 Guides Commissural Axons |
Bacterial type III protein secretion systems inject effector proteins into eukaryotic host cells in order to promote survival and colonization of Gram-negative pathogens and symbionts . Secretion across the bacterial cell envelope and injection into host cells is facilitated by a so-called injectisome . Its small hydro... | Many Gram-negative bacteria use type III secretion systems to inject bacterial proteins into eukaryotic host cells in order to promote their own survival and colonization . These systems are large molecular machines with the ability to transport proteins across three cell membranes in one step . It is believed that the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"sequencing",
"techniques",
"chemical",
"bonding",
"medicine",
"and",
"health",
"sciences",
"polyacrylamide",
"gel",
"electrophoresis",
"protein",
"interactions",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"sds",
"polyacrylamide",
"gel",
"e... | 2016 | Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus |
Long-term potentiation ( LTP ) of synaptic transmission represents the cellular basis of learning and memory . Astrocytes have been shown to regulate synaptic transmission and plasticity . However , their involvement in specific physiological processes that induce LTP in vivo remains unknown . Here we show that in vivo... | Information processing in the brain was classically thought to rely solely on neurons , whereas astrocytes , the most abundant glial cells in the brain , were considered supportive cells for neurons . However , astrocytes are known to respond to neuronal signals and regulate the function of synapses , so they may indee... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"neuroscience"
] | 2012 | Astrocytes Mediate In Vivo Cholinergic-Induced Synaptic Plasticity |
Trypomastigotes of Trypanosoma cruzi are able to invade several types of non-phagocytic cells through a lysosomal dependent mechanism . It has been shown that , during invasion , parasites trigger host cell lysosome exocytosis , which initially occurs at the parasite-host contact site . Acid sphingomyelinase released f... | Trypanosoma cruzi , is the etiological agent of a neglected tropical malady known as Chagas' disease , which affects about 8 million people in Latin America . 30–40% of affected individuals develop a symptomatic chronic infection , with cardiomyopathy being the most prevalent condition . T . cruzi utilizes an interesti... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"microbiology",
"molecular",
"cell",
"biology"
] | 2012 | Membrane Cholesterol Regulates Lysosome-Plasma Membrane Fusion Events and Modulates Trypanosoma cruzi Invasion of Host Cells |
Giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders . Although G . duodenalis can be cultured axenically , significant gaps exist in our understanding of the molecular biolo... | Giardia is the most common gastrointestinal protozoan parasite of humans . This parasite causes diarrheal disease and is correlated with post-infectious conditions such as irritable bowel syndrome . In the absence of a vaccine , treatment is limited to drugs such as metronidazole , against which clinical resistance is ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Time-Dependent Transcriptional Changes in Axenic Giardia duodenalis Trophozoites |
In this study a new computational method is developed to quantify decision making errors in cells , caused by noise and signaling failures . Analysis of tumor necrosis factor ( TNF ) signaling pathway which regulates the transcription factor Nuclear Factor κB ( NF-κB ) using this method identifies two types of incorrec... | Cell continuously receives signals from the surrounding environment and is supposed to make correct decisions , i . e . , respond properly to various signals and initiate certain cellular functions . Modeling and quantification of decision making processes in a cell have emerged as important areas of research in recent... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Extensions",
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"settings",
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"broader",
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"decision",
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"proteins",
"social",
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"signaling",
"networks",
"neuroscience",
"cognitive",
"psychology",
"mathematics",
"... | 2017 | Computation and measurement of cell decision making errors using single cell data |
Meta-analysis is an increasingly popular tool for combining multiple genome-wide association studies in a single analysis to identify associations with small effect sizes . The effect sizes between studies in a meta-analysis may differ and these differences , or heterogeneity , can be caused by many factors . If hetero... | Genome-wide association studies are an effective means of identifying genetic variants that are associated with diseases . Although many associated loci have been identified , those loci account for only a small fraction of the genetic contribution to the disease . The remaining contribution may be accounted by loci wi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"mathematics",
"statistics",
"genetics",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Interpreting Meta-Analyses of Genome-Wide Association Studies |
Tissue morphogenesis relies on proper differentiation of morphogenetic domains , adopting specific cell behaviours . Yet , how signalling pathways interact to determine and coordinate these domains remains poorly understood . Dorsal closure ( DC ) of the Drosophila embryo represents a powerful model to study epithelial... | Dorsal closure of the Drosophila embryo is used as a paradigm to study epithelial sealing and is related to wound healing . This vital process relies on the dorsal migration of the two lateral ectodermal sheets and is necessary for the protective epidermis to completely envelop the embryo . The row of cells located at ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"gene",
"regulation",
"dna",
"transcription",
"c-jun",
"n-terminal",
"kinase",
"signaling",
"cascade",
"developmental",
"biology",
"embryos",
"ectoderm",
"embryology",
"proteins",
"gene",
"expression",
"homeobox",
"biochemistry",
"signal",
"transduction",
"cell",
"biology... | 2017 | Signalling crosstalk at the leading edge controls tissue closure dynamics in the Drosophila embryo |
Micrurus snake bites can cause death by muscle paralysis and respiratory arrest , few hours after envenomation . The specific treatment for coral snake envenomation is the intravenous application of heterologous antivenom and , in Brazil , it is produced by horse immunization with a mixture of M . corallinus and M . fr... | The Elapidae family is represented in America by three genera of coral snakes: Micruroides , Leptomicrurus and Micrurus , the latter being the most abundant and diversified group . Micrurus bites can cause death by muscle paralysis and respiratory arrest few hours after envenomation . The specific treatment for Micruru... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"pharmacology",
"immunology"
] | 2010 | Diversity of Micrurus Snake Species Related to Their Venom Toxic Effects and the Prospective of Antivenom Neutralization |
The neglected tropical disease Buruli ulcer ( BU ) caused by Mycobacterium ulcerans is an infection of the subcutaneous tissue leading to chronic ulcerative skin lesions . Histopathological features are progressive tissue necrosis , extracellular clusters of acid fast bacilli ( AFB ) and poor inflammatory responses at ... | Buruli ulcer ( BU ) is a chronic necrotizing skin disease presenting with extensive tissue destruction and local immunosuppression . Standard treatment recommended by the WHO includes 8 weeks of rifampicin/streptomycin and , if necessary , wound debridement and skin grafting . In some patients satellite lesions develop... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
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] | [
"medicine",
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"diseases",
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"tropical",
"diseases",
"infectious",
"diseases",
"buruli",
"ulcer",
"medical",
"microbiology",
"biology",
"immune",
"r... | 2011 | Secondary Buruli Ulcer Skin Lesions Emerging Several Months after Completion of Chemotherapy: Paradoxical Reaction or Evidence for Immune Protection? |
Viruses are by definition fully dependent on the cellular translation machinery , and develop diverse mechanisms to co-opt this machinery for their own benefit . Unlike many viruses , human cytomegalovirus ( HCMV ) does suppress the host translation machinery , and the extent to which translation machinery contributes ... | Viruses are fully dependent on the cellular translation machinery , and develop diverse mechanisms to co-opt it for their own benefit . However , fundamental questions such as: what is the effect that infection has on the spectrum of host mRNAs that are being translated , and whether , and to what extent , a virus poss... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The Transcription and Translation Landscapes during Human Cytomegalovirus Infection Reveal Novel Host-Pathogen Interactions |
The Core Binding Factor ( CBF ) protein RUNX1 is a master regulator of definitive hematopoiesis , crucial for hematopoietic stem cell ( HSC ) emergence during ontogeny . RUNX1 also plays vital roles in adult mice , in regulating the correct specification of numerous blood lineages . Akin to the other mammalian Runx gen... | The transcription factor RUNX1 is considered a master regulator of adult and embryonic blood cell production . Mutations in RUNX1 cause defects in different blood lineages in human patients and mouse models , including leukemia and blood clotting defects due to a shortage of platelet-producing megakaryocytes . Together... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
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] | [
"blood",
"cells",
"flow",
"cytometry",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"spleen",
"immunology",
"animal",
"models",
"bone",
"marrow",
"cells",
"age",
"groups",
"adults",
"model",
"organisms",
"research",
"and",
"a... | 2016 | RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis |
The outbreak of Zika virus ( ZIKV ) in the Americas has transformed a previously obscure mosquito-transmitted arbovirus of the Flaviviridae family into a major public health concern . Little is currently known about the evolution and biology of ZIKV and the factors that contribute to the associated pathogenesis . Deter... | The current ZIKV outbreak is a major public health concern in the Americas . To further understand the virus , and to develop tools and potentially vaccines , more information on the virus strains circulating in the Americas is required . Here we describe the full-length sequence of a ZIKV isolate from a patient with c... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"and",
"Discussion"
] | [
"sequencing",
"techniques",
"medicine",
"and",
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"sciences",
"microcephaly",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"rna",
"extraction",
"microbiology",
"viruses",
"developmental",
"biology",
"rna",
"viruses",
"molecular",
"biology",
"technique... | 2016 | Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil |
Porcine circovirus 2 ( PCV2 ) is a circular single-stranded DNA virus responsible for a group of diseases collectively known as PCV2 Associated Diseases ( PCVAD ) . Variation in the incidence and severity of PCVAD exists between pigs suggesting a host genetic component involved in pathogenesis . A large-scale genome-wi... | The cost of managing Porcine Circovirus 2 ( PCV2 ) associated diseases in the US alone costs the swine industry more than $250 million a year . This virus is found in all swine populations in the US , but only a few pigs get sick and show signs of disease . Previous anecdotal field data showed differences between pig b... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"genome-wide",
"association",
"studies",
"quantitative",
"trait",
"loci",
"viral",
"transmission",
"and",
"infection",
"gene",
"regulation",
"microbiology",
"vertebrates",
"animals",
"mammals",
"genetic",
"mapping",
"genome",
"analysis",
"molecular",
"genetics",
"viral",
... | 2018 | Synaptogyrin-2 influences replication of Porcine circovirus 2 |
The “arms race” relationship between transposable elements ( TEs ) and their host has promoted a series of epigenetic silencing mechanisms directed against TEs . Retrotransposons , a class of TEs , are often located in repressed regions and are thought to induce heterochromatin formation and spreading . However , direc... | Transposable elements ( TEs ) are often thought to be harmful because of their potential to spread heterochromatin ( repressive chromatin ) into nearby sequences . However , there are few examples of spreading of heterochromatin caused by TEs , even though they are often found within repressive chromatin . We exploited... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"genetics",
"epigenetics",
"biology",
"computational",
"biology",
"genetics",
"and",
"genomics"
] | 2011 | Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms |
In the mammalian cochlea , small vibrations of the sensory epithelium are amplified due to active electro-mechanical feedback of the outer hair cells . The level of amplification is greater in the base than in the apex of the cochlea . Theoretical studies have used longitudinally varying active feedback properties to r... | The mammalian cochlea encodes sound pressure levels over six orders of magnitude . This wide dynamic range is achieved by amplifying weak sounds . The outer hair cells , one of two types of receptor cells in the cochlea , are known as the cellular actuators that provide power for the amplification . It is well known th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
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] | [
"velocity",
"stiffness",
"mechanical",
"properties",
"medicine",
"and",
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"sciences",
"classical",
"mechanics",
"vibration",
"ears",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"outer",
"hair",
"cells",
"organ",
"of",
"corti",
"inner",
"ear",
... | 2017 | Two passive mechanical conditions modulate power generation by the outer hair cells |
Natural sensory stimuli frequently consist of a fast time-varying waveform whose amplitude or contrast varies more slowly . While changes in contrast carry behaviorally relevant information necessary for sensory perception , their processing by the brain remains poorly understood to this day . Here , we investigated th... | Feedback input from more central to more peripheral brain areas is found ubiquitously in the central nervous system of vertebrates . In this study , we used a combination of electrophysiological , behavioral , and pharmacological approaches to reveal a novel function for feedback pathways in generating neural and behav... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
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"and",
"methods"
] | [
"medicine",
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"brain",
"social",
"sciences",
"electrophysiology",
"neuroscience",
"animal",
"behavior",
"ganglion",
"cells",
"zoology",
... | 2018 | Descending pathways generate perception of and neural responses to weak sensory input |
The high mortality of melanoma is caused by rapid spread of cancer cells , which occurs unusually early in tumour evolution . Unlike most solid tumours , thickness rather than cytological markers or differentiation is the best guide to metastatic potential . Multiple stimuli that drive melanoma cell migration have been... | Melanoma is feared because it spreads very rapidly when tumours are relatively small . It is not known why this metastasis is so efficient and aggressive . In particular , it is not known what drives melanoma cells to start to migrate out from the tumour . Here , we have studied the chemical signals that guide the migr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"oncology",
"biochemistry",
"lipids",
"medicine",
"and",
"health",
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"metastasis",
"cell",
"biology",
"theoretical",
"biology",
"lipid",
"metabolism",
"biology",
"and",
"life",
"sciences",
"fatty",
"acids",
"basic",
"cancer",
"research",
"molecular",
"cell",... | 2014 | Melanoma Cells Break Down LPA to Establish Local Gradients That Drive Chemotactic Dispersal |
Hemophagocytosis is a phenomenon in which macrophages phagocytose blood cells . There are reports on up-regulated hemophagocytosis in patients with infectious diseases including typhoid fever , tuberculosis , influenza and visceral leishmaniasis ( VL ) . However , mechanisms of infection-associated hemophagocytosis rem... | Anemia is one of the major clinical manifestations during visceral leishmaniasis ( VL ) , whereas mechanisms behind this symptom remain elusive . To get a better understanding of the responsible mechanism ( s ) , we have developed for the first time a mouse model of VL exhibiting anemia . Mice chronically infected with... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"blood",
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"microbiology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoan",
"life",
"cycles",
"anemia",
"animal",
... | 2016 | Hemophagocytosis in Experimental Visceral Leishmaniasis by Leishmania donovani |
The tegument protein U14 of human herpesvirus 6B ( HHV-6B ) constitutes the viral virion structure and is essential for viral growth . To define the characteristics and functions of U14 , we determined the crystal structure of the N-terminal domain of HHV-6B U14 ( U14-NTD ) at 1 . 85 Å resolution . U14-NTD forms an elo... | Human herpesvirus 6B ( HHV-6B ) , a causative agent of exanthema subitum for children and immunocompromised adults , encodes numerous tegument proteins that constitute the viral matrix . HHV-6B U14 is a tegument protein essential for viral propagation , and additionally it interacts with host factors such as tumor supp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"sequencing",
"techniques",
"dimers",
"(chemical",
"physics)",
"chemical",
"bonding",
"crystal",
"structure",
"split-decomposition",
"method",
"condensed",
"matter",
"physics",
"microbiology",
"viral",
"structure",
"multiple",
"alignment",
"calculation",
"molecular",
"biolo... | 2016 | Crystal Structure of Human Herpesvirus 6B Tegument Protein U14 |
In recent years there has been a strong development of computational approaches to mechanistically understand organ growth regulation in plants . In this study , simulation methods were used to explore which regulatory mechanisms can lead to realistic output at the cell and whole organ scale and which other possibiliti... | The growth of a plant root is driven by cell division and cell expansion occurring in spatially distinct developmental zones . Although these zones are in principle stable , depending on the conditions , their size and properties can be modulated . This has been meticulously described by kinematic studies , which have ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"biochemistry",
"developmental",
"biology",
"biochemical",
"simulations",
"plant",
"science",
"plant",
"growth",
"and",
"development",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"plant",
"physiology"
] | 2014 | Putting Theory to the Test: Which Regulatory Mechanisms Can Drive Realistic Growth of a Root? |
Drought is a major threat to plant growth and crop productivity . The phytohormone abscisic acid ( ABA ) plays a critical role in plant response to drought stress . Although ABA signaling-mediated drought tolerance has been widely investigated in Arabidopsis thaliana , the feedback mechanism and components negatively r... | Drought stress is a key environmental factor that severely reduces crop yield all over the world . The phytohormone abscisic acid ( ABA ) is known to mediate drought responses through regulating drought-responsive genes expression and stomatal closure , but the mechanisms that negatively regulate this process and preve... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"ecology",
"and",
"environmental",
"sciences",
"cellular",
"stress",
"responses",
"gene",
"regulation",
"regulatory",
"proteins",
"cell",
"processes",
"brassica",
"dna-binding",
"proteins",
"plant",
"physiology",
"plant",
"science",
"model",
"organisms"... | 2018 | Transcription factor HAT1 is a substrate of SnRK2.3 kinase and negatively regulates ABA synthesis and signaling in Arabidopsis responding to drought |
HIV-1 Vpu prevents incorporation of tetherin ( BST2/ CD317 ) into budding virions and targets it for ESCRT-dependent endosomal degradation via a clathrin-dependent process . This requires a variant acidic dileucine-sorting motif ( ExxxLV ) in Vpu . Structural studies demonstrate that recombinant Vpu/tetherin fusions ca... | Counteraction of tetherin , a host antiviral protein that blocks viral release from infected cells , is an essential attribute of HIV-1 and its related viruses . The HIV-1 accessory protein Vpu binds to tetherin , preventing its incorporation into viral particles , and targets it for ubiquitin-dependent degradation . T... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Serine Phosphorylation of HIV-1 Vpu and Its Binding to Tetherin Regulates Interaction with Clathrin Adaptors |
Dengue infection is one of the most important mosquito-borne diseases . More data regarding the disease burden and the prevalence of each clinical spectrum among symptomatic infections and the clinical manifestations are needed . This study aims to describe the incidence and clinical manifestations of symptomatic dengu... | Dengue infection is one of the most important diseases transmitted to human by mosquito bite . The disease may be mild or severe . This study reveals the occurrence and clinical features of diseases caused by dengue infection in a 3-year follow-up in school-children aged 3–14 years in Ratchaburi Province , Thailand usi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine"
] | 2012 | Dengue Infection in Children in Ratchaburi, Thailand: A Cohort Study. II. Clinical Manifestations |
Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression . Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution , facilitating detailed analyses into the genetic architecture and evolution of chromatin str... | Inside the nucleus of a cell , DNA is associated with proteins to form a complex three-dimensional structure referred to as chromatin . The structure of chromatin influences how accessible specific DNA sequences are to transcription factors , and therefore chromatin accessibility is an important determinant of gene exp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
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] | [
"genomics",
"genome",
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"comparative",
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"computational",
"biology",
"evolutionary",
"biology"
] | 2014 | Evolution and Genetic Architecture of Chromatin Accessibility and Function in Yeast |
Alternative cleavage and polyadenylation influence the coding and regulatory potential of mRNAs and where transcription termination occurs . Although widespread , few regulators of this process are known . The Arabidopsis thaliana protein FPA is a rare example of a trans-acting regulator of poly ( A ) site choice . Ana... | The ends of almost all eukaryotic protein-coding genes are defined by a poly ( A ) signal . When genes are transcribed into mRNA by RNA polymerase II , the poly ( A ) signal guides cleavage of the precursor mRNA at a particular site; this is accompanied by the addition of a poly ( A ) tail to the mRNA and termination o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA |
The control of seed germination and seed dormancy are critical for the successful propagation of plant species , and are important agricultural traits . Seed germination is tightly controlled by the balance of gibberellin ( GA ) and abscisic acid ( ABA ) , and is influenced by environmental factors . The COP9 Signaloso... | The control of seed germination and seed dormancy are critical for successful propagation of plant species , and manipulation of these processes is important for agriculture . The COP9 Signalosome ( CSN ) is a multi-subunit protein complex that regulates proteasome-mediated protein degradation in part as a regulator of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"plant",
"anatomy",
"molecular",
"probe",
"techniques",
"brassica",
"immunoblotting",
"plant",
"physiology",
"hormones",
"plant",
"science",
"model",
"organisms",
"plant",
"hormones",
"experimental",
"organism",
"systems",
"genome",
"analysis",
"molecular",
"biology",
"... | 2018 | The COP9 Signalosome regulates seed germination by facilitating protein degradation of RGL2 and ABI5 |
Efficient assimilation of alternative carbon sources in glucose-limited host niches is critical for colonization of Candida albicans , a commensal yeast that frequently causes opportunistic infection in human . C . albicans evolved mechanistically to regulate alternative carbon assimilation for the promotion of fungal ... | Most fermentative sugars like glucose , although routinely used in laboratory cell culture medium , are in fact only present at very low levels and even absent in many host niches . Therefore , assimilation of alternative nutrients is essential for the survival , proliferation and infection of most clinically important... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biofilms",
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"pathogens",
"microbiology",
"carbohydrates",
"organic",
"compounds",
"glucose",
"fungi",
"monomers",
"(chemistry)",
"experimental"... | 2017 | Mitochondrial complex I bridges a connection between regulation of carbon flexibility and gastrointestinal commensalism in the human fungal pathogen Candida albicans |
Worldwide , the theory and practice of agricultural extension system have been dominated for almost half a century by Rogers' “diffusion of innovation theory” . In particular , the success of integrated pest management ( IPM ) extension programs depends on the effectiveness of IPM information diffusion from trained far... | Food security of millions of people in the third world has faced a growing number of challenges in recent years including risks associated with emergent agricultural pests . Worldwide , the promotion of integrated pest management practices has been heavily promoted through participative methodologies relying on farmer ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computer",
"science",
"computer",
"modeling",
"social",
"and",
"behavioral",
"sciences",
"ecology",
"pest",
"control",
"sociology",
"biology",
"computational",
"sociology",
"integrated",
"control",
"agriculture"
] | 2011 | Coupled Information Diffusion–Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs |
Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments . In the same way , comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys . Toward this e... | Natural selection promotes the survival of the fittest individuals within a species . Over many generations , this may result in the maintenance of ancestral traits ( conservation through purifying selection ) , or the emergence of newly beneficial traits ( adaptation through positive selection ) . At the genetic level... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology",
"evolutionary",
"biology",
"genetics",
"and",
"genomics",
"eubacteria"
] | 2008 | Comparing Patterns of Natural Selection across Species Using Selective Signatures |
The filamentous fungus Chromocrea spinulosa ( Trichoderma spinulosum ) exhibits both self-fertile ( homothallic ) and self-sterile ( heterothallic ) sexual reproductive behavior . Self-fertile strains produce progeny cohorts that are 50% homothallic , 50% heterothallic . Heterothallic progeny can mate only with homotha... | Fungi employ one of two mating tactics for sexual reproduction: self-sterile/heterothallic species can mate only with a genetically distinct partner while self-fertile/homothallic species do not require a partner . In ascomycetes , sexual reproduction is controlled by master regulators encoded by the mating-type ( MAT ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular",
"probe",
"techniques",
"fungal",
"genetics",
"organisms",
"fungi",
"model",
"organisms",
"experimental",
"organism",
"systems",
"molecular",
"biology",
"techniques",
"dna",
"homologous",
"recombination",
"research",
"and",
"analysis",
"methods",
"saccharomyce... | 2017 | Self-fertility in Chromocrea spinulosa is a consequence of direct repeat-mediated loss of MAT1-2, subsequent imbalance of nuclei differing in mating type, and recognition between unlike nuclei in a common cytoplasm |
The ecdysone receptor is a heterodimer of two nuclear receptors , the Ecdysone receptor ( EcR ) and Ultraspiracle ( USP ) . In Drosophila melanogaster , three EcR isoforms share common DNA and ligand-binding domains , but these proteins differ in their most N-terminal regions and , consequently , in the activation doma... | Nuclear receptors are proteins that regulate gene expression in response to steroid and thyroid hormones and other small lipid-soluble signaling molecules . In many cases , nuclear receptor genes encode multiple variants ( isoforms ) that direct tissue- and stage-specific hormonal responses . The sequence differences a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"molecular",
"neuroscience",
"developmental",
"neuroscience",
"organism",
"development",
"metamorphosis",
"biology",
"signaling",
"pathways",
"neuroscience"
] | 2012 | Cryptocephal, the Drosophila melanogaster ATF4, Is a Specific Coactivator for Ecdysone Receptor Isoform B2 |
Adenocarcinoma ( AC ) and squamous cell carcinoma ( SqCC ) are two major histological subtypes of lung cancer . Genome-wide association studies ( GWAS ) have made considerable advances in the understanding of lung cancer susceptibility . Obvious heterogeneity has been observed between different histological subtypes of... | Previous genome-wide association studies ( GWAS ) strongly suggested the importance of genetic susceptibility for lung cancer . However , the studies specific to different histological subtypes of lung cancer were limited . We performed the GWAS analysis specifically for lung squamous cell carcinoma ( SqCC ) with 570 ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"oncology",
"medicine",
"cancer",
"genetics",
"squamous",
"cell",
"lung",
"carcinoma",
"lung",
"and",
"intrathoracic",
"tumors",
"genetics",
"biology",
"cancers",
"and",
"neoplasms",
"genetics",
"and",
"genomics"
] | 2013 | Genome-Wide Association Study Identifies a Novel Susceptibility Locus at 12q23.1 for Lung Squamous Cell Carcinoma in Han Chinese |
Telomerase is a telomere dedicated reverse transcriptase that replicates the very ends of eukaryotic chromosomes . Saccharomyces cerevisiae telomerase consists of TLC1 ( the RNA template ) , Est2 ( the catalytic subunit ) , and two accessory proteins , Est1 and Est3 , that are essential in vivo for telomerase activity ... | Owing to the biochemical properties of DNA polymerases , the free ends of linear chromosomes , called telomeres , cannot be replicated by the same mechanisms that suffice for the rest of the chromosome . Instead they are maintained by a telomere-dedicated reverse transcriptase called telomerase that uses its integral R... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"biochemistry",
"molecular",
"cell",
"biology",
"cell",
"division",
"cell",
"biology",
"nucleic",
"acids",
"genetics",
"molecular",
"genetics",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics",
"gene",
"function"
... | 2011 | The Saccharomyces cerevisiae Telomerase Subunit Est3 Binds Telomeres in a Cell Cycle– and Est1–Dependent Manner and Interacts Directly with Est1 In Vitro |
The lack of capacity in laboratory systems is a major barrier to achieving the aims of the London Declaration ( 2012 ) on neglected tropical diseases ( NTDs ) . To counter this , capacity strengthening initiatives have been carried out in NTD laboratories worldwide . Many of these initiatives focus on individuals' skil... | Capacity strengthening activities such as technical training for staff , student research project supervision , and equipment provision are being carried out in laboratories worldwide as part of the global effort to control neglected tropical diseases ( NTDs ) . However , these activities often focus on developing the ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"social",
"and",
"behavioral",
"sciences",
"science",
"policy",
"global",
"health",
"neglected",
"tropical",
"diseases",
"sociology",
"social",
"research",
"public",
"health",
"research",
"laboratories"
] | 2014 | A Systematic Approach to Capacity Strengthening of Laboratory Systems for Control of Neglected Tropical Diseases in Ghana, Kenya, Malawi and Sri Lanka |
Mobile group II introns are bacterial retrotransposons that are thought to have invaded early eukaryotes and evolved into introns and retroelements in higher organisms . In bacteria , group II introns typically retrohome via full reverse splicing of an excised intron lariat RNA into a DNA site , where it is reverse tra... | Group II introns are bacterial mobile elements thought to be ancestors of introns and retrotransposons in higher organisms . They consist of a catalytically active intron RNA and an intron-encoded reverse transcriptase , which function together to promote intron integration into new DNA sites in a process called “retro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"biochemistry",
"transposons",
"model",
"organisms",
"molecular",
"cell",
"biology",
"nucleic",
"acids",
"proteins",
"evolutionary",
"biology",
"genetics",
"dna",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | The Retrohoming of Linear Group II Intron RNAs in Drosophila melanogaster Occurs by Both DNA Ligase 4–Dependent and –Independent Mechanisms |
Models describing the process of stem-cell differentiation are plentiful , and may offer insights into the underlying mechanisms and experimentally observed behaviour . Waddington’s epigenetic landscape has been providing a conceptual framework for differentiation processes since its inception . It also allows , howeve... | Current emphasis on single cell analysis , especially in the context of the human and mouse cell atlas projects , is on characterizing the transcriptomic signatures of different cell states . This is clearly of great importance , as even the number of different cell types , e . g . in humans , is not known with any sat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"differentiation",
"developmental",
"biology",
"systems",
"science",
"mathematics",
"probability",
"distribution",
"stem",
"cells",
"algebra",
"epigenetics",
"reaction",
"dynamics",
"physical",
"chemistry",
"computer",
"and",
"information",
"sciences",
"animal",
"... | 2018 | Transition state characteristics during cell differentiation |
Cellular restriction factors responding to herpesvirus infection include the ND10 components PML , Sp100 and hDaxx . During the initial stages of HSV-1 infection , novel sub-nuclear structures containing these ND10 proteins form in association with incoming viral genomes . We report that several cellular DNA damage res... | The cellular DNA damage response pathway monitors damage to genomic DNA . We investigated whether cellular DNA damage response proteins can also respond to incoming viral genetic material and how they impact virus growth . Using Herpes Simplex Virus type 1 ( HSV-1 ) , we present evidence that DNA repair proteins are ac... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"microbiology",
"molecular",
"cell",
"biology"
] | 2011 | The Intrinsic Antiviral Defense to Incoming HSV-1 Genomes Includes Specific DNA Repair Proteins and Is Counteracted by the Viral Protein ICP0 |
The O-mannosyltransferase Pmt4 has emerged as crucial for fungal virulence in the animal pathogens Candida albicans or Cryptococcus neoformans as well as in the phytopathogenic fungus Ustilago maydis . Pmt4 O-mannosylates specific target proteins at the Endoplasmic Reticulum . Therefore a deficient O-mannosylation of t... | The O-mannosyltransferase Pmt4 is essential for virulence of animal and plant pathogenic fungi . This protein attaches one mannose at serine/threonine residues of cell wall and secreted proteins modulating their location and function . Thus , the crucial role of Pmt4 in fungal pathogenic development is probably caused ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"model",
"organisms",
"yeast",
"and",
"fungal",
"models",
"biology",
"microbiology"
] | 2012 | Identification of O-mannosylated Virulence Factors in Ustilago maydis |
Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks . However , transmission trees from one outbreak do not generalize to future outbreaks . Reconstruction of transmission trees is most useful to public health if i... | Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks . However , transmission trees from one outbreak do not generalize to future outbreaks . Reconstruction of transmission trees is most useful to public health if i... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"taxonomy",
"plant",
"anatomy",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"infectious",
"disease",
"epidemiology",
"pathogens",
"spatial",
"epidemiology",
"phylogenetics",
"data",
"management",
"farms",
"plant",
"science",
"p... | 2016 | Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees |
Visceral leishmaniasis is associated with significant changes in hematological function but the mechanisms underlying these changes are largely unknown . In contrast to naïve mice , where most long-term hematopoietic stem cells ( LT-HSCs; LSK CD150+ CD34- CD48- cells ) in bone marrow ( BM ) are quiescent , we found tha... | Visceral leishmaniasis ( VL ) is a chronic often fatal disease caused by the protozoan parasites Leishmania donovani and L . infantum . Progressive disease in humans and in animal models is associated with parasite replication at systemic sites , including the bone marrow ( BM ) and results in significant changes in he... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"spleen",
"immunology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"bone",
"marrow",
"cells",
"physiological",
"pr... | 2017 | TNF signalling drives expansion of bone marrow CD4+ T cells responsible for HSC exhaustion in experimental visceral leishmaniasis |
Bloom syndrome is a recessive human genetic disorder with features of genome instability , growth deficiency and predisposition to cancer . The only known causative gene is the BLM helicase that is a member of a protein complex along with topoisomerase III alpha , RMI1 and 2 , which maintains replication fork stability... | Cells contain specific protein complexes that are needed to correct errors during the replication and segregation of DNA . Impairment in the activity of these proteins can be detrimental to the viability of the cell and organism development . Bloom syndrome is an example of a genome instability disorder where cells can... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"anaphase",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"immunology",
"biological",
"cultures",
"chromatids",
"fibroblasts",
"mitosis",
"dna",
"replication",
"connective... | 2016 | Loss of RMI2 Increases Genome Instability and Causes a Bloom-Like Syndrome |
Visceral leishmaniasis ( VL ) , the most severe form of leishmaniasis , is endemic in Europe with Mediterranean countries reporting endemic status alongside a worrying northward spread . Serological diagnosis , including immunochromatographic test based on the recombinant antigen rK39 ( rK39-ICT ) and a direct agglutin... | Visceral leishmaniasis is the most severe form of leishmaniasis , a disease transmitted through the bite of an infected sandfly . Although the biggest burden of leishmaniasis is in eastern Africa and the Indian subcontinent , the disease is also endemic in parts of Europe . Previous studies have looked at performance o... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"kala-azar",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"european",
"union",
"pathogens",
"tropical",
"diseases",
"geographical",
"locations",
"microbiology",
"parasitic",
"diseases",
"retroviruses",
"viruses",
"immunodeficiency",... | 2018 | Validation of rK39 immunochromatographic test and direct agglutination test for the diagnosis of Mediterranean visceral leishmaniasis in Spain |
To understand how evolving systems bring forth novel and useful phenotypes , it is essential to understand the relationship between genotypic and phenotypic change . Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual , and it may help cr... | The phenotype of an organism comprises the set of morphological and functional traits encoded by its genome . In natural evolving systems , phenotypes are organized into mutationally connected networks of genotypes , which increase the likelihood for an evolving population to encounter novel adaptive phenotypes ( i . e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"organismal",
"evolution",
"mathematical",
"models",
"mutation",
"developmental",
"biology",
"sequence",
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"and",
"analysis",
"methods",
"sequence",
"analysis",
"random",
"walk",
"genome",
"complexity",
"sequence",
"alignment",
"bioinformati... | 2017 | The genotype-phenotype map of an evolving digital organism |
The hepatitis C virus ( HCV ) envelope glycoproteins E1 and E2 form a non-covalently linked heterodimer on the viral surface that mediates viral entry . E1 , E2 and the heterodimer complex E1E2 are candidate vaccine antigens , but are technically challenging to study because of difficulties in producing natively folded... | The function and structure of the hepatitis C virus envelope glycoprotein complex E1E2 is poorly understood because of difficulties in producing pure and correctly folded proteins for biochemical and structural analysis . Here , we use monoclonal antibodies to non-overlapping epitopes on E1E2 , as well as the CD81 co-r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Conclusion",
"Materials",
"and",
"methods"
] | [
"flow",
"cytometry",
"medicine",
"and",
"health",
"sciences",
"chemical",
"characterization",
"enzyme-linked",
"immunoassays",
"crystal",
"structure",
"chemical",
"compounds",
"immune",
"physiology",
"aliphatic",
"amino",
"acids",
"immunology",
"condensed",
"matter",
"phy... | 2017 | Probing the antigenicity of hepatitis C virus envelope glycoprotein complex by high-throughput mutagenesis |
Recent data indicate that plasticity protocols have not only synapse-specific but also more widespread effects . In particular , in synaptic tagging and capture ( STC ) , tagged synapses can capture plasticity-related proteins , synthesized in response to strong stimulation of other synapses . This leads to long-lastin... | It is thought that the main biological mechanism of memory corresponds to long-lasting changes in the strengths , or weights , of synapses between neurons . The phenomenon of long-term synaptic weight change has been particularly well documented in the hippocampus , a crucial brain region for the induction of episodic ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/computational",
"neuroscience",
"neuroscience/theoretical",
"neuroscience"
] | 2009 | State Based Model of Long-Term Potentiation and Synaptic Tagging and
Capture |
Use of tobacco products is injurious to health in men and women . However , tobacco use by pregnant women receives greater scrutiny because it can also compromise the health of future generations . More men smoke cigarettes than women . Yet the impact of nicotine use by men upon their descendants has not been as widely... | Use of tobacco products is a major public health concern throughout the world . Cigarette smoking by pregnant women receives significant attention by scientific , public health , and public policy experts because it poses health risks for the mother and her children . Although more men smoke cigarettes than women , the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"learning",
"neuropsychiatric",
"disorders",
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"chemical",
"compounds",
"adhd",
"vertebrates",
"social",
"sciences",
"mice",
"neuroscience",
"organic",
"compounds",
"animals",
"mammals",
"hormones",
"learning",
"and... | 2018 | Nicotine exposure of male mice produces behavioral impairment in multiple generations of descendants |
Chloride-transporting membrane proteins of the CLC family appear in two distinct mechanistic flavors: H+-gated Cl− channels and Cl−/H+ antiporters . Transmembrane H+ movement is an essential feature of both types of CLC . X-ray crystal structures of CLC antiporters show the Cl− ion pathway through these proteins , but ... | Chloride-proton antiport proteins of the “CLC” superfamily are transmembrane proteins that form homodimers and are used for myriad physiological purposes , all requiring the coordinated movements of Cl− anions and H+ cations in opposite directions across biological membranes . While the pathway for Cl− ions through CLC... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"biology",
"biophysics"
] | 2012 | Intracellular Proton Access in a Cl−/H+ Antiporter |
Cross-feeding , a relationship wherein one organism consumes metabolites excreted by another , is a ubiquitous feature of natural and clinically-relevant microbial communities and could be a key factor promoting diversity in extreme and/or nutrient-poor environments . However , it remains unclear how readily cross-feed... | Simple environments , even those used in laboratory experimental evolution , have proven vastly richer than originally thought , capable of generating and supporting genetic and phenotypic diversity . This was not foreseen by Gause’s seminal competitive exclusion theory , which predicted that simple single niche enviro... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"cell",
"physiology",
"carbohydrate",
"metabolism",
"chemical",
"compounds",
"cloning",
"carbohydrates",
"glucose",
"metabolism",
"organic",
"compounds",
"glucose",
"mathematical",
"models",
"cell",
"metabolism",
"metabolites",
"molecular",
"biology",
"techniques",
"populat... | 2016 | Stability of Cross-Feeding Polymorphisms in Microbial Communities |
Next generation sequencing has dramatically increased our ability to localize disease-causing variants by providing base-pair level information at costs increasingly feasible for the large sample sizes required to detect complex-trait associations . Yet , identification of causal variants within an established region o... | As next-generation sequencing ( NGS ) costs continue to fall and genome-wide association study ( GWAS ) platform coverage improves , the human genetics community is positioned to identify potentially causal variants . However , current NGS or imputation-based studies of either the whole genome or regions previously ide... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"genome",
"analysis",
"tools",
"mathematics",
"genetic",
"association",
"studies",
"statistics",
"genetics",
"biology",
"genomics",
"biostatistics",
"computational",
"biology",
"human",
"genetics"
] | 2013 | Re-Ranking Sequencing Variants in the Post-GWAS Era for Accurate Causal Variant Identification |
MicroRNAs ( miRNAs ) suppress gene expression by forming a duplex with a target messenger RNA ( mRNA ) , blocking translation or initiating cleavage . Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA , but currently available prediction methods do not address the... | MicroRNAs ( miRNAs ) are small RNA molecules that regulate post-transcriptional gene expression by binding messenger RNAs ( mRNAs ) , blocking their role in translation or marking them for degradation . To date , computational methods for predicting mRNA targets have assumed an all-or-nothing mode of miRNA-mRNA interac... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/transcriptional",
"regulation",
"computational",
"biology"
] | 2011 | Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations |
In C . elegans , removal of the germline extends lifespan significantly . We demonstrate that the nuclear hormone receptor , NHR-49 , enables the response to this physiological change by increasing the expression of genes involved in mitochondrial β-oxidation and fatty-acid desaturation . The coordinated augmentation o... | Much is known about how increasing age impairs fertility but we know little about how reproduction influences rate of aging in animals . Studies in model organisms such as worms and flies have begun to shed light on this relationship . In worms , removing germ cells that give rise to sperm and oocytes extends lifespan ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"animal",
"genetics",
"caenorhabditis",
"homeostatic",
"mechanisms",
"animals",
"physiological",
"processes",
"developmental",
"biology",
"organism",
"development",
"homeostasis",
"lipid",
"metabolism",
"lipids",
"nuclear",
"receptor",
"signaling",
"metabolis... | 2014 | Germline Signals Deploy NHR-49 to Modulate Fatty-Acid β-Oxidation and Desaturation in Somatic Tissues of C. elegans |
The arsenal in anthelminthic treatment against schistosomiasis is limited and relies almost exclusively on a single drug , praziquantel ( PZQ ) . Thus , resistance to PZQ could constitute a major threat . Even though PZQ is potent in killing adult worms , its activity against earlier stages is limited . Current in vitr... | Schistosomiasis remains a major health threat , predominantly in developing countries . Even though there has been some progress in search of new drugs , praziquantel remains the only available drug . Probably the most important advance in the search for new drugs was in vitro transformation of cercariae and their subs... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"antimicrobials",
"schistosoma",
"invertebrates",
"schistosoma",
"mansoni",
"medicine",
"and",
"health",
"sciences",
"helminths",
"drugs",
"tropical",
"diseases",
"microbiology",
"parasitic",
"diseases",
"animals",
"drug",
"screening",
"antimalarials",
"streptomycin",
"phar... | 2019 | A novel cell-free method to culture Schistosoma mansoni from cercariae to juvenile worm stages for in vitro drug testing |
Trachoma is targeted for elimination by 2020 . World Health Organization advises districts to undertake surveillance when follicular trachoma ( TF ) <5% in children 1–9 years and mass antibiotic administration has ceased . There is a question if other tools could be used for surveillance as well . We report data from a... | Trachoma , the leading infectious cause of blindness world-wide , is targeted for elimination by 2020 . The World Health Organization advises districts to undertake surveillance for trachoma when follicular trachoma ( TF ) is less than 5% in children 1–9 years . In a trachoma-endemic district that stopped its program f... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2016 | Can We Use Antibodies to Chlamydia trachomatis as a Surveillance Tool for National Trachoma Control Programs? Results from a District Survey |
Understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics . Unlike classical screening methods , analysis of genetic variation that occurs naturally in wild populations can enable rapid , genome-scale mapping of genotype to phenotype with a medium... | Many phenotypes of interest are controlled by multiple loci , and in biological systems identifying determinants of such complex traits is challenging . Here , we genotyped 112 wild isolates of Neurospora crassa and used this resource to identify genes that mediate a fundamental but poorly-understood attribute of this ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"genome",
"expression",
"analysis",
"systems",
"biology",
"functional",
"genomics",
"model",
"organisms",
"genetic",
"polymorphism",
"gene",
"identification",
"and",
"analysis",
"genetics",
"molecular",
"genetics",
"population",
"g... | 2013 | Genome Wide Association Identifies Novel Loci Involved in Fungal Communication |
Oncogenes , which are essential for tumor initiation , development , and maintenance , are valuable targets for cancer therapy . However , it remains a challenge to effectively inhibit oncogene activity by targeting their downstream pathways without causing significant toxicity to normal tissues . Here we show that del... | Oncogenes elicit driving signals required for tumor initiation , development , and maintenance and are valuable targets for cancer therapy . However , oncogenes often have essential functions in normal cellular physiology and produce intracellular proteins that are difficult to inhibit with small molecule drugs without... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"cell",
"death",
"leukemias",
"cancer",
"genetics",
"immune",
"cells",
"immunology",
"cancers",
"and",
"neoplasms",
"basic",
"cancer",
"research",
"hematologic",
"cancers",
"and",
"related",
"disorders",
"oncology",
"tumor",
"physiology",
"cell",
"growth",... | 2012 | Modulating the Strength and Threshold of NOTCH Oncogenic Signals by mir-181a-1/b-1 |
The Elongator complex promotes formation of 5-methoxycarbonylmethyl ( mcm5 ) and 5-carbamoylmethyl ( ncm5 ) side-chains on uridines at the wobble position of cytosolic eukaryotic tRNAs . In all eukaryotic organisms tested to date , the inactivation of Elongator not only leads to the lack of mcm5/ncm5 groups in tRNAs , ... | Modified nucleosides in the anticodon region of tRNAs are important for the efficiency and fidelity of translation . The Elongator complex promotes formation of several related modified uridine residues at the wobble position of eukaryotic tRNAs . In yeast , plants , worms , mice and humans , mutations in genes for Elo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"transfer",
"rna",
"cell",
"walls",
"gene",
"regulation",
"dna-binding",
"proteins",
"alleles",
"cellular",
"structures",
"and",
"organelles",
"gene",
"silencing",
"proteins",
"gene",
"expression",
"histones",
"genetic",
"loci",
"biochemistry",
"rna",
"cell",
"biology... | 2019 | SSD1 suppresses phenotypes induced by the lack of Elongator-dependent tRNA modifications |
We developed a whole-circulation computational model by integrating a transmission line ( TL ) model describing vascular wave transmission into the established CircAdapt platform of whole-heart mechanics . In the present paper , we verify the numerical framework of our TL model by benchmark comparison to a previously v... | Arterial pulse wave characteristics show associations with left ventricular hypertrophy in clinical studies . However , in such studies , measurement and signal processing errors limit assessment of causality between wave characteristics and left ventricular hypertrophy . When validated , a computational model would al... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"blood",
"anatomy",
"blood",
"vessels",
"arteries",
"simulation",
"and",
"modeling",
"cardiovascular",
"anatomy",
"physiology",
"aorta",
"biology",
"and",
"life",
"sciences",
"hypertension",
"blood",
"pressure... | 2019 | Large vessels as a tree of transmission lines incorporated in the CircAdapt whole-heart model: A computational tool to examine heart-vessel interaction |
The spontaneous dissociation of six small ligands from the active site of FKBP ( the FK506 binding protein ) is investigated by explicit water molecular dynamics simulations and network analysis . The ligands have between four ( dimethylsulphoxide ) and eleven ( 5-diethylamino-2-pentanone ) non-hydrogen atoms , and an ... | Most known drugs used to fight human diseases are small molecules that bind strongly to proteins , particularly to enzymes or receptors involved in essential biochemical or physiological processes . The binding process is very complex because of the many degrees of freedom and multiple interactions between pairs of ato... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biomacromolecule-ligand",
"interactions",
"molecular",
"dynamics",
"chemistry",
"biology",
"computational",
"chemistry",
"biophysics",
"simulations",
"biophysics"
] | 2011 | The Free Energy Landscape of Small Molecule Unbinding |
Herceptin ( trastuzumab ) is used in patients with breast cancer who have HER2 ( ErbB2 ) –positive tumours . However , its mechanisms of action and how acquired resistance to Herceptin occurs are still poorly understood . It was previously thought that the anti-HER2 monoclonal antibody Herceptin inhibits HER2 signallin... | HER2 ( ErbB2 ) is a surface protein and member of the epidermal growth factor receptor ( EGFR ) family that is overexpressed in approximately one-fifth of breast cancers . HER2-positive breast tumours tend to be very aggressive , and patients with this type of tumour have a poor prognosis . A therapeutic monoclonal ant... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"pharmacology/drug",
"resistance",
"oncology/breast",
"cancer",
"cell",
"biology/cell",
"signaling"
] | 2010 | HER2 Phosphorylation Is Maintained by a PKB Negative Feedback Loop in Response to Anti-HER2 Herceptin in Breast Cancer |
Following infection of the central nervous system ( CNS ) , the immune system is faced with the challenge of eliminating the pathogen without causing significant damage to neurons , which have limited capacities of renewal . In particular , it was thought that neurons were protected from direct attack by cytotoxic T ly... | When a virus infects the brain , it is important to quickly block viral replication without causing excessive damage to neurons , which are not easily renewed . Cytotoxic T lymphocytes ( CTL ) are one of the main actors for virus elimination . However , the question of whether CTL are indeed capable of destroying infec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"flow",
"cytometry",
"cell",
"death",
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"cellular",
"stress",
"responses",
"immune",
"cells",
"viral",
"transmission",
"and",
"infection",
"viral",
"classification",
"immunity",
"to",
"infections",
"immunology",
"m... | 2011 | Neurons are MHC Class I-Dependent Targets for CD8 T Cells upon Neurotropic Viral Infection |
Plasmacytoid dendritic cells ( pDCs ) are “natural” interferon α ( IFNα ) -producing cells . Despite their importance to antiviral defense , autoimmunity , and ischemic liver graft injury , because DC subsets are rare and heterogeneous , basic questions about liver pDC function and capacity to make cytokines remain una... | This is a detailed characterization of human liver plasmacytoid dendritic cells from patients with a chronic viral infection . It revealed that these rare innate immune cells can become point sources of multiple immune activators and pro-inflammatory mediators . This study adds new information about the fundamental pro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"flow",
"cytometry",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"organ",
"transplantation",
"immune",
"physiology",
"cytokines",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"surgical",
"and",
"invasive",
"m... | 2019 | Individual liver plasmacytoid dendritic cells are capable of producing IFNα and multiple additional cytokines during chronic HCV infection |
Tractography uses diffusion MRI to estimate the trajectory and cortical projection zones of white matter fascicles in the living human brain . There are many different tractography algorithms and each requires the user to set several parameters , such as curvature threshold . Choosing a single algorithm with specific p... | Diffusion MRI and tractography opened a new avenue for studying white matter fascicles and their tissue properties in the living human brain . There are many different tractography methods , and each requires the user to set several parameters . A limitation of tractography is that the results depend on the selection o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"diagnostic",
"radiology",
"tractography",
"nervous",
"system",
"applied",
"mathematics",
"brain",
"neuroscience",
"cerebral",
"hemispheres",
"occipital",
"lobe",
"magnetic",
"resonance",
"imaging",
"algorithms",
"simulation",
"and... | 2016 | Ensemble Tractography |
The importance of the genus Thrichomys in the retention of infection and transmission of Leishmania species is supported by previous studies that describe an ancient interaction between caviomorphs and trypanosomatids and report the natural infection of Thrichomys spp . Moreover , these rodents are widely dispersed in ... | For Leishmania , one genus among several genera belonging to the parasitic Trypanosomatidae family , many nonhuman mammals are known to be hosts in addition to humans . Most studies that describe Leishmania wild reservoirs are based on isolated descriptions of infection that can lead to misinterpretation of information... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/protozoal",
"infections",
"infectious",
"diseases/neglected",
"tropical",
"diseases"
] | 2010 | Thrichomys laurentius (Rodentia; Echimyidae) as a Putative Reservoir of Leishmania infantum and L. braziliensis: Patterns of Experimental Infection |
In order to get a comprehensive repertoire of foldable domains within whole proteomes , including orphan domains , we developed a novel procedure , called SEG-HCA . From only the information of a single amino acid sequence , SEG-HCA automatically delineates segments possessing high densities in hydrophobic clusters , a... | Spontaneous or induced folding into a specific 3D structure is a key property of proteins to perform their biological functions . Folded 3D structures of proteins perform specific functions , including interactions with other proteins . Intrinsically disordered regions also mediate interaction , gaining structure only ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Comprehensive Repertoire of Foldable Regions within Whole Genomes |
A large proportion of functional sequence within mammalian genomes falls outside protein-coding exons and can be transcribed into long RNAs . However , the roles in mammalian biology of long noncoding RNA ( lncRNA ) are not well understood . Few lncRNAs have experimentally determined roles , with some of these being li... | The best-understood portion of mammalian genomes contains genes transcribed into RNAs , which are subsequently translated into proteins . These genes are generally under high selective pressure and deeply conserved between species . Recent publications have revealed novel classes of genes , which are also transcribed i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"model",
"organisms",
"genetics",
"biology",
"computational",
"biology",
"evolutionary",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression |
In Saccharomyces cerevisiae , the essential mismatch repair ( MMR ) endonuclease Mlh1-Pms1 forms foci promoted by Msh2-Msh6 or Msh2-Msh3 in response to mispaired bases . Here we analyzed the Mlh1-Mlh2 complex , whose role in MMR has been unclear . Mlh1-Mlh2 formed foci that often colocalized with and had a longer lifet... | Lynch syndrome ( hereditary nonpolyposis colorectal cancer or HNPCC ) is a common cancer predisposition syndrome . In this syndrome , predisposition to cancer results from increased accumulation of mutations due to defective mismatch repair ( MMR ) caused by a mutation in one of the human mismatch repair genes MLH1 , M... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mutation",
"model",
"organisms",
"genetics",
"biology",
"and",
"life",
"sciences",
"yeast",
"and",
"fungal",
"models",
"research",
"and",
"analysis",
"methods"
] | 2014 | Mlh2 Is an Accessory Factor for DNA Mismatch Repair in Saccharomyces cerevisiae |
CD8+ lymphocytes play an important role in suppressing in vivo viral replication in HIV infection . However , both the extent to which and the mechanisms by which CD8+ lymphocytes contribute to viral control are not completely understood . A recent experiment depleted CD8+ lymphocytes in simian immunodeficiency virus (... | CD8+ lymphocytes play an important role in suppressing in vivo viral replication in HIV infection . However , both the extent to which and the mechanisms by which CD8+ lymphocytes contribute to viral control are not completely understood . By mathematically modeling data from a recent CD8 depletion experiment done in a... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"viral",
"transmission",
"and",
"infection",
"antiviral",
"therapy",
"immunology",
"cell",
"processes",
"microbiology",
"vertebrates",
"animals",
"mammals",
"primates",
"pre... | 2018 | CD8+ lymphocyte control of SIV infection during antiretroviral therapy |
The transcription factor ATF2 has been shown to attenuate melanoma susceptibility to apoptosis and to promote its ability to form tumors in xenograft models . To directly assess ATF2's role in melanoma development , we crossed a mouse melanoma model ( NrasQ61K::Ink4a−/− ) with mice expressing a transcriptionally inacti... | Understanding mechanisms underlying early stages in melanoma development is of major interest and importance . Recent studies indicate a role for MITF , a master regulator of melanocyte development and biogenesis , in melanoma progression . Here we demonstrate that the transcription factor ATF2 negatively regulates MIT... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/cancer",
"genetics",
"oncology/skin",
"cancers",
"cell",
"biology/cell",
"signaling"
] | 2010 | A Role for ATF2 in Regulating MITF and Melanoma Development |
The cell envelope of mycobacteria , a group of Gram positive bacteria , is composed of a plasma membrane and a Gram-negative-like outer membrane containing mycolic acids . In addition , the surface of the mycobacteria is coated with an ill-characterized layer of extractable , non-covalently linked glycans , lipids and ... | The genus Mycobacterium contains a number of important pathogens , such as Mycobacterium tuberculosis . The highly characteristic cell envelope of these bacteria plays a crucial role in the infection process . The most apparent difference with other bacteria is the recently described outer membrane composed of unique (... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"cell",
"biology",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis"
] | 2010 | Direct Visualization by Cryo-EM of the Mycobacterial Capsular Layer: A Labile Structure Containing ESX-1-Secreted Proteins |
Adenoviruses are common pathogens , mostly targeting ocular , gastrointestinal and respiratory cells , but in some cases infection disseminates , presenting in severe clinical outcomes . Upon dissemination and contact with blood , coagulation factor X ( FX ) interacts directly with the adenovirus type 5 ( Ad5 ) hexon .... | Adenoviruses are mostly considered self-limiting pathogens associated with respiratory , gastrointestinal and ocular infections; however , in immunocompromised subjects disseminated Ad infection can occur with life-threatening consequences . Many human Ads are capable of binding to coagulation factor X ( FX ) . Followi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Manipulating Adenovirus Hexon Hypervariable Loops Dictates Immune Neutralisation and Coagulation Factor X-dependent Cell Interaction In Vitro and In Vivo |
The DNA damage checkpoint and the spindle assembly checkpoint ( SAC ) are two important regulatory mechanisms that respond to different lesions . The DNA damage checkpoint detects DNA damage , initiates protein kinase cascades , and inhibits the cell cycle . The SAC relies on kinetochore-dependent assembly of protein c... | Genome integrity is assured , in part , by regulatory systems called “checkpoints” that assure that cells do not improperly progress through the cell cycle . The DNA damage checkpoint assesses the status of DNA replication and inhibits cell cycle progression when the cell makes mistakes in DNA replication or when the c... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/nuclear",
"structure",
"and",
"function",
"genetics",
"and",
"genomics/cancer",
"genetics",
"genetics",
"and",
"genomics/chromosome",
"biology"
] | 2008 | DNA Damage Activates the SAC in an ATM/ATR-Dependent Manner, Independently of the Kinetochore |
The division of cellular space into functionally distinct membrane-defined compartments has been one of the major transitions in the history of life . Such compartmentalization has been claimed to occur in members of the Planctomycetes , Verrucomicrobiae , and Chlamydiae bacterial superphylum . Here we have investigate... | The compartmentalization of cellular space has been an important evolutionary innovation , allowing for the functional specialization of cellular space . This compartmentalization is extensively developed in eukaryotes and although not as complex and developed , compartments with specialized function are known to occur... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"theoretical",
"biology",
"membranes",
"and",
"sorting",
"biology",
"microbiology",
"molecular",
"cell",
"biology"
] | 2013 | Three-Dimensional Reconstruction of Bacteria with a Complex Endomembrane System |
The rostromedial tegmental nucleus ( RMTg ) , also called the GABAergic tail of the ventral tegmental area , projects to the midbrain dopaminergic system , dorsal raphe nucleus , locus coeruleus , and other regions . Whether the RMTg is involved in sleep–wake regulation is unknown . In the present study , pharmacogenet... | Sleep–wake behavior is controlled by networks of neurons and neurotransmitters in the brain . There are multiple populations of wake-promoting neurons , but few sleep-promoting neurons have been identified . In this study , we revealed that the rostromedial tegmental nucleus , the GABAergic tail of the ventral tegmenta... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"microinjection",
"sleep",
"drugs",
"opioids",
"brain",
"brain",
"electrophysiology",
"electrophysiology",
"neuroscience",
"physiological",
"processes",
"clinical",
"medicine",
"brain",
"mapping",
"analgesics",
"bioassays",
"and",
... | 2018 | The rostromedial tegmental nucleus is essential for non-rapid eye movement sleep |
Neuronal calcium acts as a charge carrier during information processing and as a ubiquitous intracellular messenger . Calcium signals are fundamental to numerous aspects of neuronal development and plasticity . Specific and independent regulation of these vital cellular processes is achieved by a rich bouquet of differ... | In neurons , calcium ions play a dual role as charge carriers and intracellular messengers , thereby linking brain activity to cellular changes . Alterations in the electrical potential across the cell's outer membrane ( as happens , for example , when a neuron fires an action potential ) , can induce an influx of calc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"arthropods",
"eukaryotes",
"neuroscience",
"animals",
"insects"
] | 2007 | Expanding the Neuron's Calcium Signaling Repertoire: Intracellular Calcium Release via Voltage-Induced PLC and IP3R Activation |
How combinations of gene-environment interactions collectively give rise to genotype-environment interactions is not fully understood . To shed light on this problem , we genetically dissected an environment-specific poor growth phenotype in a cross of two budding yeast strains . This phenotype is detectable when certa... | Determining the genetic and molecular mechanisms that give rise to genotype-environment interaction ( ‘GxE’ ) is important for many areas of biology , including agriculture , evolution , and medicine . To help advance knowledge regarding this topic , we dissect the genetic basis of an example of GxE in which certain Sa... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"variant",
"genotypes",
"carbohydrates",
"organic",
"compounds",
"glucose",
"genetic",
"mapping",
"fungi",
"model",
"organisms",
"alcohols",
"research",
"and",
"analysis",
"methods",
"saccharomyces",
"chr... | 2016 | Gene-Environment Interactions in Stress Response Contribute Additively to a Genotype-Environment Interaction |
Complex genetic networks consist of structural modules that determine the levels and timing of a cellular response . While the functional properties of the regulatory architectures that make up these modules have been extensively studied , the evolutionary history of regulatory architectures has remained largely unexpl... | A regulatory protein can activate the expression of a target gene either directly , i . e . , by binding to the gene's promoter , or indirectly , i . e . , by altering the expression of regulators , which , in turn , bind to the target gene's promoter and induce or inhibit its transcription . Indirect regulatory circui... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"computational",
"biology/transcriptional",
"regulation",
"microbiology/microbial",
"evolution",
"and",
"genomics",
"computational",
"biology/signaling",
"networks",
"computational",
"biology/systems",
"biol... | 2008 | Evolution and Dynamics of Regulatory Architectures Controlling Polymyxin B Resistance in Enteric Bacteria |
Cutaneous leishmaniasis ( CL ) is a vector-borne parasitic disease characterized by the presence of one or more lesions on the skin that usually heal spontaneously after a few months . Most cases of CL worldwide occur in Southwest Asia , Africa and South America , and a number of cases have been reported among troops d... | Cutaneous leishmaniasis ( CL ) is a vector-borne parasitic disease transmitted by the bite of sandflies , resulting in sores on the skin . No vaccines are available , and treatment relies on chemotherapy . CL has been frequently diagnosed in military personnel deployed to Afghanistan and returning from duty . The paras... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"biology"
] | 2012 | Genetic Polymorphisms and Drug Susceptibility in Four Isolates of Leishmania tropica Obtained from Canadian Soldiers Returning from Afghanistan |
In most cell types , mitosis and cytokinesis are tightly coupled such that cytokinesis occurs only once per cell cycle . The fission yeast Schizosaccharomyces pombe divides using an actomyosin-based contractile ring and is an attractive model for the study of the links between mitosis and cytokinesis . In fission yeast... | Cytokinesis is the process by which a mother cell is physically partitioned into two daughter cells . Cytokinesis is well coordinated with segregation of the genetic material to ensure that the genome is not damaged by the cell division apparatus . How untimely cytokinesis is prevented is not fully understood , and is ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"schizosaccharomymes",
"cell",
"biology"
] | 2008 | Nuc2p, a Subunit of the Anaphase-Promoting Complex, Inhibits Septation Initiation Network Following Cytokinesis in Fission Yeast |
Internalization of the pathogenic bacterium Pseudomonas aeruginosa by non-phagocytic cells is promoted by rearrangements of the actin cytoskeleton , but the host pathways usurped by this bacterium are not clearly understood . We used RNAi-mediated gene inactivation of ∼80 genes known to regulate the actin cytoskeleton ... | Mortality from Pseudomonas aeruginosa infections , one of the leading causes of hospital acquired infections , approaches 40% , and multiple drug resistant infections are common and increasing . Internalization of P . aeruginosa by the host cell appears to play a fundamental role in the pathogenesis of this opportunist... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology",
"infectious",
"diseases",
"microbiology"
] | 2008 | RNAi Screen Reveals an Abl Kinase-Dependent Host Cell Pathway Involved in Pseudomonas aeruginosa Internalization |
In several species , including rodents and fish , it has been shown that the Major Histocompatibility Complex ( MHC ) influences mating preferences and , in some cases , that this may be mediated by preferences based on body odour . In humans , the picture has been less clear . Several studies have reported a tendency ... | There has been a longstanding hypothesis that selection may have led to mating patterns that encourage heterozygosity at Major Histocompatibility Complex ( MHC ) loci because of improved immune response to pathogens in the offspring of such matings , and , indeed , this has been observed in several model systems . Howe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology/human",
"evolution",
"evolutionary",
"biology/sexual",
"behavior",
"evolutionary",
"biology/genomics",
"immunology/genetics",
"of",
"the",
"immune",
"system",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2008 | Is Mate Choice in Humans MHC-Dependent? |
The constant bombardment of mammalian genomes by transposable elements ( TEs ) has resulted in TEs comprising at least 45% of the human genome . Because of their great age and abundance , TEs are important in comparative phylogenomics . However , estimates of TE age were previously based on divergence from derived cons... | Transposable elements ( TEs ) are interspersed repetitive DNA families that are capable of copying themselves from place to place; they have literally infested our genome over evolutionary time , and now comprise as much as 45% of our total DNA . Because of their great age and abundance , TEs are important in evolution... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"vertebrates",
"mammals",
"homo",
"(human)",
"eukaryotes",
"computational",
"biology",
"evolutionary",
"biology",
"animals",
"genetics",
"and",
"genomics"
] | 2007 | Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation |
The formation of multinucleated muscle cells through cell-cell fusion is a conserved process from fruit flies to humans . Numerous studies have shown the importance of Arp2/3 , its regulators , and branched actin for the formation of an actin structure , the F-actin focus , at the fusion site . This F-actin focus forms... | Muscle formation and homeostasis critically depend on fusion between myoblasts to create and maintain multinucleated muscle fibers . Despite the importance of this process , the mechanisms regulating myoblast fusion are not fully understood . Previous studies have shown that actin polymerization factor Arp2/3 plays a c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | The Formin Diaphanous Regulates Myoblast Fusion through Actin Polymerization and Arp2/3 Regulation |
Intellectual Disability ( ID ) disorders , defined by an IQ below 70 , are genetically and phenotypically highly heterogeneous . Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strate... | Intellectual Disability ( ID ) affects 2% of our population and is associated with many different disorders . Although more than 400 causative genes ( ‘ID genes’ ) have been identified , their function remains poorly understood and the degree to which these disorders share a common molecular basis is unknown . Here , w... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Human Intellectual Disability Genes Form Conserved Functional Modules in Drosophila |
Genomic imprints—parental allele-specific DNA methylation marks at the differentially methylated regions ( DMRs ) of imprinted genes—are erased and reestablished in germ cells according to the individual's sex . Imprint establishment at paternally methylated germ line DMRs occurs in fetal male germ cells . In prosperma... | Allele-specific DNA methylation is considered the primary mark that distinguishes the parental alleles of imprinted genes . Whereas allele-specific chromatin also exists at imprinted genes in the soma , this has not been assessed in the germ line . It will be important to understand what extent the chromatin compositio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/germ",
"cells",
"genetics",
"and",
"genomics/animal",
"genetics",
"molecular",
"biology/transcription",
"initiation",
"and",
"activation",
"genetics",
"and",
"genomics/gene",
"expression",
"molecular",
"biology/dna",
"methylation",
"genetics",
"and",... | 2010 | CTCF-Dependent Chromatin Bias Constitutes Transient Epigenetic Memory of the Mother at the H19-Igf2 Imprinting Control Region in Prospermatogonia |
Herpes Simplex Virus type 1 ( HSV-1 ) has evolved to disable the cellular DNA damage response kinase , ATR . We have previously shown that HSV-1-infected cells are unable to phosphorylate the ATR substrate Chk1 , even under conditions in which replication forks are stalled . Here we report that the HSV-1 single strande... | DNA viruses that replicate in the nucleus have been shown to both activate and inactivate various components of the cellular DNA damage response ( DDR ) . Previous reports from our laboratory and others have demonstrated that Herpes Simplex Virus ( HSV ) utilizes some aspects of the DDR while inactivating others . Para... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Herpes Simplex Virus Type 1 Single Strand DNA Binding Protein and Helicase/Primase Complex Disable Cellular ATR Signaling |
The ability to adapt to different conditions is key for Mycobacterium tuberculosis , the causative agent of tuberculosis ( TB ) , to successfully infect human hosts . Adaptations allow the organism to evade the host immune responses during acute infections and persist for an extended period of time during the latent in... | Mycobacterium tuberculosis latently infects one-third of the human population and is responsible for millions of deaths worldwide every year . The ability of the pathogen to persist in the human population stems from its capacity to adapt to host-induced stresses and adjust its metabolism to different host environments... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"medicine",
"infectious",
"diseases",
"tropical",
"diseases",
"(non-neglected)",
"tuberculosis",
"biology",
"infectious",
"disease",
"modeling",
"genetics",
"and",
"genomics"
] | 2012 | Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia |
Nuclear receptors ( NRs ) are transcription factors that are implicated in several biological processes such as embryonic development , homeostasis , and metabolic diseases . To study the role of NRs in development , it is critically important to know when and where individual genes are expressed . Although systematic ... | NRs are key molecules controlling development , metabolism , and reproduction in metazoans . Since NRs are implicated in many human diseases such as cancer , metabolic syndrome , and hormone resistance , they are important pharmaceutical targets and are under intense scrutiny to better understand their biological funct... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"danio",
"(zebrafish)",
"diabetes",
"and",
"endocrinology",
"vertebrates",
"evolutionary",
"biology",
"genetics",
"and",
"genomics"
] | 2007 | Unexpected Novel Relational Links Uncovered by Extensive Developmental Profiling of Nuclear Receptor Expression |
Many core components of the microRNA pathway have been elucidated and knowledge of their mechanisms of action actively progresses . In contrast , factors with modulatory roles on the pathway are just starting to become known and understood . Using a genetic screen in Caenorhabditis elegans , we identify a component of ... | The microRNA pathway is a post-transcriptional gene regulatory system that uses small non-coding RNAs called microRNAs to control multiple developmental and physiological processes . With the goal of unveiling factors modulating this regulatory pathway , we have undertaken the exploration of genetic interactors in the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | A New Role for the GARP Complex in MicroRNA-Mediated Gene Regulation |
Conventional methods used to characterize multidimensional neural feature selectivity , such as spike-triggered covariance ( STC ) or maximally informative dimensions ( MID ) , are limited to Gaussian stimuli or are only able to identify a small number of features due to the curse of dimensionality . To overcome these ... | Neurons are capable of simultaneously encoding information about multiple features of sensory stimuli in their spikes . The dimensionality reduction methods that currently exist to extract those relevant features are either biased for non-Gaussian stimuli or fall victim to the curse of dimensionality . In this paper we... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"algorithms",
"visual",
"system",
"computer",
"science",
"computational",
"neuroscience",
"biology",
"sensory",
"systems",
"neuroscience",
"coding",
"mechanisms"
] | 2011 | Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models |
Bacteria within biofilms secrete and surround themselves with an extracellular matrix , which serves as a first line of defense against antibiotic attack . Polysaccharides constitute major elements of the biofilm matrix and are implied in surface adhesion and biofilm organization , but their contributions to the resist... | Many bacteria have the ability to form multicellular communities , termed biofilms . An important characteristic of a biofilm is the ability of cells to synthesize and secrete an extracellular matrix . This matrix offers structural support , community organization , and added protection , often making the cells impervi... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"bacterial",
"biofilms",
"biology",
"microbiology"
] | 2013 | The Extracellular Matrix Component Psl Provides Fast-Acting Antibiotic Defense in Pseudomonas aeruginosa Biofilms |
The lack of awareness about dog-bite related rabies in the rural population of developing countries , including India , is a major impediment to controlling the incidence of disease in humans . A survey of 127 rural residents was undertaken in Shirsuphal village in western India using a structured questionnaire to asse... | The rural population in developing countries , such as India , are most vulnerable to transmission of rabies , especially due to animal-bites . The widespread trust in traditional healing practices for treating animal-bite injuries undermines the importance of seeking post-bite vaccination against rabies . In spite of ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"animal",
"types",
"livestock",
"medicine",
"and",
"health",
"sciences",
"health",
"education",
"and",
"awareness",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"india",
"pets",
"and",
"companion",
"animals",
"dogs",
"animals",
"mammals",
"healt... | 2019 | Knowledge, attitudes and practices (KAP) towards rabies and free-roaming dogs (FRD) in Shirsuphal village in western India: A community based cross-sectional study |
Eukaryotes , protozoan , and helminth parasites make extensive use of protein kinases to control cellular functions , suggesting that protein kinases may represent novel targets for the development of anti-parasitic drugs . Because of their central role in intracellular signaling pathways , cyclic nucleotide–dependent ... | Schistosomes are parasitic flatworms that inhabit the circulatory system and are the cause of a debilitating and insidious disease for millions of people worldwide . Like other complex organisms , schistosomes and other parasitic worms regulate their cell biology through extensive use of enzymes called protein kinases ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"cell",
"biology/cell",
"signaling",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/helminth",
"infections",
"biochemistry/cell",
"signaling",
"and",
"trafficking",
"structures",
"infectious",
"diseases/tropical",
"and",
"travel-associated",
... | 2009 | A Schistosome cAMP-Dependent Protein Kinase Catalytic Subunit Is Essential for Parasite Viability |
Wolbachia are widespread endosymbionts found in a large variety of arthropods . While these bacteria are generally transmitted vertically and exhibit weak virulence in their native hosts , a growing number of studies suggests that horizontal transfers of Wolbachia to new host species also occur frequently in nature . I... | Characterizing the causes of a virulence increase when a parasite jumps from one host species to another is fundamental to the understanding of disease emergence . In this context , we studied the bacterium Wolbachia wVulC , a natural symbiont of one terrestrial isopod species that becomes a pathogen when transfected i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"cell",
"biology",
"zoology",
"ecology",
"genetics",
"immunology",
"biology",
"microbiology",
"evolutionary",
"biology",
"population",
"biology",
"neuroscience",
"genetics",
"and",
"genomics"
] | 2012 | High Virulence of Wolbachia after Host Switching: When Autophagy Hurts |
Idiopathic epilepsy is a common human disorder with a strong genetic component , usually exhibiting complex inheritance . We describe a new mouse mutation in C57BL/6J mice , called frequent-flyer ( Ff ) , in which disruption of the gene encoding RNA-binding protein Bruno-like 4 ( Brunol4 ) leads to limbic and severe to... | Epilepsy is a very common brain disorder characterized by recurrent seizures , resulting from abnormal nerve cell activity in the brain . Some cases of epilepsy are caused by brain trauma , such as stroke , infection , tumor , or head injury . Others—so called “idiopathic”—do not have a clear cause . Many idiopathic ep... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"neurological",
"disorders",
"mus",
"(mouse)",
"neuroscience",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2007 | Complex Seizure Disorder Caused by Brunol4 Deficiency in Mice |
Cortical responses to sensory inputs vary across repeated presentations of identical stimuli , but how this trial-to-trial variability impacts detection of sensory inputs is not fully understood . Using multi-channel local field potential ( LFP ) recordings in primary somatosensory cortex ( S1 ) of the awake mouse , we... | Establishing the link between neural activity and behavior is a central goal of neuroscience . One context in which to examine this link is in a sensory detection task , in which an animal is trained to report the presence of a barely perceptible sensory stimulus . In such tasks , both sensory responses in the brain an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"single",
"channel",
"recording",
"medicine",
"and",
"health",
"sciences",
"engineering",
"and",
"technology",
"statistics",
"somatosensory",
"cortex",
"signal",
"processing",
"matched",
"filters",
"brain",
"social",
"sciences",
"neuroscience",
"signal",
"filtering",
"m... | 2019 | State-aware detection of sensory stimuli in the cortex of the awake mouse |
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