2023
Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species
Pearce V, Groisman E, Townsend G. Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species. Gut Microbes 2023, 15: 2221484. PMID: 37358144, PMCID: PMC10294740, DOI: 10.1080/19490976.2023.2221484.Peer-Reviewed Original ResearchConceptsMaster regulatorMicrobial populationsOrthologous transcription factorsMammalian gut microbiotaMicrobial gene expressionHuman gut symbiontHuman gut BacteroidesDistinct microbial populationsIntestinal Bacteroides speciesGut symbiontsCarbohydrate utilizationMRNA leaderTranscription factorsHost dietGut BacteroidesNutrient availabilityGene expressionMolecular pathwaysUnknown mechanismDietary sugarsBacteroides speciesFuture therapeutic interventionsRegulatorSimple sugarsPathogenic outcomes
2022
N-nitrosamines-mediated downregulation of LncRNA-UCA1 induces carcinogenesis of esophageal squamous by regulating the alternative splicing of FGFR2
Wang X, Sun M, Gao Z, Yin L, Pu Y, Zhu Y, Wang X, Liu R. N-nitrosamines-mediated downregulation of LncRNA-UCA1 induces carcinogenesis of esophageal squamous by regulating the alternative splicing of FGFR2. The Science Of The Total Environment 2022, 855: 158918. PMID: 36169023, DOI: 10.1016/j.scitotenv.2022.158918.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingCarcinogenesisCell Line, TumorCell MovementCell ProliferationDown-RegulationEpigenesis, GeneticEsophageal NeoplasmsEsophageal Squamous Cell CarcinomaGene Expression Regulation, NeoplasticHeterogeneous-Nuclear Ribonucleoprotein Group F-HHumansMicroRNAsNitrosaminesPhosphatidylinositol 3-KinasesProto-Oncogene Proteins c-aktReceptor, Fibroblast Growth Factor, Type 2RNA, Long NoncodingConceptsFibroblast growth factor receptor 2Alternative splicingEsophageal squamous cell carcinomaExact molecular mechanismsHet-1A cellsDownregulation of UCA1Epithelial-mesenchymal transitionPI3K-AKT axisFGFR2-IIIcMolecular mechanismsPI3K-AktF proteinUnknown mechanismESCC cellsESCC progressionSplicingN-nitrosamine exposureGrowth factor receptor 2Squamous cell carcinomaDigestive system tumorsRegulation levelESCC tissuesFactor receptor 2High incidence areaLncRNA UCA1A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane
Guillén-Samander A, Wu Y, Pineda SS, García FJ, Eisen JN, Leonzino M, Ugur B, Kellis M, Heiman M, De Camilli P. A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2205425119. PMID: 35994651, PMCID: PMC9436381, DOI: 10.1073/pnas.2205425119.Peer-Reviewed Original ResearchConceptsCaudate neuronsClinical manifestationsExposure of PtdSerPH domainMcLeod syndromeCell surface exposureER-PM contactsLipid dropletsTransport of lipidsPutative roleUnknown mechanismNeuronsLipid transfer proteinVPS13ALipid scramblasesTransfer proteinCytosolic loopExposurePlasma membraneCell surfaceEndoplasmic reticulumLipid transferERSyndromeDiseaseInnate and Adaptive Immunity to Transfused Allogeneic RBCs in Mice Requires MyD88.
Soldatenko A, Hoyt LR, Xu L, Calabro S, Lewis SM, Gallman AE, Hudson KE, Stowell SR, Luckey CJ, Zimring JC, Liu D, Santhanakrishnan M, Hendrickson JE, Eisenbarth SC. Innate and Adaptive Immunity to Transfused Allogeneic RBCs in Mice Requires MyD88. The Journal Of Immunology 2022, 208: 991-997. PMID: 35039331, PMCID: PMC10107373, DOI: 10.4049/jimmunol.2100784.Peer-Reviewed Original ResearchConceptsPattern recognition receptorsDendritic cellsDC activationAdaptive immunityClass of PRRsNon-ABO alloantibodiesRecipient dendritic cellsSplenic dendritic cellsMouse RBCsInflammatory cytokine responseTreatment of anemiaRBC transfusion therapyTransfused RBCsAlloantibody responsesAllogeneic RBCsSerious complicationsCytokine responsesTransfusion therapyRecognition receptorsMyD88TransfusionAlloimmunizationRBCsTRIFUnknown mechanism
2020
Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA
Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y. Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA. Molecular Cell 2020, 80: 1055-1066.e6. PMID: 33188728, PMCID: PMC7833686, DOI: 10.1016/j.molcel.2020.10.034.Peer-Reviewed Original ResearchConceptsInternal ribosome entry site RNANonstructural protein 1Host protein synthesis machineryMRNA entry channelProtein synthesis machineryCryo-EM structureProtein 1Major pathogenicity factorsDifferential expression analysisMRNA-seq dataCellular transcriptomePreinitiation complexSynthesis machineryHuman lung originTranslation inhibitionPathogenicity factorsExpression analysisSite RNAHost viabilityNSP1Protein synthesisEntry channelViral proteinsUnknown mechanismViral RNA
2019
Cediranib suppresses homology-directed DNA repair through down-regulation of BRCA1/2 and RAD51
Kaplan AR, Gueble SE, Liu Y, Oeck S, Kim H, Yun Z, Glazer PM. Cediranib suppresses homology-directed DNA repair through down-regulation of BRCA1/2 and RAD51. Science Translational Medicine 2019, 11 PMID: 31092693, PMCID: PMC6626544, DOI: 10.1126/scitranslmed.aav4508.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBRCA1 ProteinBRCA2 ProteinCell Line, TumorDNA RepairDown-RegulationE2F4 Transcription FactorFemaleGene Expression Regulation, NeoplasticHumansMice, NudePoly(ADP-ribose) Polymerase InhibitorsQuinazolinesRad51 RecombinaseReceptors, Platelet-Derived Growth FactorTumor HypoxiaVascular Endothelial Growth Factor Receptor-2Xenograft Model Antitumor AssaysConceptsHomology-directed DNA repairDNA repairE2F transcription factor 4Protein phosphatase 2ATranscription factor 4DNA repair inhibitorsPhosphatase 2ARAD51 recombinaseTranscriptional corepressorMouse tumor xenograftsSynthetic lethalityGene expressionRB2/Mouse bone marrowGrowth factor receptor inhibitionRepair inhibitorsUnknown mechanismPlatelet-derived growth factor receptor inhibitionFactor 4Human tumorsInhibitor olaparibPARP inhibitorsMutationsCombination of cediranibCancer therapy
2017
Ciliary Mechanisms of Cyst Formation in Polycystic Kidney Disease
Ma M, Gallagher AR, Somlo S. Ciliary Mechanisms of Cyst Formation in Polycystic Kidney Disease. Cold Spring Harbor Perspectives In Biology 2017, 9: a028209. PMID: 28320755, PMCID: PMC5666631, DOI: 10.1101/cshperspect.a028209.Peer-Reviewed Original ResearchConceptsPolycystin-2Autosomal dominant polycystic kidney diseaseCalcium-mediated signalsRole of ciliaDisruption of ciliaPolycystic kidney diseaseCellular processesCausal genesTransmembrane proteinTissue homeostasisCilia functionPrimary ciliaPolycystinsGenetic studiesHomeostatic maintenanceSignal integrationUnknown mechanismApical surfaceNephron structuresCiliaKidney tubule cellsIntact ciliaPrivileged compartmentActive remodelingTubule structure
2015
Feeding state-dependent regulation of developmental plasticity via CaMKI and neuroendocrine signaling
Neal S, Takeishi A, O'Donnell M, Park J, Hong M, Butcher R, Kim K, Sengupta P. Feeding state-dependent regulation of developmental plasticity via CaMKI and neuroendocrine signaling. ELife 2015, 4: e10110. PMID: 26335407, PMCID: PMC4558564, DOI: 10.7554/elife.10110.Peer-Reviewed Original ResearchConceptsNeuroendocrine signalingDevelopmental plasticityInsulin-like peptide genesDynamic subcellular localizationDauer decisionDauer formationILP genesDauer stageDevelopmental decisionsSubcellular localizationNutrient availabilityState-dependent regulationPeptide genesReproductive cycleUnknown mechanismCaMKICMK-1SignalingGenesSensory neuronsPlasticityExpressionAWCCaenorhabditisSmall neuronal networks
2013
The common hereditary elliptocytosis-associated α-spectrin L260P mutation perturbs erythrocyte membranes by stabilizing spectrin in the closed dimer conformation
Harper SL, Sriswasdi S, Tang HY, Gaetani M, Gallagher PG, Speicher DW. The common hereditary elliptocytosis-associated α-spectrin L260P mutation perturbs erythrocyte membranes by stabilizing spectrin in the closed dimer conformation. Blood 2013, 122: 3045-3053. PMID: 23974198, PMCID: PMC3811177, DOI: 10.1182/blood-2013-02-487702.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesCross-Linking ReagentsElliptocytosis, HereditaryErythrocyte MembraneHumansModels, MolecularMolecular Sequence DataMutationProtein BindingProtein MultimerizationProtein StabilityProtein Structure, SecondaryProtein Structure, TertiaryRecombinant ProteinsSpectrinConceptsHereditary elliptocytosisMembrane destabilizationLarge conformational rearrangementsGel filtration analysisMembrane proteinsTetramer assemblyHereditary pyropoikilocytosisBiophysical analysisCommon hereditary elliptocytosisConformational rearrangementsDimer conformationHelical contentTetramerization siteFiltration analysisSpectrin tetramersNovel mechanismUnknown mechanismMutationsBinding assaysSpectrinChemical crosslinkingErythrocyte shapeTetramerErythrocyte membranesMembrane
2012
Binding of the Heterogeneous Ribonucleoprotein K (hnRNP K) to the Epstein-Barr Virus Nuclear Antigen 2 (EBNA2) Enhances Viral LMP2A Expression
Gross H, Hennard C, Masouris I, Cassel C, Barth S, Stober-Grässer U, Mamiani A, Moritz B, Ostareck D, Ostareck-Lederer A, Neuenkirchen N, Fischer U, Deng W, Leonhardt H, Noessner E, Kremmer E, Grässer FA. Binding of the Heterogeneous Ribonucleoprotein K (hnRNP K) to the Epstein-Barr Virus Nuclear Antigen 2 (EBNA2) Enhances Viral LMP2A Expression. PLOS ONE 2012, 7: e42106. PMID: 22879910, PMCID: PMC3411732, DOI: 10.1371/journal.pone.0042106.Peer-Reviewed Original ResearchMeSH KeywordsAntibodies, MonoclonalAntibody SpecificityArginineCell LineDNAEpstein-Barr Virus InfectionsEpstein-Barr Virus Nuclear AntigensGene Expression Regulation, ViralHerpesvirus 4, HumanHeterogeneous-Nuclear Ribonucleoprotein KHumansImmunoprecipitationMethylationMolecular Sequence DataMultiprotein ComplexesMutant ProteinsPromoter Regions, GeneticProtein BindingProtein TransportRepetitive Sequences, Amino AcidsnRNP Core ProteinsTransfectionViral Matrix ProteinsViral ProteinsConceptsEpstein-Barr virus nuclear antigen 2Survival motor neuron (SMN) proteinHnRNP KHeterogeneous ribonucleoprotein KRG repeatsCellular proteinsSDMA-specific antibodyGel shift experimentsMotor neuron proteinHnRNP K.Cellular homologueCellular processesSequence motifsNp9 proteinsHuman endogenous retrovirus KArginine residuesNeuron proteinEBNA2 proteinShift experimentsLMP2A expressionNuclear antigen 2ProteinUnknown mechanismE. coliArginine-GlycineRole of RhoA-Specific Guanine Exchange Factors in Regulation of Endomitosis in Megakaryocytes
Gao Y, Smith E, Ker E, Campbell P, Cheng EC, Zou S, Lin S, Wang L, Halene S, Krause DS. Role of RhoA-Specific Guanine Exchange Factors in Regulation of Endomitosis in Megakaryocytes. Developmental Cell 2012, 22: 573-584. PMID: 22387001, PMCID: PMC3306542, DOI: 10.1016/j.devcel.2011.12.019.Peer-Reviewed Original ResearchConceptsGEF-H1Efficient platelet productionExchange factor GEF-H1Guanine exchange factorGEF-H1 knockdownDevelopment of aneuploidyGEF-H1 expressionMK polyploidizationExchange factorPloidy defectsAberrant mitosisDevelopmental processesExogenous expressionPolyploidizationRhoA activationEndomitotic cyclePrimary cellsUnknown mechanismMechanistic insightsECT2EndomitosisAneuploid cancersPlatelet productionMegakaryocytesDownregulation
2011
A Pathway for the Control of Anoikis Sensitivity by E-Cadherin and Epithelial-to-Mesenchymal Transition
Kumar S, Park SH, Cieply B, Schupp J, Killiam E, Zhang F, Rimm DL, Frisch SM. A Pathway for the Control of Anoikis Sensitivity by E-Cadherin and Epithelial-to-Mesenchymal Transition. Molecular And Cellular Biology 2011, 31: 4036-4051. PMID: 21746881, PMCID: PMC3187352, DOI: 10.1128/mcb.01342-10.Peer-Reviewed Original ResearchConceptsRegulation of anoikisE-cadherin complexMesenchymal transitionE-cadherinAnoikis sensitivityNuclear localizationInappropriate matrixAnoikis resistanceApoptotic responseOncogenic EMTAnoikisNRAGECellular sensitivityNovel pathwayUnknown mechanismAnkyrinEpithelial cellsEMTPathwayP14ARFCellsTbx2ComplexesGenesCytoplasm
2010
SplicerAV: a tool for mining microarray expression data for changes in RNA processing
Robinson TJ, Dinan MA, Dewhirst M, Garcia-Blanco MA, Pearson JL. SplicerAV: a tool for mining microarray expression data for changes in RNA processing. BMC Bioinformatics 2010, 11: 108. PMID: 20184770, PMCID: PMC2838864, DOI: 10.1186/1471-2105-11-108.Peer-Reviewed Original ResearchConceptsIsoform changesMRNA processingGuanyl nucleotide exchange factorMicroarray datasetsMRNA processing factorsTranscript isoform abundanceAlternative mRNA processingHG-U133Expression of HRASUnknown mechanismMicroarray expression dataHuman mammary epithelial cellsGene expression microarraysMammary epithelial cellsRNA processingExchange factorBreast cancer microarray datasetsAffymetrix HG-U133Alternative mRNABreast tumorsEGFR activationGene expressionExpression microarraysCancer microarray datasetsSpecific expression
2009
Ubiquitin-dependent lysosomal targeting of GABAA receptors regulates neuronal inhibition
Arancibia-Cárcamo I, Yuen E, Muir J, Lumb M, Michels G, Saliba R, Smart T, Yan Z, Kittler J, Moss S. Ubiquitin-dependent lysosomal targeting of GABAA receptors regulates neuronal inhibition. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 17552-17557. PMID: 19815531, PMCID: PMC2762659, DOI: 10.1073/pnas.0905502106.Peer-Reviewed Original ResearchConceptsSynaptic inhibitionGamma2 subunitInhibitory transmissionCerebral ischemiaAnoxic insultNeuronal inhibitionGABAA receptorsExcitatory currentsSynaptic sitesLysosomal targetingPathological conditionsLysosomal activityUnknown mechanismInhibitionReceptorsMolecular mechanismsIntracellular domainTargetingPathwayIschemiaNeuropathologyEndocytic pathwayInsult
2008
Heterozygous expression of myocilin glaucoma mutants increases secretion of the mutant forms and reduces extracellular processed myocilin.
Aroca-Aguilar JD, Sánchez-Sánchez F, Martínez-Redondo F, Coca-Prados M, Escribano J. Heterozygous expression of myocilin glaucoma mutants increases secretion of the mutant forms and reduces extracellular processed myocilin. Molecular Vision 2008, 14: 2097-108. PMID: 19023451, PMCID: PMC2585175.Peer-Reviewed Original ResearchConceptsWild-type myocilinWild-type proteinMyocilin mutantsMutant myocilinMutant formsProteolytic processingMissense mutant formsHEK 293T cellsMyocilin geneMutant proteinsSecretory pathwayUnidentified functionExtracellular proteinsMutantsEndoproteolytic processingRecombinant mutantsMyocilin secretionCellular fractionsHeterozygous expressionMyocilinProteinUnknown mechanismExtracellular amountSDS-PAGEHeterozygous stateThe N-Terminal Domain of Nogo-A Inhibits Cell Adhesion and Axonal Outgrowth by an Integrin-Specific Mechanism
Hu F, Strittmatter SM. The N-Terminal Domain of Nogo-A Inhibits Cell Adhesion and Axonal Outgrowth by an Integrin-Specific Mechanism. Journal Of Neuroscience 2008, 28: 1262-1269. PMID: 18234903, PMCID: PMC2856844, DOI: 10.1523/jneurosci.1068-07.2008.Peer-Reviewed Original ResearchConceptsCell adhesionFocal adhesion kinase activationN-terminal domainAxonal outgrowthInhibits cell adhesionAxonal growth conesCNS axon regenerationKinase activationCertain integrinsIntegrin activatorIntegrin beta1Widespread expressionExtracellular matrixSecond domainAlpha5 integrinUnknown mechanismIntegrinsGrowth conesNogo-A proteinCell linesAlpha6 integrinNogo-66 receptorAxonal growthAdult brainOutgrowth
2004
Targeted deletion of numb and numblike in sensory neurons reveals their essential functions in axon arborization
Huang EJ, Li H, Tang AA, Wiggins AK, Neve RL, Zhong W, Jan LY, Jan YN. Targeted deletion of numb and numblike in sensory neurons reveals their essential functions in axon arborization. Genes & Development 2004, 19: 138-151. PMID: 15598981, PMCID: PMC540232, DOI: 10.1101/gad.1246005.Peer-Reviewed Original ResearchConceptsNuclear Notch1Sensory neuronsAxon arborizationAccumulation of Notch1Conditional mouse mutantsAxon branch pointsAfferent fibersSensory gangliaAxonal arborizationAxonal lengthSevere reductionAxon lengthArborizationCre recombinaseNotch1Endocytic-lysosomal pathwayTargeted deletionSignificant increaseUnknown mechanismNeuronsOverexpression of NumbMouse mutantsGangliaNeurogenesisPathwayNon‐redundancy of cytidine deaminases in class switch recombination
Fugmann SD, Rush JS, Schatz DG. Non‐redundancy of cytidine deaminases in class switch recombination. European Journal Of Immunology 2004, 34: 844-849. PMID: 14991614, DOI: 10.1002/eji.200324418.Peer-Reviewed Original ResearchConceptsActivation-induced cytidine deaminaseClass switch recombinationAPOBEC-1Human activation-induced cytidine deaminaseSwitch recombinationCognate substratesCatalytic mutantGene conversionClose homologueProkaryotic cellsInactive mutantMurine B cellsDistinct mRNAsCytidine deaminase activityCytidine deaminasesImmunoglobulin genesDiversification mechanismsCytidine deaminaseSomatic hypermutationUnknown mechanismDeaminase activityMutantsPrecise roleActivated B cellsB cells
2003
Regulation of RAG1/RAG2‐mediated transposition by GTP and the C‐terminal region of RAG2
Tsai C, Schatz DG. Regulation of RAG1/RAG2‐mediated transposition by GTP and the C‐terminal region of RAG2. The EMBO Journal 2003, 22: 1922-1930. PMID: 12682024, PMCID: PMC154477, DOI: 10.1093/emboj/cdg185.Peer-Reviewed Original ResearchConceptsFull-length RAG2RAG2 proteinsRegulatory mechanismsC-terminal regionRAG proteinsHybrid joint formationDNA recognitionDNA transpositionCleavage functionChromosomal translocationsGTPUnknown mechanismRAG2ProteinTarget DNAPhysiological concentrationsRegulationJoint formationRAGRAG1MechanismTranslocationDNAGuanineTransposition
2000
Apoptosis and Regeneration of Hepatocytes during Recovery from Transient Hepadnavirus Infections
Guo J, Zhou H, Liu C, Aldrich C, Saputelli J, Whitaker T, Barrasa M, Mason W, Seeger C. Apoptosis and Regeneration of Hepatocytes during Recovery from Transient Hepadnavirus Infections. Journal Of Virology 2000, 74: 1495-1505. PMID: 10627561, PMCID: PMC111485, DOI: 10.1128/jvi.74.3.1495-1505.2000.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApoptosisCD4-Positive T-LymphocytesCD8-Positive T-LymphocytesDNA, ViralHepatitis BHepatitis B Virus, WoodchuckHepatitis B, ChronicInterferon-gammaLiverLiver RegenerationMarmotaMolecular Sequence DataReverse Transcriptase Polymerase Chain ReactionTumor Necrosis Factor-alphaViremiaConceptsRegeneration of hepatocytesHepadnavirus infectionTransient infectionHepatitis B virus infectionTumor necrosis factor alphaTransient hepadnavirus infectionsB virus infectionT cell accumulationNecrosis factor alphaCytokine expressionInfected hepatocytesFactor alphaT cellsVirus infectionInterferon gammaInfected liverHistologic analysisLiver tissueInfectionRecovery periodSignificant increaseHepatocytesInitial influxUnknown mechanismApoptosis
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