2024
Noncoding variants and sulcal patterns in congenital heart disease: Machine learning to predict functional impact
Mondragon-Estrada E, Newburger J, DePalma S, Brueckner M, Cleveland J, Chung W, Gelb B, Goldmuntz E, Hagler D, Huang H, McQuillen P, Miller T, Panigrahy A, Porter G, Roberts A, Rollins C, Russell M, Tristani-Firouzi M, Grant P, Im K, Morton S. Noncoding variants and sulcal patterns in congenital heart disease: Machine learning to predict functional impact. IScience 2024, 28: 111707. PMID: 39877905, PMCID: PMC11772982, DOI: 10.1016/j.isci.2024.111707.Peer-Reviewed Original ResearchNoncoding variantsCongenital heart diseaseFunctions related to neuronal developmentGene regulatory signalsH3K9me2 modificationRegulatory signalsCongenital heart disease cohortsDevelopmental pathwaysNeuronal developmentFolding patternHeart diseaseFunctional impactGenetic factorsGenesVariantsBrain developmentPredictive impactSulcal patterns
2020
Endocrine Autoimmune Disease as a Fragility of Immune Surveillance against Hypersecreting Mutants
Kohanim Y, Tendler A, Mayo A, Friedman N, Alon U. Endocrine Autoimmune Disease as a Fragility of Immune Surveillance against Hypersecreting Mutants. Immunity 2020, 52: 872-884.e5. PMID: 32433950, PMCID: PMC7237888, DOI: 10.1016/j.immuni.2020.04.022.Peer-Reviewed Original ResearchConceptsAutoreactive T cellsAutoimmune diseasesHormone secretion pathwaysBalance cell proliferationExperimental follow-upOrigin of autoimmune diseasesT cellsMutant cellsSecretion pathwayOrganismal homeostasisPresence of autoreactive T cellsRegulatory signalsTargets of autoimmune attackEndocrine autoimmune diseasesFrequent targetMutantsCell proliferationImmune surveillanceSelf-antigensAutoimmune attackFollow-upEndocrine tissuesHealthy individualsFeedback loopCellsChapter 20 Phosphorus homeostasis and related disorders
Carpenter T, Bergwitz C, Insogna K. Chapter 20 Phosphorus homeostasis and related disorders. 2020, 469-507. DOI: 10.1016/b978-0-12-814841-9.00020-8.ChaptersEndocrine fibroblast growth factorsSupply of phosphateComplex regulatory systemMolecular regulationRegulatory signalsFibroblast growth factorIntricate mechanismsPhosphate transferRegulatory systemNovel targetBone biologyMammalian boneCritical roleDistinct classesGrowth factorSkeletal mineralizationCentral rolePhosphate metabolismPrincipal mediatorEndocrine organClasses of transportersPhosphorus homeostasisBiologyTransportersLocal milieu
2018
Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins
Panda S, Setia M, Kaur N, Shepal V, Arora V, Singh D, Mondal A, Teli A, Tathode M, Gajula R, Padhy L, Shiras A. Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins. PLOS Biology 2018, 16: e2004204. PMID: 30296263, PMCID: PMC6193740, DOI: 10.1371/journal.pbio.2004204.Peer-Reviewed Original ResearchConceptsGenomic stabilityNoncoding RNAsMouse cellsBreast cancer type 1 susceptibility proteinLong intergenic noncoding RNAsIntergenic noncoding RNAsGrowth regulatory signalsLong noncoding RNAHitherto unknown mechanismEukaryotic transcriptomesMitotic regulationCellular homeostasisTranscript pairsCentrosomal proteinsRNA functionMitotic fidelityAntisense transcriptsSusceptibility proteinProtein interactionsEmbryonic developmentFunctional characterisationIndividual transcriptsBRCA1 proteinRegulatory signalsAdult tissues
2016
Inositol hexakisphosphate kinase 1 (IP6K1) activity is required for cytoplasmic dynein-driven transport
Chanduri M, Rai A, Malla A, Wu M, Fiedler D, Mallik R, Bhandari R. Inositol hexakisphosphate kinase 1 (IP6K1) activity is required for cytoplasmic dynein-driven transport. Biochemical Journal 2016, 473: 3031-3047. PMID: 27474409, PMCID: PMC5095903, DOI: 10.1042/bcj20160610.Peer-Reviewed Original ResearchConceptsInositol pyrophosphatesP150(Glued) subunit of dynactinIntermediate chainEukaryotic signaling moleculesRecruitment to membranesDynein intermediate chainP150(Glued) subunitSubunit of dynactinInositol hexakisphosphate kinase 1Inositol hexakisphosphate kinasesSerine pyrophosphorylationEndosomal sortingGolgi maintenanceVesicle transportTrafficking pathwaysVesicle movementDynein functionProtein functionMammalian cellsDiphosphoinositol pentakisphosphateDisplay defectsN-terminusRegulatory signalsMonophosphate moietyMicrotubule transport
2015
Proteomic Analysis of the Pericyte Derived Extracellular Matrix
Brown L, Sava P, Garcia C, Gonzalez A. Proteomic Analysis of the Pericyte Derived Extracellular Matrix. Cellular And Molecular Bioengineering 2015, 8: 349-363. DOI: 10.1007/s12195-015-0408-5.Peer-Reviewed Original ResearchMatrix proteinsStructural ECM proteinsBasic cellular responsesExtracellular matrix proteinsFunctional annotationProteomic analysisRegulatory signalsCell rufflingECM proteinsCellular responsesWestern blot analysisECM componentsExtracellular matrixEndothelial cell tubule formationFirst characterizationProteinMigratory velocityBlot analysisTubule formationECMNeutrophil polarizationStructural collagenVascular integrityLC/MS-MSBasement membrane
2012
A Dual Interaction between the DNA Damage Response Protein MDC1 and the RAG1 Subunit of the V(D)J Recombinase*
Coster G, Gold A, Chen D, Schatz DG, Goldberg M. A Dual Interaction between the DNA Damage Response Protein MDC1 and the RAG1 Subunit of the V(D)J Recombinase*. Journal Of Biological Chemistry 2012, 287: 36488-36498. PMID: 22942284, PMCID: PMC3476314, DOI: 10.1074/jbc.m112.402487.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAmino Acid MotifsBRCA1 ProteinCell Cycle ProteinsCell Line, TumorHistonesHomeodomain ProteinsHumansModels, BiologicalNuclear ProteinsPeptide MappingPhosphorylationProtein Structure, TertiaryRepetitive Sequences, Amino AcidTrans-ActivatorsVDJ RecombinasesConceptsDNA double-strand breaksDNA damage responseTandem BRCA1 C-terminal (BRCT) domainsC-terminusSpecific DNA double-strand breaksBRCA1 C-terminal domainC-terminal domainThreonine-rich repeatsDouble-strand breaksRAG1 subunitRAG recombinaseRAG2 proteinsDDR proteinsDamage responseRegulatory signalsBinding interfaceBreak siteHistone H2AXRAG activityRich repeatsNon-core regionsMDC1RAG1PhosphorylationSubsequent signal amplification
2007
AU-Rich-Element-Mediated Upregulation of Translation by FXR1 and Argonaute 2
Vasudevan S, Steitz JA. AU-Rich-Element-Mediated Upregulation of Translation by FXR1 and Argonaute 2. Cell 2007, 128: 1105-1118. PMID: 17382880, PMCID: PMC3430382, DOI: 10.1016/j.cell.2007.01.038.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsArgonaute ProteinsCell CycleCell LineChromatography, AffinityCulture Media, Serum-FreeEukaryotic Initiation Factor-2Genes, ReporterHumansLuciferases, FireflyMonocytesPeptide Initiation FactorsPolyribosomesProtein BiosynthesisRegulatory Sequences, Ribonucleic AcidRibonucleoproteinsRNA-Binding ProteinsSerumTumor Necrosis Factor-alphaUp-RegulationConceptsAU-rich elementsArgonaute 2Posttranscriptional regulatory systemsAffinity purification methodShRNA knockdown experimentsCell cycle arrestHuman cell linesTranslation activationRegulatory signalsMRNA stabilityGene expressionSerum starvationAU-RichFXR1Activation roleRegulatory systemProtein 1Cell linesMRNA levelsNew insightsDevelopmental consequencesTranslation conditionsUpregulationDirect evidencePurification method
1998
Defects in actin-cap formation in Vav-deficient mice implicate an actin requirement for lymphocyte signal transduction
Holsinger L, Graef I, Swat W, Chi T, Bautista D, Davidson L, Lewis R, Alt F, Crabtree G. Defects in actin-cap formation in Vav-deficient mice implicate an actin requirement for lymphocyte signal transduction. Current Biology 1998, 8: 563-573. PMID: 9601640, DOI: 10.1016/s0960-9822(98)70225-8.Peer-Reviewed Original ResearchMeSH KeywordsActinsAnimalsCell Cycle ProteinsCytoskeletonDNA-Binding ProteinsHumansJurkat CellsMiceNFATC Transcription FactorsNuclear ProteinsProto-Oncogene ProteinsProto-Oncogene Proteins c-vavReceptor-CD3 Complex, Antigen, T-CellReceptors, Antigen, T-CellSignal TransductionT-LymphocytesTranscription FactorsTranscription, GeneticConceptsMitogen-activated protein kinaseCap formationActin polymerizationGuanine nucleotide exchange factorsJun N-terminal kinaseTranscription factor NF-ATc1Vav-deficient miceActin-dependent pathwayStress-activated kinasesGrowth regulatory signalsActin cap formationAntigen receptor signalingEgr-1 geneLymphocyte signal transductionN-terminal kinaseAntigen-receptor interactionActin cytoskeletonExchange factorTranscriptional inductionSignal transductionDependent transcriptionProtein kinaseGTPase RacRegulatory signalsNull mutationThe ins and outs of virulence gene expression: Mg2+ as a regulatory signal
Groisman E. The ins and outs of virulence gene expression: Mg2+ as a regulatory signal. BioEssays 1998, 20: 96-101. PMID: 9504051, DOI: 10.1002/(sici)1521-1878(199801)20:1<96::aid-bies13>3.0.co;2-3.Peer-Reviewed Original ResearchConceptsSignal transduction systemTransduction systemCellular locationPhoP/PhoQ systemPathogen Salmonella enterica serovar TyphimuriumIntracellular pathogen Salmonella enterica serovar TyphimuriumTranscription of genesPhoP/PhoQVirulence gene expressionFacultative intracellular pathogen Salmonella enterica serovar TyphimuriumSalmonella enterica serovar TyphimuriumDifferent cell typesRegulatory hierarchyEnterica serovar TyphimuriumRegulatory signalsExtracellular environmentGene expressionHost cellsHost cuesCell typesMultiple environmentsSerovar TyphimuriumPrecise tissuePhoQTranscription
1993
‘Channelled’ pathways can be more sensitive to specific regulatory signals
Kholodenko B, Demin O, Westerhoff H. ‘Channelled’ pathways can be more sensitive to specific regulatory signals. FEBS Letters 1993, 320: 75-78. PMID: 8462681, DOI: 10.1016/0014-5793(93)81661-i.Peer-Reviewed Original Research
1984
In vivo and in vitro transcription of the Escherichia coli glutaminyl-tRNA synthetase gene.
Cheung A, Söll D. In vivo and in vitro transcription of the Escherichia coli glutaminyl-tRNA synthetase gene. Journal Of Biological Chemistry 1984, 259: 9953-9958. PMID: 6086662, DOI: 10.1016/s0021-9258(17)42791-8.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseGlutaminyl-tRNA synthetase geneTranslation initiation codon AUGInitiation codon AUGPresence of tRNATermination codon UAAGlnS geneTerminator structureTranscription initiationSynthetase geneTranscription initiatesCodons UAARegulatory signalsCodon AUGTermination sitesTranscription productsSequence analysisStructure upstreamStructural regionsTranscriptionGenesTranscriptsSynthetaseMRNAGln
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