2023
Creating Selenocysteine-Specific Reporters Using Inteins
Chung C, Söll D, Krahn N. Creating Selenocysteine-Specific Reporters Using Inteins. Methods In Molecular Biology 2023, 2676: 69-86. PMID: 37277625, DOI: 10.1007/978-1-0716-3251-2_5.Peer-Reviewed Original Research
2021
Single cell epigenetic visualization assay
Kint S, Van Criekinge W, Vandekerckhove L, De Vos WH, Bomsztyk K, Krause DS, Denisenko O. Single cell epigenetic visualization assay. Nucleic Acids Research 2021, 49: e43-e43. PMID: 33511400, PMCID: PMC8096246, DOI: 10.1093/nar/gkab009.Peer-Reviewed Original ResearchMeSH Keywords5-MethylcytosineAcetylationCell LineDNA MethylationEarly Growth Response Protein 1Epigenesis, GeneticEpigenomicsFemaleGene Expression RegulationGene SilencingHistonesHIV-1HumansImage Processing, Computer-AssistedIn Situ Hybridization, FluorescenceProvirusesReal-Time Polymerase Chain ReactionRNA, Long NoncodingSingle-Cell AnalysisConceptsEpigenetic marksEpigenetic statusGene allelesFemale somatic cellsCurrent sequencing approachesGene of interestGene-specific oligonucleotidesQuantitative fluorescent readoutTranscription stateRNA FISHHuman cell linesSomatic cellsTranscription statusTarget genesSequencing approachH3K9ac levelsDifferent genesGenesIndividual cellsAntibody-conjugated alkaline phosphataseDNA oligosSingle cellsCell linesSame cellsFluorescent readout
2020
Flow Cytometric Analyses of p53-Mediated Cell Cycle Arrest and Apoptosis in Cancer Cells
Al Zouabi NN, Roberts CM, Lin ZP, Ratner ES. Flow Cytometric Analyses of p53-Mediated Cell Cycle Arrest and Apoptosis in Cancer Cells. Methods In Molecular Biology 2020, 2255: 43-53. PMID: 34033093, DOI: 10.1007/978-1-0716-1162-3_5.Peer-Reviewed Original ResearchConceptsGene of interestCell cycle arrestCycle arrestCell typesDNA damaging agentsP53-mediated cell cycle arrestCell cycle progressionTumor suppressor p53Cellular contextEctopic expressionExogenous stressCell cycle distributionDamaging agentsCycle progressionTumor suppressorSuppressor p53Stable expressionPhenotypic analysisCell survivalCell deathGenomic damageP53 functionGenesEnvironmental insultsCycle distribution
2017
Development of an inducible platform for intercellular protein delivery
Siller R, Dufour E, Lycke M, Wilmut I, Jung YW, Park IH, Sullivan GJ. Development of an inducible platform for intercellular protein delivery. International Journal Of Pharmaceutics 2017, 522: 1-10. PMID: 28254654, DOI: 10.1016/j.ijpharm.2017.02.067.Peer-Reviewed Original ResearchConceptsNovel platformBiomolecules of interestCell penetrating peptideGene of interestHuman chorionic gonadotropin beta subunitProtein deliveryStem cell biologyChorionic gonadotropin beta subunitPenetrating peptidePotential applicationsProtein transduction domainProtein of interestGreen fluorescent proteinFusion proteinGonadotropin beta subunitEfficient uptakeN-terminal signal peptideCell culture mediumPlatformFluorescent proteinTransduction domainLack of specificityBeta subunitActive proteinFixation process
2016
Genome-wide significant loci for addiction and anxiety
Hodgson K, Almasy L, Knowles EE, Kent JW, Curran JE, Dyer TD, Göring HH, Olvera RL, Fox PT, Pearlson GD, Krystal JH, Duggirala R, Blangero J, Glahn DC. Genome-wide significant loci for addiction and anxiety. European Psychiatry 2016, 36: 47-54. PMID: 27318301, PMCID: PMC5483998, DOI: 10.1016/j.eurpsy.2016.03.004.Peer-Reviewed Original ResearchConceptsLinkage scanLinkage signalGenome-wide significant lociSignificant quantitative trait lociGenome-wide linkage scanBivariate linkage scanSignificant positive genetic correlationQuantitative trait lociGene of interestBivariate linkage analysisPositive genetic correlationAddiction phenotypeGenomic lociGenetic architectureTrait lociPleiotropic signalsSignificant lociChromosomal regionsAddiction geneticsGenetic underpinningsLinkage analysisPrevious GWASGenetic correlationsNovel regionRole of genetics
2015
Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar Septation
Cuna A, Halloran B, Faye-Petersen O, Kelly D, Crossman DK, Cui X, Pandit K, Kaminski N, Bhattacharya S, Ahmad A, Mariani TJ, Ambalavanan N. Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar Septation. American Journal Of Respiratory Cell And Molecular Biology 2015, 53: 60-73. PMID: 25387348, PMCID: PMC4566107, DOI: 10.1165/rcmb.2014-0160oc.Peer-Reviewed Original ResearchConceptsDNA methylationNormal septationGene expressionGenome-wide DNA methylation dataMajor epigenetic mechanismsLung developmentNumber of genesMouse lung developmentGene of interestDNA methylation dataGene expression dataMicroarray gene expression dataAlveolar septationCoordinated expressionEpigenetic mechanismsMethylated DNAMultiple genesMicroarray analysisMethylation dataExpression dataGenesMethylationExtracellular matrixAltered expressionAntioxidant defense
2014
A dexamethasone-inducible gene expression system is active in Citrus plants
Rossignol P, Orbović V, Irish V. A dexamethasone-inducible gene expression system is active in Citrus plants. Scientia Horticulturae 2014, 172: 47-53. DOI: 10.1016/j.scienta.2014.02.041.Peer-Reviewed Original ResearchGene expression systemExpression systemΒ-glucuronidase (GUS) reporter geneInducible gene expression systemSynthetic transcription factorsGene of interestPromoter driving expressionCrop plantsGene functionTransgenic approachesTranscription factorsCitrus plantsNew traitsReporter geneCitrus cultivarsPlantsTransgene activityGenesSynthetic glucocorticoid dexamethasoneTiming of activityGlucocorticoid receptorSuch manipulationsGlucocorticoid dexamethasoneLhGRTraits
2012
Splicing Factor ChIP and ChRIP: Detection of Splicing and Splicing Factors at Genes by Chromatin Immunoprecipitation
Sapra A, Oesterreich F, Pabis M, Listerman I, Bardehle N, Neugebauer K. Splicing Factor ChIP and ChRIP: Detection of Splicing and Splicing Factors at Genes by Chromatin Immunoprecipitation. 2012, 416-427. DOI: 10.1002/9783527636778.ch39.Peer-Reviewed Original ResearchNascent RNASplicing factorsChromatin immunoprecipitationRNA processing intermediatesMammalian tissue culture cellsRNA processing factorsRNA polymerase IIRNA processing eventsGene of interestTissue culture cellsPolymerase IIActive histoneMRNA processingIsolation of RNAProcessing factorsProcessing eventsRNA immunoprecipitationChromatinNucleic acid complexesQuantitative RT-PCRLiving cellsProcessing intermediatesRNACulture cellsImmunoprecipitation
2010
A yeast‐based recombinogenic targeting toolset for transgenic analysis of human disease genes
Bentley KL, Shashikant CS, Wang W, Ruddle NH, Ruddle FH. A yeast‐based recombinogenic targeting toolset for transgenic analysis of human disease genes. Annals Of The New York Academy Of Sciences 2010, 1207: e58-e68. PMID: 20961307, DOI: 10.1111/j.1749-6632.2010.05712.x.Peer-Reviewed Original ResearchConceptsPolycystic kidney disease 1Yeast-bacterial shuttle vectorHuman disease genesFunction of genesLarge insert DNABacterial artificial chromosomeGene of interestTransgenic analysisGenomic fragmentArtificial chromosomesDNA insertsDisease genesBiological processesShuttle vectorHuman diseasesGenesGene modificationClaspettesPClasperMouse modelValuable resourceTransgenic mouse modelTransgenic miceCritical insightsImmune system
2009
Degenerative abnormalities in transgenic neocortical neuropeptide Y interneurons expressing tau‐green fluorescent protein
Rancillac A, Lainé J, Perrenoud Q, Geoffroy H, Ferezou I, Vitalis T, Rossier J. Degenerative abnormalities in transgenic neocortical neuropeptide Y interneurons expressing tau‐green fluorescent protein. Journal Of Neuroscience Research 2009, 88: 487-499. PMID: 19830842, DOI: 10.1002/jnr.22234.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAxonsDendritesFluorescent Antibody TechniqueIn Vitro TechniquesInterneuronsLuminescent ProteinsLysineMaleMiceMice, Inbred C57BLMice, TransgenicMicroscopy, ImmunoelectronNeurodegenerative DiseasesNeuropeptide YPatch-Clamp TechniquesReverse Transcriptase Polymerase Chain ReactionSomatosensory Cortextau ProteinsConceptsLysosomal-associated membrane protein 1Bacterial artificial chromosomeGreen fluorescent proteinFluorescent proteinGene of interestElectrophysiological intrinsic propertiesTranscriptional controlTau-green fluorescent proteinArtificial chromosomesGenomic sequencesMembrane protein 1BAC transgenic miceReporter geneReporter constructsMorphological defectsLysosomal vacuolesCell typesProtein tauProtein 1Electrophysiological defectsRestricted spatial distributionElectron microscopic analysisGenesProteinTransgenic mice
2008
Addictions Biology: Haplotype-Based Analysis for 130 Candidate Genes on a Single Array
Hodgkinson CA, Yuan Q, Xu K, Shen PH, Heinz E, Lobos EA, Binder EB, Cubells J, Ehlers CL, Gelernter J, Mann J, Riley B, Roy A, Tabakoff B, Todd RD, Zhou Z, Goldman D. Addictions Biology: Haplotype-Based Analysis for 130 Candidate Genes on a Single Array. Alcohol And Alcoholism 2008, 43: 505-515. PMID: 18477577, PMCID: PMC2724863, DOI: 10.1093/alcalc/agn032.Peer-Reviewed Original ResearchConceptsWhole-genome arraysCandidate genesHigh-quality SNPsGene of interestAncestry informative markersCase/control populationInformative markersHigh-throughput assaysAverage call rateComparison of haplotypesCall rateFull haplotype informationHaplotype-based analysisHaplotype coverageHaplotype informationGenesThroughput assaysSNPsDNA qualityTag SNPsHaplotypesReplication rate
2006
Skin
Kudsi O, Pomahac B. Skin. 2006 DOI: 10.1002/9780471740360.ebs1094.Peer-Reviewed Original ResearchTissue-engineered skinSpecific design modificationsGene of interestSkin engineeringSkin substitute materialsUnlimited productionSkin alternativeSkin substitutesRecent advancementsSkin productsSplit-skin autograftsField of medicinePresent gold standardVariety of diseasesSustained lifeLarge skin areasTherapeutic agentsSuccessful step
2002
Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments
Townsend JP, Hartl DL. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biology 2002, 3: research0071.1. PMID: 12537560, PMCID: PMC151173, DOI: 10.1186/gb-2002-3-12-research0071.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremDNA-Binding ProteinsEthanolGene DeletionGene Expression ProfilingGene Expression Regulation, FungalGenotypeModels, GeneticNuclear ProteinsOligonucleotide Array Sequence AnalysisRNA, FungalRNA, MessengerSaccharomyces cerevisiae ProteinsSpecies SpecificityTranscription FactorsZincConceptsGene of interestExpression levelsGene expression levelsTwofold thresholdGene basisTranscriptional responseMicroarray comparisonsMinimal mediumExpression differencesBiological insightsMicroarray analysisEthanol shockMicroarray dataRelative mRNA levelsGenesMRNA levelsMultiple strainsBayesian analysisDevelopmental state
2000
A versatile chondrogenic rat calvaria cell line R-tTA-24 that permits tetracycline-regulated gene expression
Bergwitz C, Wendlandt T, Pötter E, Glomb I, Gras K, von zur Mühlen A, Brabant G. A versatile chondrogenic rat calvaria cell line R-tTA-24 that permits tetracycline-regulated gene expression. Histochemistry And Cell Biology 2000, 113: 145-150. PMID: 10766267, DOI: 10.1007/s004180050017.Peer-Reviewed Original ResearchConceptsTetracycline-regulated gene expressionGene expressionTetracycline-regulated gene expression systemStable transfectionChondrogenic differentiationGene expression systemGene of interestBasis of phenotypeTetracycline transactivatorGenetic manipulationHygromycin selectionExpression systemCartilage-specific proteoglycansNeomycin selectionFlexible genetic manipulationLuciferase activityType II expressionCell linesAlcian blue stainingDifferentiationCollagen type II expressionTransfectionExpressionBlue stainingGenes
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