2018
The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors
Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston R. The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics 2018, 208: 937-949. PMID: 29284660, PMCID: PMC5844342, DOI: 10.1534/genetics.117.300657.Peer-Reviewed Original ResearchConceptsIndividual transcription factorsTranscription factorsModel organismsGenome-wide binding profilesMajor model organismsKey model organismDifferent transcription factorsTissue-specific patternsFly genomeWorm genomeChromatin immunoprecipitationStock CenterRegulatory pathwaysRegulatory sitesCaenorhabditisDrosophilaOrganismsGenomeBinding profileGenesModENCODESitesGFPImmunoprecipitationVast number
2017
Bioluminescence Monitoring of Neuronal Activity in Freely Moving Zebrafish Larvae.
Knafo S, Prendergast A, Thouvenin O, Figueiredo SN, Wyart C. Bioluminescence Monitoring of Neuronal Activity in Freely Moving Zebrafish Larvae. Bio-protocol 2017, 7: e2550. PMID: 29130058, PMCID: PMC5681248, DOI: 10.21769/bioprotoc.2550.Peer-Reviewed Original Research
2015
A genetic toolkit for tagging intronic MiMIC containing genes
Nagarkar-Jaiswal S, DeLuca S, Lee P, Lin W, Pan H, Zuo Z, Lv J, Spradling A, Bellen H. A genetic toolkit for tagging intronic MiMIC containing genes. ELife 2015, 4: e08469. PMID: 26102525, PMCID: PMC4499919, DOI: 10.7554/elife.08469.Peer-Reviewed Original ResearchConceptsProtein interaction partnersGenes/proteinsProtein expression patternsUncharacterized genesGenetic toolkitIntegration cassetteMiMIC insertionsPhiC31 recombinaseProtein tagsFRT sequencesNew exonsGenetic strategiesInteraction partnersExpression patternsGenesExonsPlasmid DNAProteinMass specTagsIntronsLarge collectionGFPImmunoprecipitationMimics
2014
Differences in binding to the ILK complex determines kindlin isoform adhesion localization and integrin activation
Huet-Calderwood C, Brahme NN, Kumar N, Stiegler AL, Raghavan S, Boggon TJ, Calderwood DA. Differences in binding to the ILK complex determines kindlin isoform adhesion localization and integrin activation. Journal Of Cell Science 2014, 127: 4308-4321. PMID: 25086068, PMCID: PMC4179494, DOI: 10.1242/jcs.155879.Peer-Reviewed Original ResearchConceptsIntegrin activationKindlin-2Kindlin-3Focal adhesion proteinsFunctional differencesIntegrin-linked kinaseILK complexAdhesion proteinsF2 subdomainMolecular basisIsoform specificityComplex bindsKindlinFA targetingActivation defectsCell adhesionActivationFALocalizesKinaseGFPSignalingILKIsoformsProtein
2013
Bridging the divide
McLean PF, Cooley L. Bridging the divide. Fly 2013, 8: 13-18. PMID: 24406334, PMCID: PMC3974888, DOI: 10.4161/fly.27016.Peer-Reviewed Original ResearchConceptsRing canalsMitotic clonesSomatic tissuesDrosophila somatic tissuesFollicle cellsProtein of interestNon-recombined cellsDirect cytoplasmic connectionsDrosophila oogenesisImaginal discsGenetic toolsIntercellular exchangeProtein movementCleavage furrowCytoplasmic connectionsProteinClonesCellsMosaic cellsClonal dataOogenesisGFPTissueSix Innexins Contribute to Electrical Coupling of C. elegans Body-Wall Muscle
Liu P, Chen B, Altun Z, Gross M, Shan A, Schuman B, Hall D, Wang Z. Six Innexins Contribute to Electrical Coupling of C. elegans Body-Wall Muscle. PLOS ONE 2013, 8: e76877. PMID: 24130800, PMCID: PMC3793928, DOI: 10.1371/journal.pone.0076877.Peer-Reviewed Original ResearchConceptsUNC-9Body wall musclesC. elegans body wall muscleBody wall muscle cellsGap junctionsEpitope-tagged proteinsInnexinsTriple mutantPunctate localizationFunctions cellMutantsIntercellular junctionsDistinct populationsMuscle expressionGFPMuscle cellsJunctional currentsElectrical couplingFunctional propertiesCellsPromoterProteinSolid foundationExpressionPopulation
2012
Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion
Heinemann IU, Rovner AJ, Aerni HR, Rogulina S, Cheng L, Olds W, Fischer JT, Söll D, Isaacs FJ, Rinehart J. Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Letters 2012, 586: 3716-3722. PMID: 22982858, PMCID: PMC3473164, DOI: 10.1016/j.febslet.2012.08.031.Peer-Reviewed Original ResearchConceptsUAG codonEscherichia coli protein synthesisRelease factor 1Aminoacyl-tRNA synthetaseCellular fitnessCodon reassignmentEssential genesElongation factorPhosphoserine phosphataseProtein synthesisRF-1Protein yieldTranslation systemFactor 1CodonAccompanying lossGFPUAAGenesSynthetaseDeletionWNK4FitnessPhosphataseExpressionReprogramming human somatic cells into induced pluripotent stem cells (iPSCs) using retroviral vector with GFP.
Kim KY, Hysolli E, Park IH. Reprogramming human somatic cells into induced pluripotent stem cells (iPSCs) using retroviral vector with GFP. Journal Of Visualized Experiments 2012 PMID: 22491226, PMCID: PMC3466658, DOI: 10.3791/3804.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsInduced pluripotent stem cellsHuman somatic cellsHuman induced pluripotent stem cellsPluripotent stem cellsSomatic cellsIPSC coloniesStem cellsESC culture conditionsEmbryonic stem cellsPluripotency genesTranscription factorsRetroviral transgenesEctopic expressionGFP fluorescenceRetroviral vectorsHuman fibroblast cellsFibroblast cellsGFPCulture conditionsCellsAutologous cellsCellular sourceColoniesSurface markersReprogramming Human Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) Using Retroviral Vector with GFP
Kim K, Hysolli E, Park I. Reprogramming Human Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) Using Retroviral Vector with GFP. Journal Of Visualized Experiments 2012 DOI: 10.3791/3804-v.Peer-Reviewed Original Research
2008
Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets
Daz M, Ayala G, Len T, Zoncu R, Toomre D. Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets. Journal Of Computational Biology 2008, 15: 1221-1236. PMID: 18973437, DOI: 10.1089/cmb.2008.0055.Peer-Reviewed Original ResearchConceptsTotal internal reflection fluorescence microscopyFluorescent-tagged proteinsReflection fluorescence microscopyEndocytic proteinsBiological questionsPlasma membraneDifferent proteinsFluorescence microscopyProteinSequenceK-functionArea of fluorescenceEndocytosisFree tuning parametersGFPBiologistsColocalizationHigh spatial-temporal resolutionMembraneSpatial-temporal resolutionPoisson cluster modelCellsFluorescenceCathepsin B Is Involved in the Trafficking of TNF-α-Containing Vesicles to the Plasma Membrane in Macrophages
Ha S, Martins A, Khazaie K, Han J, Chan B, Kim S. Cathepsin B Is Involved in the Trafficking of TNF-α-Containing Vesicles to the Plasma Membrane in Macrophages. The Journal Of Immunology 2008, 181: 690-697. PMID: 18566436, DOI: 10.4049/jimmunol.181.1.690.Peer-Reviewed Original ResearchConceptsPlasma membraneIntracellular cathepsin B activityCathepsin BCathepsin B activityMouse bone marrow-derived macrophagesGene identification methodsBone marrow-derived macrophagesMarrow-derived macrophagesB activityEctopic expressionLysosomal cysteine proteinasesInnate immune responsePosttranslational processingCysteine proteinasesTNF-alphaVesiclesKey mediatorMembranePotent proinflammatory cytokineLess TNF-alphaChronic inflammatory diseaseMacrophagesMutagenesisGFPMicrobes
1999
Studies on Conditional Gene Expression in the Brain
JERECIC J, SINGLE F, KRÜTH U, KRESTEL H, KOLHEKAR R, STORCK T, KASK K, HIGUCHI M, SPRENGEL R, SEEBURG P. Studies on Conditional Gene Expression in the Brain. Annals Of The New York Academy Of Sciences 1999, 868: 27-37. PMID: 10414279, DOI: 10.1111/j.1749-6632.1999.tb11271.x.Peer-Reviewed Original Research
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