2017
STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live Cells
Erdmann RS, Toomre D, Schepartz A. STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live Cells. Methods In Molecular Biology 2017, 1663: 65-78. PMID: 28924659, PMCID: PMC6146391, DOI: 10.1007/978-1-4939-7265-4_6.Peer-Reviewed Original ResearchConceptsLive cellsMembrane-bound proteinsLipid probesGolgi dynamicsCellular functionsGolgi structureCellular organellesGolgi apparatusCeramide lipidsSuper-resolution imagingLabeling strategySTED imagingSTED microscopyCellsPhotostable fluorophoresLipidsGolgiOrganellesTwo-componentBioorthogonal reactionsProbeProteinHigh densityNovel ecto-tagged integrins reveal their trafficking in live cells
Huet-Calderwood C, Rivera-Molina F, Iwamoto DV, Kromann EB, Toomre D, Calderwood DA. Novel ecto-tagged integrins reveal their trafficking in live cells. Nature Communications 2017, 8: 570. PMID: 28924207, PMCID: PMC5603536, DOI: 10.1038/s41467-017-00646-w.Peer-Reviewed Original ResearchConceptsIntegrin functionΒ1 integrinLive cellsCell surface adhesion receptorsHeterodimeric cell-surface adhesion receptorsIntegrin endocytosisMulticellular organismsNovel powerful toolFocal adhesionsKnockout fibroblastsIntegrin activationAdhesion receptorsExtracellular loopIntegrinsTraffickingMajor mysteriesCellsTagsAdhesionHaloTagEndocytosisPowerful toolExocytosisOrganismsVesiclesHIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution
Thompson AD, Bewersdorf J, Toomre D, Schepartz A. HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution. Biochemistry 2017, 56: 5194-5201. PMID: 28792749, PMCID: PMC5854879, DOI: 10.1021/acs.biochem.7b00545.Peer-Reviewed Original ResearchConceptsLive cellsOrganelle dynamicsDiscrete organellesMultiple organellesLive-cell nanoscopyPlasma membraneDiverse processesEndoplasmic reticulumDynamic assemblyLiving cellsDynamic reorganizationOrganellesSingle-molecule switchingMembrane probeCellsMembraneMitochondriaReticulumRegulationHigh densityProbeAssemblyNew toolkitLong time periodsDivisionDifferential requirement for N‐ethylmaleimide‐sensitive factor in endosomal trafficking of transferrin receptor from anterograde trafficking of vesicular stomatitis virus glycoprotein G
Fan J, Zhou X, Wang Y, Kuang C, Sun Y, Liu X, Toomre D, Xu Y. Differential requirement for N‐ethylmaleimide‐sensitive factor in endosomal trafficking of transferrin receptor from anterograde trafficking of vesicular stomatitis virus glycoprotein G. FEBS Letters 2017, 591: 273-281. PMID: 27995606, DOI: 10.1002/1873-3468.12532.Peer-Reviewed Original ResearchConceptsVesicular stomatitis virus glycoprotein GGolgi structureDifferential requirementN-ethylmaleimide-sensitive factorConstitutive trafficking pathwayTrafficking pathwaysGlycoprotein GTransferrin endocytosisEndosomal traffickingAnterograde traffickingGolgi fragmentationMammalian cellsVesicular transportDifferent vesiclesHeLa cellsReceptor exocytosisTraffickingTransferrin receptorFusion factorKnockdownCell viabilityCentral rolePathwayCrucial roleCells
2016
The IN/OUT assay: a new tool to study ciliogenesis
Kukic I, Rivera-Molina F, Toomre D. The IN/OUT assay: a new tool to study ciliogenesis. Cilia 2016, 5: 23. PMID: 27493724, PMCID: PMC4972980, DOI: 10.1186/s13630-016-0044-2.Peer-Reviewed Original ResearchCiliary pocketCiliary transmembrane proteinsPlasma membrane invaginationsDeep plasma membrane invaginationsPrimary cilia assemblyCilia assemblyMembrane invaginationsTransmembrane proteinPrimary ciliaCellular antennaCilia lengthMolecular characterizationMost ciliaFunctional studiesCiliogenesisCiliaNew toolRPE cellsCellsAssaysAntibody accessEHD1New assayPocketConventional assaysUltra-High Resolution 3D Imaging of Whole Cells
Huang F, Sirinakis G, Allgeyer ES, Schroeder LK, Duim WC, Kromann EB, Phan T, Rivera-Molina FE, Myers JR, Irnov I, Lessard M, Zhang Y, Handel MA, Jacobs-Wagner C, Lusk CP, Rothman JE, Toomre D, Booth MJ, Bewersdorf J. Ultra-High Resolution 3D Imaging of Whole Cells. Cell 2016, 166: 1028-1040. PMID: 27397506, PMCID: PMC5005454, DOI: 10.1016/j.cell.2016.06.016.Peer-Reviewed Original ResearchConceptsCell biological researchResolution 3D imagingHigh-resolution 3D imagingOptical nanoscopeSuper-resolution microscopyThree-dimensional structureMammalian cellsNuclear poresSynaptonemal complexFluorescence nanoscopyThick samplesThin samplesBiological researchNanoscopyInferior resolutionCellular volumeWhole cellsDepth directionMolecular architecturePractical biological applicationsBiological applicationsComplex molecular architecturesResolutionNanoscopeCellsOptogenetic activation reveals distinct roles of PIP3 and Akt in adipocyte insulin action
Xu Y, Nan D, Fan J, Bogan JS, Toomre D. Optogenetic activation reveals distinct roles of PIP3 and Akt in adipocyte insulin action. Journal Of Cell Science 2016, 129: 2085-2095. PMID: 27076519, PMCID: PMC4878990, DOI: 10.1242/jcs.174805.Peer-Reviewed Original ResearchConceptsPI3KGLUT4 translocationDistinct rolesAkt-independent pathwayNew optogenetic toolsGlucose transporter 4Drug-mediated inhibitionTranslocation responseIntracellular vesiclesOverall insulin actionPlasma membraneInsulin actionN-terminusOptogenetic toolsInsulin stimulationTransporter 4Biochemical assaysAktTranslocationAdipose cellsVesiclesPathwayCIB1PIP3Cells
2015
The periciliary ring in polarized epithelial cells is a hot spot for delivery of the apical protein gp135
Stoops EH, Hull M, Olesen C, Mistry K, Harder JL, Rivera-Molina F, Toomre D, Caplan MJ. The periciliary ring in polarized epithelial cells is a hot spot for delivery of the apical protein gp135. Journal Of Cell Biology 2015, 211: 287-294. PMID: 26504168, PMCID: PMC4621837, DOI: 10.1083/jcb.201502045.Peer-Reviewed Original ResearchConceptsPrimary ciliaSurface proteinsTrans-Golgi networkPolarized epithelial cellsApical surface proteinsSNAP-tag systemBasolateral plasma membraneCell surface proteinsEpithelial cellsApical proteinsPericiliary regionGolgi networkPolarized traffickingCarrier vesiclesProtein deliveryPlasma membraneApical membraneProteinGp135Basolateral membraneCiliaMembraneHot spotsCellsTrafficking
2014
Super‐Resolution Imaging of the Golgi in Live Cells with a Bioorthogonal Ceramide Probe
Erdmann RS, Takakura H, Thompson AD, Rivera‐Molina F, Allgeyer ES, Bewersdorf J, Toomre D, Schepartz A. Super‐Resolution Imaging of the Golgi in Live Cells with a Bioorthogonal Ceramide Probe. Angewandte Chemie International Edition 2014, 53: 10242-10246. PMID: 25081303, PMCID: PMC4593319, DOI: 10.1002/anie.201403349.Peer-Reviewed Original ResearchReticulon 4 Is Necessary for Endoplasmic Reticulum Tubulation, STIM1-Orai1 Coupling, and Store-operated Calcium Entry
Jozsef L, Tashiro K, Kuo A, Park EJ, Skoura A, Albinsson S, Rivera-Molina F, Harrison KD, Iwakiri Y, Toomre D, Sessa WC. Reticulon 4 Is Necessary for Endoplasmic Reticulum Tubulation, STIM1-Orai1 Coupling, and Store-operated Calcium Entry. Journal Of Biological Chemistry 2014, 289: 9380-9395. PMID: 24558039, PMCID: PMC3969502, DOI: 10.1074/jbc.m114.548602.Peer-Reviewed Original ResearchConceptsSTIM1-Orai1 couplingER morphologyRedistribution of STIM1Store-operated calcium entryER tubulationER sheetsElevated cytoplasmicReticulon 4Functional consequencesRTN4SOCETubulationCalcium entryRecent advancesFundamental questionsSTIM1CytoplasmicHomeostasisApoptosisRegulationMechanisticallyFirst timeCellsMorphology
2012
Caveolae, Fenestrae and Transendothelial Channels Retain PV1 on the Surface of Endothelial Cells
Tkachenko E, Tse D, Sideleva O, Deharvengt SJ, Luciano MR, Xu Y, McGarry CL, Chidlow J, Pilch PF, Sessa WC, Toomre DK, Stan RV. Caveolae, Fenestrae and Transendothelial Channels Retain PV1 on the Surface of Endothelial Cells. PLOS ONE 2012, 7: e32655. PMID: 22403691, PMCID: PMC3293851, DOI: 10.1371/journal.pone.0032655.Peer-Reviewed Original ResearchConceptsFormation of diaphragmsRemoval of caveolaeDynamin-independent pathwayAbsence of caveolaeEndothelial cellsProtein levelsCellular rolesCavin-1Knockout phenotypesPlasma membraneCaveolin-1CaveolaeLung endothelial cellsCell surfaceRapid internalizationInternalization rateAbundance of structuresMice resultsTransendothelial channelsEssential componentOnly roleFenestral diaphragmsCellsClathrinTranscription
2011
Dual-mode of insulin action controls GLUT4 vesicle exocytosis
Xu Y, Rubin BR, Orme CM, Karpikov A, Yu C, Bogan JS, Toomre DK. Dual-mode of insulin action controls GLUT4 vesicle exocytosis. Journal Of Cell Biology 2011, 193: 643-653. PMID: 21555461, PMCID: PMC3166865, DOI: 10.1083/jcb.201008135.Peer-Reviewed Original ResearchMeSH Keywords3T3-L1 CellsAdipocytesAnimalsBiosensing TechniquesCarrier ProteinsExocytosisGlucose Transporter Type 4Green Fluorescent ProteinsInsulinIntracellular Signaling Peptides and ProteinsKineticsMembrane FusionMiceMicroscopy, FluorescenceMicroscopy, VideoPhospholipase DRecombinant Fusion ProteinsRNA InterferenceTransfectionTransport VesiclesVesicle-Associated Membrane Protein 2ConceptsGLUT4 storage vesiclesVesicle exocytosisInsulin-stimulated control cellsGLUT4 vesicle exocytosisPlasma membrane fusionNovel regulatory siteSingle vesicle exocytosisInsulin triggersVesicle trafficExocytic rateFusion poreSurface of adipocytesMembrane fusionRegulatory sitesPhospholipase DStorage vesiclesPore expansionExocytosisControl cellsAcute perturbationVesiclesInsulin actionVesicle characteristicsAdipocytesCells
2010
Spatial control of EGF receptor activation by reversible dimerization on living cells
Chung I, Akita R, Vandlen R, Toomre D, Schlessinger J, Mellman I. Spatial control of EGF receptor activation by reversible dimerization on living cells. Nature 2010, 464: 783-787. PMID: 20208517, DOI: 10.1038/nature08827.Peer-Reviewed Original ResearchMeSH KeywordsActinsAnimalsCell Line, TumorCell PolarityCell SurvivalCHO CellsCricetinaeCricetulusDiffusionEnzyme ActivationEnzyme StabilityEpidermal Growth FactorErbB ReceptorsGene Expression RegulationGRB2 Adaptor ProteinHumansKineticsLigandsProtein MultimerizationProtein TransportSignal TransductionThermodynamicsConceptsLigand bindingEpidermal growth factor receptor moleculeType I receptor kinaseEGF receptor activationDimer formationReceptor kinaseReceptor dimerizationDimerization dynamicsReceptor dimersLiving cellsReceptor moleculesCell marginsDimer populationSpatial controlHuman carcinomasConformation changeDimerizationCell centerReceptor activationRate of dissociationCellsBindingActivationKinaseReversible dimerization
2009
Exocyst is involved in polarized cell migration and cerebral cortical development
Letinic K, Sebastian R, Toomre D, Rakic P. Exocyst is involved in polarized cell migration and cerebral cortical development. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 11342-11347. PMID: 19549839, PMCID: PMC2708724, DOI: 10.1073/pnas.0904244106.Peer-Reviewed Original ResearchConceptsCell migrationDelivery of vesiclesNeuronal migrationVesicle tetheringExocyst complexMembrane trafficExocytic pathwayProtein complexesExocytic processExocystSpatial regulationEmbryonic developmentVesicle exocytosisSecretory vesiclesPlasma membraneTIRF microscopyPostmitotic cellsCortical neuronal migrationProper developmentCerebral cortical developmentWound assaysExocytosisVesiclesMembraneCells
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 modelCellsFluorescenceMotion tracking of the outer tips of microtubules
Hadjidemetriou S, Toomre D, Duncan J. Motion tracking of the outer tips of microtubules. Medical Image Analysis 2008, 12: 689-702. PMID: 18571462, DOI: 10.1016/j.media.2008.04.004.Peer-Reviewed Original ResearchConceptsMicrotubule assemblyCoordination of mitosisTransport of chromosomesHigh throughput quantitative studiesNumerous critical rolesMicrotubule tipsLiving cellsCell migrationStructural tracksConfocal microscopyEpifluorescent microscopyNeurodegenerative diseasesCritical roleCell pathologyMicrotubulesAssemblyCellsSequenceOuter tipChromosomesOrganellesMitosisAbnormal functionCytoplasmVesiclesRepair of injured plasma membrane by rapid Ca2+-dependent endocytosis
Idone V, Tam C, Goss JW, Toomre D, Pypaert M, Andrews NW. Repair of injured plasma membrane by rapid Ca2+-dependent endocytosis. Journal Of Cell Biology 2008, 180: 905-914. PMID: 18316410, PMCID: PMC2265401, DOI: 10.1083/jcb.200708010.Peer-Reviewed Original ResearchConceptsPlasma membraneStreptolysin OPore-forming proteinsPlasma membrane lesionsBacterial toxin streptolysin OEnhancement of endocytosisDependent endocytosisToxin streptolysin OImportant new insightsMembrane resealingLysosomal organellesEndocytosisMicrobial toxinsNovel pathwayExocytosisRepair processMembrane lesionsProteinNew insightsMembraneRapid Ca2ResealingRapid repair processCellsImmune systemAutomatic Detection of Large Dense-Core Vesicles in Secretory Cells and Statistical Analysis of Their Intracellular Distribution
Díaz E, Ayala G, Díaz ME, Gong LW, Toomre D. Automatic Detection of Large Dense-Core Vesicles in Secretory Cells and Statistical Analysis of Their Intracellular Distribution. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2008, 7: 2-11. PMID: 20150664, DOI: 10.1109/tcbb.2008.30.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsAnimals, NewbornArtificial IntelligenceCells, CulturedChromaffin CellsChromaffin GranulesComputer SimulationData Interpretation, StatisticalImage EnhancementImage Interpretation, Computer-AssistedInformation Storage and RetrievalMiceMicroscopy, ElectronModels, BiologicalModels, StatisticalPattern Recognition, AutomatedReproducibility of ResultsSecretory VesiclesSensitivity and SpecificityConceptsPlasma membraneLarge dense-core vesiclesDense-core vesiclesDifferent spatial point processesRegulated exocytosisLocation of granulesStudy of secretionIntracellular distributionCell cytoplasmSecretory cellsDysfunctional secretionDifferent cellsFunctional descriptorsDifferent cell groupsAnalysis of diseasesVesiclesCellsMembraneNovel toolCell groupsDensity of granulesGranulesExocytosisCytoplasmMorphological appearance
2005
Spying on IgE receptor signaling
Toomre D. Spying on IgE receptor signaling. Journal Of Cell Biology 2005, 171: 415-417. PMID: 16275748, PMCID: PMC2171246, DOI: 10.1083/jcb.200510105.Peer-Reviewed Original ResearchConceptsSignal transductionPlasma membrane organizationProtein-protein interactionsLipid raft microdomainsFluorescent correlation spectroscopyRaft microdomainsLipid raftsMembrane organizationIgE receptorTransductionPotential roleReceptorsCorrelation spectroscopyMicrodomainsRaftsCellsNew complexitiesComplexesDomain
2002
Dendritic cell maturation triggers retrograde MHC class II transport from lysosomes to the plasma membrane
Chow A, Toomre D, Garrett W, Mellman I. Dendritic cell maturation triggers retrograde MHC class II transport from lysosomes to the plasma membrane. Nature 2002, 418: 988-994. PMID: 12198549, DOI: 10.1038/nature01006.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigen PresentationAntigens, CDCell DifferentiationCell MembraneCells, CulturedDendritic CellsEndocytosisEndosomesHistocompatibility Antigens Class IILysosome-Associated Membrane GlycoproteinsLysosomesMembrane GlycoproteinsMiceMice, Inbred C57BLMicroscopy, VideoProtein TransportStem CellsConceptsDendritic cellsMajor histocompatibility complex (MHC) class II moleculesLive dendritic cellsImmature dendritic cellsCo-stimulatory moleculesMHC II moleculesClass II moleculesInternalized antigensInflammatory mediatorsII-peptide complexesMHC-IIT lymphocytesImmune responseMHC class II transportPeptide antigensMaturation triggerClass II transportAntigenGreen fluorescent proteinCellsLysosomal compartmentPlasma membraneLysosomesTerminal degradative compartmentMicrobial products