2024
Unraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging
Schueder F, Rivera-Molina F, Su M, Marin Z, Kidd P, Rothman J, Toomre D, Bewersdorf J. Unraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging. Cell 2024, 187: 1769-1784.e18. PMID: 38552613, DOI: 10.1016/j.cell.2024.02.033.Peer-Reviewed Original ResearchConceptsInter-organelle contactsSuper-resolutionMultiplexed super-resolution microscopyIntricate spatial relationshipsGolgi stacksMammalian cellsCellular functionsSuper-resolution microscopyPrimary ciliaSuper-resolution fluorescence microscopyCellular complexityTransient adaptationFluorescence microscopyDNA-PAINTFluorogenic labelingMolecular targetsSpatial relationshipsImagesThroughput
2019
Labeling Strategies Matter for Super-Resolution Microscopy: A Comparison between HaloTags and SNAP-tags
Erdmann RS, Baguley SW, Richens JH, Wissner RF, Xi Z, Allgeyer ES, Zhong S, Thompson AD, Lowe N, Butler R, Bewersdorf J, Rothman JE, St Johnston D, Schepartz A, Toomre D. Labeling Strategies Matter for Super-Resolution Microscopy: A Comparison between HaloTags and SNAP-tags. Cell Chemical Biology 2019, 26: 584-592.e6. PMID: 30745239, PMCID: PMC6474801, DOI: 10.1016/j.chembiol.2019.01.003.Peer-Reviewed Original Research
2018
Seeing the long tail: A novel green fluorescent protein, SiriusGFP, for ultra long timelapse imaging
Zhong S, Rivera-Molina F, Rivetta A, Toomre D, Santos-Sacchi J, Navaratnam D. Seeing the long tail: A novel green fluorescent protein, SiriusGFP, for ultra long timelapse imaging. Journal Of Neuroscience Methods 2018, 313: 68-76. PMID: 30578868, PMCID: PMC9431725, DOI: 10.1016/j.jneumeth.2018.12.008.Peer-Reviewed Original ResearchMeSH KeywordsGreen Fluorescent ProteinsHEK293 CellsHeLa CellsHumansMicroscopy, ConfocalMicroscopy, FluorescenceConceptsSuper-resolution structured illumination microscopyFluorescent proteinNovel green fluorescent proteinGreen fluorescent proteinMembrane proteinsPhotostable variantsCell biologyC-terminusStructured illumination microscopyEGFPProteinConfocal imagingSIM imagingCombination of novelIllumination microscopyKey mutationsKnown mutationsOmp25High intensity excitationMutationsLight intensityCo-operative effectSustained fluorescencePhotobleachingMisfoldingAssessing photodamage in live-cell STED microscopy
Kilian N, Goryaynov A, Lessard MD, Hooker G, Toomre D, Rothman JE, Bewersdorf J. Assessing photodamage in live-cell STED microscopy. Nature Methods 2018, 15: 755-756. PMID: 30275592, PMCID: PMC6915835, DOI: 10.1038/s41592-018-0145-5.Peer-Reviewed Original ResearchFluorescenceHeLa CellsHumansMicroscopy, FluorescenceOxidation-ReductionPhotochemical ProcessesPhotolysis
2017
Leptin Is Produced by Parathyroid Glands and Stimulates Parathyroid Hormone Secretion
Hoang D, Broer N, Sosa JA, Abitbol N, Yao X, Li F, Rivera-Molina F, Toomre DK, Roman SA, Sue G, Kim S, Li AY, Callender GG, Simpson C, Narayan D. Leptin Is Produced by Parathyroid Glands and Stimulates Parathyroid Hormone Secretion. Annals Of Surgery 2017, 266: 1075-1083. PMID: 27611607, DOI: 10.1097/sla.0000000000002004.Peer-Reviewed Original ResearchConceptsParathyroid hormone secretionParathyroid glandsHormone secretionLeptin receptorOb/ob miceDiseased parathyroid glandsDiseased parathyroid tissueDiagnosis of hyperparathyroidismParathyroid chief cellsCultured parathyroid cellsAnimal model assaysJAK2/STAT3 inhibitorPTH levelsPTH secretionPTH releaseSerum calciumSitu hybridizationLeptin uptakeProspective studySurgical interventionConfocal microscopyHyperplastic glandsParathyroid tissueBone metabolismOb miceSTED 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 ResearchMeSH KeywordsCeramidesDrug StabilityFluorescent DyesGolgi ApparatusHeLa CellsHumansImaging, Three-DimensionalMicroscopy, FluorescenceRhodaminesConceptsLive cellsMembrane-bound proteinsLipid probesGolgi dynamicsCellular functionsGolgi structureCellular organellesGolgi apparatusCeramide lipidsSuper-resolution imagingLabeling strategySTED imagingSTED microscopyCellsPhotostable fluorophoresLipidsGolgiOrganellesTwo-componentBioorthogonal reactionsProbeProteinHigh densityLong‐Term Live‐Cell STED Nanoscopy of Primary and Cultured Cells with the Plasma Membrane HIDE Probe DiI‐SiR
Thompson AD, Omar MH, Rivera‐Molina F, Xi Z, Koleske AJ, Toomre DK, Schepartz A. Long‐Term Live‐Cell STED Nanoscopy of Primary and Cultured Cells with the Plasma Membrane HIDE Probe DiI‐SiR. Angewandte Chemie International Edition 2017, 56: 10408-10412. PMID: 28679029, PMCID: PMC5576494, DOI: 10.1002/anie.201704783.Peer-Reviewed Original ResearchLong time-lapse nanoscopy with spontaneously blinking membrane probes
Takakura H, Zhang Y, Erdmann RS, Thompson AD, Lin Y, McNellis B, Rivera-Molina F, Uno SN, Kamiya M, Urano Y, Rothman JE, Bewersdorf J, Schepartz A, Toomre D. Long time-lapse nanoscopy with spontaneously blinking membrane probes. Nature Biotechnology 2017, 35: 773-780. PMID: 28671662, PMCID: PMC5609855, DOI: 10.1038/nbt.3876.Peer-Reviewed Original ResearchExcess cholesterol inhibits glucose‐stimulated fusion pore dynamics in insulin exocytosis
Xu Y, Toomre DK, Bogan JS, Hao M. Excess cholesterol inhibits glucose‐stimulated fusion pore dynamics in insulin exocytosis. Journal Of Cellular And Molecular Medicine 2017, 21: 2950-2962. PMID: 28544529, PMCID: PMC5661106, DOI: 10.1111/jcmm.13207.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell Line, TumorCell MembraneCholesterolDiabetes Mellitus, Type 2DynaminsExocytosisGene Expression RegulationGlucoseHumansInsulinInsulin-Secreting CellsMembrane FusionMiceMicroscopy, FluorescenceModels, BiologicalPhosphatidylinositol 4,5-DiphosphateSecretory VesiclesSignal TransductionConceptsFusion pore dynamicsInsulin exocytosisFusion eventsPore dynamicsGlucose-triggered insulin secretionΒ-cellsFull fusionSingle granule levelTotal internal reflection fluorescence microscopySingle exocytic eventsReflection fluorescence microscopyImpairs β-cell functionExcess cholesterolGTPase dynaminExocytic eventsRole of cholesterolPlasma membranePancreatic β-cellsMolecular mechanismsInsulin granulesCompound exocytosisFusion kineticsΒ-cell dysfunctionExocytosisType 2 diabetes
2016
Ultra-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 ResearchMeSH KeywordsAnimalsBacteriophagesCOP-Coated VesiclesCytological TechniquesGolgi ApparatusMaleMiceMicroscopy, FluorescenceSingle Molecule ImagingSpermatocytesSynaptonemal ComplexConceptsCell 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 architecturesResolutionNanoscopeCellsTwo-colour live-cell nanoscale imaging of intracellular targets
Bottanelli F, Kromann EB, Allgeyer ES, Erdmann RS, Wood Baguley S, Sirinakis G, Schepartz A, Baddeley D, Toomre DK, Rothman JE, Bewersdorf J. Two-colour live-cell nanoscale imaging of intracellular targets. Nature Communications 2016, 7: 10778. PMID: 26940217, PMCID: PMC4785223, DOI: 10.1038/ncomms10778.Peer-Reviewed Original Research
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 ResearchMeSH KeywordsCell SurvivalCeramidesColoring AgentsGolgi ApparatusHeLa CellsHumansMicroscopy, ConfocalMicroscopy, Fluorescence
2013
Live-cell imaging of exocyst links its spatiotemporal dynamics to various stages of vesicle fusion
Rivera-Molina F, Toomre D. Live-cell imaging of exocyst links its spatiotemporal dynamics to various stages of vesicle fusion. Journal Of Cell Biology 2013, 201: 673-680. PMID: 23690179, PMCID: PMC3664709, DOI: 10.1083/jcb.201212103.Peer-Reviewed Original ResearchMeSH KeywordsCell LineCell MembraneExocytosisFluorescence Recovery After PhotobleachingHeLa CellsHumansMembrane FusionMicroscopy, FluorescenceSNARE ProteinsVesicular Transport ProteinsConceptsLive-cell imagingVesicle fusionEndocytic recycling compartmentAttachment protein receptorsSNARE fusion machineryExocyst complexMembrane traffickingFusion machineryRecycling compartmentCell cortexSec8Cell protrusionsPlasma membraneVesicle attachmentFusion poreMembrane expansionProtein receptorsCell polarizationFluorescence recoverySpatiotemporal dynamicsExocystUbiquitous roleVesiclesTraffickingMorphological criteria
2012
Cellular imaging using total internal reflection fluorescence microscopy: theory and instrumentation.
Toomre D. Cellular imaging using total internal reflection fluorescence microscopy: theory and instrumentation. Cold Spring Harbor Protocols 2012, 2012: 414-24. PMID: 22474668, DOI: 10.1101/pdb.top068650.Peer-Reviewed Original ResearchConceptsTotal internal reflection fluorescence microscopyReflection fluorescence microscopyRefractive indexHigh numerical aperture objective lensNumerical aperture objective lensThinner optical planeDifferent refractive indicesDynamic cellular processesFluorescence microscopyCell fluorescent microscopyTransient intermediate statesConventional epifluorescence microscopeEvanescent fieldMembrane traffickingDeep imagingObjective lensCellular processesCytoskeleton remodelingCell cortexOptical planeCell signalingAxial resolutionOptical principlesOrganelle levelMolecular manipulationAlignment and Calibration of Total Internal Reflection Fluorescence Microscopy Systems
Toomre D. Alignment and Calibration of Total Internal Reflection Fluorescence Microscopy Systems. Cold Spring Harbor Protocols 2012, 2012: pdb.prot068668. PMID: 22474669, DOI: 10.1101/pdb.prot068668.Peer-Reviewed Original ResearchConceptsTotal internal reflection fluorescence microscopyThinner optical planeDynamic cellular processesCell fluorescent microscopyReflection fluorescence microscopyMembrane traffickingCellular processesCytoskeleton remodelingCell cortexCell signalingOrganelle levelTransient intermediate statesMolecular manipulationFluorescence microscopyRefractive indexFluorescent microscopyHigh numerical aperture objective lensFluorescence microscopy systemNumerical aperture objective lensConventional epifluorescence microscopeEpifluorescence microscopeDifferent refractive indicesCellular samplesRecent availabilityConfocal microscopeGenerating live cell data using total internal reflection fluorescence microscopy.
Toomre D. Generating live cell data using total internal reflection fluorescence microscopy. Cold Spring Harbor Protocols 2012, 2012: 439-46. PMID: 22474670, DOI: 10.1101/pdb.ip068676.Peer-Reviewed Original ResearchConceptsTotal internal reflection fluorescence microscopyReflection fluorescence microscopyThinner optical planeDynamic cellular processesFluorescence microscopyLive-cell dataCell fluorescent microscopyRefractive indexHigh numerical aperture objective lensNumerical aperture objective lensMembrane traffickingCytoskeleton dynamicsCellular processesCytoskeleton remodelingCell cortexCell signalingTime-lapse moviesDifferent refractive indicesOrganelle levelTransient intermediate statesMolecular manipulationConventional epifluorescence microscopeDeep imagingEvanescent fieldObjective lens
2011
Using light to see and control membrane traffic
Xu Y, Melia TJ, Toomre DK. Using light to see and control membrane traffic. Current Opinion In Chemical Biology 2011, 15: 822-830. PMID: 22079055, DOI: 10.1016/j.cbpa.2011.10.016.Peer-Reviewed Original ResearchDual-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 characteristicsAdipocytesCells3-D Reconstruction of Microtubules from Multi-Angle Total Internal Reflection Fluorescence Microscopy Using Bayesian Framework
Yang Q, Karpikov A, Toomre D, Duncan JS. 3-D Reconstruction of Microtubules from Multi-Angle Total Internal Reflection Fluorescence Microscopy Using Bayesian Framework. IEEE Transactions On Image Processing 2011, 20: 2248-2259. PMID: 21324778, DOI: 10.1109/tip.2011.2114359.Peer-Reviewed Original ResearchConceptsEvanescent fieldDifferent penetration depthsTIRF imagesPenetration depthSamples of microtubulesLaser beamTotal internal reflection fluorescence microscopyAxial resolutionReflection fluorescence microscopyLarge radiusIncident angleMulti-angle total internal reflection fluorescence microscopyElectron microscopy imagesTIRF dataSmall radiusTracking of microtubulesMicroscopy imagesFluorescence microscopyMicroscopyRadiusReconstruction resultsCurvilinear characteristicsZ-dimensionExperimental calibrationMicrotubule curvatureAn Expectation Maximization Based Method for Subcellular Particle Tracking Using Multi-angle TIRF Microscopy
Liang L, Shen H, De Camilli P, Toomre DK, Duncan JS. An Expectation Maximization Based Method for Subcellular Particle Tracking Using Multi-angle TIRF Microscopy. Lecture Notes In Computer Science 2011, 14: 629-636. PMID: 22003671, PMCID: PMC3648983, DOI: 10.1007/978-3-642-23623-5_79.Peer-Reviewed Original Research