2023
Cell Surface RNAs Control Neutrophil Function
Zhang N, Tang W, Torres L, Zhu L, Wang X, Ajaj Y, Wang Y, Zhang D, Kurbatov V, Zhou H, Luan Y, Kumar P, Hidalgo A, Wu D, Lu J. Cell Surface RNAs Control Neutrophil Function. Blood 2023, 142: 674. DOI: 10.1182/blood-2023-187570.Peer-Reviewed Original ResearchExtracellular RNaseCell surfaceTotal RNABona fide ligandsEndothelial cellsOuter cell surfaceTransendothelial migrationMammalian cellsSuch RNAsGlycan modificationsCellular RNAGlycoRNARNase digestionLive cellsRNAHematopoietic cellsRNase treatmentSimilar defectsIntegrin levelsConfocal microscopyRNaseGlycan fractionImportant functionsHomologuesRecombinant E-selectinRapid Quantification of First and Second Phase Insulin Secretion Dynamics using an In vitro Platform for Improving Insulin Therapy
Thoduvayil S, Weerakkody J, Sundaram R, Topper M, Bera M, Coleman J, Li X, Mariappan M, Ramakrishnan S. Rapid Quantification of First and Second Phase Insulin Secretion Dynamics using an In vitro Platform for Improving Insulin Therapy. Cell Calcium 2023, 113: 102766. PMID: 37295201, PMCID: PMC10450995, DOI: 10.1016/j.ceca.2023.102766.Peer-Reviewed Original ResearchConceptsCellular pathwaysSecretion dynamicsSmall molecule screeningLuciferase reporter systemInsulin secretion dynamicsHigh-throughput compoundInsulin secretionHigh-throughput quantificationReporter systemGenetic studiesLive cellsDistinct rolesInsulin therapyGlucose-stimulated insulin secretionSmall moleculesEffective insulin therapyPathwaySecretion
2022
Quantification of Protein Exit at the Trans-Golgi Network
Tran M, Kim Y, von Blume J. Quantification of Protein Exit at the Trans-Golgi Network. Methods In Molecular Biology 2022, 2557: 583-594. PMID: 36512239, DOI: 10.1007/978-1-0716-2639-9_35.Peer-Reviewed Original ResearchConceptsTrans-Golgi networkProtein exportSecretory pathwaySelective hooks (RUSH) systemCell biological approachesProtein of interestPulse-chase experimentsProtein exitProtein sortingExport kineticsCellular homeostasisProtein transportDifferent cargoesLive cellsBiological approachesRUSH systemProteinPathwayTraffickingHomeostasisExportCargoSortingCompartmentsCellsIn Vitro Reconstitution of the Actin Cytoskeleton Inside Giant Unilamellar Vesicles.
Chen S, Sun Z, Murrell M. In Vitro Reconstitution of the Actin Cytoskeleton Inside Giant Unilamellar Vesicles. Journal Of Visualized Experiments 2022 PMID: 36094272, DOI: 10.3791/64026.Peer-Reviewed Original ResearchConceptsGiant unilamellar vesiclesCytoskeleton networkLipid dropletsCell‐mimicking systemUnilamellar vesiclesActin cytoskeletonVitro reconstitutionGenetic regulationActin networkBiochemical regulationSynthetic biologyCellular activitiesLive cellsMixture of proteinsActin polymersLipid componentsVesiclesRegulationReconstitutionCellsCytoskeletonCell deformationMachineryBiologyQuantitative insightsBromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs
Kenworthy C, Haque N, Liou S, Chandris P, Wong V, Dziuba P, Lavis L, Liu W, Singer R, Coleman R. Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs. Biophysical Journal 2022, 121: 1738-1752. PMID: 35364106, PMCID: PMC9117891, DOI: 10.1016/j.bpj.2022.03.027.Peer-Reviewed Original ResearchConceptsChromatin remodelersChromatin statePBAF chromatin-remodeling complexSingle-molecule fluorescence microscopy studiesDifferent chromatin statesChromatin-remodeling complexRNA polymerase IIChromatin hubTranscriptional burstingPolymerase IIAcetylated nucleosomesFluorescence microscopy studiesPBAFBromodomainsNucleosomesChromatin stabilityLive cellsStable engagementRemodelersDynamic targetingDirect roleChromatinImaging revealsTargetingGenomeLive-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer
Yi E, Gujar A, Guthrie M, Kim H, Zhao D, Johnson K, Amin S, Costa M, Yu Q, Das S, Jillette N, Clow P, Cheng A, Verhaak R. Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer. Cancer Discovery 2022, 12: 468-483. PMID: 34819316, PMCID: PMC8831456, DOI: 10.1158/2159-8290.cd-21-1376.Peer-Reviewed Original ResearchConceptsExtrachromosomal DNA elementsDNA elementsUneven segregationRNA polymerase IILive-cell imagingPolymerase IIOffspring cellsGene transcriptionCell line modelsEcDNAsRandom segregationGenetic materialLiving cellsCopy numberLive cellsIndividual cellsTumor evolutionMitosisInheritance patternBreakpoint sequencesIssue featureTranscriptionFluorescent markersPatient tissuesCells
2021
Distinct roles of nuclear basket proteins in directing the passage of mRNA through the nuclear pore
Li Y, Aksenova V, Tingey M, Yu J, Ma P, Arnaoutov A, Chen S, Dasso M, Yang W. Distinct roles of nuclear basket proteins in directing the passage of mRNA through the nuclear pore. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2015621118. PMID: 34504007, PMCID: PMC8449422, DOI: 10.1073/pnas.2015621118.Peer-Reviewed Original ResearchConceptsNuclear pore complexNuclear basket proteinsNative nuclear pore complexesCopy numberDistinct rolesExport routesSingle-molecule microscopyExport kineticsPore complexNative copyNuclear exportNuclear poresExact copy numberComposite proteinsNup153Live cellsMessenger RNASpecific functionsFull complementProteinSpecific mannerNup50Specific roleExport efficiencyRNACellular Sticking Can Strongly Reduce Complex Binding by Speeding Dissociation
Davis C, Gruebele M. Cellular Sticking Can Strongly Reduce Complex Binding by Speeding Dissociation. The Journal Of Physical Chemistry B 2021, 125: 3815-3823. PMID: 33826329, DOI: 10.1021/acs.jpcb.1c00950.Peer-Reviewed Original ResearchConceptsSpliceosomal protein U1APotential binding partnerMajor cellular effectsProtein U1ABinding partnerU1 snRNACellular environmentNonspecific interactionsFörster resonance energy transferProper bindingCellular componentsResonance energy transferU1ALive cellsLarge hydrophobic surface areaMacromolecular crowdingCellular effectsHydrophobic surface areaOS cellsModel systemComplex bindingHigh binding affinityWeak nonspecific interactionsBinding affinitiesCells
2020
High-speed super-resolution imaging of rotationally symmetric structures using SPEED microscopy and 2D-to-3D transformation
Li Y, Tingey M, Ruba A, Yang W. High-speed super-resolution imaging of rotationally symmetric structures using SPEED microscopy and 2D-to-3D transformation. Nature Protocols 2020, 16: 532-560. PMID: 33318694, PMCID: PMC9382854, DOI: 10.1038/s41596-020-00440-x.Peer-Reviewed Original ResearchConceptsSpeed microscopySuper-resolution imaging techniquesDiffraction-limited resolutionComplex optical componentsSuper-resolution imagingSuper-resolution informationOptical componentsSuper-resolution microscopyBiological channelsSpeed imagingRotational symmetryFluorescent moleculesHigh spatiotemporal resolutionMicroscopy approachSymmetric structureImaging techniquesMicroscopySpatiotemporal resolutionEpifluorescence microscopeLive cellsResolutionSubcellular structuresGlobal and Site-Specific Effect of Phosphorylation on Protein Turnover
Wu C, Ba Q, Lu D, Li W, Salovska B, Hou P, Mueller T, Rosenberger G, Gao E, Di Y, Zhou H, Fornasiero EF, Liu Y. Global and Site-Specific Effect of Phosphorylation on Protein Turnover. Developmental Cell 2020, 56: 111-124.e6. PMID: 33238149, PMCID: PMC7855865, DOI: 10.1016/j.devcel.2020.10.025.Peer-Reviewed Original ResearchConceptsProtein turnoverProtein lifetimeCyclin-dependent kinase substrateStable isotope-labeled amino acidsSite-specific phosphorylationPulse-labeling approachIsotope-labeled amino acidsMass spectrometry-based methodCell fitnessKinase substratePhosphorylation sitesPhosphorylated sitesProteomic methodsCell signalingSpectrometry-based methodsLive cellsAmino acidsPhosphositesRich resourceDisease biologyLabeling approachPhosphorylationModification typesGlutamic acidTurnoverDNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells
Williams ND, Landajuela A, Kasula RK, Zhou W, Powell JT, Xi Z, Isaacs FJ, Berro J, Toomre D, Karatekin E, Lin C. DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells. Nano Letters 2020, 20: 8890-8896. PMID: 33164530, PMCID: PMC7726105, DOI: 10.1021/acs.nanolett.0c03925.Peer-Reviewed Original ResearchConceptsCopies of proteinsBrightness standardsFluorescence microscopyProtein countingMammalian cellsFluorescent proteinCopy numberLive cellsConventional quantification techniquesBiological LaboratoryFluorescence microscopeProteinDNA origamiVersatile toolCellsBiologyCurrent quantification methodsCopiesOrganic dyes
2018
Cell Volume Controls Protein Stability and Compactness of the Unfolded State
Wang Y, Sukenik S, Davis CM, Gruebele M. Cell Volume Controls Protein Stability and Compactness of the Unfolded State. The Journal Of Physical Chemistry B 2018, 122: 11762-11770. PMID: 30289261, DOI: 10.1021/acs.jpcb.8b08216.Peer-Reviewed Original ResearchAnalysis of Cell Viability by the MTT Assay.
Kumar P, Nagarajan A, Uchil PD. Analysis of Cell Viability by the MTT Assay. Cold Spring Harbor Protocols 2018, 2018: pdb.prot095505. PMID: 29858338, DOI: 10.1101/pdb.prot095505.Peer-Reviewed Original ResearchConceptsInsoluble purple formazanMitochondrial reductaseCell stressCell deathLive cellsDirect cell deathConversion of substrateMetabolic activityCell viabilityPurple formazanViability assaysNonadherent cellsPlate formatCellsAssaysMTT assayMTTChromogenic productSensitive assayReductaseToxic agentsPopular assayFormazanViabilityLarge changes
2017
How does solvation in the cell affect protein folding and binding?
Davis CM, Gruebele M, Sukenik S. How does solvation in the cell affect protein folding and binding? Current Opinion In Structural Biology 2017, 48: 23-29. PMID: 29035742, DOI: 10.1016/j.sbi.2017.09.003.Peer-Reviewed Original ResearchConceptsMild environmental changesProtein functionCellular processesProtein foldingCellular environmentProtein surface areaProtein studiesLive cellsEnvironmental changesNon-steric interactionsProtein processesNatural contextCellsInteraction typesSolute environmentFoldingProteinRecent examplesBindingRapid changesSolute compositionNovel 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 periodsDivisionSTED 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 density
2016
Avoiding artefacts when counting polymerized actin in live cells with LifeAct fused to fluorescent proteins
Courtemanche N, Pollard TD, Chen Q. Avoiding artefacts when counting polymerized actin in live cells with LifeAct fused to fluorescent proteins. Nature Cell Biology 2016, 18: 676-683. PMID: 27159499, PMCID: PMC5509211, DOI: 10.1038/ncb3351.Peer-Reviewed Original Research
2015
An Activity‐Based Probe for Studying Crosslinking in Live Bacteria
Gautam S, Kim T, Shoda T, Sen S, Deep D, Luthra R, Ferreira M, Pinho M, Spiegel D. An Activity‐Based Probe for Studying Crosslinking in Live Bacteria. Angewandte Chemie 2015, 127: 10638-10642. DOI: 10.1002/ange.201503869.Peer-Reviewed Original ResearchWall teichoic acidActivity-based probesSingle PBPLive bacteriaAntibiotic targetsCell wallFluorescent mimicTeichoic acidNatural substrateLive cellsEssential processRelative quantitationNatural crosslinksPeptidoglycanBacterial growthSpatiotemporal aspectsBacteriaExperimental toolPBPPeptide mimicsMimics
2014
Intracellular Tracking of Single Native Molecules with Electroporation-Delivered Quantum Dots
Sun C, Cao Z, Wu M, Lu C. Intracellular Tracking of Single Native Molecules with Electroporation-Delivered Quantum Dots. Analytical Chemistry 2014, 86: 11403-11409. PMID: 25341054, DOI: 10.1021/ac503363m.Peer-Reviewed Original Research
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