Featured Publications
PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infection
Xu D, Jiang W, Wu L, Gaudet R, Park E, Su M, Cheppali S, Cheemarla N, Kumar P, Uchil P, Grover J, Foxman E, Brown C, Stansfeld P, Bewersdorf J, Mothes W, Karatekin E, Wilen C, MacMicking J. PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infection. Nature 2023, 619: 819-827. PMID: 37438530, PMCID: PMC10371867, DOI: 10.1038/s41586-023-06322-y.Peer-Reviewed Original ResearchConceptsC-terminal β-barrel domainSpike-mediated fusionCell-autonomous defenseLarge-scale exome sequencingΒ-barrel domainGenome-wide CRISPRSARS-CoV-2 infectionHost cell cytosolScramblase activityPhospholipid scramblaseLive SARS-CoV-2 infectionHuman lung epitheliumPLSCR1SARS-CoV-2 USASingle-molecule switchingSARS-CoV-2 variantsExome sequencingHuman populationRestriction factorsViral RNANew SARS-CoV-2 variantsSARS-CoV-2Robust activityLung epitheliumDefense factorsChromatin expansion microscopy reveals nanoscale organization of transcription and chromatin
Pownall M, Miao L, Vejnar C, M'Saad O, Sherrard A, Frederick M, Benitez M, Boswell C, Zaret K, Bewersdorf J, Giraldez A. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023, 381: 92-100. PMID: 37410825, PMCID: PMC10372697, DOI: 10.1126/science.ade5308.Peer-Reviewed Original ResearchConceptsZygotic genome activationTranscriptional elongationExpansion microscopyRNA polymerase IIChromatin regulatory factorsEnhancer-promoter contactsGenome activationChromatin organizationNuclear organizationPolymerase IIPol IIFactor NanogTranscription factorsGene expressionRegulatory factorsChromatinNanoscale organizationNanogTranscriptionElongationNucleosomesUniversal processPromoterEmbryosEnhancerFluorogenic DNA-PAINT for faster, low-background super-resolution imaging
Chung KKH, Zhang Z, Kidd P, Zhang Y, Williams ND, Rollins B, Yang Y, Lin C, Baddeley D, Bewersdorf J. Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. Nature Methods 2022, 19: 554-559. PMID: 35501386, PMCID: PMC9133131, DOI: 10.1038/s41592-022-01464-9.Peer-Reviewed Original ResearchConceptsSlow imaging speedSuper-resolution imagingSuper-resolution microscopy methodsDNA-PAINTOptical sectioningImaging speedFast imagingNanometer resolutionDNA-based points accumulationHigh-fidelity imagesUnbound fluorophoresMicroscopy methodsDocking strandsHigh backgroundPoint accumulationNanoscale topographyProbeDMA-tudor interaction modules control the specificity of in vivo condensates
Courchaine EM, Barentine AES, Straube K, Lee DR, Bewersdorf J, Neugebauer KM. DMA-tudor interaction modules control the specificity of in vivo condensates. Cell 2021, 184: 3612-3625.e17. PMID: 34115980, PMCID: PMC8402948, DOI: 10.1016/j.cell.2021.05.008.Peer-Reviewed Original ResearchThree-dimensional adaptive optical nanoscopy for thick specimen imaging at sub-50-nm resolution
Hao X, Allgeyer ES, Lee DR, Antonello J, Watters K, Gerdes JA, Schroeder LK, Bottanelli F, Zhao J, Kidd P, Lessard MD, Rothman JE, Cooley L, Biederer T, Booth MJ, Bewersdorf J. Three-dimensional adaptive optical nanoscopy for thick specimen imaging at sub-50-nm resolution. Nature Methods 2021, 18: 688-693. PMID: 34059828, PMCID: PMC7610943, DOI: 10.1038/s41592-021-01149-9.Peer-Reviewed Original ResearchConceptsAdaptive optics schemeBest possible spatial resolutionPossible spatial resolutionOptical nanoscopyOptics schemeDiffraction limitDark stateOptical aberrationsNanoscopy methodsThin samplesThick specimenFluorescent moleculesSpatial resolutionThick specimensNanoscopeIsotropic resolutionResolutionNanoscopyPath geometryFluorescence microscopyMicroscopeMicroscopyImplementation of a 4Pi-SMS super-resolution microscope
Wang J, Allgeyer ES, Sirinakis G, Zhang Y, Hu K, Lessard MD, Li Y, Diekmann R, Phillips MA, Dobbie IM, Ries J, Booth MJ, Bewersdorf J. Implementation of a 4Pi-SMS super-resolution microscope. Nature Protocols 2020, 16: 677-727. PMID: 33328610, PMCID: PMC9118368, DOI: 10.1038/s41596-020-00428-7.Peer-Reviewed Original ResearchLight microscopy of proteins in their ultrastructural context
M’Saad O, Bewersdorf J. Light microscopy of proteins in their ultrastructural context. Nature Communications 2020, 11: 3850. PMID: 32737322, PMCID: PMC7395138, DOI: 10.1038/s41467-020-17523-8.Peer-Reviewed Original ResearchConceptsUltrastructural contextLocal protein densityConventional confocal microscopeCellular nanoarchitectureOptical contrastSpecific proteinsElectron microscopyFluorescence microscopyLight microscopyProteinBulk labelingProtein densityConfocal microscopeStandard light microscopyIntracellular spaceMicroscopyProteomeCellsNanoscaleMicroscopeNew principleDiscoveryLabelingPhysical expansionDensityAn integrated platform for high-throughput nanoscopy
Barentine A, Lin Y, Courvan E, Kidd P, Liu M, Balduf L, Phan T, Rivera-Molina F, Grace M, Marin Z, Lessard M, Rios Chen J, Wang S, Neugebauer K, Bewersdorf J, Baddeley D. An integrated platform for high-throughput nanoscopy. Nature Biotechnology 2023, 41: 1549-1556. PMID: 36914886, PMCID: PMC10497732, DOI: 10.1038/s41587-023-01702-1.Peer-Reviewed Original ResearchConceptsLarge data volumesUser-defined extensionsPlugin frameworkData compressionData volumeCamera frameFrame rateAnalysis platformAcquisition taskPlatformIntegrated acquisitionThroughputSingle-molecule localization microscopyTypical throughputHundreds of cellsThree-dimensional fluorescenceFrameworkTens of cellsLocalization microscopyWorkflow
2024
VPS13B is localized at the interface between Golgi cisternae and is a functional partner of FAM177A1
Ugur B, Schueder F, Shin J, Hanna M, Wu Y, Leonzino M, Su M, McAdow A, Wilson C, Postlethwait J, Solnica-Krezel L, Bewersdorf J, De Camilli P. VPS13B is localized at the interface between Golgi cisternae and is a functional partner of FAM177A1. Journal Of Cell Biology 2024, 223: e202311189. PMID: 39331042, PMCID: PMC11451052, DOI: 10.1083/jcb.202311189.Peer-Reviewed Original ResearchConceptsLipid transportGolgi complex proteinGolgi subcompartmentsGolgi membranesGolgi cisternaeProtein familyFunctional partnersGolgi complexKO cellsComplex proteinsFAM177A1GolgiVPS13BAdjacent membranesMutationsProteinCohen syndromeLipidOrthologsInteractorsBrefeldinMembraneOrganellesSubcompartmentsDevelopmental disordersRefining Biologically Inconsistent Segmentation Masks with Masked Autoencoders
Sauer A, Tian Y, Bewersdorf J, Rittscher J. Refining Biologically Inconsistent Segmentation Masks with Masked Autoencoders. 2024, 00: 6904-6912. DOI: 10.1109/cvprw63382.2024.00684.Peer-Reviewed Original ResearchNative architecture of a human GBP1 defense complex for cell-autonomous immunity to infection
Zhu S, Bradfield C, Maminska A, Park E, Kim B, Kumar P, Huang S, Kim M, Zhang Y, Bewersdorf J, MacMicking J. Native architecture of a human GBP1 defense complex for cell-autonomous immunity to infection. Science 2024, 383: eabm9903. PMID: 38422126, DOI: 10.1126/science.abm9903.Peer-Reviewed Original ResearchConceptsGuanylate-binding proteinsCaspase-4Surface of Gram-negative bacteriaGuanosine triphosphate hydrolysisImmunity to infectionInnate immunity to infectionCryo-electron tomographyGram-negative bacteriaImmunity proteinSignaling platformsMembrane insertionHuman cellsNative structureCombat infectionsLipopolysaccharide releaseGasdermin DExtended conformationLiving organismsProteinDefense complexCellsNative architectureGBP1BacteriaInfectionUnraveling 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 relationshipsImagesThroughputA correlative quantitative phase contrast and fluorescence super-resolution microscope for imaging molecules in their cellular context
Bao Y, Marin Z, Zhang C, Neugebauer K, Baddeley D, Shribak M, Bewersdorf J. A correlative quantitative phase contrast and fluorescence super-resolution microscope for imaging molecules in their cellular context. Biophysical Journal 2024, 123: 290a. DOI: 10.1016/j.bpj.2023.11.1808.Peer-Reviewed Original Research
2023
mRNA Editing via the Apobec1 Gene Promotes Recovery from AKI
Guo X, Velazquez H, Xu L, Cheng Z, Chen T, Tian Y, Bewersdorf J, Blanc V, Davidson N, Safirstein R, Desir G. mRNA Editing via the Apobec1 Gene Promotes Recovery from AKI. Journal Of The American Society Of Nephrology 2023, 34: 451-451. DOI: 10.1681/asn.20233411s1451b.Peer-Reviewed Original ResearchSingle cell in vivo optogenetic stimulation by two-photon excitation fluorescence transfer
Tong L, Han S, Xue Y, Chen M, Chen F, Ke W, Shu Y, Ding N, Bewersdorf J, Zhou Z, Yuan P, Grutzendler J. Single cell in vivo optogenetic stimulation by two-photon excitation fluorescence transfer. IScience 2023, 26: 107857. PMID: 37752954, PMCID: PMC10518705, DOI: 10.1016/j.isci.2023.107857.Peer-Reviewed Original ResearchThe nanoscale organization of reticulon 4 shapes local endoplasmic reticulum structure in situ
Fuentes L, Marin Z, Tyson J, Baddeley D, Bewersdorf J. The nanoscale organization of reticulon 4 shapes local endoplasmic reticulum structure in situ. Journal Of Cell Biology 2023, 222: e202301112. PMID: 37516910, PMCID: PMC10373298, DOI: 10.1083/jcb.202301112.Peer-Reviewed Original ResearchHighly Multiplexed Imaging with Speed and Fluorogenic DNA-PAINT
Schueder F, Bewersdorf J. Highly Multiplexed Imaging with Speed and Fluorogenic DNA-PAINT. Microscopy And Microanalysis 2023, 29: 1069-1069. PMID: 37613180, DOI: 10.1093/micmic/ozad067.548.Peer-Reviewed Original ResearchExtracting nanoscale membrane morphology from single-molecule localizations
Marin Z, Fuentes L, Bewersdorf J, Baddeley D. Extracting nanoscale membrane morphology from single-molecule localizations. Biophysical Journal 2023, 122: 3022-3030. PMID: 37355772, PMCID: PMC10432223, DOI: 10.1016/j.bpj.2023.06.010.Peer-Reviewed Original Research
2022
Omics goes spatial epigenomics
Schueder F, Bewersdorf J. Omics goes spatial epigenomics. Cell 2022, 185: 4253-4255. PMID: 36368304, DOI: 10.1016/j.cell.2022.10.014.Commentaries, Editorials and LettersA group approach to growing as a principal investigator
Greco V, Politi K, Eisenbarth S, Colón-Ramos D, Giraldez AJ, Bewersdorf J, Berg DN. A group approach to growing as a principal investigator. Current Biology 2022, 32: r498-r504. PMID: 35671717, DOI: 10.1016/j.cub.2022.04.082.Commentaries, Editorials and Letters