2025
Feedback between F-actin organization and active stress governs criticality and energy localization in the cell cytoskeleton
Sun Z, Zimmerberg N, Kelly P, Floyd C, Papoian G, Murrell M. Feedback between F-actin organization and active stress governs criticality and energy localization in the cell cytoskeleton. Nature Physics 2025, 21: 1290-1302. DOI: 10.1038/s41567-025-02919-4.Peer-Reviewed Original ResearchF-actin organizationF-actinNucleation-promoting factorsMyosin II motorsF-actin filamentsDynamic structural reorganizationActin cytoskeletonCytoskeletal dynamicsCellular self-organizationCell cytoskeletonBiological processesSelf-organized criticalityLiving cellsMolecular motorsCytoskeletonEnergy localizationSystem in vitroActinCondensed-matter systemsMyosinFeedback loopDistribution of energy releaseForce propagationAnderson localizationMechanical modesHighly stable planar asymmetric suspended membranes for investigating protein dynamics and membrane fusion
Bera M, Kalyana Sundaram R, Coleman J, Chatterjee A, Thoduvayil S, Pincet F, Ramakrishnan S. Highly stable planar asymmetric suspended membranes for investigating protein dynamics and membrane fusion. Nature Protocols 2025, 1-25. PMID: 40461798, DOI: 10.1038/s41596-025-01192-2.Peer-Reviewed Original ResearchMembrane fusionSingle-vesicle fusion assayMembrane fusion eventsProtein dynamics analysisMembrane fusion mechanismFluorescently labeled proteinsProtein-lipid interactionsSNARE proteinsTotal internal reflection fluorescenceFusion eventsMolecular chaperonesInvestigate protein dynamicsTime-lapse imagingCellular signalingLipid asymmetryFusion assayBiological processesLipid membranesProtein dynamicsMembrane model systemsLiving cellsMembrane environmentNear-native environmentMolecular componentsReflection fluorescenceCoarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci
Mader A, Rodriguez A, Yuan T, Surovtsev I, King M, Mochrie S. Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci. Biophysical Journal 2025, 124: 2120-2132. PMID: 40369871, PMCID: PMC12256843, DOI: 10.1016/j.bpj.2025.05.008.Peer-Reviewed Original ResearchChromatin polymerChromatin configurationLocus identityGenomic positionsLabeled lociLiving cellsLocus configurationsChromatin dynamicsMultiple lociGene locusChromatin researchChromatinLociSingle-particle trackingFluorescent labelingCorrect assignmentDynamic loopTemporal dynamicsCellsGenesModel polymersLabelingIdentityOptical Photothermal Infrared Imaging Using Metabolic Probes in Biological Systems
Shuster S, Curtis A, Davis C. Optical Photothermal Infrared Imaging Using Metabolic Probes in Biological Systems. Analytical Chemistry 2025, 97: 8202-8212. PMID: 40207400, PMCID: PMC12270000, DOI: 10.1021/acs.analchem.4c03752.Peer-Reviewed Original ResearchConceptsLive imaging of cellsSpectrally resolved imagesLiving cellsImaging of living cellsBiological systemsMultifrequency imagesAmino acid probesDynamic imaging of live cellsProbes of proteinsLive imagingConformational changes of biomoleculesConformational changesSpatial resolutionCell linesWater backgroundIdentifying biomoleculesImaging of cellsIR probeFat cellsInfrared spectraReaction mechanismCellsIn-cellInfrared SpectroscopyBiological samplesOptical photothermal infrared imaging using metabolic probes in live biological systems
Shuster S, Curtis A, Davis C. Optical photothermal infrared imaging using metabolic probes in live biological systems. Progress In Biomedical Optics And Imaging 2025, 13332: 1333208-1333208-6. DOI: 10.1117/12.3040983.Peer-Reviewed Original ResearchSpectrally resolved imagesLiving cellsImaging of living cellsReduce imaging timeMultifrequency imagesBiological systemsProtein localizationSite-specific probeDynamic imaging of live cellsMetabolic pathwaysConformational changes of biomoleculesSpatial resolutionInfrared spectraConformational changesReaction mechanismCell linesWater backgroundIdentifying biomoleculesInfrared SpectroscopyA fluorescence-based assay for measuring aminopropyltransferase activity
Singh P, Choi J, Ben Mamoun C. A fluorescence-based assay for measuring aminopropyltransferase activity. Methods In Enzymology 2025, 715: 363-388. PMID: 40382149, DOI: 10.1016/bs.mie.2025.01.067.Peer-Reviewed Original ResearchConceptsAminopropyl transferaseFluorescence-based assaySpermine synthase activityHigh-throughput chemical screeningSaccharomyces cerevisiaeFormation of spermidinePrincipal polyaminesCellular processesHigh-throughput screeningCellular functionsSubstrate analogsSpermidine synthaseDrug discovery effortsPolyamine biosynthesisLiving cellsChemical screeningEnzymeNeurodegenerative disordersPolycationic alkylaminesSynthase activityDiscovery effortsNovel inhibitorsAPT activityChemical librariesInfectious diseasesSuper‐resolution imaging of proteins inside live mammalian cells with mLIVE‐PAINT
Bhaskar H, Gidden Z, Virdi G, Kleinjan D, Rosser S, Gandhi S, Regan L, Horrocks M. Super‐resolution imaging of proteins inside live mammalian cells with mLIVE‐PAINT. Protein Science 2025, 34: e70008. PMID: 39865341, PMCID: PMC11761688, DOI: 10.1002/pro.70008.Peer-Reviewed Original Research
2024
Antagonistic nanobodies implicate mechanism of GSDMD pore formation and potential therapeutic application
Schiffelers L, Tesfamariam Y, Jenster L, Diehl S, Binder S, Normann S, Mayr J, Pritzl S, Hagelauer E, Kopp A, Alon A, Geyer M, Ploegh H, Schmidt F. Antagonistic nanobodies implicate mechanism of GSDMD pore formation and potential therapeutic application. Nature Communications 2024, 15: 8266. PMID: 39327452, PMCID: PMC11427689, DOI: 10.1038/s41467-024-52110-1.Peer-Reviewed Original ResearchConceptsMembrane insertionGasdermin DN-terminal domainCleavage of gasdermin DPore formationPro-inflammatory caspasesPyroptosis to apoptosisActivated caspase-3Caspase-1 activationTarget membraneCaspase-3Assembled poresPlasma membraneCytosolic expressionLiving cellsConformational changesEnhanced caspase-1 activityOligomerizationPotential therapeutic applicationsInflammasome activationNanobodiesPyroptosisStudy pore formationMembraneTherapeutic applicationsBacterial cell surface characterization by phage display coupled to high-throughput sequencing
Grun C, Jain R, Schniederberend M, Shoemaker C, Nelson B, Kazmierczak B. Bacterial cell surface characterization by phage display coupled to high-throughput sequencing. Nature Communications 2024, 15: 7502. PMID: 39209859, PMCID: PMC11362561, DOI: 10.1038/s41467-024-51912-7.Peer-Reviewed Original ResearchConceptsBacterial cell surfaceCell surfacePhage displayP. aeruginosa virulence factorsHigh-throughput DNA sequencingHigh-throughput sequencingPhage display panningCapacity of bacteriaCamelid single-domain antibodiesVirulence factorsDNA sequencesBacterial genotypesPhageSingle-domain antibodiesPseudomonas aeruginosaHost defenseBiological informationAntimicrobial resistanceLiving cellsSequenceChronic infectionCell surface characterizationAdaptive changesCellsBacteriaComposition Heterogeneity of Metal Ions Bound at the Oxygen-Evolving Center of Photosystem II in Living Cells
Wang J. Composition Heterogeneity of Metal Ions Bound at the Oxygen-Evolving Center of Photosystem II in Living Cells. Biochemistry 2024, 63: 1963-1968. PMID: 39037205, DOI: 10.1021/acs.biochem.4c00261.Peer-Reviewed Original ResearchConceptsX-ray free-electron lasersStructure of photosystem IIOxygen-evolving centerPhotosystem IICrystal structure of photosystem IIFree-electron laserPhotosystem II dimersPhotosystem ILight-harvesting complexesCryo-electron tomographyMetal ionsPSII samplesCryo-electron microscopyCryo-ETDimeric core complexesCryo-EMMetal ion cofactorsLiving cellsCrystal structureCryo-electronCryo-EM structureMetal-ion occupancyIon occupancySpectroscopic interpretationAsymmetric environmentProtocol for isolating and identifying small extracellular vesicles derived from human umbilical cord mesenchymal stem cells
Chen Y, Qian H, Mak M, Tao Z. Protocol for isolating and identifying small extracellular vesicles derived from human umbilical cord mesenchymal stem cells. STAR Protocols 2024, 5: 103197. PMID: 39028618, PMCID: PMC11315167, DOI: 10.1016/j.xpro.2024.103197.Peer-Reviewed Original ResearchSmall extracellular vesiclesUmbilical cord mesenchymal stem cellsHuman umbilical cord mesenchymal stem cellsIsolation of small extracellular vesiclesLipid bilayer-enclosed particlesExtracellular vesiclesMesenchymal stem cellsNanoparticle tracking analysisAtomic force microscopeStem cellsMolecular markersLiving cellsTransmission electron microscopyWestern blottingIsolatesVesiclesCellsForce microscopeNKX2-2 based nuclei sorting on frozen human archival pancreas enables the enrichment of islet endocrine populations for single-nucleus RNA sequencing
Xie G, Toledo M, Hu X, Yong H, Sanchez P, Liu C, Naji A, Irianto J, Wang Y. NKX2-2 based nuclei sorting on frozen human archival pancreas enables the enrichment of islet endocrine populations for single-nucleus RNA sequencing. BMC Genomics 2024, 25: 427. PMID: 38689254, PMCID: PMC11059690, DOI: 10.1186/s12864-024-10335-w.Peer-Reviewed Original ResearchConceptsSingle-nucleus RNA sequencingRNA sequencingNuclei sortingSnRNA-seqGene expressionEndocrine populationsFluorescence-activated nuclei sortingHuman isletsGene expression librariesNuclei isolation protocolSingle-cell RNA sequencingFrozen archival tissuesIsolated human isletsHuman pancreatic endocrine cellsSingle-cell transcriptomicsTranscriptomic studiesCytoplasmic contaminationTranscriptome profilingConclusionsOur workNKX2-2Isolated nucleiRNA integrityLiving cellsIsolation protocolPancreatic endocrine cellsMtb-Selective 5‑Aminomethyl Oxazolidinone Prodrugs: Robust Potency and Potential Liabilities
Boshoff H, Young K, Ahn Y, Yadav V, Crowley B, Yang L, Su J, Oh S, Arora K, Andrews J, Manikkam M, Sutphin M, Smith A, Weiner D, Piazza M, Fleegle J, Gomez F, Dayao E, Prideaux B, Zimmerman M, Kaya F, Sarathy J, Tan V, Via L, Tschirret-Guth R, Lenaerts A, Robertson G, Dartois V, Olsen D, Barry C. Mtb-Selective 5‑Aminomethyl Oxazolidinone Prodrugs: Robust Potency and Potential Liabilities. ACS Infectious Diseases 2024, 10: 1679-1695. PMID: 38581700, DOI: 10.1021/acsinfecdis.4c00025.Peer-Reviewed Original ResearchConceptsLinezolid-resistant mutantsDrug-resistant patientsAntitubercular activityN-acetyl metaboliteOxazolidinone prodrugMechanism of actionC3HeB/FeJ miceAntimycobacterial activityN-acetyl transferaseSusceptible to inhibitionCross-resistanceOxazolidinoneCompoundsMoleculesMammalian metabolismN-acetyltransferaseProdrugToxicityMoietyProtein synthesisLinezolidC3HeB/FeJCaseumPatientsLiving cellsOleic acid differentially affects lipid droplet storage of de novo synthesized lipids in hepatocytes and adipocytes
Castillo H, Shuster S, Tarekegn L, Davis C. Oleic acid differentially affects lipid droplet storage of de novo synthesized lipids in hepatocytes and adipocytes. Chemical Communications 2024, 60: 3138-3141. PMID: 38329230, PMCID: PMC10939124, DOI: 10.1039/d3cc04829b.Peer-Reviewed Original Research
2023
Apolipoprotein E polymorphism‐dependent effects on cellular function
Beyer B, Levine Z. Apolipoprotein E polymorphism‐dependent effects on cellular function. Alzheimer's & Dementia 2023, 19 DOI: 10.1002/alz.077424.Peer-Reviewed Original ResearchApolipoprotein EStructure:function relationshipsCombination of cell-basedIsogenic hiPSC linesTransport of lipidsSubcellular localizationE4 isoformCellular functionsFunction of apolipoprotein EBiophysical approachesLiving cellsTransport of E2Cell typesCo-localizationCentral nervous systemLipoprotein particlesIsoformsHuman astrocytesRelationship of apolipoprotein EHiPSC linesCell-basedInvestigate mechanismsApolipoproteinCellsOrganelles
2022
Ancestral archaea expanded the genetic code with pyrrolysine
Guo LT, Amikura K, Jiang HK, Mukai T, Fu X, Wang YS, O’Donoghue P, Söll D, Tharp JM. Ancestral archaea expanded the genetic code with pyrrolysine. Journal Of Biological Chemistry 2022, 298: 102521. PMID: 36152750, PMCID: PMC9630628, DOI: 10.1016/j.jbc.2022.102521.Peer-Reviewed Original ResearchConceptsAminoacylation efficiencyGenetic code expansionDomains of lifePyrrolysyl-tRNA synthetaseTRNA-binding domainFull-length enzymeNoncanonical amino acidsAmino acid substratesMolecular phylogenyDiverse archaeaCoevolutionary historyTRNA sequencesGenetic codeCode expansionDiscriminator basesMethanogenic archaeaMethanosarcina mazeiPylRSSubstrate spectrumTRNAArchaeaMultiple organismsLiving cellsAcid substratesAmino acidsAn in Vitro Cytomimetic of In‐Cell RNA Folding
Yoo H, Davis C. An in Vitro Cytomimetic of In‐Cell RNA Folding. ChemBioChem 2022, 23: e202200406. PMID: 35999178, DOI: 10.1002/cbic.202200406.Peer-Reviewed Original ResearchCounting fluorescently labeled proteins in tissues in the spinning–disk microscope using single–molecule calibrations
Liao M, Kuo Y, Howard J. Counting fluorescently labeled proteins in tissues in the spinning–disk microscope using single–molecule calibrations. Molecular Biology Of The Cell 2022, 33: ar48. PMID: 35323029, PMCID: PMC9265152, DOI: 10.1091/mbc.e21-12-0618.Peer-Reviewed Original ResearchConceptsEnd-binding protein 1Spinning-disk confocal microscopyConfocal microscopySingle-molecule imagingComplex biological phenomenaFly larvaeLiving cellsCell surfaceMicrotubule endsBiological phenomenaProtein 1Brightness of fluorophoresCytoplasmic concentrationEpifluorescence microscopeBiological systemsSensory neuronsCellsSingle moleculesAbsolute numberMolecular numberTissueLarvaeMicrotubulesEGFPProteinA Central Role for Magnesium Homeostasis during Adaptation to Osmotic Stress
Wendel B, Pi H, Krüger L, Herzberg C, Stülke J, Helmann J. A Central Role for Magnesium Homeostasis during Adaptation to Osmotic Stress. MBio 2022, 13: e00092-22. PMID: 35164567, PMCID: PMC8844918, DOI: 10.1128/mbio.00092-22.Peer-Reviewed Original ResearchConceptsResumption of growthOsmotic stressCompatible solutesCellular responsesBacillus subtilisDomains of lifeHigh salt stressCommon cellular responseEssential second messengerSpecific efflux pumpsSalt stressProtein translationOsmotic upshiftHyperosmotic stressSecond messengerHigh osmolarityReimportLiving cellsTransient growth inhibitionEfflux pumpsModel systemLive-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
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