2024
Spatiotemporal control of subcellular O-GlcNAc signaling using Opto-OGT
Ong Q, Lim L, Goh C, Liao Y, Chan S, Lim C, Kam V, Yap J, Tseng T, Desrouleaux R, Wang L, Ler S, Lim S, Kim S, Sobota R, Bennett A, Han W, Yang X. Spatiotemporal control of subcellular O-GlcNAc signaling using Opto-OGT. Nature Chemical Biology 2024, 21: 300-308. PMID: 39543398, DOI: 10.1038/s41589-024-01770-7.Peer-Reviewed Original ResearchO-GlcNAc transferaseO-GlcNAcLocalized to specific subcellular sitesResponse to insulin stimulationPost-translational modification of intracellular proteinsModification of intracellular proteinsO-GlcNAc signalingPost-translational modificationsTargeting O-GlcNAc transferaseSpatiotemporal controlMulticellular organismsOGT activityOrganelle functionO-GlcNAcylationSubcellular sitesMTORC activitySignal transductionIntracellular proteinsNutrient-sensing signalsCell signalingInsulin stimulationPlasma membraneGene expressionRegulatory mechanismsAkt phosphorylationSingle‐Cell Patch‐Clamp/Proteomics of Human Alzheimer's Disease iPSC‐Derived Excitatory Neurons Versus Isogenic Wild‐Type Controls Suggests Novel Causation and Therapeutic Targets
Ghatak S, Diedrich J, Talantova M, Bhadra N, Scott H, Sharma M, Albertolle M, Schork N, Yates J, Lipton S. Single‐Cell Patch‐Clamp/Proteomics of Human Alzheimer's Disease iPSC‐Derived Excitatory Neurons Versus Isogenic Wild‐Type Controls Suggests Novel Causation and Therapeutic Targets. Advanced Science 2024, 11: e2400545. PMID: 38773714, PMCID: PMC11304297, DOI: 10.1002/advs.202400545.Peer-Reviewed Original ResearchAbundance of individual proteinsIsogenic wild-type controlsSingle-cell (scHuman AD brainsWild-type controlsSingle-cellAlzheimer's diseaseMulticellular organismsSingle-cell physiologyAD brainTherapeutic targetIndividual proteinsProteomic informationGenetic mutationsProteinProteomicsProtein expressionHiPSC-neuronsExcitatory neuronsElectrophysiological statusDisease statesPhysiologyElectrophysiological dataNeuronsNeuronal levelAlgebraic Nexus of Fibonacci Forms and Two-Simplex Topology in Multicellular Morphogenesis
Hoyos W, Loarca H, Kahle K, Williams Z, Lamb E, Alcántara J, Kinane T, Cuevas L. Algebraic Nexus of Fibonacci Forms and Two-Simplex Topology in Multicellular Morphogenesis. Symmetry 2024, 16: 516. DOI: 10.3390/sym16050516.Peer-Reviewed Original ResearchMulticellular organismsCellular growth propertiesMulticellular morphogenesisInhibition of replicationSynthetic biologyMulticellular structuresTubular formContact inhibitionMolecular mechanismsCellular aggregatesGrowth propertiesMorphogenesisMultiple stepsFibonacci patternCell replicationReplicationCellular genesisCellsCellular arrangementPhylogenyGrowth patternMolecular propertiesAdhesionOrganizationMechanismReading the palimpsest of cell interactions: What questions may we ask of the data?
Pavlicev M, Wagner G. Reading the palimpsest of cell interactions: What questions may we ask of the data? IScience 2024, 27: 109670. PMID: 38665209, PMCID: PMC11043885, DOI: 10.1016/j.isci.2024.109670.Peer-Reviewed Original ResearchCompartmentalization of cellular processesStructure of interaction networksCell interactionsMulticellular organismsIntegrity of cellsCellular processesInteraction networkLevels of structural organizationBiological functionsBiological interpretationCell communicationInteraction dataStructural organizationWealth of dataCellsCoordination of functionsOrganizationHigher levels of structural organizationCompartmentalizationInteraction
2023
Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases
Garrison M, Jang Y, Bae T, Cherskov A, Emery S, Fasching L, Jones A, Moldovan J, Molitor C, Pochareddy S, Peters M, Shin J, Wang Y, Yang X, Akbarian S, Chess A, Gage F, Gleeson J, Kidd J, McConnell M, Mills R, Moran J, Park P, Sestan N, Urban A, Vaccarino F, Walsh C, Weinberger D, Wheelan S, Abyzov A. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Scientific Data 2023, 10: 813. PMID: 37985666, PMCID: PMC10662356, DOI: 10.1038/s41597-023-02645-7.Peer-Reviewed Original ResearchEmergence of division of labor in tissues through cell interactions and spatial cues
Adler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams T, Kaminski N, Macosko E, Regev A, Medzhitov R, Nitzan M. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Reports 2023, 42: 112412. PMID: 37086403, PMCID: PMC10242439, DOI: 10.1016/j.celrep.2023.112412.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencingMost cell typesCell-type populationsCell-cell interactionsDistinguishable expression patternsCell population levelSpatial transcriptomics dataCell interactionsLigand-receptor networkMulticellular organismsTranscriptomic dataRNA sequencingInstructive signalsExpression patternsSpecialist cellsCell typesIndividual cellsDivision of laborMultiple functionsTissue environmentSame cellsDifferent functionsPopulation levelCellsDivisionPhototaxis of Chlamydomonas arises from a tuned adaptive photoresponse shared with multicellular Volvocine green algae
Leptos K, Chioccioli M, Furlan S, Pesci A, Goldstein R. Phototaxis of Chlamydomonas arises from a tuned adaptive photoresponse shared with multicellular Volvocine green algae. Physical Review E 2023, 107: 014404. PMID: 36797913, PMCID: PMC7616094, DOI: 10.1103/physreve.107.014404.Peer-Reviewed Original ResearchConceptsVolvocine algaeGreen algaeVolvocine green algaeMulticellular speciesMulticellular organismsEvolutionary transitionsChlamydomonasVolvoxAlgaeIndividual flagellaExtracellular matrixIndividual cellsIntercellular connectionsAdaptive responsePrimary axisGoniumSwimming cellsLight levelsPhototaxisOrganismsSpeciesFlagellar responsesCell numberCellsBeat plane
2022
Integrating mechanical signals into cellular identity
Carley E, King MC, Guo S. Integrating mechanical signals into cellular identity. Trends In Cell Biology 2022, 32: 669-680. PMID: 35337714, PMCID: PMC9288541, DOI: 10.1016/j.tcb.2022.02.006.Peer-Reviewed Original ResearchConceptsDistinct gene expression programsComplex cellular programsGene expression programsLineage-committed cellsPluripotent stem cellsMulticellular organismsExpression programsCellular identityCellular programsMechanical signalsCell typesStem cellsMechanical inputCellsBiochemical inputsFunction correlationGenomeCytoskeletonOrganismsNumber of studiesImportant determinantComplex axisIdentityLarge arrayVivo
2021
Measuring Cell-Edge Protrusion Dynamics during Spreading using Live-Cell Microscopy.
Lukic N, Saha T, Lapetina S, Gendler M, Lehmann G, Koleske AJ, Gil-Henn H. Measuring Cell-Edge Protrusion Dynamics during Spreading using Live-Cell Microscopy. Journal Of Visualized Experiments 2021 PMID: 34779432, PMCID: PMC8672187, DOI: 10.3791/63157.Peer-Reviewed Original ResearchConceptsCell edge protrusionCell migrationProtrusion dynamicsKey actin regulatorsLive-cell microscopyMulticellular organismsActin regulatorsCoordinated regulationEmbryonic developmentMembrane dynamicsEssential eventRegeneration of tissuesCancer metastasisTissue invasionPathological disordersRufflesProtrusionMigrationOrganismsRegulatorHomeostasisRegulationInvasionDysregulationDynamicsAnnotation of chromatin states in 66 complete mouse epigenomes during development
van der Velde A, Fan K, Tsuji J, Moore J, Purcaro M, Pratt H, Weng Z. Annotation of chromatin states in 66 complete mouse epigenomes during development. Communications Biology 2021, 4: 239. PMID: 33619351, PMCID: PMC7900196, DOI: 10.1038/s42003-021-01756-4.Peer-Reviewed Original ResearchConceptsChromatin stateMouse epigenomesPolycomb repressive complex proteinsBivalent chromatin stateTranscription start siteRepressive mark H3K27me3Silence target genesCharacteristics of promotersChromHMM algorithmUnique epigenomeGene expression programsENCODE projectTranscribed regionsMulticellular organismsStart siteRepressed regionsActive marksMammalian developmentComplex proteinsEpigenomeTissue specificityTarget genesExpression programsCell typesIntegrated analysis
2020
Cell-Cycle-Dependent ERK Signaling Dynamics Direct Fate Specification in the Mammalian Preimplantation Embryo
Pokrass MJ, Ryan KA, Xin T, Pielstick B, Timp W, Greco V, Regot S. Cell-Cycle-Dependent ERK Signaling Dynamics Direct Fate Specification in the Mammalian Preimplantation Embryo. Developmental Cell 2020, 55: 328-340.e5. PMID: 33091369, PMCID: PMC7658051, DOI: 10.1016/j.devcel.2020.09.013.Peer-Reviewed Original ResearchConceptsFate specificationPreimplantation developmentKinase translocation reporterMammalian preimplantation embryosInner cell massEmbryonic stem cellsSingle cellsDifferent cell typesMulticellular organismsEndogenous taggingDaughter cellsNanog proteinActive ERKNanog levelsERK activityGene expressionPreimplantation embryosCell cycleTrophectoderm cellsERK inhibitionCell typesStem cellsLive embryosCell massEmbryosThe palette of techniques for cell cycle analysis
Eastman AE, Guo S. The palette of techniques for cell cycle analysis. FEBS Letters 2020, 594: 2084-2098. PMID: 32441778, PMCID: PMC9261528, DOI: 10.1002/1873-3468.13842.Peer-Reviewed Original ResearchCell cycleCell cycle analysisCell fate specificationCell division cycleCell cycle speedSingle-cell eraSingle-cell resolutionCell cycle progressionCell cycle dynamicsMulticellular organismsFate specificationCell cycle heterogeneityGenomic fidelityDivision cycleBiochemical machineryTissue homeostasisCycle progressionCellular growthCell cycle measurementsCycle analysisPalette of techniquesGenerational periodCycle dynamicsCentral roleCell numberCell Lineage Tracing and Cellular Diversity in Humans
Abyzov A, Vaccarino FM. Cell Lineage Tracing and Cellular Diversity in Humans. Annual Review Of Genomics And Human Genetics 2020, 21: 101-116. PMID: 32413272, DOI: 10.1146/annurev-genom-083118-015241.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsLineage tracingLineage mapCell lineage mapCell lineage tracingDNA methylation statusComplex biological processesMultiple cell typesMulticellular organismsCellular diversityMitochondrial DNALineage hierarchyCell lineagesBiological processesNatural variationCell typesMethylation statusLineagesNoncancerous cellsRecent studiesFetal developmentGeneral conceptual designCellsOrganismsHumansDNANovel role of dynamin‐related‐protein 1 in dynamics of ER‐lipid droplets in adipose tissue
Li X, Yang L, Mao Z, Pan X, Zhao Y, Gu X, Eckel‐Mahan K, Zuo Z, Tong Q, Hartig S, Cheng X, Du G, Moore D, Bellen H, Sesaki H, Sun K. Novel role of dynamin‐related‐protein 1 in dynamics of ER‐lipid droplets in adipose tissue. The FASEB Journal 2020, 34: 8265-8282. PMID: 32294302, PMCID: PMC7336545, DOI: 10.1096/fj.201903100rr.Peer-Reviewed Original ResearchConceptsEndoplasmic reticulumFlx/Function of Drp1Multicellular organismsPeroxisomal fissionDrp1 ablationER retentionLD dynamicsAutophagy functionER functionNovel roleDrp1LD morphologyKnockout modelsProtein 1Unilocular morphologyAdipose tissueLipid metabolismDynaminOrganellesCold exposureTissueOrganismsLarge sizeMultilocular structure
2019
Funerals and Feasts: The Immunological Rites of Cell Death.
Galimberti VE, Rothlin CV, Ghosh S. Funerals and Feasts: The Immunological Rites of Cell Death. The Yale Journal Of Biology And Medicine 2019, 92: 663-674. PMID: 31866781, PMCID: PMC6913811.BooksConceptsReceptor tyrosine kinasesCell deathMolecular mechanismsCell death modalitiesUnscheduled cell deathNon-self recognitionImportant negative regulatorDead cellsMulticellular organismsAdult organismDeath modalitiesProper immune responseNegative regulatorTyrosine kinaseMolecular processesInjury/infectionImmune responseMolecular modalitiesOmnipresent processOrganismsDefective developmentMost tissuesImmune system functionTAM familyFibrosis/scarringIntroduction to Immunology, Epidemiology, and Immunoepidemiology
Niccolai L, Ruddle N, Krause P. Introduction to Immunology, Epidemiology, and Immunoepidemiology. 2019, 3-17. DOI: 10.1007/978-3-030-25553-4_1.ChaptersIndividual multicellular organismsImmune responseMulticellular organismsRelevant health problemHealth-related eventsInflammatory diseasesSelect populationCombination of cellsHealth problemsEpidemiologic toolImmunoepidemiologyMicrobial infectionsEpidemiologyGenetic polymorphismsImmunologyEnvironmental factorsPopulationAutoimmunityMalignancyOrganismsInfectionDiversityDiseaseStudyThe microbiota regulate neuronal function and fear extinction learning
Chu C, Murdock M, Jing D, Won T, Chung H, Kressel A, Tsaava T, Addorisio M, Putzel G, Zhou L, Bessman N, Yang R, Moriyama S, Parkhurst C, Li A, Meyer H, Teng F, Chavan S, Tracey K, Regev A, Schroeder F, Lee F, Liston C, Artis D. The microbiota regulate neuronal function and fear extinction learning. Nature 2019, 574: 543-548. PMID: 31645720, PMCID: PMC6818753, DOI: 10.1038/s41586-019-1644-y.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnti-Bacterial AgentsAutistic DisorderBloodCalciumCerebrospinal FluidCuesDendritic SpinesExtinction, PsychologicalFearFecesGerm-Free LifeIndicanMaleMetabolomicsMiceMice, Inbred BALB CMice, Inbred C57BLMicrobiotaNeural InhibitionNeurogliaNeuronsPhenylpropionatesPrefrontal CortexSchizophreniaTranscriptomeVagus NerveConceptsFear extinction learningMedial prefrontal cortexExtinction learningMicrobiota-derived signalsPrefrontal cortexNeuropsychiatric disordersAdult miceSusceptibility to neuropsychiatric disordersInfluence many physiological processesGerm-free adult miceTranscranial two-photon imagingMicrobiota-derived compoundsSingle-nucleus RNA sequencingGerm-free miceComplex consortiaMulticellular organismsPostsynaptic dendritic spinesBrain healthBrain functionRNA sequencingMicrobiotaIn adulthoodGene expressionNeuronal activityPostnatal neurodevelopmentNew Twists and Turns in Bacterial Locomotion and Signal Transduction
Watts KJ, Vaknin A, Fuqua C, Kazmierczak BI. New Twists and Turns in Bacterial Locomotion and Signal Transduction. Journal Of Bacteriology 2019, 201: 10.1128/jb.00439-19. PMID: 31358610, PMCID: PMC6755736, DOI: 10.1128/jb.00439-19.Peer-Reviewed Original ResearchConceptsSignal transductionTwo-component signal transduction pathwayTwo-component signal transduction systemBacterial locomotionContribution of motilityCryo-electron tomographySignal transduction systemSystems biology approachSignal transduction pathwaysIndividual bacterial cellsMulticellular organismsProkaryotic organismsBiology approachChemosensory receptorsFlagellar motorPathogenic interactionsTransduction pathwaysTransduction systemIndividual proteinsSensing pathwaysProtein labelingBehavior of thousandsComplex ecosystemsProtein spaceLiving cellsMolecular recording of mammalian embryogenesis
Chan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG, Khodaverdian A, Yosef N, Meissner A, Weissman JS. Molecular recording of mammalian embryogenesis. Nature 2019, 570: 77-82. PMID: 31086336, PMCID: PMC7229772, DOI: 10.1038/s41586-019-1184-5.Peer-Reviewed Original ResearchConceptsCell fate mapsComplex multicellular organismsSingle totipotent cellSingle-cell readoutsSingle-cell RNA sequencing profilesEmbryonic progenitor cellsMulticellular organismsMammalian embryogenesisTranscriptional convergenceRNA sequencing profilesTotipotent cellsInternal gestationMammalian systemsAsymmetric partitioningMolecular recordersEndodermal cellsLineage tracerDevelopmental processesLineage informationMolecular recordingSequencing profilesEmbryonic originDifferent tissue typesProgenitor cellsTissue typesQuantifying protein dynamics and stability in a living organism
Feng R, Gruebele M, Davis CM. Quantifying protein dynamics and stability in a living organism. Nature Communications 2019, 10: 1179. PMID: 30862837, PMCID: PMC6414637, DOI: 10.1038/s41467-019-09088-y.Peer-Reviewed Original Research
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