2024
Local and dynamic regulation of neuronal glycolysis in vivo
Wolfe A, Koberstein J, Smith C, Stewart M, Gonzalez I, Hammarlund M, Hyman A, Stork P, Goodman R, Colón-Ramos D. Local and dynamic regulation of neuronal glycolysis in vivo. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2314699121. PMID: 38198527, PMCID: PMC10801914, DOI: 10.1073/pnas.2314699121.Peer-Reviewed Original ResearchConceptsGlycolytic stateEnergy stressEnergy metabolismConditions of energy stressDynamic regulationNeuronal functionIndividual cell typesMitochondrial localizationGenetic analysisSubcellular regionsRegulatory enzymeCell-autonomousNeuronal identityGlycolysisCell typesMetabolic stateImaging dynamic changesMetabolismLiving organismsIn vivoCellsEnergy landscapeIndividual neuronsEnzymeDynamic changes
2020
Regulation of adipose tissue inflammation by interleukin 6
Han MS, White A, Perry RJ, Camporez JP, Hidalgo J, Shulman GI, Davis RJ. Regulation of adipose tissue inflammation by interleukin 6. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 2751-2760. PMID: 31980524, PMCID: PMC7022151, DOI: 10.1073/pnas.1920004117.Peer-Reviewed Original ResearchConceptsInterleukin-6Adipose tissue inflammationLow-grade inflammationIndividual cell typesMacrophage infiltrationInflammatory cytokinesTissue inflammationGlucose disposalImmune cellsIL6 productionMouse modelChronic stateAdipose tissueMyeloid cellsTissue infiltrationReceptor αConditional expressionCell typesOxidative metabolismOpposite actionsPhysiological regulationEnergy expenditureCanonical modeInflammationSpecific cells
2019
Integrating multiomics longitudinal data to reconstruct networks underlying lung development
Ding J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N. Integrating multiomics longitudinal data to reconstruct networks underlying lung development. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2019, 317: l556-l568. PMID: 31432713, PMCID: PMC6879899, DOI: 10.1152/ajplung.00554.2018.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornChildChild, PreschoolDNA MethylationEpigenesis, GeneticFemaleGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksHigh-Throughput Nucleotide SequencingHumansImmunity, InnateInfantInfant, NewbornLungMaleMiceMice, Inbred C57BLMicroRNAsOrganogenesisProteomicsPulmonary AlveoliRNA, MessengerSingle-Cell AnalysisTranscriptomeConceptsSingle-cell RNA-seq dataLung developmentDynamic regulatory networksOmics data setsRNA-seq dataIndividual cell typesHuman lung developmentRegulatory networksDNA methylationLaser capture microdissectionEpigenetic changesExpression trajectoriesKey pathwaysCell typesActive pathwaysCapture microdissectionRegulatorKey eventsInnate immunityNew insightsSpecific key eventsPathwayComprehensive understandingProteomicsMethylationDevelopment of a 2-dimensional atlas of the human kidney with imaging mass cytometry
Singh N, Avigan ZM, Kliegel JA, Shuch BM, Montgomery RR, Moeckel GW, Cantley LG. Development of a 2-dimensional atlas of the human kidney with imaging mass cytometry. JCI Insight 2019, 4: e129477. PMID: 31217358, PMCID: PMC6629112, DOI: 10.1172/jci.insight.129477.Peer-Reviewed Original ResearchConceptsCell typesIndividual cell typesCritical baseline dataRenal cell typesMass cytometryQuantitative atlasNormal human samplesHuman kidneyRelative abundanceDevelopment of therapiesHuman kidney diseaseKidney diseaseMetal-conjugated antibodiesQuantitative interrogationScarce samplesMachine-learning pipelineDiscovery purposesFuture quantitative analysisNovel abnormalityNormal human kidneySingle tissue sectionHuman samplesRenal biopsyImmune cellsCells
2017
Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease
Lu Q, Powles RL, Abdallah S, Ou D, Wang Q, Hu Y, Lu Y, Liu W, Li B, Mukherjee S, Crane PK, Zhao H. Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease. PLOS Genetics 2017, 13: e1006933. PMID: 28742084, PMCID: PMC5546707, DOI: 10.1371/journal.pgen.1006933.Peer-Reviewed Original ResearchConceptsTissue typesNon-coding elementsNon-coding genomeComplex human diseasesLate-onset Alzheimer's diseaseIndividual cell typesRelevant tissue typesGWAS traitsTranscriptomic annotationGenome annotationFunctional annotationDNA elementsHeritability enrichmentHuman genomeLarge international consortiaVariety of cellsGenomeHuman diseasesAnnotation dataCell typesGenetic variantsOrgan system categoriesComplex diseasesSimilar localizationAnnotation
2009
Wide-field and two-photon imaging of brain activity with voltage- and calcium-sensitive dyes
Homma R, Baker BJ, Jin L, Garaschuk O, Konnerth A, Cohen LB, Zecevic D. Wide-field and two-photon imaging of brain activity with voltage- and calcium-sensitive dyes. Philosophical Transactions Of The Royal Society B Biological Sciences 2009, 364: 2453-2467. PMID: 19651647, PMCID: PMC2865128, DOI: 10.1098/rstb.2009.0084.Peer-Reviewed Original ResearchConceptsCalcium-sensitive dyeVoltage-sensitive dyeDendrites of neuronsComplex synaptic inputsDorsal brainstemCell typesBrainstem preparationBath applicationSynaptic inputsRespiratory rhythmSpike activityTwo-photon imagingMammalian brainIon-sensitive dyesIndividual neuronsTwo-photon microscopyPopulation signalsBrainstemBrain activityIndividual cell typesNeuronsBrainMembrane potentialOutput spike trainsSpike trainsWide-Field and Two-Photon Imaging of Brain Activity with Voltage and Calcium-Sensitive Dyes
Homma R, Baker BJ, Jin L, Garaschuk O, Konnerth A, Cohen LB, Bleau CX, Canepari M, Djurisic M, Zecevic D. Wide-Field and Two-Photon Imaging of Brain Activity with Voltage and Calcium-Sensitive Dyes. Methods In Molecular Biology 2009, 489: 43-79. PMID: 18839087, DOI: 10.1007/978-1-59745-543-5_3.Peer-Reviewed Original ResearchConceptsCalcium-sensitive dyeOlfactory bulb glomeruliCell typesBrain activityIndividual cell typesOlfactory receptor neuronsNerve terminalsSynaptic activityVoltage-sensitive dyeSpike activityTwo-photon imagingVivo preparationMammalian brainReceptor neuronsIndividual neuronsIon-sensitive dyesNeuronsTwo-photon microscopyBrainMembrane potentialLow sensitivitySensitive dyeNoseOutput spike trainsSpike trains
2005
Imaging Brain Activity With Voltage- and Calcium-Sensitive Dyes
Baker BJ, Kosmidis EK, Vucinic D, Falk CX, Cohen LB, Djurisic M, Zecevic D. Imaging Brain Activity With Voltage- and Calcium-Sensitive Dyes. Cellular And Molecular Neurobiology 2005, 25: 245-282. PMID: 16050036, PMCID: PMC11529562, DOI: 10.1007/s10571-005-3059-6.Peer-Reviewed Original ResearchConceptsVoltage-sensitive dyeCalcium-sensitive dyeLight sourceDark noiseVibrational noiseOptical recordingRandom emissionBrain activityFluorescent protein sensorOlfactory receptor neuronsNerve terminalsOlfactory bulbSpike activityNoise ratioCell bodiesReceptor neuronsPhotonsOpticsOptimal signalNeuronsIndividual cell typesKinds of noiseExternal sourcesVoltageCell types
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