2017
Guidelines for Genome-Scale Analysis of Biological Rhythms
Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB. Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal Of Biological Rhythms 2017, 32: 380-393. PMID: 29098954, PMCID: PMC5692188, DOI: 10.1177/0748730417728663.Peer-Reviewed Original ResearchConceptsGenome-scale analysisGenome-scale dataGenome-scale experimentsBiological rhythmsBiology approachBiology dataFuture discoveriesObvious consensusDifferent experimental designsProductive avenuesRNAProteinAbundanceComputational modelingPrimary literatureEnormous contributionClockDiscoveryRhythmMetabolitesMembrane Currents, Gene Expression, and Circadian Clocks
Allen CN, Nitabach MN, Colwell CS. Membrane Currents, Gene Expression, and Circadian Clocks. Cold Spring Harbor Perspectives In Biology 2017, 9: a027714. PMID: 28246182, PMCID: PMC5411696, DOI: 10.1101/cshperspect.a027714.Peer-Reviewed Original ResearchMeSH KeywordsAction PotentialsAnimalsCell MembraneCircadian ClocksCircadian RhythmGene Expression RegulationHumansNeuronsConceptsCircadian clockGene ClockMembrane electrical activityCyclic adenosine monophosphateCircadian clock neuronsCircadian outputClock neuronsGenetic clockGene expressionCircadian oscillatorIntracellular CaAdenosine monophosphateFeedback loopPathwayClockHuman healthAction potential firing patternsMammalianActivityAction potential firingNightly reductionsMultiple typesExpressionMembrane currentsCircadian pattern
2016
Drosophila DH31 Neuropeptide and PDF Receptor Regulate Night-Onset Temperature Preference
Goda T, Tang X, Umezaki Y, Chu ML, Kunst M, Nitabach MNN, Hamada FN. Drosophila DH31 Neuropeptide and PDF Receptor Regulate Night-Onset Temperature Preference. Journal Of Neuroscience 2016, 36: 11739-11754. PMID: 27852781, PMCID: PMC5125228, DOI: 10.1523/jneurosci.0964-16.2016.Peer-Reviewed Original Research
2014
Rhythmic control of activity and sleep by class B1 GPCRs
Kunst M, Tso MC, Ghosh DD, Herzog ED, Nitabach MN. Rhythmic control of activity and sleep by class B1 GPCRs. Critical Reviews In Biochemistry And Molecular Biology 2014, 50: 18-30. PMID: 25410535, PMCID: PMC4648372, DOI: 10.3109/10409238.2014.985815.Peer-Reviewed Original ResearchConceptsGenetic model organismClass B1 GPCRsModel organismsC. elegansMetazoan cladesMolecular roleCircadian timekeepingB1 familyMolecular mechanismsG proteinsRhythmic controlDaily rhythmsCircadian rhythmRemarkable parallelsMultiple cellsDrosophilaCladeElegansPDFRGPCRsIntercellularReceptorsOrganismsVPAC2 receptorsTimekeepingCalcitonin Gene-Related Peptide Neurons Mediate Sleep-Specific Circadian Output in Drosophila
Kunst M, Hughes ME, Raccuglia D, Felix M, Li M, Barnett G, Duah J, Nitabach MN. Calcitonin Gene-Related Peptide Neurons Mediate Sleep-Specific Circadian Output in Drosophila. Current Biology 2014, 24: 2652-2664. PMID: 25455031, PMCID: PMC4255360, DOI: 10.1016/j.cub.2014.09.077.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCalcitonin Gene-Related PeptideCircadian RhythmDrosophila melanogasterDrosophila ProteinsInsect HormonesNeuronsSleepConceptsPigment-dispersing factorNeuropeptide calcitonin gene-related peptideCalcitonin gene-related peptideGene-related peptidePDF receptorClock neuronsCircadian clock neuronsDistinct neuronal pathwaysNeuropeptide pigment-dispersing factorDorsal clock neuronsAmount of sleepHomeostatic sleep driveNeurons actsCalcitonin geneNeuronal pathwaysTiming of sleepSleepMental healthSleep driveReceptorsNovel roleCircadian rhythmDH31NeuronsLocomotor rhythm
2013
Pigment-Dispersing Factor Modulates Pheromone Production in Clock Cells that Influence Mating in Drosophila
Krupp JJ, Billeter JC, Wong A, Choi C, Nitabach MN, Levine JD. Pigment-Dispersing Factor Modulates Pheromone Production in Clock Cells that Influence Mating in Drosophila. Neuron 2013, 79: 54-68. PMID: 23849197, PMCID: PMC3955580, DOI: 10.1016/j.neuron.2013.05.019.Peer-Reviewed Original ResearchConceptsPigment Dispersing FactorClock cellsMating behaviorPheromone productionNeuropeptide Pigment Dispersing FactorPeripheral clock cellsMale sex pheromoneSex pheromone productionMolecular rhythmsPhysiological outputsNeuropeptide signalingBehavioral rhythmsCircadian mechanismsSex-specific differencesDrosophilaSex pheromoneCircadian entrainmentOenocytesCircadian systemPheromonePathwayNeuroendocrine pathwaysActivity rhythmsCellsBehavioral processes
2012
Autoreceptor Control of Peptide/Neurotransmitter Corelease from PDF Neurons Determines Allocation of Circadian Activity in Drosophila
Choi C, Cao G, Tanenhaus AK, McCarthy EV, Jung M, Schleyer W, Shang Y, Rosbash M, Yin JC, Nitabach MN. Autoreceptor Control of Peptide/Neurotransmitter Corelease from PDF Neurons Determines Allocation of Circadian Activity in Drosophila. Cell Reports 2012, 2: 332-344. PMID: 22938867, PMCID: PMC3432947, DOI: 10.1016/j.celrep.2012.06.021.Peer-Reviewed Original ResearchDeep sequencing the circadian and diurnal transcriptome of Drosophila brain
Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN. Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Research 2012, 22: 1266-1281. PMID: 22472103, PMCID: PMC3396368, DOI: 10.1101/gr.128876.111.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAnimalsBase SequenceBrainCircadian ClocksCircadian RhythmDrosophila melanogasterExonsGene Expression ProfilingMolecular Sequence AnnotationPhotoperiodRNA EditingRNA IsoformsRNA Splice SitesRNA, UntranslatedSequence AlignmentSequence Analysis, RNATranscription, GeneticTranscriptomeConceptsKey circadian genesRNA editingNoncoding RNAsCircadian genesDrosophila brainGenome-wide mapsEukaryotic circadian clocksCircadian transcriptional rhythmsSnoRNA host genesTranslational feedback loopsSmall nucleolar RNAsNovel splicing eventsAlternative splice isoformsDark diurnal cyclesFrequency of RNAPrevious microarray studyDiurnal transcriptomeDrosophila melanogaster brainTranscriptional rhythmsCircadian transcriptomeNcRNA expressionRibosomal biogenesisModENCODE consortiumSplicing eventsAlternative splicing
2011
Circadian expression of clock genes in mouse macrophages, dendritic cells, and B cells
Silver AC, Arjona A, Hughes ME, Nitabach MN, Fikrig E. Circadian expression of clock genes in mouse macrophages, dendritic cells, and B cells. Brain Behavior And Immunity 2011, 26: 407-413. PMID: 22019350, PMCID: PMC3336152, DOI: 10.1016/j.bbi.2011.10.001.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsARNTL Transcription FactorsB-LymphocytesCircadian RhythmCircadian Rhythm Signaling Peptides and ProteinsCLOCK ProteinsDendritic CellsDNA-Binding ProteinsGene ExpressionMacrophagesMiceNuclear Receptor Subfamily 1, Group D, Member 1Period Circadian ProteinsPhotoperiodSpleenTranscription FactorsConceptsMolecular clock mechanismClock genesClock mechanismGene expressionClock-controlled transcription factorsFunctional molecular clockAspects of physiologyConstant environmental conditionsMolecular clockTranscription factorsCircadian expressionB cellsEnvironmental conditionsLight-dark cycleMouse macrophagesDaily rhythmsGenesExpressionCellsDendritic cellsMurine spleenMammalsMacrophagesSplenic NK cellsImmune cellsInsect circadian clock outputs
Helfrich-Förster C, Nitabach MN, Holmes TC. Insect circadian clock outputs. Essays In Biochemistry 2011, 49: 87-101. PMID: 21819386, DOI: 10.1042/bse0490087.Peer-Reviewed Original ResearchConceptsClock neuronsDaily rhythmsCircadian clock outputBrain clockCellular clocksDrosophila fliesCircadian timekeeping systemCircadian outputEnvironmental cuesClock outputMigratory locustInsectsTimekeeping systemCircadian rhythmicitySubstantial similarityClockImpressive varietyButterfliesLocal environmentFliesClock circuitEntire lifeLocustTimekeeperPhysiologySynchronized Bilateral Synaptic Inputs to Drosophila melanogaster Neuropeptidergic Rest/Arousal Neurons
McCarthy EV, Wu Y, deCarvalho T, Brandt C, Cao G, Nitabach MN. Synchronized Bilateral Synaptic Inputs to Drosophila melanogaster Neuropeptidergic Rest/Arousal Neurons. Journal Of Neuroscience 2011, 31: 8181-8193. PMID: 21632940, PMCID: PMC3125135, DOI: 10.1523/jneurosci.2017-10.2011.Peer-Reviewed Original ResearchConceptsSynaptic inputsWhole-cell patch-clamp recordingsNicotinic acetylcholine receptor antagonistDual whole-cell patch-clamp recordingsAcetylcholine receptor antagonistNicotinic ACh receptorsSynchronous synaptic inputPatch-clamp recordingsWake-promoting neuronsLarge ventrolateral neuronsArousal neuronsSodium blockersGABAergic inputsCholinergic inputReceptor antagonistSynaptic circuitryACh receptorsNeurotransmitter receptorsBilateral inputSynaptic connectionsΑ-bungarotoxinVentrolateral neuronsContralateral pairsFiring patternsNeurons