Featured Publications
High-speed low-light in vivo two-photon voltage imaging of large neuronal populations
Platisa J, Ye X, Ahrens A, Liu C, Chen I, Davison I, Tian L, Pieribone V, Chen J. High-speed low-light in vivo two-photon voltage imaging of large neuronal populations. Nature Methods 2023, 20: 1095-1103. PMID: 36973547, PMCID: PMC10894646, DOI: 10.1038/s41592-023-01820-3.Peer-Reviewed Original ResearchConceptsNeuronal populationsLarge neuronal populationsNeural circuit functionTwo-photon voltage imagingAwake behaving miceCalcium imagingBehaving miceVoltage imagingCircuit functionNeuronsShot noise levelShot-noise limitImagingTwo-photon microscopeKilohertz frame ratesDeep-tissue imagingPopulationVoltage indicatorsField of viewMiceShot noise
2023
Odor encoding by signals in the olfactory bulb
Verhagen J, Baker K, Vasan G, Pieribone V, Rolls E. Odor encoding by signals in the olfactory bulb. Journal Of Neurophysiology 2023, 129: 431-444. PMID: 36598147, PMCID: PMC9925169, DOI: 10.1152/jn.00449.2022.Peer-Reviewed Original ResearchConceptsOlfactory bulbGlomerular responseMouse dorsalPresynaptic inputsLateral olfactory bulbSet of odorsGlomeruliOlfactory systemOdor identityOdor informationSniff onsetResponse latencyBroad tuningBulbStimulus identityLittle informationPopulationResponseEarly stagesTemporal encodingIndependent responses
2022
Dual-polarity voltage imaging of the concurrent dynamics of multiple neuron types
Kannan M, Vasan G, Haziza S, Huang C, Chrapkiewicz R, Luo J, Cardin J, Schnitzer M, Pieribone V. Dual-polarity voltage imaging of the concurrent dynamics of multiple neuron types. Science 2022, 378: eabm8797. PMID: 36378956, PMCID: PMC9703638, DOI: 10.1126/science.abm8797.Peer-Reviewed Original ResearchVoltage imaging in the olfactory bulb using transgenic mouse lines expressing the genetically encoded voltage indicator ArcLight
Platisa J, Zeng H, Madisen L, Cohen LB, Pieribone VA, Storace DA. Voltage imaging in the olfactory bulb using transgenic mouse lines expressing the genetically encoded voltage indicator ArcLight. Scientific Reports 2022, 12: 1875. PMID: 35115567, PMCID: PMC8813909, DOI: 10.1038/s41598-021-04482-3.Peer-Reviewed Original ResearchConceptsTransgenic mouse lineMouse linesOlfactory bulbSubpopulation of interneuronsVivo mammalian brainTransgenic reporter animalsTransgenic reporter miceOlfactory receptor neuronsNeuronal electrical activityVoltage indicator ArcLightGlomerular layerReporter miceMammalian brainReceptor neuronsReporter animalsHigh expression levelsElectrical activityMembrane potential changesOdorant responsesNeural activityCell populationsSingle trialExpression levelsVivo experimentsDifferent cell types
2020
A putative chordate luciferase from a cosmopolitan tunicate indicates convergent bioluminescence evolution across phyla
Tessler M, Gaffney JP, Oliveira AG, Guarnaccia A, Dobi KC, Gujarati NA, Galbraith M, Mirza JD, Sparks JS, Pieribone VA, Wood RJ, Gruber DF. A putative chordate luciferase from a cosmopolitan tunicate indicates convergent bioluminescence evolution across phyla. Scientific Reports 2020, 10: 17724. PMID: 33082360, PMCID: PMC7576829, DOI: 10.1038/s41598-020-73446-w.Peer-Reviewed Original ResearchConceptsAnimal phylaPhylum ChordataSimilar genesWidespread genesBiogeochemical roleSequence matchesPhylaBrittle starsNovel luciferaseLuciferaseTunicatesGenesLight productionCoelenterazineBioluminescenceChordataTranscriptomeVertebratesDehalogenasesPyrosomesMachineryLuciferasesBloomsPyrosomaBiochemistry
2019
Spatiotemporal dynamics of odor responses in the lateral and dorsal olfactory bulb
Baker KL, Vasan G, Gumaste A, Pieribone VA, Verhagen JV. Spatiotemporal dynamics of odor responses in the lateral and dorsal olfactory bulb. PLOS Biology 2019, 17: e3000409. PMID: 31532763, PMCID: PMC6768483, DOI: 10.1371/journal.pbio.3000409.Peer-Reviewed Original ResearchBioluminescent flashes drive nighttime schooling behavior and synchronized swimming dynamics in flashlight fish
Gruber DF, Phillips BT, O’Brien R, Boominathan V, Veeraraghavan A, Vasan G, O’Brien P, Pieribone VA, Sparks JS. Bioluminescent flashes drive nighttime schooling behavior and synchronized swimming dynamics in flashlight fish. PLOS ONE 2019, 14: e0219852. PMID: 31412054, PMCID: PMC6693688, DOI: 10.1371/journal.pone.0219852.Peer-Reviewed Original ResearchConceptsFlashlight fish
2018
Fast, in vivo voltage imaging using a red fluorescent indicator
Kannan M, Vasan G, Huang C, Haziza S, Li JZ, Inan H, Schnitzer MJ, Pieribone VA. Fast, in vivo voltage imaging using a red fluorescent indicator. Nature Methods 2018, 15: 1108-1116. PMID: 30420685, PMCID: PMC6516062, DOI: 10.1038/s41592-018-0188-7.Peer-Reviewed Original ResearchConceptsOptical toolsOptical toolboxUnparalleled temporal resolutionRed fluorescent indicatorVoltage imagingOptical electrophysiologyModest illumination intensitiesHigh-throughput strategyVoltage indicatorsIllumination intensityNew hueAcute brain slicesMultispectral imagingGreen probesSubthreshold voltageTemporal resolutionEnhanced sensitivityPostsynaptic potentialsMRuby3Brain slicesHippocampal rhythmsActivity monitorFunctional imagingImagingGEVIsGenetically encoded fluorescent voltage indicators: are we there yet?
Platisa J, Pieribone VA. Genetically encoded fluorescent voltage indicators: are we there yet? Current Opinion In Neurobiology 2018, 50: 146-153. PMID: 29501950, PMCID: PMC5984684, DOI: 10.1016/j.conb.2018.02.006.Peer-Reviewed Original Research
2017
Directed Evolution of Key Residues in Fluorescent Protein Inverses the Polarity of Voltage Sensitivity in the Genetically Encoded Indicator ArcLight
Platisa J, Vasan G, Yang A, Pieribone VA. Directed Evolution of Key Residues in Fluorescent Protein Inverses the Polarity of Voltage Sensitivity in the Genetically Encoded Indicator ArcLight. ACS Chemical Neuroscience 2017, 8: 513-523. PMID: 28045247, PMCID: PMC5355904, DOI: 10.1021/acschemneuro.6b00234.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCells, CulturedCerebral CortexElectric StimulationEmbryo, MammalianGreen Fluorescent ProteinsHEK293 CellsHumansLuminescent ProteinsMiceModels, MolecularMolecular BiologyMutagenesis, Site-DirectedMutationNeuronsPatch-Clamp TechniquesRecombinant Fusion ProteinsTransfectionVoltage-Sensitive Dye Imaging
2016
Biofluorescence in Catsharks (Scyliorhinidae): Fundamental Description and Relevance for Elasmobranch Visual Ecology
Gruber DF, Loew ER, Deheyn DD, Akkaynak D, Gaffney JP, Smith WL, Davis MP, Stern JH, Pieribone VA, Sparks JS. Biofluorescence in Catsharks (Scyliorhinidae): Fundamental Description and Relevance for Elasmobranch Visual Ecology. Scientific Reports 2016, 6: 24751. PMID: 27109385, PMCID: PMC4843165, DOI: 10.1038/srep24751.Peer-Reviewed Original ResearchConceptsSingle visual pigmentCartilaginous fishChain catsharksMarine fishPhylogenetic investigationVisual ecologyWestern AtlanticSharksCatsharkBright green fluorescenceElasmobranch behaviourVisual pigmentsPhotoreceptor cellsShark eyeSwell sharksBiofluorescenceCephaloscyllium ventriosumFishGreen fluorescenceSpeciesPotential importancePhotoreceptor propertiesEastern PacificEcologyElasmobranchsA Bright and Fast Red Fluorescent Protein Voltage Indicator That Reports Neuronal Activity in Organotypic Brain Slices
Abdelfattah AS, Farhi SL, Zhao Y, Brinks D, Zou P, Ruangkittisakul A, Platisa J, Pieribone VA, Ballanyi K, Cohen AE, Campbell RE. A Bright and Fast Red Fluorescent Protein Voltage Indicator That Reports Neuronal Activity in Organotypic Brain Slices. Journal Of Neuroscience 2016, 36: 2458-2472. PMID: 26911693, PMCID: PMC4764664, DOI: 10.1523/jneurosci.3484-15.2016.Peer-Reviewed Original ResearchConceptsVoltage indicatorsBlue-shifted channelrhodopsinRed-shifted fluorescent proteinsFluorescent voltage indicatorsWide-field fluorescence microscopyBlue excitationOptical imagingOptical electrophysiologyLow phototoxicityAutofluorescent backgroundLight photoactivationSingle-trial recordingsTemporal resolutionChannelrhodopsinIntrinsic advantagesExcitationVoltage oscillationsFluorescence microscopyOscillationsGreen indicatorsChromophoreMicroscopyResolution
2015
Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment
Gruber DF, Gaffney JP, Mehr S, DeSalle R, Sparks JS, Platisa J, Pieribone VA. Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment. PLOS ONE 2015, 10: e0140972. PMID: 26561348, PMCID: PMC4641735, DOI: 10.1371/journal.pone.0140972.Peer-Reviewed Original ResearchConceptsAcid-binding proteinFluorescent proteinFatty acid-binding proteinDuplication eventsGene duplication eventsStrong positive selectionNew fluorescent proteinsMarine environmentAdaptive evolutionEvolutionary switchCryptic genusVertebrate ordersVertebrate taxaPhylogenetic reconstructionProtein familyPhylogenetic analysisSequence motifsSister groupEvolutionary adaptationTranscriptomic analysisPositive selectionFatty acid binding proteinAcid binding proteinBinding proteinBright green fluorescenceTranscriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)
Mehr S, Verdes A, DeSalle R, Sparks J, Pieribone V, Gruber DF. Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). BMC Genomics 2015, 16: 445. PMID: 26059236, PMCID: PMC4462082, DOI: 10.1186/s12864-015-1565-6.Peer-Reviewed Original ResearchConceptsOpen reading frameAvailable genomic dataHermodice carunculataGenomic dataDe novo transcriptome assemblyNon-model organismsNovo transcriptome assemblyDeep transcriptome sequencingCoral reef ecosystemsGene Ontology termsGene expression profilingKnowledge of reproductionTranscriptome assemblyReef organismsCoral diseasesGene discoveryPhylogenetic positionReef ecosystemsTranscriptome sequencingWestern Atlantic OceanPhylogenetic analysisH. carunculataOntology termsHomology searchImmune response genes
2014
Sensory determinants of behavioral dynamics in Drosophila thermotaxis
Klein M, Afonso B, Vonner AJ, Hernandez-Nunez L, Berck M, Tabone CJ, Kane EA, Pieribone VA, Nitabach MN, Cardona A, Zlatic M, Sprecher SG, Gershow M, Garrity PA, Samuel AD. Sensory determinants of behavioral dynamics in Drosophila thermotaxis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 112: e220-e229. PMID: 25550513, PMCID: PMC4299240, DOI: 10.1073/pnas.1416212112.Peer-Reviewed Original ResearchMechanistic Studies of the Genetically Encoded Fluorescent Protein Voltage Probe ArcLight
Han Z, Jin L, Chen F, Loturco JJ, Cohen LB, Bondar A, Lazar J, Pieribone VA. Mechanistic Studies of the Genetically Encoded Fluorescent Protein Voltage Probe ArcLight. PLOS ONE 2014, 9: e113873. PMID: 25419571, PMCID: PMC4242678, DOI: 10.1371/journal.pone.0113873.Peer-Reviewed Original ResearchMeSH KeywordsAction PotentialsAmino AcidsAnimalsCells, CulturedFluorescenceFluorescent DyesGreen Fluorescent ProteinsHEK293 CellsHumansHydrogen-Ion ConcentrationKineticsLuminescent ProteinsMembrane PotentialsMicroscopy, ConfocalMutation, MissenseNeuronsPatch-Clamp TechniquesPrenylationRatsRecombinant Fusion ProteinsSpectrometry, FluorescenceThe Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon
Sparks JS, Schelly RC, Smith WL, Davis MP, Tchernov D, Pieribone VA, Gruber DF. The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon. PLOS ONE 2014, 9: e83259. PMID: 24421880, PMCID: PMC3885428, DOI: 10.1371/journal.pone.0083259.Peer-Reviewed Original ResearchConceptsFluorescent proteinCoral reef fishesRay-finned fishesNovel fluorescent proteinsColor vision capabilitiesFish lineagesAnimal treeMarine lineagesPhylogenetic distributionEvolutionary historyBony fishIntraspecific communicationLineagesExperimental biologyPhenotypic variabilityFishProteinBiofluorescenceCurrent understandingSpeciesCnidariansGenusDiscoveryBiologyTrees
2013
Fluorescent Protein Voltage Probes Derived from ArcLight that Respond to Membrane Voltage Changes with Fast Kinetics
Han Z, Jin L, Platisa J, Cohen LB, Baker BJ, Pieribone VA. Fluorescent Protein Voltage Probes Derived from ArcLight that Respond to Membrane Voltage Changes with Fast Kinetics. PLOS ONE 2013, 8: e81295. PMID: 24312287, PMCID: PMC3842285, DOI: 10.1371/journal.pone.0081295.Peer-Reviewed Original ResearchTranscriptome deep-sequencing and clustering of expressed isoforms from Favia corals
Pooyaei Mehr SF, DeSalle R, Kao HT, Narechania A, Han Z, Tchernov D, Pieribone V, Gruber DF. Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals. BMC Genomics 2013, 14: 546. PMID: 23937070, PMCID: PMC3751062, DOI: 10.1186/1471-2164-14-546.Peer-Reviewed Original ResearchGenetically Targeted Optical Electrophysiology in Intact Neural Circuits
Cao G, Platisa J, Pieribone VA, Raccuglia D, Kunst M, Nitabach MN. Genetically Targeted Optical Electrophysiology in Intact Neural Circuits. Cell 2013, 154: 904-913. PMID: 23932121, PMCID: PMC3874294, DOI: 10.1016/j.cell.2013.07.027.Peer-Reviewed Original ResearchConceptsIntact neural circuitsNeural circuitsIntact brain tissueMembrane potentialNeuronal information processingNervous systemAction potentialsBrain tissueNeuronsStudy of intracellularElectrical activityKey cellular parametersMultiple neuronsElectrical eventsSubthreshold eventsNeurite branchesOptical electrophysiologyReliable recordingCellular parametersVoltage indicatorsFluorescent voltage indicatorsBrain