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
2024
DeepVID v2: self-supervised denoising with decoupled spatiotemporal enhancement for low-photon voltage imaging
Liu C, Lu J, Wu Y, Ye X, Ahrens A, Platisa J, Pieribone V, Chen J, Tian L. DeepVID v2: self-supervised denoising with decoupled spatiotemporal enhancement for low-photon voltage imaging. Neurophotonics 2024, 11: 045007. PMID: 39474199, PMCID: PMC11519979, DOI: 10.1117/1.nph.11.4.045007.Peer-Reviewed Original ResearchDeep learning denoising methodsLeverage temporal informationSelf-supervised denoisingSuperior denoising capabilitiesReal-time inferenceLocal spatial informationSequence of framesVoltage imaging dataDenoising frameworkDenoising methodSignal-to-noise ratioDenoising capabilityExtraction branchDenoising needsBlind pixelsTemporal informationDenoisingGround truthPoisson noiseTemporal performanceCentral frameOffline versionSpatial informationDynamics of neuronal activitySignal-to-noiseDensity and distribution patterns of seafloor macrolitter in the eastern Red Sea
Martynova A, Rodrigue M, Pieribone V, Qurban M, Duarte C. Density and distribution patterns of seafloor macrolitter in the eastern Red Sea. The Science Of The Total Environment 2024, 953: 176042. PMID: 39244039, DOI: 10.1016/j.scitotenv.2024.176042.Peer-Reviewed Original ResearchItems km<sup>-2</sup> inEastern Red SeaRed SeaMarine environmentImpact of anthropogenic activitiesDensity of litterProduction of plasticsWaste management regulationsSeafloor litterLitter densityMarine ecosystemsAnthropogenic sourcesLitter categoriesAnthropogenic activitiesConservation effortsManagement regulationsWaste pollutionSurface waterWaste regulationsMaritime trafficMacrolitterLitterDistribution patternsMarineMedian densityA subdural CMOS optical device for bidirectional neural interfacing
Pollmann E, Yin H, Uguz I, Dubey A, Wingel K, Choi J, Moazeni S, Gilhotra Y, Andino-Pavlovsky V, Banees A, Parihar A, Boominathan V, Robinson J, Veeraraghavan A, Pieribone V, Pesaran B, Shepard K. A subdural CMOS optical device for bidirectional neural interfacing. Nature Electronics 2024, 7: 829-841. DOI: 10.1038/s41928-024-01209-w.Peer-Reviewed Original ResearchComplementary metal-oxide-semiconductorOptical devicesMetal-oxide-semiconductorForm factorsCMOS application-specific integrated circuitOptical stimulationApplication-specific integrated circuitIntegrated circuitsMiniature microscopeBidirectional neural interfaceOptogenetic stimulationNeural activityDevicesNeural interfacesCortical areasUltrathinSpatial-temporal precisionPrimate brainFluorescence imagingDopamine-mediated interactions between short- and long-term memory dynamics
Huang C, Luo J, Woo S, Roitman L, Li J, Pieribone V, Kannan M, Vasan G, Schnitzer M. Dopamine-mediated interactions between short- and long-term memory dynamics. Nature 2024, 634: 1141-1149. PMID: 39038490, PMCID: PMC11525173, DOI: 10.1038/s41586-024-07819-w.Peer-Reviewed Original ResearchDopamine signalingOdor cuesMemory formationLong-term memory unitsInnate valenceLong-term memory tracesMemory dynamicsConditioned odor cuesLong-term memory formationRegulate memory storageOlfactory associative conditioningShort-term memory formationMushroom body output neuronsMushroom bodiesValenced informationValence signalsMemory tracesRegulating memoryBrain structuresLearned valenceBasal gangliaDopamineSensory stimuliMemory storageSensory cuesLost in the dark: Antipatharia-Symbiodiniaceae association in the deep waters of the Red Sea
Vicario S, Terraneo T, Castano C, Chimienti G, Oury N, Vimercati S, Hume B, Marchese F, Nolan M, Eweida A, Purkis S, Rodrigue M, Pieribone V, Qurban M, Duarte C, Benzoni F. Lost in the dark: Antipatharia-Symbiodiniaceae association in the deep waters of the Red Sea. Frontiers In Marine Science 2024, 11: 1330118. DOI: 10.3389/fmars.2024.1330118.Peer-Reviewed Original ResearchBlack coralsSaudi Arabian Red SeaRed SeaDiversity of SymbiodiniaceaeRed Sea recordsEfficient photosynthetic activityDeep marine ecosystemsHigh-throughput sequencingAssociated with dinoflagellatesHeterotrophic feedingFamily SymbiodiniaceaeHard coralsITS2 regionObligate autotrophsMarine ecosystemsSymbiodiniaceaeLow light penetrationPhotosynthetic activityCommunity diversityNo significant patternCoralsSampling localitiesEvolutionary processWater environmentSymbiotic relationshipDiversity and distribution of coral gall crabs associated with Red Sea mesophotic corals
Vimercati S, Terraneo T, Marchese F, Eweida A, Rodrigue M, Pieribone V, Qurban M, Duarte C, Benzoni F. Diversity and distribution of coral gall crabs associated with Red Sea mesophotic corals. Frontiers In Marine Science 2024, 11: 1305396. DOI: 10.3389/fmars.2024.1305396.Peer-Reviewed Original ResearchSaudi Arabian Red SeaRed SeaMesophotic coralsMesophotic depthsRemotely operated vehicleCoral-associated faunaReef-building coralsSaudi Arabian coastShallow-water coralsNorthern Red SeaFamily AgariciidaeMarine biodiversityGall crabsOpecarcinusSemi-enclosed basinCoralsArabian coastObligate symbiosisNuclear markersPhylogenetic treeDecapod speciesDepth distributionSpeciesSeaGenusConsistent Symbiodiniaceae community assemblage in a mesophotic-specialist coral along the Saudi Arabian Red Sea
Vimercati S, Terraneo T, Castano C, Barreca F, Hume B, Marchese F, Ouhssain M, Steckbauer A, Chimienti G, Eweida A, Voolstra C, Rodrigue M, Pieribone V, Purkis S, Qurban M, Jones B, Duarte C, Benzoni F. Consistent Symbiodiniaceae community assemblage in a mesophotic-specialist coral along the Saudi Arabian Red Sea. Frontiers In Marine Science 2024, 11: 1264175. DOI: 10.3389/fmars.2024.1264175.Peer-Reviewed Original ResearchRed Sea coastMesophotic depthsRed SeaSaudi Arabian Red Sea coastSaudi Arabian Red SeaSymbiodiniaceae community compositionSea coastShallow water coralsRed Sea coastlineReef-dwelling organismsNorthern Red SeaGenus CladocopiumCoral speciesCoral taxaLatitudinal environmental gradientCoral coloniesSpecies-specific interactionsGenera SymbiodiniumSpecialist speciesCommunity assemblagesFarasan BanksNext generation sequencingSymbiont communitiesWater coralsEnvironmental gradientsIn situ observation on two ‘elusive’ rhodaliid siphonophores (Cnidaria; Hydrozoa; Siphonophora) from the Red Sea, including a potential new species within the genus Archangelopsis
Angulo-Preckler C, Steckbauer A, Lim K, Hissmann K, Pieribone V, Qurban M, Duarte C. In situ observation on two ‘elusive’ rhodaliid siphonophores (Cnidaria; Hydrozoa; Siphonophora) from the Red Sea, including a potential new species within the genus Archangelopsis. Frontiers In Marine Science 2024, 11: 1338782. DOI: 10.3389/fmars.2024.1338782.Peer-Reviewed Original ResearchPotential new speciesNew speciesRRNA markerTaxonomic traitsHabitat requirementsGenetic analysisColor variantsOceanic habitatsBenthic zoneLow oxygen environmentRhodaliidRed SeaGenusSpeciesHabitatIn situ observationsSiphonophoresSpecimen preservationMorphological featuresWater depthSea bedMorphological analysisSeaSequenceTraits
2023
First record of a live adult heteropod Firoloida desmarestia in the Red Sea
Angulo-Preckler C, Steckbauer A, Armelles I, Agustí S, Rodrigue M, Pieribone V, Qurban M, Duarte C. First record of a live adult heteropod Firoloida desmarestia in the Red Sea. Frontiers In Marine Science 2023, 10: 1215195. DOI: 10.3389/fmars.2023.1215195.Peer-Reviewed Original ResearchRed SeaGlobal distributionCentral Red SeaDeep sea waterSubmersible divesDiverse array of speciesShell-less mollusksEpipelagic zoneEurybathic distributionWorld's oceansObservational recordWater columnPolar regionsArray of speciesVertical migrationSeaOceanMale specimensEcological roleEcological significanceExpeditionSpeciesDiverse arrayShell-lessObservationsNew depth records and novel feeding observations of three elasmobranchs species in the Eastern Red Sea
Frappi S, Williams C, Pilcher N, Rodrigue M, Marshall P, Pieribone V, Qurban M, Duarte C. New depth records and novel feeding observations of three elasmobranchs species in the Eastern Red Sea. Frontiers In Marine Science 2023, 10: 1270257. DOI: 10.3389/fmars.2023.1270257.Peer-Reviewed Original ResearchElasmobranch speciesConservation strategiesSaudi Arabian Red SeaRed SeaGlobal population declineEffective conservation strategiesVertical distributionEastern Red SeaPresence of speciesDeep-sea habitatsDepth recordingsFishery operationsDrop cameraTrophic nicheSea habitatsPopulation declineEcological dynamicsConservation measuresFeeding observationsRemotely operated vehicleMovement patternsElasmobranchsObservation of animalsKnowledge gapsFeeding behaviorMesophotic and Bathyal Palaemonid Shrimp Diversity of the Red Sea, with the Establishment of Two New Genera and Two New Species †
Anker A, Vimercati S, Barreca F, Marchese F, Chimienti G, Terraneo T, Rodrigue M, Eweida A, Qurban M, Duarte C, Pieribone V, Benzoni F. Mesophotic and Bathyal Palaemonid Shrimp Diversity of the Red Sea, with the Establishment of Two New Genera and Two New Species †. Diversity 2023, 15: 1028. DOI: 10.3390/d15101028.Peer-Reviewed Original ResearchRed SeaNew speciesNew genusDeep-water speciesRed Sea coastRecent molecular analysesBenthic ecosystemsMesophoticBathyal zoneBathyal faunaNumerous taxaNew host recordsEvolutionary relationshipsPhylogenetic relationshipsMarine invertebratesTaxonomic revisionCaridean shrimpsRecent expeditionsSea coastDiversified familyHost recordsPalaemonid shrimpsGenetic dataDifferent generaDiversityTwo-photon voltage imaging denoising by self-supervised learning
Liu C, Platisa J, Ye X, Ahrens A, Chen I, Davison I, Pieribone V, Chen J, Tian L. Two-photon voltage imaging denoising by self-supervised learning. Progress In Biomedical Optics And Imaging 2023, 12365: 1236505-1236505-2. DOI: 10.1117/12.2648122.Peer-Reviewed Original ResearchOdor 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 typesDeepVID: A Self-supervised Deep Learning Framework for Two-photon Voltage Imaging Denoising
Liu C, Platisa J, Ye X, Ahrens A, Chen I, Davison I, Pieribone V, Chen J, Tian L. DeepVID: A Self-supervised Deep Learning Framework for Two-photon Voltage Imaging Denoising. 2022, btu4c.4. DOI: 10.1364/brain.2022.btu4c.4.Peer-Reviewed Original Research
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 Research