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
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 PacificEcologyElasmobranchs
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
The 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
Transcriptome 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 Research
2009
Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary Patterns
Gruber DF, DeSalle R, Lienau EK, Tchernov D, Pieribone VA, Kao HT. Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary Patterns. Molecular Biology And Evolution 2009, 26: 2841-2848. PMID: 19770223, PMCID: PMC2775108, DOI: 10.1093/molbev/msp194.Peer-Reviewed Original ResearchConceptsFluorescent proteinStrong positive selection pressureDivergent evolutionary pressuresDivergent evolutionary patternsMolecular phylogenetic analysisSuperfamily of proteinsPositive selection pressureCyan fluorescent proteinGreen fluorescent proteinRed fluorescent proteinNatural functionMolecular evolutionPhylogenetic analysisEvolutionary patternsEvolutionary pressureSelection pressureProtein sequencesMarine organismsCompact proteinGeographic originNovel regionBiological researchProteinOrganismsInternal region
2007
Dynamic Regulation of Fluorescent Proteins from a Single Species of Coral
Kao HT, Sturgis S, DeSalle R, Tsai J, Davis D, Gruber DF, Pieribone VA. Dynamic Regulation of Fluorescent Proteins from a Single Species of Coral. Marine Biotechnology 2007, 9: 733-746. PMID: 17955294, DOI: 10.1007/s10126-007-9025-1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnthozoaBase SequenceDNA PrimersEnvironmentGene Expression ProfilingGene Expression RegulationLuminescent ProteinsMolecular Sequence DataPhylogenyPigmentationReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionRNA, Ribosomal, 18SSensitivity and SpecificityStatistics as TopicTubulinConceptsFluorescent proteinMontastraea cavernosaSingle speciesBelizean Barrier ReefGroup of proteinsFluorescent protein familyNatural functionProtein familyDynamic regulationBarrier ReefProteinSpeciesOverall expressionCoralsPhysiological conditionsCurrent hypothesesExpressionNatural colorationReefsDistinct spectral classesColorationBetter understandingRegulationTurneffeFamily
1994
Neuropeptide role of both peptide YY and neuropeptide Y in vertebrates suggested by abundant expression of their mRNAS in a cyclostome brain
Söderberg C, Pieribone VA, Dahlstrand J, Brodin L, Larhammar D. Neuropeptide role of both peptide YY and neuropeptide Y in vertebrates suggested by abundant expression of their mRNAS in a cyclostome brain. Journal Of Neuroscience Research 1994, 37: 633-640. PMID: 8028041, DOI: 10.1002/jnr.490370510.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBrainDNA, ComplementaryGene Expression RegulationHumansIn Situ HybridizationIntestinal MucosaLampreysMolecular Sequence DataNeuropeptide YOrgan SpecificityPeptide BiosynthesisPeptide YYPeptidesPhylogenyRNA, MessengerSequence HomologySpecies SpecificityVertebrates