2025
Tunicate metatranscriptomes reveal evidence of ancient co-divergence between viruses and their hosts
Petrone M, Grove J, Parry R, Van Brussel K, Mifsud J, Dindar Z, Mei S, Shi M, Turnbull O, Marzinelli E, Holmes E. Tunicate metatranscriptomes reveal evidence of ancient co-divergence between viruses and their hosts. Current Biology 2025 PMID: 40472852, DOI: 10.1016/j.cub.2025.05.032.Peer-Reviewed Original ResearchRNA virusesCo-divergenceEvolution of structural genesVirus-host co-divergenceRNA-dependent RNA polymeraseRNA virus evolutionNegative-sense virusesPhylogenetic relationshipsSister groupEarly chordatesRNA polymeraseStructural geneAnimal evolutionEvolutionary historyTransitional taxaRNA librariesEvolutionary timescalesInvertebrate relativesVirus evolutionVirus lineagesMultiple lineagesRNAVertebratesChordatesTunicates
2019
Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes
Pham J, Ogbunugafor C, Ba A, Hartl D. Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes. MicrobiologyOpen 2019, 9: e968. PMID: 31778298, PMCID: PMC7002106, DOI: 10.1002/mbo3.968.Peer-Reviewed Original ResearchConceptsNiche breadth evolutionStructural geneNiche breadthE. coli K-12Evolution of niche breadthSignatures of selectionHost environmentFunctional gene categoriesWhole-genome sequencingEscherichia virus T4E. coli CComparison of mutationsEvolution of specializationVirus-host interactionsViral disease emergencePhage productionBacteriophage T4Gene categoriesExperimental evolutionPhage therapyBacteriophage systemsExperimental populationsGenetic determinantsEvolution experimentsPhage
2009
Cardiomyocyte Differentiation of Human Induced Pluripotent Stem Cells
Zwi L, Caspi O, Arbel G, Huber I, Gepstein A, Park IH, Gepstein L. Cardiomyocyte Differentiation of Human Induced Pluripotent Stem Cells. Circulation 2009, 120: 1513-1523. PMID: 19786631, DOI: 10.1161/circulationaha.109.868885.Peer-Reviewed Original ResearchConceptsTranscription factorsHiPS cellsCardiomyocyte differentiationCardiac-specific transcription factorsInduced pluripotent stem cellsGene expression studiesHuman induced pluripotent stem cellsStem cell linesPluripotent stem cellsCardiomyocyte differentiation potentialPluripotent stem cell lineStructural geneContracting embryoid bodiesCardiomyocyte differentiation processTranslational cardiovascular researchEmbryoid bodiesExpression studiesDifferentiation systemDifferentiation processCardiovascular regenerative medicineSarcomeric proteinsDifferentiation potentialIon channelsAdult fibroblastsFunctional properties
2003
Genetic Variability at the Human FMO1 Locus: Significance of a Basal Promoter Yin Yang 1 Element Polymorphism (FMO1*6)
Hines R, Luo Z, Hopp K, Cabacungan E, Koukouritaki S, McCarver D. Genetic Variability at the Human FMO1 Locus: Significance of a Basal Promoter Yin Yang 1 Element Polymorphism (FMO1*6). Journal Of Pharmacology And Experimental Therapeutics 2003, 306: 1210-1218. PMID: 12829732, DOI: 10.1124/jpet.103.053686.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsFlavin-containing monooxygenasesGenetic variabilityIntron 1 splice donor siteElectrophoretic mobility shift assaysYin Yang 1 (YY1) transcription factorTransient expression assaysCore binding sequenceATG start codonMobility shift assaysSplice donor siteCommon single nucleotide polymorphismsYY1 bindingStructural geneTranscription factorsStart codonShift assaysExonic sequencesChromosome 1q23Binding sequenceExpression assaysPromoter activityVariety of toxicantsBase pairsNucleotide polymorphisms
2001
Flanking regulatory sequences of the locus encoding the murine GDNF receptor, c‐ret, directs lac Z (β‐galactosidase) expression in developing somatosensory system
Sukumaran M, Waxman S, Wood J, Pachnis V. Flanking regulatory sequences of the locus encoding the murine GDNF receptor, c‐ret, directs lac Z (β‐galactosidase) expression in developing somatosensory system. Developmental Dynamics 2001, 222: 389-402. PMID: 11747074, DOI: 10.1002/dvdy.1192.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornBase SequenceChromosome MappingCloning, MolecularConsensus SequenceDrosophila ProteinsEmbryo, MammalianGanglia, SensoryGene ExpressionGene Expression Regulation, DevelopmentalGenes, RegulatorGlial Cell Line-Derived Neurotrophic Factor ReceptorsLac OperonLectinsMiceMice, TransgenicNeurons, AfferentNociceptorsPromoter Regions, GeneticProtein Structure, TertiaryProto-Oncogene ProteinsProto-Oncogene Proteins c-retReceptor Protein-Tyrosine KinasesSpinal CordTranscription Initiation SiteConceptsRegulatory domainLac Z expressionZ expressionCell type-specific expressionDistal regulatory domainEndogenous gene expressionCis-regulatory domainsTranscription initiation siteEntire structural geneSpecific regulatory domainsLac Z reporter geneStructural geneMouse genomeLateral mesodermRegulatory sequencesCpG islandsDNA sequencesPrimitive streakReporter geneFlanking sequencesCosmid contigGene expressionSpecific expressionTransgenic mouse lineInitiation siteA Quantitative-Trait Analysis of Human Plasma–Dopamine β-Hydroxylase Activity: Evidence for a Major Functional Polymorphism at the DBH Locus
Zabetian C, Anderson G, Buxbaum S, Elston R, Ichinose H, Nagatsu T, Kim K, Kim C, Malison R, Gelernter J, Cubells J. A Quantitative-Trait Analysis of Human Plasma–Dopamine β-Hydroxylase Activity: Evidence for a Major Functional Polymorphism at the DBH Locus. American Journal Of Human Genetics 2001, 68: 515-522. PMID: 11170900, PMCID: PMC1235285, DOI: 10.1086/318198.Peer-Reviewed Original ResearchConceptsQuantitative trait lociMajor quantitative trait locusMajor genetic markerH activityQuantitative trait analysisStructural geneGenotype/phenotype correlationMutational analysisExtreme phenotypesGenetic markersDBH geneHuman diseasesGenesDBH locusNovel polymorphismsCodominant inheritancePhenotype correlationUnidentified polymorphismsLociPlasma dopamine β-hydroxylase activityΒ-hydroxylase activityPolymorphismFunctional polymorphismsBeta HMajor functional polymorphisms
1999
Paternal Deletion from Snrpn to Ube3a in the Mouse Causes Hypotonia, Growth Retardation and Partial Lethality and Provides Evidence for a Gene Contributing to Prader-Willi Syndrome
Tsai T, Jiang Y, Bressler J, Armstrong D, Beaudet A. Paternal Deletion from Snrpn to Ube3a in the Mouse Causes Hypotonia, Growth Retardation and Partial Lethality and Provides Evidence for a Gene Contributing to Prader-Willi Syndrome. Human Molecular Genetics 1999, 8: 1357-1364. PMID: 10400982, DOI: 10.1093/hmg/8.8.1357.Peer-Reviewed Original ResearchMeSH KeywordsAbnormalities, MultipleAnimalsAutoantigensBrainChromosome DeletionFemaleGene ExpressionGenomic ImprintingHumansLigasesMaleMiceMice, Inbred StrainsMuscle HypotoniaMutagenesis, Site-DirectedOpen Reading FramesPedigreePhenotypePrader-Willi SyndromeRibonucleoproteins, Small NuclearRNAsnRNP Core ProteinsUbiquitin-Protein LigasesConceptsOpen reading framePartial lethalityExon 2Pathogenesis of PWSUpstream open reading framesObvious phenotypic abnormalitiesMouse chromosome 7CGenomic imprintsImprinted expressionPrader-Willi syndromeHuman translocationImprinted genesGene ContributingStructural genePaternal deficiencyChromosome 7CPaternal chromosomesGenotype/phenotype correlationHuman chromosomesMethylation patternsImprinting mutationsReading frameMultiple genesLoss of expressionSNRPN
1991
Genetic and molecular analysis of Sn, a light-inducible, tissue specific regulatory gene in maize
Tonelli C, Consonni G, Dolfini S, Dellaporta S, Viotti A, Gavazzi G. Genetic and molecular analysis of Sn, a light-inducible, tissue specific regulatory gene in maize. Molecular Genetics And Genomics 1991, 225: 401-410. PMID: 1673220, DOI: 10.1007/bf00261680.Peer-Reviewed Original ResearchMeSH KeywordsAcyltransferasesAlcohol OxidoreductasesAllelesAnthocyaninsBlotting, NorthernBlotting, SouthernCloning, MolecularDNAGene Expression RegulationGenes, PlantGenes, RegulatorLightNucleic Acid HybridizationPolymorphism, Restriction Fragment LengthRestriction MappingSequence Homology, Nucleic AcidTranscription, GeneticZea maysConceptsSuccessive duplication eventsDiverse gene familySingle ancestral geneTissue-specific regulatory genesSpecific regulatory genesTissue-specific depositionTissue-specific fashionDuplication eventsAncestral genePlant cellsR genesGene familySn locusTissue-specific accumulationExpression of SnStructural geneRegulatory genesSn geneAntisense RNA probesCDNA clonesEvolutionary derivationDistribution of anthocyaninsKb transcriptPigment synthesisNorthern analysis
1990
Linkage relationships of human arginine vasopressin-neurophysin-II and oxytocin-neurophysin-I to prodynorphin and other loci on chromosome 20.
Summar M, Phillips J, Battey J, Castiglione C, Kidd K, Maness K, Weiffenbach B, Gravius T. Linkage relationships of human arginine vasopressin-neurophysin-II and oxytocin-neurophysin-I to prodynorphin and other loci on chromosome 20. Endocrinology 1990, 4: 947-50. PMID: 1978246, DOI: 10.1210/mend-4-6-947.Peer-Reviewed Original ResearchConceptsLinkage relationshipsChromosome 20Restriction fragment length polymorphismCentre d'Etude du Polymorphisme Humain (CEPH) collectionFragment length polymorphismShort armAnonymous DNA segmentsSomatic cell hybridsLength polymorphismDistal short armSame neurosecretory granulesStructural geneTranscriptional associationsHuman genomeCell hybridsDNA segmentsLocus mapsMultilocus linkage analysisClose physical relationshipLinkage analysisSouthern blotOdds (LOD) scoreLociGenesClose linkageSpatial and Temporal Expression of Regulatory Genes in Zea mays
Tonelli C, Consonni G, Mereghetti M, Dolfini S, Dellaporta S, Viotti A, Gavazzi G. Spatial and Temporal Expression of Regulatory Genes in Zea mays. Current Plant Science And Biotechnology In Agriculture 1990, 9: 385-390. DOI: 10.1007/978-94-009-2103-0_58.Peer-Reviewed Original ResearchRegulatory genesPigmentation of flowersDifferent regulatory genesPlant defenseFlavonoid biosynthesisGene regulationStructural geneDevelopmental biologyNumerous genesZea maysSecondary metabolitesDistribution of pigmentsGenesTemporal expressionEnvironmental stimuliNutrient supplySpecific functionsBiosynthesisModel systemCoordinate wayPlantsPigmentationPhytopathogensMaysFlowers
1988
Tyrosinases of murine melanocytes with mutations at the albino locus.
Halaban R, Moellmann G, Tamura A, Kwon BS, Kuklinska E, Pomerantz SH, Lerner AB. Tyrosinases of murine melanocytes with mutations at the albino locus. Proceedings Of The National Academy Of Sciences Of The United States Of America 1988, 85: 7241-7245. PMID: 3140237, PMCID: PMC282161, DOI: 10.1073/pnas.85.19.7241.Peer-Reviewed Original ResearchConceptsAlbino locusTrans-Golgi networkWild-type melanocytesWild-type strainAbnormal posttranslational modificationsSynthesis of melaninDiminished pigmentationStructural genePosttranslational modificationsMurine melanocytesLocus mutantsKey enzymeLevels of mRNAMutantsKinetics of activationProteolytic cleavageUnstable enzymeEnzymeLociMelanocytesReduced levelsMutationsConfer susceptibilityTyrosinaseLittle enzyme
1987
Isolation and sequence of a cDNA clone for human tyrosinase that maps at the mouse c-albino locus.
Kwon BS, Haq AK, Pomerantz SH, Halaban R. Isolation and sequence of a cDNA clone for human tyrosinase that maps at the mouse c-albino locus. Proceedings Of The National Academy Of Sciences Of The United States Of America 1987, 84: 7473-7477. PMID: 2823263, PMCID: PMC299318, DOI: 10.1073/pnas.84.21.7473.Peer-Reviewed Original ResearchConceptsCDNA clonesMelanocyte cDNA libraryRelated mRNA speciesHuman tyrosinaseAmino acid sequenceSouthern blot analysisStructural geneCDNA libraryNucleotide sequenceMRNA speciesAcid sequenceGlycosylation sitesCDNA insertDeletion mutationsCell typesAmino acidsCopper bindingBlot analysisClonesMalignant melanocytesLociSequenceTyrosinaseApproximate lengthKilobasesCloning and characterization of the gene coding for cytoplasmic seryl-tRNA synthetase from Saccharomyces cerevisiae
Weygand-Durasevic I, johnson-Burke D, Söll D. Cloning and characterization of the gene coding for cytoplasmic seryl-tRNA synthetase from Saccharomyces cerevisiae. Nucleic Acids Research 1987, 15: 1887-1904. PMID: 3031581, PMCID: PMC340606, DOI: 10.1093/nar/15.5.1887.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseSingle open reading frameAbundant yeast proteinsGenomic Southern blotsNuclease S1 analysisOpen reading frameTranslation initiation codonAmino acid sequenceKb SalI fragmentNucleotide sequence analysisAT-rich sequencesYeast proteinsStructural geneCodon usageS1 analysisTATA boxInitiation codonReading frameSer geneSalI fragmentAcid sequenceExpression librarySequence analysisRich sequencesSouthern blot
1985
Cloning, nucleotide sequence, and overexpression of the bacteriophage T4 regA gene.
Adari H, Rose K, Williams K, Konigsberg W, Lin T, Spicer E. Cloning, nucleotide sequence, and overexpression of the bacteriophage T4 regA gene. Proceedings Of The National Academy Of Sciences Of The United States Of America 1985, 82: 1901-1905. PMID: 3872458, PMCID: PMC397441, DOI: 10.1073/pnas.82.7.1901.Peer-Reviewed Original ResearchConceptsRegA proteinRegA geneNucleotide sequenceProtein chemical studiesLevel of translationCorresponding genesStructural geneGene codesDNA sequencesRegulatory proteinsAcid inductionDNA fragmentsPhage M13Early genesGenesRestriction fragmentsAmino acidsProteinPAS1Same plasmidSequenceFragmentsCloningRegATranslation[8] Glutaminyl-tRNA synthetase of Escherichia coli
Hoben P, Söll D. [8] Glutaminyl-tRNA synthetase of Escherichia coli. Methods In Enzymology 1985, 113: 55-59. PMID: 3911010, DOI: 10.1016/s0076-6879(85)13011-9.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseStructural geneSpecific aminoacyl-tRNA synthetaseE. coli chromosomeAmino acidsCognate amino acidTemperature-sensitive phenotypeGlutamyl-tRNA synthetaseAminoacyl-tRNA synthetaseColi chromosomeGln-tRNAGlnDNA fragmentsProtein synthesisEscherichia coliThermolabile enzymeCellular levelGenesGln mutationSynthetaseGlnRE. coliSeparate enzymesMultistep processNegative bacteriaEnzymeTwo control systems modulate the level of glutaminyl-tRNA synthetase in Escherichia coli
Cheung A, Watson L, Söll D. Two control systems modulate the level of glutaminyl-tRNA synthetase in Escherichia coli. Journal Of Bacteriology 1985, 161: 212-218. PMID: 2578447, PMCID: PMC214858, DOI: 10.1128/jb.161.1.212-218.1985.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseEscherichia coli glutaminyl-tRNA synthetaseBeta-galactosidase structural genePost-transcriptional regulationStructural geneTranscriptional controlRegulatory mutationsTranslational levelGln-10Metabolic regulationEscherichia coliSynthetaseVivo expressionTranscriptionGrowth conditionsRegulationMRNA levelsRegulatory studiesSynthetase levelsMutationsGlnGrowth rateGenesPromoterColi
1983
Identification of two distinct regulatory regions adjacent to the human β-interferon gene
Zinn K, Dimaio D, Maniatis T. Identification of two distinct regulatory regions adjacent to the human β-interferon gene. Cell 1983, 34: 865-879. PMID: 6313211, DOI: 10.1016/0092-8674(83)90544-5.Peer-Reviewed Original ResearchConceptsIFN gene expressionBovine papilloma virusRegulatory regionsExpression of deletion mutantsGene expressionMRNA cap sitePoly(I)-poly(CCell linesStable cell linesIndependent cell linesCloned geneStructural geneDeletion mutantsLevel of expressionKinetics of inductionCap siteMouse cellsHuman beta-interferonGenesInduced expressionConstitutive levelsDeletionBeta-interferonExpressionPapilloma virus
1982
Identification of two genes immediately downstream from the polA gene of Escherichia coli
Joyce C, Grindley N. Identification of two genes immediately downstream from the polA gene of Escherichia coli. Journal Of Bacteriology 1982, 152: 1211-1219. PMID: 6183253, PMCID: PMC221628, DOI: 10.1128/jb.152.3.1211-1219.1982.Peer-Reviewed Original ResearchEscherichia coli glutaminyl-tRNA synthetase. II. Characterization of the glnS gene product.
Hoben P, Royal N, Cheung A, Yamao F, Biemann K, Söll D. Escherichia coli glutaminyl-tRNA synthetase. II. Characterization of the glnS gene product. Journal Of Biological Chemistry 1982, 257: 11644-11650. PMID: 6749844, DOI: 10.1016/s0021-9258(18)33811-0.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetasePrimary sequenceDNA sequencesAminoacyl-tRNA synthetasesManual Edman degradationExtensive sequence repeatsCarboxypeptidase B digestionEscherichia coli K12NH2-terminal sequenceSequence repeatsStructural geneGene productsCarboxyl terminusSequence homologyHomologous regionsTwo-column procedureEdman degradationColi K12B digestionSynthetaseSynthetasesTheoretical peptidesSequencePosition 550EnzymeBacteriophage T4 gene 45. Sequences of the structural gene and its protein product.
Spicer E, Noble J, Nossal N, Konigsberg W, Williams K. Bacteriophage T4 gene 45. Sequences of the structural gene and its protein product. Journal Of Biological Chemistry 1982, 257: 8972-8979. PMID: 6284751, DOI: 10.1016/s0021-9258(18)34228-5.Peer-Reviewed Original ResearchConceptsGene 45T4 late gene transcriptionT4 DNA replication complexRNA polymerase recognitionT4 DNA replicationLate gene transcriptionDNA replication complexTranslation initiation regionNucleotide sequence analysisGenes 46Protein chemistry studiesRegA proteinStructural geneSequence similarityDNA replicationPutative promoterRNA polymeraseReplication complexGene transcriptionProtein productsSequence analysisPrimary structureInitiation regionRIIB genePolymerase recognition
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