2023
The functional and evolutionary impacts of human-specific deletions in conserved elements
Xue J, Mackay-Smith A, Mouri K, Garcia M, Dong M, Akers J, Noble M, Li X, Lindblad-Toh K, Karlsson E, Noonan J, Capellini T, Brennand K, Tewhey R, Sabeti P, Reilly S, Andrews G, Armstrong J, Bianchi M, Birren B, Bredemeyer K, Breit A, Christmas M, Clawson H, Damas J, Di Palma F, Diekhans M, Dong M, Eizirik E, Fan K, Fanter C, Foley N, Forsberg-Nilsson K, Garcia C, Gatesy J, Gazal S, Genereux D, Goodman L, Grimshaw J, Halsey M, Harris A, Hickey G, Hiller M, Hindle A, Hubley R, Hughes G, Johnson J, Juan D, Kaplow I, Karlsson E, Keough K, Kirilenko B, Koepfli K, Korstian J, Kowalczyk A, Kozyrev S, Lawler A, Lawless C, Lehmann T, Levesque D, Lewin H, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu V, Marques-Bonet T, Mason V, Meadows J, Meyer W, Moore J, Moreira L, Moreno-Santillan D, Morrill K, Muntané G, Murphy W, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat N, Pfenning A, Phan B, Pollard K, Pratt H, Ray D, Reilly S, Rosen J, Ruf I, Ryan L, Ryder O, Sabeti P, Schäffer D, Serres A, Shapiro B, Smit A, Springer M, Srinivasan C, Steiner C, Storer J, Sullivan K, Sullivan P, Sundström E, Supple M, Swofford R, Talbot J, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder A, Wirthlin M, Xue J, Zhang X. The functional and evolutionary impacts of human-specific deletions in conserved elements. Science 2023, 380: eabn2253. PMID: 37104592, PMCID: PMC10202372, DOI: 10.1126/science.abn2253.Peer-Reviewed Original ResearchConceptsHuman-specific deletionHuman phenotypic traitsParallel reporterEvolutionary impactDevelopmental genesPhenotypic traitsEvolutionary mechanismsGenomic sequencesNew traitsTranscriptomic datasetsSequence altersRegulatory functionsCell typesRegulatory activityRich resourceDeletionSynaptic functionTraitsBrain developmentGenesSpeciesReporterHumansSequenceExpressionFunctional and molecular characterization of suicidality factors using phenotypic and genome-wide data
Quintero Reis A, Newton B, Kessler R, Polimanti R, Wendt F. Functional and molecular characterization of suicidality factors using phenotypic and genome-wide data. Molecular Psychiatry 2023, 28: 1064-1071. PMID: 36604601, PMCID: PMC10005939, DOI: 10.1038/s41380-022-01929-5.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesPolygenic scoringSummary association dataGenome-wide dataSNP effect sizesGenomic structural equation modelingGenetic study designsNew traitsAdmixed AmericansEffect size distributionBiological pathwaysAssociation studiesTranscriptomic featuresMolecular characterizationSusceptibility lociGenetic correlationsAssociation dataWide dataTraitsGenetic contributionEuropean ancestryCommon genetic factorsLociPhenotypeGenetic factors
2014
A dexamethasone-inducible gene expression system is active in Citrus plants
Rossignol P, Orbović V, Irish V. A dexamethasone-inducible gene expression system is active in Citrus plants. Scientia Horticulturae 2014, 172: 47-53. DOI: 10.1016/j.scienta.2014.02.041.Peer-Reviewed Original ResearchGene expression systemExpression systemΒ-glucuronidase (GUS) reporter geneInducible gene expression systemSynthetic transcription factorsGene of interestPromoter driving expressionCrop plantsGene functionTransgenic approachesTranscription factorsCitrus plantsNew traitsReporter geneCitrus cultivarsPlantsTransgene activityGenesSynthetic glucocorticoid dexamethasoneTiming of activityGlucocorticoid receptorSuch manipulationsGlucocorticoid dexamethasoneLhGRTraits
2011
Ancestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits
Chen HD, Jewett MW, Groisman EA. Ancestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits. PLOS Genetics 2011, 7: e1002184. PMID: 21811415, PMCID: PMC3140997, DOI: 10.1371/journal.pgen.1002184.Peer-Reviewed Original ResearchMeSH KeywordsAnti-Bacterial AgentsBacterial ProteinsDNA, BacterialDrug Resistance, BacterialEscherichia coliEscherichia coli ProteinsGene Expression Regulation, BacterialGene Transfer, HorizontalKineticsMagnesiumMolecular Sequence DataPhosphorylationPolymyxin BReverse Transcriptase Polymerase Chain ReactionSalmonella typhimuriumSequence Analysis, DNATranscription FactorsTransformation, BacterialConceptsGene productsPmrD proteinPmrA/PmrB systemSpecies-specific traitsPmrA/PmrBE. coliHigh phosphatase activityBacterium Escherichia coliTwo-component systemPmrA proteinPolymyxin B resistanceAncestral locusAncestral proteinAncestral geneAncestral pathwayNew traitsBiochemical activityDifferent speciesGenesPmrB proteinEscherichia coliPhosphatase activityB resistanceProteinSalmonella enterica
2009
Evolution of the neocortex: a perspective from developmental biology
Rakic P. Evolution of the neocortex: a perspective from developmental biology. Nature Reviews Neuroscience 2009, 10: 724-735. PMID: 19763105, PMCID: PMC2913577, DOI: 10.1038/nrn2719.Peer-Reviewed Original ResearchConceptsEvo-devo approachSpecies-specific adaptationsExtinct common ancestorsNew cell typesSpecies-specific differencesMutations of genesProliferative ventricular zoneMammalian evolutionDistinct migratory pathwaysCommon ancestorDevelopmental biologyCell divisionNew traitsNew cell subtypesNeural stem cellsProtomap hypothesisMouse embryosNew cytoarchitectonic areasTranscriptional factorsUnique cognitive abilitiesGene expressionDifferential enlargementDistinct traitsMigratory pathwaysCortical evolution
2008
Overcoming H-NS-mediated Transcriptional Silencing of Horizontally Acquired Genes by the PhoP and SlyA Proteins in Salmonella enterica *
Perez JC, Latifi T, Groisman EA. Overcoming H-NS-mediated Transcriptional Silencing of Horizontally Acquired Genes by the PhoP and SlyA Proteins in Salmonella enterica *. Journal Of Biological Chemistry 2008, 283: 10773-10783. PMID: 18270203, PMCID: PMC2447644, DOI: 10.1074/jbc.m709843200.Peer-Reviewed Original ResearchConceptsHistone-like nucleoid structuring proteinPagC geneSlyA proteinRNA polymeraseRNA polymerase recruitmentH-NS repressionNucleoid structuring proteinHorizontal gene transferDifferent regulatory proteinsSalmonella entericaPolymerase recruitmentTranscriptional silencingNew traitsForeign DNAGene transcriptionRegulatory proteinsUgtLRespective promotersTranscriptionPhoPRecipient organismGenesPagC promoterGene transferProtein
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