2025
Structure and evolution of photosystem I in the early-branching cyanobacterium Anthocerotibacter panamensis
Jiang H, Gisriel C, Cardona T, Flesher D, Brudvig G, Ho M. Structure and evolution of photosystem I in the early-branching cyanobacterium Anthocerotibacter panamensis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2427090122. PMID: 40366692, PMCID: PMC12107172, DOI: 10.1073/pnas.2427090122.Peer-Reviewed Original ResearchConceptsPhotosystem IAnalysis of photosystem IEvolution of Photosystem IEvolution of photosynthesisAncestor of cyanobacteriaCryo-EM structureAncestral traitPhylogenetic analysisPhotosynthesis evolutionSequence levelPhotosynthesis studiesBiochemical characterizationOxygenic photosynthesisOligomeric formsPhotosynthesisCyanobacteriaCarotenoid compositionSubunit compositionGenusCyanobacteriumAncestorSubunitSequenceIsolatesEvolution
2024
Tetrameric PilZ protein stabilizes stator ring in complex flagellar motor and is required for motility in Campylobacter jejuni
Chen Y, Tachiyama S, Li Y, Feng X, Zhao H, Wu Y, Guo Y, Lara-Tejero M, Hua C, Liu J, Gao B. Tetrameric PilZ protein stabilizes stator ring in complex flagellar motor and is required for motility in Campylobacter jejuni. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 122: e2412594121. PMID: 39793078, PMCID: PMC11725899, DOI: 10.1073/pnas.2412594121.Peer-Reviewed Original ResearchConceptsFlagellar motorPilZ domain-containing proteinsBound cyclic di-GMPCyclic di-GMPC-di-GMPDomain-containing proteinsStator unitsDi-GMPFamily proteinsSuperfamily proteinsBacterial flagellaRing assemblyCellular pathwaysCampylobacter jejuniCryoelectron tomographyCampylobacter jejuni</i>.Subtomogram averagingPilZProteinFlagellaPhylumAncestorMotilityJejuniStructural components
2021
Divergent connectomic organization delineates genetic evolutionary traits in the human brain
Bueichekú E, Gonzalez-de-Echavarri J, Ortiz-Teran L, Montal V, d’Oleire Uquillas F, De Marcos L, Orwig W, Kim C, Ortiz-Teran E, Basaia S, Diez I, Sepulcre J. Divergent connectomic organization delineates genetic evolutionary traits in the human brain. Scientific Reports 2021, 11: 19692. PMID: 34608211, PMCID: PMC8490416, DOI: 10.1038/s41598-021-99082-6.Peer-Reviewed Original ResearchConceptsEvolutionary traitsHomo sapiens lineageDN/dS ratiosPositive selectionCellular functionsEvolutionary pathwaysGene expressionGenetic expressionSapiens lineageBiological dataCo-localizationDivergent pathwaysFunctional specializationTraitsBiological qualityResting-state dataPathwayHuman brain functionSimian ancestorsExpressionConnectome organizationCognitive trajectoriesAncestorLineagesBrain functionRAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination
Gan T, Wang Y, Liu Y, Schatz DG, Hu J. RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination. Cell Reports 2021, 37: 109824. PMID: 34644584, PMCID: PMC8783374, DOI: 10.1016/j.celrep.2021.109824.Peer-Reviewed Original Research
2020
The evolution of the human brain and disease susceptibility
Pattabiraman K, Muchnik SK, Sestan N. The evolution of the human brain and disease susceptibility. Current Opinion In Genetics & Development 2020, 65: 91-97. PMID: 32629339, DOI: 10.1016/j.gde.2020.05.004.Peer-Reviewed Original ResearchConceptsGene expression patternsField of evolutionDisease risk genesNervous system developmentExtant speciesGene regulationEvolutionary changeExtinct ancestorsExpression patternsGenetic studiesMetabolic processesHuman-specific aspectsRisk genesCell typesHuman biologyEvolutionary perspectiveDisease susceptibilityNeurodegenerative disease riskNeurodegenerative diseasesDifficult hypothesisComplex processGenomicsAncestorEvolutionGenes
2018
Clonal evolution analysis of paired anaplastic and well‐differentiated thyroid carcinomas reveals shared common ancestor
Dong W, Nicolson NG, Choi J, Barbieri AL, Kunstman JW, Azar S, Knight J, Bilguvar K, Mane SM, Lifton RP, Korah R, Carling T. Clonal evolution analysis of paired anaplastic and well‐differentiated thyroid carcinomas reveals shared common ancestor. Genes Chromosomes And Cancer 2018, 57: 645-652. PMID: 30136351, DOI: 10.1002/gcc.22678.Peer-Reviewed Original ResearchConceptsCommon ancestorProgression of ATCClonal evolution analysisEvolutionary lineagesGenetic relationshipsAnaplastic thyroid carcinomaClonal analysisAncestorEvolution analysisPrivate mutationsMutationsATC tumorsLineal relationshipLineagesNormal tissuesThyroid carcinomaLandscapeFollicular thyroid carcinomaPairs
2016
A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans
Houri-Ze'evi L, Korem Y, Sheftel H, Faigenbloom L, Toker I, Dagan Y, Awad L, Degani L, Alon U, Rechavi O. A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans. Cell 2016, 165: 88-99. PMID: 27015309, DOI: 10.1016/j.cell.2016.02.057.Peer-Reviewed Original ResearchConceptsAncestral responsesSmall RNAsC. elegansRNAi responseEndogenous small RNAsSilencing of genesRNA sequencing analysisRNA inheritanceHeritable silencingRNAi factorsExposure to dsRNAManipulating genesEpigenetic responsesComplementary sequencesEpigenetic effectsGenesRNAiTransgenerational effectsSilencingRNAFeedback loopInheritance mechanismDsRNAElegansAncestor
2015
Intersecting transcription networks constrain gene regulatory evolution
Sorrells T, Booth L, Tuch B, Johnson A. Intersecting transcription networks constrain gene regulatory evolution. Nature 2015, 523: 361-365. PMID: 26153861, PMCID: PMC4531262, DOI: 10.1038/nature14613.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBinding SitesDNA-Binding ProteinsDNA, FungalEnhancer Elements, GeneticEpistasis, GeneticEvolution, MolecularGene Expression Regulation, FungalGene Regulatory NetworksGenes, FungalKluyveromycesMating FactorPeptidesPheromonesPromoter Regions, GeneticSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription FactorsConceptsGene regulatory evolutionGene regulatory networksRegulatory DNARegulatory evolutionTranscription networksCommon ancestorRegulatory networksEpistatic interactionsSpecific genesSingle proteinMutation effectsSecond pathwayCandida albicansSuch interactionsSpecific changesSaccharomycesAncestorGenesEvolutionRegulatorProteinDNAMutationsPathwayInteractionHomology in the Age of Developmental Genomics
Wagner G. Homology in the Age of Developmental Genomics. 2015, 25-43. DOI: 10.1007/978-3-7091-1862-7_2.Peer-Reviewed Original ResearchModel organismsEvolutionary biologyHomology conceptRecent common ancestorDevelopmental genomicsPhylogenetic relationshipsCommon ancestorDarwinian traditionHomologySame organOrganismsSpeciesComparative anatomyDifferent animalsBiologistsBiologyFundamental roleRichard OwenImportant roleGenomicsAncestorGenesOrgansHumansRole
2014
Whole-Body Acoel Regeneration Is Controlled by Wnt and Bmp-Admp Signaling
Srivastava M, Mazza-Curll K, van Wolfswinkel J, Reddien P. Whole-Body Acoel Regeneration Is Controlled by Wnt and Bmp-Admp Signaling. Current Biology 2014, 24: 1107-1113. PMID: 24768051, DOI: 10.1016/j.cub.2014.03.042.Peer-Reviewed Original ResearchConceptsWhole-body regenerationMolecular mechanismsLast common ancestorEarly branching positionDorsal-ventral axisYears of evolutionEnigmatic phylumBilaterian evolutionMolecular resourcesUnderlying molecular mechanismsSystemic RNAiAccessible embryosCommon ancestorHofsteniaPhylogenetic analysisVentral cellsAcoelsMolecular studiesTranscriptomePhylaRNAiPlanariansAncestorBranching positionModel system
2012
High diversity and no significant selection signal of human ADH1B gene in Tibet
Lu Y, Kang L, Hu K, Wang C, Sun X, Chen F, Kidd JR, Kidd KK, Li H. High diversity and no significant selection signal of human ADH1B gene in Tibet. Investigative Genetics 2012, 3: 23. PMID: 23176670, PMCID: PMC3528464, DOI: 10.1186/2041-2223-3-23.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsSelection signalsPositive selectionSignificant positive selectionMicro-evolutionary studiesPositive selection signalsLong-range haplotypesSino-Tibetan populationsDiversification historyADH1B geneGene diversityHaplotype diversityCommon ancestorHuman genesHigh diversityTibetan populationHaplogroupsGenesPolymorphic sitesNucleotide polymorphismsSmall populationDiversityAncestorSouthwest AsiaAlleles
2008
Pyrrolysyl-tRNA synthetase–tRNAPyl structure reveals the molecular basis of orthogonality
Nozawa K, O’Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Söll D, Nureki O. Pyrrolysyl-tRNA synthetase–tRNAPyl structure reveals the molecular basis of orthogonality. Nature 2008, 457: 1163-1167. PMID: 19118381, PMCID: PMC2648862, DOI: 10.1038/nature07611.Peer-Reviewed Original ResearchConceptsAmino acidsMolecular basisLast universal common ancestorUniversal common ancestorUAG stop codonProteinogenic amino acidsCommon ancestorSuppressor tRNAStop codonDesulfitobacterium hafnienseStandard amino acidsTRNADistinct interactionsProteinPyrrolysinePylRSSelenocysteineAncestorCodonMachineryAcidVivoPairsPhylogenetic, Structural and Functional Relationships between WD- and Kelch-Repeat Proteins
Hudson AM, Cooley L. Phylogenetic, Structural and Functional Relationships between WD- and Kelch-Repeat Proteins. Subcellular Biochemistry 2008, 48: 6-19. PMID: 18925367, DOI: 10.1007/978-0-387-09595-0_2.Peer-Reviewed Original ResearchConceptsΒ-propeller proteinsKelch repeat proteinWidespread protein familyWD-repeat proteinΒ-propeller structureΒ-propeller foldΒ-propeller domainWD repeatsMolecular functionsCommon ancestorProtein familyEvolutionary advantageDiverse familySimilar functionsProteinΒ-sheetKelchStructural motifsRepeat unitsExhibit similaritiesMotifFunctional relationshipFamilySuperfamilyAncestor
2004
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms
Ka-Shu Wong G, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier L, Yang S, Warren W, Wilson R, Brandström M, Ellegren H, Crooijmans R, van der Poel J, Bovenhuis H, Groenen M, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young J, Rogers S, Walker B, van Hateren A, Kaufman J, Bumstead N, Lamont S, Zhou H, Hocking P, Morrice D, de Koning D, Law A, Bartley N, Burt D, Hunt H, Cheng H, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi M, Andersson B, Webber C, Ponting C, Overton I, Boardman P, Tang H, Hubbard S, Wilson S, Yu J, Wang J, Yang H. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 2004, 432: 717-722. PMID: 15592405, PMCID: PMC2263125, DOI: 10.1038/nature03156.Peer-Reviewed Original ResearchConceptsSingle-nucleotide polymorphismsGenetic variation mapRed jungle fowlJungle fowlWild ancestorDomesticated linesMean nucleotide diversityDomestic chicken breedsChicken breedsNucleotide diversityChicken genomeAdaptive allelesDomestic breedsVariant sitesDomestic animalsVariation mapsBreedingFowlChickenAncestorPolymorphismGenomeKilobasesAllelesDomesticationReduced fecundity is the cost of cheating in RNA virus 6
Dennehy J, Turner P. Reduced fecundity is the cost of cheating in RNA virus 6. Proceedings Of The Royal Society B 2004, 271: 2275-2282. PMID: 15539353, PMCID: PMC1691856, DOI: 10.1098/rspb.2004.2833.Peer-Reviewed Original ResearchConceptsHost fitnessTiming of reproductionRNA bacteriophage phi6Costs of cheatingLytic growth cycleSmall burst sizeDispersal stageInterference competitionLifetime fecundityIntracellular resourcesLife historyHigher fitnessEvolved virusesReduced fecunditySolo infectionsBacteriophage phi6FecundityLytic infectionGrowth cycleAncestorBurst sizeFitnessLatent periodCheatersMultiple viruses
2001
Neocortical expansion and elaboration during primate evolution: a view from neuroembryology
Rakic P, Kornack D. Neocortical expansion and elaboration during primate evolution: a view from neuroembryology. 2001, 30-56. DOI: 10.1017/cbo9780511897085.005.Peer-Reviewed Original ResearchMammalian brain evolutionMammalian lineagesMammalian ancestorEvolutionary biologyPrimate evolutionEmbryonic developmentNeocortical evolutionLiving speciesBrain evolutionCortical evolutionNeocortical expansionAnthropoid primatesCellular mechanismsComparative anatomyNeuroembryologyPresent reviewRecent advancesEvolutionLineagesAncestorHuman mental capacitiesBiologyBrain massSpeciesPossible mechanism
1999
Evolution of a HOXB6 intergenic region within the great apes and humans
Deinard A, Kidd K. Evolution of a HOXB6 intergenic region within the great apes and humans. Journal Of Human Evolution 1999, 36: 687-703. PMID: 10330333, DOI: 10.1006/jhev.1999.0298.Peer-Reviewed Original ResearchConceptsCommon ancestorGenetic variationGenetic dataIntraspecific genetic variationHomo-Pan cladeGreat apesNuclear lociGreat ape speciesMolecular evolutionIntraspecific dataPhylogenetic reconstructionIntergenic regionIntraspecific variationDNA sequencesNucleotide substitutionsGenetic polymorphismsHomo-PanPygmy chimpanzeesApe speciesCommon chimpanzeesCladeHomo sapiens sapiensAncestorGorillasLoci
1997
Glutaminyl-tRNA synthetase.
Freist W, Gauss D, Ibba M, Söll D. Glutaminyl-tRNA synthetase. Biological Chemistry 1997, 378: 1103-17. PMID: 9372179.Peer-Reviewed Original ResearchConceptsE. coli GlnRSGlutaminyl-tRNA synthetaseGlutamyl-tRNA synthetaseMammalian enzymeCommon ancestorPositive eubacteriaCognate tRNAMultienzyme complexTRNA moleculesGlnRArtificial mutantsAcceptor stemAnticodon loopMolecular massAmino acidsCatalytic siteEnzymeSynthetaseEubacteriaArchaebacteriaTRNAMutantsOrganellesAncestorComplexes
1986
Genetic variability and divergence between cave dwelling populations of Typhlocirolana from majorca and sicily
Caccone A, Allegrucci G, Cesaroni D, Sbordoni M, de Matthaeis E, La Rosa G, Sbordoni V. Genetic variability and divergence between cave dwelling populations of Typhlocirolana from majorca and sicily. Biochemical Systematics And Ecology 1986, 14: 215-221. DOI: 10.1016/0305-1978(86)90066-9.Peer-Reviewed Original ResearchGenetic distance dataSicilian populationFreshwater systemsMarine ancestorsEvolutionary historyGenetic distanceTaxonomic statusSeparate speciesGenetic variabilityGene locusTyphlocirolanaPresent distributionSpeciesSouthern Mediterranean coastElectrophoretic analysisRecent discoveryBalearic IslandsHypogean crustaceansMediterranean coastThalassoidAncestorCrustaceansDistance dataUpper MioceneSicilian samples
1985
Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs
Grosjean H, Nicoghosian K, Haumont E, Söll D, Cedergren R. Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs. Nucleic Acids Research 1985, 13: 5697-5706. PMID: 3898020, PMCID: PMC321899, DOI: 10.1093/nar/13.15.5697.Peer-Reviewed Original ResearchConceptsSerine tRNANucleotide sequenceRecent common ancestorE. coli tRNACodon-anticodon interactionStructure-function relationshipsEubacterial originUCU codonsEvolutionary analysisCommon ancestorD-loopTRNAAnticodon stemSerine familyAnticodonGenesE. coliMinor speciesCodonMajor speciesSpeciesSequenceTRNASerAncestorSerine
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