2024
Comparative single-cell multiome identifies evolutionary changes in neural progenitor cells during primate brain development
Liu Y, Luo X, Sun Y, Chen K, Hu T, You B, Xu J, Zhang F, Cheng Q, Meng X, Yan T, Li X, Qi X, He X, Guo X, Li C, Su B. Comparative single-cell multiome identifies evolutionary changes in neural progenitor cells during primate brain development. Developmental Cell 2024, 60: 414-428.e8. PMID: 39481377, DOI: 10.1016/j.devcel.2024.10.005.Peer-Reviewed Original ResearchEvolutionary changesDistal regulatory elementsGene regulatory mechanismsExtracellular matrixSingle-cell multiomicsProgenitor cellsTranscriptional divergenceEvolutionary divergenceChromatin regionsChromatin accessibilityNeural progenitorsRegulatory elementsSequence changesTranscriptional rewiringGenetic mechanismsMouse prefrontal cortexRegulatory mechanismsPrefrontal cortexHuman neural progenitorsHuman-specific featuresUpper-layer neuronsNeural progenitor cellsChromatinCellular propertiesProgenitor proliferationCpG island turnover events predict evolutionary changes in enhancer activity
Kocher A, Dutrow E, Uebbing S, Yim K, Rosales Larios M, Baumgartner M, Nottoli T, Noonan J. CpG island turnover events predict evolutionary changes in enhancer activity. Genome Biology 2024, 25: 156. PMID: 38872220, PMCID: PMC11170920, DOI: 10.1186/s13059-024-03300-z.Peer-Reviewed Original ResearchConceptsHuman-gained enhancersCpG islandsFunction of transcriptional enhancersEvolution of biological diversityHuman CpG islandsGene regulatory changesInfluence enhancer activityCpG island contentHistone modification levelsEnhanced activitySpecies-specific activityTrait evolutionNucleotide substitutionsHistone modificationsTranscriptional enhancersMouse orthologEvolutionary changesTurnover eventsModification levelsMammalian speciesMultiple tissuesEmbryonic developmentMouse diencephalonHuman embryonic developmentSpeciesDo domain-specific protein language models outperform general models on immunology-related tasks?
Deutschmann N, Pelissier A, Weber A, Gao S, Bogojeska J, Martínez M. Do domain-specific protein language models outperform general models on immunology-related tasks? ImmunoInformatics 2024, 14: 100036. DOI: 10.1016/j.immuno.2024.100036.Peer-Reviewed Original ResearchProtein language modelsDevelopment of bioinformatics pipelinesAmino acid sequenceAntigen recognition capabilitiesBioinformatics pipelineAcid sequenceProtein functionDomain-specific modelsEvolutionary changesB cell receptorAdaptive immune system responsesImmune receptorsT cell receptorB cellsT cellsImmune system responseDownstream analytical tasksVector embeddingsRepresentation capabilityLanguage modelImmune responseEmbedding layerReceptorsAnalytical tasksToxoplasma gondii actin filaments are tuned for rapid disassembly and turnover
Hvorecny K, Sladewski T, De La Cruz E, Kollman J, Heaslip A. Toxoplasma gondii actin filaments are tuned for rapid disassembly and turnover. Nature Communications 2024, 15: 1840. PMID: 38418447, PMCID: PMC10902351, DOI: 10.1038/s41467-024-46111-3.Peer-Reviewed Original ResearchConceptsActin filamentsDynamic properties of actin filamentsProperties of actin filamentsCytoskeletal protein actinFilamentous actin networkSkeletal muscle actinCryo-EM structureIn vitro assemblyOrganelle inheritanceD-loopActin networkNucleotide exchangeLive cell imagingProteins actinSkeletal actinConserved structureEvolutionary changesActinApicomplexan parasitesAssembly contactsIntracellular parasitesMonomer dissociationApicomplexanFilamentsBiophysical properties
2020
The Epidemiological Signature of Pathogen Populations That Vary in the Relationship between Free-Living Parasite Survival and Virulence
Gomez L, Meszaros V, Turner W, Ogbunugafor C. The Epidemiological Signature of Pathogen Populations That Vary in the Relationship between Free-Living Parasite Survival and Virulence. Viruses 2020, 12: 1055. PMID: 32971954, PMCID: PMC7551987, DOI: 10.3390/v12091055.Peer-Reviewed Original ResearchConceptsFree-living survivalEvolution of virulenceParasite survivalEcology of infectious diseasesConsequences of variationPathogen populationsPillar of evolutionary theoryHost-parasite systemsInfluence several aspectsVirulenceEvolutionary changesParasite virulenceEpidemiological scaleDisease dynamicsEvolutionary theory
2017
Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine‐mapped region
López J, Lanno S, Auerbach J, Moskowitz E, Sligar L, Wittkopp P, Coolon J. Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine‐mapped region. Molecular Ecology 2017, 26: 1148-1160. PMID: 28035709, PMCID: PMC5330365, DOI: 10.1111/mec.14001.Peer-Reviewed Original ResearchConceptsD. sechelliaOA resistanceDrosophila sechelliaRNA interferenceGenetic basisEvolutionary changesTissue-specific RNA interferenceFine-mapped regionKnock down expressionGene expression analysisD. simulansSister speciesChromosome 3RGenomic regionsD. melanogasterDefence compoundsLevel of expressionToxic fruitsFat bodySpecies of fruit fliesEnvironmental plasticityGenesSeychelles IslandsFruit flyFunctional analysis
2016
An Ecological Assessment of the Pandemic Threat of Zika Virus
Carlson C, Dougherty E, Getz W. An Ecological Assessment of the Pandemic Threat of Zika Virus. PLOS Neglected Tropical Diseases 2016, 10: e0004968. PMID: 27564232, PMCID: PMC5001720, DOI: 10.1371/journal.pntd.0004968.Peer-Reviewed Original ResearchConceptsEcological niche modelsSignificant evolutionary changeEcological nichesNiche modelsGenetic shiftNative rangeSeasonality of precipitationEvolutionary changesDiurnal temperature fluctuationsEcological assessmentOccurrence datasetNorthward expansionDistribution of dengue feverHuman healthPotential establishmentClimate changeSevere threatVector speciesZika virusOutbreak of Zika virusPathogensClimatic eventsOutbreak of casesNicheNorth America
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