2021
Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions
Chandrasekaran S, Espeso-Gil S, Loh YE, Javidfar B, Kassim B, Zhu Y, Zhang Y, Dong Y, Bicks LK, Li H, Rajarajan P, Peter CJ, Sun D, Agullo-Pascual E, Iskhakova M, Estill M, Lesch BJ, Shen L, Jiang Y, Akbarian S. Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions. Nature Communications 2021, 12: 7243. PMID: 34903713, PMCID: PMC8669064, DOI: 10.1038/s41467-021-26862-z.Peer-Reviewed Original ResearchConceptsCellular stress response genesOpen chromatin domainsChromatin domain organizationRepeat-rich sequencesStress response genesRetrotransposon expansionsSPRET/EiJChromatin domainsChromosomal architectureChromosomal conformationDomain organizationAdult mouse cerebral cortexMurine germlineTranscriptional dysregulationResponse genesRegulatory mechanismsMus musculusMature neuronsNeuronal ablationStrong enrichmentMouse cerebral cortexSequenceSETDB1Single moleculesGermlineC. elegans discriminates colors to guide foraging
Ghosh DD, Lee D, Jin X, Horvitz HR, Nitabach MN. C. elegans discriminates colors to guide foraging. Science 2021, 371: 1059-1063. PMID: 33674494, PMCID: PMC8554940, DOI: 10.1126/science.abd3010.Peer-Reviewed Original ResearchConceptsCellular stress response genesCellular stress response pathwaysStress response genesStress response pathwaysPhotoreceptor genesDiverse phylaC. elegansForaging decisionsResponse pathwaysResponse genesForagingOpsinGenesPhotosensitive cellsNatural environmentCaenorhabditisHarmful bacteriaElegansPhylaOrganismsBacteriaPathwayRoundwormsCellsToxinEthanol production process driving changes on industrial strains
Nagamatsu ST, Coutouné N, José J, Fiamenghi MB, Pereira GAG, de Castro Oliveira J, Carazzolle MF. Ethanol production process driving changes on industrial strains. FEMS Yeast Research 2021, 21: foaa071. PMID: 33417685, DOI: 10.1093/femsyr/foaa071.Peer-Reviewed Original ResearchConceptsMain evolutionary driversEthanol production processMore robust strainsStress response genesSugarcane fermentationEthanol titerEthanol RedEthanol productionEvolutionary driversIndustrial yeastIndustrial fermentationMaltose transporterGenome adaptationEngineering strategiesPhylogenetic treeCorn fermentationPositive selectionSaccharomyces cerevisiaeMetal homeostasisIndustrial strainsResponse genesBiofuel productionRobust strainsNumber of copiesGenes
2020
Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells
Marczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells. Cancers 2020, 12: 2551. PMID: 32911681, PMCID: PMC7563413, DOI: 10.3390/cancers12092551.Peer-Reviewed Original ResearchTriple-negative breast cancer cellsCancer cellsBreast cancer cellsStress response genesMulti-omics landscapeCell population compositionDrug-induced cell deathMulti-omics investigationsCell linesBCL2 family inhibitorsSingle-cell analysisChromatin accessibilityGenome structureMDA-MB-231 triple-negative breast cancer cellsChromatin structureMethylation stateResponse genesFamily inhibitorsCell deathTNBC cell linesNumber variationsDefense mechanismsResistance mechanismsNew therapeutic strategiesGenes
2014
Global gene expression changes induced by prolonged cold ischemic stress and preservation method of breast cancer tissue
Aktas B, Sun H, Yao H, Shi W, Hubbard R, Zhang Y, Jiang T, Ononye SN, Wali VB, Pusztai L, Symmans WF, Hatzis C. Global gene expression changes induced by prolonged cold ischemic stress and preservation method of breast cancer tissue. Molecular Oncology 2014, 8: 717-727. PMID: 24602449, PMCID: PMC4048748, DOI: 10.1016/j.molonc.2014.02.002.Peer-Reviewed Original ResearchConceptsGlobal gene expression changesGlobal gene expressionGene expression changesGenomic signaturesResponse genesGene expressionSensitive transcriptsExpression changesStress response genesCell cycle regulationSignificant transcriptional changesExpression levelsCycle regulationTranscriptional changesIndividual probe setsInduced transcriptsAffected transcriptsProtein processingEnrichment analysis
2006
The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica
Tu X, Latifi T, Bougdour A, Gottesman S, Groisman EA. The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 13503-13508. PMID: 16938894, PMCID: PMC1557385, DOI: 10.1073/pnas.0606026103.Peer-Reviewed Original ResearchConceptsSigma factor RpoSPhoP/PhoQTwo-component systemAlternative sigma factor RpoSTwo-component regulatory system PhoP/PhoQPhoP/PhoQ.Stress response genesSalmonella enterica serovar TyphimuriumRpoS stabilityClpXP proteaseTranscriptional activatorEnterica serovar TyphimuriumRegulatory circuitsRpoS mutantResponse genesRegulatory proteinsProtein turnoverRpoSBacterial speciesEscherichia coliPhoP geneGenesSerovar TyphimuriumE. coliPhoQ
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