2022
Internode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids
Yanagui K, Camargo ELO, Abreu LGF, Nagamatsu ST, Fiamenghi MB, Silva NV, Carazzolle MF, Nascimento LC, Franco SF, Bressiani JA, Mieczkowski PA, Grassi MCB, Pereira GAG. Internode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids. Gene 2022, 828: 146476. PMID: 35413393, DOI: 10.1016/j.gene.2022.146476.Peer-Reviewed Original ResearchConceptsInternode elongationSaccharum hybridsSecondary cell wall formationDetailed transcriptome analysisCell wall formationDevelopment of plantsMolecular regulatory mechanismsEnergy caneRNA-seq analysisGrowth-related genesDifferent biological processesGene expression analysisCell wall characterizationDivision zoneTranscriptional regulationUnique genesCellulose synthesisTranscriptome analysisHigh biomass productionKey genesCell divisionWall formationBreeding programsBiomass biosynthesisExpression analysis
2021
Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue
Liu M, Yang B, Hu M, Radda JSD, Chen Y, Jin S, Cheng Y, Wang S. Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. Nature Protocols 2021, 16: 2667-2697. PMID: 33903756, PMCID: PMC9007104, DOI: 10.1038/s41596-021-00518-0.Peer-Reviewed Original ResearchConceptsSame single cellNucleome architecturesGene expressionMammalian tissuesChromatin foldingNuclear laminaSingle cellsNumerous RNA speciesDifferent biological processesSingle mammalian cellsDifferent cell typesMultiplexed imagingGenomic organizationGenomic architectureChromatin loopsGenomic regionsRNA speciesIndividual chromosomesMammalian cellsGenomic techniquesBiological processesDetailed protocolCopy numberCell typesNormal development
2012
Quantitative proteomic analysis of induced pluripotent stem cells derived from a human Huntington's disease patient
Chae JI, Kim DW, Lee N, Jeon YJ, Jeon I, Kwon J, Kim J, Soh Y, Lee DS, Seo KS, Choi NJ, Park BC, Kang SH, Ryu J, Oh SH, Shin DA, Lee DR, Tae J, Park IH, Daley GQ, Song J. Quantitative proteomic analysis of induced pluripotent stem cells derived from a human Huntington's disease patient. Biochemical Journal 2012, 446: 359-371. PMID: 22694310, DOI: 10.1042/bj20111495.Peer-Reviewed Original ResearchConceptsHD-iPSCsProteomic analysisCellular disease-modelling systemsHD-iPSCComparative proteomic analysisQuantitative proteomic analysisStress-related proteinsDifferent biological processesP53-mediated apoptotic pathwayInduced pluripotent stem cellsOxidative stress-related proteinsExpression of cytoskeletonPluripotent stem cellsDisease model systemsOxidative stressPrx familyProteomic profilesUndifferentiated stageBiological processesApoptotic pathwayNeuronal differentiationCell deathNeurodegenerative genetic disorderNeurodegeneration mechanismsProtein
2010
Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response
Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M. Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response. PLOS Genetics 2010, 6: e1000848. PMID: 20174564, PMCID: PMC2824807, DOI: 10.1371/journal.pgen.1000848.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesCaenorhabditis elegansCaenorhabditis elegans ProteinsChromatin ImmunoprecipitationEmbryo, NonmammalianEnvironmentGene Expression Regulation, DevelopmentalGenes, HelminthGenome, HelminthGreen Fluorescent ProteinsLarvaProtein BindingRecombinant Fusion ProteinsRNA Polymerase IIStarvationSurvival AnalysisTrans-ActivatorsTranscription FactorsConceptsTranscription factorsPHA-4PHA-4/FOXADiverse biological rolesDifferent biological processesBinding sitesWide IdentificationStarvation responseCellular processesChromatin immunoprecipitationRegulatory networksOrgan developmentDistinct functionsDeep sequencingBiological roleBiological processesEmbryonic pharynxEnvironmental responsesGlobal identificationEnvironmental stimuliDistinct rolesExperimental pipelineCaenorhabditisGenesCritical role
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