2024
Environmental fungi target thiol homeostasis to compete with Mycobacterium tuberculosis
Malhotra N, Oh S, Finin P, Medrano J, Andrews J, Goodwin M, Markowitz T, Lack J, Boshoff H, Barry C. Environmental fungi target thiol homeostasis to compete with Mycobacterium tuberculosis. PLOS Biology 2024, 22: e3002852. PMID: 39625876, PMCID: PMC11614215, DOI: 10.1371/journal.pbio.3002852.Peer-Reviewed Original ResearchConceptsBiosynthetic gene clusterGene clusterWhole-genome sequencingSphagnum peat bogsCollection of FungiMycobacterium tuberculosisGenome sequenceThiol stressMycobacterial speciesMtb cellsSphagnum bogFungiA productionCo-CultureInduced expressionThiol homeostasisRNAseqMtbPeat bogsSphagnumBogNatural productsMycothiolGenesVulnerable targets
2023
OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases
Sturm G, Karan K, Monzel A, Santhanam B, Taivassalo T, Bris C, Ware S, Cross M, Towheed A, Higgins-Chen A, McManus M, Cardenas A, Lin J, Epel E, Rahman S, Vissing J, Grassi B, Levine M, Horvath S, Haller R, Lenaers G, Wallace D, St-Onge M, Tavazoie S, Procaccio V, Kaufman B, Seifert E, Hirano M, Picard M. OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases. Communications Biology 2023, 6: 22. PMID: 36635485, PMCID: PMC9837150, DOI: 10.1038/s42003-022-04303-x.Peer-Reviewed Original ResearchConceptsIntegrated stress responseOXPHOS defectsMitochondrial diseaseCellular energy expenditureMitochondrial DNA instabilityPatient-derived fibroblastsMitochondrial oxidative phosphorylationCell divisionExtracellular secretionOxidative phosphorylationStress responseDNA instabilityMechanistic basisEnergetic costEpigenetic agingGeneral mechanismOXPHOSBiological agingExcess energy expenditurePotential mechanismsEnergy expenditureCellsMulti-system disorderMetabokinesRNAseq
2022
B.3 Activated gene pathways in post-infectious hydrocephalus (PIH):: proteogenomics and the PIH expressome
Isaacs A, Morton S, Movassagh M, Zhang Q, Hehnly C, Zhang L, Morales D, Townsend R, Limbrick D, Paulson J, Schiff S. B.3 Activated gene pathways in post-infectious hydrocephalus (PIH):: proteogenomics and the PIH expressome. Canadian Journal Of Neurological Sciences / Journal Canadien Des Sciences Neurologiques 2022, 49: s5-s5. DOI: 10.1017/cjn.2022.98.Peer-Reviewed Original ResearchProteins/genesGene pathwaysDifferential expressionIntegration of proteomicsGene networksOxidative stressGene setsProteogenomicsMolecular mechanismsPaenibacillus sppMolecular identificationPost-infectious hydrocephalusGenesDNA sequencingNovel insightsPathogenetic bacteriaProteomicsRNAseqViral pathogensPathwayHost responseExpressionExpressomeCerebrospinal fluidImmune systemNeural Stem Cells in Adult Mammals are not Astrocytes
Velloso F, Shankar S, Parpura V, Rakic P, Levison S. Neural Stem Cells in Adult Mammals are not Astrocytes. ASN Neuro 2022, 14: 17590914221134739. PMID: 36330653, PMCID: PMC9638700, DOI: 10.1177/17590914221134739.Peer-Reviewed Original ResearchConceptsAdult mammalian subventricular zoneNeural stem cellsMammalian subventricular zoneMammalian neural stem cellsComparative transcriptomic analysisDistinct gene expression profilesStem cellsAdult mammalian neural stem cellsGene expression profilesSingle-cell RNAseqFunction of NSCsMurine neural stem cellsSubventricular zoneTranscriptomic analysisExpression profilesAdult murine neural stem cellsCell sortingAdult mammalsFunction of astrocytesCellsNew neuronsSubtypes of astrocytesMammalsRNAseqNiche
2021
C.3 Activated Gene Pathways in Post-Infectious Hydrocephalus (PIH): Proteogenomics and the PIH Expressome
Isaacs A, Morton S, Movassagh M, Zhang Q, Hehnly C, Zhang L, Morales D, Townsend R, Limbrick D, Paulson J, Schiff S. C.3 Activated Gene Pathways in Post-Infectious Hydrocephalus (PIH): Proteogenomics and the PIH Expressome. Canadian Journal Of Neurological Sciences / Journal Canadien Des Sciences Neurologiques 2021, 48: s18-s19. DOI: 10.1017/cjn.2021.279.Peer-Reviewed Original ResearchProteins/genesGene pathwaysDifferential expressionIntegration of proteomicsGene networksOxidative stressGene setsProteogenomicsMolecular mechanismsPaenibacillus sppMolecular identificationPost-infectious hydrocephalusGenesDNA sequencingNovel insightsPathogenetic bacteriaProteomicsRNAseqViral pathogensPathwayHost responseExpressionExpressomeCerebrospinal fluidImmune systemImproved methods for RNAseq-based alternative splicing analysis
Halperin RF, Hegde A, Lang JD, Raupach EA, Legendre C, Liang W, LoRusso P, Sekulic A, Sosman J, Trent J, Rangasamy S, Pirrotte P, Schork N. Improved methods for RNAseq-based alternative splicing analysis. Scientific Reports 2021, 11: 10740. PMID: 34031440, PMCID: PMC8144374, DOI: 10.1038/s41598-021-89938-2.Peer-Reviewed Original ResearchConceptsProtein-level effectsSplicing analysisSplice eventsSplice isoformsRNAseq dataAlternative splicing analysisTissue-specific splice variantsDifferential splicing analysisGene expression levelsPathogenic splicing variantProtein level expressionSequence readsSplicing variantsSplice variantsOncogenic mutationsMass spectrometry dataSplice alterationsExpression levelsRNAseqIsoformsMelanoma datasetSpectrometry dataNovel statistical approachAnalysis resourcesMass spectrometry
2017
Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq)
Abdul-Rahman F, Gresham D. Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq). Methods In Molecular Biology 2017, 1720: 15-24. PMID: 29236248, DOI: 10.1007/978-1-4939-7540-2_2.Peer-Reviewed Original ResearchConceptsNewly transcribed RNAPopulation of RNAsMRNA decay ratesRNA spike-insRNA degradation ratesStreptavidin magnetic beadsBiotinylated RNARNA speciesUnlabeled RNARNAseq librariesSynthesized RNASpike-insRNA approachBiotinylated moleculesRNAReactive thiol groupsCultures of cellsMagnetic beadsDegradation rateDegradation rate constantLabeled populationThiol groupsTranscriptionRNAseqMultiple time points
2012
Effector CD4+ T Cell Expression Signatures and Immune-Mediated Disease Associated Genes
Zhang W, Ferguson J, Ng SM, Hui K, Goh G, Lin A, Esplugues E, Flavell RA, Abraham C, Zhao H, Cho JH. Effector CD4+ T Cell Expression Signatures and Immune-Mediated Disease Associated Genes. PLOS ONE 2012, 7: e38510. PMID: 22715389, PMCID: PMC3371029, DOI: 10.1371/journal.pone.0038510.Peer-Reviewed Original ResearchConceptsDifferential gene expressionGenome-wide association studiesGene expressionCell differentiationDisease locusT cell differentiationExpression signaturesDifferential regulation patternsDisease association signalsDisease-associated genesPromoter methylation studiesGenomic lociTransmembrane domainRegulation patternsFunctional pathwaysAssociation studiesMethylation studiesAssociated geneAbundant isoformGenesLociMolecular resolutionPromoter methylationRNAseqCritical role
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