2024
Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi
Liu T, Pyle A. Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi. Journal Of Molecular Biology 2024, 436: 168513. PMID: 38447889, DOI: 10.1016/j.jmb.2024.168513.Peer-Reviewed Original ResearchGroup I intronsAntifungal drug targetsRNA metabolismPathogenic fungiPhylogeny of fungiSelf-splicing intronsDrug targetsSystemic fungal infectionsGenetic hotspotsRiboregulatory elementsMitochondrial intronsMitochondrial genesBioinformatics pipelineC. aurisCandida aurisRelevant fungiRNA elementsAspergillus fumigatusC. albicansHousekeeping genesCandida albicansNoncoding transcriptomeCryptococcus neoformansFungal infectionsFungi
2021
Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy
Woodworth M, Ng K, Halpern A, Pease N, Nguyen P, Kueh H, Vaughan J. Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy. Nucleic Acids Research 2021, 49: e82-e82. PMID: 34048564, PMCID: PMC8373070, DOI: 10.1093/nar/gkab423.Peer-Reviewed Original ResearchConceptsHistone modificationsGenomic lociChromatin stateNon-repetitive genomic regionsRegulation of genome architectureRNA polymerase II loadingFunction of multicellular organismsMultiple histone modificationsDevelopmentally-regulated genesHistone modification levelsPopulation-averaged measurementsExpansion microscopySingle cellsGenome architectureGenomic regionsHistone marksMulticellular organismsIndividual lociEpigenetic stateHousekeeping genesGene locusLociHistoneModification levelsGenes
2017
BET N-terminal bromodomain inhibition selectively blocks Th17 cell differentiation and ameliorates colitis in mice
Cheung K, Lu G, Sharma R, Vincek A, Zhang R, Plotnikov A, Zhang F, Zhang Q, Ju Y, Hu Y, Zhao L, Han X, Meslamani J, Xu F, Jaganathan A, Shen T, Zhu H, Rusinova E, Zeng L, Zhou J, Yang J, Peng L, Ohlmeyer M, Walsh M, Zhang D, Xiong H, Zhou M. BET N-terminal bromodomain inhibition selectively blocks Th17 cell differentiation and ameliorates colitis in mice. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: 2952-2957. PMID: 28265070, PMCID: PMC5358349, DOI: 10.1073/pnas.1615601114.Peer-Reviewed Original ResearchConceptsBET proteinsActive RNA polymerase IITh17 cell differentiationProteins regulate gene transcriptionRecruitment of P-TEFbAcetyl-lysine bindingRNA polymerase IICell differentiationInflammatory disordersMature T helper cellsNaive CD4<sup>+</sup> T cellsCD4<sup>+</sup> T cellsDifferentiation of naive CD4<sup>+</sup> T cellsBlocking Th17-cell differentiationEpigenetic drug targetsT-cell transfer-induced colitisBromodomains of BET proteinsPolymerase IITreatment of inflammatory bowel diseaseT helper cellsTranscription elongationT helper 17Housekeeping genesGene locusDifferentiation of Th17
2012
Identification of condition‐specific reference genes from microarray data for locusts exposed to hypobaric hypoxia
Zhao DJ, Guo K, Kang L. Identification of condition‐specific reference genes from microarray data for locusts exposed to hypobaric hypoxia. FEBS Open Bio 2012, 2: 235-240. PMID: 23650605, PMCID: PMC3642161, DOI: 10.1016/j.fob.2012.08.001.Peer-Reviewed Original ResearchGene expression stabilityReference genesHousekeeping genesExpression stabilityGene expressionNovel candidate reference genesMicroarray dataQuantitative polymerase chain reactionLarge-scale gene expression dataClassical housekeeping genesCandidate reference genesReliable reference genesGene expression dataGenes 18STranscriptional responseStable genesExpression dataGenesΒ-actinReal-time quantitative polymerase chain reactionLocust muscleGeNormNormFinderExpressionPolymerase chain reaction
2010
Multilocus sequence analysis of Borrelia bissettii strains from North America reveals a new Borrelia species, Borrelia kurtenbachii
Margos G, Hojgaard A, Lane R, Cornet M, Fingerle V, Rudenko N, Ogden N, Aanensen D, Fish D, Piesman J. Multilocus sequence analysis of Borrelia bissettii strains from North America reveals a new Borrelia species, Borrelia kurtenbachii. Ticks And Tick-borne Diseases 2010, 1: 151-158. PMID: 21157575, PMCID: PMC3000690, DOI: 10.1016/j.ttbdis.2010.09.002.Peer-Reviewed Original ResearchConceptsMultilocus sequence analysisSequence analysisGenetic distance analysisNew Borrelia speciesBorrelia speciesDifferent transmission cyclesBorrelia bissettiiB. bissettiiLinear chromosomesPhylogenetic relationshipsEcological differencesConcatenated sequencesPhylogenetic analysisHousekeeping genesVector associationNorth AmericaInternal fragmentDistance analysisBorrelia genospeciesB. carolinensisReservoir hostsTransmission cycleI. spinipalpisIxodes pacificusRelated clusters
2009
Phylogeography of Borrelia burgdorferi in the eastern United States reflects multiple independent Lyme disease emergence events
Hoen AG, Margos G, Bent SJ, Diuk-Wasser MA, Barbour A, Kurtenbach K, Fish D. Phylogeography of Borrelia burgdorferi in the eastern United States reflects multiple independent Lyme disease emergence events. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 15013-15018. PMID: 19706476, PMCID: PMC2727481, DOI: 10.1073/pnas.0903810106.Peer-Reviewed Original ResearchConceptsB. burgdorferi populationsPhylogeographic population structurePopulation size expansionBacterial housekeeping geneDisease emergence eventsPopulation structureRange expansionHousekeeping genesB. burgdorferiDescendent clonesEuropean settlementEmergence eventsEastern United StatesSize expansionCoastal ConnecticutTick vectorGeographic extent
2008
MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi
Margos G, Gatewood A, Aanensen D, Hanincová K, Terekhova D, Vollmer S, Cornet M, Piesman J, Donaghy M, Bormane A, Hurn M, Feil E, Fish D, Casjens S, Wormser G, Schwartz I, Kurtenbach K. MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 8730-8735. PMID: 18574151, PMCID: PMC2435589, DOI: 10.1073/pnas.0800323105.Peer-Reviewed Original ResearchConceptsHousekeeping genesIntergenic spacerPopulation structureGeographic population structureChromosomal housekeeping genesMultilocus sequence typing (MLST) schemeB. burgdorferiPhylogenetic signalNorth AmericaEvolutionary relationshipsSequence typing schemeEvolutionary trajectoriesIGS locusSequence dataMLST schemeCultured isolatesGenesBorrelia burgdorferiOuter surface protein CMLST dataDistinct populationsSurface protein CBacterium Borrelia burgdorferiEuropean populationsVector-borne diseases
1999
Pathogenicity Islands and the Evolution of Salmonella Virulence
Groisman E, Blanc‐Potard A, Uchiya K. Pathogenicity Islands and the Evolution of Salmonella Virulence. 1999, 127-150. DOI: 10.1128/9781555818173.ch7.Peer-Reviewed Original ResearchSPI-1 genesPathogenicity islandDNA segmentsSPI-1Evolution of SalmonellaCultured epithelial cellsSalmonella-specific sequenceTRNA genesExport apparatusTranscriptional unitsLarge operonNonhost environmentsSecretion systemBacterial entryHousekeeping genesSalmonella virulenceHost rangeSPI-2Secretory systemHost cellsAspects of infectionNonphagocytic cellsGenesMacrophage apoptosisOperon
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