2025
Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review
Lan Y, Rancu I, Chitwood M, Sobkowiak B, Nyhan K, Lin H, Wu C, Mathema B, Brown T, Colijn C, Warren J, Cohen T. Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review. The Lancet Microbe 2025, 101094. PMID: 40228509, DOI: 10.1016/j.lanmic.2025.101094.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsGenome sequencing approachGenetic similarityGenomic dataSequencing approachGenotyping methodsPathogen geneticsGenetic methodsPathogen sequencesSampling completenessTuberculosis isolatesTransmission patternsTuberculosis casesPathogensTuberculosis transmissionM tuberculosis isolatesInfection-related mortalityEnvironmental factorsTuberculosis transmission dynamicsSpatial proximityTransmission clustersGenomeSpatial patternsTuberculosisTransmission dynamicsGenetics
2023
Genetic Overlap of Spontaneous Dissection of Either the Thoracic Aorta or the Coronary Arteries
Jeoffrey S, Kalyanasundaram A, Zafar M, Ziganshin B, Elefteriades J. Genetic Overlap of Spontaneous Dissection of Either the Thoracic Aorta or the Coronary Arteries. The American Journal Of Cardiology 2023, 205: 69-74. PMID: 37591066, DOI: 10.1016/j.amjcard.2023.07.046.Peer-Reviewed Original ResearchConceptsCorresponding molecular pathwaysSpontaneous coronary artery dissectionGenetic overlapMolecular pathwaysGenome-wide association studiesGenetic commonalityGenetic variantsThoracic aortic dissectionIndependent genesGenetic pathwaysSmooth muscle cell functionGenetic methodsAortic dissectionMuscle cell functionAssociation studiesGenetic studiesSudden deathConnective tissue genesGenesTGFβ pathwayCausative genesCoronary artery dissectionTissue genesEarly-onset myocardial infarctionBiologic processes
2021
Cas9-expressing chickens and pigs as resources for genome editing in livestock
Rieblinger B, Sid H, Duda D, Bozoglu T, Klinger R, Schlickenrieder A, Lengyel K, Flisikowski K, Flisikowska T, Simm N, Grodziecki A, Perleberg C, Bähr A, Carrier L, Kurome M, Zakhartchenko V, Kessler B, Wolf E, Kettler L, Luksch H, Hagag I, Wise D, Kaufman J, Kaufer B, Kupatt C, Schnieke A, Schusser B. Cas9-expressing chickens and pigs as resources for genome editing in livestock. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2022562118. PMID: 33658378, PMCID: PMC7958376, DOI: 10.1073/pnas.2022562118.Peer-Reviewed Original ResearchConceptsCross-species comparisonsGenome editingMolecular basis of healthFunction of Cas9Phylogenetically distant speciesTargeted gene disruptionGeneration of transgenic chickensIn vivo genome editingDistant speciesReverse geneticsDNA fragmentationGene disruptionGenetic methodsTarget genesMolecular basisCRISPR-Cas9Transgenic chickensCas9Cell typesSpeciesTranslational biomedical researchGeneticsChickenBases of healthPigs
2019
The cytoplasmic domain of MxiG interacts with MxiK and directs assembly of the sorting platform in the Shigella type III secretion system
Tachiyama S, Chang Y, Muthuramalingam M, Hu B, Barta ML, Picking WL, Liu J, Picking WD. The cytoplasmic domain of MxiG interacts with MxiK and directs assembly of the sorting platform in the Shigella type III secretion system. Journal Of Biological Chemistry 2019, 294: 19184-19196. PMID: 31699894, PMCID: PMC6916477, DOI: 10.1074/jbc.ra119.009125.Peer-Reviewed Original ResearchConceptsInner membrane ringType III secretion systemCytoplasmic domainSecretion systemCytoplasmic sorting platformForkhead-associated (FHA) domainShigella type III secretion systemDiverse bacterial pathogensDisruption of interactionsSpa47 ATPaseStructure-function relationshipsExtracellular needleEffector recognitionGram-negative bacteriaEukaryotic cellsT3SS apparatusVirulence effectorsMembrane ringSorting platformInsertional mutagenesisGenetic methodsHomologous interactionsMxiKTip complexBasal bodies
2013
Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection
Renzette N, Gibson L, Bhattacharjee B, Fisher D, Schleiss M, Jensen J, Kowalik T. Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection. PLOS Genetics 2013, 9: e1003735. PMID: 24086142, PMCID: PMC3784496, DOI: 10.1371/journal.pgen.1003735.Peer-Reviewed Original ResearchConceptsPositive selectionCongenital HCMV infectionApplication of population genetic methodsHuman cytomegalovirus evolutionViral populationsPopulation genetic methodsPopulation genetic approachesHuman cytomegalovirusModels of demographyOpen reading frameHCMV populationsHCMV infectionPatterns of variationUnrelated hostsReading frameGenome populationsWeeks gestational ageGenetic approachesGenetic methodsDNA virusesHuman hostPervasive driverHost environmentCompartmental variablesViral evolution
2011
A cell‐based screen for inhibitors of flagella‐driven motility in Chlamydomonas reveals a novel modulator of ciliary length and retrograde actin flow
Engel BD, Ishikawa H, Feldman JL, Wilson CW, Chuang P, Snedecor J, Williams J, Sun Z, Marshall WF. A cell‐based screen for inhibitors of flagella‐driven motility in Chlamydomonas reveals a novel modulator of ciliary length and retrograde actin flow. Cytoskeleton 2011, 68: 188-203. PMID: 21360831, DOI: 10.1002/cm.20504.Peer-Reviewed Original ResearchConceptsRetrograde actin flowActin flowUnicellular green alga Chlamydomonas reinhardtiiGreen alga Chlamydomonas reinhardtiiFlagella-driven motilityDrosophila S2 cellsAlga Chlamydomonas reinhardtiiTraditional genetic methodsChemical biology toolkitCell-based screenHuman disease symptomsLength of ciliaCiliary assemblyFlagellar paralysisS2 cellsIntraflagellar transportGenetic toolsFlagellar shorteningChlamydomonas reinhardtiiMammalian cellsSensory organellesGenetic methodsCiliary lengthCiliary defectsNovel modulator
2003
Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase
Laptenko O, Lee J, Lomakin I, Borukhov S. Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. The EMBO Journal 2003, 22: 6322-6334. PMID: 14633991, PMCID: PMC291851, DOI: 10.1093/emboj/cdg610.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCatalysisCross-Linking ReagentsDNA-Directed RNA PolymerasesEndoribonucleasesEscherichia coliEscherichia coli ProteinsHydroxyl RadicalModels, MolecularMolecular Sequence DataProtein ConformationProtein SubunitsSequence AlignmentSequence Homology, Amino AcidTranscription FactorsTranscription, GeneticTranscriptional Elongation FactorsConceptsN-terminal coiled-coil domainRNA polymeraseTranscription elongation factors GreANucleolytic activityRNAP secondary channelFirst transcription factorRNA hydrolysisRNAP catalytic centerCoiled-coil domainMolecular genetic methodsTerminal globular domainTranscription elongationTranscriptional pausingTranscription initiationTranscription factorsGenetic methodsKey residuesBiological roleGlobular domainCatalytic componentCatalytic centerGreAPolymeraseCatalytic actSecondary channel
2001
Identification of the transmembrane dimer interface of the bovine papillomavirus E5 protein
Mattoon D, Gupta K, Doyon J, Loll P, DiMaio D. Identification of the transmembrane dimer interface of the bovine papillomavirus E5 protein. Oncogene 2001, 20: 3824-3834. PMID: 11439346, DOI: 10.1038/sj.onc.1204523.Peer-Reviewed Original ResearchConceptsBovine papillomavirus E5 proteinE5 proteinDimer interfacePlatelet-derived growth factor β receptorEssential glutamine residueHeterologous dimerization domainGrowth factor β receptorNon-productive interactionsReceptor tyrosine phosphorylationFocus formation assayPDGF β-receptorDimerization domainHomodimeric proteinTyrosine phosphorylationGenetic methodsGlutamine residuesActive chimerasΒ receptorActive orientationFormation assaysProtein helicesProteinPosition 17ReceptorsPhosphorylation
1997
A genetic system to identify DNA polymerase β mutator mutants
Washington S, Yoon M, Chagovetz A, Li S, Clairmont C, Preston B, Eckert K, Sweasy J. A genetic system to identify DNA polymerase β mutator mutants. Proceedings Of The National Academy Of Sciences Of The United States Of America 1997, 94: 1321-1326. PMID: 9037051, PMCID: PMC19789, DOI: 10.1073/pnas.94.4.1321.Peer-Reviewed Original ResearchConceptsMutator mutantsGenetic methodsPol betaDNA synthesisAccurate DNA synthesisDNA repair processesRat pol betaWild-type pol betaEscherichia coli DNA polymerase ISpontaneous mutation frequencyDNA polymerase IAltered fidelityDNA polymerase betaMutant proteinsDNA replicationGenetic systemMammalian cellsGenetic assaysPolymerase IMutantsDNA polymerase mutantsMutator activityPolymerase mutantsBeta enzymePolymerase beta
1996
Nucleotide polymorphism, effective population size, and dispersal distances in the yellow baboons (Papio hamadryas cynocephalus) of Mikumi National Park, Tanzania
Rogers J, Kidd K. Nucleotide polymorphism, effective population size, and dispersal distances in the yellow baboons (Papio hamadryas cynocephalus) of Mikumi National Park, Tanzania. American Journal Of Primatology 1996, 38: 157-168. PMID: 31918472, DOI: 10.1002/(sici)1098-2345(1996)38:2<157::aid-ajp4>3.0.co;2-y.Peer-Reviewed Original ResearchGenetic variabilityDNA polymorphismsInbreeding effective population sizeEffective population sizeDNA sequence dataMale dispersal distancesNuclear DNA polymorphismsNucleotide heterozygosityNatural populationsRestriction fragment length polymorphismMikumi National ParkDispersal distanceWright's isolationPopulation structureSequence dataAutosomal lociGenetic methodsFragment length polymorphismPopulation dynamicsPopulation sizeNational ParkSouthern blottingLength polymorphismHuman populationYellow baboons
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