2024
Combining short- and long-read sequencing unveils geographically structured diversity in Borrelia miyamotoi
Hoornstra D, Kuleshov K, Fingerle V, Hepner S, Wagemakers A, Strube C, Castillo-Ramírez S, Bockenstedt L, Telford S, Sprong H, Platonov A, Margos G, Hovius J. Combining short- and long-read sequencing unveils geographically structured diversity in Borrelia miyamotoi. IScience 2024, 27: 110616. PMID: 39262806, PMCID: PMC11388275, DOI: 10.1016/j.isci.2024.110616.Peer-Reviewed Original ResearchComparative whole-genome sequencingCombination of IlluminaLong-read sequencingGenetically distinct populationsGenome assemblyPacBio platformPlasmid typesCore plasmidHuman pathogensGenetic basisDistinct populationsExpression sitesPlasmidGeographical originIxodes speciesGenomeIsolatesTick-borne human pathogenVector competenceStructural diversityNorth AmericaBorrelia miyamotoiPacBioIlluminaVirulenceThe RRE-REV module has no effect on the packaging efficiency of cas9 and Gag proteins into nanomedic virus-like particles
Kruglova N, Komkov D, Mazurov D, Shepelev M. The RRE-REV module has no effect on the packaging efficiency of cas9 and Gag proteins into nanomedic virus-like particles. Доклады Российской Академии Наук Науки О Жизни 2024, 515: 64-70. DOI: 10.31857/s2686738924020121.Peer-Reviewed Original ResearchRev expression plasmidVirus-like particlesEmpty control plasmidGene therapy of human diseasesGag proteinTherapy of human diseasesGene therapyViral Gag proteinTarget cellsControl plasmidProtein levelsCas9 nucleaseGenome editingGagEfficiency of genome editingMethods of genome editingExpression of Cas9Plasmid constructsCotransfectionHuman diseasesPlasmidCell lysatesNuclear export
2022
Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways
Rafei R, Koong J, Osman M, Al Atrouni A, Hamze M, Hamidian M. Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways. FEMS Microbes 2022, 3: xtac027. PMID: 37332503, PMCID: PMC10117892, DOI: 10.1093/femsmc/xtac027.Peer-Reviewed Original ResearchComplex evolutionary historyEvolutionary historyMetabolic pathwaysHybrid assembly approachConjugative transfer systemOxford Nanopore sequencingLarge plasmidsMetabolic modulesComplete sequenceMetabolism modulesAntibiotic resistance genesAncestral structureIllumina MiSeqNanopore sequencingResistance genesPossible ancestorAntibiotic resistanceGlobal clone 2PlasmidMultiple antibiotic resistanceClone 2Important pathogenResistance islandsKb plasmidSequence types
2019
Folate-Decorated Polyamidoamine Dendrimer Nanoparticles for Head and Neck Cancer Gene Therapy
Xu L, Yang H. Folate-Decorated Polyamidoamine Dendrimer Nanoparticles for Head and Neck Cancer Gene Therapy. Methods In Molecular Biology 2019, 1974: 393-408. PMID: 31099016, DOI: 10.1007/978-1-4939-9220-1_26.BooksConceptsGene therapyGene delivery systemsNeck cancer gene therapyCancer gene therapyDelivery systemNanoparticle carriersGene deliveryDendrimer nanoparticlesHigh biocompatibilityGene transfectionKnockdown efficiencyTumor targetingSuitable platformFolic acidIRDye 800CWSustained retentionGeneration 4DendrimersNanoparticlesBioimagingCarriersBiocompatibilityHereinPlatformPlasmid
2018
Draft Genome Sequence of an Erwinia tracheiphila Isolate from an Infected Muskmelon (Cucumis melo)
Shapiro L, Andrade A, Scully E, Rocha J, Paulson J, Kolter R. Draft Genome Sequence of an Erwinia tracheiphila Isolate from an Infected Muskmelon (Cucumis melo). Microbiology Resource Announcements 2018, 7: 10.1128/mra.01058-18. PMID: 30533754, PMCID: PMC6256489, DOI: 10.1128/mra.01058-18.Peer-Reviewed Original ResearchInfected muskmelonDraft genome sequenceBacterial plant pathogensCucumis meloChromosome contigPlasmid contigsEastern North AmericaGenome sequencePlant pathogensE. tracheiphilaGenetic variationErwinia tracheiphilaContigsGenomeCucumisNorth AmericaMuskmelonBacteriophageErwiniaPlasmidPathogensSequenceIsolates
2016
Folic acid-decorated polyamidoamine dendrimer mediates selective uptake and high expression of genes in head and neck cancer cells
Xu L, Kittrell S, Yeudall WA, Yang H. Folic acid-decorated polyamidoamine dendrimer mediates selective uptake and high expression of genes in head and neck cancer cells. Nanomedicine 2016, 11: 2959-2973. PMID: 27781559, PMCID: PMC5144492, DOI: 10.2217/nnm-2016-0244.Peer-Reviewed Original ResearchConceptsNeck cancer cellsCancer cellsFR-dependent mannerEnhanced gene expressionGene expressionSame binding siteCellular uptakeGenesDelivery of genesBinding sitesHigh expressionFree FASuitable vectorPlasmidDNA plasmidsCellsTransfection resultsExpressionTransfection efficiencySelective uptakeUptakeFolate receptorHigh levelsVectorFA
2015
Isocost Lines Describe the Cellular Economy of Genetic Circuits
Gyorgy A, Jiménez J, Yazbek J, Huang H, Chung H, Weiss R, Del Vecchio D. Isocost Lines Describe the Cellular Economy of Genetic Circuits. Biophysical Journal 2015, 109: 639-646. PMID: 26244745, PMCID: PMC4572570, DOI: 10.1016/j.bpj.2015.06.034.Peer-Reviewed Original ResearchConceptsGenetic circuitsRibosome binding site strengthsBinding site strengthsPlasmid copy numberProduction of proteinsInduced genesCellular economyCopy numberReporter genePlasmidLiving cellsGenesRegulatory pathProteinTranslation resourcesSite strengthProtein concentrationRibosomeLinesEffects of such couplingCells
2014
Antibiotic resistance correlates with transmission in plasmid evolution
Turner PE, Williams ES, Okeke C, Cooper VS, Duffy S, Wertz JE. Antibiotic resistance correlates with transmission in plasmid evolution. Evolution 2014, 68: 3368-3380. PMID: 25351426, DOI: 10.1111/evo.12537.Peer-Reviewed Original ResearchConceptsCarbon source utilizationPreliminary sequence analysisAntibiotic resistance correlatesFitness assaysQuantitative traitsSelection pressureBacterial hostsResistance levelsPhenotypic performancePlasmid-bearing cellsGenetic rearrangementsTransfer operonSequence analysisPlasmid evolutionPlasmid conjugationCommon competitorPhenotypic correlationsShufflon regionTetracycline resistance transposonAutonomous replicatorPlasmidHorizontal transmissionDivergencePlasmid resistancePlasmid lineages
2005
Mitochondrial DNA depletion analysis by pseudogene ratioing
Swerdlow R, Redpath G, Binder D, Davis J, VandenBerg S. Mitochondrial DNA depletion analysis by pseudogene ratioing. Journal Of Neuroscience Methods 2005, 150: 265-271. PMID: 16118020, DOI: 10.1016/j.jneumeth.2005.06.023.Peer-Reviewed Original ResearchConceptsPlasmid clonesCell linesTreated with ethidium bromideCopies of mtDNAPolymerase chain reactionMtDNA copy numberPCR-based analysisPolymerase chain reaction productsU251 human glioma cell lineMtDNA pseudogenesAmplified mtDNAMitochondrial DNAMtDNAMtDNA depletionGenomic DNACopy numberHuman glioma cell linesPseudogenesGlioma cell linesEthidium bromidePrimersPlasmidClonesDNAChain reactionInducible Gene Expression Using an Autoregulatory, Tetracycline‐Controlled System
Shockett P, Schatz D. Inducible Gene Expression Using an Autoregulatory, Tetracycline‐Controlled System. Current Protocols In Cell Biology 2005, 27: 20.8.1-20.8.10. PMID: 18228465, DOI: 10.1002/0471143030.cb2008s27.Peer-Reviewed Original ResearchConceptsInducible gene expressionSelectable markerGene expressionSecond selectable markerCell linesFibroblast cell lineTransient transfectionGene protein expressionResultant clonesStable linesMarker plasmidPlasmidProtein expressionAdherent cellsTransactivatorExpressionTransfectionCellsTargetGenesSupport protocolClonesLinesMarkersAutoregulatory
2002
Inducible Gene Expression Using an Autoregulatory, Tetracycline‐Controlled System
Shockett P, Schatz D. Inducible Gene Expression Using an Autoregulatory, Tetracycline‐Controlled System. Current Protocols In Molecular Biology 2002, 60: 16.14.1-16.14.9. PMID: 18265300, DOI: 10.1002/0471142727.mb1614s60.Peer-Reviewed Original ResearchConceptsInducible gene expressionSelectable markerGene expressionSecond selectable markerCell linesFibroblast cell lineTransient transfectionGene protein expressionResultant clonesStable linesMarker plasmidPlasmidProtein expressionAdherent cellsTransactivatorExpressionTransfectionCellsTargetGenesSupport protocolClonesLinesMarkersAutoregulatoryCryptic plasmids of Mycobacterium avium: Tn552 to the rescue
Kirby C, Waring A, Griffin T, Falkinham J, Grindley N, Derbyshire K. Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue. Molecular Microbiology 2002, 43: 173-186. PMID: 11849545, DOI: 10.1046/j.1365-2958.2002.02729.x.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBlotting, SouthernDNA Transposable ElementsDNA, BacterialDNA, CircularMolecular Sequence DataMutagenesis, InsertionalMycobacterium aviumMycobacterium bovisMycobacterium smegmatisPlasmidsReplication OriginRestriction MappingSequence Analysis, DNASequence Homology, Nucleic AcidConceptsEssential genetic toolsCryptic plasmidGenetic toolsOpportunistic pathogen Mycobacterium aviumGenetic exploitationTransposon insertionConjugative relaxaseTransposition systemSelectable markerExtrachromosomal DNAGenetic analysisHost rangePlasmid genesPlasmid originBacterial speciesPlasmid establishmentCircular DNAPlasmidMycobacterium smegmatisGenesMycobacterial plasmidsDNAReplicationMycobacterium aviumRescue
1997
Insulin-like growth factor II stimulates cell proliferation through the insulin receptor
Morrione A, Valentinis B, Xu S, Yumet G, Louvi A, Efstratiadis A, Baserga R. Insulin-like growth factor II stimulates cell proliferation through the insulin receptor. Proceedings Of The National Academy Of Sciences Of The United States Of America 1997, 94: 3777-3782. PMID: 9108054, PMCID: PMC20517, DOI: 10.1073/pnas.94.8.3777.Peer-Reviewed Original ResearchConceptsInsulin receptorSerum-free mediumType 1 insulin-like growth factor receptorCell proliferationInsulin-like growth factor receptorR cellsIGF-IIWild-type counterpartsGrowth factor receptorGrowth factor supplementationInsulin-like growth factor IITargeted disruptionFactor receptorGrowth factor IIFactor supplementationGrowth factorPlasmidAdditional plasmidsCellsReceptorsFactor IIProliferationGenesIGF1RFibroblasts
1992
Effective vectors for transformation, expression of heterologous genes, and assaying transposon excision in transgenic plants
Jones J, Shlumukov L, Carland F, English J, Scofield S, Bishop G, Harrison K. Effective vectors for transformation, expression of heterologous genes, and assaying transposon excision in transgenic plants. Transgenic Research 1992, 1: 285-297. PMID: 1338696, DOI: 10.1007/bf02525170.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid OxidoreductasesBase SequenceCloning, MolecularDNA Transposable ElementsDrug ResistanceEscherichia coliGenetic TechniquesGenetic VectorsGlucuronidaseMolecular Sequence DataOligodeoxyribonucleotidesPlantsPlants, Genetically ModifiedPlasmidsPromoter Regions, GeneticProtein Sorting SignalsRestriction MappingTransformation, GeneticConceptsTransgenic plantsHeterologous genesNopaline synthaseCauliflower mosaic virus 35S promoterΒ-glucuronidase gene expressionPlant cell transformationActivity of transposonsPlant molecular biologyBinary vector constructsSelection marker geneTransgene of interestPlant transformationHeterologous expressionSynthase promoterEffective vectorPolyadenylation sequenceReading frameTransposon excisionMarker genesGene expressionCell transformationMolecular biologyVector constructsGenesPlasmid
1991
Ultraviolet Mutagenesis of a Shuttle Vector Plasmid in Repair Proficient and Deficient Human Cells
Seidman M, Brash D, Settharam S, Kraemer K, Bredberg A. Ultraviolet Mutagenesis of a Shuttle Vector Plasmid in Repair Proficient and Deficient Human Cells. 1991, 183-192. DOI: 10.1007/978-1-4615-3732-8_23.ChaptersDNA sequence dataRecombinant DNA revolutionStudy of mutagenesisDeficient human cellsMechanisms of mutagenesisMammalian genomesNature of mutationsMammalian cellsShuttle vector plasmidSequence dataProkaryotic systemDNA revolutionShuttle vectorHuman cellsMutagenesisVector plasmidRepair proficientMutagenic agentsUltraviolet mutagenesisGenomeCellsFundamental questionsEnormous bodyGeneticsPlasmid
1990
Differences in the extent of activation of Epstein-Barr virus replicative gene expression among four nonproducer cell lines stably transformed by OriP/BZLF1 plasmids
Gradoville L, Grogan E, Taylor N, Miller G. Differences in the extent of activation of Epstein-Barr virus replicative gene expression among four nonproducer cell lines stably transformed by OriP/BZLF1 plasmids. Virology 1990, 178: 345-354. PMID: 2171186, DOI: 10.1016/0042-6822(90)90331-k.Peer-Reviewed Original ResearchConceptsCell linesEffects of mutationsStable cell linesExtent of activationProtein functionCellular genesGene productsExtrachromosomal plasmidsGene expressionNonproducer cell linesExpression vectorEarly antigenEarly genesGenesLymphoid cell linesCellular subclonesEBV early genesReplicative gene expressionX50-7 cellsZEBRA proteinPlasmidZebraBZLF1 gene productLatent EBVEBV genesConditional Mutations Occur Predominantly in Highly Conserved Residues of RNA Polymerase II Subunits
Scafe C, Martin C, Nonet M, Podos S, Okamura S, Young R. Conditional Mutations Occur Predominantly in Highly Conserved Residues of RNA Polymerase II Subunits. Molecular And Cellular Biology 1990, 10: 1270-1275. DOI: 10.1128/mcb.10.3.1270-1275.1990.Peer-Reviewed Original ResearchRNA polymerase II largest subunitRNA polymerase mutantsAmino acid residuesRPB1 geneLarge subunitInvariant residuesEucaryotic organismsPolymerase mutantsConditional mutationsYeast cellsSequence analysisAcid residuesRPB2RPB1MutationsCold sensitivityResiduesYeastMutantsCellsHomologyPlasmidGenesRNASubunit
1989
The 44P Subunit of the T4 DNA Polymerase Accessory Protein Complex Catalyzes ATP Hydrolysis
Rush J, Lin T, Quinones M, Spicer E, Douglas I, Williams K, Konigsberg W. The 44P Subunit of the T4 DNA Polymerase Accessory Protein Complex Catalyzes ATP Hydrolysis. Journal Of Biological Chemistry 1989, 264: 10943-10953. PMID: 2786875, DOI: 10.1016/s0021-9258(18)60410-7.Peer-Reviewed Original ResearchConceptsAccessory proteinsATP hydrolysisDNA-dependent ATP hydrolysisT4 DNA polymerase accessory proteinsDNA polymerase accessory proteinPolymerase accessory proteinsTotal cellular proteinAccessory protein complexProtein complexesCellular proteinsPlasmid resultsSubunitsProteinATPase activityOverexpression plasmidProductive interactionInduction of cellsPlasmidSpecific activityComplexesSubcomplexInductionGenesOverexpressionATPase
1987
Stimulation of cellular DNA synthesis by wild type and mutant bovine papillomavirus DNA
Jaskulski D, Kaczmarek L, DiMaio D. Stimulation of cellular DNA synthesis by wild type and mutant bovine papillomavirus DNA. Biochemical And Biophysical Research Communications 1987, 148: 86-91. PMID: 2823817, DOI: 10.1016/0006-291x(87)91079-5.Peer-Reviewed Original ResearchMutational analysis of open reading frame E4 of bovine papillomavirus type 1
Neary K, Horwitz B, DiMaio D. Mutational analysis of open reading frame E4 of bovine papillomavirus type 1. Journal Of Virology 1987, 61: 1248-1252. PMID: 3029420, PMCID: PMC254088, DOI: 10.1128/jvi.61.4.1248-1252.1987.Peer-Reviewed Original ResearchConceptsBovine papillomavirus type 1Papillomavirus type 1E4 proteinLate gene expressionMouse C127 cellsAmino acid sequenceAcid sequenceExtrachromosomal plasmidsBiological activityC127 cellsMutational analysisGene expressionFoci formationORF E2ORFProteinViral DNAMutationsSoft agaroseCellsMutantsType 1Papilloma formationDNAPlasmid
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