plasmids

Summary

Summary: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.

Top Publications

  1. pmc One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
    K A Datsenko
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    Proc Natl Acad Sci U S A 97:6640-5. 2000
  2. doi Enzymatic assembly of DNA molecules up to several hundred kilobases
    Daniel G Gibson
    The J Craig Venter Institute, Synthetic Biology Group, Rockville, Maryland, USA
    Nat Methods 6:343-5. 2009
  3. ncbi Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae
    M S Longtine
    Department of Biology, University of North Carolina, Chapel Hill 27599 3280, USA
    Yeast 14:953-61. 1998
  4. pmc Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study
    Karthikeyan K Kumarasamy
    Department of Microbiology, Dr ALM PG IBMS, University of Madras, Chennai, India
    Lancet Infect Dis 10:597-602. 2010
  5. pmc An archaeal immune system can detect multiple protospacer adjacent motifs (PAMs) to target invader DNA
    Susan Fischer
    Department of Biology II, Ulm University, 89069 Ulm, Germany
    J Biol Chem 287:33351-63. 2012
  6. pmc Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site
    Asma Hatoum-Aslan
    Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 108:21218-22. 2011
  7. doi The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA
    Josiane E Garneau
    Departement de Biochimie, de microbiologie et de bio informatique, Faculte des sciences et de genie, Groupe de Recherche en Ecologie Buccale, Faculte de Medecine Dentaire, Felix d Herelle Reference Center for Bacterial Viruses, Universite Laval, Quebec City, Quebec G1V 0A6, Canada
    Nature 468:67-71. 2010
  8. ncbi Prokaryotic toxin-antitoxin stress response loci
    Kenn Gerdes
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Nat Rev Microbiol 3:371-82. 2005
  9. pmc Dissemination of clonally related Escherichia coli strains expressing extended-spectrum beta-lactamase CTX-M-15
    Teresa M Coque
    Hospital Universitario Ramon y Cajal, Madrid, Spain
    Emerg Infect Dis 14:195-200. 2008
  10. pmc DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways
    Zengyi Shao
    Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Nucleic Acids Res 37:e16. 2009

Detail Information

Publications379 found, 100 shown here

  1. pmc One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
    K A Datsenko
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    Proc Natl Acad Sci U S A 97:6640-5. 2000
    ..with 36- to 50-nt extensions that are homologous to regions adjacent to the gene to be inactivated and template plasmids carrying antibiotic resistance genes that are flanked by FRT (FLP recognition target) sites...
  2. doi Enzymatic assembly of DNA molecules up to several hundred kilobases
    Daniel G Gibson
    The J Craig Venter Institute, Synthetic Biology Group, Rockville, Maryland, USA
    Nat Methods 6:343-5. 2009
    ..This assembly method can be used to seamlessly construct synthetic and natural genes, genetic pathways and entire genomes, and could be a useful molecular engineering tool...
  3. ncbi Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae
    M S Longtine
    Department of Biology, University of North Carolina, Chapel Hill 27599 3280, USA
    Yeast 14:953-61. 1998
    ..We describe here a new set of plasmids that serve as templates for the PCR synthesis of fragments that allow a variety of gene modifications...
  4. pmc Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study
    Karthikeyan K Kumarasamy
    Department of Microbiology, Dr ALM PG IBMS, University of Madras, Chennai, India
    Lancet Infect Dis 10:597-602. 2010
    ..We investigated the prevalence of NDM-1, in multidrug-resistant Enterobacteriaceae in India, Pakistan, and the UK...
  5. pmc An archaeal immune system can detect multiple protospacer adjacent motifs (PAMs) to target invader DNA
    Susan Fischer
    Department of Biology II, Ulm University, 89069 Ulm, Germany
    J Biol Chem 287:33351-63. 2012
    ..only a few species have been investigated to elucidate the precise mechanisms for the defense of viruses or plasmids. Approximately 90% of all sequenced archaea encode CRISPR/Cas systems, but their molecular details have so far ..
  6. pmc Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site
    Asma Hatoum-Aslan
    Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 108:21218-22. 2011
    ..We also show that maturation is mediated by specific cas genes distinct from those genes involved in primary processing, showing that this event is directed by CRISPR/Cas loci...
  7. doi The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA
    Josiane E Garneau
    Departement de Biochimie, de microbiologie et de bio informatique, Faculte des sciences et de genie, Groupe de Recherche en Ecologie Buccale, Faculte de Medecine Dentaire, Felix d Herelle Reference Center for Bacterial Viruses, Universite Laval, Quebec City, Quebec G1V 0A6, Canada
    Nature 468:67-71. 2010
    ..and Archaea have developed several defence strategies against foreign nucleic acids such as viral genomes and plasmids. Among them, clustered regularly interspaced short palindromic repeats (CRISPR) loci together with cas (CRISPR-..
  8. ncbi Prokaryotic toxin-antitoxin stress response loci
    Kenn Gerdes
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Nat Rev Microbiol 3:371-82. 2005
    Although toxin-antitoxin gene cassettes were first found in plasmids, recent database mining has shown that these loci are abundant in free-living prokaryotes, including many pathogenic bacteria...
  9. pmc Dissemination of clonally related Escherichia coli strains expressing extended-spectrum beta-lactamase CTX-M-15
    Teresa M Coque
    Hospital Universitario Ramon y Cajal, Madrid, Spain
    Emerg Infect Dis 14:195-200. 2008
    We analyzed 43 CTX-M-15-producing Escherichia coli isolates and 6 plasmids encoding the blaCTX-M-15 gene from Canada, India, Kuwait, France, Switzerland, Portugal, and Spain. Most isolates belonged to phylogroups B2 (50%) and D (25%)...
  10. pmc DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways
    Zengyi Shao
    Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Nucleic Acids Res 37:e16. 2009
    ....
  11. ncbi Identification of plasmids by PCR-based replicon typing
    Alessandra Carattoli
    Department of Infectious, Parasitic and Immune Mediated Diseases, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161 Rome, Italy
    J Microbiol Methods 63:219-28. 2005
    The epidemiological importance of tracing plasmids conferring drug resistance prompted us to develop a PCR method based on replicons (inc/rep PCR) of the major plasmid incompatibility groups among Enterobacteriaceae...
  12. ncbi Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant
    P P Cherepanov
    Universitat Oldenburg, Germany
    Gene 158:9-14. 1995
    ..This system was applied in the construction of an E. coli endA deletion mutation which can be transduced by P1 to the genetic background of interest using TcR as a marker. The transductant can then be freed of the TcR if required...
  13. doi Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain
    Benjamin A Rogers
    The University of Queensland, UQ Centre for Clinical Research, Herston, 4006, Brisbane, Australia
    J Antimicrob Chemother 66:1-14. 2011
    ..Phenotypic detection of the ST131 clone is not possible and DNA-based techniques, including MLST and PCR, are described...
  14. pmc Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms
    Susanne Erdmann
    Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK 2200 Copenhagen N, Denmark
    Mol Microbiol 85:1044-56. 2012
    ..The results underline the complex dynamics of CRISPR-based immune systems within a population infected with genetic elements...
  15. ncbi The diversity of conjugative relaxases and its application in plasmid classification
    Maria Pilar Garcillán-Barcia
    Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria CSIC IDICAN, Santander, Spain
    FEMS Microbiol Rev 33:657-87. 2009
    ..Bacterial conjugation is an efficient and sophisticated mechanism of DNA transfer among bacteria. While mobilizable plasmids only encode a minimal MOB machinery that allows them to be transported by other plasmids, conjugative plasmids ..
  16. pmc Extended-spectrum beta-lactamases: a clinical update
    David L Paterson
    Infectious Disease Division, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
    Clin Microbiol Rev 18:657-86. 2005
    ..The presence of ESBLs carries tremendous clinical significance. The ESBLs are frequently plasmid encoded. Plasmids responsible for ESBL production frequently carry genes encoding resistance to other drug classes (for example, ..
  17. doi CRISPR/Cas, the immune system of bacteria and archaea
    Philippe Horvath
    Danisco France SAS, BP10, F 86220 Dangé Saint Romain, France
    Science 327:167-70. 2010
    ..palindromic repeats (CRISPR) form peculiar genetic loci, which provide acquired immunity against viruses and plasmids by targeting nucleic acid in a sequence-specific manner...
  18. pmc Genome stability of Lyme disease spirochetes: comparative genomics of Borrelia burgdorferi plasmids
    Sherwood R Casjens
    Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
    PLoS ONE 7:e33280. 2012
    ..Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297...
  19. pmc Recombineering: a homologous recombination-based method of genetic engineering
    Shyam K Sharan
    Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
    Nat Protoc 4:206-23. 2009
    ..coli genome can be subcloned by gene retrieval using recombineering. Most of these constructs can be made within about 1 week's time...
  20. ncbi Emergent properties of reduced-genome Escherichia coli
    György Pósfai
    Institute of Biochemistry, Biological Research Center, H 6726 Szeged, Hungary
    Science 312:1044-6. 2006
    ..beneficial properties: high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains...
  21. ncbi Recombinant protein expression in Escherichia coli
    F Baneyx
    Department of Chemical Engineering University of Washington Box 351750, Seattle, WA 98195, USA
    Curr Opin Biotechnol 10:411-21. 1999
    ..coli, together with serendipitous discoveries and the availability of improved genetic tools are making this bacterium more valuable than ever for the expression of complex eukaryotic proteins...
  22. ncbi The CTX-M beta-lactamase pandemic
    Rafael Canton
    Servicio de Microbiologia, Hospital Ramon y Cajal, 28034 Madrid, Spain
    Curr Opin Microbiol 9:466-75. 2006
    ..These structures have been located in narrow and broad host-range plasmids belonging to the same incompatibility groups as those of early antibiotic resistance plasmids...
  23. pmc Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers
    Soley Gudbergsdottir
    Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200N Copenhagen, Denmark
    Mol Microbiol 79:35-49. 2011
    ..Moreover, the relatively high incidence of single-spacer deletions observed for S. islandicus suggests that an additional more directed mechanism operates in this organism...
  24. pmc GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules
    Alejandro Sarrion-Perdigones
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas, Universidad Politecnica de Valencia, Valencia, Spain
    PLoS ONE 6:e21622. 2011
    ..The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily ..
  25. pmc Plasmid-mediated quinolone resistance: a multifaceted threat
    Jacob Strahilevitz
    Department of Clinical Microbiology and Infectious Diseases, Hadassah Ein Kerem, Jerusalem 91120, Israel
    Clin Microbiol Rev 22:664-89. 2009
    ..Of concern, these genes are not yet being taken into account in resistance screening by clinical microbiology laboratories...
  26. ncbi A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes
    Carsten Janke
    CRBM, CNRS FRE2593, 1919 Route de Mende, F 34293 Montpellier cedex 5, France
    Yeast 21:947-62. 2004
    ..This new toolbox should help to speed up the analysis of gene function in yeast, on the level of single genes, as well as in systematic approaches...
  27. pmc Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes
    Diya Sen
    Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies IBEST, University of Idaho, Moscow, ID 83844 3051, USA
    Appl Environ Microbiol 77:7975-83. 2011
    Broad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants...
  28. pmc Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli
    Yoshitoshi Ogura
    Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889 1692, Japan
    Proc Natl Acad Sci U S A 106:17939-44. 2009
    ..We found many lambdoid phages, IEs, and virulence plasmids that carry the same or similar virulence genes but have distinct evolutionary histories, indicating that ..
  29. ncbi Stochastic gene expression in a single cell
    Michael B Elowitz
    Laboratory of Cancer Biology, Center for Studies in Physics and Biology, Rockefeller University, New York, NY 10021, USA
    Science 297:1183-6. 2002
    ..These results establish a quantitative foundation for modeling noise in genetic networks and reveal how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation...
  30. ncbi The ClosTron: a universal gene knock-out system for the genus Clostridium
    John T Heap
    Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    J Microbiol Methods 70:452-64. 2007
    ..The procedure is highly efficient and reproducible, and should revolutionize functional genomic studies in clostridia...
  31. doi A modular system for Clostridium shuttle plasmids
    John T Heap
    BBSRC Sustainable BioEnergy Centre, School of Molecular Medical Sciences, Centre for Biomolecular Sciences, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    J Microbiol Methods 78:79-85. 2009
    ..The transfer and maintenance of recombinant, replicative plasmids into various species of Clostridium has been reported, and several elements suitable as shuttle plasmid ..
  32. ncbi Prions affect the appearance of other prions: the story of [PIN(+)]
    I L Derkatch
    Laboratory for Molecular Biology, Department of Biological Sciences, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, IL 60607, USA
    Cell 106:171-82. 2001
    ..Importantly, the de novo appearance of Rnq1::GFP prion aggregates also requires the presence of other prions, suggesting the existence of a general mechanism by which the appearance of prions is enhanced by heterologous prion aggregates...
  33. pmc Analysis of the resistome of a multidrug-resistant NDM-1-producing Escherichia coli strain by high-throughput genome sequencing
    Laurent Poirel
    Service de Bacteriologie Virologie, Hopital de Bicetre, 78 rue du General Leclerc, 94275 Le Kremlin Bicetre cedex, France
    Antimicrob Agents Chemother 55:4224-9. 2011
    ..These resistance genes were located on three additional plasmids, of 160 kb (IncA/C), 130 kb (IncF), and 110 kb (IncI1)...
  34. ncbi Localization of ASH1 mRNA particles in living yeast
    E Bertrand
    Department of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Mol Cell 2:437-45. 1998
    ..Video microscopy demonstrated that She1p/Myo4p moved particles to the bud tip at 200-440 nm/sec. Therefore, the ASH1 3'UTR-dependent particle serves as a marker for RNA transport and localization...
  35. pmc An efficient recombination system for chromosome engineering in Escherichia coli
    D Yu
    Gene Regulation and Chromosome Biology Laboratory and Mouse Cancer Genetics Program, National Cancer Institute, Division of Basic Science, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 97:5978-83. 2000
    ..Gene disruptions and modifications of both the bacterial chromosome and bacterial plasmids are possible...
  36. ncbi A synthetic oscillatory network of transcriptional regulators
    M B Elowitz
    Department of Molecular Biology and Physics, Princeton University, New Jersey 08544, USA
    Nature 403:335-8. 2000
    ..Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks...
  37. pmc A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast
    U Gueldener
    Heinrich Heine Universitat, Institut fur Mikrobiologie, Universitatsstrasse 1, Geb 26 12 01 64, 40225 Dusseldorf, Germany
    Nucleic Acids Res 30:e23. 2002
    ..The set of disruption cassettes and Cre expression plasmids described here represents a significant further development of the marker rescue system, which is ideally suited ..
  38. pmc Targeted transcriptional activation of silent oct4 pluripotency gene by combining designer TALEs and inhibition of epigenetic modifiers
    Sebastian Bultmann
    Department of Biology, Center for Integrated Protein Science Munich CIPSM, Ludwig Maximilians University Munich, Germany
    Nucleic Acids Res 40:5368-77. 2012
    ..These results show that dTALEs in combination with chemical manipulation of epigenetic modifiers facilitate targeted transcriptional activation of epigenetically silenced target genes...
  39. doi Extended-spectrum β-lactamase-producing Escherichia coli from retail chicken meat and humans: comparison of strains, plasmids, resistance genes, and virulence factors
    Jan A J W Kluytmans
    Laboratory for Medical Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
    Clin Infect Dis 56:478-87. 2013
    ..Now, we have extended the analysis with plasmid replicons, virulence factors, and highly discriminatory genomic profiling methods...
  40. doi Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants
    Laura Villa
    Department of Infectious, Parasitic and Immuno Mediated Diseases, Istituto Superiore di Sanita, Rome, Italy
    J Antimicrob Chemother 65:2518-29. 2010
    IncF plasmids are frequently encountered in clinical enterobacterial strains associated with the dissemination of relevant antimicrobial resistance and virulence genes...
  41. doi DNA vaccines: an historical perspective and view to the future
    Margaret A Liu
    ProTherImmune, Lafayette, CA, USA
    Immunol Rev 239:62-84. 2011
    ....
  42. doi Plasmids foster diversification and adaptation of bacterial populations in soil
    Holger Heuer
    Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institut Federal Research Centre for Cultivated Plants, Braunschweig, Germany
    FEMS Microbiol Rev 36:1083-104. 2012
    It is increasingly being recognized that the transfer of conjugative plasmids across species boundaries plays a vital role in the adaptability of bacterial populations in soil...
  43. pmc Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000
    Helene Feil
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:11064-9. 2005
    ..5 mbp in size, composed of a circular chromosome and two plasmids. Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes ..
  44. pmc Genetic features of blaNDM-1-positive Enterobacteriaceae
    Laurent Poirel
    Service de Bacteriologie Virologie, Hopital de Bicetre, 78 rue du General Leclerc, 94275 Le Kremlin Bicetre cedex, France
    Antimicrob Agents Chemother 55:5403-7. 2011
    ..The bla(NDM-1) plasmids coharbored a variety of resistance determinants, including β-lactamase genes, quinolone resistance genes, and ..
  45. doi CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation
    Devaki Bhaya
    Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305, USA
    Annu Rev Genet 45:273-97. 2011
    ..Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its potential for biotechnological applications and understanding evolutionary dynamics are discussed...
  46. pmc Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria
    M Herrero
    GBF National Research Centre for Biotechnology, Braunschweig, Federal Republic of Germany
    J Bacteriol 172:6557-67. 1990
    ..of foreign genes into the chromosomes of gram-negative eubacteria was developed by combining in two sets of plasmids (i) the transposition features of Tn10 and Tn5; (ii) the resistances to the herbicide bialaphos, to mercuric ..
  47. pmc The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients
    Matthew T G Holden
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
    J Bacteriol 191:261-77. 2009
    ..The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen...
  48. pmc New vector for efficient allelic replacement in naturally nontransformable, low-GC-content, gram-positive bacteria
    Maryvonne Arnaud
    Unité de Biologie des Bactéries Pathogènes à Gram Positif, Institut Pasteur, Paris, France
    Appl Environ Microbiol 70:6887-91. 2004
    ..The plasmid was used in Staphylococcus aureus, Listeria monocytogenes, and Bacillus cereus to efficiently construct mutants with or without an associated antibiotic resistance gene...
  49. pmc Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system
    Tomas Sinkunas
    Department of Protein DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
    EMBO J 30:1335-42. 2011
    ..foreign nucleic acids by utilizing small guide crRNAs (CRISPR RNAs) to interfere with invading viruses and plasmids. In Escherichia coli, Cas3 is essential for crRNA-guided interference with virus proliferation...
  50. pmc Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids
    Anton V Bryksin
    Department of Biochemistry, Center for Fundamental and Applied Molecular Evolution, Emory University, Atlanta, Georgia 30322, USA
    Biotechniques 48:463-5. 2010
    ..Phusion DNA polymerase was used for the amplification and fusion reactions, so both reactions were easy to monitor and optimize...
  51. pmc Human induced pluripotent stem cells free of vector and transgene sequences
    Junying Yu
    Morgridge Institute for Research, Madison, WI 53707 7365, USA
    Science 324:797-801. 2009
    ..These results demonstrate that reprogramming human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors and removes one obstacle to the clinical application of human iPS cells...
  52. pmc Outer-surface protein C of the Lyme disease spirochete: a protein induced in ticks for infection of mammals
    Dorothee Grimm
    Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South Fourth Street, Hamilton, MT 59840, USA
    Proc Natl Acad Sci U S A 101:3142-7. 2004
    ..The induction of a spirochetal virulence factor preceding the time and host in which it is required demonstrates a developmental sequence for transmission of this arthropod-borne pathogen...
  53. ncbi Improved gfp and inaZ broad-host-range promoter-probe vectors
    W G Miller
    University of California, Department of Plant and Microbial Biology, Berkeley 94720, USA
    Mol Plant Microbe Interact 13:1243-50. 2000
    ..The vector suite was augmented with derivatives of the kanamycin-resistant gfp promoter-probe plasmids that encode Gfp variants with different half-life times.
  54. pmc MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms
    Yan Zeng
    Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 100:9779-84. 2003
    ..These data suggest that miRNAs and siRNAs can use similar mechanisms to repress mRNA expression and that the choice of mechanism may be largely or entirely determined by the degree of complementary of the RNA target...
  55. pmc The genome of Rhizobium leguminosarum has recognizable core and accessory components
    J Peter W Young
    Department of Biology, University of York, York, UK
    Genome Biol 7:R34. 2006
    ..We have sequenced the genome of R. leguminosarum biovar viciae strain 3841...
  56. ncbi RF cloning: a restriction-free method for inserting target genes into plasmids
    Fusinita van den Ent
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    J Biochem Biophys Methods 67:67-74. 2006
    ..The absence of any alterations to the protein as well as the simplicity of both the primer design and the procedure itself makes it suitable for high-throughput expression and ideal for structural genomics...
  57. pmc Analysis of mutation in human cells by using an Epstein-Barr virus shuttle system
    R B DuBridge
    Mol Cell Biol 7:379-87. 1987
    ..A total of 33 of 34 lacI nonsense mutations and 26 of 27 missense mutations involve G X C to A X T transitions. These data provide support for the mutational theory of cancer...
  58. pmc A highly efficient recombineering-based method for generating conditional knockout mutations
    Pentao Liu
    Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
    Genome Res 13:476-84. 2003
    ..systems have recently been developed that now make it possible to subclone or modify DNA cloned into plasmids, BACs, or PACs without the need for restriction enzymes or DNA ligases...
  59. pmc Detection of plasmid-mediated AmpC beta-lactamase genes in clinical isolates by using multiplex PCR
    F Javier Pérez-Pérez
    Center for Research in Anti Infectives and Biotechnology, Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, Nebraska 68178, USA
    J Clin Microbiol 40:2153-62. 2002
    ..In conclusion, a multiplex PCR technique was developed for identifying family-specific ampC genes responsible for AmpC beta-lactamase expression in organisms with or without a chromosomal AmpC beta-lactamase gene...
  60. pmc Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids
    Bruce Humphrey
    Bristol Centre for Antimicrobial Research, Department of Cellular and Molecular Medicine, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
    BMC Microbiol 12:53. 2012
    Understanding the survival of resistance plasmids in the absence of selective pressure for the antibiotic resistance genes they carry is important for assessing the value of interventions to combat resistant bacteria...
  61. pmc Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids
    Mart Krupovic
    Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Departement de Microbiologie, Institut Pasteur, Paris, France
    PLoS ONE 8:e49044. 2013
    ..into genetic diversity and dynamics of mobile genetic elements in these environments we have sequenced five new plasmids from different Thermococcus strains that have been isolated from geographically remote hydrothermal vents...
  62. pmc PSI:Biology-materials repository: a biologist's resource for protein expression plasmids
    Catherine Y Cormier
    The Virginia G Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85287 6401, USA
    J Struct Funct Genomics 12:55-62. 2011
    ..asu.edu ) sequence-verifies, annotates, stores, and distributes the protein expression plasmids and vectors created by the Protein Structure Initiative (PSI)...
  63. pmc Histone H3-variant Cse4-induced positive DNA supercoiling in the yeast plasmid has implications for a plasmid origin of a chromosome centromere
    Chu Chun Huang
    Section of Molecular Genetics and Microbiology and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 108:13671-6. 2011
    ....
  64. pmc Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant
    Shital A Tripathi
    Mascoma Corporation, Lebanon, NH 03755, USA
    Appl Environ Microbiol 76:6591-9. 2010
    ..thermocellum, a microbe that holds an exciting and promising future in the biofuel industry and development of sustainable energy resources...
  65. pmc A simplified system for generating recombinant adenoviruses
    T C He
    The Howard Hughes Medical Institute, 424 North Bond Street, Baltimore, MD 21231, USA
    Proc Natl Acad Sci U S A 95:2509-14. 1998
    ..After transfections of such plasmids into a mammalian packaging cell line, viral production is conveniently followed with the aid of green fluorescent ..
  66. pmc The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair
    Peter C Fineran
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
    Proc Natl Acad Sci U S A 106:894-9. 2009
    ..This is the first demonstration of a novel mechanistic class of TA systems and of an Abi system functioning in different bacterial genera, both with implications for the dynamics of phage-bacterial interactions...
  67. doi Pushing and pulling in prokaryotic DNA segregation
    Kenn Gerdes
    Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
    Cell 141:927-42. 2010
    ..par) locus encodes an actin homolog called ParM, which forms dynamically unstable filaments that push plasmids apart in a process reminiscent of mitosis...
  68. ncbi A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation
    Kyoung Hee Choi
    Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
    J Microbiol Methods 64:391-7. 2006
    ..Not surprisingly, the method also allows for very efficient transformation with replicative plasmids, with transformation efficiencies ranging from 10(7) to >10(11) transformants per microgram of DNA...
  69. pmc Nasty viruses, costly plasmids, population dynamics, and the conditions for establishing and maintaining CRISPR-mediated adaptive immunity in bacteria
    Bruce R Levin
    Department of Biology, Emory University, Atlanta, Georgia, United States of America
    PLoS Genet 6:e1001171. 2010
    ..mechanism, bacteria with CRISPR regions carrying copies of the DNA of previously encountered phage and plasmids abort the replication of phage and plasmids with these sequences...
  70. ncbi Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe
    J Bahler
    Department of Biology, University of North Carolina, Chapel Hill 27599 3280, USA
    Yeast 14:943-51. 1998
    ..We also constructed a series of plasmids containing the kanMX6 module, which allows selection of G418-resistant cells and thus provides a new heterologous ..
  71. pmc What traits are carried on mobile genetic elements, and why?
    D J Rankin
    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    Heredity (Edinb) 106:1-10. 2011
    ....
  72. pmc Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom, all belonging to the international O25:H4-ST131 clone
    Neil Woodford
    ARMRL, Centre for Infections, Health Protection Agency, London, United Kingdom
    Antimicrob Agents Chemother 53:4472-82. 2009
    We determined the complete nucleotide sequences of three plasmids that encode CTX-M extended-spectrum beta-lactamases (ESBLs) in pulsed-field gel electrophoresis-defined United Kingdom variants (strains A, C, and D) of the internationally ..
  73. pmc Construction of an eae deletion mutant of enteropathogenic Escherichia coli by using a positive-selection suicide vector
    M S Donnenberg
    Department of Medicine, University of Maryland School of Medicine, Baltimore 21201
    Infect Immun 59:4310-7. 1991
    ..These results confirm the role of the eae gene in the attaching and effacing activity of EPEC and establish the utility of a new system for the construction of deletion mutations...
  74. pmc Mobility of plasmids
    Chris Smillie
    Institut Pasteur, Microbial Evolutionary Genomics, CNRS, URA2171, F 75015 Paris, France
    Microbiol Mol Biol Rev 74:434-52. 2010
    b>Plasmids are key vectors of horizontal gene transfer and essential genetic engineering tools...
  75. doi Creation of a bacterial cell controlled by a chemically synthesized genome
    Daniel G Gibson
    The J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Science 329:52-6. 2010
    ..The new cells have expected phenotypic properties and are capable of continuous self-replication...
  76. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
    ..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
  77. ncbi Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
    M McClelland
    Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA
    Nature 413:852-6. 2001
    ..Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets...
  78. pmc The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation
    Julien Guglielmini
    Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France
    PLoS Genet 7:e1002222. 2011
    ..Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ICE) in prokaryotes ..
  79. ncbi The genome of the natural genetic engineer Agrobacterium tumefaciens C58
    D W Wood
    Department of Microbiology, University of Washington, 1959 NE Pacific Street, Box 357242, Seattle, WA 98195, USA
    Science 294:2317-23. 2001
    ..the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A...
  80. ncbi Two-step red-mediated recombination for versatile high-efficiency markerless DNA manipulation in Escherichia coli
    B Karsten Tischer
    Cornell University, Ithaca, NY, USA
    Biotechniques 40:191-7. 2006
    ....
  81. doi Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system
    Kirill A Datsenko
    Waksman Institute, Piscataway, New Jersey 08854, USA
    Nat Commun 3:945. 2012
    ..system that functions by acquisition of short fragments of DNA (mainly from foreign invaders such as viruses and plasmids) and subsequent destruction of DNA with sequences matching acquired fragments...
  82. pmc A dynamic, mitotic-like mechanism for bacterial chromosome segregation
    Michael A Fogel
    Genetics Program, Tufts University School of Medicine, and Howard Hughes Medical Institute, Boston, Massachusetts 02111, USA
    Genes Dev 20:3269-82. 2006
    ..These data suggest that ParAI forms a dynamic structure that pulls the ParBI-bound chromosome to the pole in a process analogous to anaphase of eukaryotic mitosis...
  83. ncbi The composite genome of the legume symbiont Sinorhizobium meliloti
    F Galibert
    UMR6061-CNRS, , , , F-35043 Rennes Cedex, France
    Science 293:668-72. 2001
    ..The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments...
  84. pmc Epitope tagging of chromosomal genes in Salmonella
    S Uzzau
    Centre de Genetique Moleculaire, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France
    Proc Natl Acad Sci U S A 98:15264-9. 2001
    ..The procedure described here should be applicable to a wide variety of Gram-negative bacteria and is particularly suited for the study of intracellular pathogens...
  85. pmc Borrelia burgdorferi OspC protein required exclusively in a crucial early stage of mammalian infection
    Kit Tilly
    Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
    Infect Immun 74:3554-64. 2006
    ..We conclude that OspC is indispensable for establishing infection by B. burgdorferi in mammals but is not required at any other point of the mouse-tick infection cycle...
  86. doi The ClosTron: Mutagenesis in Clostridium refined and streamlined
    John T Heap
    BBSRC Sustainable BioEnergy Centre, School of Molecular Medical Sciences, Centre for Biomolecular Sciences, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    J Microbiol Methods 80:49-55. 2010
    ..com; the out-sourced construction of re-targeted intron plasmids has become cost-effective as well as rapid; and the combination of constitutive intron expression with direct ..
  87. doi Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains
    M A Leverstein-Van Hall
    Department of Medical Microbiology, University Medical Centre Utrecht, The Netherlands
    Clin Microbiol Infect 17:873-80. 2011
    ..Therefore, distribution of ESBL genes, plasmids and strain genotypes in Escherichia coli obtained from poultry and retail chicken meat in the Netherlands was ..
  88. pmc The human gut mobile metagenome: a metazoan perspective
    Brian V Jones
    Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
    Gut Microbes 1:415-31. 2010
    ..TRACA system in conjunction with a comparative metagenomic approach, we have recently explored the pool of plasmids associated with the human gut mobile metagenome...
  89. pmc Complete DNA sequence, comparative genomics, and prevalence of an IncHI2 plasmid occurring among extraintestinal pathogenic Escherichia coli isolates
    Timothy J Johnson
    Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, 1802 Elwood Drive, VMRI 2, Iowa State University, Ames, IA 50011, USA
    Antimicrob Agents Chemother 50:3929-33. 2006
    ..coli isolates...
  90. pmc Novel cassette-based shuttle vector system for gram-positive bacteria
    Emmanuelle Charpentier
    Molecular Pathogenesis Program, Skirball Institute of Biomolecular Medicine, NYU Medical Center, New York, USA
    Appl Environ Microbiol 70:6076-85. 2004
    ..Questions about gene dosage, complementation, and cis-trans effects can now be conveniently addressed, so that this system constitutes an effective tool for studying gene regulation of staphylococci in various ecosystems...
  91. pmc Site-specific chromosomal integration of large synthetic constructs
    Thomas E Kuhlman
    Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544 1014 USA
    Nucleic Acids Res 38:e92. 2010
    ....
  92. pmc Dissemination of blaKPC-2 by the spread of Klebsiella pneumoniae clonal complex 258 clones (ST258, ST11, ST437) and plasmids (IncFII, IncN, IncL/M) among Enterobacteriaceae species in Brazil
    Leonardo Neves Andrade
    Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Brazil
    Antimicrob Agents Chemother 55:3579-83. 2011
    ..pneumoniae clonal complex 258 (CC258) clones (ST258, ST11, and ST437) and a diversity of plasmids (IncFII, IncN, and IncL/M, two untypeable plasmids carrying Tn4401a or Tn4401b) successfully disseminated among ..
  93. ncbi IRES-dependent second gene expression is significantly lower than cap-dependent first gene expression in a bicistronic vector
    H Mizuguchi
    Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
    Mol Ther 1:376-82. 2000
    ..e., care should be taken regarding the decreased capacity of IRES-dependent downstream gene expression as well as in determining which gene should be positioned as the first or second gene in a bicistronic vector...
  94. pmc De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
    Josephine A Reinhardt
    Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Genome Res 19:294-305. 2009
    ..syringae pan-genome, a corresponding contraction of the core genome, and a further diversification of the type III effector complement for this important plant pathogen species...
  95. ncbi Insertion sequences in prokaryotic genomes
    Patricia Siguier
    Laboratoire de Microbiologie et Génétique Moléculaires UMR5100 CNRS Campus Université Paul Sabatier 118, route de Narbonne, F 31062 Toulouse Cedex, France
    Curr Opin Microbiol 9:526-31. 2006
    ..g. plasmids and viruses) and the factors which influence this, and appreciation of the different transposition mechanisms in ..
  96. doi Generation of mouse induced pluripotent stem cells without viral vectors
    Keisuke Okita
    Center for iPS Cell Research and Application CiRA, Institute for Integrated Cell Material Sciences, Kyoto University, Kyoto 606 8507, Japan
    Science 322:949-53. 2008
    ..Here, we report the generation of mouse iPS cells without viral vectors. Repeated transfection of two expression plasmids, one containing the complementary DNAs (cDNAs) of Oct3/4, Sox2, and Klf4 and the other containing the c-Myc cDNA, ..
  97. pmc Efficient gene transfer in C.elegans: extrachromosomal maintenance and integration of transforming sequences
    C C Mello
    Department of Cellular and Developmental Biology, Harvard University, Cambridge, MA 02138
    EMBO J 10:3959-70. 1991
    ..Integration of the injected DNA, though relatively rare, was reproducibly achieved when single-stranded oligonucleotide was co-injected with the double-stranded DNA...
  98. pmc AmpC beta-lactamases
    George A Jacoby
    Lahey Clinic, Burlington, Massachusetts 01805, USA
    Clin Microbiol Rev 22:161-82, Table of Contents. 2009
    ..Transmissible plasmids have acquired genes for AmpC enzymes, which consequently can now appear in bacteria lacking or poorly expressing ..
  99. ncbi Conjugative transfer by the virulence system of Legionella pneumophila
    J P Vogel
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
    Science 279:873-6. 1998
    ..The dot virulence genes encoded a large putative membrane complex that functioned as a secretion system that was able to transfer plasmid DNA from one cell to another...
  100. pmc The CGView Server: a comparative genomics tool for circular genomes
    Jason R Grant
    Department of Agricultural, Food and Nutritional Science, University of Alberta, Canada
    Nucleic Acids Res 36:W181-4. 2008
    ..The CGView Server can be accessed at http://stothard.afns.ualberta.ca/cgview_server/..

Research Grants77

  1. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  2. Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone Receptors
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2013
    ..They both exhibit repressive effects on HSV-1 [unreadable] genes. In Aim 2, we will generate a series of mutant plasmids with partial deletion of HSV-1 Repeat Element-1 (RE-1) to study the boundary effect of CTCF on LAT and [..
  3. Non-viral Genetic Modification of Antigen-presenting Cells in Allografts
    Wilson S Meng; Fiscal Year: 2011
    ..Successful completion of the study will lead to improved health outcome of a significant number of patients by decreasing the need for indefinite use of non-specific immunosuppressants in transplant recipients. ..
  4. MOLECULAR BASIS OF REOVIRUS PATHOGENESIS
    Terence S Dermody; Fiscal Year: 2013
    ..abstract_text> ..
  5. Novel DNA-Launched Attenuated Vaccine for VEE Virus
    PETER M PUSHKO; Fiscal Year: 2012
    ..If successful, this technology can potentially transform the field of live attenuated vaccines for many viral diseases. ..
  6. Present Homologous and Heterologous Antigen with Hepatitis E Virus
    R Holland Cheng; Fiscal Year: 2012
    ....
  7. Characterization of new toxins (YmgD and YdfD) from E.coli, targeting cell wall
    Hisako Masuda; Fiscal Year: 2012
    ..The first such example was found in plasmids and bacteriophage, and required for "post-segregational killing'(15, 17)...
  8. CHEMISTRY AND BIOLOGY OF PLATINUM ANTICANCER DRUGS
    Stephen J Lippard; Fiscal Year: 2013
    ..Pt-DNA adducts will be studied with site-specifically modified nucleosomes in vitro and with platinated reporter plasmids in live cells following transfection...
  9. Regulation of Astrocyte TIMP-1 in HIV-Associated Dementia
    JEREL ADAM FIELDS; Fiscal Year: 2011
    ..Aim 2 will be completed by combining pathway-specific inhibitors with a panel of luciferase expression plasmids, CAAT-binding factor overexpression plasmids and pathway-indicating plasmids with and without HAD-relevant ..
  10. Regulation of insulins by the Rhox5 homeobox gene supports spermatogenesis
    James Maclean; Fiscal Year: 2009
    ..Transient transfection of Rhox5 expression plasmids increased the activity of Ins2 promoter-driven luciferase reporter constructs...
  11. Mechanism of Irradiation Pulmonary Fibrosis
    Joel S Greenberger; Fiscal Year: 2012
    ..Project Narrative This irradiation application addresses a critical problem in managing the side effects of thoracic radiotherapy for lung and esophagus cancer. ..
  12. Regulation of EBV Latency by EBNA1
    Paul M Lieberman; Fiscal Year: 2013
    ..More detailed understanding of EBNA1 is further justified by its potential value as a target for therapeutic intervention in diseases and cancers associated with EBV latent infection. ..
  13. DRUG RESISTANCE AND PTERIDINE METABOLISM IN LEISHMANIA
    Stephen M Beverley; Fiscal Year: 2010
    ..These studies have yielded new opportunities for chemotherapeutic attack and new directions for future study of pteridine metabolism and biology. [unreadable] ..
  14. ENZYMOLOGY OF ANTIBIOTIC RESISTANCE
    Richard Armstrong; Fiscal Year: 2009
    ..Plasmid encoded versions of FosA and FosX have been found in multi-drug resistant plasmids Serratia marcescens and P. putida...
  15. Chronic Granulomatous Lung Inflammation Elicited by Carbon Nanotubes
    Mary Jane Thomassen; Fiscal Year: 2013
    ..numbers in: (a) macrophage-specific PPAR?-null versus wild-type mice;and (b) mice treated with lentivirus-PPAR? plasmids, PPAR? agonist rosiglitazone;or PPAR? antagonist BADGE versus untreated mice...
  16. The Role of the Nuclear Lamina in Chromatin Organization and Gene Expression in N
    Marcos Estecio; Fiscal Year: 2012
    ..a method to study the chromatin binding to the nuclear lamina (LAD-Seq) that is independent from engineered plasmids transfection and applicable to primary, uncultured cells...
  17. Cellular functions of the essential PcrA helicase in Staphylococcus aureus
    Saleem A Khan; Fiscal Year: 2013
    ..aureus. Since PcrA is a conserved protein, the knowledge gained from these studies could be used in the future for the development of drugs against S. aureus and other Gram-positive human pathogens. ..
  18. Growth Factor and Antiapoptotic Gene Delivery to Human Islets
    Ram I Mahato; Fiscal Year: 2012
    ..This will decrease the number of islets required to achieve normoglycemia in type I diabetic patients. ..
  19. Endemic maintenance of relapsing fever genotypes.
    Michael Bela Teglas; Fiscal Year: 2013
    ..The bacterium utilizes a reserve of pseudogenes located on multiple plasmids that allow recombinant variants to be expressed during successive waves of spirochetemia...
  20. Centromere Structure and Function in Candida albicans
    Judith G Berman; Fiscal Year: 2012
    ..Furthermore, we have constructed CEN-plasmids that will be useful for many applications...
  21. Disruption of Autonomic Pathways in Left Atrium by Inhibition of G Proteins
    Alan H Kadish; Fiscal Year: 2010
    ..We propose to use a new method to treat AF, by inhibiting the function of the nerves that are critical to the genesis of this arrhythmia. By using a new inhibitory protein, we will selectively block these nerves in the left atrium. ..
  22. Novel Bacillus subtilis based spore vaccine to tuberculosis
    Subramanian Dhandayuthapani; Fiscal Year: 2013
    ..Finally, we will test whether mice with these immunization groups are protected against challenge doses of live M. tuberculosis H37Rv. ..
  23. National surveillance of emerging MDR in pediatric Enterobacteriaceae infections
    Danielle M Zerr; Fiscal Year: 2013
    ..and is concerning both because it limits the antimicrobials available to treat infections and because plasmids are readily transferable between organisms, creating a threat for rapid spread of resistance...
  24. Multiplex Serodiagnostic Protein Microarray
    PHILIP LOUIS FELGNER; Fiscal Year: 2012
    ..Deliverables generated from this project include plasmids, customized protein microarrays in a modular multiplex format, purified recombinant proteins and lateral flow (..
  25. Defining evolutionary trajectories: Molecular adaptation to antibiotic resistance
    ADIL YOUSIF SHAMOO; Fiscal Year: 2012
    ..Mobile genetic elements such as transposons, conjugative transposons and plasmids act as vectors between microbial populations and can spread resistance beyond the agricultural or clinical ..
  26. Structures of RNA processing and Silencing Enzymes in Prokaryotes
    Hong Li; Fiscal Year: 2013
    ..a variety of defense systems to protect themselves from selfish genetic elements (phages, transposons, and plasmids)...
  27. HTLV-1 &Cellular Factors in Neuroinflammatory Disease
    Brian Wigdahl; Fiscal Year: 2013
    ..to interact with these factors independently have been performed using transiently transfected viral reporter plasmids or in cell lines that do not represent the primary target for HTLV-1 in vivo...
  28. Regulations of DNA Alkylation/Deamination Damage Repair
    Rabindra Roy; Fiscal Year: 2013
    ..Furthermore, this knowledge will allow us eventually to devise strategies for modulating MPG expression for chemopreventive and therapeutic purposes. ..
  29. Genomic profiling of yeast resistance to AFB1, a P450-activated carcinogen
    MICHAEL THOMAS FASULLO; Fiscal Year: 2013
    ..We will introduce plasmids that express human CYP1A2 into the ~5,000 diploid homozygous single-deletion and heterozygous single-deletion ..
  30. Role of H-Ras in Retinal Cell Death in Diabetes
    Renu A Kowluru; Fiscal Year: 2013
    ..The central hypothesis will be tested using active plasmids, siRNAs and pharmacological inhibitors in isolated cells, and in vitro findings will be validated in in vivo ..
  31. Development of transformed lactobacilli as a microbicide
    Richard B Markham; Fiscal Year: 2010
    ..Those VHH will then be expressed from plasmids and/or the bacterial chromosome of Lactobacillus rhamnosus GR-1 and Streptococcus gordonii...
  32. C/EBP, atrogin-1, and muscle wasting
    Per Olof Hasselgren; Fiscal Year: 2009
    ..protein degradation and expression of atrogin-1 and MuRF1 is tested by transfecting cultured muscle cells with plasmids expressing wild-type C/EBP[unreadable] or C/EBP[unreadable] with mutations of specific acetylation or ..
  33. Biophysics of Drug Interactions with Viral Episomes
    James K Bashkin; Fiscal Year: 2013
    ....
  34. Development of CNS-targeted AAV vectors
    MIGUEL S ESTEVES; Fiscal Year: 2012
    ..of CNS-targeted AAV vectors to foster the development of highly effective gene therapy approaches to treat many childhood, adult, and geriatric neurological diseases currently beyond the reach of modern medicine ..
  35. Role of TRPM1 (Melastatin1) in the Biology of Human Melanocytes
    Vijayasaradhi Setaluri; Fiscal Year: 2012
    ..To address these issues, we generated TRPM1 expression (constitutive and tet-inducible) shRNA plasmids and antibody reagents...
  36. Advancing a Lead Candidate Hantavirus Pulmonary Syndrome DNA Vaccine
    JAY WILLIAMS HOOPER; Fiscal Year: 2013
    ..We have developed a candidate HPS vaccine. The vaccine is a DNA vaccine consisting of two plasmids that encode the surface glycoproteins of ANDV and SNV...
  37. Disruption of Autonomic Pathways in the Left Atrium by Inhibition of G-proteins
    Rishi Arora; Fiscal Year: 2013
    ..Using minigenes (plasmids) that can express these G-protein inhibitory peptides on both a short and long term basis, the proposed studies ..
  38. Delivery of biologically active nucleic acids to epidermal cells
    ROGER L contact KASPAR; Fiscal Year: 2010
    ..If the goal of this work succeeds, it is expected that the pace of new research and development of nucleic treatments for skin disease will accelerate greatly, spawning many new jobs and small companies. ..
  39. Hepatic Non-viral Gene Therapy
    Leaf Huang; Fiscal Year: 2013
    ..S/MAR sequence will be incorporated into the IFN-[unreadable]2b plasmid to prolong the gene expression. The goal is to develop a once-a-month IFN gene therapy for the HBV hepatitis patients. ..
  40. Feedback and Hormonal Regulation of Hepatic HMG-CoA Reductase
    GENE CHARLES NESS; Fiscal Year: 2010
    ..examined by either over expressing hepatic HMGR or by knocking it down with hydrodynamic tail vein injections of plasmids containing HMGR cDNA or siRNA...
  41. Development of Site-Specific Mutagenesis in Coxiella burnetti
    JAMES EVANS SAMUEL; Fiscal Year: 2012
    ..The proposed project outlined several strategies to develop genetic tools for characterization of gene functions and will aid the development of a vaccine as national security goal. ..
  42. Polymorphisms of estrogen-metabolizing genes in kidney cancer
    Yuichiro Tanaka; Fiscal Year: 2013
    ..The following experiments will be performed: (a) Development of EMG wild-type plasmids by cloning and generation of polymorphic variants using site-directed mutagenesis, (b) Transfection of promoter ..
  43. Development of Small Heat Shock Proteins as Therapeutic Agents in the Eye
    JONATHAN MARK PETRASH; Fiscal Year: 2010
    ..Our proposed studies could substantially improve the quality of life of affected patients by preventing vision loss and associated financial burdens due to lost productivity and increased medical expenses. ..
  44. Interactions between P. aeruginosa and autophagy in Airway epithelial cells
    INDHIRA H DE LA ROSA; Fiscal Year: 2013
    ..In addition, we have received plasmids encoding some of the P. aeruginosa T3SS effector proteins (5, 6), which are responsible for the T3SS toxicity (5)...
  45. Role of Polyamine Oxidase in Apoptosis Studies with RNA Interference
    GLENN KUEHN; Fiscal Year: 2009
    ....
  46. CONTROL OF BACTERIAL TOXINS BY VIRUSES AND PLASMIDS
    Randall K Holmes; Fiscal Year: 2013
    ..tuberculosis and potential value as chemotherapeutic agents for treatment of tuberculosis. ..
  47. Nontoxigenic Clostridium difficile as an Oral Vaccine for C. difficile Infection
    DALE NICHOLAS GERDING; Fiscal Year: 2013
    ..abstract_text> ..
  48. Functional role of RAG2 H3K4me3 interaction in V(D)J recombination
    Marjorie A Oettinger; Fiscal Year: 2013
    ..Our goal is to understand the normal steps in development and how errors in the process lead to immune deficiency syndromes and lymphoid tumors, with the hope of preventing or treating such diseases. ..
  49. Mechanisms and regulation of serine resolvases
    Phoebe A Rice; Fiscal Year: 2012
    ..Sin is encoded by many large multi-resistance plasmids of Staph. aureus, and is thought to promote their stable maintenance by resolving replicon dimers into monomers...
  50. Intracellular immunization strategy in inhibit HCV related liver cancer
    Srikanta Dash; Fiscal Year: 2010
    ..If this project becomes successful then it can lead to a potential therapy to treat chronic hepatitis C infection and prevent liver cancer. ..
  51. HCV in Alcoholics
    Jack R Wands; Fiscal Year: 2011
    ..this inhibitory effect of ethanol was completely reversed by co-immunization with an IL2 or GM- CSF expression plasmids following genetic immunization suggesting that dendritic cells (DCs) could be involved in these abnormal immune ..
  52. Targeting stress-mediated pathways in the treatment of muscle insulin resistance
    Paige C Geiger; Fiscal Year: 2013
    ....
  53. Structure and mechanism of CRISPR interference.
    Ailong Ke; Fiscal Year: 2013
    ..CRISPR drives adaptation to harmful invading nucleic acids - such as conjugative plasmids, transposable elements and phages - using an RNA-mediated interference (CRISPR interference) mechanism with ..
  54. NEUROBIOLOGY OF VARICELLA ZOSTER VIRUS
    Donald Gilden; Fiscal Year: 2013
    ....
  55. LANA and Cellular Gene Expression
    ROLF F RENNE; Fiscal Year: 2013
    ..More specifically, we study how LANA supports the replication of the viral genome and how it helps to recruit the above mentioned factors. ..
  56. Plasmid-Mediated Quinolone Resistance
    George A Jacoby; Fiscal Year: 2013
    ..gram-negative bacteria from around the world and to be typically incorporated into integrons on multiresistance plasmids. This resubmission application builds on our prior studies to obtain a deeper and more detailed understanding of ..
  57. CRISPR Cas genes and Legionella pneumophila infection
    Nicholas P Cianciotto; Fiscal Year: 2013
    ..Thus, by using Lpn a a new model organism, we will probe for novel functions of the CRISPR/Cas locus that seek to shift current research paradigms. ..
  58. Toxoid adjuvant CRM197 production in a stable reduced genome E. coli strain
    Frederick R Blattner; Fiscal Year: 2012
    ..These improvements could have a wide impact on production of pharmaceutical protein products and ultimately broaden access to vaccines for at-risk populations who need them. ..
  59. Targeted DNA Nanoparticles in Brain
    David M Yurek; Fiscal Year: 2010
    ..DNA compacting techniques will be used to form nanoparticles containing condensed DNA plasmids with diameters in the range of 8-12 nanometers...
  60. Development of Breast Cancer Vaccines
    WEI ZEN NONE WEI; Fiscal Year: 2013
    ..to Her-2, we formulated DNA vaccines that express both human Her-2 and heterologous rat Neu sequences in separate plasmids or as single hybrid constructs that encode Her-2/neu fusion proteins...
  61. Improvement of Organ Function after Severe Hypovolemia
    Ping Wang; Fiscal Year: 2013
    ..These proposed studies should open up a new research field for the development of innovative therapeutic agents as resuscitation adjuncts for victims with traumatic hemorrhage. ..
  62. DNA Pro-Drug Technology in Localized Wound Healing and Tissue Regeneration
    Arthur A Decarlo; Fiscal Year: 2011
    ....
  63. PAIRING OF HOMOLOGOUS SEQUENCES IN DROSOPHILA
    KENT GOLIC; Fiscal Year: 2002
    ..The FLP recombinase will be supplied in the form of a synthetic mRNA coinjected with the plasmid library. Plasmids containing sequences promoting plasmid/chromosome pairing should be favored for integration; these sequences ..
  64. MODELS OF IN VIVO MYOMETRIAL GENE TRANSFER
    Gregory Christman; Fiscal Year: 2001
    ..Together, these studies will provide in vivo efficacy and safety data for the future clinical application of gene therapy in uterine myometrium. ..
  65. Bacterial heme transport and hemoglobin expression
    Douglas Henderson; Fiscal Year: 2009
    ..Our hypothesis is that hemoglobin production can be increased by transforming E. coli with plasmids containing human hemoglobin genes and heme transport genes from a Gram-negative bacterium, and supplying heme in ..
  66. ANTIBIOTIC SUSCEPTIBILITIES OF PERIODONTAL BACTERIA
    Clay Walker; Fiscal Year: 1993
    ..intermedius and E. corrodens to determine if plasmids encode for resistance in these organisms...
  67. Mechanisms of Sequence-Based Resistance to Viruses and Plasmids in Eubacteria
    Erik J Sontheimer; Fiscal Year: 2010
    ..the locus suggests that it specifies resistance not only to bacteriophages but also to staphylococcal conjugative plasmids. Given the clinical importance of staphylococci and the experimental tractability of S...
  68. Pilot trial of a DNA vaccine encoding PAP in patients with prostate cancer
    Douglas McNeel; Fiscal Year: 2009
    ..This is consequently relevant to the development of other anti-tumor vaccines. ..
  69. Prevention of neointimal thickening by Mst1
    Junichi Sadoshima; Fiscal Year: 2006
    ..stents made of noncombustible magnesium and a proprietary technique to coat the stents with mammalian expression plasmids, which can be efficiently delivered to vascular smooth muscle cells (VSMCs), the technique successfully utilized ..
  70. Regulated Osteochondrogenesis of Human Mesenchymal Stem Cells Using Gene Delivery
    Antonios Mikos; Fiscal Year: 2009
    ..Each of these plasmids will be complexed with a novel polymeric gene delivery vector developed in our laboratory (a conjugate of ..
  71. VIRULENCE IN COXIELLA BURNETTII
    HERBERT THOMPSON; Fiscal Year: 1999
    ..In aim 1, organisms will be transformed to ampicillin resistance using a mixture of plasmids en masse via electroporation. These plasmids carry the C...
  72. IMMUNE CONTROL OF CAE LENTIVIRUS
    Donald Knowles; Fiscal Year: 2005
    ..Therefore, the second objective of this proposal is to evaluate virus replication following CAEV challenge of goats co-immunized with plasmid DNA expressing CAEV env and tat genes and caprine IFN. ..
  73. Prevention of diabetes by pDNA encoded with IL-10
    Jagdish Singh; Fiscal Year: 2010
    ..The proposed study will contribute towards the development of a high efficiency and low toxicity non-viral gene delivery vehicle in order to deliver plasmid encoding IL-10 gene for prevention of type 1 diabetes. ..
  74. STRUCTURE AND GENETIC CONTROL OF COLICINES
    Donald Helinski; Fiscal Year: 2005
    ..along with the plasmid specific initiation protein in the initiation of replication of RK2 and narrow-host-range plasmids P1 and F will be determined...
  75. Structural mechanism of DNA segregation by the pSK41 par system
    Maria Schumacher; Fiscal Year: 2010
    ..Essential to this process are the accurate movement and positioning of chromosomes and plasmids to daughter cells at cell division...
  76. Y ENTEROCOLITICA VIRULENCE PLASMID
    John Morris; Fiscal Year: 1991
    ....
  77. Plasmid pXO2 Replication in Bacillus anthracis
    Saleem Khan; Fiscal Year: 2005
    Bacillus anthracis is an important human pathogen and a potential biological weapon. Two large plasmids, pXO1 and pXO2 play a major role in the virulence of this organism...