escherichia coli

Summary

Summary: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections.

Top Publications

  1. pmc EcoCyc: a comprehensive view of Escherichia coli biology
    Ingrid M Keseler
    SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Nucleic Acids Res 37:D464-70. 2009
  2. 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
  3. ncbi Protein production by auto-induction in high density shaking cultures
    F William Studier
    Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
    Protein Expr Purif 41:207-34. 2005
  4. 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
  5. pmc Coding-sequence determinants of gene expression in Escherichia coli
    Grzegorz Kudla
    Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 324:255-8. 2009
  6. pmc Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
    Yuichi Taniguchi
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 329:533-8. 2010
  7. pmc Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    D Allan Drummond
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 134:341-52. 2008
  8. doi Genome evolution and adaptation in a long-term experiment with Escherichia coli
    Jeffrey E Barrick
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
    Nature 461:1243-7. 2009
  9. ncbi Network motifs: simple building blocks of complex networks
    R Milo
    Departments of Physics of Complex Systems and Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100
    Science 298:824-7. 2002
  10. pmc Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
    Ido Yosef
    Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
    Nucleic Acids Res 40:5569-76. 2012

Detail Information

Publications346 found, 100 shown here

  1. pmc EcoCyc: a comprehensive view of Escherichia coli biology
    Ingrid M Keseler
    SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Nucleic Acids Res 37:D464-70. 2009
    EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the regulatory network of E. coli...
  2. 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
    We have developed a simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s)...
  3. ncbi Protein production by auto-induction in high density shaking cultures
    F William Studier
    Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
    Protein Expr Purif 41:207-34. 2005
    ..coding sequences cloned under control of a T7lac promoter efficiently produce a wide variety of proteins in Escherichia coli. Investigation of factors that affect stability, growth, and induction of T7 expression strains in shaking ..
  4. 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...
  5. pmc Coding-sequence determinants of gene expression in Escherichia coli
    Grzegorz Kudla
    Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 324:255-8. 2009
    ..When expressed in Escherichia coli, GFP protein levels varied 250-fold across the library...
  6. pmc Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
    Yuichi Taniguchi
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 329:533-8. 2010
    ..with single-molecule sensitivity using a newly constructed yellow fluorescent protein fusion library for Escherichia coli. We found that almost all protein number distributions can be described by the gamma distribution with two ..
  7. pmc Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    D Allan Drummond
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 134:341-52. 2008
    ....
  8. doi Genome evolution and adaptation in a long-term experiment with Escherichia coli
    Jeffrey E Barrick
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
    Nature 461:1243-7. 2009
    ..Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations...
  9. ncbi Network motifs: simple building blocks of complex networks
    R Milo
    Departments of Physics of Complex Systems and Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100
    Science 298:824-7. 2002
    ..The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web...
  10. pmc Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
    Ido Yosef
    Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
    Nucleic Acids Res 40:5569-76. 2012
    ..Here we describe a robust assay in Escherichia coli to explore the hitherto least-studied process, adaptation...
  11. 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...
  12. pmc Nascentome analysis uncovers futile protein synthesis in Escherichia coli
    Koreaki Ito
    Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
    PLoS ONE 6:e28413. 2011
    ..Pulse-labeled nascent polypeptides of Escherichia coli form a characteristic line below the main diagonal line, because each of them had contained a tRNA of nearly ..
  13. pmc Simple and highly efficient BAC recombineering using galK selection
    Søren Warming
    Mouse Cancer Genetics Program, National Cancer Institute Frederick, MD 21702 1201, USA
    Nucleic Acids Res 33:e36. 2005
    Recombineering allows DNA cloned in Escherichia coli to be modified via lambda (lambda) Red-mediated homologous recombination, obviating the need for restriction enzymes and DNA ligases to modify DNA...
  14. doi Small CRISPR RNAs guide antiviral defense in prokaryotes
    Stan J J Brouns
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands
    Science 321:960-4. 2008
    ..Our results demonstrate that the formation of mature guide RNAs by the CRISPR RNA endonuclease subunit of Cascade is a mechanistic requirement for antiviral defense...
  15. pmc The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates
    David A Rasko
    Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201, USA
    J Bacteriol 190:6881-93. 2008
    ..This study examined the pangenomic content of Escherichia coli. Six distinct E...
  16. ncbi Pathogenic Escherichia coli
    James B Kaper
    Center for Vaccine Development, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    Nat Rev Microbiol 2:123-40. 2004
    Few microorganisms are as versatile as Escherichia coli. An important member of the normal intestinal microflora of humans and other mammals, E. coli has also been widely exploited as a cloning host in recombinant DNA technology. But E...
  17. pmc The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli
    Rimantas Sapranauskas
    Institute of Biotechnology, Vilnius University, Graiciuno 8, LT 02241 Vilnius, Lithuania
    Nucleic Acids Res 39:9275-82. 2011
    ..Here, we show that the S. thermophilus CRISPR3/Cas system can be transferred into Escherichia coli and provide heterologous protection against plasmid transformation and phage infection...
  18. pmc Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter
    L M Guzman
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Bacteriol 177:4121-30. 1995
    ..We have exploited the tight regulation of the PBAD promoter to study the phenotypes of null mutations of essential genes and explored the use of pBAD vectors as an expression system...
  19. ncbi FACS-optimized mutants of the green fluorescent protein (GFP)
    B P Cormack
    Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305 5402, USA
    Gene 173:33-8. 1996
    We have constructed a library in Escherichia coli of mutant gfp genes (encoding green fluorescent protein, GFP) expressed from a tightly regulated inducible promoter...
  20. doi Microbial production of fatty-acid-derived fuels and chemicals from plant biomass
    Eric J Steen
    Joint BioEnergy Institute, Emeryville, California 94608, USA
    Nature 463:559-62. 2010
    ..Here we demonstrate the engineering of Escherichia coli to produce structurally tailored fatty esters (biodiesel), fatty alcohols, and waxes directly from simple ..
  21. pmc Rapid and simple determination of the Escherichia coli phylogenetic group
    O Clermont
    Laboratoire d études de génétique bactérienne dans les infections de l enfant EA3105, Universite Denis Diderot Paris 7, Hopital Robert Debre, Paris, France
    Appl Environ Microbiol 66:4555-8. 2000
    Phylogenetic analysis has shown that Escherichia coli is composed of four main phylogenetic groups (A, B1, B2, and D) and that virulent extra-intestinal strains mainly belong to groups B2 and D...
  22. pmc Sex and virulence in Escherichia coli: an evolutionary perspective
    Thierry Wirth
    Department of Molecular Biology, Schumannstrasse 21 22, Max Planck Institut für Infektionsbiologie, 10117 Berlin, Germany
    Mol Microbiol 60:1136-51. 2006
    Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals and birds...
  23. pmc Microbial laboratory evolution in the era of genome-scale science
    Tom M Conrad
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 0412, USA
    Mol Syst Biol 7:509. 2011
    ....
  24. pmc Comparison of 61 sequenced Escherichia coli genomes
    Oksana Lukjancenko
    Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark
    Microb Ecol 60:708-20. 2010
    b>Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp...
  25. ncbi Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans
    L Timmons
    Department of Embryology, Carnegie Institution of Washington, 115 West University Parkway, Baltimore, MD 21210, USA
    Gene 263:103-12. 2001
    ....
  26. doi Programming cells by multiplex genome engineering and accelerated evolution
    Harris H Wang
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 460:894-8. 2009
    ..We applied MAGE to optimize the 1-deoxy-D-xylulose-5-phosphate (DXP) biosynthesis pathway in Escherichia coli to overproduce the industrially important isoprenoid lycopene...
  27. doi Multidimensional optimality of microbial metabolism
    Robert Schuetz
    Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
    Science 336:601-4. 2012
    ..Consistent with flux data from evolved Escherichia coli, we propose that flux states evolve under the trade-off between two principles: optimality under one given ..
  28. pmc Mauve: multiple alignment of conserved genomic sequence with rearrangements
    Aaron C E Darling
    Department of Computer Science, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Genome Res 14:1394-403. 2004
    ..We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution...
  29. 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
    b>Escherichia coli sequence type 131 (ST131) is a worldwide pandemic clone, causing predominantly community-onset antimicrobial-resistant infection...
  30. ncbi Synonymous codon usage in Escherichia coli: selection for translational accuracy
    Nina Stoletzki
    Ludwig Maximilan Universität, Biocenter, Planegg Martinsried, Germany
    Mol Biol Evol 24:374-81. 2007
    ..Using several data sets, we find evidence that codon use in Escherichia coli is biased to reduce the costs of both missense and nonsense translational errors...
  31. ncbi Bacterial persistence as a phenotypic switch
    Nathalie Q Balaban
    Laboratory of Living Matter and Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 305:1622-5. 2004
    ..We investigated the persistence of single cells of Escherichia coli with the use of microfluidic devices...
  32. ncbi Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements
    Francisco J M Mojica
    Divisón de Microbiología, Departamento de Fisiologia, Genética y Microbiología, Universidad de Alicante, Campus de San Vicente, E 03080, Spain
    J Mol Evol 60:174-82. 2005
    ..All these biological traits could be influenced by the presence of specific spacers. CRISPR loci can be visualized as mosaics of a repeated unit, separated by sequences at some time present elsewhere in the cell...
  33. ncbi The complete genome sequence of Escherichia coli K-12
    F R Blattner
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Science 277:1453-62. 1997
    The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function...
  34. pmc Structure of Escherichia coli Hfq bound to polyriboadenylate RNA
    Todd M Link
    Department of Biochemistry and Molecular Biology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030 4009, USA
    Proc Natl Acad Sci U S A 106:19292-7. 2009
    ..Here, we report the crystal structure of Escherichia coli Hfq bound to the poly(A) RNA, A(15). The structure reveals a unique RNA binding mechanism...
  35. pmc Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    Nathan E Lewis
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Nat Rev Microbiol 10:291-305. 2012
    ..These methods have enabled genome-scale analysis of microbial metabolism for numerous basic and applied uses, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour...
  36. doi Negative epistasis between beneficial mutations in an evolving bacterial population
    Aisha I Khan
    Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
    Science 332:1193-6. 2011
    ..the effects of epistasis on fitness for the first five mutations to fix in an experimental population of Escherichia coli. Epistasis depended on the effects of the combined mutations--the larger the expected benefit, the more ..
  37. 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
    ..These results suggest that the method is potentially applicable to a large number of strains to trace the diffusion of specific multi-drug resistance plasmids in different environments...
  38. doi Persister cells
    Kim Lewis
    Department of Biology and Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts 02115, USA
    Annu Rev Microbiol 64:357-72. 2010
    ..Toxin/antitoxin (TA) modules are involved in persister formation in Escherichia coli. The SOS response leads to overexpression of the TisB toxin and persister formation...
  39. 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
    Phage-based Escherichia coli homologous recombination 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...
  40. pmc The biomass objective function
    Adam M Feist
    GT Life Sciences, Inc, 10520 Wateridge Circle, San Diego, CA 92122, USA
    Curr Opin Microbiol 13:344-9. 2010
    ..Here we review fundamental issues associated with its formulation and use to compute optimal growth states...
  41. 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
    ..determinants have been developed for the construction of insertion and deletion mutants of cloned genes in Escherichia coli. In both cassettes, the resistance determinants are flanked by the short direct repeats (FRT sites) required ..
  42. pmc Genomic analysis of a key innovation in an experimental Escherichia coli population
    Zachary D Blount
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
    Nature 489:513-8. 2012
    ..the evolution of a novel trait, aerobic citrate utilization (Cit(+)), in an experimental population of Escherichia coli. Here we analyse genome sequences to investigate the history and genetic basis of this trait...
  43. pmc Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding
    Kevin S Myers
    Microbiology Doctoral Training Program, University of Wisconsin Madison, Madison, Wisconsin, USA
    PLoS Genet 9:e1003565. 2013
    ..Such combinatorial regulation may allow Escherichia coli to respond rapidly to environmental changes and confer an ecological advantage in the anaerobic but nutrient-..
  44. doi Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
    Harry Yim
    Genomatica, Inc, San Diego, California, USA
    Nat Chem Biol 7:445-52. 2011
    ..the first direct biocatalytic routes to BDO from renewable carbohydrate feedstocks, leading to a strain of Escherichia coli capable of producing 18 g l(-1) of this highly reduced, non-natural chemical...
  45. doi Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    Shota Atsumi
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, California 90095, USA
    Nature 451:86-9. 2008
    ..Here we present a metabolic engineering approach using Escherichia coli to produce higher alcohols including isobutanol, 1-butanol, 2-methyl-1-butanol, 3-methyl-1-butanol and 2-..
  46. pmc Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
    Erdal Toprak
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 44:101-5. 2012
    ..We analyzed the evolution of resistance in Escherichia coli under selection with single drugs, including chloramphenicol, doxycycline and trimethoprim...
  47. pmc Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011
    Yonatan H Grad
    Department of Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 109:3065-70. 2012
    ..Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest ..
  48. doi Microbial biosynthesis of alkanes
    Andreas Schirmer
    LS9, Inc, 600 Gateway Boulevard, South San Francisco, CA 94080, USA
    Science 329:559-62. 2010
    ..Heterologous expression of the alkane operon in Escherichia coli leads to the production and secretion of C13 to C17 mixtures of alkanes and alkenes...
  49. pmc A one pot, one step, precision cloning method with high throughput capability
    Carola Engler
    Icon Genetics GmbH, Biozentrum Halle, Halle, Germany
    PLoS ONE 3:e3647. 2008
    ....
  50. pmc High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics
    Oleksii Sliusarenko
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Mol Microbiol 80:612-27. 2011
    ..Using MicrobeTracker, we discover that the dynamics of the extensively studied Escherichia coli Min oscillator depends on Min protein concentration, unveiling critical limitations in robustness within the ..
  51. doi Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA
    Cynthia M Sharma
    Institute for Molecular Infection Biology, Research Centre of Infectious Diseases, University of Wurzburg, Germany
    Mol Microbiol 81:1144-65. 2011
    ..Rather, GcvB rewires primary transcriptional control circuits and seems to act as a distinct regulatory node in amino acid metabolism...
  52. pmc Bacterial charity work leads to population-wide resistance
    Henry H Lee
    Howard Hughes Medical Institute, Center for BioDynamics, Boston, Massachusetts 02115, USA
    Nature 467:82-5. 2010
    ..Here we follow a continuous culture of Escherichia coli facing increasing levels of antibiotic and show that the vast majority of isolates are less resistant than ..
  53. doi The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex
    Beom Seok Park
    Department of Chemistry, KAIST, Daejeon, 305 701, Korea
    Nature 458:1191-5. 2009
    ..The TLR4-MD-2-LPS structure illustrates the remarkable versatility of the ligand recognition mechanisms employed by the TLR family, which is essential for defence against diverse microbial infection...
  54. pmc Second-order selection for evolvability in a large Escherichia coli population
    Robert J Woods
    Department of Zoology, Michigan State University, East Lansing, MI 48824, USA
    Science 331:1433-6. 2011
    ..To test this hypothesis, we revived a frozen population of Escherichia coli from a long-term evolution experiment and compared the fitness and ultimate fates of four genetically ..
  55. ncbi Protein translocation across the bacterial cytoplasmic membrane
    Arnold J M Driessen
    Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Haren, The Netherlands
    Annu Rev Biochem 77:643-67. 2008
    ..This review summarizes the present knowledge of the mechanism and structure of the Sec translocase, with a special emphasis on unresolved questions and topics of current research...
  56. ncbi The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    R Mahadevan
    Genomatica, Inc, Bioprocessing Division, 5405 Morehouse Drive, Suite 210, San Diego, CA 92121, USA
    Metab Eng 5:264-76. 2003
    ..These methods also provide an efficient and robust method to calculate the range of flux distributions that can be derived from quantitative fermentation data...
  57. pmc The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
    Gene Wei Li
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA
    Nature 484:538-41. 2012
    ..Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes...
  58. doi The twin-arginine translocation (Tat) protein export pathway
    Tracy Palmer
    Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
    Nat Rev Microbiol 10:483-96. 2012
    ..In the Gram-negative bacterium Escherichia coli, this complex task can be achieved by using only three small membrane proteins: TatA, TatB and TatC...
  59. pmc A synchronized quorum of genetic clocks
    Tal Danino
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
    Nature 463:326-30. 2010
    ..Furthermore, it provides a specific model system for the generation of a mechanistic description of emergent coordinated behaviour at the colony level...
  60. pmc Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
    Jonathan A Bernstein
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:9697-702. 2002
    Much of the information available about factors that affect mRNA decay in Escherichia coli, and by inference in other bacteria, has been gleaned from study of less than 25 of the approximately 4,300 predicted E. coli messages...
  61. pmc The transcription unit architecture of the Escherichia coli genome
    Byung Kwan Cho
    Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
    Nat Biotechnol 27:1043-9. 2009
    ..abundance, 5' sequences and translation into proteins to determine the organizational structure of the Escherichia coli K-12 MG1655 genome...
  62. pmc Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage
    Karine Prévost
    Department of Biochemistry, RNA Group, University of Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
    Genes Dev 25:385-96. 2011
    ..Thus, beyond translation initiation block, sRNA-induced mRNA cleavage requires several unexpected steps, many of which are determined by structural features of the target mRNA...
  63. pmc Phenotypic landscape of a bacterial cell
    Robert J Nichols
    University of California, San Francisco, 94143, USA
    Cell 144:143-56. 2011
    ....
  64. pmc Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    Marie Touchon
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
    PLoS Genet 5:e1000344. 2009
    The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change...
  65. ncbi Engineering and characterization of a superfolder green fluorescent protein
    Jean Denis Pédelacq
    Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Nat Biotechnol 24:79-88. 2006
    ..The fluorescence of Escherichia coli cells expressing each of eighteen proteins from Pyrobaculum aerophilum as fusions with superfolder GFP was ..
  66. pmc Translation efficiency is determined by both codon bias and folding energy
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 107:3645-50. 2010
    ..Using the Escherichia coli and Saccharomyces cerevisiae transcriptomes, we conducted a genome-scale study aiming at dissecting the ..
  67. ncbi Multistability in the lactose utilization network of Escherichia coli
    Ertugrul M Ozbudak
    Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 427:737-40. 2004
    ..Here we present the phase diagram of the bistable lactose utilization network of Escherichia coli. We use this phase diagram, coupled with a mathematical model of the network, to quantitatively investigate ..
  68. doi The RpoS-mediated general stress response in Escherichia coli
    Aurélia Battesti
    Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA
    Annu Rev Microbiol 65:189-213. 2011
    Under conditions of nutrient deprivation or stress, or as cells enter stationary phase, Escherichia coli and related bacteria increase the accumulation of RpoS, a specialized sigma factor...
  69. pmc Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence
    Ekaterina Semenova
    Waksman Institute, Piscataway, NJ 08854, USA
    Proc Natl Acad Sci U S A 108:10098-103. 2011
    ..Here, we show that in the case of Escherichia coli subtype CRISPR/Cas system, the requirements for crRNA matching are strict only for a seven-nucleotide seed ..
  70. pmc Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin
    Stefan Pukatzki
    Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 104:15508-13. 2007
    ..to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4...
  71. pmc Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    Bryson D Bennett
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    Nat Chem Biol 5:593-9. 2009
    ..Here we use LC-MS/MS to quantify more than 100 metabolite concentrations in aerobic, exponentially growing Escherichia coli with glucose, glycerol or acetate as the carbon source...
  72. pmc Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans
    R S Kamath
    Wellcome CRC Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
    Genome Biol 2:RESEARCH0002. 2001
    ..It has previously been shown that RNAi can also be achieved by feeding worms Escherichia coli expressing dsRNA corresponding to a specific gene; this mode of dsRNA introduction is conventionally ..
  73. pmc A microhomology-mediated break-induced replication model for the origin of human copy number variation
    P J Hastings
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS Genet 5:e1000327. 2009
    ....
  74. pmc Probing transcription factor dynamics at the single-molecule level in a living cell
    Johan Elf
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 316:1191-4. 2007
    Transcription factors regulate gene expression through their binding to DNA. In a living Escherichia coli cell, we directly observed specific binding of a lac repressor, labeled with a fluorescent protein, to a chromosomal lac operator...
  75. doi Bacterial persistence and toxin-antitoxin loci
    Kenn Gerdes
    Center for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, United Kingdom
    Annu Rev Microbiol 66:103-23. 2012
    ..Recent research has shown that persistence of the model organism Escherichia coli depends on toxin-antitoxin (TA) loci...
  76. doi Assembly of bacterial ribosomes
    Zahra Shajani
    Departments of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biochem 80:501-26. 2011
    ..In this review, we present a brief history of the early work on ribosome assembly in Escherichia coli, including a description of in vivo and in vitro intermediates...
  77. ncbi A comprehensive library of fluorescent transcriptional reporters for Escherichia coli
    Alon Zaslaver
    Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Israel
    Nat Methods 3:623-8. 2006
    ..coli, including putative internal promoters within previously known operons, such as the lac operon. This library can serve as a tool for accurate, high-resolution analysis of transcription networks in living E. coli cells...
  78. ncbi Multiple sigma subunits and the partitioning of bacterial transcription space
    Tanja M Gruber
    Department of Microbiology and Immunology, University of California, Genentech Hall, 600 16th St, San Francisco, San Francisco, California 94143, USA
    Annu Rev Microbiol 57:441-66. 2003
    ..We use the sigma repertoire of Escherichia coli, Bacillus subtilis, Streptomyces coelicolor, and cyanobacteria to illustrate the different strategies ..
  79. pmc CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage
    Alexander V Yakhnin
    Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
    Mol Microbiol 87:851-66. 2013
    Csr is a conserved global regulatory system that controls expression of several hundred Escherichia coli genes. CsrA protein represses translation of numerous genes by binding to mRNA and inhibiting ribosome access...
  80. 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
    ..We constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated...
  81. doi Structural basis for CRISPR RNA-guided DNA recognition by Cascade
    Matthijs M Jore
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
    Nat Struct Mol Biol 18:529-36. 2011
    ..In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade...
  82. pmc Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis
    Michael A Kohanski
    Howard Hughes Medical Institute, Boston University, Boston, MA 02215, USA
    Mol Cell 37:311-20. 2010
    ..This work establishes a radical-based molecular mechanism whereby sublethal levels of antibiotics can lead to multidrug resistance, which has important implications for the widespread use and misuse of antibiotics...
  83. pmc Design parameters to control synthetic gene expression in Escherichia coli
    Mark Welch
    DNA2 0, Menlo Park, CA, USA
    PLoS ONE 4:e7002. 2009
    ..Protein-coding sequences are commonly re-designed to enhance expression, but there are no experimentally supported design principles...
  84. pmc ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
    Markus Wiederstein
    Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
    Nucleic Acids Res 35:W407-10. 2007
    ..ProSA-web is accessible at https://prosa.services.came.sbg.ac.at...
  85. ncbi Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis
    C E Outten
    Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
    Science 292:2488-92. 2001
    ..To test this, we determined the mechanism of zinc sensors that control metal uptake or export in Escherichia coli and calibrated their response against the thermodynamically defined free zinc concentration...
  86. ncbi Silver nanoparticles as antimicrobial agent: a case study on E. coli as a model for Gram-negative bacteria
    Ivan Sondi
    Center for Marine and Environmental Research, Ruder Boskovic Institute, Zagreb, Croatia
    J Colloid Interface Sci 275:177-82. 2004
    ..These nontoxic nanomaterials, which can be prepared in a simple and cost-effective manner, may be suitable for the formulation of new types of bactericidal materials...
  87. ncbi Antimicrobial effects of silver nanoparticles
    Jun Sung Kim
    Laboratory of Toxicology, Seoul National University, Seoul, Korea
    Nanomedicine 3:95-101. 2007
    ..The antimicrobial activity of Ag nanoparticles was investigated against yeast, Escherichia coli, and Staphylococcus aureus...
  88. doi The molecular diversity of adaptive convergence
    Olivier Tenaillon
    Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697, USA
    Science 335:457-61. 2012
    To estimate the number and diversity of beneficial mutations, we experimentally evolved 115 populations of Escherichia coli to 42.2°C for 2000 generations and sequenced one genome from each population...
  89. pmc Emergence of metallo-β-lactamase NDM-1-producing multidrug-resistant Escherichia coli in Australia
    Laurent Poirel
    Service de Bacteriologie Virologie, INSERM U914, Hopital de Bicetre, Assistance Publique Hopitaux de Paris, 78 rue du General Leclerc, Le Kremlin Bicetre Cedex, France
    Antimicrob Agents Chemother 54:4914-6. 2010
    A multidrug-resistant Escherichia coli isolate recovered in Australia produced a carbapenem-hydrolyzing β-lactamase. Molecular investigations revealed the first identification of the bla(NDM-1) metallo-β-lactamase gene in that country...
  90. ncbi Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili
    L A Pratt
    Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
    Mol Microbiol 30:285-93. 1998
    We have used Escherichia coli as a model system to investigate the initiation of biofilm formation. Here, we demonstrate that E. coli forms biofilms on multiple abiotic surfaces in a nutrient-dependent fashion...
  91. doi Precise manipulation of chromosomes in vivo enables genome-wide codon replacement
    Farren J Isaacs
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 333:348-53. 2011
    ..MAGE) to site-specifically replace all 314 TAG stop codons with synonymous TAA codons in parallel across 32 Escherichia coli strains...
  92. doi Adding new chemistries to the genetic code
    Chang C Liu
    The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biochem 79:413-44. 2010
    ..pairs has led to the addition of approximately 70 unnatural amino acids (UAAs) to the genetic codes of Escherichia coli, yeast, and mammalian cells...
  93. doi The population genetics of commensal Escherichia coli
    Olivier Tenaillon
    INSERM U722 and Université Paris 7 Denis Diderot, Paris 75018, France
    Nat Rev Microbiol 8:207-17. 2010
    The primary habitat of Escherichia coli is the vertebrate gut, where it is the predominant aerobic organism, living in symbiosis with its host...
  94. pmc Quake: quality-aware detection and correction of sequencing errors
    David R Kelley
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:R116. 2010
    ..Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake...
  95. ncbi Macromolecular crowding: obvious but underappreciated
    R J Ellis
    Dept of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK
    Trends Biochem Sci 26:597-604. 2001
    ..Positive results of crowding include enhancing the collapse of polypeptide chains into functional proteins, the assembly of oligomeric structures and the efficiency of action of some molecular chaperones and metabolic pathways...
  96. pmc Automated design of synthetic ribosome binding sites to control protein expression
    Howard M Salis
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    Nat Biotechnol 27:946-50. 2009
    ..Experimental validation of >100 predictions in Escherichia coli showed that the method is accurate to within a factor of 2.3 over a range of 100,000-fold...
  97. 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
    A recombination system has been developed for efficient chromosome engineering in Escherichia coli by using electroporated linear DNA...
  98. pmc Emergent bistability by a growth-modulating positive feedback circuit
    Cheemeng Tan
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
    Nat Chem Biol 5:842-8. 2009
    ..circuit consisting of mutant T7 RNA polymerase (T7 RNAP*) that activates its own expression in the bacterium Escherichia coli. Although activation by the T7 RNAP* is noncooperative, the circuit caused bistable gene expression...
  99. pmc Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks
    Xionglei He
    Department of Ecology and Evolutionary Biology, Ann Arbor, Michigan, USA
    Nat Genet 42:272-6. 2010
    ..positive and negative epistatic interactions amongst biochemical reactions within the metabolic networks of Escherichia coli and Saccharomyces cerevisiae using flux balance analysis...
  100. ncbi Darwinian evolution can follow only very few mutational paths to fitter proteins
    Daniel M Weinreich
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Science 312:111-4. 2006
    ..This implies that the protein tape of life may be largely reproducible and even predictable...
  101. pmc Composability of regulatory sequences controlling transcription and translation in Escherichia coli
    Sriram Kosuri
    Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 110:14024-9. 2013
    ..The ease and scale this of approach indicates that rather than relying on prediction or standardization, we can screen synthetic libraries for desired behavior. ..

Research Grants78

  1. Fatty acid related regulation of enteric infectious disease
    FREDRICK JON KULL; Fiscal Year: 2012
    ..Preliminary analysis has indicated that a number of pathogenic bacteria, including several types of Escherichia coli, Salmonella typhi, Salmonella typhimurium, Shigella flexneri, and Yersinia enterocolitica, contain A/X ..
  2. Molecular Basis of E. coli Adhesins in Bladder Disorders
    Scott J Hultgren; Fiscal Year: 2013
    ..S., ~85% of which are caused by uropathogenic Escherichia coli (UPEC)...
  3. Salmonella Vaccines Against Bacterial Enteropathogens
    Roy Curtiss; Fiscal Year: 2013
    ..8 (WHO) to 2.2 (UNESCO) million are due to infections with enteric pathogens including Salmonella, Escherichia coli and Shigella sp., and other entero-pathogens such as Yersinia sp...
  4. Novel Bioconjugate Vaccines to Prevent Staphylococcus aureus Infection
    JEAN CLAIRE LEE; Fiscal Year: 2013
    ..This protein glycosylation system has been functionally transferred into Escherichia coli, and it allows the conjugation of an antigenic polysaccharide to a designer protein of choice through an N-..
  5. 4th ASM Conference on Prokaryotic Cell Biology and Development
    Susan S Golden; Fiscal Year: 2012
    ..The core subject matter involves five widely and successfully studied systems: Escherichia coli (cell division, cytoskeletal structures, cell wall biosynthesis), Bacillus subtilis (cell cycle regulation, ..
  6. The Electricidal Effect, a Novel Anti-Biofilm Strategy
    Robin Patel; Fiscal Year: 2013
    ..aeruginosa, S. aureus, and S. epidermidis, three isolates each of Escherichia coli and Enterococcus faecalis, and single isolates of each of Streptococcus mutans species group and Candida ..
  7. Colitis Induced by immune responses to luminal bacteria-mouse
    Ryan B Sartor; Fiscal Year: 2012
    ..Selective colonization of germ-free IL-10-/- mice with Escherichia coli or Enterococcus faecalis induces different phenotypes of colitis for each bacteria. E. coli and E...
  8. Adherent Escherichia coli and associated virulence genes in children with IBD
    Sandra C Kim; Fiscal Year: 2010
    ..10 deficient (IL-10-/-) mice selectively colonized (monoassociated) with non-pathogenic strains of Escherichia coli (NC101) or Enterococcus faecalis (OG1RF) develop different phenotypes of colitis with clear regional and ..
  9. Cellular functions of the essential PcrA helicase in Staphylococcus aureus
    Saleem A Khan; Fiscal Year: 2013
    ..PcrA is related to the Escherichia coli UvrD and Rep helicases and is known to be essential for UV DNA repair in Bacillus subtilis. In B...
  10. Rho-Modifying Cytotoxic Necrotizing Factor of E. coli
    ALISON DAVIS O'BRIEN; Fiscal Year: 2013
    ..CNF1 and a membrane-lytic toxin, hemolysin (Hly), are often co- expressed by Escherichia coli strains that cause urinary tract infections (UTIs), i.e., cystitis or pyelonephritis, or acute prostatitis...
  11. MECHANISM AND CONTROL OF UREA BIOSYNTHESIS
    Frank M Raushel; Fiscal Year: 2011
    ..enzyme has recently been implicated in the biosynthesis of an extracellular death factor peptide, NNWNN, in Escherichia coli. The role of AsnA in the formation of this very unusual peptide will be determined...
  12. LIPID A MODIFICATION SYSTEMS IN GRAM-NEGATIVE BACTERIA
    Pei Zhou; Fiscal Year: 2012
    ..b>Escherichia coli lipid A is synthesized on the cytoplasmic surface of the inner membrane by a conserved pathway of nine ..
  13. Reciprocal Control of Motility and Adherence in UTI
    Harry L Mobley; Fiscal Year: 2013
    ..The most common uropathogen, Escherichia coli, can cause acute cystitis or pyelonephritis in the uncomplicated urinary tract...
  14. National surveillance of emerging MDR in pediatric Enterobacteriaceae infections
    Danielle M Zerr; Fiscal Year: 2013
    ..PUBLIC HEALTH RELEVANCE: We propose to study antibiotic resistance in Enterobacteriaceae bacteria (such as Escherichia coli and Klebsiella pneumoniae) that produce urinary tract and bloodstream infections in children, by analyzing ..
  15. Exploiting deep ocean biology for biomedical discovery
    David C Rowley; Fiscal Year: 2011
    ..of both ATCC and clinical strains of multiple drug resistant Staphylococcus aureus, Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae...
  16. Bacterial Stress Responses to Intestinal Inflammation
    JONATHAN JAMES HANSEN; Fiscal Year: 2013
    ..Isolates of Escherichia coli (E...
  17. Challenges in beta-Lactamase Mediated Resistance
    Robert A Bonomo; Fiscal Year: 2013
    ..These [unreadable]-lactamases are found in ceftazidime resistant Klebsiella pneumoniae, Escherichia coli, Enterobacter spp., Acinetobacter baumannii, and Pseudomonas aeruginosa...
  18. Catalytic inactivation of miRNA function by customized RNase P-based ribozymes
    DANIEL R contact SCHOENBERG; Fiscal Year: 2010
    ..Our research design exploits the properties of M1 RNA, the catalytic subunit of Escherichia coli RNase P...
  19. Regulation of Streptomyces differentiation and antibiotic production by SoxR
    Monica Chander; Fiscal Year: 2010
    ..SoxR has traditionally been known as the mediator of an oxidative stress response in Escherichia coli and Salmonella enterica, but this role may be restricted to enteric bacteria...
  20. Novel gene-silencing therapeutics for multidrug-resistant gram-negative pathogens
    DAVID ELIHU GREENBERG; Fiscal Year: 2013
    ..This group includes the Gram-negative pathogens Acinetobacter baumannii and Escherichia coli. A new paradigm in antibiotic discovery and design has recently been shown effective against numerous ..
  21. Deciphering of the Toxin-Antitoxin Systems in E. coli
    Masayori Inouye; Fiscal Year: 2012
    ..For this reason, I propose to carry out thorough investigation of the toxin-antitoxin systems in Escherichia coli as a model bacterium, which surprisingly contains as many as twenty two independent toxin-antitoxin systems ..
  22. Re-Wiring Cellular Metabolism to Control Biofilm Formation and Virulence BY...
    Thomas K Wood; Fiscal Year: 2011
    ..Here, we will use a simple model system (pathogenic and non-pathogenic Escherichia coli along with pseudomonads and sulfur-reducing bacteria) that allows us to investigate biofilm formation and ..
  23. Photocrosslinking characterization of heat-labile toxin glycoreceptors
    Amberlyn M Wands; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Enterotoxigenic Escherichia coli (ETEC) is endemic to developing countries, in which acute infectious diarrhea is the second most common cause of childhood death, and millions of traveler's per ..
  24. Short-term responses to temperature changes in Escherichia coli
    Christine A White Ziegler; Fiscal Year: 2010
    ..molecular biology approaches to explore the short-term response of both commensal and pathogenic strains of Escherichia coli to these temperatures...
  25. Structure and mechanism of CRISPR interference.
    Ailong Ke; Fiscal Year: 2013
    ..far sequenced, including important human pathogens such as Campylobacter human jejuni, Clostridium botulinum, Escherichia coli, Listeria monocytogenes, Mycobacterium tuberculosis and Yersinia pestis...
  26. SHIGA-TOXINS: PRE-CLINICAL ANIMAL MODEL DEVELOPMENT AND THERAPEUTIC TESTING
    Shinichiro Kurosawa; Fiscal Year: 2011
    DESCRIPTION (provided by applicant): Shiga-like toxin producing enterohemorrhagic Escherichia coli (EHEC) strains are recognized as the most common cause of outbreaks and regional sporadic cases of bloody diarrhea and hemolytic uremic ..
  27. Toxoid adjuvant CRM197 production in a stable reduced genome E. coli strain
    Frederick R Blattner; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): Scarab Genomics has developed valuable reduced-genome strains of Escherichia coli in which multiple deletions remove from the genome much unwanted and all potentially hazardous DNA...
  28. Soft Metal, Disulfide, and Cysteine Stresses in Escherichia coli
    James A Imlay; Fiscal Year: 2013
    ..the mechanisms by which soft metals, cystine import, and cysteine accumulation can perturb the fitness of Escherichia coli. These three distinct stresses are connected by the central involvement of cysteine chemistry...
  29. Characterization of wild-type and mutant initiation/elongation complexes in Esche
    Carlos Bustamante; Fiscal Year: 2012
    ..few years we have developed novel methods and approaches to study transcription by RNA polymerase (RNAP) of Escherichia coli (Eco)...
  30. TERPENE CONDENSATION REACTIONS
    CHARLES POULTER; Fiscal Year: 2009
    ..To facilitate our work, we are developing a collection of genetically engineered strains of Escherichia coli that permit us to rapidly produce and purify multimilligram quantities of prenyltransferases for study in our ..
  31. Lipid Translocating Glycosyltransferases in Congenital Neurological Disease
    PETER AB ORLEAN; Fiscal Year: 2010
    ..DPS-GT is then expressed in Escherichia coli as fusions to green fluorescent protein, allowing a gel mobility shift assay that distinguishes folded from ..
  32. The roles of MKP-1 in Gram-negative bacterial sepsis and colitis
    Yusen Liu; Fiscal Year: 2010
    ..Surprisingly, when infected with Escherichia coli, MKP-1-/- mice exhibited substantially greater bacterial burdens than do wild-type mice in spite of a more ..
  33. The Abeta protein of Alzheimer's Disease is an antimicrobial peptide
    Robert D Moir; Fiscal Year: 2013
    ..A[unreadable] inhibits the growth of eight clinically important microorganisms, including Candida albicans, Escherichia coli, Staphylococcus epidermidis, Streptococcus pneumoniae, Staphylococcus aureus, Listeria monocytogenes, ..
  34. REGULATION OF LIPID METABOLISM IN BACTERIA
    Charles O Rock; Fiscal Year: 2013
    ..The basic blueprint for bacterial membrane lipid biosynthesis is established by decades of research with Escherichia coli. However, there are numerous and significant differences in lipid metabolism between Gram-positive and Gram-..
  35. Allosteric regulation of the sensory protease DegS
    RANDALL VERNON MAULDIN; Fiscal Year: 2011
    ..The Ce envelope-stress response pathway is a RIP system found in Escherichia coli and many other Gram-negative bacteria...
  36. Regulation of the Poly Sialic Virulence Factor
    ERIC ROSS VIMR; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Extraintestinal pathogenic Escherichia coli (ExPEC) are major pathogens in mostly the very young, aged or immunocompromised human population resulting in tens of thousands of deaths each year and ..
  37. Understanding of a Family of Bacterial Transcription Factors
    Hwan Youn; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): The Escherichia coli cAMP receptor protein (CRP) has been the model transcription factor for our understanding of ligand sensing, DNA recognition and transcriptional regulation...
  38. BIOSYNTHESIS AND FUNCTION OF LIPOPOLYSACCHARIDES
    Pei Zhou; Fiscal Year: 2013
    ..b>Escherichia coli lipid A is synthesized on the cytoplasmic surface of the inner membrane by a conserved pathway of nine ..
  39. Spin labeling of MsbA
    Candice S Klug; Fiscal Year: 2012
    ..is the ABC transporter for lipid A that is found in the inner membranes of Gram-negative bacteria such as Escherichia coli, Salmonella typhimurium, and Vibrio cholerae...
  40. Stomate-based innate immunity against bacterial infection in Arabidopsis
    Maeli Melotto; Fiscal Year: 2012
    ..Specifically, stomata close in response to Escherichia coli O157:H7 and Pseudomonas syringae pv. tomato (Pst) DC3000 or bacterial PAMPs...
  41. Regulation of Pore Formation by Type III Secretion System
    Gloria I Viboud; Fiscal Year: 2010
    ..Shigella spp., Yersinia enterocolitica, Y. pseudotuberculosis and enteropathogenic Escherichia coli as well agents causing severe pneumonia, like the opportunistic bacteria Pseudomonas aeruginosa, or the ..
  42. Structural Biology of Enterotoxin Secretion from Bacterial Cells
    WILHELMUS G J HOL; Fiscal Year: 2013
    ..by applicant): Infections of Vibrio cholerae can result in death within a few hours, while enterotoxigenic Escherichia coli (ETEC) is in the third world a major cause of infant diarrhea and death due to dehydration...
  43. Reactivity epitopes of ribonuclease III substrates
    ALLEN WHITALL NICHOLSON; Fiscal Year: 2010
    ..The mechanism of RNase III activation will be analyzed using an in vitro translation system. Along with Escherichia coli RNase III, this project will employ Aquifex aeolicus RNase III and Thermotoga maritima RNase III, for which ..
  44. BIOGENESIS AND INHIBITION OF BIOFILM-ASSOCIATED BACTERIAL AMYLOID
    Scott J Hultgren; Fiscal Year: 2013
    ..Amyloid fibers called curli are critical in the formation of a biofilm extracellular matrix by uropathogenic Escherichia coli (UPEC). This fiber is made up of the major subunit CsgA, and a minor subunit CsgB...
  45. Validating metabolic pathways in the intracellular pathogen Chlamydia trachomatis
    DEREK JAMES FISHER; Fiscal Year: 2010
    ..AroG, AroDE, and AroA) using genetic and biochemical approaches, including complementation studies in Escherichia coli null mutants, enzyme assays using purified recombinant proteins, and inhibitor assays;2) detecting chorismate ..
  46. Optimization of novel pyranopyridine efflux pump inhibitors
    Son Truong Nguyen; Fiscal Year: 2013
    ..pyranopyridine (MBX-2319) that enhances the antibacterial activity of FQ and beta-lactam antibiotics against Escherichia coli, Shigella flexneri, Salmonella enterica, Enterobacter cloacae, and Klebsiella pneumoniae by inhibiting the ..
  47. Structural and Biochemical Studies of LpxC Inhibition
    Pei Zhou; Fiscal Year: 2012
    ..Many of the potent inhibitors of Escherichia coli LpxC are relatively inactive against divergent LpxC enzymes, especially that from Pseudomonas aeruginosa, the ..
  48. Deciphering ExPEC Virulence Mechanisms
    Matthew A Mulvey; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): Extraintestinal pathogenic Escherichia coli (ExPEC) cause a diverse array of diseases including urinary tract infections, sepsis, and neonatal meningitis. These infections affect 6.7 to 8...
  49. Micro-patterned surfaces for reducing the risk of catheter-associated UTI
    SHRAVANTHI REDDY; Fiscal Year: 2012
    ..Phase I the Sharklet R&D team demonstrated this new concept by reducing colonization of uropathogenic Escherichia coli with in vitro via testing of three Sharklet micro-patterns relative to a smooth surface and by successfully ..
  50. EHEC-induced actin rearrangement and Stx2 translocation across epithelium
    John M Leong; Fiscal Year: 2012
    ..PUBLIC HEALTH RELEVANCE: Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important food-borne pathogen in North America, Europe and Japan (79)...
  51. Genetic Approaches to Lipid Metabolism
    John E Cronan; Fiscal Year: 2013
    ..Although many aspects of bacterial lipid metabolism were first worked out in the paradigm Escherichia coli, other bacteria differ from E. coli in various aspects...
  52. Interactions of Enteropathogenic E Coli with Intestinal Epithelial Cells
    Gail A Hecht; Fiscal Year: 2013
    ..Enteropathogenic Escherichia coli (EPEC) is a foodborne non-invasive pathogen that causes diarrhea...
  53. DNA-Binding Protein Discovery by the Combinatorial Method REPSA
    Michael van Dyke; Fiscal Year: 2013
    ..For example, while the bacteria Escherichia coli strain K12 has 4364 open reading frames, only about half of these genes have been well characterized by ..
  54. Novel components of iron sulfur cluster biosynthesis pathways
    Gareth P Butland; Fiscal Year: 2013
    ..are formed by specific biosynthesis pathways such as the iscRSUhscBAfdx operon and sufABCDSE operon in Escherichia coli. Our long term goal is to determine a complete set of factors involved in FeS cluster biosynthesis in the ..
  55. Determining vaccine candidacy of LT and STa toxoid fusions against enterotoxigeni
    Weiping Zhang; Fiscal Year: 2010
    Enterotoxigenic Escherichia coli (ETEC) strains are categorized as priority B pathogens by NIAID...
  56. The population genetics of antibiotic resistance in multi-drug environments
    Roy Kishony; Fiscal Year: 2013
    ..phenotyping, this device will enable us to characterize the genotypic and phenotypic pathways of replicate Escherichia coli populations evolving high level of resistance to individual drugs (Aim 1), and to test how adaptation is ..
  57. Mechanism/Regulation of Intestinal Thiamin Uptake
    Hamid M Said; Fiscal Year: 2013
    ..Furthermore, we have examined the effect of the enteropathogenic Escherichia coli (EPEC) and found significant inhibition in thiamin uptake...
  58. Maneuvering of Macrophage Function By Escherichia coli K1
    PRASADARAO V NEMANI; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Bacterial meningitis due to Escherichia coli K1 is a serious illness of the central nervous system. It is the most common pathogen causing meningitis in premature infants (46%)...
  59. Escherichia coli and Colorectal Carcinogenesis
    Michael S Donnenberg; Fiscal Year: 2010
    ..Our preliminary data suggest that Escherichia coli and in particular E. coli strains that have the E...
  60. Structural and Dynamical Response of Escherichia coli to Osmotic Stress
    James C Weisshaar; Fiscal Year: 2010
    ..In the longer term, our methods can be extended to the study of time-dependent drug effects on cytoplasmic organization and protein diffusion at a new level of detail. ..
  61. NMR Studies of Structures and Dynamics of Proteins
    Arthur G Palmer; Fiscal Year: 2013
    ..RNase H) by comparing the structural, dynamical and enzymatic properties of homologous proteins derived from Escherichia coli and the extremely thermophilic bacterium Thermus thermophilus...
  62. Bordetella adenylate cyclase toxin: the role of cell interaction in toxin functio
    JOSHUA CLARK EBY; Fiscal Year: 2013
    ..of pore-forming bacterial protein toxins that are produced by other pathogenic bacteria such as uropathogenic Escherichia coli. Here, we will characterize the basic mechanisms of cell binding by AC toxin and show that these mechanisms ..
  63. Molecular Modulation of Catalytic Sites of Escherichia coli F1Fo ATP Synthase
    Zulfiqar Ahmad; Fiscal Year: 2009
    ..0 million kg of ATP in a 75-year life span. In its simplest form, Escherichia coli contains eight different subunits. It can be separated into two sectors F1 and Fo...
  64. MECHANISM OF CARBOHYDRATE TRANSPORT IN BACTERIA
    Milton Saier; Fiscal Year: 2000
    Enteric bacteria such as Escherichia coli and Salmonella species are principal causative agents of diarrhea, dysentery, urinary tract infections, meningitis in children, septicemia, enteric fevers, an pneumonia...
  65. S. typhimiurium Vaccine Against Bacterial Enteropathogens
    Roy Curtiss; Fiscal Year: 2007
    ..2 million are the result of infections by Salmonella and other related bacterial enteropathogens including Escherichia coli and Shigella species, and less closely related enteropathogens such as Vibrio cholerae, Campylobacter jejuni ..
  66. SHIGA-LIKE TOXIN OF ESCHERICHIA COLI
    ALISON O BRIEN; Fiscal Year: 1991
    b>Escherichia coli can cause diarrhea by several distinct mechanisms. A newly recognized group of E. coli cause hemorrhagic colitis and the hemolytic uremic syndrome. These enterohemorrhagic E...
  67. Bacterial heme transport and hemoglobin expression
    Douglas Henderson; Fiscal Year: 2009
    Our long-term goal is to produce large amounts of recombinant human hemoglobin in Escherichia coli to allow commercial production of the protein for formulation of hemoglobin-based oxygen carriers which will be used for blood ..
  68. ESCHERICHIA COLI LT-RELATED ENTEROTOXINS
    RICHARD FINKELSTEIN; Fiscal Year: 1991
    ..k.a. LTs) from diarrheagenic strains of Escherichia coli of human (H) origin; LT from strains of E. coli of porcine (P) origin; a distinct LT, LT-II, from an E...
  69. REGULATION BY THE ESCHERICHIA COLI SMALL RNA, DSRA
    DARREN SLEDJESKI; Fiscal Year: 2002
    DsrA is a small, stable, untranslated RNA that is conserved between Escherichia coli, Klebsiella pneumoniae, and Salmonella typhimurium. DsrA RNA regulates two different global regulatory networks...
  70. Glycosylation of full-length antibodies in Escherichia coli
    ADAM FISHER; Fiscal Year: 2009
    ..Full-length monoclonal antibodies (immunoglobulins) can be produced in Escherichia coli that are functionally similar to those produced in mammalian cells except in the ability to bind macrophage ..
  71. E COLI TRANSLOCATION ACROSS INTESTINAL EPITHELIUM
    Michelle Pietzak; Fiscal Year: 2003
    ..D., Dr. Pietzak will continue to pursue her basic investigations into the mechanisms by which Escherichia coli (E. coli) is able to translocate across intestinal epithelium and cause sepsis. E...
  72. Humanizing N-linked glycosylation in Escherichia coli
    ADAM FISHER; Fiscal Year: 2009
    ..jejuni asparagine-linked (Nlinked) protein glycosylation system can be functionally transferred into Escherichia coli, giving the recipient E. coli cells the ability to glycosylate proteins...
  73. THE CLONAL NATURE OF CYTOTOXIGENIC E. COLI
    THOMAS WHITTAM; Fiscal Year: 1992
    ..research is to define the clonal population structure and genetic relationships of pathogenic forms of Escherichia coli, with special reference to cytotoxin-producing strains that only recently have been linked to enteric disease ..
  74. THE CLONAL NATURE OF CYTOTOXIGENIC E. COLI
    THOMAS WHITTAM; Fiscal Year: 1991
    ..research is to define the clonal population structure and genetic relationships of pathogenic forms of Escherichia coli, with special reference to cytotoxin-producing strains that only recently have been linked to enteric disease ..
  75. TREATMENT INTERVENTIONS FOR HEMORRHAGIC COLITIS
    Edgar Boedeker; Fiscal Year: 1999
    DESCRIPTION The broad aim of this application is to use a new animal model of enterohemorrhagic Escherichia coli (EHEC) infection to develop prophylactic and therapeutic regimens to prevent and treat EHEC disease...
  76. VIRUL FACTORS OF UROPATH ESCHERICHIA COLI
    Peter Redford; Fiscal Year: 2003
    b>Escherichia coli is the most common cause of community-acquired urinary tract infections, resulting in an estimated eight million physician visits a year in the United States. It is also a leading cause of nosocomial infections...
  77. DNA METHYLATION AND PILI GENE REGULATION
    David Low; Fiscal Year: 2006
    ..and PapI orchestrate the reversible switch between OFF and ON Pap pili expression states in uropathogenic Escherichia coli (UPEC)...
  78. Pathogenicity of Shiga Toxin-Producing E. coli
    ALISON O BRIEN; Fiscal Year: 2007
    DESCRIPTION (provided by applicant): Enterohemorrhagic Escherichia coli (EHEC) O157:H7 belongs to a subset of Shiga toxin-producing E coli (STEC) that makes Shiga toxin (Stx) type 1 or type 2 (or a variant thereof), or both toxins, ..