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Microbial Gene Essentiality: Protocols and Bioinformatics

  • Book
  • © 2008

Overview

Editors:
  1. Andrei L. Osterman

    1. Burnham Institute for Medical Research, La Jolla

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  2. Svetlana Y. Gerdes

    1. Fellowship for Interpretation of Genomes (FIG), Burr Ridge

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    You can also search for this editor in PubMed   Google Scholar

  • Offers a comprehensive, up-to-date collection of all the main strategies of experimental genome-scale gene essentiality analysis
  • Contains a detailed description of the procedures as well as a discussion of potential difficulties and failures
  • Includes chapters on statistical analysis of the generated datasets and their integration into existing genomic databases
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 416)

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Table of contents (31 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Introduction

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Overview of Whole-Genome Essentiality Analysis

      • Karen Joy Shaw
      Pages 3-8

  3. Experimental Protocols

    1. Front Matter

      Pages 9-11
      Download chapter PDF

    2. Populational Genome-Wide Essentiality Screens

      1. Transposon-Based Strategies for the Identification of Essential Bacterial Genes
        • William S. Reznikoff, Kelly M. Winterberg
        Pages 13-26
      2. Identification and Analysis of Essential Genes in <i>Haemophilus influenzae</i>
        • Sandy M.S. Wong, Brian J. Akerley
        Pages 27-44
      3. Transposon Site Hybridization in <i>Mycobacterium tuberculosis</i>
        • Jeffrey P. Murry, Christopher M. Sassetti, James M. Lane, Zhifang Xie, Eric J. Rubin
        Pages 45-59
      4. Essential Genes in the Infection Model of <i>Pseudomonas aeruginosa</i> PCR-Based Signature-Tagged Mutagenesis
        • François Sanschagrin, Irena Kukavica-Ibrulj, Roger C. Levesque
        Pages 61-82
      5. Whole-Genome Detection of Conditionally Essential and Dispensable Genes in <i>Escherichia coli</i> via Genetic Footprinting
        • Michael D. Scholle, Svetlana Y. Gerdes
        Pages 83-102
      6. Generating a Collection of Insertion Mutations in the <i>Staphylococcus aureus</i> Genome Using <i>bursa aurealis</i>
        • Taeok Bae, Elizabeth M. Glass, Olaf Schneewind, Dominique Missiakas
        Pages 103-116
      7. Multipurpose Transposon Insertion Libraries for Large-Scale Analysis of Gene Function in Yeast
        • Anuj Kumar
        Pages 117-129

    3. Systematic Collections of Knockout Mutants

      1. How to Make a Defined Near-Saturation Mutant Library. Case 1: <i>Pseudomonas aeruginosa</i> PAO1
        • Michael A. Jacobs
        Pages 133-152
      2. Comparing Insertion Libraries in Two <i>Pseudomonas aeruginosa</i> Strains to Assess Gene Essentiality
        • Nicole T. Liberati, Jonathan M. Urbach, Tara K. Thurber, Gang Wu, Frederick M. Ausubel
        Pages 153-169
      3. The Construction of Systematic In-Frame, Single-Gene Knockout Mutant Collection in <i>Escherichia coli</i> K-12
        • Tomoya Baba, Hirotada Mori
        Pages 171-181
      4. The Applications of Systematic In-Frame, Single-Gene Knockout Mutant Collection of <i>Escherichia coli</i> K-12
        • Tomoya Baba, Hsuan-Cheng Huan, Kirill Datsenko, Barry L. Wanner, Hirotada Mori
        Pages 183-194
      5. A Novel, Simple, High-Throughput Method for Isolation of Genome-Wide Transposon Insertion Mutants of <i>Escherichia coli</i> K-12
        • Takeyoshi Miki, Yoshihiro Yamamoto, Hideo Matsuda
        Pages 195-204
      6. High-Throughput Creation of a Whole-Genome Collection of Yeast Knockout Strains
        • Angela M. Chu, Ronald W. Davis
        Pages 205-220
      7. Analysis of Genetic Interactions on a Genome-Wide Scale in Budding Yeast: Diploid-Based Synthetic Lethality Analysis by Microarray
        • Pamela B. Meluh, Xuewen Pan, Daniel S. Yuan, Carol Tiffany, Ou Chen, Sharon Sookhai-Mahadeo et al.
        Pages 221-247

    4. Genome Minimization

      1. Scarless Engineering of the <i>Escherichia coli</i> Genome
        • Tamás Fehér, Ildikó Karcagi, Zsuzsa Győrfy, Kinga Umenhoffer, Bálint Csörgő, György Pósfai
        Pages 251-259
      2. Minimization of the <i>Escherichia coli</i> Genome Using the Tn<i>5</i>-Targeted Cre/<i>loxP</i> Excision System
        • Byung Jo Yu, Sun Chang Kim
        Pages 261-277
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Keywords

About this book

Microbial Gene Essentiality: Protocols and Bioinformatics contains a comprehensive collection of experimental and computational strategies and techniques for microbial genome-scale essentiality studies, developed and presented by the leading groups in the field. In addition to wet-lab protocols, the book describes (i) statistical methods essential for planning successful large-scale essentiality screens, as well for data evaluation and analysis; (ii) in-silico prediction of gene essentiality using genome-scale reconstructed metabolic models; and (iii) data integration and comparative analysis in the context of genomic databases. This volume provides researchers with a first-stop guide for choosing the most appropriate strategy for planned essentiality studies. Experimental and computational aspects are equally important in genome-scale gene essentiality analysis, as in all other genomic technologies, and Microbial Gene Essentiality: Protocols and Bioinformatics reflects both of these aspects. All protocols follow the successful Methods in Molecular Biology™ series format, each offering an introduction outlining the principles behind the techniques, step-by-step instructions, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding pitfalls, and are intended for both novice and expert scientists.

Editors and Affiliations

  • Burnham Institute for Medical Research, La Jolla

    Andrei L. Osterman

  • Fellowship for Interpretation of Genomes (FIG), Burr Ridge

    Svetlana Y. Gerdes

Bibliographic Information

  • Book Title: Microbial Gene Essentiality: Protocols and Bioinformatics

  • Editors: Andrei L. Osterman, Svetlana Y. Gerdes

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-321-9

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2008

  • Hardcover ISBN: 978-1-58829-378-7Published: 04 February 2008

  • Softcover ISBN: 978-1-61737-529-3Published: 19 November 2010

  • eBook ISBN: 978-1-59745-321-9Published: 08 April 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 486

  • Topics: Biochemistry, general, Cell Biology, Human Genetics

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