Microbial Gene Essentiality: Protocols and Bioinformatics / Edition 1

by Andrei L. Osterman, Svetlana Y. Gerdes

Overview

Microbial Gene Essentiality: Prools 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 prools, 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: Prools and Bioinformatics reflects both of these aspects. All prools 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.

Product Details

ISBN-13:	9781588293787
Publisher:	Springer-Verlag New York, LLC
Publication date:	02/04/2008
Series:	Methods in Molecular Biology , #416
Edition description:	2008
Pages:	486
Product dimensions:	7.20(w) x 10.00(h) x 1.30(d)

Table of Contents

Overview of Whole-Genome Essentiality Analysis.- Experimental Prools.- Transposon-Based Strategies for the Identification of Essential Bacterial Genes.- Identification and Analysis of Essential Genes in Haemophilus influenzae.- Transposon Site Hybridization in Mycobacterium tuberculosis.- Essential Genes in the Infection Model of Pseudomonas aeruginosa PCR-Based Signature-Tagged Mutagenesis.- Whole-Genome Detection of Conditionally Essential and Dispensable Genes in Escherichia coli via Genetic Footprinting.- Generating a Collection of Insertion Mutations in the Staphylococcus aureus Genome Using bursa aurealis.- Multipurpose Transposon Insertion Libraries for Large-Scale Analysis of Gene Function in Yeast.- How to Make a Defined Near-Saturation Mutant Library. Case 1: Pseudomonas aeruginosa PAO1.- Comparing Insertion Libraries in Two Pseudomonas aeruginosa Strains to Assess Gene Essentiality.- The Construction of Systematic In-Frame, Single-Gene Knockout Mutant Collection in Escherichia coli K-12.- The Applications of Systematic In-Frame, Single-Gene Knockout Mutant Collection of Escherichia coli K-12.- A Novel, Simple, High-Throughput Method for Isolation of Genome-Wide Transposon Insertion Mutants of Escherichia coli K-12.- High-Throughput Creation of a Whole-Genome Collection of Yeast Knockout Strains.- Analysis of Genetic Interactions on a Genome-Wide Scale in Budding Yeast: Diploid-Based Synthetic Lethality Analysis by Microarray.- Scarless Engineering of the Escherichia coli Genome.- Minimization of the Escherichia coli Genome Using the Tn5-Targeted Cre/loxP Excision System.- Construction of Long Chromosomal Deletion Mutants of Escherichia coli and Minimization of the Genome.- Identification of Essential Genes in Staphylococcus aureus by Construction and Screening of Conditional Mutant Library.- Techniques for the Isolation and Use of Conditionally Expressed Antisense RNA to Achieve Essential Gene Knockdowns in Staphylococcus aureus.- of Conditional Lethal Amber Mutations in Escherichia coli.- Bioinformatics.- Statistical Methods for Building Random Transposon Mutagenesis Libraries.- Statistical Evaluation of Genetic Footprinting Data.- Modeling Competitive Outgrowth of Mutant Populations: Why Do Essentiality Screens Yield Divergent Results?.- Statistical Analysis of Fitness Data Determined by TAG Hybridization on Microarrays.- Profiling of Escherichia coli Chromosome Database.- Gene Essentiality Analysis Based on DEG, a Database of Essential Genes.- Detection of Essential Genes in Strepoccus pneumoniae Using Bioinformatics and Allelic Replacement Mutagenesis.- Design and Application of Genome-Scale Reconstructed Metabolic Models.- Predicting Gene Essentiality Using Genome-Scale in Silico Models.- Comparative Approach to Analysis of Gene Essentiality.

Editorial Reviews

Reviewer: Omer Iqbal, MD, FACC, FESC (Loyola University Medical Center)
Description: This book reflects the editors' ideas of development and application of a variety of techniques, especially the experimental and computational aspects, for genome-scale analysis of gene essentiality in diverse microorganisms. The first of the book's two parts, on experimental protocols, is divided into four sections covering population genome-wide essentiality screens (8 chapters), systematic collections of knockout mutants (7 chapters), genome minimization (6 chapters), and conditional knockouts (3 chapters). The second part of the book on bioinformatics is divided into two sections, statistics (4 chapters) and data integration and modeling (6 chapters).
Purpose: According to the editors, "this book provides researchers with a first-stop guide for choosing the most appropriate strategy for their planned essentiality studies." Their purpose is fulfilled in this well written, well illustrated book.
Audience: It is intended for new investigators in the area of microbial gene essentiality, and it may be of interest to graduate students and researchers in this area.
Features: An introduction provides an overview of whole-genome essentiality analysis and a preview of the essence of each chapter, which readers will find very useful. Each chapter begins with a summary and key words and ends with a concise conclusion interspersed with numerous illustrations. The book provides the essence of the main strategies of experimental genome-scale gene essentiality analysis, a detailed description of the procedures including a discussion of potential difficulties and failures, and adequate coverage of statistical analysis of the generated datasets and their integration into existing databases. It covers essential concepts of comparative genomics and mutant analysis which help elucidate the role of specific genes in the life cycle of an organism. It deals with the development and application of a variety of techniques, especially the experimental and computational aspects, for genome-scale analysis of gene essentiality in diverse microorganisms. The illustrations will facilitate the understanding of intricate details, but color illustrations would have added a new dimension and would have greatly enhanced the book.
Assessment: This book is quite unique in providing complex intricate details of protocols and bioinformatics related to microbial gene essentiality in a clear, easy to understand way. The book will be if immense use to new investigators in this area and will greatly facilitate the identification of novel antibacterial and antifungal drug targets. There are very few books in this growing area and hence this book will be of much use to new investigators and students.

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