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This book 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. It contains detailed description of the procedures, discussion of potential difficulties and failures. All prools follow the successful Methods in Molecular Biology™ series format.
This book 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. It contains detailed description of the procedures, discussion of potential difficulties and failures. All prools follow the successful Methods in Molecular Biology™ series format.
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.
Table of Contents
INTRODUCTION
1. Karen Joy Shaw. Overview of Whole Genome Essentiality Analysis
Part I. EXPERIMENTAL PROTOCOLS
I.1 Populational genome-wide essentiality screens
2. Bill Reznikoff and Kelly Winterberg. Transposon-based strategies for the identification of essential bacterial genes.
3. Sandy M.S. Wong and Brian J. Akerley: Identification and analysis of essential genes in Haemophilus influenzae.
4. Jeffrey P. Murry, Christopher M. Sassetti, James M. Lane, Zhifang Xie, and Eric J. Rubin "Transposon site hybridization TraSH. in Mycobacterium tuberculosis"
5. François Sanschagrin, Irena Kukavica-Ibrulj, and Roger C. Levesque Essential genes in the infection model of P.aeruginosa PCR-based signature-tagged mutagenesis
6. Michael Scholle, Svetlana Gerdes "Whole-genome detection of conditionally essential and dispensable genes in E. coli via genetic footprinting"
7. Taeok Bae, Elizabeth Marland Glass, Olaf Schneewind, and Dominique Missiakas Generating a Collection of Insertion Mutations in the S. aureus Genome Using bursa aurealis
8. Anuj Kumar Multipurpose Transposon Insertion Libraries for Large-Scale Analysis of Gene Function in Yeast
I.2. Systematic collections of knockout mutants
9. Michael Jacobs "How to: make a defined near-saturation mutant library. Case one: Pseudomonas aeruginosa PAO1"
10. Nicole T. Liberati, Jonathan M. Urbach, Tara K. Thurber, Gang Wu, and Frederick M. Ausubel Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality.
11. Tomoya Baba and Hirotada Mori "The Construction of Systematic In- frame, Single-gene Knockout Mutant Collection in Escherichia coli K-12"
12. Tomoya Baba, Hsuan-Cheng Huan, Kirill Datsenko, Barry L. Wanner, and Hirotada Mori: "The Applications of Systematic In- frame, Single-gene Knockout Mutant Collection of Escherichia coli K-12"
13. Takeyoshi Miki, Yoshihiro Yamamoto, and Hideo Matsuda. A Novel, Simple, High-throughput Method for Isolation of Genome-wide Transposon Insertion Mutants of Escherichia coli K12
14. Angela M. Chu and Ronald W. Davis "High-throughput creation of a whole-genome collection of yeast knockout strains"
15. Pamela B. Meluh, Xuewen Pan, Daniel S. Yuan, Carol Tiffany, Ou Chen, Sharon Sookhai-Mahadeo, Xaioling Wang, Brian Peyser, Rafael Irizarry, Forrest Spencer, and Jef D. Boeke Analysis of Genetic Interactions on a Genome-Wide Scale in Budding Yeast: Diploid-based Synthetic Lethal Analysis by Microarray dSLAM.
I.3 Genome minimization
16. Tamás Fehér, Ildikó Karcagi, Zsuzsa Gyorfy, Kinga Umenhoffer, Bálint Csörgo and György Pósfai "Scarless engineering of the Escherichia coli genome"
17. Byung Jo Yu, and Sun Chang Kim: Minimization of the Escherichia coli genome using Tn5-targeted Cre/loxP excision system
18. Jun-ichi Kato and Masayuki Hashimoto Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome
I.4 Conditional knockouts
19. Dezhong Yin and Yinduo Ji. "Identification of essential genes in Staphylococcus aureus by construction and screening of conditional mutant library"
20. Allyn Forsyth and Liangsu Wang Techniques for the Isolation and Utilization of Conditionally Expressed Antisense RNA to Achieve Essential Gene Knockdowns in the Pathogen Staphylococcus aureus
21. Christopher D. Herring Introduction of conditional lethal amber mutations in Escherichia coli
Part II. BIOINFORMATICS
II.1. Statistics
22. Oliver Will "Statistical Methods for Building Random Transposon Mutagenesis Libraries"
23. Gábor Balázsi Statistical evaluation of genetic footprinting data
24. Alexander Grenov and Svetlana Gerdes Modeling competitive outgrowth of mutant populations: Why do different techniques yield divergent lists of essential genes?
25. Brian D. Peyser, Rafael A. Irizarry, and Forrest A. Spencer "Statistical Analysis of Fitness Data Determined by TAG Hybridization on Microarrays"
II.2 Data integration and Modeling
26. Yukiko Yamazaki, Hironori Niki and Jun-ichi Kato "Profiling of E. coli Chromosome PEC. Database"
27. Chun-Ting Zhang, and Ren Zhang "Gene essentiality analysis based on DEG, a database of essential genes"
28. Jae-Hoon Song and Kwan Soo Ko. Detection of Essential Genes in Strepoccus pneumoniae Using Bioinformatics and Allelic Replacement Mutagenesis
29. Isabel Rocha, Jochen Förster, and Jens Nielsen "Design and application of genome-scale reconstructed metabolic models".
30. Andrew R. Joyce and Bernhard Ø. Palsson Predicting gene essentiality using genome-scale in silico models.
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.
Special Features:
Table of Contents
INTRODUCTION
1. Karen Joy Shaw. Overview of Whole Genome Essentiality Analysis
Part I. EXPERIMENTAL PROTOCOLS
I.1 Populational genome-wide essentiality screens
2. Bill Reznikoff and Kelly Winterberg. Transposon-based strategies for the identification of essential bacterial genes.
3. Sandy M.S. Wong and Brian J. Akerley: Identification and analysis of essential genes in Haemophilus influenzae.
4. Jeffrey P. Murry, Christopher M. Sassetti, James M. Lane, Zhifang Xie, and Eric J. Rubin "Transposon site hybridization TraSH. in Mycobacterium tuberculosis"
5. François Sanschagrin, Irena Kukavica-Ibrulj, and Roger C. Levesque Essential genes in the infection model of P.aeruginosa PCR-based signature-tagged mutagenesis
6. Michael Scholle, Svetlana Gerdes "Whole-genome detection of conditionally essential and dispensable genes in E. coli via genetic footprinting"
7. Taeok Bae, Elizabeth Marland Glass, Olaf Schneewind, and Dominique Missiakas Generating a Collection of Insertion Mutations in the S. aureus Genome Using bursa aurealis
8. Anuj Kumar Multipurpose Transposon Insertion Libraries for Large-Scale Analysis of Gene Function in Yeast
I.2. Systematic collections of knockout mutants
9. Michael Jacobs "How to: make a defined near-saturation mutant library. Case one: Pseudomonas aeruginosa PAO1"
10. Nicole T. Liberati, Jonathan M. Urbach, Tara K. Thurber, Gang Wu, and Frederick M. Ausubel Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality.
11. Tomoya Baba and Hirotada Mori "The Construction of Systematic In- frame, Single-gene Knockout Mutant Collection in Escherichia coli K-12"
12. Tomoya Baba, Hsuan-Cheng Huan, Kirill Datsenko, Barry L. Wanner, and Hirotada Mori: "The Applications of Systematic In- frame, Single-gene Knockout Mutant Collection of Escherichia coli K-12"
13. Takeyoshi Miki, Yoshihiro Yamamoto, and Hideo Matsuda. A Novel, Simple, High-throughput Method for Isolation of Genome-wide Transposon Insertion Mutants of Escherichia coli K12
14. Angela M. Chu and Ronald W. Davis "High-throughput creation of a whole-genome collection of yeast knockout strains"
15. Pamela B. Meluh, Xuewen Pan, Daniel S. Yuan, Carol Tiffany, Ou Chen, Sharon Sookhai-Mahadeo, Xaioling Wang, Brian Peyser, Rafael Irizarry, Forrest Spencer, and Jef D. Boeke Analysis of Genetic Interactions on a Genome-Wide Scale in Budding Yeast: Diploid-based Synthetic Lethal Analysis by Microarray dSLAM.
I.3 Genome minimization
16. Tamás Fehér, Ildikó Karcagi, Zsuzsa Gyorfy, Kinga Umenhoffer, Bálint Csörgo and György Pósfai "Scarless engineering of the Escherichia coli genome"
17. Byung Jo Yu, and Sun Chang Kim: Minimization of the Escherichia coli genome using Tn5-targeted Cre/loxP excision system
18. Jun-ichi Kato and Masayuki Hashimoto Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome
I.4 Conditional knockouts
19. Dezhong Yin and Yinduo Ji. "Identification of essential genes in Staphylococcus aureus by construction and screening of conditional mutant library"
20. Allyn Forsyth and Liangsu Wang Techniques for the Isolation and Utilization of Conditionally Expressed Antisense RNA to Achieve Essential Gene Knockdowns in the Pathogen Staphylococcus aureus
21. Christopher D. Herring Introduction of conditional lethal amber mutations in Escherichia coli
Part II. BIOINFORMATICS
II.1. Statistics
22. Oliver Will "Statistical Methods for Building Random Transposon Mutagenesis Libraries"
23. Gábor Balázsi Statistical evaluation of genetic footprinting data
24. Alexander Grenov and Svetlana Gerdes Modeling competitive outgrowth of mutant populations: Why do different techniques yield divergent lists of essential genes?
25. Brian D. Peyser, Rafael A. Irizarry, and Forrest A. Spencer "Statistical Analysis of Fitness Data Determined by TAG Hybridization on Microarrays"
II.2 Data integration and Modeling
26. Yukiko Yamazaki, Hironori Niki and Jun-ichi Kato "Profiling of E. coli Chromosome PEC. Database"
27. Chun-Ting Zhang, and Ren Zhang "Gene essentiality analysis based on DEG, a database of essential genes"
28. Jae-Hoon Song and Kwan Soo Ko. Detection of Essential Genes in Strepoccus pneumoniae Using Bioinformatics and Allelic Replacement Mutagenesis
29. Isabel Rocha, Jochen Förster, and Jens Nielsen "Design and application of genome-scale reconstructed metabolic models".
30. Andrew R. Joyce and Bernhard Ø. Palsson Predicting gene essentiality using genome-scale in silico models.
| Book: | Microbial Gene Essentiality: Protocols & Bioinformatics: Methods In Molecular Biology |
| Author: | Osterman |
| ISBN: | 1588293785 |
| ISBN-13: | 9781588293787 |
| Binding: | Hardbound |
| Publishing Date: | 2008-02-01 |
| Publisher: | cbspd |
| Language: | English |
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