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Microbial gene essentiality : protocols and bioinformatics / edited by Andrei L. Osterman and Svetlana Y. Gerdes. — Totowa, N.J. : Humana Press, c2008. – (58.17/M592/v.416) |
Contents
Contents
Preface v
Contributors xi
Introduction
1 Overview of Whole-Genome Essentiality Analysis
Part I Experimental Protocols
IA Populational Genome-Wide Essentiality Screens
2 Transposon-Based Strategies for the Identification of Essential Bacterial Genes
3 Identification and Analysis of Essential Genes in Haemophilus influenzae
4 Transposon Site Hybridization in Mycobacterium tuberculosis
5 Essential Genes in the Infection Model of Pseudomonas aeruginosa PCR-Based Signature-Tagged Mutagenesis
6 Whole-Genome Detection of Conditionally Essential and Dispensable Genes in Escherichia coli via Genetic Footprinting
7 Generating a Collection of Insertion Mutations in the Staphylococcus aureus Genome Using bursa aurealis
8 Multipurpose Transposon Insertion Libraries for Large-Scale Analysis of Gene Function in Yeast
IB Systematic Collections of Knockout Mutants
9 How to Make a Defined Near-Saturation Mutant Library. Case 1: Pseudomonas aeruginosa PAO1
10 Comparing Insertion Libraries in Two Pseudomonas aeruginosa Strains to Assess Gene Essentiality
11 The Construction of Systematic In-Frame， Single-Gene Knockout Mutant Collection in Escherichia coli K-12 Tomoya Baba and Hirotada Mori 171
12 The Applications of Systematic In-Frame， Single-Gene Knockout Mutant Collection of Escherichia coil K-12
13 A Novel， Simple， High-Throughput Method for Isolation of Genome- Wide Transposon Insertion Mutants of Escherichia coli K-12
14 High-Throughput Creation of a Whole-Genome Collection of Yeast Knockout Strains
15 Analysis of Genetic Interactions on a Genome-Wide Scale in Budding Yeast: Diploid-Based Synthetic Lethality Analysis by Microarray
IC Genome Minimization
16 Scarless Engineering of the Escherichia coli Genome
17 Minimization of the Escherichia coli Genome Using the Tn5-Targeted Cre/IoxP Excision System
18 Construction of Long Chromosomal Deletion Mutants of Escherichia coli and Minimization of the Genome
ID Conditional Knockouts
19 Identification of Essential Genes in Staphylococcus aureus by Construction and Screening of Conditional Mutant Library
20 Techniques for the Isolation and Use of Conditionally Expressed Antisense RNA to Achieve Essential Gene Knockdowns in Staphylococcus aureus
21 Introduction of Conditional Lethal Amber Mutations in Escherichia coil
Part II Bioinformatics
IIA Statistics
22 Statistical Methods for Building Random Transposon Mutagenesis Libraries
23 Statistical Evaluation of Genetic Footprinting Data
24 Modeling Competitive Outgrowth of Mutant Populations: Why Do Essentiality Screens Yield Divergent Results?
25 Statistical Analysis of Fitness Data Determined by TAG Hybridization on Microarrays
IIB Data Integration and Modeling
26 Profiling of Escherichia coil Chromosome Database
27 Gene Essentiality Analysis Based on DEG， a Database of Essential Genes
28 Detection of Essential Genes in Streptococcus pneumoniae Using Bioinformatics and Allelic Replacement Mutagenesis
29 Design and Application of Genome-Scale Reconstructed Metabolic Models
30 Predicting Gene Essentiality Using Genome-Scale in Silico Models
31 Comparative Approach to Analysis of Gene Essentiality
