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(TM) 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.

Overview of Whole-Genome Essentiality Analysis.- Experimental Protocols.- 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 Streptococcus 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.