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TitleMicrobial Gene Essentiality: Protocols and Bioinformatics [electronic resource]
Author edited by Andrei L. Osterman, Svetlana Y. Gerdes
ImprintTotowa, NJ : Humana Press, 2008
Connect tohttp://dx.doi.org/10.1007/978-1-59745-321-9
Descript XIV, 486 p. online resource

SUMMARY

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


CONTENT

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


Life sciences Human genetics Biochemistry Cell biology Life Sciences Biochemistry general Cell Biology Human Genetics



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