Gene Essentiality: Methods and Protocols

ISBN-13: 9781493923977 / Angielski / Twarda / 2015 / 248 str.

Long Jason Lu

Opis

This volume opens by covering two main types of approaches widely used to determine essential genes: single-gene knockouts and transposon mutagenesis, in both prokaryotes and Candida albicans. Given the significant advancement in the computational predictions of microbial essential genes, the second half of the book examines four main types of approaches: comparative genomics, supervised machine learning, constraint-based methods, and corrections of transposon mutagenesis data, as well as databases and servers that are often used in studying gene essentiality. Written in the highly successful Methods in Molecular Biology series format, chapters include an introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Authoritative and up-to-date, Gene Essentiality: Methods and Protocols will aid researchers who wish to further our knowledge in this vital field of study.

Spis treści

1. Microarray Transposon Tracking for the Mapping of Conditionally Essential Genes in Campylobacter jejuni

            Martin Stahl and Alain Stintzi

 

2. Identifying Essential Streptococcus sanguinis Genes Using Genome-Wide Deletion Mutation

            Lei Chen, Xiuchun Ge, and Ping Xu

 

3. Defining Essential Genes and Identifying Virulence Factors of Porphyromonas gingivalis by Massively-Parallel Sequencing of Transposon Libraries (Tn-seq)

            Brian A. Klein, Margaret J. Duncan, and Linden T. Hu

 

4. Identification of Essential Genes and Synthetic Lethal Gene Combinations in Escherichia coli K-12

            Hirotada Mori, Katsushi Yokoyama, Rikiya Takeuchi, Kazuichi Makishi, Wataru Nomura, Yuta Otsuka, Hitomi Dose, and Barry L. Wanner

 

5. Identification of Genes Essential for Leptospirosis

            Thanatchaporn Bartpho and Gerald L. Murray

 

6. Identifying Essential Genes in Mycobacterium tuberculosis by Global Phenotypic Profiling

            Jarukit E. Long, Michael DeJesus, Doyle Ward, Richard E. Baker, Thomas Ioerger, and Christopher M. Sassetti

 

7. Essential Genes in the Infection Model of Pseudomonas aeruginosa-PCR-Based Signature-Tagged Mutagenesis

            Irena Kukavica-Ibrulj and Roger C. Levesque

 

8. Genome-Wide Synthetic Genetic Screening by Transposon Mutagenesis in Candida albicans

            Brooke N. Horton and Anuj Kumar

 

9. An Integrated Machine-Learning Model to Predict Prokaryotic Essential Genes

            Jingyuan Deng

 

10. A Statistical Framework for Improving Genomic Annotations of Transposon Mutagenesis (TM) Assigned Essential Genes

            Jingyuan Deng

 

11. A Proposed Essential Gene Discovery Pipeline: A Campylobacter jejuni Case Study

            Mark Reuter, Duncan J.H. Gaskin, and Aline Metris

 

12. Computational Prediction of Essential Metabolic Genes Using Constraint-Based Approaches

            Georg Basler

 

13. Three Computational Tools for Predicting Bacterial Essential Genes

            Feng-Biao Guo, Yuan-Nong Ye, Lu-Wen Ning, and Wen Wei

 

14. Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes

            Feng Gao, Hao Luo, Chun-Ting Zhang, and Ren Zhang

 

15. A Novel Essential Domain Perspective for Exploring Gene Essentiality

            Yulan Lu, Yao Lu, Jingyuan Deng, Hui Lu, and Long Jason Lu