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Gene Essentiality

Methods and Protocols

  • Book
  • © 2015

Overview

Editors:
  1. Long Jason Lu

    1. Cincinnati Children’s Hospital Medical Center, Cincinnati, USA

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  • Includes cutting-edge methods and protocols for the study of microbial gene essentiality
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1279)

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Table of contents (15 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

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

    • Martin Stahl, Alain Stintzi
    Pages 1-14

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

    • Lei Chen, Xiuchun Ge, Ping Xu
    Pages 15-23

  4. 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, Linden T. Hu
    Pages 25-43

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

    • Hirotada Mori, Tomoya Baba, Katsushi Yokoyama, Rikiya Takeuchi, Wataru Nomura, Kazuichi Makishi et al.
    Pages 45-65

  6. Identification of Genes Essential for Leptospirosis

    • Thanatchaporn Bartpho, Gerald L. Murray
    Pages 67-77

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

    • Jarukit E. Long, Michael DeJesus, Doyle Ward, Richard E. Baker, Thomas Ioerger, Christopher M. Sassetti
    Pages 79-95

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

    • Irena Kukavica-Ibrulj, Roger C. Levesque
    Pages 97-123

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

    • Brooke N. Horton, Anuj Kumar
    Pages 125-135

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

    • Jingyuan Deng
    Pages 137-151

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

    • Jingyuan Deng
    Pages 153-165

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

    • Mark Reuter, Duncan J. H. Gaskin, Aline Metris
    Pages 167-181

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

    • Georg Basler
    Pages 183-204

  14. Three Computational Tools for Predicting Bacterial Essential Genes

    • Feng-Biao Guo, Yuan-Nong Ye, Lu-Wen Ning, Wen Wei
    Pages 205-217

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

    • Feng Gao, Hao Luo, Chun-Ting Zhang, Ren Zhang
    Pages 219-233

  16. Discovering Essential Domains in Essential Genes

    • Yulan Lu, Yao Lu, Jingyuan Deng, Hui Lu, Long Jason Lu
    Pages 235-245

  17. Back Matter

    Pages 247-248
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Keywords

About this book

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.

Editors and Affiliations

  • Cincinnati Children’s Hospital Medical Center, Cincinnati, USA

    Long Jason Lu

Bibliographic Information

  • Book Title: Gene Essentiality

  • Book Subtitle: Methods and Protocols

  • Editors: Long Jason Lu

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-2398-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-2397-7Published: 31 January 2015

  • Softcover ISBN: 978-1-4939-4862-8Published: 05 October 2016

  • eBook ISBN: 978-1-4939-2398-4Published: 30 January 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 248

  • Number of Illustrations: 27 b/w illustrations, 15 illustrations in colour

  • Topics: Human Genetics, Microbial Genetics and Genomics

  • Industry Sectors: Biotechnology, Pharma

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