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
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.
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
Microarray Transposon Tracking for the Mapping of Conditionally Essential Genes in Campylobacter jejuni.- Identifying Essential Streptococcus sanguinis Genes Using Genome-Wide Deletion Mutation.- Defining Essential Genes and Identifying Virulence Factors of Porphyromonas gingivalis by Massively-Parallel Sequencing of Transposon Libraries (Tn-seq).- Identification of Essential Genes and Synthetic Lethal Gene Combinations in Escherichia coli K-12.- Identification of Genes Essential for Leptospirosis.- Identifying Essential Genes in Mycobacterium tuberculosis by Global Phenotypic Profiling.- Essential Genes in the Infection Model of Pseudomonas aeruginosa-PCR-Based Signature-Tagged Mutagenesis.- Genome-Wide Synthetic Genetic Screening by Transposon Mutagenesis in Candida albicans.- An Integrated Machine-Learning Model to Predict Prokaryotic Essential Genes.- A Statistical Framework for Improving Genomic Annotations of Transposon Mutagenesis (TM) Assigned Essential Genes.- A Proposed Essential Gene Discovery Pipeline: A Campylobacter jejuni Case Study.- Computational Prediction of Essential Metabolic Genes Using Constraint-Based Approaches.- Three Computational Tools for Predicting Bacterial Essential Genes.- Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes.- A Novel Essential Domain Perspective for Exploring Gene Essentiality.
Inhaltsverzeichnis
Microarray Transposon Tracking for the Mapping of Conditionally Essential Genes in Campylobacter jejuni.- Identifying Essential Streptococcus sanguinis Genes Using Genome-Wide Deletion Mutation.- Defining Essential Genes and Identifying Virulence Factors of Porphyromonas gingivalis by Massively-Parallel Sequencing of Transposon Libraries (Tn-seq).- Identification of Essential Genes and Synthetic Lethal Gene Combinations in Escherichia coli K-12.- Identification of Genes Essential for Leptospirosis.- Identifying Essential Genes in Mycobacterium tuberculosis by Global Phenotypic Profiling.- Essential Genes in the Infection Model of Pseudomonas aeruginosa-PCR-Based Signature-Tagged Mutagenesis.- Genome-Wide Synthetic Genetic Screening by Transposon Mutagenesis in Candida albicans.- An Integrated Machine-Learning Model to Predict Prokaryotic Essential Genes.- A Statistical Framework for Improving Genomic Annotations of Transposon Mutagenesis (TM) Assigned Essential Genes.- A Proposed Essential Gene Discovery Pipeline: A Campylobacter jejuni Case Study.- Computational Prediction of Essential Metabolic Genes Using Constraint-Based Approaches.- Three Computational Tools for Predicting Bacterial Essential Genes.- Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes.- A Novel Essential Domain Perspective for Exploring Gene Essentiality.
Klappentext
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.nAuthoritative and up-to-date, Gene Essentiality: Methods and Protocols will aid researchers who wish to further our knowledge in this vital field of study.
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
