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© 2015

Prokaryotic Systems Biology

  • Nevan J. Krogan, PhD
  • Mohan Babu, PhD

Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 883)

Table of contents

  1. Front Matter
    Pages i-ix
  2. Ana Popovic, Anatoly Tchigvintsev, Hai Tran, Tatyana N. Chernikova, Olga V. Golyshina, Michail M. Yakimov et al.
    Pages 1-20
  3. Karine Dufresne, Catherine Paradis-Bleau
    Pages 41-76
  4. Cedoljub Bundalovic-Torma, John Parkinson
    Pages 77-96
  5. Viktor Deineko, Ashwani Kumar, James Vlasblom, Mohan Babu
    Pages 135-154
  6. Hirotada Mori, Rikiya Takeuchi, Yuta Otsuka, Steven Bowden, Katsushi Yokoyama, Ai Muto et al.
    Pages 155-168
  7. Omar Wagih, Leopold Parts
    Pages 169-185
  8. Charles Calmettes, Andrew Judd, Trevor F. Moraes
    Pages 255-270
  9. Colin A. Cooper, Iain L. Mainprize, Nicholas N. Nickerson
    Pages 295-315
  10. Back Matter
    Pages 317-319

About this book

Introduction

This book focuses on innovative experimental and computational approaches for charting interaction networks in bacterial species. The first part of the volume consists of nine chapters, focusing on biochemical and genetics and genomics approaches including yeast two hybrid, metagenomics, affinity purification in combination with mass spectrometry, chromatin-immunoprecipitation coupled with sequencing, large-scale synthetic genetic screens, and quantitative-based mass spectrometry strategies for mapping the bacterial physical, functional, substrate, and regulatory interaction networks needed for interpreting biological networks, inferring gene function, enzyme discovery, and identifying new drug targets.

The second part comprises five chapters, covering the network of participants for protein folding and complex enzyme maturation. It also covers the structural approaches required to understand bacterial intramembrane proteolysis and the structure and function of bacterial proteins involved in surface polysaccharides, outer membrane, and envelope assembly.

This volume concludes with a focus on computational and comparative genomics approaches, especially network-based methods for predicting physical or functional interactions, and integrative analytical approaches for generating more reliable information on bacterial gene function. This book provides foundational knowledge in the understanding of prokaryotic systems biology by illuminating how bacterial genes f

unction within the framework of global cellular processes. The book will enable the microbiology community to create substantive resources for addressing many pending unanswered questions, and facilitate the development of new technologies that can be applied to other bacterial species lacking experimental data. ​ ​

Keywords

genomics integrative biology prokaryotes proteomics systems biology

Editors and affiliations

  • Nevan J. Krogan, PhD
    • 1
  • Mohan Babu, PhD
    • 2
  1. 1.Cellular and Molecular PharmacologyUniv of California, San FranciscoSAN FRANCISCOUSA
  2. 2.Department of BiochemistryUniversity of ReginaReginaCanada

About the editors

Nevan Krogan, PhD, is a professor at the UCSF School of Medicine in the Cellular Molecular Pharmacology department. Dr. Krogan’s lab focuses on applying global proteomic and genomic approaches to formulate hypotheses about various biological processes, including transcriptional regulation, DNA repair/replication and RNA processing. His lab at UCSF is now developing and applying methodologies to create genetic and physical interactions between pathogenic organisms, including HIV, Mtb, and Dengue, and their hosts, which is providing insight into the human pathways and complexes that are being hijacked during the course of infection.

Mohan Babu, PhD, is an Assistant Professor in the Department of Biochemistry at the University of Regina. Dr. Babu currently holds a CIHR New Investigator award and is a Maud-Menten Finalist of the CIHR Institute of Genetics. He is a member of the Canadian Society of Microbiology, Human Proteome Organization, and Canadian National Proteomics Network. Dr. Babu has developed and applied advanced proteomic, functional genomic, and bioinformatic methods to characterize genome-wide protein and epistatic interaction networks in the budding yeast and gram-negative bacterium, and mammalian cell systems. His group also developed advanced proteomics using affinity purification coupled with mass spectrometry technology to analyze the molecular composition of protein complexes and interactions 

related to major diseases in humans. 

Bibliographic information

  • Book Title Prokaryotic Systems Biology
  • Editors Nevan J. Krogan, PhD
    Mohan Babu, PhD
  • Series Title Advances in Experimental Medicine and Biology
  • Series Abbreviated Title Adv Exp Med Biol
  • DOI https://doi.org/10.1007/978-3-319-23603-2
  • Copyright Information Springer International Publishing Switzerland 2015
  • Publisher Name Springer, Cham
  • eBook Packages Biomedical and Life Sciences Biomedical and Life Sciences (R0)
  • Hardcover ISBN 978-3-319-23602-5
  • Softcover ISBN 978-3-319-79508-9
  • eBook ISBN 978-3-319-23603-2
  • Series ISSN 0065-2598
  • Series E-ISSN 2214-8019
  • Edition Number 1
  • Number of Pages IX, 319
  • Number of Illustrations 3 b/w illustrations, 55 illustrations in colour
  • Topics Systems Biology
    Proteomics
    Bacteriology
  • Buy this book on publisher's site
Industry Sectors
Biotechnology
Pharma