Microbial Systems Biology Methods and Protocols
Systems biology is the study of interactions between assorted components of biological systems with the aim of acquiring new insights into how organisms function and respond to different stimuli. Although more and more efforts are being direct
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MOLECULAR BIOLOGY
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes: http://www.springer.com/series/7651
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Microbial Systems Biology Methods and Protocols
Edited by
Ali Navid Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
Editor Ali Navid Biosciences and Biotechnology Division Physics and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore, CA, USA
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-826-9 e-ISBN 978-1-61779-827-6 DOI 10.1007/978-1-61779-827-6 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2012937211 ª Springer Science+Business Media, LLC 2012 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com)
Preface Revolutionary advances in high-throughput bioanalytical technologies have made it possible to shift the focus of biological studies away from a limited number of high-priority processes to those where the organism of interest, be it a bacterium, an infected host cell, a patient, or a multi-scale combination of all can be examined as a “system.” These forms of analyses are the primary focus of the new field of systems biology. Systems biology is a broad term used to describe the study of the interactions of a large number of disparate biochemical processes with the aim of garnering new insights into how organisms respond to different stimuli. Although more and more efforts are being directed toward examining the entirety of biological processes in complex multicellular organisms, the bulk of systemlevel analyses conducted to date have focused on the biology of microbes. The purpose of this book is to introduce the reader to some of the established and state-of-the-art technologies that are being used to study microbial systems biology. Although the majority of techniques that have been detailed in this book can easily be accessed by most investigators, some forms of systems biology analyses still require outsourcing to specialized centers. For example, NanoSIMS technology is not widely available and only a handful of labs operate this equipment. Similarly, genetic seque
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