Synthetic Gene Networks Methods and Protocols

The rapid expansion of synthetic biology is due to the design and construction of synthetic gene networks that have opened many new avenues in fundamental and applied research. Synthetic Gene Networks: Methods and Protocols provides the necessary informat

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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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Synthetic Gene Networks Methods and Protocols

Edited by

Wilfried Weber BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland

Martin Fussenegger Department of Biosystems Science and Engineering, ETH Zurich, University of Basel, Basel, Switzerland

Editors Wilfried Weber BIOSS Centre for Biological Signalling Studies University of Freiburg Freiburg, Germany and Department of Biosystems Science and Engineering ETH Zurich Basel, Switzerland [email protected]

Martin Fussenegger Department of Biosystems Science and Engineering ETH Zurich University of Basel Basel, Switzerland [email protected]

ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-411-7 e-ISBN 978-1-61779-412-4 DOI 10.1007/978-1-61779-412-4 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2011940329 © 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 The rapid expansion of synthetic biology showing exponentially growing publication numbers is based on the design and construction of synthetic gene networks opening many new avenues in fundamental and applied research. In this book, we provide comprehensive information to design and construct synthetic gene networks in different host backgrounds. In the first section, we focus on design concepts to devise synthetic gene networks and how mathematical models can be applied to the predictable engineering of desired network features while taking into account inherent cellular imponderability like noise and stochastic fluctuations. The second section highlights the construction and validation of biologic tools ranging from engineering the codon usage to the development and validation of sophisticated RNA-based switches. In the third section, strategies are described to optimize and streamline the host cell for optimized network performance. The last section forms a synthesis of the previous