Synthetic Gene Networks : Methods and Protocols

Part I. Design Strategies for Synthetic Gene Network

1. In silico Implementation of Synthetic Gene Networks

Maria Andrea Marchisio

2. Standardization in Synthetic Biology

Kristian M. Müller and Katja M. Arndt

3. Robust Optimal Design of Synthetic Biological Networks

Dirk Lebiedz, Marcel Rehberg, and Dominik Skanda

4. Predicting Synthetic Gene Networks

Diego di Bernardo, Lucia Marucci, Filippo Menolascina, and Velia Siciliano

Part II. Development and Characterization of the Synthetic Biology Toolbox

5. Reprogramming a GFP Reporter Gene Subjects it to Complex Lentiviral Gene Regulation

Frank Notka and Ralf Wagner

6. A High-throughput Microfluidic Method for Generating and Characterizing Transcription Factor Mutant Libraries

Marcel Geertz, Sylvie Rockel, and Sebastian J. Maerkl

7. Identifying and Optimizing Intracellular Protein-protein Interactions using Bacterial Genetic Selection

Dujduan Waraho and Matthew P. DeLisa

8. Zinc-finger Nucleases Based Genome Engineering to Generate Isogenic Human Cell Lines

Anne-Kathrin Dreyer and Toni Cathomen

9. RNA-based Networks: Using RNA Aptamers and Ribozymes as Synthetic Genetic Devices

Julia E. Weigandm Alexander Wittmann, and Beatrix Suess

10. MicroRNA Circuits for Transcriptional Logic

Madeleine Leisner, Leonidas Bleris, Jason Lohmueller, Zhen Xie, and Yaakov Benenson

11. Light-regulated Gene Expression in Yeast

Laszlo Kozma-Bognar, Anita Hajdu, and Ferenc Nagy

12. Light-controlled Gene Switches in Mammalian Cells

Fuzhong Zhang, Kristian M. Müller, G. Andrew Woolley, and Katja M. Arndt

13. Expressed Protein Modifications: Making Synthetic Proteins

Birgit Wiltschi

Part III. Optimizing the Host Systems

14. Using Transcription Machinery Engineering to Elicit Complex Cellular Phenotypes

Amanda M. Lanza and Hal S. Alper

15. Streamlining of a Pseudomonas putida Genome using a Combinatorial Deletion Method Based on Mini-transposon Insertion and the Flp-FRT Recombination System

Audrey Leprince, Danielle Janus, Victor de Lorenzo, and Vitor Martins dos Santos

16. Transposon-based and Plasmid-based Genetic Tools for Editing Genomes of Gram-negative Bacteria

Esteban Martinez-García and Víctor de Lorenzo

Part IV. Implementation of Synthetic Gene Networks in Different Host Systems

17. Synthetic Networks: Oscillators and Toggle Switches for Escherichia coli

Nicolas Perry and Alexander J. Ninfa

18. Studying Microbial Communities in Biofilms

Katie Brenner

19. Quantitative Analysis of the Spatiotemporal Dynamics of a Synthetic Predator-prey Ecosystem

Stephen Payne, Robert Phillip Smith, and Lingchong You

20. Drosophila S2 Schneider Cells - A Useful Tool for Rebuilding and Redesigning Approaches in Synthetic Biology

Jianying Yang and Michael Reth

21. Synthetic Gene Networks in Plant Systems

Astrid Junker and Björn H. Junker

22. Design and Construction of Synthetic Gene Networks in Mammalian Cells

Maria Karlsson, Wilfried Weber, Martin Fussenegger

23. Synthetic Gene Networks as Blueprint for Smart Hydrogels

Michael M. Kämpf and Wilfried Weber

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 information to design and construct synthetic gene networks in different host backgrounds. Divided into four convenient sections, this volume focuses on design concepts to devise synthetic gene networks and how mathematical models can be applied to the predictable engineering of desired network features. The volume continues by highlighting the construction and validation of biologic tools, describing strategies to optimize and streamline the host cell for optimized network performance, and covering how optimally designed gene networks can be implemented in a large variety of host cells ranging from bacteria over yeast and insect cells to plant and mammalian cell culture. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, Synthetic Gene Networks: Methods and Protocols serves as an invaluable resource for established biologists, engineers, and computer scientists or novices just entering into the rapidly growing field of synthetic biology