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
