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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, Synthetic Gene Networks: Methods and Protocols focuses on design concepts to devise synthetic gene networks and how mathematical models can be applied to the predictable engineering of desired network features. Gene Networks: Methods and Protocols 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
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. Muller 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. Muller, 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-Garcia and Victor 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 Bjorn 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. Kampf and Wilfried Weber
