Synthetic Gene Networks: Methods and Protocols (Methods in Molecular Biology)

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(TM) 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. Mller 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. Mller, 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-Garca and Vctor 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 Bjrn 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. Kmpf and Wilfried Weber