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Synthetic gene networks : methods and protocols / edited by Wilfried Weber, Martin Fussenegger. — New York : Humana Press, c2012. – (58.17/M592/v.813) |
Contents
CONTENTS
Preface
Contributors
PART I DESIGN STRATEGIES FOR SYNTHETIC GENE NETWORK
1 In Silico Implementation of Synthetic Gene Networks
2 Standardization in Synthetic Biology
3 Robust Optimal Design of Synthetic Biological Networks
4 Predicting Synthetic Gene Networks
PART II DEVELOPMENT AND CHARACTERIZATION OF THE SYNTHETIC BIOLOGY TOOLBOX
5 Reprogramming a GFP Reporter Gene Subjects It to Complex Lentiviral Gene Regulation 85
6 A High-Throughput Microfluidic Method for Generating and Characterizing Transcription Factor Mutant Libraries 107
7 Identifying and Optimizing Intracellular Protein-Protein Interactions Using Bacterial Genetic Selection
8 Zinc-Finger Nucleases-Based Genome Engineering to Generate Isogenic Human Cell Lines 145
9 RNA-Based Networks: Using RNA Aptamers and Ribozymes as Synthetic Genetic Devices
10 MicroRNA Circuits for Transcriptional Logic
11 Light-Regulated Gene Expression in Yeast
12 Light-Controlled Gene Switches in Mammalian Cells
13 Expressed Protein Modifications: Making Synthetic Proteins
PART III OPTIMIZING THE HOST SYSTEMS
14 Using Transcription Machinery Engineering to Elicit Complex Cellular Phenotypes
15 Streamlining of a Pseudomonas putida Genome Using a Combinatorial Deletion Method Based on Minitransposon Insertion and the Flp-FRT Recombination System
16 Transposon-Based and Plasmid-Based Genetic Tools for Editing Genomes of Gram-Negative Bacteria 267
PART IV IMPLEMENTATION OF SYNTHETIC GENE NETWORKS IN DIFFERENT HOST SYSTEMS
17 Synthetic Networks: Oscillators and Toggle Switches for Escherichia coli 287
18 Studying Microbial Communities in Biofilms 301
19 Quantitative Analysis of the Spatiotemporal Dynamics of a Synthetic Predator-Prey Ecosystem 315
20 Drosophila S2 Schneider Cells: A Useful Tool for Rebuilding and Redesigning Approaches in Synthetic Biology 331
21 Synthetic Gene Networks in Plant Systems 343
22 Design and Construction of Synthetic Gene Networks in Mammalian Cells 359
23 Synthetic Gene Networks as Blueprint for Smart Hydrogels 377
Index 391
