Synthetic Gene Networks

Methods and Protocols

Editors:

ISBN: 978-1-61779-411-7 (Print) 978-1-61779-412-4 (Online)

Table of contents (23 protocols)

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  1. Front Matter

    Pages i-xi

  2. Design Strategies for Synthetic Gene Network

    1. Front Matter

      Pages 1-1

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      Pages 3-21

      In Silico Implementation of Synthetic Gene Networks

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      Pages 23-43

      Standardization in Synthetic Biology

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      Pages 45-55

      Robust Optimal Design of Synthetic Biological Networks

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      Pages 57-81

      Predicting Synthetic Gene Networks

  3. Development and Characterization of the Synthetic Biology Toolbox

    1. Front Matter

      Pages 83-83

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      Pages 85-106

      Reprogramming a GFP Reporter Gene Subjects It to Complex Lentiviral Gene Regulation

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      Pages 107-123

      A High-Throughput Microfluidic Method for Generating and Characterizing Transcription Factor Mutant Libraries

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      Pages 125-143

      Identifying and Optimizing Intracellular Protein–Protein Interactions Using Bacterial Genetic Selection

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      Pages 145-156

      Zinc-Finger Nucleases-Based Genome Engineering to Generate Isogenic Human Cell Lines

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      Pages 157-168

      RNA-Based Networks: Using RNA Aptamers and Ribozymes as Synthetic Genetic Devices

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      Pages 169-186

      MicroRNA Circuits for Transcriptional Logic

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      Pages 187-193

      Light-Regulated Gene Expression in Yeast

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      Pages 195-210

      Light-Controlled Gene Switches in Mammalian Cells

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      Pages 211-225

      Expressed Protein Modifications: Making Synthetic Proteins

  4. Optimizing the Host Systems

    1. Front Matter

      Pages 227-227

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      Pages 229-248

      Using Transcription Machinery Engineering to Elicit Complex Cellular Phenotypes

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      Pages 249-266

      Streamlining of a Pseudomonas putida Genome Using a Combinatorial Deletion Method Based on Minitransposon Insertion and the Flp-FRT Recombination System

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      Pages 267-283

      Transposon-Based and Plasmid-Based Genetic Tools for Editing Genomes of Gram-Negative Bacteria

  5. Implementation of Synthetic Gene Networks in Different Host Systems

    1. Front Matter

      Pages 285-285

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      Pages 287-300

      Synthetic Networks: Oscillators and Toggle Switches for Escherichia coli

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      Pages 301-314

      Studying Microbial Communities in Biofilms

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      Pages 315-330

      Quantitative Analysis of the Spatiotemporal Dynamics of a Synthetic Predator–Prey Ecosystem

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      Pages 331-341

      Drosophila S2 Schneider Cells: A Useful Tool for Rebuilding and Redesigning Approaches in Synthetic Biology

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