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This volume provides clear and direct protocols to implement automated Design-Build-Test-Learn (DBTL) into synthetic biology research. Chapters detail techniques to model and simulate biological systems, redesign biological systems, setting up of an automated biolaboratory, step-by-step guide on how to perform computer aided design, RNA sequencing, microfluidics -using bacterial cell free extracts, live mammalian cells, computational and experimental procedures, metabolic burden, computational techniques to predict such burden from models, and how DNA parts can be engineered in mammalian cells to sense, and respond to, and intracellular signals in general. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Synthetic Gene Circuits: Methods and Protocols aims to ensure successful results in the further study of this vital field.
List of contents
Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits.- Stochastic Differential Equations for Practical Simulation of Gene Circuits.- Using Models To (Re-)Design Synthetic Circuits.- Automated bio-circuit design with SYNBADm.- Setting up an Automated Biomanufacturing Laboratory.- Computer-aided Design and Pre-validation of Large Batches of DNA Assemblies.- Computer-aided Planning for the Verification of Large Batches of DNA Constructs.- Characterizing Genetic Parts and Devices using RNA Sequencing.- Steady-State Cell-Free Gene Expression with Microfluidic Chemostats.- A Microfluidic/Microscopy-Based Platform for On-Chip Controlled Gene Expression in Mammalian Cells.- Optimal Experimental Design for Systems and Synthetic Biology Using Amigo.- A Cyber-Physical Platform for Model Calibration.- Prediction of cellular burden with host-circuit models.- A Practical Step-by-Step Guide for Quantifying Retroactivity in Gene Networks.- Engineering Sensors for Gene Expression Burden.- Engineering Protein-based Parts for Genetic Devices in Mammalian Cells.
