Menolascina F. (Ed.) Synthetic Gene Circuits: Methods and Protocols

Springer, 2021. — 356 p. — (Methods in Molecular Biology 2229). — ISBN 978-1-0716-1031-2.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.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 Biocircuit 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 AMIGO2
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