Main description:

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.

Contents:

1. Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits

Madalena Chaves and Hidde de Jong

2. Stochastic Differential Equations for Practical Simulation of Gene Circuits

Jesus Pico, Alejandro Vignoni, and Yadira Boada

3. Using Models To (Re-)Design Synthetic Circuits

Giselle McCallum and Laurent Potvin-Trottier

4. Automated bio-circuit design with SYNBADm

Irene Otero-Muras and Julio R. Banga

5. Setting up an Automated Biomanufacturing Laboratory

Marilene Pavan

6. Computer-aided Design and Pre-validation of Large Batches of DNA Assemblies Valentin Zulkower

7. Computer-aided Planning for the Verification of Large Batches of DNA Constructs Valentin Zulkower

8. Characterizing Genetic Parts and Devices using RNA Sequencing

Deepti Vipin, Zoya Ignatova, and Thomas E. Gorochowski

9. Steady-State Cell-Free Gene Expression with Microfluidic Chemostats

Nadanai Laohakunakorn, Barbora Lavickova, Zoe Swank, Julie Laurent, and Sebastian J. Maerkl

10. A Microfluidic/Microscopy-Based Platform for On-Chip Controlled Gene Expression in Mammalian Cells

Mahmoud Khazim, Elisa Pedone, Lorena Postiglione, Diego di Bernardo, and Lucia Marucci

11. Optimal Experimental Design for Systems and Synthetic Biology Using Amigo2

Eva Balsa-Canto, Lucia Bandiera, and Filippo Menolaschina

12. A Cyber-Physical Platform for Model Calibration

Lucia Bandiera, David Gomez Cabeza, Eva Balsa-Canto, and Filippo Menolascina

13. Prediction of cellular burden with host-circuit models

Evangelos-Marios Nikolados, Andrea Y. Weisse, and Diego A. Oyarzun

14. A Practical Step-by-Step Guide for Quantifying Retroactivity in Gene Networks

Andras Gyorgy

15. Engineering Sensors for Gene Expression Burden

Alice Boo and Francesca Ceroni

16. Engineering Protein-based Parts for Genetic Devices in Mammalian Cells

Giuliano Bonfa, Federica Cella, and Velia Siciliano