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Synthetic Gene Circuits

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Filippo Menolascina

    1. School of Engineering, Institute for Bioengineering, University of Edinburgh, Edinburgh, UK

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2229)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

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

    • Madalena Chaves, Hidde de Jong
    Pages 1-40

  3. Stochastic Differential Equations for Practical Simulation of Gene Circuits

    • Jesús Picó, Alejandro Vignoni, Yadira Boada
    Pages 41-90

  4. Using Models to (Re-)Design Synthetic Circuits

    • Giselle McCallum, Laurent Potvin-Trottier
    Pages 91-118

  5. Automated Biocircuit Design with SYNBADm

    • Irene Otero-Muras, Julio R. Banga
    Pages 119-136

  6. Setting Up an Automated Biomanufacturing Laboratory

    • Marilene Pavan
    Pages 137-155

  7. Computer-Aided Design and Pre-validation of Large Batches of DNA Assemblies

    • Valentin Zulkower
    Pages 157-166

  8. Computer-Aided Planning for the Verification of Large Batches of DNA Constructs

    • Valentin Zulkower
    Pages 167-174

  9. Characterizing Genetic Parts and Devices Using RNA Sequencing

    • Deepti Vipin, Zoya Ignatova, Thomas E. Gorochowski
    Pages 175-187

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

    • Nadanai Laohakunakorn, Barbora Lavickova, Zoe Swank, Julie Laurent, Sebastian J. Maerkl
    Pages 189-203

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

    • Mahmoud Khazim, Elisa Pedone, Lorena Postiglione, Diego di Bernardo, Lucia Marucci
    Pages 205-219

  12. Optimal Experimental Design for Systems and Synthetic Biology Using AMIGO2

    • Eva Balsa-Canto, Lucia Bandiera, Filippo Menolascina
    Pages 221-239

  13. A Cyber-Physical Platform for Model Calibration

    • Lucia Bandiera, David Gomez-Cabeza, Eva Balsa-Canto, Filippo Menolascina
    Pages 241-265

  14. Prediction of Cellular Burden with Host–Circuit Models

    • Evangelos-Marios Nikolados, Andrea Y. Weiße, Diego A. Oyarzún
    Pages 267-291

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

    • Andras Gyorgy
    Pages 293-311

  16. Engineering Sensors for Gene Expression Burden

    • Alice Boo, Francesca Ceroni
    Pages 313-330

  17. Engineering Protein-Based Parts for Genetic Devices in Mammalian Cells

    • Giuliano Bonfá, Federica Cella, Velia Siciliano
    Pages 331-346

  18. Back Matter

    Pages 347-353
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Keywords

About this book

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.


Editors and Affiliations

  • School of Engineering, Institute for Bioengineering, University of Edinburgh, Edinburgh, UK

    Filippo Menolascina

Bibliographic Information

  • Book Title: Synthetic Gene Circuits

  • Book Subtitle: Methods and Protocols

  • Editors: Filippo Menolascina

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1032-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1031-2Published: 07 January 2021

  • Softcover ISBN: 978-1-0716-1034-3Published: 07 January 2022

  • eBook ISBN: 978-1-0716-1032-9Published: 06 January 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 353

  • Number of Illustrations: 7 b/w illustrations, 87 illustrations in colour

  • Topics: Human Genetics, Biotechnology, Biological Techniques

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