Synthetic Biology: Methods and Protocols

ISBN-13: 9781071636572 / Angielski

Jeffrey Carl Braman

Spis treści

Part I: Gene Circuits and Biochemical Pathways

 

1. Plant engineering to enable platforms for sustainable bioproduction of terpenoids

Jacob D. Bibik and Björn Hamberger

 

2. Compartmentalized Terpenoid Production in Plants Using Agrobacterium-mediated Transient Expression

Jacob D. Bibik, Abigail E. Bryson, and Björn Hamberger

 

3. Design Principles for Biological Adaptation: A Systems and Control-Theoretic Treatment Priyan Bhattacharya, Karthik Raman, and Arun K. Tangirala

 

4. Construction of Xylose-Utilizing Cyanobacterial Chassis for Bioproduction Under Photomixotrophic Conditions

Xinyu Song, Yue Ju, Lei Chen, and Weiwen Zhang

 

5. Allosteric-Regulation-Based DNA Circuits In Saccharomyces Cerevisiae To Detect Organic Acids And Monitor Hydrocarbon Metabolism In Vitro

Michael Dare Asemoloye and Mario Andrea Marchisio

 

6. dCas12a:Pre-crRNA: A New Tool To Induce mRNA Degradation In Saccharomyces Cerevisiae Synthetic Gene Circuits

Lifang Yu and Mario Andrea Marchisio

 

Part II:  Genome Editing and Modification

 

7. CRISPRi-Driven Genetic Screening for Designing Novel Microbial Phenotypes

Minjeong Kang, Kangsan Kim, and Byung-Kwan Cho

 

8 Enzymatic Preparation of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase and Its Applications

Guanyuan Wang, Yuhui Du, and Tingjian Chen

 

9. Single-Nucleotide Microbial Genome Editing Using CRISPR-Cas12a

Ho Joung Lee and Sang Jun Lee

 

10. Multiplex Marker-less Genome Integration in Pichia pastoris using CRISPR/Cas9

Jucan Gao, Jintao Cheng, and Jiazhang Lian

11. Genome Editing, Transcriptional Regulation and Forward Genetic Screening Using CRISPR-Cas12a Systems in Yarrowia lipolytica

Adithya Ramesh, Sangcheon Lee and Ian Wheeldon

 

12. An Improved Method for Eliminating or Creating Intragenic Bacterial Promoters

Ellina Trofimova, Dominic Y. Logel, and Paul R. Jaschke

 

13. Genetic Code Expansion in Pseudomonas putida KT2440

Tianyu Gao, Jiantao Guo, and Wei Niu

 

14. Genome-Wide Screen for Enhanced Noncanonical Amino Acid Incorporation in Yeast

Briana R. Lino and James A. Van Deventer

 

15. Positive Selection Screens for Programmable Endonuclease Activity using I-SceI

Michael A. Mechikoff, Kok Zhi Lee, and Kevin V. Solomon

 

16.  CRISPR-Cas9-mediated Genome Editing in

Paenibacillus polymyxa

Giulia Ravagnan, Meliawati Meliawati, and Jochen Schmid

 

Part III: Genome Language and Computing

17. Programming Juxtacrine-Based Synthetic Signaling Networks in a Cellular Potts Framework

Calvin Lam and Leonardo Morsut

 

18. Encoding Genetic Circuits with DNA Barcodes Paves the Way for High-throughput Profiling of Dose-response Curves of Metabolite Biosensors

Huibao Feng, Yikang Zhou and Chong Zhang

 

19. Machine Learning for Biological Design

Tom Blau and Iadine Chades and Cheng Soon Ong

 

20. A machine learning approach for predicting essentiality of metabolic genes

Lilli J Freischem and Diego A Oyarzún

 

21. The Causes for Genomic Instability And How To Try And Reduce Them Through Rational Design Of Synthetic DNA

Matan Arbel-Groissman, Itamar Menuhin-Gruman, Hader Benshoshan, Doron Naki, Shaked Bergman, Yarin  Udi, and Tamir Tulle

 

22. Genetic Network Design Automation with LOICA

Gonzalo Vidal, Carolus Vitalis, Tamara Matúte, Isaac Núñez, Fernán Federici, and Timothy J. Rudge

 

23. Flapjack: Data Management and Analysis for Genetic Circuit Characterization

Carolus Vitalis, Guillermo Yáñez Feliú, Gonzalo Vidal, Macarena Muñoz Silva, Tamara Matúte, Isaac Núñez , Fernán Federici, and Timothy J. Rudge

 

Part IV: Molecular Assembly

24. In Vivo DNA Assembly Using the PEDA Method

Tianyuan Su, Qingxiao Pang, and Qingsheng Qi

 

25. Cell-Free Synthesis and Quantitation of Bacteriophages

Antoine Levrier, Steven Bowden, Bruce Nash, Ariel Lindner, and Vincent Noireaux

 

26. Multimodal Control of Bacterial Gene Expression by Red and Blue Light

Stefanie S. M. Meier, Elina Multamäki, Américo T. Ranzani, Heikki Takala, and Andreas Möglich

 

27. In silico design, in vitro construction and in vivo application of synthetic small 

regulatory RNAs in bacteria

Michel Brück, Bork A. Berghoff, and Daniel Schindler

Blurb

This second edition provides new and updated techniques and applications associated with synthetic biology. Chapters guide readers through the creation and regulation of gene circuits, manipulation of biochemical pathways, genome editing and modification, creating genome language and computing, as well as molecular assembly.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 key tips on troubleshooting and avoiding known pitfalls.

 Authoritative and cutting-edge, Synthetic Biology: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.