Synthetic biology : methods and protocols

著者

    • Braman, Jeffrey Carl

書誌事項

Synthetic biology : methods and protocols

edited by Jeffrey Carl Braman

（Methods in molecular biology / John M. Walker, series editor, 1772）（Springer protocols）

Humana Press, c2018

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注記

Includes bibliographical references and index

内容説明・目次

内容説明

This detailed book explores a few of the plethora of techniques and applications associated with the unique branch of science known as synthetic biology. Chemists, biologists, and engineers engaged in this multidisciplinary field of study will be guided in 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 for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible protocols, plus troubleshooting tips and explanations of how to avoid pitfalls, all written by experts who have published their work in peer-reviewed journals. Authoritative and practical, Synthetic Biology: Methods and Protocols provides key guidance and ideas for conducting your own synthetic biology projects.

目次

Part I: Gene Circuits and Biochemical Pathways 1. Re-Factoring Glycolytic Genes for Targeted Engineering of Catabolism in Gram-Negative Bacteria Alberto Sanchez-Pascuala, Pablo I. Nikel, and Victor de Lorenzo 2. Negative Regulation Gene Circuits for Efflux Pump Control Daniel A. Charlebois, Junchen Diao, Dmitry Nevozhay, and Gabor Balazsi 3. Methods for Generating Microbial Co-Cultures that Grow in the Absence of Fixed Carbon or Nitrogen Matthew J. Smith and Matthew B. Francis 4. Synthetic Biology with an All E. coli TXTL System: Quantitative Characterization of Regulatory Elements and Gene Circuits Ryan Marshall and Vincent Noireaux 5. Transformation of an Exotic Yeast Species into a Platform Organism: A Case Study for Engineering Glycolipid Production in the Yeast Starmerella bombicola Sofie Lodens, Marilyn De Graeve, Sophie L.K.W. Roelants, Sofie L. De Maeseneire, and Wim Soetaert 6. Sortase A-Assisted Metabolic Enzyme Ligation in Escherichia coli for Enhancing Metabolic Flux Takuya Matsumoto, Tsutomu Tanaka, and Akihiko Kondo Part II: Genome Editing and Modification 7. Construction of CRISPR Libraries for Functional Screening Carsten-P. Carstens, Katherine A. Felts, and Sarah E. Johns 8. Targeted Genome Editing Using DNA-Free RNA-Guided Cas9 Ribonucleoprotein for CHO Cell Engineering Jongoh Shin, Namil Lee, Suhyung Cho, and Byung-Kwan Cho 9. Dynamic Management of Codon Compression for Saturation Mutagenesis Gur Pines and Ryan T. Gill 10. Designed Transcriptional Regulation in Mammalian Cells Based on TALE- and CRISPR/dCas9 Tina Lebar and Roman Jerala 11. Combinatorial Evolution of DNA with RECODE Zhen Kang, Wenwen Ding, Peng Jin, Guocheng Du, and Jian Chen 12. Genome Editing in Penicillium chrysogenum Using Cas9 Ribonucleoprotein Particles Carsten Pohl, Laszlo Mozsik, Arnold J.M. Driessen, Roel A.L. Bovenberg, and Yvonne Nygard 13. Targeted Gene Knockout Using Nuclease-Assisted Vector Integration: Hemi- and Homozygous Deletion of JAG1 Michael Gapinske, Nathan Tague, Jackson Winter, Gregory H. Underhill, Pablo Perez-Pinera 14. Programming Biomaterial Interactions Using Engineered Living Cells Keith C. Heyde and Warren C. Ruder 15. Rapid Control of Genome Editing in Human Cells by Chemical-Inducible CRISPR-Cas Systems Kaiwen Ivy Liu, Muhammad Nadzim Bin Ramli, Norfala-Aliah Binte Sutrisnoh, and Meng How Tan 16. Production of a Human Cell Line with a Plant Chromosome Naoki Wada, Yasuhiro Kazuki, Kanako Kazuki, Toshiaki Inoue, Kiichi Fukui, and Mitsuo Oshimura 17. Bacterial Genome Editing with CRISPR-Cas9: Taking Clostridium beijerinckii as an Example Zhong-Tian Zhang, Pablo Jimenez-Bonilla, Seung-Oh Seo, Ting Lu, Yong-Su Jin, Hans P. Blaschek, and Yi Wang 18. CRISPR-Cas9-Mediated Genome Editing and Transcriptional Control in Yarrowia lipolytica Cory Schwartz and Ian Wheeldon 19. Construction and Integration of a Synthetic MicroRNA Cluster for Multiplex RNA Interference in Mammalian Cells Tingting Wang and Zhen Xie Part III: Genome Language and Computing 20. Bio-Algorithmic Workflows for Standardized Synthetic Biology Constructs Angel Goni-Moreno and Victor de Lorenzo 21. Engineering Genomes with Genotype Specification Language Erin H. Wilson, Chris Macklin, and Darren Platt 22. Automated Visualization of Genetic Designs Using DNAplotlib Vittorio Bartoli, Daniel O.R. Dixon, and Thomas E. Gorochowski 23. DNA-Based Analog Computing Daniel Fu, Shalin Shah, Tianqi Song, and John Reif Part IV: Molecular Assembly 24. DNA Assembly with the DATEL Method Zhen Kang, Wenwen Ding, Peng Jin, Guocheng Du, and Jian Chen 25. EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology Hung-En Lai, Simon Moore, Karen Polizzi, and Paul Freemont 26. Designing and Assembling Plasmids for Construction of Escherichia coli Biosensor for Vibrio cholerae Detection Maciej B. Holowko and Chueh Loo Poh 27. A Rapid Combinatorial Approach to Assembling Synthetic Prokaryotic and Eukaryotic Protein Expression Vectors Rebecca Mullinax, Sarah Johns, Denise Rhodes, Vivian Zhang, Nancy McKinney, Katie Felts, Carsten Carstens, and Peter Sheffield 28. Standardized Cloning and Curing of Plasmids Ida Lauritsen, Se Hyeuk Kim, Andreas Porse, and Morten H.H. Norholm 29. STAR: A Simple TAL Effector Assembly Reaction Using Isothermal Assembly Sabine Gogolok, Ute Koeber, and Steven M. Pollard

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