Synthetic metabolic pathways : methods and protocols
著者
書誌事項
Synthetic metabolic pathways : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 1671）（Springer protocols）
Humana Press : Springer Nature, c2018
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注記
Includes bibliographical references and index
"This Humana Press imprint is published by Springer Nature. The registered company is Springer Science+Business Media LLC"--T.p.verso
内容説明・目次
内容説明
This volume outlines key steps associated with the design, building, and testing of synthetic metabolic pathways for optimal cell factory performance and robustness, and illustrates how data-driven learning from these steps can be used for rational cost-effective engineering of cell factories with improved performance. Chapters are divided into four sections focusing on the four steps of the iterative design-build-test-learn cycle related to modern cell factory engineering. 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 practical, Synthetic Metabolic Pathways: Methods and Protocols aims to ensure successful results in the further study of this vital field.
目次
Part I: Parts and Models for Designing Synthetic Metabolic Pathways
1. Parts characterization for tunable protein expression
Michael S. Klausen and Morten O. A. Sommer
2. Enzyme Nicotinamide Cofactor Specificity Reversal Guided by Automated Structural Analysis and Library Design
Jackson K.B. Cahn, Sabine Brinkmann-Chen, and Frances H. Arnold
3. Bacterial Genome Editing Strategy for Control of Transcription and Protein Stability
Ida Lauritsen, Virginia Martinez, Carlotta Ronda, Alex Toftgaard Nielsen, and Morten H. H. Norholm
4. An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization
Sean M. Halper, Daniel P. Cetnar, and Howard M. Salis
5. Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design
Mohammad Mazharul Islam and Rajib Saha
6. Extended Metabolic Space Modeling
Pablo Carbonell, Baudoin Delepine, and Jean-Loup Faulon
7. Computational Methods to Assess the Production Potential of Bio-based Chemicals
Miguel A. Campodonico, Sumesh Sukumara, Adam M. Feist, and Markus J. Herrgard
Part II: Building and Refactoring Synthetic Metabolic Pathways
8. Multiplex Genome Editing in Escherichia coli
Sheila Ingemann Jensen and Alex Toftgaard Nielsen
9. Designing and Implementing Algorithmic DNA Assembly Pipelines for Multi-gene Systems
Szu-Yi Hsu and Michael J. Smanski
10. An adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism
Tian Zhang and Pier-Luc Tremblay
11. CRISPR-Cas9 toolkit for Actinomycete Genome Editing
Yaojun Tong, Helene Lunde Robertsen, Kai Blin, Tilmann Weber, and Sang Yup Lee
12. Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast using CasEMBLR
Tadas Jakociunas, Emil D. Jensen, Michael K. Jensen, and Jay D. Keasling
13 A modified Gibson assembly method for cloning large DNA fragments with high GC contents
Lei Li, Weihong Jiang, and Yinhua Lu
14 Coupling Yeast Golden Gate and VEGAS for efficient assembly of the violacein pathway in Saccharomyces cerevisiae
James Chuang, Jef D. Boeke, and Leslie A. Mitchell
Part III: Screening and Selection of Synthetic Metabolic Pathways
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15 Multi-capillary Column Ion Mobility Spectrometry of Volatile Metabolites For Phenotyping Of Microorganisms
Christoph Halbfeld, Joerg Ingo Baumbach, Lars M. Blank, and Birgitta E. Ebert
16 Selection of Highly Expressed Gene Variants in Escherichia coli using Translationally-coupled Antibiotic Selection Markers
Maja Rennig, Daniel O. Daley, and Morten H. H. Norholm
17. Design, Engineering, and Characterization Of Prokaryotic Ligand-binding Transcriptional Activators as Biosensors in Yeast
Francesca Ambri, Tim Snoek, Mette L. Skjoedt, Michael K. Jensen, and Jay D. Keasling
18. A Capture-SELEX Strategy for Multiplexed Selection of RNA Aptamers against Small Molecules
Lasse H. Lauridsen, Holger B. Doessing, Katherine S. Long, and Alex T. Nielsen
19. High-throughput Microfluidics for the Screening Of Yeast Libraries
Mingtao Huang, Haakan N. Joensson, and Jens Nielsen
20. Growth-Coupled Carotenoids Production Using Adaptive Laboratory Evolution
Luis H. Reyes and Katy C. Kao
Part IV: Learnings from Design-Build-Test-based Projects
21. Two scale 13C Metabolic Flux Analysis for Metabolic Engineering
David Ando and Hector Garcia Martin
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