Systems Metabolic Engineering: Methods and Protocols

ISBN-13: 9781627032988 / Miękka / 2013 / 474 str.

Alper, Hal S.

Opis

With the ultimate goal of systematically and robustly defining the specific perturbations necessary to alter a cellular phenotype, systems metabolic engineering has the potential to lead to a complete cell model capable of simulating cell and metabolic function as well as predicting phenotypic response to changes in media, gene knockouts/overexpressions, or the incorporation of heterologous pathways. In Systems Metabolic Engineering: Methods and Protocols, experts in the field describe the methodologies and approaches in the area of systems metabolic engineering and provide a step-by-step guide for their implementation. Four major tenants of this approach are addressed, including modeling and simulation, multiplexed genome engineering, 'omics technologies, and large data-set incorporation and synthesis, all elucidated through the use of model host organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions on 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.Comprehensive and cutting-edge, Systems Metabolic Engineering: Methods and Protocols serves as an ideal guide for metabolic engineers, molecular biologists, and microbiologists aiming to implement the most recent approaches available in the field.

Spis treści

Part I: Modeling and Simulation Tools

 

 

 

1. Genome-Scale Model Management and Comparison

 

            Stephan Pabinger and Zlatko Trajanoski

 

 

 

2. Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED

 

            Scott Devoid, Ross Overbeek, Matthew DeJongh, Veronika Vonstein, Aaron A. Best, and Christopher Henry

 

 

 

3. Metabolic Model Refinement Using Phenotypic Microarray Data

 

            Pratish Gawand, Laurence Yang, William R. Cluett, and Radhakrishnan Mahadevan

 

 

 

4. Linking Genome-Scale Metabolic Modeling and Genome Annotation

 

            Edik M. Blais, Arvind K. Chavali, and Jason A. Papin

 

 

 

5. Resolving Cell Composition through Simple Measurements, Genome-Scale Modeling, and a Genetic Algorithm

 

            Ryan S. Senger and Hadi Nazem-Bokaee

 

 

 

6. A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism)

 

            Evangelos Simeonidis, Sriram Chandrasekaran, and Nathan D. Price

 

 

 

7. Kinetic Modeling of Metabolic Pathways: Application to Serine Biosynthesis

 

            Kieran Smallbone and Natalie J. Stanford

 

 

 

8. Computational Tools for Guided Discovery and Engineering of Metabolic Pathways

 

            Matthew Moura, Linda Broadbelt, and Keith Tyo

 

 

 

9. Retrosynthetic Design of Heterologous Pathways

 

            Pablo Carbonell, Anne-Gaëlle Planson, and Jean-Loup Faulon

 

 

 

Part II: Genome Engineering Tools

 

 

 

10. Customized Optimization of Metabolic Pathways by Combinatorial Transcriptional Engineering

 

            Yongbo Yuan, Jing Du, and Huimin Zhao

 

 

 

11. Adaptive Laboratory Evolution for Strain Engineering

 

            James Winkler, Luis H. Reyes, and Katy C. Kao

 

 

 

12. Trackable Multiplex Recombineering for Gene-Trait Mapping in E. coli

 

            Thomas J. Mansell, Joseph R. Warner, and Ryan T. Gill

 

 

 

Part III: Systems-Level ‘Omics Tools

 

 

 

13. Identification of Mutations in Evolved Bacterial Genomes

 

            Liam Royce, Erin Boggess, Tao Jin, Julie Dickerson, and Laura Jarboe

 

 

 

14. Discovery of Post-Transcriptional Regulatory RNAs Using Next Generation Sequencing Technologies

 

            Grant Gelderman and Lydia M. Contreras

 

 

 

15. 13C-based Metabolic Flux Analysis: Fundamentals and Practice

 

            Tae Hoon Yang

 

 

 

16. Nuclear Magnetic Resonance Methods for Metabolic Fluxomics

 

            Shilpa Nargund, Max E. Joffe, Dennis Tran, Vitali Tugarinov, and Ganesh Sriram

 

 

 

17. Using Multiple Tracers for 13C Metabolic Flux Analysis

 

            Maciek R. Antoniewicz

 

 

 

18. Isotopically Nonstationary 13C Metabolic Flux Analysis

 

            Lara J. Jazmin and Jamey D. Young

 

 

 

19. Sample Preparation and Biostatistics for Integrated Genomics Approaches

 

            Hein Stam, Michiel Akeroyd, Hilly Menke, Renger H. Jellema, Fredoen Valianpour, Wilbert H.M. Heijne, Maurien M.A. Olsthoorn, Sabine Metzelaar, Viktor M. Boer, Carlos M.F.M. Ribeiro, Philippe Gaudin, and Cees M.J. Sagt

 

 

 

Part IV: Integrating Large Datasets for Modeling and Engineering Applications

 

 

 

20. Targeted Metabolic Engineering Guided by Computational Analysis of Single Nucleotide Polymorphisms (SNPs)

 

            D.B.R.K. Gupta Udatha, Simon Rasmussen, Thomas Sicheritz-Pontén, and Gianni Panagiotou

 

 

 

21. Linking RNA Measurements and Proteomics with Genome-Scale Models

 

            Christopher M. Gowen and Stephen S. Fong

 

 

 

22. Comparative Transcriptome Analysis for Metabolic Engineering

 

            Shuobo Shi, Tao Chen, and Xueming Zhao

 

 

 

23. Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation

 

            Kazuharu Arakawa and Masaru Tomita