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Systems Metabolic Engineering Hal S. Alper

Systems Metabolic Engineering By Hal S. Alper

Systems Metabolic Engineering by Hal S. Alper


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Summary

This book describes the methodologies and approaches in systems metabolic engineering and provides a step-by-step guide for their implementation. Includes readily reproducible laboratory protocols and tips on troubleshooting.

Systems Metabolic Engineering Summary

Systems Metabolic Engineering: Methods and Protocols by Hal S. Alper

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 (TM) 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.

Table of Contents

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-Gaelle 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-Ponten, 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

Additional information

NLS9781493962921
9781493962921
1493962922
Systems Metabolic Engineering: Methods and Protocols by Hal S. Alper
New
Paperback
Humana Press Inc.
2017-04-30
474
N/A
Book picture is for illustrative purposes only, actual binding, cover or edition may vary.
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