Systems Metabolic Engineering: Methods and Protocols

by Hal S. Alper (Editor)

Overview

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 Prools, 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 prools, and tips on troubleshooting and avoiding known pitfalls.

Comprehensive and cutting-edge, Systems Metabolic Engineering: Methods and Prools serves as an ideal guide for metabolic engineers, molecular biologists, and microbiologists aiming to implement the most recent approaches available in the field.

Product Details

ISBN-13:	9781627032988
Publisher:	Springer-Verlag New York, LLC
Publication date:	02/16/2013
Series:	Methods in Molecular Biology , #985
Edition description:	2013
Pages:	474
Product dimensions:	7.01(w) x 10.00(h) x 0.05(d)

Table of Contents

Genome-Scale Model Management and Comparison.- Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED.- Metabolic Model Refinement Using Phenotypic Microarray Data.- Linking Genome-Scale Metabolic Modeling and Genome Annotation.- Resolving Cell Composition through Simple Measurements, Genome-Scale Modeling, and a Genetic Algorithm.- A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism).- Kinetic Modeling of Metabolic Pathways: Application to Serine Biosynthesis.- Computational Tools for Guided Discovery and Engineering of Metabolic Pathways.- Retrosynthetic Design of Heterologous Pathways.- Customized Optimization of Metabolic Pathways by Combinatorial Transcriptional Engineering.- Adaptive Laboratory Evolution for Strain Engineering.- Trackable Multiplex Recombineering for Gene-Trait Mapping in E. coli.- Identification of Mutations in Evolved Bacterial Genomes.- Discovery of Post-Transcriptional Regulatory RNAs Using Next Generation Sequencing Technologies.- ¹³C-based Metabolic Flux Analysis: Fundamentals and Practice.- Nuclear Magnetic Resonance Methods for Metabolic Fluxomics.- Using Multiple Tracers for ¹³C Metabolic Flux Analysis.- Isotopically Nonstationary ¹³C Metabolic Flux Analysis.- Sample Preparation and Biostatistics for Integrated Genomics Approaches.- Targeted Metabolic Engineering Guided by Computational Analysis of Single Nucleotide Polymorphisms (SNPs).- Linking RNA Measurements and Proteomics with Genome-Scale Models.- Comparative Transcriptome Analysis for Metabolic Engineering.- Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation.