Metabolic Flux Analysis Methods and Protocols

About this book

Metabolic Flux Analysis: Methods and Protocols opens up the field of metabolic flux analysis to those who want to start a new flux analysis project but are overwhelmed by the complexity of the approach. Metabolic flux analysis emerged from the current limitation for the prediction of metabolic fluxes from a measured inventory of the cell. Divided into convenient thematic parts, topics in this essential volume include the fundamental characteristics of the underlying networks, the application of quantitative metabolite data and thermodynamic principles to constrain the solution space for flux balance analysis (FBA), the experimental toolbox to conduct different types of flux analysis experiments, the processing of data from ¹³C experiments and three chapters that summarize some recent key findings.

Written in the 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 protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Metabolic Flux Analysis: Methods and Protocols presents protocols that cover a range of relevant organisms currently used in the field, providing a solid basis to anybody interested in the field of metabolic flux analysis.

Contents

Part I. Models - Stoichiometry, Network Generation
1. Stoichiometric Modelling of Microbial Metabolism Lars Kuepfer
2. Tapping the Wealth of Microbial Data in High-Throughput Metabolic Model Reconstruction Ric Colasanti, Janaka N. Edirisinghe, Tahmineh Khazaei, Jose P. Faria, Sam Seaver, Fangfang Xia, and Christopher Henry

Part II. Thermodynamics - A Step Beyond MFA
3. Constraining the Flux Space using Thermodynamics and Integration of Metabolomics Data Keng Cher Soh and Vassily Hatzimanikatis
4. NExT - Integration of Thermodynamic Constraints and Metabolomics Data into a Metabolic Network Veronica Sofia Martinez and Lars Keld Nielsen

Part III. Experiments - Design Considerations, Fermentation, Analytics
5. Customization of ¹³C-MFA Strategy According to Cell Culture System Lake-Ee Quek and Lars Keld Nielsen
6. Quantitative Metabolomics Using ID-MS Aljoscha S. Wahl, Reza Maleki Seifar, Angela ten Pierick, Cor Ras, Jan van Dam, Joseph J. Heijnen, and Walter M. Van Gulik
7. Determining the Biomass Composition of a Sponge Holobiont for Flux Analysis Jabin Watson, Bernard Degnan, Sandie Degnan, and Jens O. Kromer
8. Successful Down-Sizing for High-Throughput ¹³C-MFA Applications Birgitta E. Ebert and Lars M. Blank
9. Labelling Analysis for ¹³C MFA Using NMR Spectroscopy Paula Jouhten and Hannu Maaheimo
10. GC-MS Based ¹³C Metabolic Flux Analysis Judith Becker and Christoph Wittman
11. Dynamic Cell Respiration & CO₂ Labeling Analysis Using Membrane-Inlet Mass Spectrometry Tae Hoon Yang

Part IV. ¹³C Fluxomics Data Processing
12. Correction of MS Data for Naturally Occurring Isotopes in Isotope Labelling Experiments Pierre Millard, Fabien Letisse, Serguei Sokol, and Jean-Charles Portais
13. Steady-State ¹³C Fluxomics Using OpenFLUX Lake-Ee Quek and Lars Keld Nielsen
14. Flux Visualization Using VANTED/FluxMap Christian Krach, Astrid Junker, Hendrik Rohn, Falk Schreiber, and Bjorn H. Junker

Part V. Examples
15. Metabolic Flux Analysis for Escherichia coli by Flux Balance Analysis Yu Matsuoka and Kazuyuki Shimizu
16. ¹³C-Metabolic Flux Analysis for Escherichia coli Yu Matsuoka and Kazuyuki Shimizu
17. 3C-Based Metabolic Flux Analysis of Recombinant Pichia pastoris Pau Ferrer and Joan Albiol

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