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, José 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
Verónica Sofía Martínez 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. Krömer
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 Björn 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