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.

InhaltsangabePart 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 Processing12. 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

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