Metabolic flux analysis : methods and protocols
著者
書誌事項
Metabolic flux analysis : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 1191）（Springer protocols）
Humana Press, c2014
- hbk.
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注記
Includes bibliographical references and index
内容説明・目次
内容説明
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.
目次
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. Kroemer
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 Bjoern 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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