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Metabolic Flux Analysis

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Jens O. Krömer

    1. Centre for Microbial Electrosynthesis (CEMES), Advanced Water Management Centre, University of Queensland, St. Lucia, Brisbane, Australia

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  2. Lars K. Nielsen

    1. AIBN, University of Queensland, St. Lucia, Brisbane, Australia

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    You can also search for this editor in PubMed   Google Scholar

  3. Lars M. Blank

    1. Biology Department, RWTH Aachen University, Aachen, Germany

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1191)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xii
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  2. Models: Stoichiometry, Network Generation

    1. Front Matter

      Pages 1-1
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    2. Stoichiometric Modelling of Microbial Metabolism

      • Lars Kuepfer
      Pages 3-18

    3. 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 et al.
      Pages 19-45

  3. Thermodynamics: A Step Beyond MFA

    1. Front Matter

      Pages 47-47
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    2. Constraining the Flux Space Using Thermodynamics and Integration of Metabolomics Data

      • Keng Cher Soh, Vassily Hatzimanikatis
      Pages 49-63

    3. NExT: Integration of Thermodynamic Constraints and Metabolomics Data into a Metabolic Network

      • Verónica Sofía Martínez, Lars K. Nielsen
      Pages 65-78

  4. Experiments: Design Considerations, Fermentation, Analytics

    1. Front Matter

      Pages 79-79
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    2. Customization of 13C-MFA Strategy According to Cell Culture System

      • Lake-Ee Quek, Lars K. Nielsen
      Pages 81-90

    3. Quantitative Metabolomics Using ID-MS

      • S. Aljoscha Wahl, Reza Maleki Seifar, Angela ten Pierick, Cor Ras, Jan C. van Dam, Joseph J. Heijnen et al.
      Pages 91-105

    4. Determining the Biomass Composition of a Sponge Holobiont for Flux Analysis

      • Jabin Watson, Bernard Degnan, Sandie Degnan, Jens O. Krömer
      Pages 107-125

    5. Successful Downsizing for High-Throughput 13C-MFA Applications

      • Birgitta E. Ebert, Lars M. Blank
      Pages 127-142

    6. Labelling Analysis for 13C MFA Using NMR Spectroscopy

      • Paula Jouhten, Hannu Maaheimo
      Pages 143-164

    7. GC-MS-Based 13C Metabolic Flux Analysis

      • Judith Becker, Christoph Wittmann
      Pages 165-174

    8. Dynamic Analysis of CO2 Labeling and Cell Respiration Using Membrane-Inlet Mass Spectrometry

      • Tae Hoon Yang
      Pages 175-194

  5. 13C Fluxomics Data Processing

    1. Front Matter

      Pages 195-195
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  6. 13C Fluxomics Data Processing

    1. Correction of MS Data for Naturally Occurring Isotopes in Isotope Labelling Experiments

      • Pierre Millard, Fabien Letisse, Serguei Sokol, Jean-Charles Portais
      Pages 197-207

    2. Steady-State 13C Fluxomics Using OpenFLUX

      • Lake-Ee Quek, Lars K. Nielsen
      Pages 209-224

    3. Flux Visualization Using VANTED/FluxMap

      • Christian Krach, Astrid Junker, Hendrik Rohn, Falk Schreiber, Björn H. Junker
      Pages 225-233

  7. Examples

    1. Front Matter

      Pages 235-235
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Keywords

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.

Editors and Affiliations

  • Centre for Microbial Electrosynthesis (CEMES), Advanced Water Management Centre, University of Queensland, St. Lucia, Brisbane, Australia

    Jens O. Krömer

  • AIBN, University of Queensland, St. Lucia, Brisbane, Australia

    Lars K. Nielsen

  • Biology Department, RWTH Aachen University, Aachen, Germany

    Lars M. Blank

Bibliographic Information

  • Book Title: Metabolic Flux Analysis

  • Book Subtitle: Methods and Protocols

  • Editors: Jens O. Krömer, Lars K. Nielsen, Lars M. Blank

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-1170-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2014

  • Hardcover ISBN: 978-1-4939-1169-1Published: 03 September 2014

  • Softcover ISBN: 978-1-4939-4159-9Published: 17 September 2016

  • eBook ISBN: 978-1-4939-1170-7Published: 01 September 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 316

  • Number of Illustrations: 19 b/w illustrations, 51 illustrations in colour

  • Topics: Biochemistry, general, Enzymology

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