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Mathematical Modeling of Isotope Labeling Experiments for Metabolic Flux Analysis

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Plant Metabolism

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1083))

Abstract

Isotope labeling experiments (ILEs) offer a powerful methodology to perform metabolic flux analysis. However, the task of interpreting data from these experiments to evaluate flux values requires significant mathematical modeling skills. Toward this, this chapter provides background information and examples to enable the reader to (1) model metabolic networks, (2) simulate ILEs, and (3) understand the optimization and statistical methods commonly used for flux evaluation. A compartmentalized model of plant glycolysis and pentose phosphate pathway illustrates the reconstruction of a typical metabolic network, whereas a simpler example network illustrates the underlying metabolite and isotopomer balancing techniques. We also discuss the salient features of commonly used flux estimation software 13CFLUX2, Metran, NMR2Flux+, FiatFlux, and OpenFLUX. Furthermore, we briefly discuss methods to improve flux estimates. A graphical checklist at the end of the chapter provides a reader a quick reference to the mathematical modeling concepts and resources.

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Acknowledgments

This work was funded by the National Science Foundation (award number IOS 0922650).

Author information

Authors and Affiliations

  1. University of Maryland, College Park, MD, USA

    Shilpa Nargund

  2. Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA

    Ganesh Sriram

Authors
  1. Shilpa Nargund
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  2. Ganesh Sriram
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Editor information

Editors and Affiliations

  1. Engineering, University of Maryland Dept. Chemical & Biomolecular, College Park, Maryland, USA

    Ganesh Sriram

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Author Contributions

SN and GS conceived the chapter. SN wrote a draft of the manuscript and prepared most of the figures. GS wrote sections of the manuscript, prepared Fig. 3, critically edited the manuscript and prepared the final version. Both authors approved the final version of the manuscript.

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Nargund, S., Sriram, G. (2014). Mathematical Modeling of Isotope Labeling Experiments for Metabolic Flux Analysis. In: Sriram, G. (eds) Plant Metabolism. Methods in Molecular Biology, vol 1083. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-661-0_8

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  • DOI: https://doi.org/10.1007/978-1-62703-661-0_8

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-660-3

  • Online ISBN: 978-1-62703-661-0

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