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Open Access Research article

13C labeling experiments at metabolic nonstationary conditions: An exploratory study

Sebastian Aljoscha Wahl1*, Katharina Nöh2 and Wolfgang Wiechert3

Author Affiliations

1 Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany

2 Fermentation Technology, Institute of Biotechnology 2, Research Centre Jülich GmbH, Jülich, Germany

3 Department of Simulation, Institute of Systems Engineering, University of Siegen, Siegen, Germany

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BMC Bioinformatics 2008, 9:152  doi:10.1186/1471-2105-9-152

Published: 18 March 2008

Abstract

Background

Stimulus Response Experiments to unravel the regulatory properties of metabolic networks are becoming more and more popular. However, their ability to determine enzyme kinetic parameters has proven to be limited with the presently available data. In metabolic flux analysis, the use of 13C labeled substrates together with isotopomer modeling solved the problem of underdetermined networks and increased the accuracy of flux estimations significantly.

Results

In this contribution, the idea of increasing the information content of the dynamic experiment by adding 13C labeling is analyzed. For this purpose a small example network is studied by simulation and statistical methods. Different scenarios regarding available measurements are analyzed and compared to a non-labeled reference experiment. Sensitivity analysis revealed a specific influence of the kinetic parameters on the labeling measurements. Statistical methods based on parameter sensitivities and different measurement models are applied to assess the information gain of the labeled stimulus response experiment.

Conclusion

It was found that the use of a (specifically) labeled substrate will significantly increase the parameter estimation accuracy. An overall information gain of about a factor of six is observed for the example network. The information gain is achieved from the specific influence of the kinetic parameters towards the labeling measurements. This also leads to a significant decrease in correlation of the kinetic parameters compared to an experiment without 13C-labeled substrate.