Estimation of Bidirectional Metabolic Fluxes from MS and NMR Data Using Positional Representations

Marcos J. Arauzo-Bravo (marara@dali.eis.uva.es)
Kazuyuki Shimizu (shimi@bse.kyutech.ac.jp)

Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan


Abstract

It is quite important to estimate the metabolic flux distribution (MFD) vectors in vivo, and to investigate the effect of culture environments on the flux distributions to uncover the metabolic regulation mechanism of microbial cells. The conventional approach is to compute the MFD using the stoichiometric equations and the measured specific rates (input and output variables). However, this method cannot give the MFD for the complex metabolic network which includes cyclic pathways. In the present investigation, we considered the method of analysing the metabolic fluxes based on 13C tracer experiments. In particular, we compared the different techniques of estimating the bidirectional fluxes in the metabolic networks, studying their applicability with respect to the different types of data formats obtained through GC-MS (gas chromatography-mass spectrometry) and NMR (nuclear magnetic resonance) measurements in labeling experiments. It was found that some techniques cannot be applied for GC-MS and NMR data. In the present research, therefore, a new preprocessing method for MS and NMR data was developed, to solve some of the problems encountered in the conventional approaches.

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Japanese Society for Bioinformatics