Respiratory Metabolism in Heterotrophic Plant Cells as Revealed by Isotopic Labeling and Metabolic Flux Analysis

2017 ◽  
pp. 247-260
Author(s):  
Martine Dieuaide-Noubhani ◽  
Dominique Rolin
Keyword(s):  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Plant Cells ◽  
Isotopic Labeling ◽  
Flux Analysis ◽  
Respiratory Metabolism

scholarly journals OpenMebius: An Open Source Software for Isotopically Nonstationary13C-Based Metabolic Flux Analysis

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Shuichi Kajihata ◽  
Chikara Furusawa ◽  
Fumio Matsuda ◽  
Hiroshi Shimizu
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Simulated Data ◽  
Isotopic Labeling ◽  
Metabolic Model ◽  
Cell Physiology ◽  
Flux Analysis

Thein vivomeasurement of metabolic flux by13C-based metabolic flux analysis (13C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a13C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas13C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary13C metabolic flux analysis (INST-13C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-13C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-13C-MFA. Confidence intervals determined by INST-13C-MFA were less than those determined by conventional methods, indicating the potential of INST-13C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-13C-MFA.

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