OpenMebius: An Open Source Software for Isotopically Nonstationary 13C-Based Metabolic Flux Analysis. (11th June 2014)

• Record Type: Journal Article
• Authors: Kajihata, Shuichi; Furusawa, Chikara; Matsuda, Fumio; Shimizu, Hiroshi
• Other Names: Robert Martin Academic Editor.
• Is Part Of: BioMed research international. Volume 2014(2014)
• Publication Date: 2014-06-11
• Subjects: Medicine -- Periodicals; Biology -- Periodicals; Biotechnology -- Periodicals; Life sciences -- Periodicals; 610.5
• DOI: 10.1155/2014/627014
• Languages: English
• ISSNs: 2314-6133

Abstract

Abstract : The in vivo measurement of metabolic flux by 13 C-based metabolic flux analysis ( 13 C-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 a 13 C-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. Whereas 13 C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary 13 C metabolic flux analysis (INST- 13 C-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- 13 C-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- 13 C-MFA. Confidence intervals determined by INST- 13 C-MFA were less than those determined by conventional methods, indicating the potential of INST- 13 C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST- 13 C-MFA.