convISA: A simple, convoluted method for isotopomer spectral analysis of fatty acids and cholesterol

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Title: convISA: A simple, convoluted method for isotopomer spectral analysis of fatty acids and cholesterol
Author(s): Tredwell, GD
Keun, HC
Item Type: Journal Article
Abstract: Isotopomer spectral analysis (ISA) is a simple approach for modelling the cellular synthesis of fatty acids and cholesterol in a stable isotope labelling experiment. In the simplest model, fatty acid biosynthesis is described by two key parameters: the fractional enrichment of acetyl-CoA from the labelled substrate, D, and the fractional de novo synthesis of the fatty acid during the exposure to the labelled substrate, g(t). The model can also be readily extended to include synthesis via elongation of unlabelled shorter fatty acids. This modelling strategy is less complex than metabolic flux analysis and only requires the measurement of the mass isotopologues of a single metabolite. However, software tools to perform these calculations are not freely available. We have developed an algorithm (convISA), implemented in MATLAB™, which employs the convolution (Cauchy product) of mass isotopologue distributions (MIDs) for ISA of fatty acids and cholesterol. In our method, the MIDs of each molecule are constructed as a single entity rather than deriving equations for individual isotopologues. The flexibility of this method allows the model to be applied to raw data as well as to data that has been corrected for natural isotope abundance. To test the algorithm, convISA was applied to 238 MIDs of methyl palmitate available from the literature, for which ISA parameters had been calculated via other methods. A very high correlation was observed between estimates of the D and g(t) parameters from convISA with both published values, and estimates generated by our own metabolic flux analysis using a simplified stoichiometric model (r=0.981 and 0.944, and 0.996 and 0.942). We also demonstrate the application of the convolution ISA approach to cholesterol biosynthesis; the model was applied to measurements made on MCF7 cells cultured in U-13C-glucose. In conclusion, we believe that convISA offers a convenient, flexible and transparent framework for metabolic modelling that will help facilitate the application of ISA to future experiments.
Publication Date: 2-Oct-2015
Date of Acceptance: 10-Sep-2015
URI: http://hdl.handle.net/10044/1/44734
DOI: http://dx.doi.org/10.1016/j.ymben.2015.09.008
ISSN: 1096-7184
Publisher: Elsevier
Start Page: 125
End Page: 132
Journal / Book Title: Metabolic Engineering
Volume: 32
Sponsor/Funder: Commission of the European Communities
Funder's Grant Number: 266838
Copyright Statement: © 2015, Elsevier Ltd. All rights reserved. This manuscript is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/
Keywords: Science & Technology
Life Sciences & Biomedicine
Biotechnology & Applied Microbiology
Isotopomer spectral analysis
Metabolic flux
Fatty acid
Cholesterol
CELLS
BIOSYNTHESIS
METABOLISM
FLUX
Cholesterol
Fatty acid
Isotopomer spectral analysis
Metabolic flux
Algorithms
Cell Line
Cholesterol
Fatty Acids
Glucose
Humans
Isomerism
Isotope Labeling
MCF-7 Cells
Palmitates
Reproducibility of Results
Spectrum Analysis
Cell Line
Humans
Cholesterol
Glucose
Fatty Acids
Palmitates
Spectrum Analysis
Reproducibility of Results
Isotope Labeling
Isomerism
Algorithms
MCF-7 Cells
Biotechnology
1003 Industrial Biotechnology
Publication Status: Published
Appears in Collections:Division of Surgery
Division of Cancer
Faculty of Medicine



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