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Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions

Paper ID Volume ID Publish Year Pages File Format Full-Text
31817 44841 2006 24 PDF Available
Title
Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions
Abstract

13C metabolic flux analysis (MFA) has become an important and powerful tool for the quantitative analysis of metabolic networks in the framework of metabolic engineering. Isotopically instationary 13C MFA under metabolic stationary conditions is a promising refinement of classical stationary MFA. It accounts for the experimental requirements of non-steady-state cultures as well as for the shortening of the experimental duration. This contribution extends all computational methods developed for classical stationary 13C MFA to the instationary situation by using high-performance computing methods. The developed tools allow for the simulation of instationary carbon labeling experiments (CLEs), sensitivity calculation with respect to unknown parameters, fitting of the model to the measured data, statistical identifiability analysis and an optimal experimental design facility.To explore the potential of the new approach all these tools are applied to the central metabolism of Escherichia coli. The achieved results are compared to the outcome of the stationary counterpart, especially focusing on statistical properties. This demonstrates the specific strengths of the instationary method. A new ranking method is proposed making both an a priori and an a posteriori design of the sampling times available. It will be shown that although still not all fluxes are identifiable, the quality of flux estimates can be strongly improved in the instationary case. Moreover, statements about the size of some immeasurable pool sizes can be made.

Keywords
Instationary 13C metabolic flux analysis; 13C labeling experiment; 13C labeling dynamics; Parameter identifiability; Optimal experimental design; E. coli
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Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions
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Publisher
Database: Elsevier - ScienceDirect
Journal: Metabolic Engineering - Volume 8, Issue 6, November 2006, Pages 554–577
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us