Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions
Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions
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DOI：
10.1016/j.ymben.2006.05.006
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发表时间：
2006-11-01
影响因子：
8.4
通讯作者：
Wiechert, Wolfgang
中科院分区：
文献类型：
--
作者：
Noeh, Katharina;Wahl, Aljoscha;Wiechert, Wolfgang
在代谢工程的框架下，碳13代谢流分析（MFA）已成为定量分析代谢网络的一个重要而有力的工具。在代谢固定条件下的同位素非固定C-13 MFA是经典固定MFA的一个很有前途的改进。它解释了非稳态培养的实验要求以及实验持续时间的缩短。这一贡献通过使用高性能计算方法，将所有为经典的固定C-13 MFA开发的计算方法扩展到非固定情况。所开发的工具允许模拟非稳态碳标记实验（克莱斯），灵敏度计算相对于未知参数，拟合模型的测量数据，统计可识别性分析和最佳的实验设计facility.To探索新的方法的潜力，所有这些工具都适用于大肠杆菌的中央代谢。所取得的成果相比，固定对应的结果，特别是侧重于统计特性。这证明了非平稳方法的具体优势。提出了一种新的排序方法，使先验和后验设计的采样时间。它将表明，虽然仍然不是所有的通量是可识别的，通量估计的质量可以大大提高在非平稳的情况下。此外，可以对一些不可测量的池大小的大小进行声明。(c)2006年爱思唯尔公司All rights reserved.
C-13 metabolic flux analysis (MFA) has become an important and powerful too] for the quantitative analysis of metabolic networks in the framework of metabolic engineering. Isotopically instationary C-13 MFA under metabolic stationary conditions is a promising refinement of classical stationary MFA. It accounts for the experimental requirements of no n-steady-state cultures as well as for the shortening of the experimental duration. This contribution extends all computational methods developed for classical stationary C-13 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. (c) 2006 Elsevier Inc. All rights reserved.