Dataset Information

Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches.

ABSTRACT: Metabolic pathway modeling plays an increasing role in drug design by allowing better understanding of the underlying regulation and controlling networks in the metabolism of living organisms. However, despite rapid progress in this area, pathway modeling can become a real nightmare for researchers, notably when few experimental data are available or when the pathway is highly complex. Here, three different approaches were developed to model the second part of glycolysis of E. histolytica as an application example, and have succeeded in predicting the final pathway flux: one including detailed kinetic information (white-box), another with an added adjustment term (grey-box) and the last one using an artificial neural network method (black-box). Afterwards, each model was used for metabolic control analysis and flux control coefficient determination. The first two enzymes of this pathway are identified as the key enzymes playing a role in flux control. This study revealed the significance of the three methods for building suitable models adjusted to the available data in the field of metabolic pathway modeling, and could be useful to biologists and modelers.

SUBMITTER: Lo-Thong O

PROVIDER: S-EPMC7417601 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches.

Lo-Thong Ophélie O Charton Philippe P Cadet Xavier F XF Grondin-Perez Brigitte B Saavedra Emma E Damour Cédric C Cadet Frédéric F

Scientific reports 20200810 1

Metabolic pathway modeling plays an increasing role in drug design by allowing better understanding of the underlying regulation and controlling networks in the metabolism of living organisms. However, despite rapid progress in this area, pathway modeling can become a real nightmare for researchers, notably when few experimental data are available or when the pathway is highly complex. Here, three different approaches were developed to model the second part of glycolysis of E. histolytica as an ...[more]

PMID: 32778715

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Project description:In any membrane filtration, the prediction of permeate flux is critical to calculate the membrane surface required, which is an essential parameter for scaling-up, equipment sizing, and cost determination. For this reason, several models based on phenomenological or theoretical derivation (such as gel-polarization, osmotic pressure, resistance-in-series, and fouling models) and non-phenomenological models have been developed and widely used to describe the limiting phenomena as well as to predict the permeate flux. In general, the development of models or their modifications is done for a particular synthetic model solution and membrane system that shows a good capacity of prediction. However, in more complex matrices, such as fruit juices, those models might not have the same performance. In this context, the present work shows a review of different phenomenological and non-phenomenological models for permeate flux prediction in UF, and a comparison, between selected models, of the permeate flux predictive capacity. Selected models were tested with data from our previous work reported for three fruit juices (bergamot, kiwi, and pomegranate) processed in a cross-flow system for 10 h. The validation of each selected model's capacity of prediction was performed through a robust statistical examination, including a residual analysis. The results obtained, within the statistically validated models, showed that phenomenological models present a high variability of prediction (values of R-square in the range of 75.91-99.78%), Mean Absolute Percentage Error (MAPE) in the range of 3.14-51.69, and Root Mean Square Error (RMSE) in the range of 0.22-2.01 among the investigated juices. The non-phenomenological models showed a great capacity to predict permeate flux with R-squares higher than 97% and lower MAPE (0.25-2.03) and RMSE (3.74-28.91). Even though the estimated parameters have no physical meaning and do not shed light into the fundamental mechanistic principles that govern these processes, these results suggest that non-phenomenological models are a useful tool from a practical point of view to predict the permeate flux, under defined operating conditions, in membrane separation processes. However, the phenomenological models are still a proper tool for scaling-up and for an understanding the UF process.

Dataset Information

Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches.

Publications

Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches.

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