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Flexible Nets to Improve GEM Cell Factories by Combining Kinetic and Proteomics Data

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Computational Methods in Systems Biology (CMSB 2024)

Abstract

Alzheimer’s disease is expected to reach a prevalence of 152 million people worldwide caused by the aggregation of amyloid \(\beta \)-proteins leading to apoptosis of neurons and loss of cognitive function. Although there is no effective treatment for this disease, molecules such as scyllo-inositol have been shown to be promising. Bacillus subtilis has been proposed as a suitable organism for the production of scyllo-inositol. Metabolic computational models have proven useful in the prediction of the production of a metabolite. However, most genome-scale metabolic models lack detailed parameters and tend to overestimate the production of a metabolite with respect to the consumption of medium resources. In order to reduce the solution space and, hence, obtain a more realistic model, additional constraints from experimental data can be added to the model. This work exploits the modeling capabilities of Flexible Nets to model the production of scyllo-inositol in a genome-scale metabolic model of Bacillus subtilis that has been previously enriched with proteomic and enzymatic data. We assess how these constraints limit the scyllo-inositol production to more realistic levels. Moreover, the integration of different types of constraints allowed us to uncover which one of them limits the production of scyllo-inositol for a given growth rate.

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Correspondence to Jorge Lázaro .

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Lázaro, J., Júlvez, J., Zanghellini, J. (2024). Flexible Nets to Improve GEM Cell Factories by Combining Kinetic and Proteomics Data. In: Gori, R., Milazzo, P., Tribastone, M. (eds) Computational Methods in Systems Biology. CMSB 2024. Lecture Notes in Computer Science(), vol 14971. Springer, Cham. https://doi.org/10.1007/978-3-031-71671-3_11

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  • DOI: https://doi.org/10.1007/978-3-031-71671-3_11

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