Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity
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| Formato: | Recurso digital |
| Lenguaje: | inglés |
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2010
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| _version_ | 1866901193821782016 |
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| author | Tortajada, Marta |
| author_facet | Tortajada, Marta |
| contents | <p>The research validates a simplified constraint-based stoichiometric model of Pichia pastoris metabolism using experimental datasets, focusing on maximum theoretical growth yields and the consistency between model predictions and measurements. It demonstrates the model's ability to estimate non-measured fluxes, highlighting its utility in scenarios with limited data.</p> <p>Constraint-based models enable structured cellular representations in which intracellular kinetics are circumvented. These models, combined with experimental data, are useful analytical tools to estimate the state exhibited (the phenotype) by the cells at given pseudo-steady conditions.ResultsIn this contribution, a simplified constraint-based stoichiometric model of the metabolism of the yeast Pichia pastoris, a workhorse for heterologous protein expression, is validated against several experimental available datasets. Firstly, maximum theoretical growth yields are calculated and compared to the experimental ones. Secondly, possibility theory is applied to quantify the consistency between model and measurements. Finally, the biomass growth rate is excluded from the datasets and its prediction used to exemplify the capability of the model to calculate non-measured fluxes.ConclusionsThis contribution shows how a small-sized network can be assessed following a rational, quantitative procedure even when measurements are scarce and imprecise. This approach is particularly useful in lacking data scenarios.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_14773993 |
| institution | Zenodo |
| language | eng |
| publishDate | 2010 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity Tortajada, Marta Pichia pastoris Constraint-based model Metabolism Data scarcity Stoichiometric model <p>The research validates a simplified constraint-based stoichiometric model of Pichia pastoris metabolism using experimental datasets, focusing on maximum theoretical growth yields and the consistency between model predictions and measurements. It demonstrates the model's ability to estimate non-measured fluxes, highlighting its utility in scenarios with limited data.</p> <p>Constraint-based models enable structured cellular representations in which intracellular kinetics are circumvented. These models, combined with experimental data, are useful analytical tools to estimate the state exhibited (the phenotype) by the cells at given pseudo-steady conditions.ResultsIn this contribution, a simplified constraint-based stoichiometric model of the metabolism of the yeast Pichia pastoris, a workhorse for heterologous protein expression, is validated against several experimental available datasets. Firstly, maximum theoretical growth yields are calculated and compared to the experimental ones. Secondly, possibility theory is applied to quantify the consistency between model and measurements. Finally, the biomass growth rate is excluded from the datasets and its prediction used to exemplify the capability of the model to calculate non-measured fluxes.ConclusionsThis contribution shows how a small-sized network can be assessed following a rational, quantitative procedure even when measurements are scarce and imprecise. This approach is particularly useful in lacking data scenarios.</p> |
| title | Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity |
| topic | Pichia pastoris Constraint-based model Metabolism Data scarcity Stoichiometric model |
| url | https://doi.org/10.5281/zenodo.14773993 |