Dataset Information

Shene2020 - flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium

ABSTRACT: Modelo_mod3_032020.m is a Matlab code used for the simulation of the growth curve of Antarctic thraustochytrid Oblongichytrium sp. RT2316-13. The model is based on the genome scale model adapted for the strain that is found in the Excel file ExcelAurant_28102019.xlsx. Flux balance analysis is used to predict the specific growth rate of the biomass, specific synthesis of neutral lipids and specific consumption rate of the nutrients. The code crea_modelo.m transform the excel file into the array model_T.mat used in by Modelo_mod3_032020.m This model was used to generate data presented in the manuscript Dynamic flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium sp. RT2316-13, 2020, Carolina Shene, Paris Paredes, Liset Flores, Allison Leyton, Juan A. Asenjo, Yusuf Chisti, Biotechnology and Bioengineering, DOI: 10.1002/bit.27463.

SUBMITTER: Carolina Shene

PROVIDER: MODEL2006010001 | BioModels | 2020-07-16

REPOSITORIES: BioModels

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Dataset's files

Source:

			Action	DRS
	MODEL2006010001?filename=ExcelAurant_28102019.xlsx	Xlsx
	MODEL2006010001?filename=Modelo_mod3_032020.m	Other
	MODEL2006010001?filename=crea_modelo.m	Other
	MODEL2006010001?filename=curva8.txt	Txt
	MODEL2006010001?filename=imprimeResultadosDual.m	Other

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Project description:Background: Cell line specific, genome-scale metabolic models enable rigorous and systematic in silico investigation of cellular metabolism. Such models have recently become available for Chinese hamster ovary (CHO) too. However, a key ingredient, namely an experimentally validated biomass function that summarizes the cellular composition, was so far missing in all genome-scale metabolic models of CHO cell lines. Here, we close this gap by providing extensive experimental data on the biomass composition of 13 parental and producer CHO cell lines under various conditions.Results: We report protein, lipid, DNA, RNA and carbohydrate content, cell dry mass, and protein and lipid composition. Furthermore, we present meticulous data on exchange rates between cells and environment and provide detailed experimental protocols on how to determine all of the above. The biomass composition is converted into cell line and condition specific biomass functions for usage in cell line specific, genome-scale metabolic models of CHO. Finally, flux-balance analysis (FBA) is used to demonstrate consistency between in silico predictions and experimental analysis.Conclusions: Our study reveals a strong variability of the total protein content and cell dry mass across cell lines. Yet, the relative amino acid composition is independent of the cell lines and conditions and thus needs not be explicitly measured for each new cell line. In contrast, the lipid composition is strongly influenced by the growth media and needs to be determined for each case. These cell line specific variations in the biomass composition have a small impact on growth rate predictions with FBA, as inaccuracies in the predictions are typically dominated by inaccuracies in the exchange rate spectra. Cell specific biomass variations become only important if the experimental errors in the exchange rate spectra drop below twenty percent. Links:All data and code for data processing are available at <a href='http://dx.doi.org/10.17632/g3wz7spyc9.1' rel='noopener noreferrer' target='_blank'>Data Mendeley</a>.Cell line specific metabolic models were deposited in <a href='https://www.ebi.ac.uk/biomodels/(Chelliah et al, 2014)' rel='noopener noreferrer' target='_blank'>BioModels</a>, identifiers are listed in the study sample table.

Dataset Information

Shene2020 - flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium

Dataset's files

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