The aim of this project is to simulate vitamin D production in yeast (Saccharomyces cerevisiaea), as well as optimise the reaction in various ways such as optGene, and FSEOF. Furthermore, manual knockouts have been utilised to attempt optimization. The pathway used is from a research paper, using zymosterol (a native metabolite) as precursor to produce 7-Dehydrocholesterol, which is a precursor to vitamin D. This is done through three reactions, with a final concentration reached of 0.041 mmol gDW-1 h-1. The optimization analyses used did not lead to any useful optimization method. Such analyses include manual knock-outs based on literature research, media optimizations as well as co-factor swapping. Furthermore, more automated methods were attempted. The initial automated methods did not yield fruitful optimization, however with more time they may lead to higher production of the desired compound.
This project is organized with the text of the report being presented in the file Report.ipynb and the code for the results presented are located in different files across the repository. The project code is meant to be read in the following order:
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0-Code_Memote.ipynb - this document covers the memote analyses of four different yeast models.
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1-Code_Heterologous-pathway.ipynb - this document covers the model and addition of the heterologous reactions.
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2-Code_PPP.ipynb - this document covers the phenotypic phase plan analysis of manual knock-outs.
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3-Code_Carbon-sources.ipynb - this document covers analysis of what carbon source may be most efficient.
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4-Code_Automatic-optimization.ipynb - This document covers automatic optimization attempts such as optGene
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5-Code_FSEOF.ipynb - This document covers FSEOF analysis of the model
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6-Code_Co-factor.ipynb - This document covers cofactor-swapping optimization analysis
The metabolic models that are used are located in the "data" folder, the memote analysis are in the "memote" folder, and the figures are located in the "figures" folder.