levdopa_synthesis

Central metabolism-scale flux balance, thermodynamic, and stoichiometric analysis of engineered L-DOPA synthesis in E. coli.

Final project for Thayer School of Engineering at Dartmouth College ENGS 161, Metabolic Engineering, Winter 2020.

Lauch the Presentation!

• https://russell-stewart.github.io/levdopa_synthesis/presentation.slides.html

Supplemental Materials: View the Repo

• https://github.com/russell-stewart/levdopa_synthesis

Analysis Notebooks

The following Jupyter notebooks contain the analysis done for the project:

• FBA analysis.ipynb: Flux balance analysis
• thermodynamics.ipynb: Black box and open box thermodynamic analyses
• black box stoichiometry.ipynb: Black box stoichiometric analyses

Required Dependencies

• Jupyter Lab
• Equilibrator
• Equilibrator-Pathway
• Cobra
• Pandas
• Numpy
• Matplotlib
• Escher
• SBtab

External data

The following external metabolomics datasets are used in this project

• BiGG Models
  • E. coli core http://bigg.ucsd.edu/models/e_coli_core
• Relevant KEGG Pathways
  • https://www.kegg.jp/kegg-bin/show_pathway?map01063
  • https://www.kegg.jp/kegg-bin/show_pathway?org_name=eco&mapno=00400&mapscale=&show_description=hide
  • https://www.kegg.jp/kegg-bin/show_pathway?map00030

References

• Journal Articles
  • http://jpet.aspetjournals.org/content/jpet/195/3/453.full.pdf
  • https://apps.who.int/iris/bitstream/handle/10665/93142/EML_18_eng.pdf;jsessionid=BCB6FBC3AFB8913EB126C251473F6D05?sequence=1
  • https://www.nature.com/articles/srep30080
  • https://link.springer.com/article/10.1007/s10295-011-0973-0
• Patents
  • https://patents.google.com/patent/US20060141587A1/en?oq=US20060141587A1-2