====== Bio production ======

** 5th of October - Patrick Boyle (Ginkgo Bioworks) **\\
[[http://bio.academany.org/files/Patrick_Boyle_How_to_grow_almost_anything_2016.pdf|class slides]]
[[http://connectmedia.waag.org/AcadeMany/bio-2016/10/05/index.html|Recordings]]
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How do you tailor the metabolism of a microbe to make a product? People have been tweaking microbial metabolism since the advent of fermented foods like beer, bread, and cheese. Over the last century, new tools have been transforming this process into an engineering discipline. In this class, we will explore the latest tools and approaches to designing microbial metabolism.
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How does engineering in biology differ from engineering in other fields? What design principles can be applied to microbes, which are products of evolution? How do we find good biological parts? How do we know if an engineered microbe is performing as expected? We will review Design, Build, and Test strategies appropriate for engineering the metabolism of microbes.
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===== Background reading =====
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PDFs available if requested
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[[http://www.ncbi.nlm.nih.gov/pubmed/22037345|General review of synthetic biology tools and methods for metabolic engineering]]

[[http://www.ncbi.nlm.nih.gov/pubmed/17710092|Commentary on lessons learned during the development of synthetic chemistry, and how that may influence the development of synthetic biology]]

==== Bonus Background reading ====
[[https://www.sciencemag.org/content/349/6252/1095.abstract|Recent publication on the production of opiods in yeast]]

[[http://www.pnas.org/content/109/3/E111.short|Engineering yeast to produce the anti-malarial drug artemisinin]]

[[http://pubs.acs.org/doi/abs/10.1021/ja809461u|Publication on the use of DNA synthesis and bioinformatics to discover novel enzymes]]

[[http://www.sciencedirect.com/science/article/pii/S0168165612002933|Review article on common pathways that are engineered in microbes to produce plant natural products]]

==== Software (not required for assignment) ====
[[https://opencobra.github.io/|Open source software for modeling metabolic networks]]

==== Assignment ===
Design a biosynthetic route to produce a small molecule in an organism. See the class slides for tools and examples. Choose a target compound and answer the following questions:

1. What chassis and pathway will you use?
2. How will you measure product formation?
3. What chassis enzymes would you modify?