Engineering Biology

Registry of standard biological parts

Tuning transcription, translation degradation

Tune Gene expression: DNA transcription, mRNA translation.

• Tuning transcription:
  • Tune promoter regions. Operator and activator sequences.
  • transcription factors, inducers to tune the activity of the promoter region.
• Tuning translation:
  • Tune RBS (see mRNA translation). Translation regulated by changing mRNA secondary structure.
  • Tune codon usage. Some codons, that give rise to the same amino acid may result in more efficient translation. Due to abundance of tRNA (be careful with comptetition for the same tRNA, which can change their availability), change in secondary structure. There can be problems with Protein folding, as protein folding can depend on translation speed. RNA stability
• Tuning Protein degradation. Use tags that label proteins for faster degradation.

Reporters.

• $\beta$-galactosidase (encoded by lacZ)
• $\beta$-glucoronidase. Similar. (GUS)
• Luciferase, luciferin
  • Bacterial luciferase
  • Green fluorescent protein. Many colours obtained by Artificial selection.

Craig Venter, George Church

3D bioprinting

Design of biological circuits and systems

Control theory and control systems, depends on a lot of the theory and knowledge of Systems biology

https://autodeskresearch.com/groups/bionano

http://www.synthace.com/

http://ginkgobioworks.com/

http://www.nanalyze.com/2016/03/3-companies-building-nanorobot-factories/

(Lecture Notes in Artificial Intelligence volume 5777) Kampis, Karsai, Szathmáry-Advances in Artificial Life_ Darwin Meets von Neumann, Part 1(2011)

Xenobiology. Craig Venter, George Church

https://serotiny.bio/