The parts that we created.
For our project, we created 9 distinct composite parts (see Design for more information). Each of them is a reporter system that can be induced with SCFAs or a donwstream metabolite of SCFAs.
| # | Name | Part Number |
|---|---|---|
| 1 | Acetate-GFP | BBa_K4930014 |
| 2 | Acetate-BFP | BBa_K4930015 |
| 3 | Acetate-RFP | BBa_K4930016 |
| 4 | Propionate-GFP | BBa_K4930017 |
| 5 | Propionate-BFP | BBa_K4930018 |
| 6 | Propionate-RFP | BBa_K4930019 |
| 7 | Butyrate-GFP | BBa_K4930020 |
| 8 | Butyrate-BFP | BBa_K4930021 |
| 9 | Butyrate-RFP | BBa_K4930022 |
SCFA serve as signal molecules and energy source for bacteria. Therefore we cannot look at our expression system in isolation but have to consider certain environmental factors that could influence the SCFA triggered expression of the reporter. Acetate specifically is a key player in the glucose metabolism, the question is now how much influence does a glucose rich environment (medium) have on the fidelity of our expression system. We created our model to be able to quantify exactly how much effect a glucose rich medium would have on the reporter expression triggered through acetate.
Our model represents the basic metabolism of an E. coli cell and can be utilized by other iGEM teams in the future to check for metabolic influences on their experiments (see Model for more).
Designing Primers is a critical task in synthetic biology. While several computational tools exist, they are often lacking configuration options or use private algorithms. Moreover, various industry-standard primer calculation tools we tested gave wildly different results. To alleviate this and understand the specifics of such a program, we coded a simple primer calculator ourselves (see Software for more).