This was a really busy week in the lab. All three teams made really good progress, and we all really appreciated finally being able to do something practical for the project.
The XylE team miniprepped plasmids containing the XylE gene, which was used for assays for C2,3O activity. They also used 3A assembly to join the J23101 (promoter), XylE and pSB1C3 together. At the same time, they started the construction of the GFP-XylE fusion protein.
The surface protein team spent the week cloning the double terminator (B0014) part into pSB1C3, which will be needed at various points in the assembly strategy.
On Tuesday we were lucky enough to meet Jay Keasling, who was really inspiring and very positive about our project. We were plied with drinks by our advisors (which we had no objection to) and then ended the night with a few drinks at the union.
Here's a photo of the team with Jay Keasling:
The modellers had a busy day on Tuesday, with meetings with Dr Bultelle and Dr Stan to discuss the abnormal behaviour of the output amplification model as well as the ComD receptor signalling. Once viable reaction rate constants have been entered into the output amplification model, it started exhibiting strange behaviour. Sometimes it was showing negative concentration values! When discussing the issue with advisers, several solutions were suggested. Finally, it was found that our system was stiff and required different solver. Initial steps were made in direction of developing the display protein signalling model. This was withheld towards the end of the week, since it was pointed out that sensitivity analysis should be performed on output amplification model to determine the key constants that we should aim to get measured in the lab.
Kirill bought a strawberry cheesecake for Cake Friday.