Monday morning was spent preparing a presentation for the advisors. In the meeting, we discussed the project so far, what existing parts in the registry we could use, and how we could model the system.
On Tuesday morning, our very own supervisor, Chris Hirst, gave us a tutorial on how to use PlasmaDNA for In silico cloning. We then talked about the approximate time frames for standard assembly.
Tuesday night was our first movie night! We were all in need of a break from work, so we ordered pizza, watched a film and chilled out.
For the rest of the week, we set about putting together our DNA cassettes for synthesis, and we also defined the genes in the B. subtilis genome into which we would integrate the DNA cassettes. We also researched Dif sites, which would allow us to remove antibiotic resistance genes after the cassettes had integrated into the genome (see the Human Practices Report for more information on this).
We also started modelling how fast our system would actually be, depending on whether it was a one-step or a two-step amplification. Initially, online sources were explored for guidance on how to start modelling. Introductory lecture given by Dr Guy-Bart Stan proved being very useful. From there, first steps towards creating a model using Michaelis-Menten kinetics were made.
We presented our progress so far at a meeting on Thursday. We explained why we wanted to use the Dif sites in our DNA cassettes, and what DNA we wanted to get synthesised.
On Friday, we started researching catechol 2,3 dioxygenase (C2,3O), which is an enzyme that produces a yellow product very quickly on addition of its substrate, catechol. It is coded for by the gene XylE and was already in the registry, so we started thinking about it as a potential candidate for our output.
Anita made a fantastic banoffee pie for Cake Friday and Wolf held a much needed party on the Saturday. He cooked amazing burgers and we had our first game of horse-racing!