This week we started designing primers and refining the assembly strategy.
The Modellers have been working throughout the week on implementing the output amplification model. They have been exploring different environments to do it in, such as: MatLab or TinkerCell. They decided to go with MatLab to have better understanding of the observed behaviour. They have decided to model 1,2,3 step amplification systems. They again run into a problem of determining rate constants required for the models.
On Thursday, we had a meeting with Professor Paul Freemont, co-director of the CSynBI. He made us realise that we could have been working much more efficiently, and advised us to set objectives for each week. His words were taken as constructive criticism and we actually ended up working much more successfully after the meeting, by dividing up topics to research and communicating with each other more effectively.
After the meeting, we split up into dry lab and wet lab teams. Within the dry lab team were the modellers, Anita and Piotr, and Ben, who worked on the Wiki and other design strategies for the project. Within the wet lab team, there were 3 different pairs, which each started working on a different part of the assembly strategy. Nick and Maddie formed the XylE Team, Kirill and Kyasha formed the Vector Team and Harriet and Florian made up the Surface Protein Team. Wolf and Ben were also given the task of overseeing the project so that everything ran smoothly.
The XylE team started work in the lab on Thursday afternoon, transforming E. coli with a vector containing XylE, and working on the promoter, part J23101.
The Vector Team had the task of assembling the AmyE vector and the PyrD vector, which could then be used to integrate any piece of DNA directly into the B. subtilis genome, and at the same time, disrupt essential genes (see the Human Practices Report for more information). We used these vectors for testing constructs as well as the final assembly. Kirill decided to take on the AmyE vector, and Kyasha assembled the PyrD vector.
Nick brought in Krispy Kreme donuts for Cake Friday!