Team:Imperial College London/Notebook/week4



This is our diary page which records the daily activities of the team. Click on the links below to see a summary of events and activities happening each week.

Week 4: 25th July to 31st July

Monday, 25th July

We arrived at Norwich for the UK iGEM meet-up. We presented our project to the other UK teams and gained valuable feedback. The other teams presented their projects as well and we gained new insights into their projects. Many parts of their presentations were pretty relevant to our project. For instance, one team was making a kill switch which we would also need as part of our project. There was a great exchange of ideas and opinions and it surely was a fruitful day for us as we gathered advice and learned from others.

In the evening, we mingled with students from the other teams and had loads of fun activities. After that, we had a great time and team bonding session at the clubs.

Tuesday, 26th July

This was the second day of the UK iGEM meet-up. We had four interesting talks on synthetic biology. In particular, we picked up many good points from one of the talks on human practice. It reminded us of the many ethical issues and responsibilities that we bear and should take into account into our project as we dealt with synthetic biology. Another talk by James Brown from Cambridge was also very relevant and useful to our project. We were very impressed by some of the great images of plant root growth and the modelling of the individual root cells. Ming and Rebecca also successfully collected the seeds that we need for our project. On the train back to London, we went through many of the great ideas and information that we had gathered during the meet-up. We also drew up plans and set up experiment timetables for the week.

Wednesday, 27th July

Today we had a meeting with the professors to update them on our progress. We also had the RCA group with us to talk about their ideas. The main feedback from the meeting was that we need to figure out our kill switch or containment mechanism asap for the human practices so that it can actually inform our design rather than be tagged on. This is for the containment of bacteria in soil as well as the issue of horizontal gene transfer. We also found out that Prof Kitney knows everyone.

Koby and CJ showed us an amazing logo designed by Koby. CJ did loads of research into public policy and media around GMO, which is on the blog now embedded in our wiki.

We had good news form Ming today, our baby Arabidopsis are ready to be experimented on! We also recieved the YFP seeds from Nottingham.

Chris and Nick started work in the lab, preparing plates etc. fun fun. We finally finished the questions to email to Claire.

I had sushi for lunch.

Thursday, 28th July

Today everyone made big progress.

Nikki redefined the problem our project wants to solve; she suggested that it might be better if we don’t focus on solving desertification completely, but integrate our project with green plant process to help in re-vegetation.

Chris found a paper, which describes the auxin production in a cell. So we are going to have journal club tomorrow to discuss about it. And he also transformed three plasmids into E.coli, which can be used later for Gibson Assembly.

Ming and Rebekka were taking care of the seeds. Rebekka also contacted Dr. Robert Cariffiths at the Centre for Ecology and Hydrology about soil microbiology. While, Ming helped us ding research about modeling of branch of root. Many thanks for Ming from modeling team!!

Nick found James Chapel today. James showed him how to deal with wide-field microscopy.

Thank you Frank for introducing us the Chemotaxis guy Luke Tweedy, he generously helped us a lot in Chemotaxis modeling. Franks also had good news for us: he found a new developed version of kill switch.

Nina was modeling the auxin production today and I was modeling the chemotaxis animation. The bad news is I don’t know why the bacteria are moving away from chemoattractant. I wish I could fix it tomorrow.

Finally, Yuanwei’s efforts were visible, please go to Imperial iGEM Wiki 2011.

Friday, 29th July

First, happy birthday to Ming again

Chris,Nick and Rebekka

finished the auxin production overview for our wiki MCPs protein arrived from Spain wetlab: transforming the cells


uploaded the live news finished the sponsorship page and the brainstorming page the dessertification description page will be finished soon


abstract for the homepage blog reading the information about other relative iGem projects

Si and Nina

finished the animation to demonstrate the bacterial population dynamics 1000 bacteria are re-directed with the presence of chemoattractant as the radius goes further, the chemoreceptors are not sensitive enough to detect malate therefore, random(Levy) walks the auxin synthesis pathway is modelled with a set of ODEs change of the concentration of [E],[S],[ES],[EI],[P] with respect to time several parameters are needed to finish the model


help the modeling team with the Michaelis-Menten kinetics


progression in kill-switch we need your help to model it !