Difference between revisions of "Team:Toulouse/Notebook"

The following weeks were spent brainstorming. Everyone presented at least two project ideas. Here are a few examples of projects reviewed:

Two projects were still in course to be chosen, the use of ice nucleating proteins to purify water and the creation of a bio trap against the parasitic mite Varroa destructor. This last one was chosen to be our project on the grounds that it was the most feasible. Based on bibliography, the initial idea was to build an engineered bacteria which will have to produce butyrate to attract the parasite. The following weeks were the subject of extensive research on the topic.

Moreover, it was time to choose attributions to make the project management easier, below in the table, the main assignments.

We held our first meeting without instructors to discuss the design of the constructions needed to create the engineered bacteria. Our reflexion led us to the conclusion that our construction would depend on the bee life cycle. We therefore started searching for beekeepers that would agree to discuss with us.

We met with Dr Boucher Christian HDR, DR1 INRA retired since 2012 and amateur beekeeper. The fact that Dr Boucher was both a researcher and a beekeeper made this meeting really beneficial for us. We learned every important stages in a bee life and how the varroa affected it. We also learned more about the beekeeping activity and the treatments used to fight against the parasite. Furthermore we have been able to discuss our early genetic design and how to improve it.

In conclusion of this meeting we decided that the bacteria should not produce both attractive and toxic molecules at the same time. These productions should be cyclic to have the least effect on bee’s life cycle since formate is also toxic at a lesser extent for bees.

During the whole week we searched for means to produce our molecules cyclically. We found a way to produce our molecules on a circadian rhythm which allows us to produce toxic molecules during the night when bees are a lot less active.
Since we agreed on the regulation constructions we started to look for means to build our construction.
We also started to think about our logo and decided that Louise Gody will create our logo since she is capable of drawing using a graphical tablet.
We also started to organize our search for financial help. To do so we designed a booklet explaining our project and what iGEM is.

We started searching for each individual gene by first looking on the iGEM registry.
Know that the design of our construct was agreed upon we also starded thinking about what our device would look like. Since our bacteria needed to perceive red light we decided to place our device at the entry of the beehive where bees need to passe to enter and go out the beehive.

We realised that the number of genes that we needed to obtain and the cloning work that followed was too high. We therefore decided to synthesize the sequences needed to realise our genetic construction.

Laetitia Chaumont and Benoit Pons went to Vacbio EA 4357 a laboratory studying Varroa destructor. Dr Angelique Vetillard allowed us to test the actual effect of concentrations of butyrate on Varroa. The results were inconclusive. However since butyrate is a very volatile molecule we conducted experiments in a Petri dish, we decided to set up a more optimized protocol to assess the attraction of varroa by butyrate

We finished the design of our constructions and send it to our instructors for verifications. In parallel we started training ourselves on basic synthetic biology protocols, making competent cells, biobrick transformations, DNA extractions,…

Modeling has started. We attempted to determine which metabolic pathways both molecules are taking part. This gave us the opportunity to have an overview of their roles and effects.
Everybody is training to master the different protocols of synthetic biology and optimize them.
Our constructs were finally ordered via Biobasic who allowed us discount price.