Team:Toulouse/Notebook
Notebook
February
02/02/2015
First team meeting, our instructors informed us on the competition and how the team is organized. Our first mission was to prepare a presentation for the next week on the following themes:
- Previous subjects. What are the themes explored by iGEM? Give examples of good projects and explain why they won?
- Biobricks? What are they? What’s their advantages? What are the materials send by iGEM? How does the registry work?
- Competition and deadlines. How does the competition works and what are the important deadlines?
Those presentations gave us the opportunity to understand more about the iGEM competition and to get to know each other (since we don’t all come from the same institutions)
Our first team meeting
09/02/2015
Every group of two or three students presented one of the subjects seen above. Every presentation was followed by a Q&A so that everyone understood clearly the topic.
16/02/2015
The next step was to present every week, two new project ideas. The presentations were divided in the following parts.
- Context
- Goal
- Originality
- Strategy
- Difficulty
- Modeling
- Device
- Benefit
- Ethic
- Planning
- Why is this project going to win?
From february to may
The following weeks were spent brainstorming. Everyone presented at least two project ideas. Here are a few examples of projects reviewed:
- Creation of a rapid detection kit for hepatitis
- Degradation of Lignin
- Use of ice nucleation proteins for water desalination
- Creation of a small domestic pollution detector
- ...
May
05/05/2015
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.
| Trouche Blandine | Finance |
|---|---|
| Tanchon Melany | Modeling |
| David Melissa | Events |
| Pons Benoit | Press |
| Etcheberry Thomas | Logistics |
| Le Scornet Alexandre | Registry, Biobricks |
| Pons Marine | Experiences |
| David Anthony | Power Point Presentation |
| Gody Louise | Wiki |
| Chaumont Laetitia | Ethic |
13/05/2015
Two members of our team participated in the Toulouse Exposcience. They presented a poster on synthetic biology and the iGEM competition. They also organized banana DNA extraction experiences for children. This successful event was a good opportunity for us to start learning how to design a poster and to communicate about synthetic biology.
15/05/2015
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.
18/05/2015
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.
25/05/2015
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.
June
01/06/2015
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.
15/06/2015
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.
06/06/2015
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
06/06/2015
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,…
29/06/2015
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.
July
01/07/2015
We designed a new protocol to assess whether butyrate is an attractive molecule for varroas [↗]
02/07/2015
Our project was in a popular newspaper “Metronews”.
04/07/2015
Our project made the cover of a popular local newspaper “La Dépèche”.
06/07/2015
Laetitia Chaumont initiated cytotoxicity tests of butyrate and formate. The purpose of those tests are to assess whether choosen E.coli strain could withstand various butyrate/formate concentrations.
In parallel Melany Tanchon determined the maximum productions of butyrate/formate. Those results are directly linked to the undergoing cytotoxicity tests.
We also initiated the creation of the plans that would be used to 3D print our device. In order to achieve this Valentin Girin used the software Catia to model our device.
Finally, our crowdfunding campaign was launched via the platform Ulule. Goal: €1,200
09/07/2015
We skyped with the iGEM Ankara 2015 high school team who is also working on Varroa destructor. We decided to establish database about the parasite infestation in France and in Turkey.
13/07/2015
Following the newspaper articles published we discovered a forum of beekeepers discussing our project on the web. Our project raised questions about DNA manipulations and beekeepers were curious and interpellate. We decided to engage the conversation with them and answer all of their questions.
20/07/2015
Melissa David, Melany Tanchon and Louise Gody went to Brussels to attend the ExpoScience International (ESI 2015)for the whole week. They presented our project and synthetic biology to people coming from all around the world.
August
04/08/15
References
