Difference between revisions of "Team:Toulouse/Notebook"
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| − | + | <li> We Skyped with the iGEM Ankara team which is also working on Varroa destructor. We exchanged on our different strategies, and decided to start a collaboration with us in order to combine our efforts to fight against varroa and to gather some data about the mite. See <a target="_blank" href="https://2015.igem.org/Team:Toulouse/Collaborations#ankara"> "Collaborations" </a> part for more information. </li> | |
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Revision as of 00:19, 18 September 2015
Notebook
January
During this period, we were informed by iGEM toulouse instructors of what this competition is, and what was expected of us.
From february to may
02/02
First team meeting, our instructors informed us on the competition more specifically 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 are 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
We also created our mail address and a google drive to organise our files online.
02/09
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.
02/16
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?
Until 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
05/04
Our youngest instructor and team mother Mathilde Béraud went with Benoît Pons to the FSIE committee, and thanks to their intervention, we obtained € 4000 !
05/05
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 |
05/13
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.
05/15
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.
05/18
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.
05/25
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
06/01
We started searching for each individual genes by first looking on the iGEM registry.
Knowing that the design of our construct was agreed upon we also started 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 hive where bees need to enter the beehive.
06/05
We realised that our work would be too heavy seeing the number of genes needed to obtain and the cloning work required.. We therefore decided to synthesise the sequence needed to realise our construction.
06/06
Laetitia Chaumont, Benoit Pons and Mathilde Beraud went to Vacbio EA 4357 a laboratory studying varroa. Dr Vetillard allowed us to test the actual effects different concentrations of butyrate on Varroa. The results were inconclusive. However two parameters should be improved because butyrate is a very volatile molecule and we conducted experiments in a petri dish, that is why we decided to set up a more optimised protocol to assess the attraction of varroa by butyrate.
06/22
We finished the design of our constructions and send it to our instructors for checking. In parallel we started training ourselves on basic synthetic biology protocols such as making competent cells, biobrick transformation…
06/29
- Modeling started. We attempted to determine which metabolic pathways our molecules are taking part. This gave us the opportunity to have an overview of their roles and effects.
- Everybody trained to master the different protocols of synthetic biology. Our constructs were finally ordered via Biobasic which offered us a discount price.
- Laetitia Chaumont initiated cytotoxicity test. The purpose of those tests are to assess whether our bacteria could withstand various butyrate/formate concentration
- In parallel Melany Tanchon determined the production 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 for the modeling of our device.
- Our crowdfunding campaign was launched via the Ulule platform.
- We Skyped with the iGEM Ankara team which is also working on Varroa destructor. We exchanged on our different strategies, and decided to start a collaboration with us in order to combine our efforts to fight against varroa and to gather some data about the mite. See "Collaborations" part for more information.
- We stored two bacterial strains BW25113 and MG1665 in a glycerol solution.
- Laetitia Chaumont obtained a meeting with Vincent Grégoire Delory, the ethician of Toulouse White Biotechnology (TWB).
- We did a bacterial culture monitoring thanks to an Optical Density (OD) reading and culture plating.
- We did again a cytotoxicity test of formic acid.
- We did a bacterial culture monitoring thanks to an Optical Density (OD) reading and culture plating.
- We did a cytotoxicity test of butyric acid.
- We did a bacterial culture monitoring thanks to an Optical Density (OD) reading and culture plating.
- We did a cytotoxicity test of butyric acid.
July
07/01
We designed a new protocol to assess whether butyrate is an attractive molecule for varroas. Thanks to M. Patrick Chekroun who made a glass T-tube, we were able to define the attraction power of butyrate. See "Protocols" part
07/02
Our project was in a popular newspaper “Metronews”.
07/04
Our project made the cover of a popular local newspaper “La Dépèche”.
07/06
07/08
First competent cells success by Benoît Pons!!
07/09
07/13
Following the newspaper articles published we discovered a forum of beekeepers discussing about our project on the web. A lot of them were perplexed by our project. We decided to engage the conversation with them and answer all of their questions.
07/14
We prepared precursor molecules for a M9 medium, and also did a cytotoxicité test of formic acid thanks to a plate reader.
07/16
We realised two tests: one is a test culture on BW25113 strain on aerobic and micro aerobic conditions. The other permits to determine the cytotoxicity of formic acid.
07/17
07/18
07/20
Melissa David, Melany Tanchon and Louise Gody went to Brussels to attend the international Exposciences for the whole week. They presented our project and synthetic biology to people coming from all around the world.
07/21 & 07/22
07/23
07/24
07/27
07/29
07/30
07/31
August
04/08/15
September
References
