Team:Toulouse INSA-UPS/Notebook
Notebook
Here is an overview over the accomplishments and the challenges we had to manage during our project.
Week of December 14th to 20th
Project
This week marks the creation of the 2021 team. After the responses to our applications we had the first meeting with our PI, in which a first distribution of roles was proposed:
Maxence: Finance/Modelo/Wiki
Margaux: Entrepreneurship
Romane: Wiki/Modelo
Thomas: Experimentation
Romain: Human Practices
Camille: Organisation/Communication
We started to get in touch with each other and presented the ideas of the topics we had proposed in our applications.
Week of December 21th to 27th
Project
This week corresponded to the first week of the end-of-year vacations. We continued to develop our application projects while trying to find other potential topics.
Week of December 28th to 03rd
Project
During the last week of the year we continued our research work on topics.
Week of January 04th to 10th
Project
First week of the year and first real meeting with all the supervisors. The final roles have been assigned:
Maxence: Finance/Modelo
Margaux: Entrepreneurship
Romane: Wiki/Modelo
Thomas: Experimentation /Wiki
Romain: Human Practices
Camille: Organisation/Communication
Week of January 11th to 17th
Project
We continued the brainstorming effort and began holding more meetings per week.
Week of January 18th to 24th
Project
The brainstorming effort continued this week. This is the first week where we started making slideshows to further present our topic ideas.
First meeting of the student team in real life, we strengthened our ties around board games!
Week of January 25th to 31th
Project
This was the first week where a subject on the violet was discussed during a brainstorming meeting. We also started to have meetings with scientists to discuss the topic.
Team Building
We met the 2020 team where we had a lot of fun playing together!
Week of February 01st to 07th
Project
To optimize the brainstorming, and to refocus our research, we started to have mini-meetings during the week with the supervisors by dividing up the topics.
Week of February 08th to 14th
Project
This is the first time that the creation of a sustainable and modular fragrance has been discussed in a meeting.
Team Building
Second meeting of the team in real, we played board games.
Week of February 15th to 21th
Project
At this point of the brainstorming we had only 2 potential topics left, one on azo-dyes
treatment and one on violet.
We came close to choose the violet topic but left the
azo-dye topic for one last week.
Week of February 22th to 28th
Project
We continued to dig into our 2 potential topics. Towards the end of the week we met with a chemist for the azo-dyes topic and we concluded that it would be complicated to do.
Week of March 01st to 07th
Project
This week marks the final selection of our topic on violet.
We met for the first time with L'Occitane (a cosmetics company). This meeting helped us to
evolve our subject and to focus more on the agreements in perfumery rather than on a
perfume.
From this week on we were sure to participate in the competition this year.
Team Building
We organized a meal to get together.
Week of March 08th to 14th
Project
This week a new supervisor joined the team. Philippe Urban working on yeast whose team provided us with our yeast strain. The INSA students spoke to us for the first time about a friend of theirs who was interested in our subject and who could join us.
Week of March 15th to 21th
Project
This week was very important for the team as we welcomed a new member, Manon. She was assigned to the communication department to help Camille. The project has also evolved tremendously. During the weekly meeting we presented to the supervisors the idea of using S. elongatus to co-culture with our yeast.
Week of March 22th to 28th
Project
It’s during this week that we began to construct our design and our bricks, first with schemes. Thomas helped us with Benchling to work on the design. We met for the first time Denis Jallet, our future advisor, who confirmed our idea of working with cyanobacteria.
Week of March 29th to 04th
Project
Denis accepted to join our team as an advisor to help us with the cyanobacteria in our project. We made our first GANTT to see if our project could be realisable in our experimentation time.
Week of April 05th to 11th
Project
It’s during this week that for the first time we put our design on Benchling. We also focus our search to talk with cyanobacteria experts and see what materials we would need.
Week of April 12th to 18th
Project
This week we met many specialists to help us with our design and advise us about the
materials for the cyanobacteria.
We started to search for the name of our project and our
logo!
Week of April 19th to 25th
Project
For the first time, we were able to meet our supervisors in real life to talk about the
design of our project. The composition of the team was modified with the departure of
Romain. This week we met our 3 advisors Amandine, Thibault and Younes!
We contacted for
the first time iGEM IISER Pune to establish a collaboration.
We worked on our 2-minutes
presentation video.
Week of April 26th to 02nd
Project
We presented the storyboard of our 2-minutes video to Eglantine, who was willing to help us
with the animation part.
Since we were ahead of schedule with the design and organization
of the project, the supervisors decided to suspend the weekly meetings and put the project
on hold for a while so that we could focus on our final exams.
This week, the project was
named Elixio!
Week of May 03rd to 09th
Project
We did not have a meeting this week.
Although the project was paused to allow us to
concentrate on our exams, some tasks were not stopped. We continued to work on the video
presentation and we had to order material for the beginning of the experiments.
Week of May 10th to 16th
Project
We did not have a meeting this week.
The effort on the project process continued.
Some
orders for the beginning of the experiments have started to arrive. Thomas and Camille went
to Ambre's laboratory to repel strains containing plasmids of interest.
Week of May 17th to 23th
Project
The 2 members of the team coming from the university finished their year during this
week.
We started going to the lab to drop off equipment and to sort out what was left of
the 2020 team.
Week of May 24th to 30th
Project
After the break for exams we resumed our weekly meetings. INSA members have finished their exams too.
Collaboration
For the first time we had a meeting with iGEM Pune to meet them and see how we could work together
Week of May 31th to 06th
Project
This marks the beginning of our internship!
pFLEUR: Amplification of the first block HygR and Z3eV by PCR to open the
vector of integration pCfB3038 XII-1.
pVIOLETTE: Amplification of NsR, ofCCD1, Lcye and the vector of integration
pCfB3040 XII-4 by PCR . First In Fusion performed and failed. A second test was carried out
at the end of the week.
pFRAMBOISE-fused: Amplification of the first block NeoR and pTet and PCR to
open the vector of integration pCfB3034 X-3. First In Fusion performed.
pCONCOMBRE: amplification of blocks LOX and HPL by PCR. LacI amplification
by PCR colony on a cyanobacteria strain. The integration vector PCR failed due to a problem
in the design of the primers, new ones have been ordered.
Cyanobacteria cultures: The first kinetics of cyanobacteria growth have been done this week.
Human Practices
Margaux and Camille made a podcast on the radio Campus FM to talk about our project and to
highlight biotechnologies.
Manon, Margaux and Camille participated to the Exposcience, an
exhibition allowing young students to present scientific projects. This allowed us to share
our project with the general public.
Safety training
Thomas, Manon, Maxence and Romane have been trained in the use of the autoclave.
Sanitary precaution
In order to carry out our experiments in the best conditions, we decided to vaccinate the 6 of us as soon as possible. Maxence had already received his 2 doses of vaccine. This week Manon and Margaux received their first and last dose of vaccine.
Week of June 07th to 13th
Project
pFLEUR: Second attempt of In Fusion by changing the quantities of the DNA
fragments, 2 clones obtained were sent for sequencing.
pVIOLETTE: Last In Fusion failed. Attempted a new strategy by performing
PCR overlaps to assemble the LcyE and ofCCD1 fragments, but that did not work.
pFRAMBOISE-fused: Amplification of the vector obtained with the first In
Fusion and attempt at a new In Fusion to finish the construction.
pCONCOMBRE: In Fusion analysis by PCR and enzymatic digestion showed that
the construct was assembled. Sequencing showed mutations in the construct.
Cyanobacteria cultures: We continued to perform the culture tests on our cyanobacteria.
Safety training
We have received training in laboratory safety.
Sanitary precaution
Romane had her first and last dose of vaccine and Thomas and Camille their first.
Week of June 14th to 20th
Project
pFLEUR: First attempt at In Fusion failed.
pVIOLETTE: Failure of the second attempt of In Fusion. Fragments for the In
Fusion were re-amplified and purified on gel. Another In Fusion was attempted.
pFRAMBOISE-fused: Success of the last In Fusion. Amplification of the other
fragments, RtTA and Crty, to continue the construction.
pCONCOMBRE: Amplification of the vector with the new primers. Attempt of an
In Fusion with the 3 fragments and the vector.
Yeast Cre-Lox: We tried to perform a cre-lox on our yeast strain to remove a
resistance.
Cyanobacteria cultures: We continued to perform the culture tests on our
cyanobacteria.
Video
We started shooting footage for our 2-minutes presentation video.
Week of June 21th to 27th
Project
pFLEUR: Sequencing showed that the construct was good for one strain. In
Fusion to perform the second part of the construct was attempted.
pVIOLETTE: New primers have been ordered to try a new strategy, an In
Fusion in 2 steps, to achieve the construction. The first In Fusion of the next strategy was
attempted.
pFRAMBOISE-fused: Analysis of clones obtained with the latest In
Fusion.
pCONCOMBRE: Further sequencing showed that the construct had no mutation
and was finished. The helper strain was constructed for triparental conjugation to introduce
the construct into our cyanobacteria strain.
Yeast Cre-Lox: The first attempt at cre-lox failed. We also realized that
the glycerol stock we were working with was contaminated. So we re-stocked our strain to try
the cre-lox again.
Cyanobacteria cultures: The effort to control cyanobacteria cultures
continued.
Video
We finished the shooting of our 2-minutes presentation video, only remaining to edit it.
Collaboration
A meeting between our dry lab and the one in Pune was held to see how we could help each
other.
We also participated in the first Phototroph meetup, by presenting our
subject.
Week of June 28th to 04th
Project
pFLEUR: The only clone obtained with the last In Fusion had a mutation in
one of the fragments.
pVIOLETTE: The first In Fusion of the new strategy succeeded. The second
step, another In Fusion to integrate the last fragment into the construction, was
attempted.
pFRAMBOISE-fused: We ordered primers to sequence the construct.
pCONCOMBRE: Attempt to integrate pConcombre into the cyanobacteria.
Yeast Cre-Lox: We had problems with phleomycin. This antibiotic was normally
used to select the strains that have integrated the plasmid of interest allowing us to
perform the cre-lox. We had to reorder phleomycin.
Cyanobacteria cultures: After several weeks of cultivation we
started trying to measure the sucrose produced by our cyanobacteria.
Human Practices
We tested the game in the team, with the students and the supervisors.
Week of July 05th to 11th
Project
pFLEUR: A new sequencing was attempted on the strain obtained with the last
In Fusion.
pVIOLETTE: The last In Fusion failed.
pFRAMBOISE-fused: Clones were sent for sequencing.
pCONCOMBRE: The PCR colonies to see if there were integrations in the
cyanobacterial genome failed.
Yeast Cre-Lox: We received a new stock of phleomycin, a new cre-lox was
attempted.
Cyanobacteria cultures: We changed the pH of our culture medium to try to
increase the growth rate of the cyanobacteria.
Video
We were able to see the first drafts of the editing of our 2 minutes video.
Communication
We shared a press release in order to present our project with the public.
Collaboration
We started the meetings to begin organizing the Symposium on Phototrophic Organisms with iGEM Pune, HKU iGEM and iGEM Stony Brook.
Human practices
We started programming the production of our game. We also considered the interventions we could make to test it, in a high school or with visually impaired people.
Week of July 12th to 18th
Project
pFLEUR: Sequencing confirmed that the last In Fusion was successful, this
genetic construct was completed.
pVIOLETTE: Another In Fusion failed. Another strategy is attempted.
pFRAMBOISE-fused: The last sequencing was missing 20 bp. To be sure that
the construction was finished, new primers were ordered and a new sequencing was performed.
pCONCOMBRE: New strategies are being attempted to verify PCR integration,
including DNA extraction from cyanobacteria.
Yeast Cre-Lox: We still had problems with phleomycin, we tried to perform
some tests by adjusting the pH of the antibiotic.
Cyanobacteria cultures: We changed the pH of our culture medium to
try to increase the growth rate of the cyanobacteria.
Communication
Journalists contacted us by phone, two articles about our project appeared in the press.
Collaboration
We had another meeting for the organisation of the Symposium in which we divided the tasks.
Human practices
We found a scent rehabilitation program for people affected by covid or affected by chemotherapy. We thought it would be interesting to contact someone in charge of this program to learn more.
Week of July 19th to 25th
Project
pVIOLETTE: Fragment amplification for the new In Fusion strategy.
pFRAMBOISE-fused: The sequencing validated that the construction was finished.
pCONCOMBRE: Failure of the verification PCRs. Another method of DNA extraction is attempted and new primers for PCRs are ordered.
Yeast integration: As the pFLEUR construction was finished we tried to integrate it into the genome of S. cerevisiae.
Yeast Cre-Lox: As we could not make our cre-lox with the phleomycin
resistant plasmid we ordered another plasmid to make it with the hygromycin resistance.
Cyanobacteria cultures: We detected sucrose in our culture medium
by HPLC.
Communication
A journalist came to write a report on us at the laboratory.
Collaboration
Meeting between our dry lab and those of Pune to make an assessment of our partnership.
We
also had a meeting with all the French teams to discuss the organization of the French meet
up and we decided to do it online.
We participated to the second phototrophic meetup.
Denis and Amandine participated as
speakers.
Human practices
We have finished the cards in our deck. Robertet, our sponsors, offered to provide us with scent vials for our game.
Sponsor
We had a visit from Robertet, one of our sponsors. We gave them an update on our progress and showed them where we were working.
Week of July 26th to 01st
Project
pVIOLETTE: We received new gblocks to perform a new In Fusion strategy. The In Fusion with the new strategy failed.
pFRAMBOISE-notfused: Preparation of the fragments to build by In Fusion the backup construction, pFRAMBOISE-notfused
pCONCOMBRE: A method to extract DNA from cyanobacteria was finally successful but other primers had to be ordered for genotyping.
Yeast integration: The pFLEUR integration failed and we had a problem with the selection marker of this integration (hygromycin).
Yeast Cre-Lox: Failure of the last tentative.
Cyanobacteria cultures: We were able to improve the saturation OD of our
cultures with a new BG-11 culture medium.
As we were having problems working with our yeast strain we met Hélène Martin-Yken who gave
us a lot of advices and a new strain of S. cerevisiae.
Collaboration
We had another meeting to talk about the organisation of the Symposium.
Human practices
We finished writing the rules of our game.
Week of August 02nd to 08th
Project
pVIOLETTE: The same In Fusion as last week was retried, after verification by sequencing we finally finished this construction!
pFRAMBOISE-notfused: The construction was sent to sequencing.
pCONCOMBRE: The PCRs finally worked, and the construct seemed to be integrated into the genome of our cyanobacterium but new primers have been ordered to confirm it.
Yeast integration: We tried a new protocol to attempt to integrate our constructs in our yeast, without success.
Yeast Cre-Lox: After several failures of the Cre-Lox, we realized that the
selection with neomycin, to see whether or not the Cre-Lox worked, was not the right one and
that we should use G418 instead.
Cyanobacteria cultures: We managed again to increase the OD of our
cultures.
Week of August 09th to 15th
Project
pFRAMBOISE-notfused: The sequencing results showed that the construction was globally successful, one area was not sequenced. New primers were ordered to cover the unsequenced area.
pCONCOMBRE: The new primers did not remove the doubt about the integration, new primers were ordered.
Yeast integration: We tried again to integrate pViolette and pFleur in our yeast strain without success.
Yeast Cre-Lox: We still had selection problems with antibiotics and we
performed more Cre-Lox trials.
Cyanobacteria cultures: We had a better growth rates in our cultures.
Collaboration
We participated in the Symposium allowing us to present our project and to attend workshops.
Week of August 16th to 22th
Project
pFRAMBOISE-notfused: The sequencing showed that the construction was correct and finished.
pCONCOMBRE: With the new primers one arm of the integration still could not be amplified. As all fragments were integrated and the strain was well resistant to the antibiotic selection, we considered that the integration was successful.
Yeast integration: We tried again to integrate our constructions in the yeast without success.
Yeast Cre-Lox: We finally managed to perform our Cre-Lox allowing us to try
to integrate pFramboise in the yeast.
Cyanobacteria cultures: We ordered new LEDs to have a better light source
in our cultures.
Human practices
The cards of the game were at last finished. We found someone who can produce the pieces of our game.
Week of August 23th to 29th
Project
It was Manon's last week in the lab with us.
Yeast integration: We tried a new protocol to integrate one of our
constructions in our yeast.
Cyanobacteria cultures: We measured the sucrose secretion with our new
lights, but it was still not optimal.
Co-culture: We have performed our first co-culture tests. We grew our
strain with yeast in the co-culture medium.
Video
We showed the team presentation video to our supervisors for the first time.
We went
to Grasse for the weekend, the capital of perfume. We visited the company of Robertet, one
of our sponsors. We took advantage of the city heritage to start shooting shots for our
20-minutes presentation video.
Team building
As we were close to Canne we took the opportunity to go and eat in a restaurant by the
sea.
Week of August 30th to 05th
Project
Yeast integration: After weeks of trials with the new protocol, we finally succeeded in integrating two of our constructions, pVIOLETTE and pFLEUR, into two yeast strains.
Cyanobacteria cultures: We continued to try to improve the sucrose secretion
of our strains.
Co-culture: The yeasts grew well in the co-culture medium. We wondered how
we would count our 2 organisms when we put them together in the culture.
Video
At the beginning of the week we came back to Toulouse after our weekend at Grasse.
Week of September 06th to 12th
Project
This week Thomas, Camille and Manon were back to school.
Maxence, Margaux and Romane
continued the experiments on all 3 of them.
The priority was to induce the production of
our molecules and to try to detect them. We had for the first time access to the
GC-MS.
Yeast integration: After successfully integrating pVIOLETTE we then
successfully integrated pFLEUR into the same yeast strain. We also succeeded to integrate in
another strain pFRAMBOISE-notfused
Cyanobacteria cultures: The effort continued to improve sucrose secretion.
Collaboration
Thomas and Camille presented during the French meetup that we partly organized with all the
French teams.
Human Practices
We received the pieces of our game.
Week of September 13th to 19th
Project
Yeast integration: The last transformation of the summer was done to build our final yeast strain by integrating pFRAMBOISE-fused.
Detection: We were finally able to detect the β-ionone produced by a yeast strain carrying the pFRAMBOISE-notfused construction. We were also able to detect carotene which are degradation compounds of lycopene and precursors of our ionones.
Cyanobacteria cultures: We were able to detect an increased secretion of sucrose.
Video
We filmed more shots of our video in the lab.
Human Practices
We were able to produce our game board! Thomas himself used the laser printer to produce
them.
Week of September 20th to 26th
Project
That was the last week of experiments of the project.
Yeast integration: After our 4 months of experimentation and in the last
week of our internship we finally succeeded to produce our final yeast strain with the 3
integrations!
Detection: This week we were able to detect the 2 others ionones of our
project, the ɑ-ionone and the dihydro-β-ionone.
Cyanobacteria cultures: We have done our last cyanobacteria cultures.
Video
We continued to film shots of our 20-minutes video presentation.
Week of September 27th to 03rd
Project
As the experiments were finished we could focus on the valorization of our results. We all
got together to do a fake wiki freeze in order to make progress on the wiki writing.
Human practices
We had the opportunity to test our game in an association for visually impaired people. This
allowed us to get feedback on the game and to see how we could adapt it so that they could
play it.
Communication
We went to present our project and for the first time our results to the CBI.
Week of October 04th to 10th
Project
We made a second fake Wiki freeze in order to continue to progress on our website
Video
We continued shooting for our 20 minutes video presentation.
Human practices
We tested our game with some friends. They gave us very good feedback on our game.
Week of October 11th to 17th
Project
We made a third fake Wiki freeze in order to definitely finish our website!
Human practices
We went to a high school class to talk to them about synthetic biology and our project and to let them test our board game.
Week of October 18th to 24th
Project
After weeks of work, we finally succeeded in finishing our website !
Thank you for reading this notebook to the end. As a reward, here is one of our best photos taken in the lab during summer!
