Team:Toulouse INSA-UPS/Notebook
Notebook
Here is an overview over the accomplishments and the challenges we had to manage during our project.
If you want to learn more about our brainstorming stage, from december to march, check out our description page here.
To know more about our collaborations click here, and about our two partnerships click here.
Week of December 9th to 15th
Project
We held the first meeting where we met the rest of the team and some of the advisors (Pierre and Eliot were still in Japan for their exchange semester). We also defined some team roles:
- Arno: Wiki leader
- Cécilia: Finances
- Laura: Organization
- Laurène: Communication
- Solène: Human Practices
Week of December 16th to 22th
Project
We had our second meeting where we were introduced to the judging handbook. Each of us thought of a possible project before joining the team so we briefly presented them to the rest of the team.
Week of January 6th to 12th
Project
We met again after the Christmas break, and continued discussing our possible projects ideas: a tumoral biodetector, production of vitamins, algae treatment, spider silk production…
Human Practices
We were invited to the “Soirée des talents Toulousains 2019”, an award ceremony for Toulouse inhabitants of the year 2019 organized by Toulouse Métropole. It was the perfect opportunity to start team building, and also to network with local entrepreneurs.
Week of January 13th to 19th
Project
We started searching possible ways to fund our project, and continued discussing our possible ideas between us.
Week of January 20th to 26th
Project
During this week's meeting, we had the idea for the first time of using electrosynthesis in our project.
Week of February 3rd to 9th
Project
Out of the eight project ideas we decided to dismiss some of them: toxic red mud treatment, algae treatment, tumoral biodetector.
Human Practices
We attended TWB start-up day, this event brings together European key players in the biotech start-up business. We also had the chance to meet and chat with Randy Rettberg, the iGEM president.
Week of February 10th to 16th
Project
As we continued exploring all our ideas, we decided to stop searching about the production of spider silk. We also decided to merge our idea about vitamin production and space to produce nutrients for astronauts.
Team building
We finally met Eliot and Pierre, who came back from their semester in Japan and we had a lovely team Building dinner with previous iGEMERS (iGEM Toulouse 2018, 2017).
Week of February 24th to 1st of March
Human Practices
We had our first meeting with Alain Maillet, scientific leader at MEDES - Institute for Space Medicine and Physiology. We discussed about the loss of nutritional value of food over time and also about the available resources in a space station. You can learn more about it [here].
Week of March the 2nd to 8th of March
Project
Brainstorming continued. We focused on the production of nutrients in space for astronauts and a possible solution for the sharka virus.
Week of March 16th to 22nd
Covid-19
On the 16th of march our country started a lockdown due to COVID-19, from now on all our meetings will be held remotely.
Project
After a long discussion with the whole team, we decided that we will work on the production of molecules in space for our project. We will grow two microorganisms in coculture: Clostridium ljungdahlii PETC (an acetogen) and Saccharomyces cerevisiae (a yeast).
Human Practices
We interviewed Jean-Marie François, specialist in Saccharomyces cerevisiae. For more information click [here].
We also Interviewed Benjamin Erable, responsible for research at CNRS, specialist in electroactive biofilms. For more information click [here].
Week of March 23rd to 29th
Project
We designated Eliot as our modeling leader. We started brainstorming on which molecules we want to produce in space.
Week of March 30th to 5th of April
Project
We started searching which are the available resources that we could use in space for our project.
Week of April the 6th to 12th
Project
This week, we focused on different vitamins that would be interesting to produce in space, we thought about producing vitamin D, vitamin K, vitamin A, or vitamin E.
Human Practices
For our Human Practices, we decided to focus on how synthetic biology is essential for long-duration space travel.
Week of April the 13th to 19th
Project
We have chosen Pierre as our entrepreneurship leader, and Solène as our Ethics leader. We also decided on our project name: iGEMINI. Brainstorming about the molecules we want to produce continued. This week, in addition to working on vitamins, we also searched what flavoring molecules we could synthesize.
Human Practices
We interviewed Dr. Gilles Truan, the head of the Molecular and Metabolic Engineering (I2M) team and responsible for the Metabolic Engineering axis which includes three TBI teams. You can learn more about this interview [here].
Week of April 20th to 26th
Project
We decided on producing provitamin A, and as flavoring molecules we wanted to produce limonene, geraniol and brazzein.
Week of April 27th to 3rd of May
Project
Optogenetics systems were chosen to let astronauts select the flavor they prefer. There would be two LEDs colors: red and blue.
Week of May 4th to 10th
Project
We started designing our experimental plan for the summer
Week of May the 11th to 17th
Project
We started designing the sequences we want to clone. We also had our second meeting with Alain Maillet where we got the wonderful news that the French National Centre for Space Studies (CNES) wanted to sponsor our project!
Human Practices
We interviewed Dr. Natalie Ley (Head of the Microbiology Research Unit, coordinator of the Space Life Science program at SCK-CEN) and Dr. Rob Van Houdt (specialist in genetic engineering at Microbiology Research Unitat at SCK-CEN). For more information click [here].
Week of May the 18th to 24th
Project
We continued designing the sequences we want to clone.
Human Practices
We had our third meeting with Alain Maillet, this time we discussed the recycling system that is currently in place at the international space station.
Week of May 25th to 31th
Project
We kept designing the sequences we wanted to clone.
Human Practices
We discussed with Marie-Pierre Escudié, our Ethics advisor, to decide what we want to achieve for our integrated human practices and public and education engagement. You can read the full interview [here].
Week of June 1st to 7th
Project
We finished our sequences design using Benchling.
Human Practices
We participated at Exposcience, an exposition for young scientists in Occitanie, where we presented our project and discussed it with middle school students.
Collaborations and Partnerships
AshesiGhana iGEM team
New techniques developed for space could be used on Earth and have a major impact on a world where the population is growing and where resources are diminishing. For these two major reasons, we wondered about the possible use of our production device on earth. We looked for areas in the world where vitamin A deficiency is present and found out that Africa is part of these areas, so we contacted Team iGEM AshesiGhana. In our first meeting with AshesiGhana iGEM Team we presented both of our projects and talked about potential collaborations. Some ideas came up, for instance, to give a survey to Ghanaian people about the acceptability of our vitamin production device.
Week of June 8th to 14th
Project
We were finally able to go to the lab! Five out of the eight team members started, we wore masks all day and made sure we were keeping safe distances between us. We got our first genetic elements from Gilles Truan. During this first week, we finished designing all the primers that we will need, we ran the order for our DNA sequences with IDT, and started designing our fermentation protocols.
Entrepreneurship
We had our first online meeting with Le Catalyseur, to start talking about how we could create a start-up from our project.
Week of June 15th to 21th
Project
The whole team is back in the lab! As always we followed the rules established by our university: face masks at all times, safe distances between us, and often hands washings. We did the security training required by TBI.
Human Practices
We had our first meeting with Arnaud Cockx, Gas-Liquid Reactor Engineering professor at INSA Toulouse, to discuss our bioreactor, read the full interview [here].
Collaborations and Partnerships
AshesiGhana iGEM team
We created our Google Drive work space to write down our ideas about our partnership.
Week of June 22nd to 28th
Project
Clonings
Plasmids
Amplification and verification of all the plasmids that we were given to us.
tHmg1-CrtE
Amplification and purification from the plasmid by PCR.
CrtYBekI
Size problem with our plasmid amplification.
Rose Brazzein
Amplification of one of the fragments from the plasmid by PCR.
Cococulture
First cultures with Saccharomyces cerevisiae on acetate and ethanol.
Collaborations and Partnerships
AshesiGhana iGEM team
AshesiGhana team have created our slack work space in order to easily exchange information between our teams. We talked about attaining both silver and gold medals criteria.
Week of June 29th to 5th of July
Project
Clonnings
tHmg1-CrtE
Infusion of the three fragments into pUC19.
CrtYBekI
Amplification of the fragment, then cloning into pUC19.
Rose/Brazzein
Amplification of fragments.
Cococulture
First culture monitoring yeast with a medium containing 60% acetate and 40% ethanol,
Collaborations and Partnerships
We participated in the German Meetup on the 4th and 5th of July, where we presented our team and our poster. We got first place in the poster competition and won a 5000€ centrifuge ! It was amazing to be able to meet with other teams and learn about their projects.
Week of July 6th to 12th
Project
Clonings
We received all the DNA blocks from IDT, so we can finally start all the constructions that were not started yet.
tHmg1-CrtE
Infusion of the other three fragments into pUC19.
CrtYBekI
Fail of Last week’s cloning.
Rose/Brazzein
Amplification of the fragment by PCR and subcloning in pUC19.
Red regulation
Amplification of four fragments by PCR and cloning into pUC19. Negative results.
Lemon
Amplification of the fragment by PCR and subcloning in pUC19. Negative results.
Cococulture
Test of different media concentrations for the growth of S. cerevisiae.
Human Practices
We had a meeting with Arnaud Cockx to talk about the modelling of our project.
We interviewed former Astronaut Phillipe Perrin, we talked about nutrition in space. To watch the full interview click [here].
Collaborations and Partnerships
iGEM France
Meeting with all the iGEM teams in France. iGEM Grenoble suggested doing a video with all the teams which sounds very exciting!
AshesiGhana iGEM team
This was an update meeting on what we have done. We have created a file « notebook » to follow our meeting through the year. We discussed resources that are available in Ghana that we could use for our Vitamin A production device. We thought to do an experiment for the iGEM Ghana team and advised them to use the sponsorship with IDT and get 20kb free of DNA.
Concordia iGEM team
We had our first meeting with the Concordia iGEM team where we presented both of our projects and talked about potential collaborations. Some ideas came up. We then created a Google drive work space as well as a Slack to easily communicate with all the members of each team.
Entrepreneurship
We had a meeting with Le Catalyseur in order to discuss our project potential risks, and their solutions.
Week of July 13th to 19th
Project
Clonings
CrtYBekI
For both parts of the construction: fragments were cloned and transformed into E. coli stellar cells. One of the clones has been sequenced with positive results.
Rose/Brazzein
For one of the inserts we did a miniprep, but it turned out negative. On the other hand, we sent the other inserts to be sequenced.
Lemon
We did the same cloning again and verified the transformation by enzymatic digestion. Sadly, none of the clones have the insert, which means that we have to rethink our design.
Red regulation
After retesting our strategy we decided to design a new strategy with more but smaller blocks.
Blue regulation
We finally received the plasmids containing some of the fragments.
Human Practices
We had a meeting with Alain Maillet at CNES, to discuss the progress of our project.
Week from the 20th to 26th of July
Project
Clonings
Rose/Brazzein
We got our sequencing results: the sequence for the rose is good!
As for the other part of our insert, brazzein, we unfortunately didn’t get any positive results so we redesigned our strategy.
Red regulation
We amplified the fragments by PCR.
Blue regulation
The fragments were amplified by PCR from the plasmids we received last week.
Human Practices
On Monday, we were interviewed with France 3 Occitanie, a local television channel. We interviewed Karen Dhanraj and Romain Maillet who are specialists about the nutritive aspect of the yeast. The interview report is available [here].
On Thursday we interviewed Dr. Brigitte Godard, the European astronaut’s doctor. For the full interview click [here].
On Saturday we had the opportunity to discuss with former astronaut Jean-Jacques Favier, we talked about our project and how it could be implemented in space. For the full interview click [here].
Collaborations and partnerships
Concordia iGEM team
As both of our projects are related to space, we decided to establish partnership goals such as creating a contribution document for future iGEM teams or doing an experiment for them. We also did the plan for our contribution document and separate for both of our teams the work. This contribution is a guide for future iGEM teams.
Entrepreneurship
We had our third meeting with Le Catalyseur where they presented us with what is a business model.
Week of July 27th to 2nd of August
Project
Clonings
tHmg1-CrtE
Both blocks have been purified and ligated together to produce the final construction.
CrtYBekI
New strategy for one of the intermediaries, so the fragments were amplified by PCR, cloned into pUC19 and transformed into E. coli stellar cells.
Red regulation
Fragments were amplified using new oligos.
Blue regulation
We continued testing different PCR methods for the fragments. For one of the blocks an InFusion cloning into pUC19 was done, but it didn’t work.
Cocolture
Yeast culture monitoring with different concentrations of glucose, acetate and ethanol to know its growth rate.
Preparation of Clostridium ljungdahlii medium.
Human Practices
Interview with Romain Charles, astronaut’s support who participated on Mars 500 (a project that simulated the conditions that will be encountered by a crew on Mars). To read more about this interview click [here].
We were interviewed by La dépêche du Midi, a regional daily newspaper published in Toulouse.
Collaborations and partnerships
AshesiGhana iGEM Team
They have sent emails to NGOs that are working on nutrition in Africa. We gave constructive and analytic feedback on their design process as well as informations about coastal erosion in France and Europe. We also have created a new channel in the shared slack for implementation because we think that we can help them on that part.
Week of August 3rd to 9th
Project
Clonings
tHmg1-CrtE
Colonies were verified by enzymatic digestion, we are ready to insert into the yeast.
CrtYBekI
Last week’s colonies were digested and we did an InFusion cloning to add a new fragment to the construction.
Red regulation
Amplified fragments were purified, cloned into pUC19 and transformed into E. coli stellar cells. Unfortunately none of the clones presented the insert.
Blue regulation
InFusion cloning was performed, but we did not get any positive results.
Collaborations and partnerships
Concordia iGEM team
The goal of this meeting was to present to some of our team members the software Astrobio created by Concordia iGEM team. To give them a first feedback.
Pittsburgh iGEM team
With the iGEM Pittsburgh team, we exchanged on both of our projects as we are using two different regulation systems. We pointed out some advantages and drawbacks on both systems.
Week of August 10th to 16th
Project
Clonings
tHmg1-CrtE
We tried yeast transformation of the tHmg1-CrtE construction, but it didn’t work.
CrtYBekI
We got the results that last week cloning did not work.
Limonene
We retried the cloning with a new strategy, but unfortunately it didn’t work
Blue regulation
We retried the first part of the blue regulation, but we found out that some of the fragments are too small to be amplified by PCR.
Collaborations and partnerships
AshesiGhana iGEM team
We had feedback from the design team about advices that we gave them two weeks ago. We gave them some names of companies that are using bioluminescence bacteria (Glowee) and enzymes that are degrading plastic (Carbios). The survey about the acceptability of our Vitamin A production device has been sent to people in Ghana thanks to the iGEM Ghana team.
Pittsburgh iGEM team
We were invited to participate on their podcast « Bluetooth bacteria », that you can listen [here].
Video
We visited La cité de l’espace, to decide which scenes we wanted to shoot there for our videos.
Week from the 17th to 23rd of August
Project
Clonings
CrtYBekI
The blocks were cloned into E. coli stellar cells by InFusion, we will know the results next week.
Limonene
Fragments were purified once again to try a new strategy.
Cococulture
Bacteria
We finally received the bacteria at the end of the week, but it had spent too much time at room temperature during the delivery process and it didn’t grow correctly.
Yeast
We tried different acetate concentrations and measured the growth rate.
Collaborations and partnerships
Concordia iGEM team
The meeting goal was to give feedback from the other part of our team about their database. This feedback was really useful for them because the other team members did not have previous knowledge on how Astrobio database works.
We also attended their conference about microbes and cell agriculture for sustainable food production which was really interesting.
Week of August 24th to 30th
Project
Clonings
tHMG1-CrtE
Saccharomyces cerevisiae gal+ and gal- strains were transformed with the β-carotene boosters (Hmg1 and CrtE) at the beginning of the week. By the end of the week we had some clones! And none in the negative control plates. Clones were verified by genomic PCR, and we had positif results. We are done with this construction!
Video
From Tuesday to Friday we shot with Rémy for our video deliverables. We finished shooting all the clips for the promotion video (and the narration) and we started some scenes of the presentation video.
Week of August 31th to 6th of September
COVID-19
From there on, we had two big problems. First, only five members of the team were left working in the lab, since the other three had to go back to class. Worse, the pandemic stroke back in the Toulouse student community and the five survivors had to miss some weeks when they were experiencing Covid-19 symptoms or while waiting for the test results.
Project
Clonings
There were less and less hands in the lab and we were running out of time. We had a difficult decision to make and decided to stop working on the blue and red regulation, to focus more time and effort on the other constructions.
CrtYBekI
Last week clones could be OK! They were sent to be sequenced.
Rose and brazzein
We performed a bulk PCR test on the numerous clones and all turned out negative.
Limonene
We checked the fragment insertion for the lemon gene, but it gave negative results.
Cococulture
We started setting up the system for the coculture with the help of Christine Lafforgue, professor at INSA Toulouse.
Bacteria
We had a meeting with Jason Whitham to try to solve our problems on why Clostridium ljungdahlii wasn’t growing. We concluded that all our protocols need to be optimized. To read the full interview click [here].
Yeast
We followed three cultures of yeast so we can understand how the two substrates are consumed. We then ran an HPLC batch analysis of acetate and ethanol.
We also tested the growth of yeast in a media closer to the media that will be used for the coculture, unfortunately we forgot to add NTA (that helps to dissolve the metals) so nothing grew, but we will restart with a new medium.
Human Practices
We discussed with Jason Whitham, expert in anaerobic fermentation, about how to make Clostridium ljungdahlii grow, he gave some very useful tips, to learn more about it click [here].
We sent the first part of our video game followed up with some questions to a pedagogical inspector who diffused it to many french high school teachers.
Collaborations and partnerships
Concordia iGEM team
We talked about the design of the contribution document and mentioned using Canva.
Calgary iGEM team
iGEM Calgary contacted us to talk about our projects together because they also work on yeast that produces provitamin A. We had an interesting meeting talking about a potential collaboration.
Week of September 7th to 13th
Project
Clonings
tHmg1+CrtE
We prepared the preculture of the transformed yeast and the non-transformed in YNB+Acetate for the quantification of GGPP next week.
CrtYBekI
We now can combine the two parts of the vitamin A into one.
Rose and brazzein
We got the results of the sequencing, unfortunately two bases have been deleted in the ORF.
Coculture
Bacteria
We prepared the medium for the bacteria.
Yeast
We measured the growth rate and the specific consumption rates of ethanol and acetate. We followed three cultures of yeast on the coculture medium in order to know the growth rate.
Human Practices
We had a meeting with Stéphane Guillouet for the culture condition and monitoring with limitation of oxygen. We decided that we will perform a batch and then a chemostat. Click [here] to know more about it.
Collaborations and partnerships
Concordia iGEM team
The goal of this meeting was to agreed on the maximum number of pages for the contribution document.
Entrepreneurship
We had our fourth meeting with Le Catalyseur where we discussed our business model.
Week of September the 14th to 20th
Project
Clonings
tHmg1+CrtE
The pre-cultures for the quantification of GGPP did not grow enough. So we had to restart the experiment.
CrtYBekI
Both parts of the construction were assembled. Next step: yeast (which already has tHMG1-CrtE) transformation.
Coculture
Clostridium ljungdahlii
We finally received the fresh strain of Clostridium ljungdahlii. We prepared the reactor for the experiments next week.
Week of September 21st to 27th
Project
Clonings
We had to make a difficult decision once again, and decided to fully focus on the production of β-carotene, so we stopped working on the two different tastes.
tHmg1+CrtE
Good news, our GGPP assess is successful and our construction is increasing its pool by a whopping five-times.
CrtYBekI
Our transformants are not orange as expected. Sadly, the sequencing easily explained it: our clones had a non-detected before mutation creating a shift in the ORF, preventing any expression of our enzyme.
Coculture
Bacteria
We inoculated the reactor with Clostridium ljungdahlii and monitored the growth by measuring the OD and HPLC analysis.
Human Practices
We did our conference with La Citée de l’espace and three experts (Brigitte Godard, the European astronaut’s doctor, Yves Gourinat, professor at ISAE-SUPAERO, and Gilles Truan, expert in synthetic biology) on Wednesday about microbiology and space, to learn more about it click [here].
During the weekend, we went to La Citée de l’espace to present our exhibition and to talk with the general public about our project and the iGEM competition, click [here] to read more about our itinerant exhibition.
Entrepreneurship
We had our fourth meeting with Le Catalyseur where we continued the discussion about our business model.
Video
Rémy came this week to shoot the last scenes for our presentation video.
Week from the September 28th to 4th of October
Project
Clonings
Concordia's experiment
We performed an experiment for iGEM Concordia as part of our partnership, where we looked at the fluorescence evolution after adding a stress factor. We could observe some fluorescence in all conditions, so we conclude that there is no right change in the gal10 promoter activity under these different stress conditions.
Collaborations and partnerships
AshesiGhana iGEM team
We talked together about the gold criteria « Partnership » and we agreed to do it due to the numerous meetings we had and the work we have done. We decided to wait until 50 answers for the survey for the iGEM Ghana team to start analyzing the results. We also created a document to both work on each other wiki partnership page.
Concordia iGEM team
We chose a final template for our contribution document to start implementing it with the work we have done.
German Meetup
We received the SIGMA centrifuge we won by getting the first prize in the poster presentation during the German Meetup organized by iGEM Marburg.
Week from October 5th to 11th
Human Practices
We visited Leon Blum High School in Villefranche-de-Lauragais where we presented synthetic biology and our video game to the students. We received lots of useful feedback.
Week of October 12th to 18th
Entrepreneurship
We had our last meeting with Le Catalyseur, they helped us organize our last weeks of iGEM by defining all the tasks we still had to do, and assigning a responsible person for each of them.
Wiki
We did our first “fake wiki freeze”.
Week of October 19th to 25th
Video
We finished recording the narration parts of our presentation video.
Wiki
We did our second “fake wiki freeze”.
Week of October 25th to 31st
Wiki
We spent these last days finishing our wiki, by the wiki freeze all the team learnt how to script pages using HTML.
