Week of January 3rd to 9th

On 07/01/2022 was our first team meeting. The advisors and the students of the 2021 edition met the student team of the 2022 edition. The competition was presented and each student and advisor was designated to be responsible for an aspect of the project: Communication (Charline), Wiki (Morgane), Experimentation (Guillaume), Entrepreneurship (Samy), Human Practices (Juliette), Modelisation (Raphaël), Finances (Thomas) and Organization (Laure).

During the week, the team brainstormed to find as many project ideas as possible to discuss during the next meeting.

Week of January 10th to 16th

This week we continued to brainstorm on the many ideas we had. Each student worked on 2 to 4 different projects. Of all our ideas, here are the one we have retained at this time:

• - Sound and bacterias, can microorganisms hear?
• - Production of antivenom
• - Treat a disease of cassava by decreasing the viral load of an insect
• - Create a biofilter for used water
• - Looking for the weaknesses of slime mold
• - Treatment of melon downy mildew
• - Production of a microbial deodorant
• - Treatment of sclerosis
• - Production of fabric with microbial cellulose
• - Valorization of the byproducts of wine fermentation
• - Detection and treatment of allergies

Week of January 17th to 23th

Morgane, Charline and Juliette attended the first meeting about the Exposcience Occitanie 2022 event. On 16/01, Thomas flew to Thailand for 4 months to study for an exchange but he kept working with us from there. On 19/01/2022, the very first online meeting took place with students only. This week, we brainstormed on how to use aptamers to detect IgE antibodies. We also talked about using a biofilm as a cream for desensitization. On January the 14th, Raphaël came back from his Erasmus in Barcelona.

Week of January 24th to 30th

The brainstorming continued. This week, only 4 project ideas were remaining:

• - Valorization of CO2 in wine fermentation
• - Detection of odors with bacterias
• - Creating microorganisms that can hear
• - Detecting and treating allergies.

This week, on January the 20th, Laure came back from her Erasmus semester in Athens.

Week of January 31th to February 6th

Brainstorming continued. During the weekly meeting, we talked about using DARPin in our project but we did not know yet for which purpose.

Week of February 07th to 13th

Brainstorming continued. During the weekly meeting, we had the idea of organizing an event at INSA as a mini-Jamboree with all the French iGEM teams and in partnership with the school EUR Bioeco.
We discovered the basic principles of HTML with Younes, a former iGEMer who kindly took the time to explain how the wiki works.

Week of February 14th to 20th

We participated in the school opening day to present the iGEM competition and the results of the INSA-UPS 2021 iGEM team to secondary school’s students with Margaux Haon, a member of the 2021’s team.

We organized our first team building evening in real life around a raclette cheese.

Week of February 21th to 27th

During a brainstorming session, we talked about converting the CO2 of wine fermentation into methanol by electrolysis. We also started to discuss detecting allergies by agglutination of two microorganisms around IgE molecules. Even with a lot of research, we had trouble finding a promising idea for the two other projects (Detect odors with bacterias/Make microorganisms hear).

Week of February 28th to March 6th

We had the first meeting with Luana, Saber and Lucie, three doctoral students who helped us for the rest of the project.

We decided during the weekly meeting to focus only on two ideas: valorization of CO2 from wine fermentation and detection and treatment of allergies.

Week of March 07th to 13th

This week we focused on detecting all the challenges and difficulties we could encounter with each project (CO2 valorization or allergy detection and treatment). It seemed there were more difficulties with CO2 valorization so we tried to get more help from experts during the next week.

Week of March 14th to 20th

We met several professionals to discuss our ideas for the competition and ask questions about our projects. Two specialists in electrochemistry explained to us how difficult it is to use electrochemistry to convert CO2 in methanol. On the other hand, Chloé Beuraud, a researcher in immunology, seemed very enthusiastic about our allergy project idea. That is why, among other reasons, we chose allergy detection and treatment as our official project for 2022 edition of iGEM with a vote.

Week of March 21th to 27th

Now that we have chosen our project, each student met their referent instructor to talk more precisely about their responsibility in the project (modeling, communication, HP, entrepreneurship, experimentations, wiki).

Week of March 28th to 03rd

Week of April 04th to 10th

This week, we began the design of the project. The first step was to determine which allergens we would produce and to imagine which biobricks would be needed.

Week of April 11th to 17th

On April the 14th, we met Dr. Gabrielle Potocki-Veronese (Research Director at TBI) to talk about how to use microdroplets to screen hundreds of allergens for IgE detection.
We met members of the EUR Bioeco school to present our idea of organizing a French Meet-Up as a mini-Jamboree with them. They liked the idea and agreed to collaborate with us and to sponsor the event.

Week of April 18th to 24th

On this week, we registered the team for the competition and paid the fee so the adventure officially begun! Now we knew which experiments would have to be conducted for the project during the summer, we had to design the main biobricks to be created and started to design them on Benchling. As we will do our experiments in INSA’s laboratory this summer, Samy and Guillaume, who are UPS students, came to visit the lab.

Week of April 25th to May 01st

Among several logo ideas, we voted for the one that will represent us during all the season. The design continued, we brainstormed to define our experiments and the needed DNA sequences and started a list of all we needed to order for the summer internship.

Week of May 02nd to 08th

This week, we imagined the first design of our mascot Daisy, a cheerleader dressed as an IgE and wearing our colors.

We met a lot of experts to talk about our project and try to detect issues as soon as possible to have the time to find some solution before the beginning of the experiments. We also ordered our sequences on IDT so that we could receive them at the beginning of the internship.

Week of May 09th to 15th

This week we met Dr. Alain Liné who works on aggregation models and brainstormed on the model we could make and how to adapt the general model to our aggregation system. We went to the lab to check what material was left from the previous year, what we could use for our project and what we would miss if we did not order it.

Week of May 16th to 22th

We met members of the EUR bioeco school, our sponsor for the meetup to organize the event and prepare the communication around it. We also met a few days later to continue the preparation and imagine an first schedule for the three-day meetup. As our exams are in a few days we haven't worked as much as the previous weeks on the design.

Week of May 23th to 29th

On Tuesday, Thomas came back to Toulouse from his exchange semester in Thailand so he was able to begin the experiment the next week. On the weekend, Juliette and Charline built models of our bacterias displaying allergens or DARPin. They were very useful for presentation videos and to explain our project playfully to the public during science popularization events. We were passing our respective exams and could not wait to begin the experiments.

Week of May 30th to June 05th

We began our internship! During the next four months we will work on iGEM projects all day in the lab. It was a very intense week. We received a lot of material, conducted a few training experiments and worked hard on HP, modeling draft, sponsor research, meet-up organization and communication.

Week of June 06th to 12th

On the weekend, we attended Exposcience, an event to popularize science to children. It was a great occasion to talk about microbiology, synthetic biology, iGEM and our project Daisy but also to discover a lot of scientific projects conducted by children from 8 to 18 years old in France, Germany and Luxembourg.

On Monday we received our sequences from IDT! So we began the PCR for sequences and plasmid so that we could clone them in our bacterias the next week, hopefully.

Here is a scheme of the evolution of the experiments. Each week, another scheme will be presented to track our progress. We first started with a biomolecular experiment to construct our plasmid and then we performed biochemistry and aggregation experiments. The steps in blue are not finished yet while the green ones are.

Week of June 13th to 19th

On Monday we met Dr Gabrielle Potocki-Veronese to talk again about microfluidics for our project. She explained to us in detail the patented technology she worked on and we discussed how to use it to screen aggregate. If we have good results in August, we will use their microfluidic device in September.

This week we received the sequencing result of our first construction and we can affirm we successfully constructed a pET21 plasmid with OmpA_DARPin_sfGFP insert.

Week of June 20th to 26th

On Monday, we transformed E. coli Tuner (DE3), our strain for expression, for the first time!

Week of June 27th to July 03st

On the 1st to 3rd of July, was the European Meet-Up in Hambourg. We took a plane to Frankfurt but never managed to reach Hamburg because our flight was canceled. After 48h traveling, we came back to Toulouse tired and frustrated because we could not attend the meetup. However, we sent our poster some days ago and earnt the Best Poster Prize!

We had our first fluo results! It means we successfully expressed the OmpA-DARPin-sfGFP fusion protein. We will have to check if it is on the membrane. We started Interlab experiments! The first cloning results were unsuccessful but we will try again next week.

Week of July 04th to 10th

The 7-8-9 of July was the French Meet-Up on our campus. Thanks to Charline, Juliette and our sponsor EUR Bioeco, all went well. It was amazing to discover all the french projects and exchange on our experience through the iGEM adventure! We did less experiments this week to make the most of the Meet-Up.

We designed the primer to suppress sfGFP and added fluorescent genes to our plasmids. We are on the way for our final constructions. After discussing with our advisor Alain Liné, it seemed our aggregation model will be harder to create than predicted. We will be the first to modelize the aggregation of two different bacteria so it was a big challenge.

Week of July 11th to 17th

For the first time, we ran our aggregation model this week. We also had the proof that our protein of interest is exported on the membrane thanks to the Ompa-DARPin-sfGFP construction.

We started filming our presentation video. Here is a vue of the back stage with Thomas explaining how our bacteria will aggregate.

Week of July 18th to 24th

We made a photoshoot for our wiki and social media but we were not always very focused.

We finally constructed OmpA-DARPin and OmpA-arah2 plasmids! In the next week we will use them for aggregation experiments!

Week of July 25th to 31st

On this week, we performed our first agregation experiment! However, the results do not allow us to conclude on the presence of specific aggregates. We also successfully constructed the OmpA-Derp1 sequence and checked that it did not kill the cell.

Week of August 01st to 07th

We started the filming of the popular science series named “Cracking Allergies”. The aim of these 10 videos is to provide content about allergies, to understand them and live with them. On this occasion, our HP leader Juliette created a new model in polystyrene.

We continued our experiment to check the exportation of our protein of interest, tried to aggregate our strains of E. coli and tried to insert a gene for fluorescence in the plasmid we previously created. However, we had a lot of difficulties and did not obtain successful results.

This week, we encountered the iGEM Thessaloniki team from Greece. We discussed how we could helped each other in our projects and to collaborate until the Giant Jamboree.

Week of August 08th to 14th

We found out the DARPin sequence we have been working on for 3 months was not optimal! This gene was essential for our project so we will have to correct all our plasmid. This will probably make us fall behind schedule but it likely explains why we had poor results the past weeks.

We started the operation "Saving Daisy!".

As we wait for the delivery of our new sequences, we work hard on Modeling, Entrepreneurship, and Human Practices aspects of the project and the wiki.

A journalist and a cameraman came at the lab to make a TV report about our project and team.

Week of August 15th to 21th

The writing work has started for the wiki with the Description, Collaboration, Attribution and Team pages. At the same time, the strategy to synthesize the missing sequence of the DARPin was designed and primers were ordered. We worked all summer in the school’s lab and as the classes will start next week, we made some space in the classrooms to let the laboratory staff prepare the first school day.

Week of August 22th to 28th

We observed blue fluorescence of our strains expressing BFP, so we now know the gene is correctly expressed and that the promoter ihfB800 is working. A journalist from “20 minutes”, a French newspapers, spent time in our lab for an interview and took photos of our lab. Our PI have chosen the speakers for the presentation. Laure, Charline, Juliette and Thomas will present the project at the Jamboree. Juliette has finished making the majority of the video of the serie Cracking Allergies, and Charline sent our 2 min video. The DARPin was rebuilt and showed good results on PCR screening. This is the last week of experiments for Samy and Guillaume, then they will go back to university.

Week of August 29th to September 04th

To finish experiments, there was only two weeks left and we were reduced to 5 now in lab, so we decided to change the lab organization:

• - Raphaël and Thomas would make surface controls of bacteria
• - Laure would make with Sophie Lajus aggregation on droplets
• - Charline was responsible to insert the mScarlet and conduct assays on FACS
• - Juliette would make last aggregation assays with news parameters.

A special attention was given to the wiki redaction, the wiki freeze being in one month and half. Thomas has paid the inscription to the Jamboree.

Week of September 05th to 11th

This week, we worked hard to finish our experiments. Unfortunately, FACS and droplets did not give significant results, there was still no aggregation or there was aggregation on negative controls.
We organized a trip to the Atlantic Ocean to relax before working hard for the final run toward the Wikifreeze in the following weeks. We slept and ate a lot, the rest of the time we were relaxing on the beach and playing with waves. We had a good time even though our car’s battery broke down and we came back with a suspicion of COVID.

Week of September 12th to 18th

Here is the last week for lab work, and this week we stayed in the lab later than usual to try to finish the draft of the majority of the wiki redaction. The first fake wiki freeze was going to take place at the end of the week so we spent a full Saturday rushing to write the wiki at Laure’s family home and without Juliette, because she was sick.

Week of September 19th to 25th

For all students class has started, so it became harder to meet all the deadlines but we still managed it so far. Laure, Thomas and Charline went to a high school to explain synthetic biology to the students, talk about the biologies in superior studies and run and experience at the high school laboratory. On the weekend, we met again to work together on the wiki. We started to add most of the content on Gitlab.

Week of September 26th to 02nd

This was a stressful week! The wiki freeze is very close now and we want to give our best to have the perfect website. We also worked hard to complete all our parts in the registry. We gathered almost everyday this week to work together and stay motivated but the most efficient day was on saturday when we almost finished all the pages.

Week of October 03rd to 09nd

This was a stressful week! The wiki freeze is very close now and we want to give our best to have the perfect website. We also worked hard to complete all our parts in the registry. We gathered almost everyday this week to work together and stay motivated but the most efficient day was on saturday, the day we called a fake wiki freeze when we almost finished all the pages.

Week of October 10th to 16th

We checked one last time every detail of the wiki and the registry to be ready for the wiki freeze and started to prepare the final presentation. Thank you for reading the entire Notebook. As a reward, here are two memes from Raphaël.