Team:Ionis Paris/Partnership

Partnership

Partnership - IGEM IONIS

Partnership
Team IONIS Paris
Team IISER Tirupati
Introduction

In May, during the lockdown, the Indian team IISER Tirupati communicated on the fact they were working on antimicrobial resistance (AMR). We contacted them to first, set up a conference call, to talk about both of our projects to see if a partnership could be possible.

The idea was to help each other out throughout the competition on a scientific point of view (as we were both working on projects linked to AMR), and in any other way possible (communicating on our projects, fundraising, advice etc.).

The IISER Tirupati team’s project, called Coli Kaze, tackles AMR in a different way compared to BacTail. Their aim is to engineer bacteria to render them capable of degrading the antibiotics (Sulfonamides) found in the excreta of chicken and turkey. Once the mission accomplished, the goal is to program the death of the chassis whose lysis would be induced by arabinose.

The first conference call between iGEM IISER Tirupati and iGEM IONIS in May 2020
Establishing our partnership

Since April, The IISER Tirupati team had doubts about getting into the lab until the end of the iGEM competition due to the Covid-19 pandemic. Thanks to our calls and project presentations, we were aware that part of their project was to develop a kill switch in order to kill their chassis at the end of the antibiotic degradation.

Since our team was also interested in using a kill switch that would be activated when our chassis had accomplished its mission of killing the target pathogen (cf.phase 3) , we started talking about a potential partnership on this point especially.
We agreed on the following partnership: the IISER Tirupati team would design the theoretical part of the kill switch (cf.BioBricks) and in exchange our team would do the wet lab experiments for them. In order to accomplish this partnership, we had dozens of zoom calls with their team to exchange on our projects.

Conference call between Omkar (IISER Tirupati), Lucie (IONIS Paris) and Elliot (IONIS Paris) in regard to the kill switch

Numerous calls with Team IISER Tirupati were first dedicated to planning and preparing the implementation of their experiments in our lab. These were especially done with Omkar.

To start, both of our teams had to agree on the experiments that should and could be run, considering the available equipment. Next, our lab team proceeded to writing up the protocols and listing of every single item and consumable needed:

- For the construct, the IISER TIRUPATI Team ordered fragments thanks to the IDT sponsorship and requested the shipment to be to our laboratory instead of theirs
- For the experimental kits, enzymes and bacteria, IISER Tirupati ordered them as well thanks to the NEB sponsorship. The products were sent to our lab
- For the consumables, equipment and some other products already in our possession, our team provided them for this partnership

We then began to run the experiments beginning of September, with daily calls to keep Team IISER Tirupati advised on the current status of the experiments but also exchange on the results, possible problems, trouble-shoot and get advice from them. In addition to that, weekly follow-up documents were written by us and sent to them so they could keep summaries of the workflow and track the progress.

Key Meetings in our Partnership in regard to the wet lab
September 25th 2020
Final meeting between both of our teams to recapitulate the partnership, experiments and results!
September 8th 2020
Last check-up of the products needed, those already in our possession, those furnished by NEB and IDT for free and those left to buy.
Conducting experiments with 3 calls/week
September 2nd 2020
Additional information about the workflow + First check-up of the products needed, those already in our possession, those furnished by NEB and IDT for free and those left to buy.
September 1st 2020
Third check-up of the workflow for the experiments of the project.
August 26th 2020
Second check-up of the workflow for the experiments of the project.
August 4th 2020
First check-up of the workflow for the experiments of the project.
July 16th 2020
Call between the laboratory members of each iGEM team to discuss about the feasibility of this partnership concerning the experiments.

Link for the wet-lab results for the experiments conducted during this partnership

Check Results
Help on designing the tank for Coli Kaze
A part of our team helped IISER Tirupati team to design a tank for their project. They wanted to make a tank that can be used to grow the cells and use them as antibiotic degrading machinery. In order to do the 3D modelling fusion 360 software was used as it is free, easy to use and is cloud-based.
The basic design of the tank had three components: two chambers and one dome. We modelled a 2D circle that we extruded to form a 3D cylinder. Then, we obtained a dome by designing a 2D semicircle and revolving it by 180°. This completed the top chamber. Another chamber was made in the same way below that except that it had two holes, one for inlet and one for the outlet.
A separation plate with two holes punched was added in between. Two small curved pipes of appropriate lengths were joined to the separation plate where the holes were punched to facilitate the movement of fluid from the top chamber to the bottom chamber. A rotor was added to both chambers so that homogeneity is maintained throughout.
Conclusion


The last conference call between our teams before the wiki freeze (October 25th 2020)
All in all, we keep an amazing memory of this partnership. The joy coming from succeeded experiments, following several fails, was two times more important because the satisfaction was shared between both our teams. We are so grateful that we worked on such a partnership as it allowed us to learn new things, exchange on our projects and meet incredible iGEMers. If COVID-19 had never existed, it would have been such a pleasure to meet the IISER Tirupati team in real life at the Giant Jamboree in Boston! Maybe one day we will be able to meet for real...
We invite you to go check out team IISER Tirupati’s wiki!
https://2020.igem.org/Team:IISER-Tirupati_India