Team:Grenoble-Alpes/Collaborations

NeuroDrop

Collaborations

Collaboration with iGEM Nantes

Collaboration with other iGEM teams was a big part of this project. It showed the teams’ spirit and the importance of sharing information to give out the best results in science.

We worked on collaborations with many teams: the first one with iGEM Nantes was based on a scientific level and artistic level. The second one with iGEM TU Dresden was based on human practices level. We have also participated in an international collaboration.

The idea behind the collaboration with iGEM Nantes started with a goal of testing the flexibility and the validity of our software protocols. Their project aimed at creating a biological clock by transforming E.coli bacteria to respond with different fluorescence proteins upon the presence of varied concentration of sugars in the medium.

We tested 6 different transformed bacteria with 4 plasmids:

  • pLAC/GFP
  • pSRL/RFP
  • pARA/CFP
  • pRIB/YFP
  • pLAC/GFP + pSRL/RFP
  • pARA/CFP + pRIB/RFP

These plasmids are DNA sequences that code for fluorescent proteins (GFP, RFP, CFP, YFP) that get activated with the presence of the corresponding sugars (lactose, sorbitol, arabinose, ribose).

The activation of the fluorescence was tested with different concentrations of sugars in time. These concentrations are:

  • 0.2mM (saturated solution)
  • 0.02mM
  • 0.05mM
  • 0.005mM

The measurements of fluorescence intensity were made every 10 minutes for about 3 hours, so as to see the evolution in time. In other words, to understand how the bacteria indicate the time with different fluorescence.

Software collaboration with iGEM Nantes

Lisa from iGEM Nantes also came to visit us. She tested our software and hardware first hand and gave her insight to improve the whole device. Her remarks were very pertinent in terms of simplifying the interface for beginners and adding explanation for each step in the definition phase of the protocols. She was also introduced to the hardware device and each of its parts.

Remarks from Lisa

When Lisa came to see us, she tested the software. As we wanted to see if she was able to use it without any help we didn’t explained to her how it worked, nor how the device worked. Here is a picture of her creating a protocol:

The whole video of what she did is accessible here:

From this basis we changed our software and took into account most of the remarks she did. We also corrected a few bugs that we hadn’t seen while developing and testing the software, and that she detected.

The correction we made to the software thanks to Lisa are the following:

  • We changed the way we could select a volume when pipetting a solution. We previously had used a widget from which we could select the volume with a precision of 0.5µL, now we are using an entry box where the user can write the volume he wants. If what he entered is too precise or it causes problems afterwards, the software advises the user and offers to correct his input so the hardware can perform the action.
  • When choosing to measure the luminescence of the sample, we can ask the software to wait between measurements. Before Lisa came and tested the device, we had used an entry box where the user could type the number of milliseconds he wanted the hardware to wait between two measurements. Thanks to Lisa’s remark, we changed that so the user can select the unit in which he wants to define the waiting time (either milliseconds, seconds or minutes).
  • At the end of a protocol, we have to ask the machine to execute it. Before Lisa came, the user had to select the USB port to which the device was connected. This proved to be quite difficult and we found a way to change that so the software automatically detects the hardware.
  • We also noticed that applying a protocol could mean applying the same series of actions over and over again. This was quite a long task before Lisa made the remark, and so we added a command that could allow the user to apply a secondary protocol in a main protocol.
  • We also noticed, while Lisa was using the software that it didn’t detect values that were either too high or too low when pipetting. This lead us to create new controls in the software to make sure that the user didn’t ask the machine to do things it wasn’t meant to do.
  • In the protocol window we also detected a few bugs, mainly when reaching the first and the last position. Those bugs were corrected and the appearance of the protocol window was slightly modified to correct this problem.

Result

Lisa's visit helped us a lot in perfecting our software and thanks to all her remarks, we made lots of changes to it. The end result is a software that is more stable, without being more difficult to use.

To prove that, we did the same exact operations Lisa did when she came to visit us, and here is the result:

Collaboration with iGEM Dresden

The second collaboration with iGEM TU Dresden consisted in translating a scientific script for a video used in human practices into 2 different languages: French and Arabic to maximize the audience to their project.

We believe that presenting a speech in different languages is a key nowadays to reach new people and get them to understand our objectives. It could even help us to come up with new ideas and to give out the best possible results.

The languages we translated their script to are ones of the most used all over the world. They can reach a big population, whether it be students, professionals or the general public.

Collaboration with iGEM Costa Rica, Tübingen, TAS Taipei teams

In this collaboration, we have been challenged to boost and promote the 17 Sustainable Development Goals (SDG). So, we had to categorize our project by choosing the 4 most related goals, and then promote it on our social media.

Our project was put in the following categories: Good health and well-being (#3), Quality education (#4), Industry, Innovation and Infrastructure (#9), Partnerships for the goals (#17). Thinking about these goals while we were working on our project, was a good reminder of our initial thoughts and had always put us back on the right track.

To promote this incredible initiative, we have therefore challenged four other teams (iGEM Moscow, Poitiers, Nantes and Eindhoven teams) to do the same for their respective projects.

iGEM Art Exhibition with iGEM Nantes

During the competition, iGEM Nantes reached us to participate in an international exhibition about synthetic biology; iGEM teams willing to participate had to send a piece of Art linked with their project. We decided to take part in this collaboration through our common project with the Dutch artist Maurice Mikkers.

“Hum… a snowflake? Ahaha no? So may be… is this a picture of the moon?”

The answer given by Inès when she was asked what was represented on that picture is quite similar to the one given by other people. It’s true this delicate ramifications, these little pyramids could be the one of snow or a planet. But actually, what you have in front of you is a crystallized tear.

This tear was created by iGEM Grenoble. Very common and yet unknown liquid, tears were tailor-made to illustrate our project of detection of biomarkers in very low concentrated fluids. The curiosity raised by tears drove us to demonstrate the ability of the project through the detection of alpha synuclein, a protein involved in Parkinson disease hidden in our tears.

During the lab experimentation, our team had to reconstituted fake tears and realized how poetic this liquid can be: it represents our human emotions of course, but we found out it could be even more beautiful under a microscope.

We discovered its unexpected beauty thanks to Maurice Mikkers and his project, Imaginarium of Tears1. With his biological background, the artist from The Netherlands decided to study the richness of tears from another perspective: through his microscope, he takes pictures of crystallized tears of people. All unique, these beautiful photographs shows how tears are under-used material which can reveal much more than we presume.

Microscope is the tool of the biologist, camera the one of the artist: we believe its approach is a very poetic way to raise awareness about the richness of tears, shows the possibilities unlocked by synthetic biology and reinforces bonds between science and society.

“I believe we should embrace our tears, be they happy or unhappy ones, because they are one of the true expressions of ourselves and your connection to the world.”2

Maurice Mikkers

Lucie from iGEM Nantes at the Art Exhibition.

1 Maurice Mikkers. (2019). Imaginarium of Tears: https://imaginariumoftears.com/#tears

2 Maurice Mikkers. (2015). TEDxAmsterdam, How do tears turn into art?: https://www.youtube.com/watch?v=7VRzn8hc5mc