Template:Groningen/Collaborations

Meetups

European Meetup

Vilnius

The Vilnius iGEM team invited us to join in the first biohackathon organized in Lithuania. The topic of the hackathon: create something to make the life of a biologist in the lab easier. Since we are a very diverse team including many members with a background in a computational field, we gladly accepted their invitation.

We selected a delegation of our team to participate in the biohackathon and set to brainstorming. As we were throwing around some ideas for the hackathon in our office, some of our lab experts came to us. They told us they were making buffers for the lab, and that they were wondering if it would be possible to automate this task. This initial thought spawned the idea of buffy the bufferbot, our automatic buffer adjusting robot.

Soon we flew to Vilnius, Lithuania and were greeted by the the Vilnius iGEM team’s charming Lina and Ieva, who graciously hosted us during the weekend. The biohackathon took part from friday till sunday, and was concluded by pitches from every team. It was decided that we would create the brains of “buffy” at the hackathon and work on the hardware aspects of the project after we returned to Groningen. We presented a demo of our project, which uses carefully designed machine intelligence to keep track of the pH of the buffer and to make predictions of how best to adjust this pH to reach the desired goal. After careful deliberations, the judges awarded our team the prize for the best pitch!

Concluding the hackathon, there was a fruitful meeting between the present iGEM teams, Groningen, Lund, Helsinki and the Vilnius team themselves. We discussed our projects and offered each other useful feedback. We look forward to seeing all the teams again during the Giant Jamboree and we are especially grateful for the Vilnius team’s amazing hospitality.

The software component of buffy the bufferbot can be found at: https://github.com/ezmagon/buffy

Collaborations

Vilnius

After the Hackathon in Vilnius we decided to work on a collaboration with them, where we did some modeling for them. A molecular dynamics model was setup for the Vilnius 2018 iGEM team to study a part of their system. The system in question consists of a fusion transmembrane protein (OmpA+anti-GFP) in a pure DOPC bilayer in the presence of GFP. The fusion transmembrane protein should bind GFP and should display it on the outer side of the membrane.

To start, the structure of OmpA had to be reconstructed as parts of it are missing in the crystal structure. This was achieved using the “modeller” software, a python module for homology modeling. The same structure was used as the reference structure and so the filled in structure only serves to complete the molecule.

Next, the fusion protein was constructed. The sequences of OmpA and anti-GFP were joined exactly where they will be fused according to the DNA sequence designed by the Vilnius team, using PyMOL.

Then the fusion protein was coarse grained by the martinize script, producing a well calibrated coarse grained bead mapping for the fusion protein in the MARTINI 2 forcefield. The fusion protein was then inserted in a DOPC bilayer constructed by the insane.py script. GFP was also coarse grained using martinize and inserted in the system containing the fusion protein and the DOPC bilayer, after which the system was solvated with regular water beads. 150mM equivalence of NaCl was added to neutralize the system. For both coarse grained structures, an elastic network was applied with a cutoff of 0.5nm such that the beta-barrels of the proteins are maintained.

The MD system for the Vilnius 2018 iGEM team. On the left is shown the fused OmpA+anti-GFP inserted in a DOPC lipid bilayer and on the right the coarse grained structure of GFP.

Common parameters for martini were used for minimization and equilibration, and the model was setup to run for about 10 microseconds with berendsen temperature coupling and Parrinello-Rahman pressure coupling. The system runs at 300 K and a pressure of 1 bar.

The building process is documented on the project’s github page: https://github.com/Ezmagon/vilnius-collab

Bordeaux

We decided to collaborate with the Bordeaux iGEM team because of the strong parallels between our projects. We were both trying to use cellulose to produce an industrially useful platform molecule (2,5-Furandicarboxyclic acid, in their case). With such strong similarities, we felt we would have a lot to discuss about the ethical considerations of our projects.

The collaboration began when David, from Bordeaux, sent our team a Facebook message. Over the next weeks we had skype sessions until it was eventually decided that we would visit them in Bordeaux in late August. They would present the extensive research they had done about the ethics of GMOs and the use of non-edible biomass. In return, we would use the expertise of the chemists on our team and university to improve their protocols and to teach them how to effectively use an HPLC machine.

The Groningen team took a plane to Bordeaux from Schiphol Amsterdam on Friday the 24th of August. Upon arrival we were picked up by David who drove us to the Chateau (Castle) d’Eck where two of us would be sleeping throughout our stay and the conference would take place. The two other members of our team would sleep with David at a typical French student residence. After dropping off our luggage, David took us to a restaurant where we met a few more members of the Bordeaux team. We got to know each other and discuss our projects more informally over a pleasant meal followed by a small digestive.

The next day, after a light lunch, we started working on our collaboration in earnest. Saturday we would work on the chemistry part. Jacques gave a presentation on his findings concerning the extraction and characterization of FDCA from the cellular mixture. Together with Hemant Kumar (University of Groningen) he had evaluated the Bordeaux protocol and came up with a number of improvements and recommendations for safe practice. A separate protocol for HPLC (High Performance Liquid Chromatography) was also suggested.

Following this, a presentation about HPLC was given. It started with the basic chemical principles that govern this type of measurement, as the Bordeaux team is mostly biologists with no chemical expertise. Then the layout of the machine was explained. Finally, the interpretation of the measurements and troubleshooting were explained via the fundamental parameters of HPLC; resolution, selectivity, retention and efficiency. By the end of the presentation, the Bordeaux team felt confident about their eventual use of the HPLC. A question and answer session followed the presentations.

The following day, in the same chamber from chateau d’Eck, we discussed the ethics part of our collaboration. This was started with presentation by Anais, David and Inez about the progress their team had made towards understanding the ethical implications of their project. This involved brief summaries of the conferences they organized and the experts they went to visit.

Next we had a general discussion about the ethics of GMO use, contrasting the differing societal and governmental attitudes between France and the Netherlands. The French team also presented the results of a survey they had conducted to investigate public opinion on GMO use. Matthijs and Jan-Marten then proceeded to ask a list of questions the Dutch team had prepared. Once answered, we tried to summarize the main insights of the interview and presentations via a discussion that was filmed.

To celebrate a successful collaboration we had some wine from the castle’s vineyard and then went to downtown Bordeaux, where we sat by the Garonne and socialized over a picnic dinner. On Monday, we slept in and then went on a day trip to the countryside with the Bordeaux team. We first visited the lake of Biscarrosse. While the bulk of the group relaxed by the beach; Jacques, Jan Marten and Vincent went on a “geocache hunt” (a type of scavenger hunt) in the surrounding countryside. Towards the beginning of the evening we drove towards the fantastic sand dune of Pilat, Europe’s biggest sand dune. After an exhausting climb we celebrated by drinking a well-deserved beer and watching the sunset.

Tuesday was the last day of our stay in Bordeaux. After a short tour through the city, the team had a crepe lunch and said their goodbyes. David drove the team to the Bordeaux airport for what would be a hectic journey back to the Netherlands.

In conclusion:

• - The Bordeaux team had a clear outline for the extraction and quantification of their target molecule from the cell mixture.
• - The Bordeaux team learned the theoretical basis behind HPLC and how to troubleshoot a bad separation.
• - The Groningen team gained insight into the ethics of GMO use and what tools can be used to investigate that.
• - Both teams gained a list of experts who could be consulted for issues regarding ethical use of biomass, GMO-related ethics, and chemical processing of cellulose.