Team:Tuebingen/Collaborations
Collaborations
Interactions with other teams worldwide
Scientific research is a field that lives on teamwork, not only inside your own research group but especially in collaboration with other researchers from all over the world. iGEM itself is already very internationally organized and therefore we are extremely thankful to all the different teams we got the chance to meet during our project. We shaped each other's work and were able to learn a lot about the differences and similarities between cultures and countries.
CCU Taiwan: As Guests on AMPodacst
In Human Practices, we collaborated with CCU Taiwan on the 21st of September. Since both our teams wanted to tackle the problem of antimicrobial resistance in some way, although a very different one, we invited them to star in one of our podcast episodes (for more information on the interview, please click here ). Working together not only interdisciplinary – our interviewees were from all different fields and managed parts of the team which required different expertise – but also internationally, in this case, proved to be very helpful for our HP work. Together, we talked for quite some time and got an insight into their work and their approach to iGEM and science. To get a glimpse into the workings of another team was rather interesting and we could learn from them through comparison as well as by listening to their journey so far. We consider broadening your horizon and being open to other concepts (no matter if those are scientific, structural, or plainly concepts of communication) a major part of learning and growing through the iGEM competition. Our collaboration with CCU Taiwan played a big role in this since we also collaborated with them in Drylab which is explained below. Through their insights and explanations, we were able to reflect on our work, but also us as a team, which was very important. Thanks to our collaborative endeavor, we gained inspiration for future projects and learned through our differences.
CCU Taiwan: Simulating their antimicrobial peptides (AMPs) inside our scaffold
As part of our collaboration with CCU Taiwan, we inserted their peptides into our scaffold and ran a Molecular Dynamics simulation to determine the stability of the construct.
Our first step was to build the sequence. After a few iterations of sequence building and structure prediction using AlphaFold (as described in “Model”), we were able to get a good structure for one of the peptides, namely Buforin II-C, in combination with our scaffold. The other peptides sadly did not yield useful structures. The general problem with the peptides was their size. At just above 20 amino acids, they are pretty big to be used in our scaffold. Therefore, we had to split the sequence between loops 5 and 6 of our scaffold, also inserting an extra glycine to preserve the cis/trans-configuration of the peptide. The final sequence is shown in figure 2 and the structure of the construct is shown in figure 3 .
The root-mean-square deviation (RMSD) vs MCoTI-II (same procedure as in Model ) was calculated as 1.687 Å and shows a good similarity between the two structures. All disulfide bonds were correctly predicted.
Afterward, we ran a 10 ns coarse-grained simulation of the peptide in water to calculate its RMSD and radius of gyration over time. Both are measures as to how stable the structure is. The RMSD over time is shown in figure 4 , the radius of gyration in figure 5 . A movie of the simulation can be found in figure 6 .
Both the RMSD and radius of gyration are stable over time, which implies that the structure is stable.
Overall, this shows that grafting of their peptide Buforin II-C into our scaffold could be feasible. However, it is not clear if the bioactivity of the peptide would be conserved, as it had to be split between two loops of the scaffold due to its size.
We would like to say a big thank you to CCU Taiwan for the opportunity to run a simulation with their peptides! The collaboration has given us important insight into the limits and opportunities of our scaffold.
German Meetup: Sharing Ideas with Like-Minded
The iGEM teams Bonn and Kaiserslautern invited us to the German Meetup, a great chance to meet other German teams and get to know each other.
Meeting other teams was quite motivating since our project had already taken shape. However, meeting with others, who are at a similar point and with similar issues to face, encouraged us to now really get started. The first part of the meetup was structured into four different breakout rooms we could join. The first focused on biotechnological production of healthy sugar substitutes, in the second room we could discuss ethical issues in biotechnology in general and in animal testing, another one was about collaborations and in the last room we exchanged ideas and advice on finding suitable sponsors.
We benefited greatly from the exchange of experience on how to contact sponsors in an efficient way and could also give advice based on our own experience. At the end of this breakout session, we had collected a bunch of tricks and tips we used during the whole iGEM cycle to raise enough money for our project and also for the next team.
The highlight of the meetup was the breakout session about collaborations. We really enjoyed brainstorming with the other teams about potential collaborations and social media projects. It was a quite creative process where we evaluated all sorts of projects. Many with a humorous attitude, trying to make it easier for also non-natural scientists to get in contact with synthetic biology. It was a very nice atmosphere, which reminded us again how far-reaching iGEM is. The exchange with the others helped us to think outside the box.
It further inspired us to pursue our podcast idea and participate in Team Duesseldorf's postcard project as you can see further down on this page. Last but not least we want to thank the iGEM teams from Bonn and Kaiserslautern very much for organizing this fun and at the same time very informative evening.
IISER Kolkatta: Collaboration Turned into Partnership
iGEM Team IISERK contacted us through Instagram as both of our teams' projects revolve around AMPs as a possible alternative to antibiotics. Despite the time difference we held several meetings to get to know one another personally and our mutual projects in more detail. Having a deeper insight, we figured out how we could complement each other’s work throughout the year, especially in the Drylab part of the projects.
As several members of their team have high expertise with simulation software and modeling in general, they offered us their support in this regard. Meanwhile, we got the opportunity to have access to the supercomputer of the federal state of Baden-Württemberg and by that we could run simulations for team IISERK, which they couldn’t have completed in the short timeframe of the iGEM competition otherwise.
Throughout several meetings for planning and designing of the models and simulations, it became obvious that what in the beginning was planned as a short collaboration developed into a partnership with mutual contributions of expertise and time from both teams. We are extremely thankful to iGEM team IISERK for reaching out to us in the beginning as well as for the ongoing support of each other's work and for the friendships that evolved from this.
Maastricht Journal Initiative: Such a Great Opportunity
When we first read about the journal initiative by the iGEM Team from Maastricht, we were directly hooked by the idea to be able to publish our own work. After some considerations and as our practical work in the laboratory had only just started when the submission deadline was arising, we decided to write a review paper about a topic, which is closely linked to our project this year. We chose to write about antimicrobial peptides (AMPs) for bioengineering and their possible applications, challenges, and future perspectives. Our review revolves around the work former iGEM teams have conducted with AMPs and it was fascinating to see what interesting and challenging projects other teams have focused on before.
Furthermore, as a peer-review was also part of the journal writing process, we got the chance to read about the inspiring projects of two other iGEM teams (team Calgary and team Athens) and had the opportunity to give them some feedback on their papers as well, as they provided us with suggestions for improvement of our review.
We want to thank iGEM Calgary and iGEM Athens very much for their constructive feedback, which was extremely helpful for us, not only in regard for this writing but also in face of possible future publications one might write. Special thanks go to the MSP Maastricht team for giving us and other iGEM teams this great opportunity with their proceeding journal and for the perfectly organized peer-review process, we are beyond grateful.
iGEM Ioannina: Working towards the Same Goal
Another collaboration at the earlier stages of our project was between our team and the iGEM team from Ioannina, Greece. We became aware of our mutual projects because we both focused on possible alternatives to antibiotics due to the increasing problem of antibiotic resistance worldwide. Thus, we were quite curious in what way they planned to tackle the issue.
Together we shared our thoughts and presented our projects to each other and with just a few meetings we gained a lot from this exchange of ideas. We ended up giving advice on different aspects of our work to each other, not only regarding human practices (for example team Ioannina shared their expertise with podcast production and question design with us) but also on a more general level with the design of the projects itself. The meetings were quite fruitful and we felt very inspired afterward, especially in the design of educational content on social media, and our ideas helped them in their project design, shaping and refining its form through the discussion.
Social Media: The Small Things Matter
But not only the big projects matter. Connections to all the iGEM teams around the globe can be found in small things. Such as the iJET project of iGEM team Darmstadt, the Monument challenge from GO Paris-Saclay, or the postcard project from iGEM Duesseldorf. Here we get to hear and see each other, learn more about our respective cities and projects, be creative, and - of course - have fun together. Since iGEM is not just a competition, but a community all over the world and these little challenges showed us that we have friends everywhere.
About Us
We are the iGEM Team Tuebingen, a group of motivated students who are working on creating a fast screening platform for stabilized peptides. We are aiming to provide a system that gives everyone the ability to stabilize peptides such as antimicrobial peptides to create better medical agents.
