Introduction

Throughout our iGEM journey, we have engaged with a lot of iGEM teams. Often, these engagements took the form of small, but also sometimes considerably large collaboration. On this page, we will address all of the collaboration activities our team has participated in during the iGEM competition. Also, our ‘main’ collaboration with the Sydney team is introduced on this page. For a more elaborate description of the specifics regarding this collaboration, we advise you to check out our modelling page!

Nanobuddies

iGEM Sydney

We have made pretty good friends with other iGEM teams throughout the competition, especially after meet-ups such as the iGEM European meet-up; more on this later. Our good friends that we met in Hamburg, the Freiburg team, made us aware that there was another team named: ‘nanobuddies’!? Naturally, we created a meme about their similar name and they soon contacted us back. We organized a meeting to just have a friendly chat and talk about our projects. What we did not know before the meeting (figure 1) was that this would eventually lead to a very interesting cross-continental collaboration!

Figure 1. Our first of many meetings with the Sydney 2022 iGEM team.

We found out that Sydney's project was very similar to what we were doing with our modeling project. We were developing an in silico approach to test nanobody binding affinity. On one hand, we were developing a high throughput nanobody folding (using an alpha fold-like algorithm) and docking approach. On the other hand, we were developing a code which can find nanobodies that bind to a given antigen input. This code makes use of sequences and certain chemical features (pH and hydrophobicity). The bottleneck of our modelling project consisted of the big nanobody synthetic library, for which we were implementing a clustering and filtering algorithm to reduce the size of our database to a more manageable size.

The Sydney team had the same objective that we set out with our modelling in the sense that we both were looking to generate a nanobody library in order to find the best binder to a given antigen. However, they were developing a nanobody library through a gene shuffling approach.

Considering that our aims were highly similar, we organized a collaboration between our two teams. With our collaboration, we set out to:

• Input their nanobodies in our algorithms and find out whether our model also predicts similar binding affinities.
• Find out which nanobodies bind best to a given antigen, and look into whether we receive similar results experimentally.

We conducted structure generation and docking with the data that the Sydney team has sent us, and shared our results with the Sydney team. We then were able to align our results, and uncovered some interesting findings.

As mentioned before, for the specific fruits that our collaboration bore, check out our modelling page

Dutch iGEM Meet-up

Our team participated in the Dutch iGEM Meet-up in Utrecht. The Centre for Living Technologies organized the Dutch iGEM meet with the support of iGEM WUR and iGEM TU/e.This event provided a common platform for the Dutch iGEM teams to come together, network, and explore collaboration. Keynote speakers Randy Rettberg (President of iGEM foundation) and Kyra Delsing (Rathenau Instituut, The Netherlands) spoke about what iGEM has to offer. All Dutch teams also presented their project and research so far, this allowing for nice moments of feedback from fellow researchers and their supervisors. The day ended with a brainstorming speedround session, in which participants shared experiences and advice.

Benelux

Mini-Jamboree

On the 18th of October, iGem TU-Eindhoven organized a Benelux Mini-Jamboree to practice our presentation skills and answering questions from the judges. Every iGEM team from the Benelux (Belgium, The Netherlands, Luxembourg) is invited to this event. Unfortunately, we cannot post any nice pictures or descriptions of the event, since it will take place after the Wiki freeze. We are, however, looking forward to meeting some iGEM teams already at the Mini-Jamboree in Eindhoven!

The iGEM Map

For this collaboration, we submitted a self-drawn character that represented our project. We chose to make a cartoon of our genetically modified bacteria: limosilactobacillus reuteri. They are the knight in shiny armor for the poultry industry and for us! Our knight represents us at Groningen in the global iGEM map, created by the iGem team NTHU_Taiwan. The global map was created to promote the importance of synthetic biology and show where all the experiments take place. Once you navigate over the map and you click on a character, a project description will pop-up and provide more information about that certain iGEM project. Our contribution can be seen in (figure 2).

Figure 2. Our contribution to the NTHU Taiwan team.

Synthetic Biology Colouring book

The synthetic biology coloring book was created on the initiative of iGem Usafa, America. It depicts the different problems researchers face and require to solve while working in the field of synthetic biology. The coloring book contains 12 different iGEM projects from 7 countries around the world. For this collaboration, it was asked of us to draw a small cartoon and description about our project. Once the coloring book was finished, we printed it out and used it as a giveaway at the Science fair ‘Zpannend Zernike’ (figure 3) after the children had performed the experiment with us. The stories were written in English, but some parents told us that they would translate it and use it as a fun, sciency bedtime story! iGEM Usafa requested to take a picture of the coloring book at the Science fair. They combined all the collaboration pictures and sent them to everyone as well (figure 4).

Figure 3. The coloring book created on the initiative of iGEM Usafa contains our contribution.

Figure 4. Some iGEM teams with the coloring book. On the left, we have Ronald and Bindert from our team. The topright is the Usafa team themselves, and below is the iGEM team of Wageningen.

Synthetic Biology Magazine

This collaboration was organized by the iGEM team UNSW_Sydney, Australia, as part of their education and communication efforts. The idea is to create a magazine of interesting articles on synthetic biology from around the world in different languages. This magazine will be written in English and the regional language of the specific iGEM project to make all information regarding synthetic biology more accessible. We sent in a paragraph of our Dutch blog and included an English translation of it as well. The end product shows articles of several iGEM teams from around the world (figure 5). We are very content with the end result!

Figure 5. Tell me about Synthetic Biology Magazine on synthetic biology by UNSW_Sydney, which we submitted our contribution for.

Picture Book

We received a request from a group consisting of the iGEM teams from McGill, Cornell and Queen’s universities regarding an educational booklet. For this we’ve collected several electron microscope images of our favorite bacteria (limosilactobacillus reuteri), and some interesting/fun facts about it. This information we’ve submitted to their questionnaire from which they would make an educational booklet containing all the favorite bacteria for all partaking iGEM teams.

Patented Nanobodies

While reading into scientific literature to find a solution for the spread of avian influenza virus, we stumbled upon an article of Dr. Simon Hufton: ‘The breadth of cross subtype neutralization activity of a single domain antibody to influenza hemagglutinin can be increased by antibody valency’ [1]. The nanobodies of this article were suitable for our project, but fall within their patent PCT/GB2012/052164. We reached out to Dr. Hufton and asked for permission to use the nanobodies and pNIBS-1 vector to experiment for ‘Nanobuddy’. Luckily, he was willing to provide R1a-A5, R1a-B6 and NB7-14 as mono- and bivalent versions in pNIBS-1 entailing sequence information as well.

Providing Data

Over the course of the iGEM competition, we received many requests to help other iGEM teams with their project by filling in their questionnaires. We participated in as many as we could, since we find it important to help other scientists out. In figure 6 below there is an overview of the forms and questionnaires we filled in throughout the iGEM project.

Figure 6. This table shows the date on which the questionnaire was filled in, the iGEM team that sent out the questionnaire and what was discussed in the questionnaire.