Team:Utrecht/Collaborations

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• Aachen
• ETHZürich
• München
• Tar
• NRC

Collaboration iGEM team Aachen 2018 - iGEM Biotechnology Conference

On 20th September, we organized the iGEM Biotechnology Conference in collaboration with iGEM Team Aachen. In keeping with the spirit of iGEM this conference was ‘valorisation’-themed and was intended to bring public engagements and collaboration opportunities together. During the iGEM meet-up in Munich, we came in contact with the iGEM team from Aachen and ran our idea of a possible collaboration on the conference by them. They were very enthusiastic right away and already had many ideas.

After the meet-up in Munich, we started Skyping with them weekly to keep each other updated. We divided the tasks and both started with our search for speakers, companies and funding. Our team arranged the venue and facilities, catering services, ticket sales, two speakers (Dr. Silvia Mihaila and Dr. Mauro Muraro) and two companies (Single Cell Discoveries and Mimetas). Team Aachen arranged two speakers (Dr. Aljoscha Wahl and Dr. Karel Olavarria Gamez) and designed the flyers. They also helped with designing the powerpoint for the conference. Together we promoted the conference on Facebook, Instagram and Twitter, as well as face-to-face promotion both in Germany and the Netherlands.

Before the conference, we had two meetings in Utrecht to sort problems and to get to know each other even better. We had a lot of fun during these meet-ups and during the iGEM Biotechnology Conference itself. We are happy we managed to organize such a successful conference together, with about 60 paying participants!

Collaboration with iGEM team ETH Zurich 2018

This year, the iGEM team from ETH Zurich is developing an autonomous robot that uses biosensors as its control element to follow molecule gradients in the air to detect their source. To speed up their biosensors, they are also aiming to exploit and modify the natural Tar-receptor-based chemotaxis system of E. coli.

During the European iGEM Meetup in July, we came to the conclusion that both of our teams were working on chemotaxis-based biosensors. Although our projects are based on somewhat different methods and applications, we did struggle with similar complications at the time. For those reasons, we decided to stay in touch and update each other about problems and solutions, which formed the base for our collaboration. An example of our similar approaches was found in the way both our teams dealt with our intended use of split luciferase. Both teams intended to use reconstitution of a split luciferase as a way to create a read-out signal from the chemotaxis pathway. Unfortunately, we found out that luciferase could not be split again after reconstitution, making this approach impossible. These findings were shared between teams, after which we composed a strategy to find alternative approaches for this problem. We split up this task and shared outcomes with each other, which lead to our current solution to this issue.

In the future, we also aim to integrate our engineered bacteria in the autonomous robot AROMA from Zürich. We hope their biosensor will improve the range of detectable concentrations, while also broadening the range of substrates that could potentially be bound.

European meetup in Munich (20 – 22/7/18)

During the European iGEM meetup 2018 in Munich (20th - 22nd July 2018), we contributed to the organisation by organising a Teambuilding Workshop for approximately 40 students in total. This workshop was inspired by both Amy Edmonson’s TEDx talk: ‘How to turn a group of strangers into a team?’ and the story about the Thailand cave rescue. We discussed the ways people with different cultural and academic backgrounds who did not know each other before, had to work together in one team to achieve their mutual goals similar as in the Thailand cave rescue. This truly reflects the collaboration within any iGEM team: all individual team members of the separate iGEM teams have one common goal: make the project succeed and win as much medals as possible at the Giant Jamboree, and teams consist of members with different cultural and academic backgrounds. In situations comparable to the Thailand cave rescue, especially good communication within a group of strangers, is essential in order to complete the task.

After the theoretical part, the participants got the chance to experience how difficult it is to communicate in a group of strangers by completing the ‘blindfolded rope square task’. In teams of 10 members, they had to make a perfect square out of a 15 meter rope within a 20 minute time limit, without knowing each other’s names. For this challenge each individual was blindfolded while holding the rope, which they were not allowed to let go of. Almost every team managed to make a perfect square in time.

After the task, we evaluated the problems and findings, which arose during the task. The main conclusion was that structure and good communication is very important, regulated by a leader who guides the whole group by making sure everyone understands the task, evaluates if the task has been performed correctly and channels all the input of the group. This conclusion is also applicable in their own iGEM teams.

Tar-Transformation

Figure 1. Colony PCR of 6 Tar expressing colonies.

Since the Tar receptor plays a central role in our project, we opted to use the biobricks BBa_K777000 and BBa_K777001. After isolation from the distribution kit and subsequent transformation of these parts to E. coli DH5-alpha we performed a colony PCR on several clones using the VF and VR primers, to confirm the presence of the Tar construct in our bacteria. The results of this screening showed the presence of a DNA fragment of 1200 bp, even though the expected fragment size should be 1762 bp (Figure 1). Sequencing results showed the presence of a GFP coding sequence downstream of an undefined region that presumably contains a promoter sequence. These results were confirmed by examining the plates under the fluorescence binoculars.

We hypothesized that this was due to inconsistency in our DNA distribution kit, since we did not isolate any GFP expressing constructs, with the exception of constructs that were already used for the interlab study. Because these constructs were isolated on a separate occasion, we asked other iGEM teams if they could replicate these results. The Dutch teams from Eindhoven and Groningen decided to help us by testing theses parts from their kit and sharing their results with us. From these results it became clear that the parts BBa_K777000 and BBa_K777001 from their kits showed no fluorescence at all (Figure 2 and 3).

Since we really needed these parts to complete the methylation part of our project, team Groningen decided to send their parts to us. The effort that both teams put into helping us is a perfect example of the iGEM spirit. We would like to thank both teams for their time and effort!

Figure 2: Results of team Eindhoven. Left shows no fluorescence of colonies transformed with BBa_K777000. Similarly, the right picture shows no fluorescence for colonies transformed with BBa_K777001.

Figure 3: Results of team Eindhoven. Left shows no fluorescence of colonies transformed with BBa_K777000. Similarly, the right picture shows no fluorescence for colonies transformed with BBa_K777001.