Collaborations with other iGEM teams

During the year we've been involved in many extensive collaborations. We have hosted an iGEM conference for the Nordic countries, had scientific collaborations with BGU Israel, ETH Zürich and University of Freiburg, written articles for the Amoy newsletter, helped CGU Taiwan with modelling, worked on digital collaboration platforms with Pasteur Paris and Aalto-Helsinki and participated in a global collaboration on human practice surveys.

Nordic iGEM Conference

In collaboration with Uppsalas iGEM team, we organized and hosted a meet-up for 60 students from eight Nordic iGEM teams. Teams present at the Nordic iGEM Conference were Oslo, SDU Danmark, Aalto Helsinki, Linkoping, Copenhagen, Gothenbug as well as Uppsala and us, Stockholm. We also had the pleasure to have Randy Rettberg, presedent of the iGEM foundation, in our company for the conference.

Our Nordic iGEM Conference was a three day long event. We had a mini-Jamboree, complete with project presentations and a prize – the famous Golden Pipette! There were also workshops, fabulous dinners and great bar-crawl in Uppsala. It was a great experience, and the Nordic iGEM Conference will return next year!

Read more about the Nordic iGEM Conference and see pictures

BGU Israel

Together with BGU Israel we have worked on a possible Affibody based application of their idea for cancer therapy. Their system is delivered to mammalian cells with AAV vectors and triggers expression or knockout when two cancer-related promoters are highly active simultaneously. One method of therapy could be to specifically target cancer cells with a toxin. Since Affibody molecules can be engineered to bind almost any protein with high specificity and affinity, it might be possible to direct these toxins towards cells that express Affibody molecules on their surface. To try this concept, we decided that our team would design a membrane-bound Affibody that BGU Israel would then attempt to express on the surface of mammalian cells using their AAV vectors.

Our design used a system of GPI-anchoring common in membrane proteins of mammalian cells. We based our design on Human protein DAF, encoded by the CD55 gene. A 34 amino acid long signal peptide at the N terminal precedes the actual protein, which is then followed by a second 28 amino acid long signal peptide at the C terminal. The N-terminal signal directs the protein to the ER, and the C-terminal signal is removed in the ER and is replaced with a GPI anchor. Addition of a DAF-derived signal has been shown to lead to GPI anchoring of fusion proteins. ¹

In addition to the signal peptide, we also added a short linker sequence and a FLAG-tag on the N-terminal of the Affibody. On the C-terminal, we also added a linker that ended with Serine, which is the site of cleavage for the signal peptide. This gene was then synthesized as a gBlock by IDT and expressed by BGU Israel.

Amoy

Last year the iGEM team from Xiamen University together with the team from Paris Bettencourt University founded the Newsletter platform. Through this iGEM team from all over the world could share information about their project and discuss issues concerning it and synthetic biology in general. For this year’s version of the Newsletter iGEM Amoy contacted iGEM Stockholm to include us in the 2015 issue. We contributed with five articles concerning setting-up a team, germline modifications and a description of our project and an update on our progress.

CGU Taiwan

The CGU Taiwan team was referred to us by the Delft University of Technology team. They needed help with the modeling part of their project. They had to knock out a gene in the GPCR pathway, which in normal circumstances would be active. We introduced them to Matlab and SimBiology as well and helped them model the GPCR pathway with the eliminated gene. They were also interested in projecting the boundary condition for liquid-liquid interphase diffusion, using partial differential equations. We offered to research their reactions and to try to find kinetic parameters of the processes present in the CGU’s current project. We suggested utilisation of Newmann no-flux partial differential equation useful as a boundary condition for this type of diffusion, previously used also by Zurich IGEM team 2012.

Design of the pathway performed by Stockholm iGEM team

Global collaboration on human practice surveys

CGU Taiwan involved the Stockolm team into a broader collaboration, evaluating public recognition of iGEM projects. Except for CGU Taiwan and Stockholm iGEM teams, the following teams collaborated on this:

• Technische Universität Berlin (Berlin)
• Beijing Institute of Technology (BIT)
• University of São Paulo (Brasil_USP)
• The Chinese University of Hong Kong
• University of Leicester
• Tianjin University (Tianjin)
• Université de Toulouse (Toulouse)
• University College London (UCL)

Our role was to come up with questions for a survey and coordinate the technical work on the survey. An example of our contribution is depicted in the figure below. In a related collaboration, we also hosted a survey on our servers for iGEM Nankai and provided them with technical support.

University of Freiburg

In the context of developing novel technologies for diseases diagnostics, we contacted Freiburgs iGEM team who are developing a DNA Microarray to screen for several different diseases at the same time. Their project is based on the coating of a Nickel surface with a certain disease antigen and the binding to the antibodies of a patient’s serum. In our collaboration, we have sent the team in Freiburg His-tagged HER-2 Affibody molecule, a strong molecular binder for the breast cancer antigen. This will allow to screen directly for current diseases in the patient as the indirect detection via serum antibodies can also give false positive results due to old infections.

ETH Zürich

The project of ETH Zürich is in the field of cancer cell detection. Besides several intensive Skype conversations in which both groups have been helping with advice and reflections, we have also established a physical scientific collaboration in which the iGEM Group Stockholm characterizes their biobrick part, a lactate sensing circuit. We test with pure lactate and likely also with lactate expressing tumor cells. In return, the iGEM Group ETH Zürich is using our chimeric receptors to bind to HER-2 expressing tumor cells in order to sense the surrounding lactate levels.

Pasteur Paris and Aalto-Helsinki

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