Collaborations with other iGEM teams

During the year we have 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 modeling, 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 the collaboration with Uppsalas iGEM team, we organized and hosted a meet-up for 60 students from eight Nordic iGEM teams. Teams participating in the Nordic iGEM Conference were Oslo, SDU Danmark, Aalto Helsinki, Linköping, Copenhagen, Gothenbug as well as Uppsala and us, Stockholm. We also had a pleasure to have Randy Rettberg, president of the iGEM foundation, with us during the conference.

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

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 simultaneously highly active. One method of the 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 utilized a system of GPI-anchoring that is common in membrane proteins of mammalian cells. We based our design on a human protein DAF, encoded by the CD55 gene. A 34-amino-acid-long signal peptide at the N-terminus precedes the actual protein, which is then followed by a second 28-amino-acid-long signal peptide at the C-terminus. The N-terminus signal directs the protein to the ER, and the C-terminus signal is removed from the ER and then replaced with a GPI anchor. In addition, a DAF-derived signal has been shown to lead to GPI anchoring of fusion proteins. ¹

Subsequently, we have also added a short linker sequence and a FLAG-tag on the N-terminus of the affibody. On the C-terminus, we have 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. The construct was expressed by the BGU Israel team. While expression of the Affibody was confirmed, it did not appear to be localised to the membrane. More results are available on the BGU Israel 2015 wiki.

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 ETH Zürich 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 Freiburg 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 patients 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. Apart from several fruitful Skype conversations in which both groups have been helping each other with advice and reflections, we have also established a physical scientific collaboration in which the iGEM Group Stockholm characterized their biobrick part, a lactate sensing circuit. We tested the circuit with pure lactate and also with lactate expressing tumor cells. In return, the iGEM Group ETH Zürich offered to investigate on binding capacity of our EnvZ-affibody chimera expressing TOP 10 strains to HER-2 expressing cancer cells.

Aalto-Helsinki

Several members expressed their will not to use Facebook for various reasons, and along with personal reasons the fact that Facebook lacks key functions for streamlined collaboration and possibilities to customize. Discussions regarding other means of communication started and the idea of the Hub arose as a common place for teams to discuss and collaborate both within the team and with other teams, specifically including Institut Pasteur from Paris.

We assumed that the communication problems weren’t only issues in Stockholm and Aalto-Helsinki, but to get more information about the communication platforms and collaborating practices within iGEM teams, Aalto-Helsinki launched a team questionnaire. The questionnaire consisted of multiple choice questions and aimed to gather information about the different platforms teams used to communicate with other teams and also how teams find each other to start collaborations. By August 5th 23 teams had replied to the questionnaire. Of these only one team felt there was no need for a better collaboration platform.

Following the discussions a network was set up by the Stockholm iGEM team using the open source. In many ways, the Hub mimicked a regular social network. However, some functions have been added such as a better word processor. People could join different platforms and make one space for each team, sub-team responsibility, wetlab work, cross team collaboration etc. In each platform users were able to post text, pictures and links to share them with each other. People were also able to post to everyone in the open forum to ask for help or reach out for a certain collaboration. As the Hub was used for iGEM communication alone, there would be no unnecessary distractions.

It however worked quite similarly to Facebook and most of team members would find it easy to use the Hub as they already used Facebook. It would also remove the necessity of multiple platforms for intra- and interteam communication as was the case with Aalto-Helsinki at that moment. It would also solve the problem of communicating with the teams in countries where there may not be access to Facebook, or where Facebook may not be popular. If HumHub would be spread out through the headquarters, teams would be encouraged to use it and the communication between teams would likely be much easier. If HumHub became the norm of communication within iGEM, it could be adopted by new teams fast and with little effort and it could also function as a means to find other teams to work with. Eventually, if everything was focused on one platform, noticing new messages and replying to them could have been more accessible.

Team:Stockholm/Collaborations