UR igem wiki


  • Linköpings Universitet Partnership
  • Since the LiU iGEM Linköping Universitet and our team met in August 2020 via an introductory meeting on Zoom, we maintained weekly interactions in order to achieve a set of shared goals that were essential to both of our projects. Our teams collaborated in three key areas: modeling (i.e. reports, variables, and beta-testing), software (i.e. biomarker database), and wet-lab (i.e. antibody design).

    Modeling Partnership

    With regards to modeling, both teams were highly involved in helping each other. We had been looking for a method to find the significance of our model variables, for which Linköping suggested principal component regression. This suggestion greatly helped us focus on important variables in our model, allowing us to obtain data about our models more efficiently. Linköping’s constructive feedback on our modeling reports helped us make our Wiki more accessible to a variety of audiences by providing advice on how to clarify concepts and equations used. Lastly, we beta tested Linköping’s ClusteRy web tool to help their team develop their software. Particularly, we identified a bug in the workflow and suggested ways in which they could make their website more friendly to non-experts in RNA matrices. In this way, we both contributed to each other’s modeling efforts to help each other improve our models and achieve our goals.

    Software Partnership

    For software, we worked together to help each other create functional databases which are part of our projects. Our team designed a biomarker database to make it easier for future teams to find information about conditions that they are interested in. After sending an email out to other iGEM teams to gather information, we learned that Linköping was also looking to create a similar database. While their database registers RNA expression matrices to identify potential biomarkers, our database collects information on various aspects of biomarkers in known diseases. For example, for each biomarker, our database specifies the type of biological molecule a specific biomarker is, why a team did or did not select that biomarker for use in their project, what kind of sample the team used to measure or detect their biomarker, etc. We are grateful to Linköping for their contribution in our database; they added 10 entries to our database, making up over 30% of our database!

    Wet Lab Partnership

    Wet lab was another area where Linköping and Rochester collaborated. Linköping used our team’s BioBrick BBa_K3346002 and SnapGene instructions to design a microbially produced antibody for their lateral flow assay (LFA). Our new plug-and-play BioBrick method and modified constructs provides other teams with a method to create full-length monoclonal antibodies for use in their project using E. coli SHuffle, an modified strain with an oxidative cytoplasm and additional chaperone proteins to allow for proper formation of disulfide bonds in the monoclonal antibodies. Linköping was able to follow the instructions that our team created about how to use our plug-and-play method to design a BioBrick for their own project at low cost, demonstrating the functionality of our method and the usefulness of our system to other teams. This inspired Linköping to use an immunoassay for the design of their project and guidance in creating a novel BioBrick for their team.

    Our partnership with Linköping was very significant in that it helped us successfully implement our modeling, software, and wet-lab objectives. This ultimately got us closer to development of a novel, non-invasive diagnostic for endometriosis.

    Our science manager, Emily Laskey, and modeling manager, Linh Hoang, working on our partnership with the Project Leader of the Linköpings Universitet team, Alexander Johansson, in a Zoom meeting.

  • SDU Denmark Partnership
  • Initiative: Gender Reproductive Health Care

    We were excited to collaborate with the University of Southern Denmark (SDU Denmark) team as our projects covered the same human body system - the reproductive system - and both teams were working on diagnostics in reproductive health. While they were engineering a diagnostic for prostate cancer, and we were engineering that for endometriosis, we could still contribute to each other’s projects mutually.
    We connected the SDU Denmark team with a urologist Dr. Divya Ajay from our local medical center, the University of Rochester Medical Center (URMC), specializing in prostate treatment. The team communicated with Dr. Ajay via emails and received valuable insight into their project. She explained to the team the US’ perspective on prostate cancer in terms of diagnosis and treatment approaches. SDU Denmark also learned that these factors are influenced by the health care system, which in the US is mainly private whereas in Denmark public. SDU Denmark connected us with a gynecologist Dr. Martin Rudnicki from Odense University Hospital, specializing in endometriosis diagnosis and treatment in Denmark. Dr. Rudnicki provided us with feedback on our educational materials for endometriosis outreach and outlined how endometriosis was being approached in Denmark.
    In addition to gaining knowledge about reproductive illnesses and treatments from doctors, we also exchanged corresponding contact information about foundations that address the diseases of our respective interests. We provided the SDU Denmark team with a thorough list of Men’s Wellness and Prostate Cancer foundations in the USA to further foster their interest in how the US manages prostate cancer. The SDU Denmark team connected us with a Danish Endometriosis Organisation (Endometrioseforeningen). It is a volunteer-run support foundation for people with endometriosis. This organization also supports endometriosis research in Denmark and contributes to the awareness of the disease in the health care institutions. During the meeting with a representative from the Endometriose Organisation, we learned that in Denmark, endometriosis treatment starts with various alternatives such as physical exercises and nutritional adjustments, and invasive treatment comes as a last resort. This is not the case in the USA. As a result, in our outreach educational materials on endometriosis, we included information on the benefits of nutritional improvements as an attempt to alleviate endometriosis-related pain. Additionally, one of our team members created a dance piece that was meant to raise awareness of endometriosis and in a method that promoted physical activity for those with the disease.
    Upon explaining to SDU Denmark our outreach initiatives to spread awareness of endometriosis through educational material accessible to people of all ages, the team was inspired to direct their Policy and Practice and Outreach efforts towards education on prostate cancer for the public. SDU Denmark thus created an educational initiative to guide men in climatic age on how to go through andropause.
    We are grateful to the SDU Denmark team for discussing with us our project directions, connecting us with a doctor from Denmark and a member from the Endometriosis Organization. Additionally, we would like to thank the team for contributing to our language Accessibility Project by translating endometriosis facts into Danish.