Team:KU ISTANBUL/Partnership



The Partnership part was written with mutual efforts of iGEM Athens & iGEM KU_ISTANBUL

Introduction by iGEM Athens

During this odd year, iGEMers around the world wanted to connect with each other more than ever, especially after the announcement that the Giant Jamboree will be held online. The need for a feeling of community, but also for collaboration partners pushed our team to look for other iGEM teams that work with light (electromagnetic radiation) and matter interactions. While searching through the database of the Maastricht Journal initiative, during early summer, we(iGEM Athens) stumbled upon the work of iGEM KU Istanbul. We were initially drawn to their work because we found biological lasers an interesting topic, a bit relative to our project. We decide to contact them and the rest is history!

Our partnership was built upon different stages of our project development, from helping each other understand the problems we address, to assisting the design of our solutions and defining their future perspectives. We arranged a first get-to-know teleconference, where we introduced ourselves and our work, but also discussed how the pandemic had affected us, the mutual difficulties we were facing and the constant changes we were going through. After that first meeting, our team realized that the situation and the problems young students and scientists face are very similar. Besides the pandemic effects, the financial issues both of our teams experienced, brought us together and helped shape our partnership. The main characteristics that prevailed were mutual support, empathy and communication to help each other meet our goals.

Our first meeting

At our following meetings, we presented our projects to each other in detail and exchanged valuable feedback. It was one of our first presentations for our team and we really appreciated the experience and the welcoming atmosphere. During those meetings, we discussed the extra needs each team had and iGEM KU Istanbul was in need of some parts from last year’s distribution kit. We gladly checked if we still had all those parts from iGEM Athens 2019 team and since we were not planning to use them, we mailed them those parts. In addition, the team of iGEM KU Istanbul was the first team to enthusiastically participate at our flyer translation on dyes.

Translated flyer in Turkish

Just another meeting :)

After those meetings we found ourselves arranging a series of interviews, by suggesting to each other and helping contacting experts related to our fields, in order to get feedback from them. More specifically, the Istanbul team introduced us to Yilmaz Aslan, a Turkish former art teacher and artist, to talk about how the end product we are creating can be used by students. Full interview can be found here .

Interview with Yilmaz Aslan

Similarly, we introduced the Istanbul team to Dr Mara Simopoulou, an Associate Professor of Physiology and Clinical Embryologist/Geneticist at Athens Medical School to help them understand the challenges of In Vitro Fertilisation (IVF) and how their laser could contribute to the characterisation of oocytes.

Dr. Mara Simopoulou interview

They also found a thesis that provided detailed information on the accidents related to that specific field in Turkey, a neighbor country to Greece. They also got out of their ways to help us translate parts of that thesis and to focus on what is directly related to our project, even during our not-so-rare after midnight working schedule.

Finally our collaboration evolved with mutual help on wiki building and content proofreading. The feedback acquired was crucial for the presentation of our teams.

Project collaboration

Our partnership could not be completed without collaborating to link our projects. Since both of our teams have not completed our projects due to the circumstances that prevailed due to the pandemic, our partnership focused on a potential future interaction and the design of future experiments.

It would be of significant importance for the Morphæ project that we are able to track the bacteria, as gliding motility has been linked to structural colour. Therefore, combining our work with the Living Laser was the way to achieve real time tracking! In order for this to happen, Flavobacteria cells need to produce reflectin in the periplasmic membrane as well as to express green fluorescent protein (GFP). After cells reach this state, the laser is pointed towards them, and can be tracked!

Genetic engineering

To accomplish this, we firstly need to genetically engineer the flavobacteria to produce the above proteins in the desired cell compartment, but we would also need the hardware equipment from KU Istanbul team’s project.

For the genes design and insert, the following procedure is followed. The OPH signal peptide is designed to transfer the reflectin to the periplasmic membrane [1].

Additionally we used the promoter, RBS and terminator, to ensure its successful translation at Flavobacterium species. The same procedure was followed for the GFP without the signal peptide, as it was not needed. Those genes are incorporated into the Himar transposon that is found in pHimarErm1 plasmid, using Type IIS assembly (level 2) standard. The two plasmids containing transcriptional units (GFP and reflectin) are inserted with conjugation in the flavobacteria using the E. coli S17-1 as the donor of plasmid, following the same protocol as the one described in detail in the project description tab of iGEM Athens. After conjugation occurs, the two transcriptional units are transported into the Flavobacterium species genome.

Plasmid design for GFP

Plasmid design for Reflectin

Below, the hardware of KU Istanbul that will be used to track the cells is described in detail.


After all that communication, mutual help and support as well as the bond created between the two teams, we promised to meet in person after the pandemic! Until then, the least we could do to celebrate our shared experience was to stream the Giant Jamboree together and enjoy the event connected!

[1](Versatile signal peptide of Flavobacterium-originated organophosphorus hydrolase for efficient periplasmic translocation of heterologous proteins in Escherichia coli).