Team:Berlin diagnostX/Collaborations


IIT Delhi

Together with IIT Delhi we were increasing each other’s Social Media impact, jointly built up an RNA isolation and purification pipeline in India and helped each other with circling samples and research equipment between India, Germany and the US.

How everything came into existence:
In the beginning of 2017 Berlin diagnostX launched their Facebook Page. Back then the team did not even know whether they would ever participate in the iGEM competition. They were a group of students lacking funding and a laboratory, but were planning on building a diagnostic test for Taenia Solium. They wanted to do so within the framework of the iGEM competition. Since social media is an important factor to gain financial support, Noa from Berlin diagnostX contacted iGEM IIT Delhi to ask whether they would be willing to share each others posts to gain more followers and increase the reach of our posts. This small-scale collaboration worked promoting each other on social media. This initial collaboration laid the foundation for our extensive collaboration – because without this pre-existing contact, Berlin diagnostX may not have skyped with iGEM IIT Delhi before travelling to India.

A first Gasp of transcontinental research
Later in 2017 Henrik and Dimi of Team diagnostX flew to India to establish new research cooperations. Because their journey would lead them through Delhi they contacted iGEM IIT to visit their lab and exchange research ideas. Throughout a first skype call with Kshitij and Tarun, all got along so well, that the idea emerged to jointly build a pipeline, that would allow local PCR and RNA isolation of/on lysed, non-infectious S1-security level samples, that Berlin diagnostX planned to acquire from India.
With that in mind Berlin diagnostX tried to order some RNA isolation kits and PCR reagents to the lab of iGEM IIT but it turned out that multinational companies like NEB, ThermoFisher and QIAGEN are unable to send a bill to Germany and to deliver the products to India. At this point iGEM IIT helped and bought the kits for Berlin diagnostX from a local reseller.

Jointly established RNA isolation pipeline at IIT:
After visiting physicians and villages in the area of Varanasi and meeting people affected by T. solium, Dimi and Henrik went to IIT Delhi to establish RNA isolation in the lab of iGEM IIT Delhi. Having the option to perform RNA isolation was crucial for diagnostX because the laboratories in Varanasi did not have the proper equipment for RNA isolation. The chances were high that isolation of RNA was necessary for export. The team from Delhi organised a student dorm for Henrik and Dimi to stay in and thus allowing them to work day and night on improving an RNA isolation protocol that ultimately yielded high quality RNA.

Championing international trade and safety regulations:
Once Dr. Mishra of the Heritage Institute for Medical Sciences received a tapeworm sample containing eggs from Taenia Solium and processed them, the Berlin Team had to transport the RNA-sample from India to Germany for sequencing. Due to a change in the Indian trade policy in June 2015, no company, hospital or physician could send samples abroad without obtaining an “Import Export Code”. Obtaining this code is bureaucratic and complicates taxation. For this reason, despite having the sample and a carrier with expertise in the field (World Courier, an AmerisourceBergen company), diagnostX was unable to transfer the sample to Germany. At this point iGEM IIT Delhi supported the Berlin team again by shipping the sample to IIT and subsequently exporting it with permission of the IIT. This shipping procedure took over two months and the joint effort of the Berlin and Delhi iGEM teams to complete but it was a key step to the transcriptome data and the sensor described by iGEM Berlin diagnostX.

The team TU Darmstadt contacted the team Berlin diagnostX in search of background information on wound care and healing for their project. Since the body of the team Berlin is made up of medical students it was delighted to help.
During an initial Skype meeting both teams talked about their ideas and plans for the iGEM competition and gave each other helpful feedback. When the conversation fell on wound care and healing the Team Berlin reinforced its willingness to share knowledge gained in medical school and to consult experts to answer the special questions the team TU Darmstadt had.
In the following weeks an active email exchange took place in which the team TU Darmstadt shared the questions they had and the areas they were most interested in. The following Skype webinar was based on those questions and covered many different areas regarding wound healing. The topic that were discussed involved different types of wounds ranging from stab wounds to burn wounds, wound microenvironments and of course the application and clinical role of wound hydrogels.

During an initial Skype meeting both realised that they were working on replicating the same algorithm to score possible sensor candidates and rank them by likelyhood of success prior to the in vitro screening. In the following email exchange both teams provided each other insight into their understanding of the methods described in the extended methods of this ( paper. In addition the team EPFL iGEM shared the information they gathered from a meeting with one of the authors of the aforementioned paper. Those efforts combined led to the development of the toehold designer software in each team.
Since both teams also worked with cell free expression they exchanged protocols with insights gathered from previous experiments. The team EPFL iGEM shared their protocol of how to produce an own cell lysate. The team diagnostX on the other hand shared protocols for freeze-drying cell free expression systems and rehydrating them.

Due to the close proximity of Berlin and Potsdam collaboration between team Potsdam and team Berlin diagnostX was a breeze. The first contact happened in June and both teams soon exchanged information regarding the projects and the challenges of being a first time contender in the iGEM competition. The electronic contact was soon followed by a personal meeting playing a couple of rounds of volleyball in the heart of Berlin. Some members of team Potsdam also participated in a workshop organised by team diagnostX and the Boston Consulting Group to learn how to acquire new sponsors and advisors. On the other hand team Potsdam provided the vector pSB1C3 when team diagnostX had difficulties with their vector.