Team:TU Delft/Collaborations
Collaborations
Sharing and collaborating with other iGEM teams
Overview
Because our project is a fundamental one, there were a lot of teams that were interesting to collaborate with. For the next years we expect that by making an organized biofilm structure, a lot of teams can use the method we designed this year. During the development of our project, we received a lot of ideas and input from other teams - what is useful for a biofilm and what not. Also we helped other teams by sharing the knowledge we have about biofilms and even printed a biofilm for another team. For sharing this knowledge we had several skype different teams, we helped with organizing different events where we talked to other teams, and we eventually went to Groningen to make a biofilm for them.
Dutch iGEM Teams Meeting
Preparatory starting course for all the Dutch iGEM teams of 2015
On the 26th and 27th of March 2015 there were two training days for all the iGEM teams of the Netherlands. The teams invited were Groningen, TU Eindhoven, and TU Delft. Both days were filled with different lectures, on the 26th at the University of Groningen, and on the 27th at TU Delft.
We left the Delft station early in the morning, prepared for a long train ride. Without any delays we arrived in Groningen by 11am and were warmly welcomed with tea,coffee, and biscuits. Aljoscha Wahl started with a general introduction to iGEM, and we were introduced to the members of the other teams. It was really nice to meet them all and learn about all the different backgrounds. The first speaker was Renske van Raaphorst who gave a lecture about how to be successful in iGEM. She had participated in the iGEM competition in 2012 with the team of Groningen, and won the grand prize that year. She summarized what they had done and how their project had proceeded from beginning to end. It was very surprising how many obstacles they encountered and how they solved them. She gave us a few good tips how to approach problems and avoid stress moments. Clement Gallay continued with a general introduction about bio bricking. I thought that a lot of what she told was already known, since nearly everyone had a biology background. Yet it was a nice abstract about what we would be doing in the lab this summer.
Time flew by and at the beginning of the afternoon we got lunch in the canteen. It was a great moment to talk to the other team members and ask about their projects and experiences so far. After the lunch every team gave a short presentation about their project and their progression so far. That was a moment we could give comments and ask questions. Because we didn't have our final idea yet, it was a nice opportunity to hear different opinions about subjects we had in mind. Although the other teams were already a lot further than us, we are sure we can still catch up with them.
The day continued with a presentation by Anna Lauxen from the Groningen team 2014. She also gave us a lot of tips that were very practical. Maarten van den Nieuwenhof followed with an informative lecture about Human Practices in iGEM. Lastly Bayu Jayawardhana informed us about modeling in iGEM. He described the importance of modeling in Biology in general and the importance for iGEM. After the last presentation of the first day, we stayed a while to have dinner with the team of Groningen. They ordered large pizza’s with beer and we had a nice time with the other teams about the long, but educating day. We went home satisfied. On the way back we had a little bit of troubles, but thanks to the beautiful singing voice of Hector we were able to come home without extra costs.
On the second day, the iGEM courses were hosted at the TU Delft campus. Unfortunately due to disruptions with the trains, the Groningen team were unable to join the gathering. Luckily, the team of TU Eindhoven was able to come to with the other half of their group, so there were a lot of new faces for us, and many introductions. At 10.30 we started with a lecture by Anne Meyer about tuning and troubleshooting engineered genetic circuits. It also included many tips and tricks to avoid problems. Aljoscha Wahls followed up with a presentation about Network Motives, a kinetic perspective. Timon Idema started his presentation about physics and modeling behind the iGEM project, and how you had to ask the right questions to use modelling as a tool. He also gave information about how the judges evaluate the modeling tract. After taking up so much new knowledge, it was time for a lunch provided by the TU Delft.
After lunch Anne Meyer continued with a lecture about all the things the jury like and dislike in the iGEM competition. Since she had participated as a judge in the iGEM competition, she was able to gives a lot of useful information that we definitely would use. The last item on the agenda was a practical course in modelling, where we were given some exercises with matlab to see how modelling worked in practice. This gave a lot of insight for students who had never worked with matlab or modelling before. To close the two day lectures, everyone was invited for drinks afterwards in one of the popular bars.
All in all the two days were very informative, we got a lot of useful tips and tricks. Besides that we have a lot of fun. It was also very nice to meet the other teams and hear their project. We would like to thank all the participating teams, old iGEM members and lecturers for their time and energy in organizing and joining the educating and informative subjects.
RIVM and Rathenau Instituut
National Institute for Public Health and the Environment together with the Rathenau Instituut, organized meetings for the Dutch teams to discuss human practices.
For the second time, the RIVM (Governmental agency for public health and environment) and Rathenau organized a discussion about “Synthetic biology in action”. All the Dutch iGEM teams were actively involved in organizing the event. We had two preparation meetings of which the first meeting was about what we wanted to achieve and what the iGEM teams could mean for the discussion. In the second meeting, all the Dutch teams practiced their pitch that they wanted to present at the event. It was really inspiring and lovely to see what the other teams had accomplished during the previous months.
7th of September 2015
On the 7th of September it was time for the real event. The invited public consisted of people who had expertise in government affairs, synthetic biology, and industries, and therefore look at synthetic biology from different perspectives. The aim of the day was to create a discussion about the advances in technology that have the potential to have an influence on a large scale.
Introduction to synthetic biology from different viewpoints
The day started with an introduction into synthetic biology, taught by Jack Pronk, a professor at the TU Delft. He gave a lot of insights in what kind of opportunities synthetic biology could give in terms of research and development. The next talk was given by Dr. Bart Wesselink, RIVM. He discussed the meaning of sustainability in the biobased economy and industry. He succeeded in relating the subject of synthetic biology to the social and economical impacts of a biobased way of thinking. The last presenter was Dr. Dirk Stemerding, senior researcher “technology assessment” at the Rathenau institute, who expressed feelings surrounding the implications of synthetic biology and that social debate is necessary. He related this thought to the Ecover case, a producer of cleaning products. Ecover did not want to use any palm oil for their products and therefore decided to use genetically modified algae for the production of oil. However, this raised a lot of resistance by people who thought oil produced by genetically modified algae was not ‘natural’, while palm oil was. According to Stemerding, this case illustrated an early warning. This talk was the most related to what we understand as the main goal of the “Policy and Practice analysis” of iGEM. We, as an iGEM team, should encourage debate, education and maybe even acceptance.
Could we add the three images here?
iGEM teams and related discussions
After a short break the stage was room for the Dutch iGEM teams to pitch their projects, and what their views were of iGEM in the synthetic biology world. First to start was our project, represented by Max van ‘t Hof and Michelle Post and our DIY printer. iGEM aims to be a platform that informs the world about synthetic biology, via students who are open-minded about ethical issues, it can reach a large public. This combined with full transparency on all achievement reached by its participants, in both our wiki and the iGEM database. We described our concerns about being transparent and therefore being an open source for non-iGEM’ers. We explained the issue about anybody being able to access information about synthetic biology and in that way being able to recreate entire experiments. All iGEM teams must comply to this transparency to be able to fulfill medal requirements. We mentioned that our 3D printer could be recreated by anybody, because a manual will be placed on their website stating all the steps to create this machine out of children’s toys. Our finalstatement was as followed:
“The open source mentality of iGEM is not so threatening as that this system should be forbidden”.
The public had been handed out green/red cards, to indicate if they dis- or agreed with this statement. The public was almost entirely unanimous in agreeing with the Delft’s students. Besides the agreement, there was a technical philosopher who said that although we should aim to an open source system to stimulate innovation, we should also be aware of the risks related to such a system. Although we agreed on this point, we were also very glad to see that almost everyone saw the benefits in an open source system as used byby the iGEM community.
The next team was Groningen who talked about their biofilm used for the production of blue energy; the production of energy based on the difference in salt concentration between salt and fresh water. They stated that it should be possible to allow GMOs outside closed circuits. The public was a bit more hesitant in agreeing with this. The public mentioned that it is unpredictable what the effect of these GMOs will be on the environment. Pronk added that naturally occurring microorganisms will in most cases outcompete the GMOs.
The third team was Amsterdam, who explained their project incorporating symbiosis between E. coli and cyanobacteria to produce biofuels.The costs of biofuels are not favorable compared to current fossil fuels due to the production costs. Therefore, the students from the capital stated that they believe that the Netherlands should invest in such innovations, even if it would lead to a less favorable economical situation in the near future.
The last Dutch team was Eindhoven, who introduced their modular device to biosense diseases. Their statement was that the patent regulations should not apply for applied research. This was met with the most ambiguity throughout the audience. There were comments stating that patents were only used if the “new” products made with the help of patented items, had to be payed for, and not if used only for research.
Drinks and acknowledgements
The day was finalized with drinks and an opportunity for the audience to mingle and discuss further with other professionals. It gave us an unique chance to talk with people who deal with these kind of issues on a daily basis. We also had the insight that the discussion could even be more fruitful by introducing more specific statements. Moreover, a lot of people agreed that the open source system has a lot of promises, but that we should look at the consequences and at each case specifically. This is also related to the aim of our tool; to see what the acceptance and feeling of the public is towards each iGEM project specifically.
We would like to thank the RIVM and Rathenau institute for making this day possible. A special thanks to Virgil Rerimassie, Korienke Smit and Jaco Westra! And also to Loesje Praktijken for making the nice pictures!
Cooperations
Throughout the year we cooperated with a number of national and international iGEM teams
test
On the 12th of June we had contact for the first time with a team outside the Netherlands. We arranged a Skype meeting with them for an hour. We explained our project, and they explained their project. We had just started in the lab, and it was very interesting to hear how far they were in the process and what their experience was so far. CGU team was further in the development of the plasmids. In their iGEM project they try to develop an organism that can detect Oral squamous cell carcinoma (OSCC). They use the idea of the TU Delft team of 2012, the snifferomyces project.
Unfortunately our projects are now too different, so there was no reason to exchange plasmids. They had some questions for us about the modeling, because our model was already quite developed at that time. It was a good experience, and nice to meet another team!
On the 4th of August we had a Skype conversation with the iGEM team of NCTU. After 15 minutes of getting the technology to work, we finally can talk. We started with sharing our project topics. Jenny Gee, one of the team members held a comprehensive presentation of their project. What we noticed and surprised us is that it seems that most of the teams have a lot of members. However, our team consist only of nine(9) members, we seem to be quite on track. We are all now working at least 40 hour a week on iGEM, and it was nice to hear that NCTU team also does. They are arranging a big event among the Asian iGEM teams. For us that’s maybe also an idea, to arrange one more time an event among the Dutch teams. It was a nice conversation, we had fun meeting them and seeing how far other teams are in their project.
Oh the 24th of June we received a message via Facebook from Kyle Sam Bennett of the Oxford iGEM Team. They contacted us because we were both working with biofilms. In their project they focus on the breakdown of biofilms in the urinary tract in order to treat Urinary Tract Infections. For testing the breakdown, they need biofilms with their modified bacteria. Because we also create biofilms with a modified E. Coli bacteria, with the help of a 3D printer, our projects fit really well.
Our project can be a good support for theirs. With the use of our printer in combination with the vector with the curli gene inserted in their modified bacteria, they can print biofilms in the structure. A second subject in which we can help each other is to discuss the safety of the projects. We finally decided to induce the biofilm formation with rhamnose. The last collaboration point with Oxford was about the modeling. We had in total 2 skype meetings, and a few times contact by email. We shared ideas.
The iGEM team of Aix-Marseille Université asked us to participate on their survey about chewing gum. Examples of questions in their survey were:
- How much bubble gum do we consume all around the world during a year?
- Does your country have a way of removing bubble gum from the streets?
- What is your definition of GMO (genetically modified organism)?
Where most teams ask for the opinion of other iGEM teams, this team wants us to go and ask around for other people to answer the question. The guidelines for doing the survey are below. On the 26th of August we heard that we provided enough answers to earn the Bronze medal. We are really glad to hear that we gave the team enough input and we are curious to see what they did with the answers for the progress of their project.
