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. Some of these can be seen on the Policy and Practice page under iGEM Community section. For this we collaborated with the Berlin, KU Leuven and Amsterdam teams.
Moreover, 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.
Testing Biolinker
Throughout the policy and practice assessment, it became clear that the strong point of our printer was that it could be used for different types and strains of bacteria. We believed that it was important to test this hypothesis. At the RIVM/Rathenau discussion meeting preparation we learnt more about what the other teams were planning on making. A popular direction was biofilms such as the team of University of Groningen.
The iGEM Groningen team were creating a biofilm that would be used to create energy out of salt and fresh water. Their plan was to create an ion-selective biofilm that would be placed as a barrier between the two types of water, to ensure that an electro potential gradient would develop. This gradient would then be converted into energy called Blue Energy. Their biofilm had to therefore be ion-selective and robust. But they had a couple of troubles with creating a stable biofilm containing their engineered selective bacteria, Bacillus subtilis 3610 comI strain. They wanted to create a membrane that would be able to maintain itself, making it very sustainable and cheap. The two teams believed that combining their projects would lead to a good result, as well as it being important to help out a fellow iGEM team to test their hypothesis. .
Just before the track decisions were made, we contacted the iGEM team of Groningen through Skype, on the 17th of August, to discuss the possibilities of a collaboration between us. Like we mentioned in our policy and practice assessment, it became clear that a strong point of their printer could potentially be the usage for different types and strains of bacteria. .
On the 1st of september, Marit, Anne and Biolinker (our 3D-printer) travelled to Groningen to execute several experiments. The aim of the two teams were as followed: We wanted to prove that our 3D-printer can be called an open source platform technology, by letting the team of Groningen print their bacteria. The team of Groningen wanted to create a stable biofilm containing their biofilm-forming bacteria, by using our 3D-printer to improve the biofilm.
Two experiments were therefore designed. The first experiment was printing with the bacteria in alginate in a certain structure. By adding calcium chloride to the alginate, a gel forms with the bacteria encased. By using a plate filled with LB agar, the bacteria would be able to survive and create a biofilm. The team members of Groningen printed with their own bacteria, B.subtilis, in a form of their own choosing. The Groningen team prepared beforehand their own bioink (Sodium alginate+bacteria), calcium chloride and LB agar plates.
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To make the solution they pasteurized 100 mL of 1%(w/v) sodium alginate with appropriate antibiotic, and autoclaved 100 mL of 0,1M calcium chloride to acquire sterile solutions. The LB agar plates were made using standard protocols. They had grown their bacteria overnight in 5 mL LB with appropriate antibiotic. The overnight culture was then spun down, and the supernatant was discarded. The pellet was then resuspended in 100µL LB and mixed with 500µL sterile sodium alginate to make the bioink, and transferred into a 1mL syringe Before printing on the LB agar, 500µL calcium chloride was added to enable formation of the hydrogel.
The Groningen team then proceeded with printing with their self-made bioink. They were able to print on two agar plates, in the form of a house and a flower. They noted that the controls of the printer, weren’t very user friendly, but after a while they got the hang of it. In the end they agreed that the Biolinker was functioning as a 3D printer. .
The second experiment, was measuring the selectivity of alginate. The membrane should only let sodium ions (Na+) ions pass through to be a selective bio-membrane. Since the previous experiment proved that the 3D-printer was able to print the bacteria in the gel, the next aim was to prove that the printing of a biofilm made of alginate would be selective. The Groningen drew a square on carrier material, on which they printed the alginate in “full color”. The alginate filter was then placed in a self-made voltmeter system, where the filter would separate the fresh from salt water. This separation of salt and fresh was not acquired. This was due to the salt water added on one side of the alginate filter, it leaked to the other side, which didn’t allow the possibility of adding fresh water. The voltmeter did measure a voltage of 10 mV, but the Groningen team stated that the this was caused by the carrier material, which produces a voltage of around 10-12 mV by itself. Therefore it could not be concluded that the alginate filter was selective for sodium ions.
Thanks to the help of Gronigen, we are able to state that our Biolinker (3D-printer) is indeed an open-source platform technology, since Groningen was able to print their bacteria, B.subtilis, by themselves. The Groningen team wasn’t able to prove that their filter was selective for ions, due to the fact that the filter made let water molecules pass through.
We would like to thank the iGEM Groningen team for their time, bacteria and for the great dinner we had afterwards.
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.
Cooperations
Throughout the year we cooperated with a number of national and international iGEM teams
We received a request from the iGEM team Aalto-Helsinki to fill in a questionnaire. This questionnaire was about modeling in combination with experiments. Because our modeling is quite extensive, this questions gave us a lot of insight in how we can best implement modeling with science. So we were pleased to help them.
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.
