Team:Aalto-Helsinki/Gold

Meeting with experts

When our team started brainstorming for the project idea, our general knowledge of what would be feasible and what wouldn’t was quite insufficient. We had a many meetings right in the beginning of our project just to hear from different experts what they consider to be synthetic biology, what they thought of our various ideas and how they would proceed with the project. Especially talking with our primary PI Markus Linder directed our brainstorming and ideation, which finally led up to the final design of the project. Even though many experts gave us advice and guided our brainstorming, deciding about the topic and more precise plans were left for ourselves.

When we had decided on the top three project ideas, we met with researchers working with these different subjects as a part of the background research we did about the different options. We found about the Cyanobacteria research group of the University of Helsinki and met with them. And what a goldmine it was! Thanks to input from Kaarina Sivonen and her group, the decision about our project subject was finalized. We much appreciate that they truly dared to turn some of our ideas down, if they thought that these ideas wouldn’t result in a successful project. With ideas where they saw potential they encouraged us enormously. They have also helped us during the course of our project - for example the degradation part of our project would not have ended up being what it is without their help. We also practiced our Boston presentation and got feedback on that from them.

As we didn’t have much experience on protein production in yeast and as it was in a focal role in our project, we needed some help in planning our enzyme constructs. Alexander Frey from Aalto University turned out to be a great help in this. He helped us decide what kind of signal sequences we should have for protein secretion. He also questioned our choice to use yeast at all in the enzyme production, and made us broaden our thinking and justify our ideas. Putting much thought into justifications for our choices at this point of our project turned out to be very useful, since after that, we didn’t need to regret that we should have done something in a completely different way.

If the Cyanobacteria group and professor Frey along with his group affected the degradation aspect of our project the most, Jussi Jäntti and his research group from VTT likely contributed the most to the detection part. They gave us valuable input on our thoughts of harnessing the yeast stress response, and for example commented on our transporter constructs and gave ideas on tags to facilitate the verification of its expression. They also gave us input on our results and gave ideas on possibilities to take things further, e.g. giving the idea about using flow cytometry to verify stress promoter functionality. Without them we probably wouldn’t have thought to use flow cytometry, which ended up providing important support and verification for our other results!

Even though our team had students from fields ranging from biotechnology to mathematics, there wasn’t anyone who really understood both fields well enough to have a clear idea of what modelling is like in the field synthetic biology. That’s why meeting Merja Oja, who works with modeling biological systems, was very important in the beginning of our project. After that we were able to also think about the modelling part of our project and how it could support the experimental parts of our work. We ended up creating two different models: molecular and mathematical model about our detection. Integrating modeling as part of our project provided also interesting new challenges for our mathematicians.

Meeting with SYKE

The most valuable information from our meeting with Finnish Environment Institute was that we learned what kind of solutions already exist for the blue green algae problem. It came up that all the present methods dealt with the problem causing algal blooms, eutrophication. There was thus a real need for solution like our that could be effective in a smaller scale. This convinced us that we were on right track with the degradation.

We also discussed current detection methods and according to them, all the available detection methods are rather expensive and hardly any of them is available for the public. They guided us to plan our detection device so that it would correspond to the current need - being available for the public and not be too expensive. If the use of GMOs was legal, our yeast based detection system would provide an easy and affordable solution.

It was also nice to hear that there was no available method for the present day to get rid of the cyanobacteria or the toxins. All the present methods dealt with the problem by nipping it in the bud, i.e. fighting eutrophication but, none tried to get rid of the toxins once they have been produced. They gave us a an advise that one measurement should cost less than 25 euros in order for it to be an improvement to existing methods. We used these aspects when choosing the best option of our preliminary detection methods to continue with. We can honestly say that their input affected our choice of using modified yeast as detection chassis organism.

We also talked about the possibility to use genetically modified yeast as a sensor in the natural environment and it was nice to hear that they didn’t turn this idea down even if it is not allowed by the Finnish legislation at the moment. This gave us additional courage to choose our GMO yeast sensor construct to become out topic.

Besides affecting our choice of topic, SYKE gave us information about how we could develop our project after the proof of concept. We talked quite a lot about what kind of models are used now to follow cyanobacterial movement in seas and the development of algal blooms. From this conversation, we got an idea to develop their Levävahti sensor app. This was supposed to be part of our project, but unfortunately time constraints prevented us from doing this. Perhaps after the Giant Jamboree we might have time for this.

Interviewing people on the streets of Helsinki

From interviewing people in the streets, we learned that public knowledge about synthetic biology was rather restricted. Most people associated it with man-made biology or just something that they need to know nothing about. Based on this, we really thought that there was a need to increase knowledge about synthetic biology. We didn’t leave this on the level of thought, as we tried to raise the level of knowledge by talking in university lectures and in a biology olympiad training camp and by telling about synthetic biology in magazine and radio interviews. In the beginning, we didn’t really understand how scary and strange a branch synthetic biology seems to be for people not involved in it, but during the project we started to understand this. It is probably also one reason for why investors are not so easily attracted on projects related to this branch - they don’t know about its existence. Our team participated also in a bioeconomy seminar hosted by VTT, where this subject was brought up. It was discussed that communication really is the key when trying to create business in this field, and that researchers should learn how to communicate about this seemingly outlandish field to the general public. For this reason, too, we see a huge need to spreading knowledge, and we hope that in some years, it will start to show.

Besides gaining information about the need of synthetic biology outreach, we wanted to see what people know about blue green algae and if it has caused problems for them. All of interviewed people were familiar with it but didn’t know much about the health or economic problems it causes. Still, as each of the interviewed people had encountered blue-green algae, it means that our project can touch their lives and why not to facilitate their life in the future?

We didn’t change much in our project topic itself based on the interviews but we increased the importance of talking to the public. Additionally, as we learned how restricted the knowledge about our topic is, we have been able to adjust our presentations better for the audiences. Some of the most important modifications we did in our presentations to people with little biological background was dismissing almost all scientific terms, assuming no background information, focusing on what we can achieve with our project instead of the exact methodology, and leaving more time for questions. One result of our efforts to communicate with the non-scientific community was our project introduction video “Matti and the cyanobacteria” found on our Project page.

iGEM meetups

We participated in two iGEM meetups, the ones in Stockholm and Paris, which gave us many of things to consider in our project. In Stockholm we participated in an ethics workshop. This gave us a lot to think, since our project’s final product was designed to be a genetically engineered organism used outside the lab. We want to stir up the conversation about GMO legislation, and be part of the discussion about how GMOs could be used outside of the lab and by general public. More about our ethical considerations can be read below.

In both meetups, we were presented with the idea of patenting one’s work. In Stockholm, the SDU team couldn’t present their full project because they were in the process of patenting it. In Paris we participated in a panel discussion where part of the discussion was about patents and the openly communicated nature of iGEM projects. After hearing about this, we reconsidered our project from a broader point of view and decided to look into business aspects of it. Although neither the topic of our project nor the nature of iGEM made patenting seem like a relevant concern, we nevertheless thought it would be useful to gain an understanding of this aspect. We met up with Merja Penttilä from VTT to discuss these subjects. We received a lot of valuable information which would prove useful if at some point our project was developed forward and commercialization was a relevant question.

Meeting with companies

We got a chance to practise our presenting skills when we met with different companies and tried to convince them to sponsor us. What we got from them was advice on how to give presentations and how to emphasize our strongest points. We also got good practise on how to communicate with people who don’t have much background in biology, not to mention synthetic biology. Later in the project, we had a meeting with Algol, one of sponsors, where we presented our results. We were asked great questions on how we are going to motivate our choices and how we plan to explain the results at the Jamboree. Even though our presentation there was for people who don’t have a biological background, we had to think of e.g. how to explain that cyanobacteria are a problem for people who don’t live in Finland and have the same problems with it as we do.

When we met with companies, there was also a lot of discussion of the potential commercialization of our project, which meant patenting our idea. As discussed above, our conclusion was that it didn’t seem relevant to our project.