16. November 2016 Lucie Studená

iGEM Competition

Now when my 'dream internship' is over, I can share a few thoughts about how it all was and what have I learned from there. As probably expected the experience was quite different than how I was imagining it.

The summer was filled with amazing feelings about finally finding my ideal specialisation and about my personal discovery that there is a way to do molecular biology and still make directly useful things as engineers do (that is also why much of synthetic biology it is often called genetic engineering). However it was also a lot of pain and frustration about results and to be fair, we think that as a bunch of undergraduates with limited research experience we were sometimes left to our own fate a bit.

So how it all started? On the 27th of June, the team assembled for the first time. We had just one brief meeting in a pub before the exams so most of us were complete strangers to each other. But everybody was very keen and we got a crash course about what synthetic biology actually is and what is expected from us. I was quite surprised by how relaxed the programe was, we finished early on many days and went for teas a lot. It definitely hasn't happened again after that first week. We were brainstorming the ideas of what to do and we were faced with the huge breadth of synthetic biology field plus a few constrains and opportunities of working on plants. Moreover each of us had some idea about what are we expected to finish with, but it was very vague and different from what others thought. It is funny to look back at our discussions and see that one day some of us thought that our goal was to “make a BioBrick”. No, they expected a real project, but built from BioBricks and making new BioBricks in the process.

The crash course was planned for the first two weeks but happened just the first one. Faced with the timescale of 9 weeks left and the knowledge that many other teams have started much earlier, some even last summer or before, we were more and more worried that we still don't have any feasible specific idea. To be fair, I knew that time already that I would look back to the first two weeks with certain nostalgy. Yes, it was frustrating not to know what our summer will be about, but which undergraduate has the chance of getting money and labspace and of suggesting whichever project they like, discussing the most crazy ideas how to save the world and eventually actually attempting to make them real? I kind of loved that and felt like we shouldn't stress ourselves that much yet, it may even kill productivity. But that is what happens if we have amazingly keen and ambitious team.

At the beginning of second week, I came up with the first a little more specific idea for the group. I got inspired by two articles which have tackled the problem of oxygenation of biomaterials. They tried to put algae into hydrogels and it worked surprisingly well. I wanted to take it from there and try to make “bioplasters”, biomaterials which would produce wound healing and protecitng substances via algae straight into the wound. The idea was well adopted by the group but our academic organiser (Prof Jim Haseloff) didn't like it because of possibility of working with animal tissues and containment legal requirements. Seeing it from today's perspective, I am glad we didn't do it, because it would have been even harder to get advisers for this.

My second idea was to make homoplasmy in chloroplasts easier. They have many copies of DNA and it takes ages to put our genes of interest into all of them. I wanted something which would actively insert our genes into all copies. In theory it should happen in a few hours instead of 2-3 months. This idea wasn't solely mine, I just said the first thought and others quickly added CRISPR/Cas9 molecular cutting tool into it. It was then taken forwards and it was relatively wise to choose something that people in our department can help us with. Despite the fact they didn't actually have time, which we were yet to find out. The first goal – choosing a project – was done.

We all got very excited for the idea. During the summer it shifted into making a whole toolbox for chloroplast transformation (putting foreign genes into the DNA of algal chloroplast, not the main genome). Some of our engineers have worked on their own challenges, building a do-it-yourself gene gun and incubator, others have turned into molacular biologists. We realised that managing relationships in the group was by far not the easiest part and sometimes was a cause of frustration. But it was a valuable life lesson of empathy and teamwork.

We have learned a lot from the literature in the first 4 weeks however we had a huge problem to take our project off practically. Our academic organiser didn't have much time because of leading his own lab and advisers were lovely and numerous but none of them had time to engage with the project beyond specific questions on problems encountered. Basically there was not anybody sitting with us for a while, pointing out obvious mistakes in our plans which we didn't have experience with and telling us that we can actually start and how to do that. So we have spent many days and nights designing our DNA sequences and then still needed to fix them when they came because the website was unclear. Moreover we got a bare lab so needed to manage orders of even the most basic consumables and finance, and get somebody to give us induction for all the techniques. Molecular biology is in that sense much less predictable and needs more leading from experienced professionals than the DIY hardware. Luckily, in the middle of the project we got one adviser inducing us into techniques and another who got involved time-to-time with planning and fixing our design mistakes. Since then the project moved on much quicker but constrained by the the lack of established grounds for chloroplast work and speed algae can grow (still much better than plants!) we had just one try for making it work.

But we tried hard, spent almost the whole summer in the lab and in the end put our project together. We found a way to present well what we have achieved and in the end I must say I was quite excited about what we have brought to the final Jamboree in Boston, despite we couldn't reach the results of well-led overgraduate teams working on something for even two years. The university term has already started when we were finishing our website and preparing presentation. It all sequestered a lot of our time and energy. Lovely times come when after 8-hour flight and 3-hour waiting at the border and solving the issues with the hotel, we finally got into our rooms, at 5am of UK time, and decided our presentation needed complete redoing, before we go to sleep.

However the Jamboree was amazing! We went to numerous presentations of other teams in the competition and I gained so much extra new motivation for the whole synthetic biology field! There was a lot of diversity, teams working on medicine, environment, foundational advance, hardware and much more, their projects taking between three months and two years, students of all ages and from all around the world. Some presentations were really amazingly rehearsed, some posters with beautiful design, judges nice and interested people and creating a great atmosphere. Many teams struggled more then us if they were coming from developing regions or didn't have access to lab and money. The Jamboree was the final drop in my decision that synthetic biology is the right way for me.

Finally, the project is over. We got a gold medal for it and a special prize for the best overgraduate plant synthetic biology project which was more than we expected. I would be very interested in actually finishing our homoplasmy idea which was too ambitious for three months, but for now, I am busy catching up with university work, getting good enough grades to build interesting future, applying for masters of PhD courses and starting new projects. I think I have gained a lot this summer and all the frustration had some valuable lessons for me. It was a real independent and truly our project, we got experience with many techniques including managing a whole lab. We were probably a little intruding when collecting advice and materials but also got a lot of contacts and nice experiences with people around our department and elsewhere in the UK. I went to my first real conference and a few slightly less official ones, given many presentations, documented, learned a lot about people and teams and got a few good friends (I am sure we will hate each other a little less when this term is over! :D)

If you are interested in our project, check our website here: http://2016.igem.org/Team:Cambridge-JIC

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