Team:KULeuven/Evaluation

From 2008.igem.org

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Our road towards the golden dream ...

At the end of a project people often tend to look only at the results. But the road towards these results is just as important, especially if other students will discover the same path next year. Therefore we want to reflect on our obtained results and the path towards them.

During the summer period we divided our team into two major groups: a lab team and a modeling team. The work in the dry lab resulted in an extensive model of our full system. Building the main model backbone was finished during the first six - seven weeks. During these weeks the model was gradually built and updated several times. A lot of time and effort was put into searching the literature for biologically relevant values of all parameters. There were a few parameters where we couldn't find any values, in those cases we had to make an educated guess. We made sure that even in those cases there were references to papers and sources that allowed us to make these estimates. Every subsystem was extensively tested and simulated before we connected them to each other. This was very tricky because every part had to be in tune with the others and tinkering with one part often messed up our entire system. Hereafter we further investigated the diffusion of HSL into the medium and the effect of multiple cells on the behaviour of a single cell. This resulted in one of our own written software tools: a multi-cell toolbox. During the entire summer, our modeling team made a beautiful wiki on which our progress and results could be consulted at any time: we've been working as "open source" as possible.

While the modeling team was busy building and simulating Dr. Coli, the lab team was trying to connect the different BioBricks. Unfortunately, our lab team was very often withheld from a fast progress:

punching the bricks: We punched a lot of BioBricks and transformed and electroporated many cells with the DNA from the distribution binder, but we couldn't grow any cells. Apparently the DNA concentration on the paper was too low. When we received a glycerolstock of the DNA from the iGEM HQ, this problem was solved and we could start.
ligation problems with BBa_B0015: In the beginning we cut BBa_B0015 with XbaI and EcoRI. It appeared to be impossible to ligate this part to another one. When we tried to ligate BBa_B0015 that was cut with XbaI and PstI, this was successful.
adjustments by the modeling team to the DNA sequence of different subsystems: While the modeling team was building the model, they often saw by simulations a malfunctional subsystem. This resulted in many changes of the DNA sequences of the different subsystems. A good example is the memory. Our first memory would probably have switched automatically from state zero to state one, which would make it completely useless. This resulted in a totally new memory system.
Many ribosome binding sites were upregulated or downregulated. All these changes made many ligations useless and a lot of work had to be redone. This was the main reason the lab team couldn't keep up with the modeling team. But we did not have any other choice then to carry on with the work, because we had a very ambitious project and only 3 months time... As an advice for the team of next year, we recommend to start modeling as soon as possible so that changes to the system don't lead to too much useless work.

Despite these obstacles, the lab team could finish different parts which resulted in some great biobricks.

We created 6 new parts:
- GFP-LVA (BBa_K145015)
- T7 RNA polymerase (BBa_K145001)
- T7 RNA polymerase with UmuD tag (BBa_K145014)
- Antisense LuxI (BBa_K145013)
- Hybride promoter (BBa_K145150)
- CcdB (BBa_K145151)

We created 4 devices:
- input (BBa_K145201)
- output (BBa_K145205)
- reset (BBa_K145300)
- invertimer (BBa_K145302)

We characterized the GFP-LVA (BBa_K145015), the input (BBa_K145201) and the output (BBa_K145205).

We introduced a new concept: A filter mechanism that filters out background signals. It is based on a mechanism that also exist in nature: a coherent feed forward loop with AND-gate.

When it comes to the iGEM judging criteria, we believe we have fulfilled many different requirements like submitting the physical DNA of a new biobrick: GFP with a LVA-tag. Furthermore this biobrick works fine and has an experimentally proven faster degradation rate than GFP without the LVA-tag. Based on these experiments we could even characterize the biobrick by determining its degradation constant. Besides these lab criteria we also made an effort to make a contribution to the world of Ethics and Human Practices in synthetic biology by outlining and detailing an issue about these two subjects related to our project. Our approach is based on the Three Laws of Robotics formulated by Isaac Asimov halfway the twenthieth century. We were also proud to see some of our wiki-tools show up on other team's wikis. Based on all these facts, we started dreaming of a golden medal...

Personal Evaluation

Maarten

A once in a life time opportunity broadening my view in different aspects

As a civil engineer, I started this project without a precise view on the work I was expected to do. It was a step in the dark. At the end, I can say that this once in a life time opportunity, has broadened my view in many aspects:

Till now I've only modelled based on the "black box system"-principle. This was the first time in my student carreer that I helped building a white box model based on biological laws.
This project was a nice introduction into the world of synthetic biology which was unknown to me.
Working in a team with people form very different backgrounds is very representative to the real world. This experience will certaintly help me in my future working career.

As you can see, I'm glad I joined the project.

Nathalie

Being a chemist who also took some biochemistry courses and who is interested in about anything scientific, this project really fascinated me. I was thrilled at the thought of working on a scientific project for one summer. And it didn't disappoint me. The whole thing of synthetic biology, the brainstorm to find and deepen our project, the working in the lab, the interactions with the modeling,... it was all very interesting. I have learned a lot in those three months, especially about the broad field of synthetic biology.

But what I loved the most was the multidisciplinarity of the whole project. I would never be able to do all that modeling and IT stuff (wiki, designing logos,...) myself. I probably wouldn't even like it - I want to be in the wet lab from time to time. Although, I daresay, I was a bit jealous of the excellent results of the modelers. But eventually, after a long period of hard labor, the wet lab also produced some results. And there's another thing I've learned - having patience is essential if you work in a wet lab.

Jonas

As a more modeling-aimed biochemist I've had the privilege of finding myself as some sort of corpus callosum ;) between the lab hemisphere on one hand and the modeling hemisphere on the other. This allowed me to fully enjoy and assist in the fantastic things that happened on both sides of the brain/team. Communicating between fields and keeping both teams on the same track was truly a very fulfilling experience.

I also liked the many brainstorming sessions we had and spent a lot of my exam-time on the wiki brainstorm section. Creating genetic circuits with the desired properties by puzzling with genetic bricks allowed me to, fully and in an extremely creative manner, employ the things that I had learned during my education. It felt great to put this knowledge into practice.

The thing that I will carry with me the longest however was the experience of working in our multidisciplinary team. 11 incredible people with completely different backgrounds combined and, as we say here, 'all with their noses pointed in the same direction'; creating one hell of a project.

Andim

This project gave me the opportunity to discover the big world of synthetic biology, which might become my own research area in the future.

Through the whole summer period we worked hard to realize our dream, our project. Especially during the first meetings we had, I had the feeling for the first time, that we as students had the chance not only to bring up new ideas but also to make them come true.

During the project, I worked mainly in the wetlab. It was a real challenge to get the expected results. We had to be patient enough to reach them. Eventhough sometimes we felt down, we never lost our motivation.

I believe we succeeded most of our project in the best way we could. I am proud and happy that I could contribute to that.

Jan

Earlier this year I got to know of "synthetic biology". The concept of building up your own biological system from basic biobricks immediately appealed to me. Also the idea to be part of the foundation of a relatively new discipline, that has gotten a burst of growth and attention the last years, seemed very exciting to me. Working at this with people with different skills would only contribute to a great project.

As I'm a bio-engineer, I was mainly occupied in the wetlab. In the beginning we had some failures to work through though. But we learned by experience and advice from our advisors and later on we circumvented or solved our earlier problems. The experience I acquired during those summer months was inexpensible. As our system was very big we didn't succeed in completing everything, neverthless we got a great lot done and working.

At the start I thought the modeling people would have a pretty difficult task as the modeling of biological systems is also relatively new, so I could only be in awe for the great job they did in generating realistic models.

Last but not least, it was a very enriching experience to work with an interdisciplinary team with such great and motivated people. I really learned things from everybody and everybody found something to do which he or she was comfortable with. Now I'm looking forward to the jamboree in november which will be the cherry on the cake we baked together.

Benjamien

When I first heard about iGEM, my first thought was:

I want to contribute to this fascinating science and compete in this interesting competition!

And look, here I am. For me, this summer was an amazing experience, and I hope the adventure is not over yet. Not only a window on molecular biology and gene technology was created and my problem-solving abilities were sharpened in the synergy that arose between the engineers and me, a scientist.

I hope to learn a lot more at the Jamboree and I hope that our team achieves a nice result there.

Stefanie

When I first heard about the project, I was thrilled. It was something I really wanted to contribute to. It was a great opportunity to get working experience in a real-life wet lab.

My main contribution to the project as a bio-engineer was building our Dr. Coli in the wet lab. Together with the other team members we were able to work out our concepts in a real living organism. I was extremely happy when the first fluorescent colonies were grown. We actually succeeded to build our own theoretically engineered system inside a bacteria!

During the project I not only learned about the technical stuff directly linked to our system, but also a lot about myself. I'm now sure, more than ever, that my place is in the wet lab. I just love to be there and hopefully I will get the opportunity to do research in the field of synthetic biology.

Working with people from different backgrounds was challenging in the beginning, but at the end we ended up as good friends. Thanks to all of you for this great summer!

Hanne

Months ago, in June, when we were discussing what we wanted to do this summer, I was a bit worried how twelve people with such different backgrounds ever could work together. Don’t get me wrong, I was very excited about working in a multidisciplinary team, but I wondered how we could come to a symbiosis between wet and dry lab. After a few days I discovered that my worries were completely misplaced and I started to feel at ease within this diverse group.

In the very beginning we had some brainstorms on what our project would be, and to my great surprise, I was one of the founders of Dr. Coli. Somewhere at the end of one of those meetings, I got the wild idea of a bacteria that could produce and regulate its own drug-production. The rest is history, as four months later, we’ve managed to create our Dr. Coli!

As a biochemist I was really excited to get the chance to extend my lab skills and learn more about being an actual member of an exciting research. We had to cope with some great disappointments but luckily we achieved some new things too! It was nice to know that we weren’t on our own, as we could discuss our progress with our advisors during weekly meetings. They guided us and gave some practical guidance when we encountered difficulties. At the end of our period in the lab, I alternated my work overthere with some research on human practice and ethical aspects of synthetic biology. It was very interesting to get in touch with those problems, as when you are working so hard in the lab it is sometimes hard to think about the possible consequences of your work.

It was nice to see that the twelve of us, although so different, really started to form a group. Now I’m really looking forward to the Jamboree, it will be a nice ending of an amazing experience!

Elke

In the three months we worked together, I have gained a lot of respect for my team mates. All the things like modeling, building the wiki, engineering our bio-brick scheme, engineering primers,.... are all things I tried to help with, but other members of my team are a lot better at this because of their different background. But I watched, listened and learned a lot of them.

As a bio-engineer, I spend most of my iGEM-time in the lab. It was very nice that we could do everything ourselves. The first month was a bit disappointing because the transformations and elektroporations didn't succeed. But then, things started to go well and we went wild when we had fluorescent colonies for the first time. It's an amazing feeling when an experiment you worked very hard on gives a good result.

Nick

At first I saw iGEM as a unique opportunity to get in touch with the latest scientific hype: synthetic biology. As a student in Mathematical Engineering it would be a real challenge to model something I've never done before: molecular biology. I also thought of it as good experience for my engineering career: learning to work with many people from different backgrounds to reach an extraordinary goal.

During the project I learned that there's so much that you aren't taught in university and there's still an enormous amount of knowledge out there, that was so new to me. I got to know the basics of molecular biology and learned to think in terms of transcription speed, dissociation constants, complexation reactions, ... All this was needed to build a realistic model of our project: Dr. Coli. Hundreds of simulations were run to check the working of our model, to analyze the results, to optimize our scheme. At the end of the summer, we reached our goal and delivered a working model with several simulations of Dr. Coli.

When I look back to this summer @ KUL I can truly say that it was a rewarding experience that it has taught me many things and hopefully we can win some prizes with our Dr. Coli!

Antoine

Unaware of a large portion of biological concepts, I must say it wasn't that hard for me to work throught this project. IGEM embraces the spirit of bringing together distinctive disciplines and have them cooperate. Though my work was primarily restricted to modeling and IT-management, I got a taste of the real lab work. It was an experience worth trying and gave me a deep understanding in how our wet lab people had a tough nut to crack, given the vast complexity of our system on a biological level.

Looking back, I believe as a civil engineer I got the opportunity to give my input towards the final model, meaning modeling isn't just an add-on in synthetic biology, but is capable of pointing out fundamental errors when it comes to functionality and behaviour of biological systems. I had memorable times working with biochemists and bio-engineers, in the end, we wouldn't have pulled it off without them, they truly formed a bridge between the wet and dry lab.

In total, I got to taste the ideal world of modeling, the challenging task of working in the lab, and the more creative side of helping out with the wiki. Not to mention I've discovered a whole new array of delicious sandwiches, during the many many days we've spent on this project.

Dries

Working on this project with people how have different scientific backgrounds, was a fantastic learning experience. As a physics engineer in nanotechnology, my background in biochemistry is really basic but by modeling this system I have gained some new insides and I am happy to have been able to contribute to this project any way I could. I’ve enjoyed working together with everyone from the team and I hope we’ll get some prizes in Boston.