fredag 5 november 2010

The first days at iGEM Jamboree, Cambridge MA, hosted by MIT

Let me tell you what happened these two days.

I flew with Antonio to Boston via Amsterdam. The landing at Amsterdam felt extremely dangerous. It started with the wings shooting two jet streams from below the wings; next you knew, the plane started to bounce randomly like it was caught in a turbulence. Well one could've believed it was indeed turbulence, before seeing the plane was actually 50 m above the ground, at most. Then came the landing. The first touchdown pushed the plane right back into the air, like an athlete's final step on the ramp when doing the long jump. Fortunately, this time the athlete didn't fall over. It was the worst landing I ever experienced.

The flight to Boston from Amsterdam had its AC turned a bit too low. I couldn't help my runny nose. Once we landed, Antonio was "random selected" by the border control. I waited for him outside, and he was angry why I didn't try to find him. Well, I said, if he got sent back to Europe, I don't wanna follow him by claiming to be his friend. The road from Logan airport to Hyatt Regency in Cambridge was long and painful. The hotel turned out to be 15 min from the nearest public transport and food. So strategically located, I thought. Now you have no choice but to buy their expensive food, like the 20$ breakfast buffet.

On Friday, me and Antonio got ourselves haircut. I also bought the iPad for my friend, draining my HSBC bank account almost empty. In the evening we tried to practice the presentation at MIT, and saw another group having their presentation. To our horror, our presentation lacked a lot of information. We spent hours correcting them all. Today we finally got over with the presentation. It was alright.

Actually it was not "alright". One day ago, I thought that me, Antonio and Hsin-Ho are the only ones representing Uppsala. However, Bing and Imityaz got their US visa approved last-minute. The pity was, Nagarjun who made the modeling couldn't come. We convinced Bing to take part of our presentation. Imityaz was persuaded into explaining the modeling. And he got so nervous during the presentation that it was almost funny to watch. When being asked a question that was expected to come from the judges, he tried to point at the huge screen 30 meters away with his fingers. I'm not saying my part was flawless either. I got a bit high in the midst and dragged out my part like always. If things stopped there, then we would've thought our presentation was "alright".

When the next team took over, we were totally stunned. At least I knew I was.

Imperial College London tried to create a biosensor for fast detection of Schistosoma parasite. It was done through a simple protein-protein interaction mechanism. They incorporated engineering designs and modules into the project, something Prof. John March at Cornell also taught me. The most scary part was, by the end of their presentation, they showed a "prototype" of their biosensor. Actually it was just a fake prototype, a wooden model showing how the product should look like. With their over 50 slides, we wondered how they could keep the presentation to less than 20 minutes. When I saw how the guys were alternating paces from fast to slow to fast, I realized how much they must have practiced the entire speech and timed it perfectly. Maybe they even planned ahead as much as knowing which minute shall finish with which slide. Their over 50 slides finished almost exactly on 20 minutes. My first impression of the overall project along with its presentation is summarized in one word.


Yes flawless indeed.

Compared to Imperial College London, our presentation looked like a pathetic attempt to sneak into this prestigious International competition. It was like a kid showing the mother the first poem he wrote, while your brother just composed something Shakespeare-ish. We looked like a bunch of fools.

After the break, an even stronger Cambridge showed up. They submitted 20 parts, recorded stunning footage of what their genetic product was capable of, and wrote a RFC for future BioBrick standards. On the way to Jamboree, they wrote three biochemical calculator and file conversion tools. Other than software, the Cambridge people even invented a device for bioluminescence measurement. The Cambridge team of iGEM 2010 is pure awesomeness.

After all the presentations, it was poster session. To cut the diary short, I'll just explain what I found out about the other teams. Things that the future iGEM team of Uppsala should know about.

Rumor say Heidelberg ran a 4 million SEK project. Each member gained 20 000 euro for completing iGEM, and they have 20 members. Uppsala's budget is around 2 % of theirs. Heidelberg's studies involved testing of viral strains on mice, which in itself is expensive enough.

Slovenia submitted 151 new parts to the registry. They won iGEM twice already. Uppsala this year: of the 6 parts to be submitted, only 2 got submitted.

Cambridge got most of their funding directly or indirectly through the university sector. One of their advisors is a lab director with extensive connections to the biotech-industry (my guess is he's Gos Micklem). He could personally get all the sophisticated equipments borrowed from companies to campus for wetwork over the summer. Our lab certainly didn't have all the equipments, nor the same kind of connections.

BIOTEC Dresden came up with a smart reporter system to normalize the fluorescence expression to a reference. They made a construct where the expression of YFP is induced; on the same construct, they inserted a constitutive RFP generator, using the red fluorescence as the reference value to the yellow fluorescence. The result was great. Apart from the companies they contacted, the university department offered them frequent and free sequencing. The Rudbeck lab at Uppsala was such a bitch about sequencing and getting the primers. While they agreed to sequence our construct, they did not want to make the necessary primers for us. So we had to ask some company to make our primers. In the end there was so much hassle that we never sequenced anything.

Imperial College London had all the company contacts taken care of by the university administration, as well as all the lab equipments. Furthermore, they received money for working and living over the summer.

Students from UCL had to contact the companies on their own, as told by a person from Imperial College London.

Chris Andersen of Berkeley is a judge at iGEM this year. His students worked on a cool project, and an open source program called Clotho. A super-senior of the Berkeley team told me how good it is for coordinating group works in synthetic biology. Uppsala students used Google Wave. The useful information was easily drown among the useless information. Mostly it wasn't up-to-date.

It seems like Cornell did something relatively trivial this year, they used a few somewhat non-conventional fluorescent proteins so they could contribute to the parts registry. We should have submitted all our intermediate parts, if they weren't in the registry already.

That's all for now. Tomorrow I'll check out Slovenia, UCSF, MIT, Harvard and some other big shots in this field.

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