Friday, November 15, 2013

Impressions from iGEM WCJ 2013

The International Genetically Engineered Machine competition, or iGEM, is an annual event in which teams of undergraduates compete to develop the best synthetic biology project. Their results are presented, and prizes awarded, at conference events dubbed iGEM jamborees. 

The iGEM 2013 event featured hundreds of teams. After qualifying at regional jamborees in North America, Asia, Latin America, and Europe, many teams converged at the Stata Center in MIT between November 1st and November 4th for the World Championship Jamboree.

I attended (as a volunteer) the Championship Jamboree this year. It was a great experience, and is something I recommend to anybody that is interested in the field of synthetic biology but cannot themselves join an iGEM team. In the rest of this post, I will share my impressions of the Jamboree and highlight some of my favorite teams and projects from this year.

If you are interested in learning more about all of this year's projects, and see their presentations from the World Championship Jamboree, you can visit the iGEM 2013 livestream channel for archived videos. HD videos and other files (including photos) should be or will be available on the main iGEM website. (For example, the finalists and medalists presentations are available, both video and poster files).

What do you think about iGEM, and which team or project was your favorite? Please share your thoughts in a comment below!

Note: I do not own, or claim any rights to, the official iGEM logo shown above; it was taken from

Overall Impressions: 

I had attended iGEM once before, back in 2006 (as a spectator, not a participant). This was one of the first iGEM competitions, and it is impressive to note how much the even has grown since them. While I enjoyed the 2006 Jamboree (there was only one that year; no regional events), the projects were more ambitious and exciting this year. This is to be expected, of course, since teams can build upon the work presented in previous years. Despite having only a summer to complete the work, the ability to use bio-bricks from their predecessors allows many of these teams to successfully execute their designs and achieve the aims of their project.

Most of the presentations were delivered with style and enthusiasm. In fact, some of the teams opened with a sort of sales pitch, at times directed to the judges specifically. At the risk of over-hyping their results, this presentation style was a breath of fresh air. Far from the often dull talks found in academic halls, these presentations were energizing and can captivate a wide range of audiences. This last point is particularly important, since the synthetic biology teams are composed of people from various backgrounds (molecular biology, engineering, computer programming, and even a philosopher). My lovely girlfriend, who does not share my scientific background, also volunteered for the event. Even she was engaged by these teams and their presentations, appreciating both what they have accomplished and its significance. 

Several of the people I talked with at the event shared the opinion that the presentations, and the entire field of synthetic biology, is to some extent over-hyped. However, this was not a reflection to them of how important synthetic biology will be in the future, but rather for how it is discussed and presented today. It was interesting to see this admission, and it is one that I partly share myself. For example, the novelty of standard assembly of bio-bricks is/was over-sold; this technology is not a breakthrough innovation by synthetic biologists, but rather an application of well known restriction enzyme cloning technology. Despite this, the potential of synthetic biology, rather than the technical details, deserves any and all the hype it commands. 

Finally, the focus of the projects has evolved from 2006 to 2013. While some projects are still somewhat whimsical demonstrations of technical prowess (which are themselves important for advancing the field of synthetic biology), many of the teams successfully completed a project that have serious commercial applications. In fact, these teams often presented economic analysis and even a business plan to demonstrate how their innovations can be used in industry to solve real world problems. In the following section, I highlight some of my favorite teams and projects, many of which had commercial potential.

My favorite teams (that didn't win)

It is hard to select just a few teams to highlight, since so many of the projects were compelling. Indeed, I was impressed by the gold medalist team from Heidelberg, who introduced an important innovation: a standard way for arranging non-ribosomal peptide synthetases (NRPS). The diversity of building blocks for non-ribosomal peptides are orders of magnitude higher than the 20 natural amino acids  used in translation. 

Below are some of my favorite teams that did not receive a medal, or at least did not place in the top three. Nonetheless, I found the presentation exciting, and the project was both interesting and impressive.

UC Berkeley: Blue Genes
The team from Berkeley engineered E. coli to produce a soluble form of indigo, as well as the enzyme needed to convert it into the insoluble dye form. In short, they generated a (relatively) business ready technology to dye blue jeans from growing an E. coli culture, instead of chemical treatment of molecules found in oil. This was a great project for a number of reasons. First, the project was straightforward application of synthetic biology to an industrial problem, and one in which effect of the engineered organism should not pose any risk concerns to human health. Second, through the course of the project the team actually characterized a new protein sequence (so a bit of basic science was mixed in!). Finally, during the presentation, a piece of cloth dyed with E. coli produced indigo was passed around. I can attest to the fact that it was indeed blue!

UNITN Trento: B. Fruity
Most people are familiar with the plant hormone ethylene, even if they don't realize it. This gas is produced by plants and fruits, and causes fruits to ripen quicker. Many fruits are harvested before they are ripe, and then made to ripen on command by exposure to the gas. This is also the reason why placing an apple with other fruit in a paper bag will cause them to ripen faster (the gas builds up inside the bag). The Trento team exported the ethylene production pathway from plants into Bacillus, engineered it to be induced by blue light, and dubbed the resulting microbe Bacillus Fruity (or B. Fruity). In addition, a version that produces the chemical MeSA, which slows down the ripening process, was also created. The group imagined two different ways such microbes can be used; in a specially designed bag or in a fruit vending machine. Most importantly, it provides a way for the consumer to command the production / application of ethylene at home, without the need for large and dangerous industrial tanks of the gas.

UIUC Illinois: Cardiobiotics
Several of the teams this year focus on engineering a more beneficial probiotic. The team from illinois focused not on digestive health, but on cardiovascular disease by introducing a probiotic that can alter the metabolism of L-carnitine, a metabolite associated with increased risk for atherosclerosis. By using a proven probiotic chassis, E. coli Nissle 1917, the group also mitigated some of the safety concerns and risks associated with such an application (although for human consumption, strict measures of safety and efficacy must be met). Considering the prevalence of cardiovascular disease, and a unwillingness by some to reduce their risk factors by modifying their diet, a cardiobiotic may eventually be the answer (or at least part of it).

University of Alberta: Map Men
This project was an exercise and demonstration in the power of biocomputing. In brief, the team developed two different strategies for biological based computation of the optimal path in the traveling salesman problem (a classic problem in computer science / programming). In both, the initial constraints of the problem was reflected in the initial concentrations of DNA fragments or oligos used; the most common DNA construct recovered represented the optimal solution to the problem. Arguably the most impressive feature of this project was the ability of this biocomputing strategy to outperform normal computation of the solution (i.e. using a computer) when the problem was scaled to be more complex. 

Which iGEM team was your favorite? Please share your thoughts as a comment below.

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