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November 19, 2009

Gold, silver medals for UW teams in the International Genetically Engineered Machine competition

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You could call it a Lego competition for the biological sciences.

To those in the know, it’s called iGEM, or International Genetically Engineered Machine competition, which challenges undergraduates to build novel biological systems that actually operate within living cells.

A UW team of five undergraduates, four graduate student advisors and one faculty member, received a gold medal for its work, most of which occurred in UW laboratories throughout the summer.

A second UW team was composed of one undergraduate student, an 11-year-old unmatriculated UW student, and a group of advisers. That team, which was focused on software, literally did use Lego pieces to build a device to replace expensive lab equipment for assembling biological parts.

This is just the second year the UW has participated in iGEM. In their first year, students garnered a bronze medal. This year’s results, along with the teams’ entries, can be viewed online here. The iGEM Jamboree, the culminating event of the competition, took place Oct. 31 to Nov. 2 at MIT.

Faculty adviser to the first team Eric Klavins, associate professor of electrical engineering, summarizes the goal of iGEM as “getting bacteria to do neat things.” In reality, undergraduates are performing genetic engineering experiments that, a generation ago, were considered exotic and required expertise in a number of disciplines. Now, the technical job of modifying the genetic components of bacteria is done according to well-developed recipes. “This is very well worked out, and many of the tools that the students are using actually come in standard kits,” Klavins says.

Teams that want to compete for the top prizes are encouraged to set lofty goals. This year’s grand prize winner, from Cambridge University, developed a system for determining when a water sample is contaminated, by developing bacteria that would turn various colors to indicate which contaminant was present. This system could be used in remote locations that are unfriendly to sensitive and power-hungry precision instruments.

“The iGEM competition stimulates research in synthetic biology, no doubt about that,” says Herbert Sauro, associate professor of bioengineering and adviser to the second team. “There are so many ideas that come out, you can’t avoid getting some really innovative concepts. You get these things that people [in the research community] would say ‘Oh , you couldn’t do that,’ but then you get these young things trying and they get halfway there.”

The undergraduates on the first UW team — one junior and four seniors — came from biochemistry, bioengineering, physics, and molecular and developmental biology. A background in the biological sciences was not essential for participating on the team. Indeed, the only UW courses that address the emerging field of synthetic biology are in engineering. This makes sense, Klavins says, because synthetic biology is based on taking standardized parts and putting them together in living systems — in the case of iGEM, those living systems are usually bacteria.

The second team was dominated by a surprising force, Gabriel See, an 11-year-old who is currently taking an advanced course in mathematical biology and has been working with UW mentors since he was 8 years old.

“He’s quite interesting,” Sauro said. “He would show me his calculations because he was doing three-dimensional trigonometry to figure out how to control the two motors to get from one part of the plate to the other part of the plate. It was quite sophisticated mathematics.”

See’s team ended up earning a silver medal. You can watch him demonstrating the Lego device here. The iGEM contests began in 2003, and each year the standardized parts developed by participating teams are entered into the Registry of Standard Biological Parts — very much like a hardware store for synthetic biology. The registry now boasts about 5,000 parts. Every team entering the competition is given about 1,000 parts as kind of a starter kit, although teams are not limited to using only what they are given, nor are they limited to items from the registry. As part of the project, each team usually ends up making five to 10 new parts, which become part of the registry for following years.

“This centralization, standardization and interchangeability of genetic parts is the key piece of technology that allows undergrads to play around with very advanced genetic engineering projects,” says Justin Siegel, a graduate student advisor in biochemistry.

For example, last year one team developed a part which, when inserted in a bacterium, caused gas bubbles (technically, they’re called vesicles) to form. This year, another team hooked up this part in such a way that, when the bacteria encountered arsenic in a water sample, the arsenic was picked up by the bacteria, which produced a gas vesicle and floated to the surface, where it could be skimmed off, thereby removing the arsenic from the water.

“The iGEM competition is a fantastic learning experience,” says Ingrid Swanson, a graduate student in microbiology. “It’s not just great for undergraduates, but also for graduate students, who learn how to organize and lead a team.” It was Swanson who was the inspiration behind the first iGEM team. “It sounded like a lot of fun,” she said, so she began putting together a team of advisors and willing faculty members, including Klavins and Sauro.

This year’s first team was selected and began meeting in the spring and, with the help of graduate advisors, selected a suitable project in the “wet lab” category.

Their project was to find a simpler, quicker way to purify proteins. “Many enzymatic reactions in industrial processes, and most research in biochemical labs, require pure proteins,” says Siegel. “We still use the same steps for isolating proteins that have been in place for over 20 years. The process has approximately 12 steps and takes about four hours for a skilled worker to complete.” The goal was to use a new method which, by genetically modifying bacteria, could help isolate proteins in about ten minutes with no highly specialized equipment.

The students divided the project into three phases and each team began working in the lab by the end of Spring Quarter.

One of the most important lessons they learned was to be thorough and methodical. For example, it turned out that one of the off-the-shelf parts from the registry did not perform as advertised, so they spent a great deal of time describing the characteristics of this part and why it failed to meet expectations. It turned out that this incidental “discovery” was one of the team’s more significant findings.

The team members realized time was short. They could be found in the labs early in the morning and late at night any day of the week, including weekends.

Still, when their deadline came, they had not reached their goal. It turns out that very few teams actually achieve their objectives, Siegel says. “There’s a good deal of luck involved.” Even so, the entire team, including advisors and faculty, was energized by the experience. The gold medal award was based upon meeting a specified number of benchmarks in the overall process.

“The students grew so much,” says Swanson. “If they had had more time, the project could have worked.” Klavins commented, “If I had the money I’d create 10 iGEM teams.”Already, there have been positive results from the competition. All graduating seniors from last year’s team have had their career choice influenced by the competition — two are now working in synthetic biology laboratories — while an electrical engineering major is now employed in an immunology lab. And all of this year’s team’s seniors are applying to graduate school in synthetic biology.

“I’d love to have more faculty from more departments involved in coming years, and I’d like to recruit students who are as young as possible, so they can stay with the competition for a number of years,” Klavins says. “Eventually, we’d like to build the base for a synthetic biology program at the UW.”

This year’s iGEM teams received financial support from the departments of Electrical Engineering and Bioengineering.