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Making (and breaking) it big: UW iGEM students and mentors lead the way in synthetic biology

Jan 2012 | Michelle 1,806 Comments

The 2011 iGEM team. Photo from the team website, by Joe Oh of the Daily.

This is the final article in a series on education and outreach at UW. Check out previous articles here and here


Think back on 2011.

What did you do last year?

Did you engineer E. coli to make diesel fuel? Or make an enzyme that breaks down gluten so well it’s hundreds of times more effective than what’s currently in clinical trials? Clone genes from deep-ocean magnetotactic bacteria and play with fluorescent magnet-sensing proteins in E. coli?

The 2011 University of Washington iGEM team did.

And when they presented this phenomenal work in synthetic biology at the iGEM Americas Regional and World Championship Jamborees this fall, they were named the grand prize winners of both. All in all, not a bad year for the team of 23 undergraduates, especially considering the grunt work was carried out during one summer.

“They get more done in three months than most graduate students do in a year—maybe even in their entire graduate careers,” says Matt Smith, an MCB student and mentor for the UW iGEM team during the past two years.

iGEM (that’s short for International Genetically Engineered Machine competition) started in 2004 at MIT and has rapidly grown to include over 160 teams from universities all over the world. The goal of the program is to immerse undergraduates in science that tackles real life problems with synthetic biology (building biological systems). And they don’t mess around. The competition regularly showcases a vast and impressive array of bioengineered technologies, from arsenic biosensors to bacteria that can count. In just a few short years, UW has emerged as a consistent frontrunner in the competition.

The UW iGEM team was founded by Ingrid Swanson Pultz, a graduate student in Microbiology who has mentored them each year since. The first team was made up of seven undergraduates and won a bronze medal at the end of the year jamboree. In the following two years, UW earned gold medals for their projects, last year winning Best Health or Medicine Project for the two different pathogen-killing agents they developed.

With this year’s team bringing home top awards all over again, it’s safe to say that UW is on a roll with this synthetic biology stuff.

Each year, the team gets started in January, Pultz explains. While most students are science and engineering majors, their background in biology varies, so the goal early on is to cover the basics of molecular biology (gene transcription/translation, cloning, etc.) so that they can begin brainstorming synthetic biology projects. “We don’t do an iGEM bootcamp here at UW,” says Pultz, although she notes that some other schools do. “Actually, a lot of the teaching comes from other students; they teach each other and help each other out.” In the spring, when students have a solid background, they scour the literature and begin proposing potential projects aimed at solving real-world problems. By summer, they’ve picked several projects and subprojects to tackle in the lab.

Summertime is crunch time. iGEM teams across the world receive “toolkits” of biological parts for engineering their organisms. The UW team sets up shop in whatever open lab space is available for the current year (which, the mentors note, is always a crucial factor; this year they were able to use Biochemistry department’s teaching labs). Working in teams, the students quickly become acquainted with the challenges of science: no guarantees, lots of failure, plenty of troubleshooting, and—with perseverance—a few successes. Maybe even great ones.

In the fall, iGEM teams give formal presentations of their work at regional jamborees, and the top teams advance to the international competition in November.

From the 2011 UW iGEM website

Each of projects that the UW team featured in its presentation this year is impressive in its own right. First, through genetic manipulation and a lot of hard work optimizing growth conditions, they engineered E. coli to produce the full spectrum of alkane molecules present in diesel fuel. Which means they’ve come up with a system for renewable production of fuel that’s compatible with our current oil-centric infrastructure. Not bad.*

The team didn’t stop there. They wanted to tackle the problem of gluten intolerance, for which the only current solution is adoption of a gluten-free diet. There is a therapeutic now in clinical trials—an enzyme that breaks down gluten—but it doesn’t work well at acidic pH (which, for a treatment that needs to operate in stomach acid, means there’s room for improvement.) The iGEMers combed the literature and learned of a protease isolated from acidophilic bacteria. The students reasoned that the enzyme should work well in acidic conditions, and when they it out on  gluten and found that it broke it down decently well. Using FoldIt (link http://fold.it/portal/) to guide them through mutagenesis experiments, the iGEM team reengineered the enzyme to work nearly 800 times better than the one in clinical trials, at the pH of stomach acid. (And they patented it.) Not too bad at all.

UW’s summer effort paid off so well that they didn’t have time to cover all of their projects** in detail in their presentation (linked here; UW starts at 1:08), which was appropriately dubbed “Make It or Break It: Diesel Production and Gluten Destruction, the Synthetic Biology Way.” The iGEM judges were thoroughly impressed, and UW was awarded the grand prize of the entire international competition.

Winning feels pretty good, says undergraduate Sydney Gordon, a senior in Biochemistry and one of the team members who presented UW’s work at the competition. “It’s been really satisfying,” she says, “we’ve been putting a lot of work in, and so it’s nice to have such a big payoff.” Along the way, though, the team members have gained skills outside of molecular biology: “I feel confident that I can give a good presentation, and that I can explain science to my friends and family.” (And to us; Sydney described the 2011 projects to me in vivid detail for this article.)

iGEM puts great emphasis on sharing science with others. Teams design websites detailing the year’s efforts, and they spend months honing their presentation for competition. In their “spare time” the UW team also made sure to give back to the community (or, in their words, “introduce people to the awesomeness of synthetic biology”), which included paying a visit to a Seattle grade school and simulating genetic engineering with hands-on activities.

Because tinkering with biology means generating new forms of life, iGEM teams are also required to address the greater implications of their work in terms of public safety: what would happen if their inventions escaped the lab? What will the environmental or societal impacts be? These are big issues to tackle, but as Pultz explains, it’s all part of “students learning to think about things for themselves.”

While the undergrads fuel every phase of the iGEM endeavor, guiding them throughout are a handful of graduate and postdoc mentors (along with the support of PIs who generously donate reagents, lab space, and expertise; this year, the Baker, Klavins and Sauro labs served as iGEM hosts). The experience of mentoring iGEM is radically different from typical grad student teaching requirements, in a good way.

Pultz emphasizes the differences between mentoring for iGEM and other teaching experiences (which she has quite a lot of—she won a teaching award through her department after TAing). Unlike lab courses, where every detail is planned and everyone, even the students, know the “experiment” will probably work, with iGEM “we have students doing research that we don’t know how to fix. There’s no guarantee that it will work. But it’s really fun,” Pultz says with a smile.

Speaking of how mentoring can benefit grad students, Smith says, “It’s what we came here for. We want to be able to one day lead a group in doing awesome science. iGEM gives us the chance to do that right now.”

Smith adds, “We get to be PIs, essentially. We help them with the projects, advise them on doing science. We become project advisors, and they get to do more science than they ever have in their classes, and they get to present to a wider audience than most graduate students do. Everyone moves up.”

Given the combination of brilliantly creative students and passionate mentors, it seems UW is ready to keep moving forward, and moving up.



The UW iGEM team is seeking new members for 2012. If you’re interested, please contact Aaron Chevalier at a.chevalie@gmail.com.



**They also had a lot of fun with genes from bacteria that sense and align with magnetic fields. Check out a video here.

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