Students prepare for final round of bioengineering competition

Students from UC Berkeley will have the opportunity to pit their animation software-created simulations of molecular processes against those of other teams in the world championship of the International Genetically Engineered Machine competition to be held from Nov. 5 to 7.

The UC Berkeley team’s project focuses on engineering artificial biosensors and inserting them into bacteria, according to Terry Johnson, a lecturer in the UC Berkeley department of bioengineering and an adviser on the team. The team is heading to the championship after advancing from the Americas Regional Jamboree — held in Indianapolis, Ind. from Oct. 8 to 10 — with 26 other teams.

Students on the team, which is made up of seven undergraduate researchers and three advisers, have been working on the project since June. Teams have access to a registry of DNA “parts” that teams in past competitions have designed and uploaded to the database. The parts are interchangeable and can be used by teams to address various life sciences problems, Johnson said.

“Students spend the summer working on a synthetic bioengineering project, many making use of the registry of parts,” Johnson said. “What that is is if you design a part, you upload it to iGEMcentral — that way you build up a database and people draw on that. If you’re forming a new team, you can search the database and use parts to tackle problems — the problems are all over the map.”

Team Berkeley decided to focus on engineering artificial biosensors. While numerous biosensors are found naturally in bacteria, the team was interested in having bacteria serve as a notifier for scientists, Johnson said.

“There are plenty of biosensors in bacteria naturally, but you might want biosensors in bacteria to react to something it might not normally,” he said. “We’re currently working on an estrogen biosensor. Groundwater that has been polluted with estrogen could be engineered so that biosensors react to it, which would notify us. It’s something that has a variety of uses, both manufacturing and environmental.”

Though the team started out with a number of different biosensors, it has been focusing on the estrogen biosensor as the championship approaches.

“Estrogen is what we’ve done the most work on and is most developed,” said Gabriel Lopez, graduate student and an adviser on the team. “We still need to figure out some details to make it work the way we want it to.”

Team members were pleased with their performance at the regional competition, where they were awarded best poster for their informational graphic and given a gold medal.

“We’re really happy with the results so far,” said Chris Anderson, an assistant professor in the UC Berkeley bioengineering department and an adviser on the team. “We’re hoping we’ll have some extra results (in the final round) that will make us real contenders — we’re really psyched.”

In order to convey the project in an easy-to-understand manner, the team turned to Maya, an animation software developed by software company Autodesk that is known for being used in the last 16 movies that won the Academy Award for Best Visual Effects, to create simulations of the relevant molecules and bacteria. The software was made relevant to teams participating in the competition thanks to a molecular plugin — called Molecular Maya — tailored for biovisualization, the visualization of biological systems.

“We have actually a pretty cool animation,” said UC Berkeley junior Miriam McQuade. “We’re pretty excited about them. They’re beautiful.”