CMU students compete in synthetic biology competition

Carnegie Mellon’s multidisciplinary approach allow s students from different fields of study to come together and work on projects. This past year, four students from the Carnegie Institute of Technology and the Mellon College of Science joined forces to participate in the International Genetically Engineered Machine (iGEM) Competition. The group enjoyed success at the regional level held in Pittsburgh and was selected as one of the four teams out of 43 to advance to the competition’s international jamboree this past weekend in Cambridge, Mass.

The team, which came together last October, consists of sophomore electrical and computer engineering and biomedical engineering double major Peter Wei; senior electrical and computer engineering and biomedical engineering double major Jesse Salazar; sophomore biological sciences major Eric Pederson; and junior chemical engineering and biomedical engineering double major Yang Choo.

Their instructors were Cheemeng Tan, a post-doctoral fellow with the Ray and Stephanie Lane Center for Computational Biology, and Natasa Miskov-Zivanov, an adjunct faculty member with the department of electrical and computer engineering.

The iGEM competition motivates students from around the world to develop projects in synthetic biology. Pederson explained it as “projects that take parts from different organisms and mixing them to get what you want qualify."

After spending a month exploring different project ideas for the competition, the team settled on a project that expanded on work researchers at Carnegie Mellon had already briefly explored. After securing lab time in March, the team finally got to work. Their research aimed to quantitatively measure the a cell’s amount of a protein that was discovered at Carnegie Mellon.

Pederson explained the science behind what their project aimed to accomplish: “Promoters are regions in our DNA that have regulatory functions that can impact what goes on inside our cells.” DNA codes for tens of thousands of proteins to be made by cells, but only a select number of these proteins will be made by the cells at any one time. The controlling factors are these promoter regions which act as on and off switches that tell the cell when to make or stop making a protein depending on if it is needed or not.

In modern biology, researchers incorporate and manipulate promoters in cells to increase or decrease the concentration of specific proteins to force a certain change within the cell. Pederson compared promoters to the engine of a car in “how a mechanic wouldn’t want to put a Hummer engine inside a Prius because it would destroy the chassis.” Similarly, a scientist wouldn’t want to use the wrong promoter to force a specific change in the cell because it might cause the wrong proteins to be made and cause the cell to die.

Once they had decided on a project, Tan and Pederson collected data through fluorescence microscopy, where certain dyes bind to proteins and glow. This allows researchers to use microscopes to measure the amount of dye present and subsequently determine how much protein is present in the cell. Wei explained that he used the data to “develop a quantitative measure using time course curves that pinpoint when all the dye has binded to the proteins in the cell.”

Currently, researchers can perform experiments such as Western Blotting and use protein purification techniques to collect the proteins in the cell and measure their concentration. However, these techniques require breaking open the cells to collect the proteins. The quantitative measures that the Carnegie Mellon iGEM team developed to measure utilized promoters and dyes didn’t require killing the cells; Pederson believes it “can save scientists a lot of extra work, time, and money.”

The multidisciplinary project allowed team members from a variety of backgrounds to get involved and contribute to its success. Wei said that before joining the project he had a small interest in biology, which motivated him to get involved. He felt that joining a project like this “was the most effective method to getting into a field you know nothing about.”

Both Pederson and Salazar felt that “the competition was just a prologue” and they felt very proud of how much they had already accomplished.