Multidisciplinary Student Team Advances to iGem's World Championship Jamboree


October 25, 2012

A team of CIT and Mellon College of Science students believes that building blocks can be turned into a biosensor to measure cellular activities. Based on their performance at the International Genetically Engineered Machine (iGEM) Competition's Americas East Regional Jamboree, held earlier this month at Duquesne University, they're well on their way to proving just that.

Using a kit of interchangeable biological parts and a fundamental knowledge of synthetic biology, the CMU students created a biosensor that can measure cellular activities. Not only did they win a gold medal and prize for Best Biobrick Measurement Approach at the Pittsburgh event, but they also earned a spot as one of four regional finalists (from a field of 43) that will move on to the World Championship Jamboree Nov. 2–5 in Cambridge, Mass.

Synthetic biology is a field that aims to engineer biological systems to perform functions that don't exist in nature. For the iGEM competition, teams were given a toolkit of biological building blocks and asked to design and build a synthetic biological system.

"Synthetic biology is a lot like having a set of different Lego blocks. Although each block has a different function and nature, they can be linked to each other using the rules of synthetic biology," said Yang Choo, a junior chemical engineering and biomedical engineering major. "We put together different blocks not normally found together in nature to create a system that reports on the course of biological processes taking place in a cell."

The work for the 2012 iGEM competition began this past summer, when 190 teams from 34 countries designed and built synthetic biology systems from a kit of standard biological parts. This fall, student teams from around the world are presenting their work to be judged in regional jamborees in Amsterdam; Hong Kong; Bogota, Colombia; Pittsburgh; and Palo Alto, Calif. The top teams in each of these regional events will compete in the iGEM World Championship Jamboree.

The CMU team includes Choo; sophomore Peter Wei and senior Jesse Salazar, both electrical and computer engineering and biomedical engineering majors; sophomore Eric Pederson, a biological sciences major; and their instructors Cheemeng Tan, a Lane Post-doctoral fellow in the Ray and Stephanie Lane Center for Computational Biology; and Natasa Miskov-Zivanov, an adjunct ECE faculty member who led the effort to create CMU's iGEM team.

The student team brought together diverse interdisciplinary interests and expertise to build a biosensor using a fluorogen-activating RNA sequence called "Spinach" and a fluorogen-activating protein. The sensor glows brighter in response to cellular activities like transcription and translation. Using a mathematical model developed by Wei, the students analyzed the fluorescence results and determined the efficiency of several promoters in bacteria. The team says it should be helpful for synthetic biologists, as it provides a way for them to measure how much of a product their cell is producing. For example, synthetic biology has been used to create E. coli cells that produce biofuel; the CMU team's sensor could be incorporated into the cell and would glow brighter based on the amount of biofuel produced, giving an easily read indicator of the cell's efficiency.

"Our sensor allows us to quickly and accurately look at RNA and protein levels in a cell in real-time, which has many potential applications in biotechnology, medicine, cell biology and genetics," Pederson said. "Comparatively speaking, it is a cheap and fast alternative to expensive RNA and protein analysis equipment."

The project also had an outreach component in which CMU students were encouraged to create a tool to help teach high schoolers about synthetic biology. Salazar created a circuit board that mimicked the biosensor developed by the team. The electronic circuit was adopted by DNAZone, the outreach program of CMU's Center for Nucleic Acids Science and Technology, to teach high school students about synthetic biology.

The team was advised by Chemistry Professor Catalina Achim, Electrical and Computer Engineering Professor Diana Marculescu, Biological Sciences Professor Aaron Mitchell and Biomedical Engineering Assistant Professor Ge Yang. CMU's iGEM team has been supported by CMU's College of Engineering, Mellon College of Science, School of Computer Science, Center for Nucleic Acids Science and Technology, Molecular Biosensor and Imaging Center, and the Ray and Stephanie Lane Center for Computational Biology.

Jocelyn Duffy and Chriss Swaney