Research Team Scores Big for Bio-Computer That Sorts “Burnt Pancakes”
Members of the iGEM research team with three of their four trophies. (front l-r) Erin Zwack ’08 and Lance Harden '09 (back l-r) Karmella Haynes and Samantha Simpson '09. (Adam Martin photo)
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11/23/2006
Contact: Bill Giduz 704/894-2244 or bigiduz@davidson.edu
by Adam Martin ' 06
For more information on the iGEM Jamboree, visit this site.
The annual international Genetically Engineered Machine competition, or iGEM Jamboree, has been likened to the World Cup of synthetic biology. Thirty-five teams of scientists representing institutes of higher education from across the globe converged on the campus of the Massachusetts Institute of Technology recently to show off their research in this new field of DNA manipulation, and hopefully be recognized for their effort.
Davidson, one of just three small colleges involved, won a lion’s share of accolades for a project that turned E. coli bacteria into a rudimentary computer to solve a complex math puzzle called the “Burnt Pancake Problem.” Davidson was one of just three teams to win four awards, and was recognized by the judges to have one of the top six projects overall.
The honors culminated six months of work by three Davidson students– Erin Zwack ’08, Lance Harden ’09, and Samantha Simpson ’09—and Sabriya Rosemond, a junior from Hampton University. They worked with direction from Malcolm Campbell, associate professor of biology and director of the James G. Martin Genomics Program, as well as King Associate Professor of Mathematics Laurie Heyer, and Karmella Haynes, a postdoctoral fellow and visiting assistant professor of biology. Haynes and two of the summer researchers are funded through a large, multi-year grant to Davidson by the Howard Hughes Medical Institute (HHMI).
Creating Biological Tools
Synthetic biology has emerged from genomics research as a distinct scientific field that seeks to engineer living systems for a variety of applications. One application, designed by this year’s iGEM grand-prize winning team from the University of Ljubljana in Slovenia, modified mammalian cells to reduce the body’s excessive response to infection, which can lead to a sometimes fatal condition called sepsis that is one of the top ten causes of death in the United States. Another team manipulated microbes to detect arsenic levels in well water, a problem that affects 100 million people around the world, especially in poorer nations.
Davidson’s “Burnt Pancake” project brought home second-prize awards in three categories–Best Part (or constructed piece of DNA), Best Poster, and Best Cooperation and Collaboration. It also won third prize for Best Conquest of Adversity. Davidson shared the latter three awards with Missouri Western College, with whom the Davidson team collaborated.
“The Burnt Pancake Problem is a puzzle in which a scrambled stack of pancakes burnt on one side must be sorted into smallest to largest order, with all the burnt sides down, by successively flipping parts of the stack,” explained Heyer. “To solve the problem with E. coli, we represented a stack of pancakes by segments of DNA separated by places where DNA can be cut and flipped 180 degrees.” For more on the project, visit the 2006 Davidson team’s wiki site.
Simpson, a sophomore from Ohio, said that “flipping” essentially means turning genes on and off. “The ability to reverse the orientation of particular genes could have huge potential for preventing some genetic diseases in the future,” she said.
Applications Built with BioBricks
Each team began their projects last summer with access to the same toolkit of 500 “BioBricks”—snippets of DNA that have been proven to accomplish certain tasks. By combining and manipulating the given pieces in their projects, teams also built new BioBricks.
The Davidson BioBrick part used to change the orientation of certain genes was one of eleven new parts built by the Davidson team. The “Best Part” second prize was awarded to an insulating plasmid that Haynes constructed after the summer research students identified a pervasive problem with the plasmid provided by the BioBrick registry. The improved version will be adopted by many teams next year.
All the new BioBricks created in the course of teams’ projects are being added to the registry at MIT, and will be available to all scientists who are similarly willing to share the results of their research. In the last two years, the number of total parts in the MIT registry has increased from 200 to 1,000, all developed by participants in the iGEM competitions.
Student Work Attracts Professional Attention
Davidson’s project caught the eyes of several prominent biologists, engineers, and mathematicians. The Davidson students fielded questions one-on-one with leaders in the field such as George Church, a Harvard professor of genetics, and Drew Endy, assistant professor at MIT in Biological Engineering and an organizer of the iGEM Jamboree.
“After our presentation to the whole conference, during the Q&A session, professors and industry professionals were making comments about our research, rather than asking for clarification,” said Harden. “They threw out ideas on how to extend it and get past our latest obstacles. I think they really saw promise in our research.”
“It was incredible to see our students being treated as colleagues by people around the world who were buying into their project,” said Campbell. “Our students were smooth and professional, and a professor from Chiba University in Japan even said he wanted to use our idea and parts in a project next year.”
The students attribute part of their success to the preparation with Haynes before the competition, and this fall in weekly lab meetings. “She asked us lots of specific science-related questions that other scientists would want to know. She really drilled us,” said Simpson.
Harden agreed, “Haynes was instrumental to our success,” he said. Harden also said the attention and the prizes gave him an exciting feeling of working on the cutting edge. He said, “It really feels like we are driving the field of synthetic biology.”
Davidson is a highly selective independent liberal arts college for 1,700 students. Since its establishment in 1837 by Presbyterians, the college has graduated 23 Rhodes Scholars and is consistently ranked in the top ten liberal arts colleges in the country by U.S. News and World Report magazine.
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