Students build bio-circuits

Four University students presented their designs for biological machines last November at MIT in a federally funded, 10-week competition in the developing field of synthetic biology.

The 2004 Synthetic Biology Competition Jamboree marked the end of a contest between students from five schools — Boston University, Caltech, MIT, Princeton and the University of Texas at Austin — to "design and build a genetically encoded finite state machine."

In other words, students designed basic processors with biological materials. Some teams successfully created machines that executed a programmed output in response to stimuli. Others simulated an output response with individual components of a machine.

"The idea was to set up a friendly competition to take students who don't know much about synthetic biology and teach them how to design genetic circuits," said electrical engineering professor Ron Weiss, adviser to the two Princeton teams.

Each team at the Jamboree consisted of either undergraduates only or a combination of undergraduate and graduate students, all of whom specialized in various engineering and science disciplines.

Vikram Vijayan '07, Allen Hsu '06 and Lawrence Fomundam, a University of Maryland student, received the "Best Simulations" award for simulating a genetic program that enables E. coli bacteria to find their way through a maze.

"The programming is performed by inserting a synthetic gene network into the E. coli," Vijayan said in an email. "Basically, the user can draw a maze on a Petri dish using bacteria, and the bacteria will execute an algorithm to highlight the path between the beginning and end of the maze."

Vijayan and Hsu have continued their project, dubbed "A-Mazing E. coli," as independent work in the electrical engineering department.

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The other team representing Princeton, comprised of Aditi Shrivastava '06, Sarah Welch '06 and Jee-Won Lee of Duke University, created Simon 1.0, a network of three bacterial strains. Like the children's game Simon, in which a player tries to memorize and mimic a sequence of flashing colored buttons, Simon 1.0 is a biological device that recognizes patterns. It fluoresces when chemical stimuli are received in the correct order.

"If certain chemicals are entered in one specific sequence, then it gives a 'yes' as an output by yellow fluorescence," Shrivastava said.

Shrivastava and her teammates used BioBricks, modules of bacterial DNA from the MIT database, for Simon 1.0.

The project won the "Best Finite State Machine" award.

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Teams from other universities presented innovative projects as well. Caltech students built a strain of yeast that detects different concentrations of caffeine by manipulating ribonucleic acid (RNA). A team from UT Austin designed photosensitive cells that produced the "world's first biological photograph of the phrase 'Hello World,'" according to MIT professor Drew Endy.

Endy, who organized the competition with the help of Weiss, MIT colleague Tom Knight and professors from other universities, plans to launch an expanded version of the competition, renamed "iGEM" (for "intercollegiate Genetically Engineered Machine"), this summer.

"One of the goals of the competition is to develop a community that works together to engineer biology," Endy said.

He said that another objective is to expose students to a relatively new field and influence them to continue research in synthetic biology.

Students said they felt the experience of the competition was a valuable one.

"For me the most rewarding part was actually getting a few things to go correctly in lab," Vijayan said. "In fact, I hope to continue doing independent work at Princeton in related fields where I will similarly be able to get experience with both lab work and computation work."

Shrivastava, who was not familiar with biological devices prior to last summer, also enjoyed the project. "It was really cool for me because it was my first introduction to high-level biology in a lab," she said.

Weiss recruited students for Princeton's two teams by distributing fliers to his engineering students. Fomundam and Won, the two non-Princetonian team members, joined their respective groups during Princeton's Research Experience for Undergraduates summer program.

"The first few weeks were spent teaching [the students] what synthetic biology was," Weiss said. Several graduate students helped him deliver lectures and come up with project ideas for the Princeton teams.

"The students did a great job," Weiss continued. "They really learned a lot over the summer. We trained them in the issues that may be in research later on in the biology industry and taught them that genetically manipulating cells will have an impact."