Team puts E. coli to work in computing

by Patricia Bow

A team of UW students was in Boston November 3-4 to take part in the fifth annual International Genetically Engineered Machines (iGEM) competition hosted by the Massachusetts Institute of Technology. They were one of 58 undergraduate teams from universities all over the world, including Harvard, Berkeley, Peking, and Valencia, as well as six Canadian universities.

Each team’s goal was to build a biological device by modifying the genes of living cells. The UW team worked on their project — “Compucoli,” a basic computing element called a half-adder — over the summer and fall, using a standard kit of DNA parts supplied to each team. A half-adder is an essential part of the arithmetic logic unit in a computer’s CPU. In a conventional computer it’s made of silicon; the UW half-adder relies on E. coli to work. When the students subjected the bacteria to different combinations of the chemical tetracycline and red light, the presence or absence of which represented binary 1 or 0 signals, the bacteria produced fluorescent proteins coloured red or green, or produced no protein. These three results represented the sums of 2, 1, or 0, respectively.

This is the third year UW’s team has taken part in iGEM, and the first time on their own: the last two years, they collaborated with the University of Toronto team. The full UW group includes about 15 active undergrad members from engineering, mathematics, and science. Three grad students and postdocs have served as advisers, and professors such as Trevor Charles, biology, allowed the students to use their labs.

Peking won the competition overall. The top Canadian team was from the University of Alberta, who were working on an alternative fuel based on E. coli. While the UW team did not complete their Compucoli project and so did not win one of the major prizes, they came away with a silver medal for participation and the quality of their idea and presentation. Components of their new biological device were added to the Registry of Standard Biological Parts for students to use in future competitions.

While the team members did not receive academic credit for the project, the experience was rewarding in other ways, says team spokesperson Kathy Lam, a fourth-year biomedical sciences student. Working in the lab, the students learned about tools and techniques — such as using enzymes to cut DNA and splice the pieces back together — that were new to most of them. Other students used mathematical modelling to assess and predict protein levels for each combination of inputs, to determine if the design would work before it was constructed in the lab.

“The most valuable part of the competition was seeing the really novel and innovative projects of some of the other teams,” says Danielle Nash, also in fourth-year biomedical sciences. “There are so many things that can be done with synthetic biology that I wouldn't have thought possible.”

Lam says they plan to restart the team early in 2008. “We feel we need more time to work on a project, so we would like to try to make the iGEM project a year-round effort. It may even be something that co-op students can apply to,” she says. “And this coming year, we plan to be more ambitious with the kind of project that we choose to take on.” Interested students may email uwigem@gmail.com.

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First VP mourned; United Way update

UW's first vice-president (academic), Theodore L. (Ted) Batke, died November 2. He was a faculty member in chemical engineering almost from the university's beginnings, arriving in September 1957, and was later also appointed to the department of philosophy as his academic interests grew broader. Meanwhile, he played a series of key roles, including membership in the Academic Advisory Committee that persuaded founding president Gerry Hagey and the earliest board of governors to buy a parcel of land that's now the main campus. Tradition also has it that he suggested the name "University of Waterloo" for what until then was the Waterloo College Associate Faculties. Batke (pictured; photo by Personal Studio from UW archives) was VP (academic) from the fall of 1961 until August 1967, then served a year under the title "vice-president (development)", in charge of building the campus. He retired in 1982, UW's 25th anniversary year, and received an honorary Doctor of Laws degree that year.

Happiness and relief come across in this announcement, received yesterday afternoon: “The University of Waterloo United Way Campaign has reached its goal! As of November 13, the university has raised $175,999.27. That's 103.5% of our goal. The United Way team would like to send a big thank you out to everyone who has supported this years campaign and all the volunteers who helped make this campaign a great success.” From the United Way office, Stacey Ritzer adds that “Donations will gladly be accepted up until December 12.” She also advises that this Friday, the University Club is hosting a special United Way lunch from 11:30 to 2:00. “All gratuities from this special buffet will be donated to United Way. The menu can be viewed online. Call ext. 33801 to make reservations.”

A brief announcement covers a big gift to UW’s Renison College: “a gift of $500,000,” the college says, “to name the Keiko and Charles Belair and Family Centre for East Asian Studies. The gift is the largest donation made to the College since its founding in 1959. Both prominent members of the K-W community, Charles and Keiko Belair have been longstanding supporters of the arts and education. Charles is a professional photographer and Rotarian, while Keiko Belair, once an instructor in Renison's East Asian studies program, was instrumental in the founding of both the program and Renison's annual East Asian Studies Festival. She expressed her delight at having the opportunity to give back to an institution and a community that had made both herself and her husband feel so welcome. The gift will be directed toward college capital initiatives.”

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GIS Day, astronaut's lecture, and more

UW today joins in worldwide activities marking Geographic Information Systems Day. Activities are centred in the Environmental Studies II building, where the main foyer will be transformed into a map gallery displaying UW students’ and faculty’s GIS projects (10:30 to 2:30). “Brought back by popular demand,” says Eva Dodsworth of the map library, “the posters will be judged by all and winners of the best posters will be announced at the end of the day. There will be several GIS-related workshops offered in the morning and research discussions in the afternoon. All students, faculty and staff are invited.” The map library is sponsoring today’s activities along with the Mapping, Analysis and Design unit in environmental studies. More information, and a chance to register in advance, can be found online.

Canadian astronaut Roberta Bondar (left) is on campus today, here to deliver the 2007 Hagey Lecture — this year's event in a series that dates back to 1970, bringing to campus prominent academic and quasi-academic speakers for a major formal lecture in the Humanities Theatre. The series was launched to honour the retirement of UW's founding president, Gerry Hagey, and over the years has brought to campus such figures as Margaret Atwood, David Suzuki, John Ralston Saul, Michael Ignatieff, John Polanyi and Frank Gehry. This year's speaker, born in Sault Ste. Marie, is a neurology researcher with degrees from Guelph, Western, Toronto (PhD) and McMaster (MD), and flew on the space shuttle Discovery in January 1992. This afternoon at 2:30 she'll give a student colloquium (on the third floor of the Student Life Centre) under the title "Suspended in Air: The Reality of Human Space Flight". Tonight at 8:00 comes the main lecture in Humanities: "When We Get to Mars, Will Our Legs Be Flippers? What Space Medicine Teaches Canadians about Life on Earth". Admission is free.

The men's rugby Warriors didn't quite make it into the league championships this fall, but they've come out well in the end-of-season awards from Ontario University Athletics. Excerpts from an OUA announcement: "The University of Waterloo’s Athar Zia is honored with the Rookie of the Year award following a remarkable first season at center. Zia’s tackling-breaking skills and aggressive defense helped lead the Warriors to the playoffs before succumbing to Western in a match that saw Zia score the lone Waterloo try. . . . Waterloo Head Coach Tom Mandich is recognized as Coach of the Year as the Warriors played to a 3-2 record this year, including a 13-11 victory over McMaster in the final week of play, and a quarter-final playoff berth." Named to the provincial all-star team were Zia, Daniel Jilek, Andy Reitzel, Adrian Lui and Jeff Robinson.

And . . . there's good news for those who prefer to read the Daily Bulletin through an RSS feed rather than on the web. "The Daily Bulletin RSS feed is functioning properly again," says my technical colleague Megan McDermott. "We have fixed a bug that prevented the date from updating properly. RSS readers should now see a notification for the Daily Bulletin when it is published. We apologize for the inconvenience." She goes on: "Some of you may be wondering what this RSS thing is. RSS stands for Really Simple Syndication or Rich Site Summary and is also referred to as a feed or newsfeed. RSS allows you to receive notifications when new material on a website is published. This way, you don't have to keep going back to sites to check and see if new articles have been posted. I t's a great way to follow your favourite news sites or blogs, as well as a variety of other types of information that is frequently updated. Look for the little orange icon which indicates that an RSS feed is available, and click on it to subscribe. To read your feeds, you can use your web browser's built-in functionality, or you can use online readers such as Bloglines or Google Reader."

CAR

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