Team presents its bacterial factory

Somil Bhargava, Erica Tiberia and Danielle Nash report on their trip to Cambridge, Massachusetts

The Massachusetts Institute of Technology has issued a challenge: can biological systems be engineered in the same way as electrical and software systems? The University of Waterloo has answered the call.

The International Genetically Engineered Machines competition, hosted at MIT, is an undergraduate competition in which student teams compete to build biological devices from the genetic level. iGEM has become a driving force in the emerging cross-disciplinary field called Synthetic Biology. This nascent area of applied science stems from applying engineering approaches to biological systems to design and construct synthetic systems with new functions.

DNA “parts” used and produced by each team are designed using a standard format to ensure compatibility during assembly. All parts submitted by each year’s iGEM teams are stored in the Registry of Standard Biological Parts. This Registry allows biological parts to be accessed and interchanged almost as easily as a set of gears or a box of screws.

At the beginning of the summer, each team receives a DNA Parts Kit containing these standardized parts from the Registry. The competition is open-ended, so each team decides on a project of their own choosing and works throughout the year to design and construct build their biological device. Teams are free to use the parts provided or to construct their own new parts. At the iGEM Jamboree, a conference held at the beginning of November, competing teams meet to present their design and results in front of a global audience of teams from around the world.

Beginning with five teams in 2004, the competition has since rapidly expanded to 84 teams from more than 20 countries in the 2008 competition. Attendance at the Jamboree reached over 800 people this year. The majority of participants were undergraduate students with vivid imaginations regarding the potential of synthetic biology. Some particularly interesting applications proposed and constructed by the participating undergrad students include synthetic blood made from bacteria, solutions for HIV and cancer utilizing specific molecular receptors, sensors for toxins in the environment, and a computational device capable of solving complex mathematical problems. This year's finalists presented projects using bacteria to emulate kidney activity, generate electricity and develop vaccines.

The UW iGEM team consists of many undergraduate students and also several faculty advisors spanning the Faculties of Science, Engineering, and Math. The team attended and presented this year's project at the Jamboree on November 8 and 9 and earned a bronze medal standard for their hard work and contributions. (Photo: some of the 15 Waterloo students who attended the event.)

This year, the UW iGEM team designed a genome-free cell expression system, which basically acts as a safe bacterial factory for producing useful compounds in response to an environmental signal. The applications of this project are numerous because it can be modified to produce essentially any protein desired, acting as a compound production and delivery system for agricultural, industrial or therapeutic use.

We are looking for motivated and innovative students to form the 2009 team. We’re wrapping up this term with some preliminary brainstorming for new project ideas, and during the winter term we will decide on a project and focus on the design phase. We will move full force into the lab phase at the start of spring term. Current team members will be holding a brainstorming session today from 5:45 to 7:00 in Rod Coutts Hall room 306. Anyone interesting in sharing their ideas for the 2009 project is welcome to attend.

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Success story for 'refer-a-student' site

by Beth Bohnert, from the @Waterloo e-newsletter for UW alumni

Engineering student Joel Koscielski (right) was referred to UW by his supervisor, Tyler Alexander (BASc '06), who knows mechanical aptitude when he sees it. That's why he pointed Koscielski to UW.

As the supervisor of a welding engineering group who is also responsible for filling co-op positions, Alexander has seen quite a few students come and go. But he couldn't help being impressed by the talent and drive that the young man brought to his summer job at Centerline, a Windsor, Ontario, manufacturer that produces custom-designed welding and metalworking equipment.

Tyler appreciated Koscielski’s natural mechanical ability and the way he applied the skills he'd learned as part of his high school robotics team. In fact, it wasn't long before Joel was handling the tasks of a full-time machinist. "Joel wanted to make the most of his experience at Centerline," Alexander says. "Some students just put in their time, but you could see Joel was looking ahead."

And when Koscielski had questions about university engineering programs, Alexander was happy to share his experiences at UW. "Everybody talks about how intensive UW's engineering program is; I wanted to make sure Joel heard about the positive aspects of the program as well as the challenges," he says.

"UW's co-op program really appealed to me," says Koscielski. "I like the hands-on aspect and the chance to solve real problems."

Alexander passed the student’s name to UW's recruitment team via the Refer-A-Student program, an initiative that allows alumni to recommend outstanding students who they believe will not only benefit from a UW education, but will also be an asset to the university and to the broader community. Koscielski applied to UW and the rest, as they say, is history.

Today, he is settling in to his first term in UW's mechanical engineering program. He's looking forward to his co-op placements, where he hopes to gather perspectives on different industries before he decides to specialize. Eventually, he intends to be part of an innovative, fast-paced industry such as wind power production. And Alexander has no doubt that he will make the most of his UW experience.

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And a rainbow of other news today

"The One Waterloo Campaign is hosting an afternoon event this Thursday," writes Heather Fitzgerald, director of UW's student life office. She advises that "The Queer Community Is Part of My Community" is "open to all members of the University of Waterloo, and is an opportunity for our campus to demonstrate its collective support for the queer community on campus. Our community recognizes that when negative events occur, such as the vandalism of the Rainbow Flag during October's Queer Pride Week, the impact is felt by the entire UW community, not just the queer community. We encourage everyone to visit us on Thursday, November 27, between 12:30 and 2:30 p.m. in the Student Life Centre Great Hall. You will have an opportunity to sign your name and leave a message of support on a banner."

As announced just the other day, the new "E-way" web site, for use by departments ordering office supplies from Corporate Express, is now in operation. But "as with all new rollouts, there are a few kinks," reports Donna Foreman of the procurement and contract services department. One difficulty has prevented some users from signing in, although existing passwords are supposed to work; another problem involves return authorization numbers. "They have set up a team of IT people to work on this problem," says Foreman, adding that if users have run into other difficulties, "any issues at all", they should e-mail her — deforema@ uwaterloo.ca — and somebody will take action.

An invitation from Colin Ellard of the department of psychology: "The Research Laboratory for Immersive Virtual Environments (RELIVE) is currently recruiting participants for a study of how we explore and form preferences for different styles of houses. If you choose to participate, you will have a chance to walk around inside some virtual house interiors while wearing a head-mounted display. You will also be asked to complete some questionnaires describing your experiences in the virtual homes. We will also ask you some questions about your background (age, occupation, education, and cultural background). The study takes approximately 60 minutes and you will be reimbursed in the amount of $15 for your time. For further details, please contact us at housepreferencestudy@gmail.com. This study has been reviewed by, and received ethics clearance through, the Office of Research Ethics, University of Waterloo."

Frances Westley, who heads UW’s Social Innovation Generation project, gave one of the keynote addresses (left) at the second annual Conference on Social Entrepreneurship, sponsored by the Laurel Centre for Social Entrepreneurship and held in mid-November. About 200 people took part, reports Suzanne Gardner of the organizing committee. The weekend kicked off on Friday night with a lecture from media star Marc Kielburger of Free the Children. “After an engaging and impassioned speech about his own experiences living and working in developing countries,” she says, “Kielburger stayed for over an hour longer to chat with each and every attendee waiting in the massive line up to meet him! Throughout the rest of the weekend there were talks about keys to success, attracting and retaining talent, decreasing high school drop-out rates, (the ever important) revenue generation, and much more. Key leaders in the areas of health, education, and international development came together to talk about their efforts, successes and challenges. With non-stop keynotes, workshops, and panel discussions, everyone was tired out by the end — tired, but inspired.”

The engineering faculty's e-newsletter reports that Ladan Tahvildari of electrical and computer engineering will be publications chair of the 31st IEEE/ACM International Conference on Software Engineering being held in May 2009 in Vancouver. "ICSE is the premier software engineering conference," it notes, "providing a forum for researchers, practitioners and educators to present and discuss the most recent innovations, trends and experiences in the field of software engineering."

Sheila Oberholzer, a former staff member in food services in Ron Eydt Village, died June 17, the human resources department advises. She worked in what was then called "Village II" from September 1989 to her retirement in March 1997.

CAR

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