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Channeling undergraduate enthusiasm

It is the rare undergraduate engineering student who knows what a polymerase chain reaction (PCR) machine is, let alone how to build one. But that is exactly the kind of experience the CreateIT Collaboratory brings to students at Oregon State.

“I had heard of PCR in my high school biology class, but I only knew what it did, not how it worked,” said Hayden Bialek, a junior in electrical and computer engineering. None of his group mates had heard of a PCR machine before embarking on a summer research project to build one for Matthew Johnston, assistant professor of electrical and computer engineering.

A PCR machine is a diagnostic tool used in biology and clinical labs primarily to diagnose viral infections. During the PCR process, samples are marked with a dye and then heated and cooled 30 times. If the target virus is present, the DNA will replicate and the dye will show up brighter.

Video of the CreateIT Collaboratory project to build a PCR machine.

Professor Johnston specializes in developing electronic devices that have applications in fields like chemistry, biology and medicine and he has often worked with PCR machines. He knew that access to PCR machines was limited because they use expensive technology that can be operated only by highly trained technicians.

“That means this very usable technology exists primarily in major pathology labs, hospital labs, and testing centers. It can’t be used in very rural areas, and it can’t be used in the developing world because it’s too expensive and too complicated,” Johnston said.

He brought the idea of building a low-cost, portable PCR machine to the CreateIT Collaboratory, a lab in the School of Electrical Engineering and Computer Science where students take ideas from industry and research and develop them to prototypes under the guidance of the lab director, Don Heer.

By the end of the project, the team of undergraduates built two different working prototypes of a PCR machine. The first prototype used the camera in an Android tablet to perform the same functions that are typically done by expensive, specialized optical instruments. The downside to the first prototype was that after just one run the battery would be exhausted.

For the second prototype the team designed a custom heating element that would use a lot less power for the heating and cooling cycles. The low-power device could only perform the PCR process and not the optical analysis, so a second step would be needed to for that part. But the advantage would be for situations where electricity was not readily available.

“We tested it for three runs and it only dropped the battery by about five percent. So you could throw it in your backpack and go off in the middle of nowhere for quite a few days and it will continue running,” said Justin Martinez, a senior in electrical and computer engineering.

I came into the Collaboratory with a lot of interest and excitement to do things but not a lot of direction and knowledge, and that’s what the Collaboratory gave me.
– Jacob Dawes

The project allowed students to gain valuable hands-on experiences. For Bialek, who had just finished his freshman year when he started in the Collaboratory, everything was new to him. He began by helping to test the microcontroller code, but eventually took over that portion of the project. Beyond specific skills, he learned how you go from a concept to a finished product. “I was not prepared for the intensity of that process,” he said.

Jacob Dawes, who was the main app developer for the Android tablet, said he didn’t know anything about Android programming when he started. “I came into the Collaboratory with a lot of interest and excitement to do things but not a lot of direction and knowledge, and that’s what the Collaboratory gave me,” said Dawes, a senior in electrical and computer engineering.

Martinez, who had been working in the lab for three years, took on the role of project manager and mentor. He says his experience in the Collaboratory helped him succeed during his internship at Biotronik this summer. “You gain a lot of fundamental skills and an intuition about how your part of the project is going to have an impact on others,” he said.

Johnston said that it would have been hard for him to supervise the project in his own lab. “The Collaboratory has a great infrastructure with prototyping tools and maker tools, and there are six other students in there who are working on related projects. So there’s a lot of institutional knowledge that makes these kinds of projects doable,” he said.

Although many of the projects at the CreateIt Collaboratory are industry sponsored, this one was purely research. The student’s work successfully demonstrated that a low-cost, portable PCR machine is possible.  Bialek and Dawes also had the opportunity to present their work at the IEEE Engineering Medicine & Biology Society International Student Conference in Ottawa, Canada. It was a transforming experience for both of them who were excited to see the other research presented there.

“Going to the conference really opened my eyes to the depth of the field, and how many things you could do especially if you pursue graduate school,” Bialek said. “And it really encouraged me to go into graduate school.”

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