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2012



May 22, 2012

Engineering Students Take a Plunge Into . . . Biology

 

Engineering Project Adds Important Piece to Learning Center

The completion of a piezoelectric oligonucleotide synthesizer and microarrayer device, or POSaM, by a group of engineering seniors will add an important component to the Microarray Teaching and Learning Center at JMU.

Established in 2009 with a $249,211 grant from the National Science Foundation, the center supports curricular innovations at a consortium of regional colleges in the Shenandoah Valley. The grant helped purchase a microarray reader and fund the student project to build the POSaM device, said Dr. Louise Temple, a professor of integrated science and technology who secured the NSF grant.

More than 150 students per year in biology and bioinformatics courses at three four-year colleges and two community colleges will use the equipment in inquiry-based or research-oriented classes. The students include science and education majors and students in general education classes. In addition to the students, participating teachers receive training in a summer workshop designed to familiarize them with the equipment and to assist in developing teaching, learning and assessment materials. About 20 undergraduate science faculty participate in intensive technological and educational training experiences.

The learning center will bring together students in biology, computer science and engineering courses to promote the understanding of multi-disciplinary approaches to problem solving, Temple said. The center and related educational activities will also serve an increasingly diverse undergraduate student population and facilitate the advancement in many different fields of study.

 

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How many picoliters of fluid are required to synthesize a section of DNA?

That's not exactly the type of question five engineering majors expected to encounter when they began their studies four years ago. But the five students designing and building a piezoelectric oligonucleotide synthesizer and microarrayer, or POSaM device for short, can tell you now.

The device will create DNA samples for biology research and employ ink-jet printing technology to "print" the samples on glass slides similar to microscope slides. Faculty and students at JMU and other area colleges will use the slides for gene expression testing and comparative genomics. The technology also will be used in teacher training.

"Only really big schools and commercial centers make DNA," said ISAT Professor Louise Temple, who has spent thousands of dollars purchasing DNA samples for her research in bacterial pathogenesis, bacterial virus discovery and genomic analysis. With the POSaM device, many of those samples will be produced at JMU.

Temple, who secured a National Science Foundation grant that is funding the project, proposed that JMU engineering students build a microarrayer. "I figured it would be so cool for students to build one of these and then we can have this capability, we could service people in our region, we could do all kinds of things," she said.

Zack Murter and Taylor Clark were sold on the idea as soon as they heard about it from one of their professors during their sophomore year. They discussed it with some of their classmates and the team came together in about an hour.

"I picked this project because it sounded like the most challenging," Murter said. "I wanted something that was going to challenge me and all of my friends."

The project, which has required fabricating original parts and working with vendors to secure others, has lived up to the challenge. The design is based on a POSaM device created by the Hood Laboratory in 2004, but the majority of the components in the JMU model are different, said Jared Price.

One of the many head-scratching problems occurred during testing, when the team wanted to see if the print nozzles were working.  "We couldn't see the fluid and we decided it was entirely possible it was evaporating, because the droplets are so small, before it even hit the surface underneath it," said Tim Eisenhardt. "It's on such a different scale that's not covered in our classes. We don't have a test question where it's, 'How many picoliters of fluid are going to synthesize DNA?'"

Eisenhardt, who has a job lined up after graduation with a government defense contractor, is happy to be part of the team. "Being able to discuss this project pretty much nailed me that job," he said, noting that in his interview he was able to discuss interfacing systems and dealing with various vendors. "It showed that I had the ability to tackle a project that I didn't know all of the core competencies involved, but I could bring people together to accomplish it."

The cross-disciplinary nature of the project attracted Christina DiMarino, who plans to go to graduate school. "This project is about working across disciplines, it's about working with other people in biology, in chemistry and computer science," she said. A second team of students, comprised of ISAT major Mary Kathryne Dickinson, biotechnology major Laura Lorenz and computer science major Ryan Farrell, is preparing the genomic information for the first project.

Price, who also is planning on attending graduate school, said the project has required everyone's talents, along with a bit of fortitude. "I think everybody heard oligonucleotide and was just kind of blown away because nobody knew what it meant." Due to the team's limited biology background—none have taken it since high school—it took some time to grasp the explanations being given by biologists, he said.

So how many picoliters of fluid are required to synthesize a section of DNA? Well, it's quite simple really. The POSaM device is being designed to print 9,800 different spots (oligonucleotides) of 20 mer (DNA bases) long. Each droplet will be about six picoliters, so it will take 1,176,000 picoliters of fluid to create a full array.

Published Feb. 9, 2012