Biological Sciences student helps stop invasive weed

January 26, 2015

Shaun Harper’s research journal

About six months ago, Biological Sciences student Shaun Harper began an independent research project with his faculty mentor, Dr. Melissa Hills. We’ve been following Shaun for more than six months now as he collected samples of an invasive weed in the summer, learned how to extract DNA from his samples, compiled his findings and ran into a few bumps along the way.

Here is a timeline of his story:

July 4, 2014—Grants and frozen plants

Shaun Harper has a big smile on his face. He’s received an Undergraduate Student Research Initiative (USRI) grant, collected samples of garlic mustard—the invasive weed he’s planning to study—from two sites in Edmonton and one in St. Albert, frozen them in liquid nitrogen, stored them in the minus 80 degree freezer and ordered the rest of the materials he needs to do his research.

Now he just needs the DNA extraction kit to arrive so he can get started.

“I’m estimating it will take about 75 to 100 hours to do all extractions and hoping to finish them by mid-September,” says Shaun. “It’s really exciting to be part of something that could be quite big. Garlic mustard hasn’t spread throughout Canada yet, but there is some on Vancouver Island, some in Ontario and in the eastern U.S. Who knows? It could turn into something huge—it would be pretty awesome if we could get collaboration throughout Canada and other researchers looking into this invasive species.”


July 23, 2014—Battling nerves and extracting DNA

The DNA kit arrived and Shaun is working on his third set of DNA extractions from his garlic mustard as his research supervisor Melissa Hills watches.

“It’s hard to have someone looking over your shoulder, but today, I’m trying to sit back and quietly watch what he’s doing,” says Melissa. “It’s obviously a bit uncomfortable for him, but I’m doing this so I can provide input, comments and suggestions. Molecular biology involves a lot of little steps and you have to be very precise—the best thing is to be focused and not to be interrupted so it will be easier for Shaun when he can do this on his own—after a few times it will be like second nature.”

Shaun starts by grinding the plant tissue with a mortar and pestle, adds a solution to help the DNA become soluble in liquid, incubates it on a heating block for 10 minutes, adds RNAse to degrade the RNA (which they don’t want), then follows several additional steps to get rid of everything else and leave just the DNA.

September 15, 2014—Overcoming hurdles

There’s been a bump in the road. Remember that mid-September target to finish the extractions? That’s not going to happen.

“The DNA yields from my samples were lower than we hoped, so we ended up having to try a few different things,” says Shaun. “I didn’t get as far along as I would have liked during the summer.”

So Shaun and Melissa tried using different reagents to break down the material more. It didn’t work.

They tried ordering coarse sea sand to help with the process of grinding the plant material. It didn’t really work either.

But Shaun isn’t discouraged. “It’s really just the scientific process. I expected that there would be some hurdles, but waiting for materials to arrive has affected my original plan.”

He modified the schedule and plans to do about 16 DNA extractions a week—a couple of days during the week and a day on the weekend.

Even if the yields don’t increase, it should be okay. “It’s not perfect, but the amounts I have will be fine. The next step of the process doesn’t require that much DNA, but it will use up almost all that I have. If I make a mistake, I don’t’ have too much wiggle room, so it’s kind of stressful—if I had more I could play around with it and if I mess up or do something wrong I could go back.”

The good news? Shaun’s confidence in the lab has increased significantly. “I’m on my seventh extraction, but I’m feeling good about it right now. After 10 or 20 more, I’ll have the entire process down pat and I won’t have any more anxiety.”

September 23, 2014—Hitting the books

Research—even biology research—doesn’t just happen in the lab.

“I’m working on the literature review now—compiling articles and references. By the end of the year I will have compiled between 50 and 100 references,” says Shaun.

He says he’s being careful with his schedule, but he’s not stressed about it. “You need to invest quite a bit of time into it, but it’s manageable. Really, time management is the key.”

October 9, 2014—Welcome good news

Good news! The DNA levels turned out to be okay after all. “The gels actually look fine and it’s possible the earlier readings may have been wrong. I’ve done 12 samples since doing the gels and it seems like we’ve figured out the problem.”

Today Shaun looks like a pro in the lab. 

November 21, 2014—Student Research Week application deadline

Shaun is still working on extracting DNA, but he’s getting closer. With midterms underway and finals looming, his writing is on hold, but he’s confident that everything will get done.

He is signed up to do a poster presentation on Tuesday, January 27 at Student Research Week. Stop by and visit him in the Multipurpose Room (6-106) between 9 and 10:30 a.m. .

January 15, 2015—Preparing for Student Research Week

Let the writing begin. “I’ve written a smaller version of what my final paper will include and am getting feedback from my faculty mentor,” says Shaun.

As soon as he has the final text ready, he will use one of the two poster templates provided and send it out for printing.

On Tuesday, January 27, Shaun will be ready to talk about his research at the Student Research Week poster presentations.

“While public speaking isn’t my strong suit and I’m starting to feel a little nervous, I’m preparing myself for the experience and really want to do an excellent job of presenting and talking about my research.”

Shaun says that with convocation only a few months away, there are only positive things to draw from this research experience—whether it leads him on to graduate school or directly into the work world.

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