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DNA Barcoding: A Teacher’s Perspective

Allison Granberry
Teacher, Hostos-Lincoln Academy of Science, Bronx, NY

Previous articles in this series addressed genetic imprinting and DNA methylation. The DNA Learning Center at Cold Spring Harbor Laboratory (DNALC) makes this technology amenable for student research. In addition to simplified lab protocols and bioinformatics tools, the DNALC developed the Urban Barcode Project (UBP) as a model for how to involve large numbers of students in biodiversity studies using DNA barcodes. In this article, I'll provide a teacher's perspective on the UBP and how students used it to answer the questions, "How much ginkgo is in your herbal medicine?" and "How many ant species live in NYC?"


Background

During the first year of the UBP in 2011–12, 75 teams—comprising 218 students from 30 high schools—presented their projects at 2 poster sessions held at the American Museum of Natural History (AMNH). Ten finalist teams were then selected by a jury of experts in biodiversity, conservation biology, DNA barcoding, and education to give oral presentations. Among the finalists were teams from 2 of NYC's selective science high schools and teams mentored by AMNH scientists. With this sort of competition, I was shocked when my teams walked away with first- and fourth-place prizes! I'd never done any scientific research or even attended a science fair before becoming involved with the UBP, so this was really a case of "the little engine that could."

The first-place team, composed of seniors Bobby Glover, Mary Acheampong, and Marisa VanBrakle (see Figure 1), studied gingko dietary supplements they had collected at herbal shops around the city. The team found that most of the products contained no gingko DNA, but most did contain rice DNA. Some of the products appeared to contain potentially toxic plant products, including the plant belladonna that has been linked to previous poisonings in NYC.




Figure 1   UBP 2011–12 first-place winners: (left to right) Bobby Glover, Mary Acheampong, and Marisa VanBrakle.
Figure 1   UBP 2011–12 first-place winners: (left to right) Bobby Glover,
Mary Acheampong, and Marisa VanBrakle.



The fourth-place team, with Kavita Bhikhi (11th grade), Lachoy Harris (12th grade), and Hillary Ramirez (10th grade), used Keebler® Sandies® Pecan Shortbread cookies as bait to collect 256 ants from St. Mary's Park, located across the street from their school. Harris explains, "We basically wanted to find out how diverse were the populations of ants within an urban community because the park is located in a very urban neighborhood." Although a research paper had recently identified 11 ant species living in the median of Broadway, my student team found only 3 species in St. Mary's Park.

But the ant team didn't stop! There was more to find out about NYC ants. Ramirez explains, "One of our biggest unanswered questions was whether collecting in very cool temperatures in October 2012 affected our results. So we thought that maybe trying it in warmer temperatures would result in greater [ant] diversity." They found support for this hypothesis when they identified 4 additional species among an impressive 869 ants collected in summer 2012. Their determination and impressive command of ant research won them first place among 41 teams—113 students from 19 high schools—that competed in the 2012–13 UBP (see Figure 2).




Figure 2   UBP 2012–13 first-place winners Kavita Bhikhi and Hillary Ramirez present their poster to judge Jesse Ausubel, Vice President, Alfred P. Sloan Foundation.
Figure 2   UBP 2012–13 first-place winners Kavita Bhikhi and Hillary Ramirez present
their poster to judge Jesse Ausubel, Vice President, Alfred P. Sloan Foundation.



Being a UBP teacher mentor

I became involved with the UBP in 2011 when I saw an advertisement for a 1-day summer teacher-training workshop on DNA barcoding. I thought it would be great to join the competition since most of my students had never even held a micropipette before! Bobby said, "We've done research but it was never this intense. Nothing more than the eighth grade exit project."

Although my school does not have the facilities to perform DNA barcoding experiments, we attend Open Labs at the Harlem DNA Lab and other teams borrow DNALC equipment footlockers, which have everything from reagents to pipettes to PCR machines. The students then work on their projects after school throughout the academic year. I like how DNA barcoding incorporates the Science and Engineering Practices in the Next Generation Science Standards and addresses the Common Core. The students learn skills such as asking questions, planning and carrying out investigations, analyzing and interpreting data, constructing explanations, engaging in argument from evidence, and obtaining, evaluating, and communicating information.

I help the students with the proposal writing but then quickly encourage them to make the projects their own. By the time we get to developing the posters, there is a real shift—they are totally in charge of the presentation. It is really nice to see them take ownership.

The most difficult part of mentoring is keeping the students organized and getting them to write everything down. Some findings might not initially seem important to record, but those details often turn out to be the most useful! It is also important to stress to students that many different skills are needed for any research project. Some might like writing more than organizing samples; others might prefer computers to bench work. Although all students should try all parts of a project, in the end what appeals to each student might be very different.


Benefits of independent student research

I have noticed that being part of the UBP greatly affects my students. They take personal responsibility for their data and learn what it means to be part of a scientific community. They learn the importance of understanding the process of science and not just memorizing facts. I myself have also learned a great deal. Before this experience, I had only a very limited knowledge about DNA, PCR, primers, or analyzing sequence data. I also know much more about ants now!

The students gained valuable laboratory skills, which will help them in their future studies. Five members of the teams are in college now, with a sixth soon to follow. As Hillary explains, "I may want to do research in the future so having the skills before going into college, it would really be helpful."

Beyond scientific research and college applications, the students also acquire some important life lessons. Harris reflects that, "It takes a lot of discipline and concentration to do that work. When you're getting results that are not good or not what you want, that's frustrating but you have to move past that. I think the work that we did is not just DNA barcoding but it's also things that we'll use in our lives. You just can't give up on the things that make us frustrated."

The students' perception of urban habitats has also greatly changed. Bhikhi told me, "There are about 15,000 ant species and I learned that the environment can have a lot of biodiversity. When we started studying last year, we thought that biodiversity in an urban environment does not exist. And this year we've completely shifted away from that idea and we're seeing that biodiversity in urban environments can exist and we've seen that it does exist by studying these ants."

So, how many species of ants are there in NYC? The truth is no one yet knows, but the ant team wants to find out. They hope to better answer that question by expanding their project to include student teams working in other NYC boroughs. Stay tuned for their results.

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