Dr. Malcolm Campbell's genomics class, from left: Laura McCoy, Dr. Campbell, Puneet Lakhmani, Dylan Coughtrey, Alexis Valauri-Orton, Leland Taylor, Lauren Ivey, William Green. (David Boraks/DavidsonNews.net)

By DAVID BORAKS
DavidsonNews.net

Puneet Lakhmani (left) and Alexis Valauri-Orton

In a Davidson College biology classroom the other day, Alexis Valauri-Orton and Puneet Lakhmani stood before fellow students and researchers and explained their analysis of a gene called Nhx1 that among other things gives blueberries their color.

Using newly available data on the genome of blueberries from the N.C. Research Campus in Kannapolis, they explained how they studied the gene and what they’d found. The Nhx1 gene that Ms. Valauri-Orton and Mr. Lakhmani studied also can affect how berries ripen and their health benefits for humans.

The students eventually will get a grade for their work from their professor, A. Malcolm Campbell. But their work also could have value in the real world: Their one-semester study is part of a larger project to publish and explain the entire blueberry genome.

In college undergraduate science labs, students typically learn by duplicating research already done elsewhere and confirming the results. Professor Campbell’s course this spring let students participate in the real-world blueberry genome project thanks to a unique collaboration with N.C State University researchers at the N.C. Research Campus.

Listening to presentations, from left, were researchers Allan Brown, Garron Wright, Mark Burke and Davidson professor Malcolm Campbell. (David Boraks/DavidsonNews.net)

Dr. Allan Brown, an assistant professor with N.C. State’s Plants for Human Health Institute at the Research Campus, is leading an effort to sequence the blueberry genome. He said he’s studying blueberries because they are “an important crop in North Carolina.”

And the health benefits of blueberries have been highlighted in other research. What the seven Davidson students have been doing this semester is to help annotate the genome – to help explain the functions and characteristics of small sections of the gene sequence.

The project is an important one, and could lead to a better understanding of blueberries to improve cultivation, boost production, or even make blueberries healthier, larger or hardier.

The class was not in a “wet” lab, working with the blueberries themselves. Instead, it involved computer analyses of the blueberry genome developed by the N.C. State team – long strings of letters that represent the sequence of genes. The students’ job – and that of other researchers in Kannapolis – now is to look more closely at those strings and explain what they mean.

Dr. Campbell, who oversees an international network called the Genome Consortium for Active Teaching, said he has offered a genomic annotation class in previous years, but this was the first time students worked with data from a current ongoing research project.

Dr. Brown contacted him in 2010 and explained that he had unpublished data from the blueberry gene sequencing project.  “It hadn’t been annotated before, and we could participate in the annotation,” Dr. Campbell said.

Said Dr. Brown: “This saves resources for us and it provides a great opportunity for the students. It’s a win-win for research and education.”

Dr. Brown’s research is still in process and has yet to be published. It’s a bit early to say for sure, but some of the students’ work eventually could wind up in a research paper in which Dr. Brown and his colleagues announce the blueberry gene sequence to the world, Dr. Campbell said.

“The students get more value from doing real research as opposed to going through something that’s already been done – and validating it,” he said.

The students presented their work to Dr. Brown and several associates during a class on April 12 in Davidson College’s Chambers Building.

Mark Burke, director of informatics at the David H. Murdock Research Institute on the N.C. Research Campus, said the students’ work is an important part of the blueberry project. “What they’re doing is a lot of what we’re doing. They’re basically helping us with a step. The annotation is the longest phase of any (genome) project,” he said.

Sophomore biology major Laura McCoy said the class gave her important experience in conducting independent research, though at times it seemed like “a whole lot of trial and error,” she said. “I’ve always been interested in genetics, so I thought genomics would be interesting to do a project.”

Dr. Malcolm Campbell has taught the genomics class for several years. (David Boraks/DavidsonNews.net)