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Purified DNA

Test tubes with pipette

Three sophomores were summer student assistants in Duke University’s neuroscience lab, where they converted small chunks of frozen bird flesh into tubes of purified DNA that was then sent to China for full-genome sequencing. Their work was a part of the Avian Phylogenomics Project, an international scientific effort that compared the whole genomes of 48 bird species.

DURHAM, NC – For scientific findings to soar to new heights, there’s often a lot of repetitive, meticulous groundwork to be done first. Such is the case with the ambitious Avian Phylogenomics Project, which is doing whole-genome comparisons on a scale never before seen in vertebrates.

The project, which is literally rewriting the family tree of birds, is based on summer lab work by three Duke undergraduates, a high school student and untold boxes of fresh gloves.

“I didn’t know the intensity of the project at first,” said Nisarg Dabhi, a sophomore from Long Island who hasn’t picked his major yet, but who also hasn’t left the lab. “But then it felt like I was working on something really important.”

Dabhi spent the summer working with sophomores Ruth Melka and Louis Li and East Chapel Hill HS student David Gu in Erich Jarvis’ neuroscience lab at the Bryan Research Building. (Melka blogged about her experience, which was supported by the Howard Hughes Medical Institute.)

The student assistants were converting small chunks of frozen bird flesh collected by the Smithsonian Institution and other organizations around the world into carefully labeled little tubes of purified DNA that was then sent to China for full-genome sequencing at BGI (formerly the Beijing Genomics Institute).

The lab is kept very clean and the razor blades, trays and tubes used to mince and grind the flesh into a pink slurry are single-use. The team changes gloves constantly, keeps careful records and labels new tubes at every step of the way.Moving quickly is really important, explains Carole Parent, the lab research analyst who set up the assembly line and supervised the students. There are enzymes in the flesh that will degrade the DNA, and they start working the moment the sample thaws, she said. Contamination with errant DNA from earlier samples or lab-workers is also a huge concern.

Getting the little chunk of frozen bird flesh out of the tube isn’t always easy. In addition to various small implements, the lab workers took to whacking them on the counter repeatedly, a sound that eventually piqued the curiosity of workers in other labs up and down the hall. At first, Li says, he was supervised doing “entry level stuff,” but pretty soon he was working on his own. Each sample took 15 steps. In a good  day, Li said he could do about 24 specimens.After being ground up, each specimen goes through several steps of laboratory chemistry and spinning in a centrifuge to liberate about 50 micrograms of DNA and discard everything else. Louis Li, a sophomore biology major and pre-med from Philadelphia mostly did that part during his summer.

“It was interesting to see how much time and effort goes into making sure everything is as efficient as possible,” Li said. “I was learning exactly what goes into running a lab.” Which has him thinking of clinical medicine at this point, not basic science.

It was tedious, they all admit, but they brought in speakers to play Jack Johnson. “And we had dry ice,” Dabhi said. “That’s always fun for a little bit.”

Information provided by Duke University