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Hao Trinh (Photo: Jesse Cantley)

DNA sequencer in lab gives CSUEB students competitive edge

  • June 26, 2012

It took scientists with the Human Genome Project 13 years to figure out the order in which billions of DNA building blocks, called bases, line up in the human genome. Today, equipment such as the Next Generation DNA Sequencer –– about the size of a large printer –– used in Professor Chris Baysdorfer’s biology lab at Cal State East Bay can accomplish the same task in a couple of  hours.

“(In) the biology department –– I’ve been here 25 years –– we’ve always provided undergraduate and graduate students the latest technology,” said Baysdorfer, a molecular biologist. “We’ve had a DNA sequencing class as long as I’ve been here, which, by the way, is something no other CSU has.”

The genome is the complete set of DNA that makes up an individual organism, such as a tabby cat, gorilla or California black oak tree. By studying the genome, whether of a plant or human, students working in the Biological Core Facility lab at CSUEB, where the DNA sequencer is kept, gain technical and scientific experience that gives them an edge over the competition when they later apply for graduate school and professional opportunities, Baysdorfer said.

“It makes a huge difference when our students go for job interviews,” he explained. “Their marketability goes immediately up.”

It’s one of several things student Hao Trinh appreciates about the lab time she’s accumulated as an assistant in Baysdorfer’s lab. Trinh graduated in early June with a B.S. in biological science with a cell and molecular biology option. She returns to CSUEB in the fall as a biotech certificate student with future plans to pursue a Ph.D.

“We do experiments involving DNA isolation,” said Trinh, who has isolated DNA from herself, her mother and from plant samples. “It’s a lot of hands-on work in Dr. B’s lab … It’s good experience.”

In the “language” of DNA sequencing, there are four letters representing nucleotides, the chemical building blocks that contain the information in DNA. They are: A, C, G and T.

“DNA sequencing is determining the arrangement of those letters,” Baysdorfer explains. “There are 3 billion letters in a human genome.”

Collecting the DNA is simple. A student simply spits into a large glass tube.

Operating the DNA sequencer also is a straightforward process, said Baysdorfer and his students. It’s preparing the chip containing a DNA sample, however, that is challenging and time consuming.

If his students worked full time, he said, preparing the sample would take three days.

“We have to do a lot of steps to get DNA isolated,” Trinh said.

For Trinh, the process was interesting, she said, because she also tested her mother’s DNA and compared the results. Trinh didn’t make any unexpected medical discoveries, but an unusual sequencing pattern evident in both women’s samples confirmed that the woman who raised her is indeed her biological mother.

Analyzing the results of DNA sequencing can yield a host of health data, such as a proclivity toward developing a specific disease. But not every carrier of a gene for arthritis, for instance, will go on to develop the condition. There is plenty of research yet to be conducted in the field, along with social and ethical considerations to discuss as a society, Baysdorfer observed.

"This massively parallel chip-based DNA sequencing machine allows us to inexpensively and rapidly sequence entire genomes and represents the ‘wave of the future’ for genomic diagnostic medicine,” Baysdorfer said.

“This almost looks like a toy, and yet this is the most advanced sequencer,” said Baysdorfer. “This technology is revolutionizing medicine.”

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California State University, East Bay is the San Francisco East Bay Area's high-access public university of choice. CSUEB serves the region with campuses in Hayward and Concord, a professional development center in Oakland, and an innovative online campus. With an enrollment of more than 14,000, the University offers a nationally recognized freshman year experience, award-winning curriculum, personalized instruction, and expert faculty. Students choose from among more than 100 professionally focused fields of study for which the University confers bachelor's and master's degrees, as well as an Ed.D. in education. Named a "Best in the West" college, as well as a Best Business School, by the influential Princeton Review, Cal State East Bay is among the region's foremost producers of teachers, business professionals and entrepreneurs, public administrators, health professionals, literary and performing artists, and science and math graduates.

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