Unlocking the Gene’s Secrets

Keck Foundation grant helps modernize the study of biology

Assistant professor Nate Jue checks his phone as he walks to his lab. “I’ve got great news!” he tells his colleague, assistant professor Eric Crandall, as they pass in the hallway.

Jue just received confirmation that an acquaintance’s test for cancer is negative. But the determination was done using conventional, invasive means.

In the future, Jue says a small blood sample and hardware that fits in your pocket will reveal “trace biomarkers in your blood ... they will be able to determine whether or not you might have indicators for cancer.”

That future may be arriving in Jue’s lab in the Chapman Science Academic Center.

Keck Foundation grant

Last summer Jue announced a $300,000 award from the W. M. Keck Foundation to help modernize the way CSUMB teaches biology. Instead of working at the genetic level, CSUMB students will now be able to work at the genome level and use a relatively new field of study to analyze large sets of data.

But according to Jue, this will not be limited to a single course, as it is with most universities. “We’re really trying to affect our entire biology major,” Jue says.

In addition, Jue and eight other colleagues see this as an interdisciplinary tool. This means a student attending any class in the School of Natural Sciences will be able to “apply the methodologies of genomics and bioinformatics to the type of biology” that interest them.

Understanding genes

Genomics allows a researcher to understand the entire set of genes in a cell or organism. The genome is the blueprint for how an organism builds and maintains itself, and genomics allows a researcher to draw that blueprint.

But acquiring that information means analyzing enormous data sets on dedicated servers.

The core of Keck is to implement course-based undergraduate research experiences into classes
Professor Jue

Bioinformatics allows a researcher to use computer software to pour through data sets in the hundreds of terabytes.

Jue teaches both in his course work. “People like me who do both will be more common in the future,” he says.

Analyzing DNA strands

In Jue’s lab on the third floor of the Chapman building, he pulls out a device the size of a stapler called a MinION. It can produce a sequence of DNA strands thousands of chains long in just a few minutes.

This device connects to a laptop via a USB cable. “It means you could conduct real-time monitoring of ebola breakouts in Africa” rather than wait for results to be sent back to labs in developed countries, he says.

In the next room is a much larger device called MiSeq that can sequence millions of chains.

Jue’s primary research is on genetic diversity of marine life (1). He and his students will use these tools to identify and understand how genetic changes affect organisms.

But these tools are the same for any concentration in biology. “You can be a genome/bioinformatics person who does ecology or cancer research,” explains Jue. “All those things apply.”

And that is a different skill set than what is traditionally taught in biology.

Nate Jue in his lab working with hardware

Professor Nate Jue uses a MinION gene sequencer in laboratory.

Genomics and bioinformatics

When Jue was an undergraduate, the “high tech” in his classroom was the ability to study the biology of cells using fluorescence and microscopes.

“When I was an undergrad in the late 1990’s, genetics was still pretty limited in what it could do,” Jue remembers. “The human genome wasn’t officially sequenced at that point.”

That wouldn’t come until 2001; the advance cost $3 billion. “Now it costs about a $1,000 to sequence the human genome,” Jue says.

That’s because of technological advancement, not just demand. Over time, the cutting-edge tools in the classroom became tools of the trade in the industry.

With Jue’s lab equipment, today’s students will be able to enter contemporary biological professions where genomics is an established field and bioinformatics is the tool of the trade.

More research opportunities

The Keck grant allows Jue and his colleagues to develop more research opportunities for undergraduates.

“The core of Keck is to implement course-based undergraduate research experiences into classes,” Jue explains.

The Undergraduate Research Opportunities Center (UROC) has successfully developed that for students involved in UROC research. Jue and his colleagues want to democratize that for the rest of the student body in collaboration with UROC.

He first has to build the infrastructure with the sequencers, the hardware that allows students to identify DNA.

Next comes creating a new concentration in the biology major in genomics and bioinformatics.

Lastly, Jue and his colleagues will blend these new fields into the entire biology curriculum.

It has already led to opportunities to conduct important research, including a study of the genome of great white sharks, conducted with scientists from the Monterey Bay Aquarium.

Viral genomes

Studying marine viruses has a distinct advantage, especially for new students.

“Viral genomes are a lot smaller than [animal or plant] genomes,” says Jue.

We’re really trying to affect our entire biology major.
Professor Jue

Freshmen could go out on the Monterey Bay, take some samples and come back to the lab to study them with new equipment.

In addition, there’s a real need.

“We know very little about marine viruses in general,” he explains. Because bacteria found in the ocean are a main source of carbon, it’s important to understand when marine viruses infect bacteria and kill them off.

Researchers like Jue use genomic techniques to improve our understanding of the diversity of life.

“In the past, you would have focused on just one virus or perhaps just one gene; now you can take a water sample and amplify one gene to identify what organisms are in the Monterey Bay or describe the entire genomes of organisms such as viruses in order to deepen our understanding of ecosystem biology." (2)

That gene could come from a larva, a red tide or even a whale, according to Jue.

“We’ll hopefully get a better understanding of what the viral dynamics are out in the ocean.”

Footnotes

(1) Updated from the print version to more broadly reflect Professor Jue's overall research interests.

(2) Updated to further describe the technique.