Allan Brown

Scientific coalition studies plants’ role in fighting disease

July 28, 2014

By Hannah Miller

View the article as published in the Charlotte Observer.

View the article as published in the Raleigh News & Observer.

In the worldwide search to learn more about plants’ role in fighting human disease, an unusual coalition has formed at North Carolina Research Campus in Kannapolis.

It’s made up of academic and industrial scientists from General Mills, Dole Foods, UNC Charlotte and N.C. State’s Plants for Human Health Institute – and 40 student interns from 12 colleges and two Cabarrus County high schools.

Called the Plant Pathways Elucidation Project (P2EP), it has received nearly $2 million in gifts from academic and industrial sponsors. Duke Energy, a multiyear sponsor, recently announced a $150,000 grant for this year’s program.

Various studies indicate that compounds in certain foods offer protection from diseases, including heart disease, cancer, Parkinson’s disease, Type 2 diabetes, cataracts, age-related macular degeneration and even waning mental powers.

The scientists and scientists-to-be are approaching their task at the “bare bones” level, said Dr. Mary Ann Lila, director of the Plants for Human Health Institute and part of the P2EP leadership team.

To trace the chemical pathways involved in compound creation, they’re sequencing the genomes, or mapping the DNA makeup, of blueberries, strawberries, broccoli and oats, something that’s never been done before.

“We wanted to ask simple questions,” Lila said. “What kind of product does a plant make? How does it make it? And then in the end, what good is that product for human health?”

Interns have been a big part of the project since it began last year.

“It gives them a taste of what we do and, hopefully, such an interest that they will pursue this later on,” said N.C. State’s Allan Brown. He’s one of six scientists who mentor both the interns and the seven graduate students who lead them.

Besides, he said, “extra pairs of hands” come in handy when sequencing something as complicated as the 12,000 or so DNA fragments in the blueberry genome.

Some students work in teams that concentrate on one or another of the four foods, others in a bioinformatics section that uses computers to organize the project’s findings.

A tremendous amount of data has been generated in the two-year project, said mentor Rob Reid of UNCC’s Bioinformatics Research Services Division. Once it’s collected, “then you have to start mining that data.”

Much of it has to do with anthocyanins, compounds that give blueberries and strawberries their rich color. They are antioxidants, capable of trapping and neutralizing free radicals – rogue molecules that cause cell damage and are implicated in various diseases, including cancer.

Glucosinolates, another subject of study, are compounds found in broccoli and other cruciferous vegetables. They’re thought to guard against inflammation.

Compounds being studied are “very, very complex phytochemicals (plant chemicals),” said Lila. In blueberries, for instance, “The interaction between them is what really packs the punch.”

Learning by doing

Students are learning to present their research both to each other and to the public.

Every Friday, there’s what Lila calls an “all hands on deck” meeting where teams present the results of their week’s work.

And at the end of last summer, a scientific journal, Frontiers in Genetics, published a paper written by that season’s interns. It was “Students’ Perspective on Genomics: From Sample to Sequence Using the Case Study of Blueberry.”

“It’s almost unheard of to be able to publish anything after three months of work,” said Lila.

P2EP, which starts accepting student applications each March, “is an incredible career opportunity,” Lila said.

Once interns graduate, she said, “They’re going to be golden in the marketplace.”

Even now, their work is contributing to what they and their mentors hope will be the development of plants grown specifically for disease-fighting ability.

Ground rules specify that it’s an “open source” project – meaning that nothing is proprietary and results will be available to scientists all over the world.

Once you know how a plant makes a compound, said Lila, then you can use traditional breeding techniques “to make a plant that’s better able to make that compound.”

THE PROCESS: GRAPES POINT THE WAY

Students studying blueberry anthocyanin are confronted with what bioinformatics mentor Dr. Rob Reid calls “mystery pieces” of DNA. They set out to answer these questions: 1) Do the pieces have genes involved in anthocyanin production? and 2) Where on the entire genome – and on what chromosome – do they belong?

For the first question, they consult available literature on grapes, another highly colored, anthocyanin-rich fruit whose genome has already been sequenced.

In doing so, said P2EP Director Mary Ann Lila, students learn critical thinking. “How do we make sense of the literature that’s out there? How do we glean from it what we need?”

Computers help them to determine whether their blueberry pieces have similar, and therefore relevant, genes.

In the lab, students load the pieces into gels and run an electric current through them to produce a score based on their size.

Existing data on blueberries have already assigned scores to some of the genome’s fragments, or scaffolds, and they’re represented by small slips of paper on a genome map posted outside the office of mentor Allan Brown.

If students determine that one of their fragments has a score close to one on the chart, they will post a slip of paper representing it nearby. If the score is exactly the same, it will be “right next to it” on both the map and the genome, Brown said.

After three weeks of work, students had put about 100 fragments on the map, out of the 12,000 in the entire genome.

But, said Brown, “These ones are the biggest pieces. If we can get to 500 by the end of summer, I’ll be real excited.”

A similar process is being followed with the other foods, and Lila said that the oats genome, while not completely sequenced, “is getting really close.”

For information: www.p2ep.org.

 

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