UTA team’s genome research with reptiles could yield clues to human health

Fort Worth Star-TelegramJune 14, 2013 

ARLINGTON — It would come in handy, it’s safe to say, if humans could freeze nearly solid, or go more than a few short minutes without oxygen, and not suffer catastrophic injury.

The Western painted turtle can. In the northern reaches of its range, which stretches from northern Mexico to southern Canada, it spends its winters hibernating below the surface of ice-locked ponds and still feels quite chipper come spring.

What is the turtle’s secret? Thanks to an international project to sequence its genome, evolutionary biologists — including Todd Castoe and Matthew Fujita at the University of Texas at Arlington — now have a better idea. If they are right, doctors might one day possess advanced knowledge of how to treat certain human diseases.

Castoe and Fujita were among nearly 60 co-authors of a paper published in the journal Genome Biology this spring that described the findings from the genome sequencing, only the second full genetic mapping on a reptile.

The researchers found that the painted turtle’s genes used for tolerance of extreme cold and oxygen deprivation are common to all vertebrates but that they are more active in turtles that experience the extreme conditions. One gene that humans share became 130 times more active in turtles subjected to low-oxygen environments.

Further study of the turtle genome could yield clues related to human health and well-being, particularly oxygen deprivation, hypothermia and longevity.

“It’s very hard to do research on people,” said Pamela Jansma, dean of the UTA College of Science, “but if you know that animals have a similar gene pairing, you can study how those genes trigger responses to environmental stimuli. You can map that to humans, and you can then imagine developing gene therapies to address certain diseases.”

Key biological insights

For years, UT Arlington has been an important player in amphibian and reptile research, said Jonathan Campbell, chairman of the biology department and an international authority in the field. Scientists worldwide use the university’s 6,000-square-foot Amphibian and Reptile Diversity Research Center, which opened in 2005 at a cost of more than $1 million and houses nearly 150,000 specimens.

As UT Arlington makes a push for Tier One research status, attracting top-notch faculty members and giving them cutting-edge technology to do their work are among the top priorities.

Castoe, 35, a native of the Mid-Hudson Valley in New York, and Fujita, 33, who is from Pinole, a small town in the San Francisco Bay Area, joined the College of Science in September.

They had barely learned their way around campus before the university announced in late February that it was getting a $7.5 million gift from Shimadzu Scientific Instruments. One of the three components of the Shimadzu Institute for Research Technologies will be the Center for Imaging, which will be housed in the Life Science Building.

In recent weeks, the College of Science also bought a $125,000 sequencing instrument called MiSeq that allows researchers to work exponentially faster than before.

It will be useful in a wide variety of research, including levels of gene expression, said Jill Castoe, Todd Castoe’s wife and the director of UTA’s Genomics Core Facility.

“That provides insight into biological processes and functions — from a snake’s unique digestive characteristics to the ways coral react to the effects of ocean warming,” she said.

Genomics “has incredible explanatory power at multiple levels,” Campbell said. Fujita and Castoe “have taken a unique approach to studying the natural history of reptiles and amphibians — they see that the incredible diversity of lizards and snakes and frogs we see in the wild, in our own gardens, translates to genomic diversity that we have not even begun to explore,” he said.

Slithery critters

The painted-turtle research team was led by Brad Shaffer from the University of California, Los Angeles, and involved scientists from the Washington University School of Medicine in St. Louis, Iowa State University and several other institutions.

The Western painted turtle “used the machinery that all vertebrates have, but they modified it to build a better organism,” Shaffer told the Los Angeles Times. “These are genes and pathways that we have too, but we are not using them in the same way.”

Turtles have been around for more than 210 million years, scientists believe, and in that time they have not changed much. The sequencing project found that the turtle’s genome has evolved much more slowly than that of humans and even more slowly than that of other reptiles.

Todd Castoe’s expertise and data on snake genes helped lead to that conclusion.

Fujita showed that large regions of the turtle’s genome show characteristics more similar to that of birds or mammals than to some other reptiles, like lizards — a finding that implies turtles have diverse genomic characteristics.

Understanding how the turtle’s body form has been so successful is especially important in light of the extinction danger faced by numerous turtle species, Fujita said.

Castoe and Fujita trace their interest in critters that slither and crawl back to a fascination and fear of them when they were kids. Fujita, in fact, kept as many lizards and turtles as pets as he could.

Nowadays their work is not restricted to the lab. They often take field trips to observe and gather specimens — old-fashioned get-your-hands-dirty adventure.

Why is the work important?

“If I give you a computer and ask you to tell me how it works, you can take it apart and get some idea,” Castoe said. “But if I give you another kind of computer, a Dell, a couple of laptops, and you take them apart, too, then you will have a better idea of how it works.”

Fujita offers a dreamier explanation.

“The lizards and snakes and frogs and toads you see in your back yard have important relevance not only by stirring the excitement in young children but also to inform science and society about the world and, ultimately, ourselves,” he said.

“This is one reason to build an appreciation for the natural world so that we can continue learning from it.”

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