MDI Biological Laboratory to play key role in skate genome project

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SALISBURY COVE – Lying on the bottom of a tank of water so cold that it would be frozen if it were not so salty, a skate doesn’t look like the celebrity of the animal world that it may soon become.

In fact, it looks like nothing so much as a Jell-O mold gone wrong … until it starts to move, wings undulating as it flutters across the tank like a silk scarf riding the breeze.

The skate, an ancient animal that marine biologists frequently describe as a “flattened shark,” has been selected by the National Institutes of Health to have its genes sequenced, like man, mouse and fruit fly before it. And the Mount Desert Island Biological Laboratory in Bar Harbor will play a key role in the $20 million to $40 million federally funded project, the lab announced this week.

The genetic code – the instructions for making a skate – will be revealed only with years of effort, but could lead to a better understanding of genes that developed in the skate millions of years before dinosaurs roamed the earth and geologic ages before similar genes appeared in the early humans.

When biologists study skates and their close relatives, sharks and rays, they are literally peering backward in evolutionary time – back to the development of the first jaws in fishes, as well as the first pressurized circulatory systems (what gives us blood pressure), and the first immune systems capable of producing antibodies in response to illness.

“This animal has its origins 450 million years ago,” said David Barnes, a microbiologist who serves as associate director of the Center for Marine Functional Genomic Studies at MDI Bio Lab.

“They represent an early solution to a lot of the problems that we have to solve in our own bodies,” said Barnes, who will be one of several scientists nationwide working jointly on the skate genome research.

And the relative simplicity of biological systems that evolved first in skates makes them far easier to research than their human counterparts.

“You can actually look [at skates] and see the minimum set of genes that controls these systems,” said Geoff Spencer, spokesman for the National Human Genome Research Institute, the division of NIH that oversees genetic sequencing.

Scientists at the Mount Desert Island Biological Laboratory first saw the research potential for skates and sharks more than 70 years ago. Since then, the creatures have been used to develop eye drops to treat glaucoma and medications for hypertension, said lab spokeswoman Jerilyn Bowers.

The pre-existing research, including sequences from a handful of skate genes, will be “a great resource,” for the project, Spender said.

And with a complete understanding of skate genes, that research will only expand, Bowers said.

Lynn “Kip” Kippax, spokesman for Gov. John Baldacci, said Friday that the biomedical research made possible by the skate genome project is precisely what the governor has in mind when he speaks of building Maine’s “creative economy.”

The little skate, the particular species chosen for this research, is abundant in the Gulf of Maine. Mottled brown and spiny, they are designed to blend into the sandy ocean bottom where they spend their lives. Anyone who has taken a mid-summer swim in a deep Atlantic harbor has blindly shared the water with skates, and countless beachcombers have picked up their leathery egg cases, known as “mermaid purses.”

Researchers will collect wild skates from throughout the Gulf of Maine, Nova Scotia to Cape Cod, then observe the animals to choose a healthy individual that seems to be “representative” of the population. All genetic sequencing – including the Human Genome Project in 2000 – relies on blood and tissue samples from a single individual. While multiple samples would account for some of the tremendous genetic variation that exists in nature, it could also result in confusion, Barnes explained.

Genome sequencing means that scientists are transcribing the pattern of four individual chemicals – known by their initials G, T, A and C – that repeat to make up the familiar spiraling ladder known as the DNA double helix, which is found within each chromosome, at the heart of every cell.

The result of tens of millions of dollars worth of research will look something like this: ACGAAATCGG, with thousands of these different-sized segments of code representing individual genes.

Genome mapping, which is presently being done as part of the Human Genome Project, is the long scientific process that comes after the headlines. It consists of figuring out what each of these genes does.

Sequencing begins on a computer, where hundreds of thousands of tiny vials of genetic material are scanned by lasers. The images are fed through software that identifies the strings of bases, then compares individual genes to a database containing partial gene sequences from more than 40,000 species. The skate genome will likely take “huge rooms full of [computers]” months to analyze, Barnes said.

Sometimes a gene from a new animal is so similar to one well known in humans or mice that computers know exactly what it does. Other strings of code need a human brain to tease out their identity, so scientists like Barnes step in to fine-tune the genetic sequence, which usually takes several years.

“There are always some new genes and there is always some gray area,” Barnes said.

Humans have about 35,000 genes, some bacteria as few as 500, but until the sequencing is done, scientists have no idea how many skates will turn out to have, Barnes said.

“There’s no reason to believe that we’re going to find [fewer] genes just because it’s an older organism,” Barnes said.

“The idea that humans have more genes than other animals has turned out not to be true,” he said.

Humans also have many of the same genes as other animals. Mice share more than 90 percent of their genes with humans. Skates, sharks and rays are believed to share somewhere between 40 and 70 percent of their genetic material, he said.

The ancient genes that humans lack give these fish characteristics that have been lost in evolution, and if regained, could provide medical miracles.

For example, sharks and skates are all but invulnerable to infection and they rarely grow cancerous tumors. These fishes also have the ability to re-grow their kidneys. Genetic research completed at MDI Bio Lab suggests that humans may actually have retained this regeneration gene, but that it is “turned off” in infancy.

The National Human Genome Research Institute is funding the mapping of animal genomes, one at a time, in hopes of giving this sort of research a head start.

“The only reason we sequence any of these animal organisms is to understand humans,” Spencer said.

Already, gene sequences have been completed for the dog, mouse, honey bee, rat, chicken, fruit fly and sea urchin, as well as for numerous worms, bacteria and fungi; while macaques, orangutans, kangaroos, cows, domestic cats and platypuses are in the pipeline along with skates, according to Spencer.

It may be three years or more before the skate genome is complete, Barnes said.

And if other species are any indication, the skate that gives its genes to the project could then be in demand for scientific research. That Adam or Eve of skates will be kept at MDI Bio Lab for the remainder of its life.

“I guess we’ll have to name it,” Barnes said. “It will be the daddy of all skate research.”