UD profs study human genome using ancient marine creatures

Researchers, including university professors, are attempting to identify the genome sequence of the oldest known jawed vertebrate in hopes of discovering potential medical benefits to humans.

The little skate, which has existed for 450 million years, is a marine animal similar to a ray that researchers believe has the closest genetic coding to the human. It also has the ability to regenerate its limbs.

In 2006, five Northeastern states including Delaware began work on a project called the North East Cyberinfrastructure Consortium. The university contributes to the project's progress by examining the little skate.

Computer and information sciences professor Shawn Polson, a researcher at the university and coordinator of the Bioinformatics Core Facility in the Center for Bioinformatics and Computational Biology, has been involved in the project for approximately one year.

Polson believes the little skate's regenerative properties could be valuable to human medicine.

"As the cellular and molecular mechanisms of these adaptations become better understood, there is the potential for this research to lead to new medicines and other treatments for organ damage and other degenerative disease in humans," Polson said.

The ultimate goal of the project will be to annotate the completed sequence. Annotating involves locating all of the skate's individual genes and determining what their function is.

Since beginning work on the project, Polson and his team, led by biological sciences professor Cathy Wu, have also been able to assemble the little skate's mitochondrial genome, which is separate from the main genome.

James Vincent, director of the Bioinformatics Core for the Vermont Genetics Network, also pointed towards the little skate's regenerative properties as being potentially beneficial to humans.

"The fact that this animal still has the ability and humans don't might tell us something about why humans lost it," Vincent said.

According to Vincent, the consortium seeks to create a fiber optic infrastructure to better share research between each region and then to sequence and annotate the little skate's genome.

"Sequencing is the process of chopping up the genome into tiny parts and putting it back together to get sequence of DNA," Vincent said.

He compared the process to chopping a book into 20 word excerpts, shuffling those pieces up, and putting them back in order to make sense. Currently, this work is being conducted at the University of Vermont.

As the project progresses, many researchers are needed to complete the sequencing, especially the annotation processes. In order to find these highly-specialized individuals, the consortium has held three workshops, two of them in Delaware.

"We have done this not only to help build a team to annotate this genome, but to teach critical skills that will help these researchers to perform other bio-informatic projects in our states," Polson said.

Members of the consortium communicate constantly about their research. In addition to video conferencing once a week, all contributors meet in person at important research stages.

It is estimated the project will take approximately one more year to complete, according to Vincent.

"That's not too bad when you consider it took 13 [years] to sequence the human genome," he said.