RIC researchers collaborating with Northeast consortium on genome project

The Merson lab: Erika Clift, left, Janis Hall, Rebeka Merson and Mike Jastram. (Photo: Gene St. Pierre)

The Merson lab: Erika Clift, left, Janis Hall, Rebeka Merson and Mike Jastram. (Photo: Gene St. Pierre)
Do mermaid’s purses, those shiny egg cases that wash up on the beach, hold important clues to how birth defects and diseases are caused and how they might be prevented?

Rebeka Merson, associate professor of biology at RIC, believes they do.

Merson, along with RIC student Mike Jastram, recently participated in a five-day bioinformatics workshop at the University of Delaware, the first of three planned meetings to map the genome of the little skate, a flat-bodied fish with a slender tail.

RIC professor Rebeka Merson and student Mike Jastram
review data from their experiments.
The event was sponsored by the Northeast Cyberinfrastructure Consortium (NECC), which includes educators and participants from universities and colleges in New Hampshire, Maine, Rhode Island, Vermont and Delaware.

The skate genome project, said Merson, “provides a large data set to allow us to understand the relationship between early vertebrates and humans, and once we have the genome in hand, we can look at DNA sequences that influence health effects from exposure to environmental chemicals."

"The blueprint for the development of an organism is located in its genome, which comes in the form of DNA packaged on chromosomes," Merson said. The human genome was first sequenced in 1999.

Merson’s lab at RIC studies environment chemical stress and understanding the evolution of gene families involved in the response to those chemicals. She and her students study the embryos of sharks, rays and skates.

The knowledge gained about the connection between biological development and exposure to environmental chemicals is critical to learning about some of the underlying causes of birth defects and illnesses in humans.

Merson employs a two-pronged approach to research: bioinformatics and experimentation in the lab.

Bioinformatics uses computer science, mathematics and statistics to analyze biological information. It has been “a hot field, and it’s getting hotter,” said Merson, who added that it was an “invaluable” tool for the study of biology.

In her lab work for the skate genome project, Merson focuses on what beachcombers commonly call the mermaid’s purse, those rectangular, leather-like pouches that contain the embryos of skates and sharks.

A skate egg case is observed under a microscope.
“We’re using the skate egg cases as a model to determine how the environmental chemicals impact development,” said Merson.

Skate eggs are a particularly good research choice because are easy to keep alive in a tank, and by simply scraping the egg case, researchers can get a ringside seat to observe the embryo in various stages of development.

To that end, she is attempting to understand the effect that contaminated sediments from Narragansett Bay and, possibly, sediments and water samples from the oil-polluted Gulf of Mexico, have on the skate embryos that reside inside the cases.

Why study sharks and skates? Merson explains that humans and most mammals have just one Aryl Hydrocarbon Receptor (AHR), which performs multiple functions such as vascular development in the liver and kidneys, immune cell function and protein regulation.

The skate is one of the fish being studied in Merson's lab.
AHR is a cellular protein that binds to some dioxins, PCBs and PAHs, chemicals found in pesticides, industrial solvents and crude oil. These toxins, which enter the environment by the burning of waste and fossil fuels, are linked to cancer and other adverse health effects in humans and wildlife.

Once activated by a chemical, AHR proteins regulate numerous genes, including some of the cytochrome P450 genes, which are the code for enzymes that can alter the structure of the chemical that activated the receptor. In some cases, these alterations promote the elimination of toxins from the body, but in other instances make the chemical even more toxic.

Humans and most mammals have just one AHR; in contrast, sharks and skates have at least four AHRs encoded by separate genes.

Her research focuses on the partitioning of functions among these AHRs, providing an experimental approach that will allow scientists to “tease apart” the various roles of the AHRs, to better understand how the protein works and how that might apply to humans.

Merson added that her research is important for another reason. “The skate and other organisms like it have been strategically selected because they represent branches on the tree of life that have not been studied on a genomics level, and are not well understood,” she said.

Merson also notes that the NECC workshop and genome research also benefit her students. “This project is an excellent opportunity to train students in the scientific method and applying bioinformatics methods on real data,” she said.

RIC sophomore Mike Jastram is the self-described “computer nerd” in Merson’s lab. His task is to interface between the “wet lab” work done with sharks, and the genetic information from other organisms that has become available.

Mike Jastram studies a computer readout.
Through his brief exposure to bioinformatics with Merson and the NECC workshops, he has already has been able to decipher the gene structure of a spiny dogfish shark AHR.

Jastram finds the skate genome project important because currently, the lab depends on “distantly-related organisms” such as humans or mice, for references against genetic information from sharks.

“But the little skate is comparatively a close cousin to the sharks we study,” he said. “A complete picture of its genome would advance our research by leaps and bounds.”

To better aid her in her observations and experiments, Merson will soon have a three-dimensional close-up view of her subject cells: a laser-scanning confocal microscope. The $330,000 instrument will enable her to look not only through the cell, but also at various “slices” inside it, giving her a clearer picture of its status as a dying or multiplying entity.

The NECC project, which is funded by INBRE (IDeA Networks of Biomedical Research) and EPSCoR (Experimental Program to Stimulate Competitive Research) grants, will meet again in October in Maine. At that workshop, researchers will be learning new techniques in bioinformatics and experimentation, and work as a group on the genome data, Merson said.