Code Breakers

Code Breakers
Dr. Mark Fast, UPEI, is on a Genome Atlantic-led project team that is developing better feed for healthier farmed salmon.

Genome Atlantic is helping Atlantic Canada companies use genomic insights for better resource development

Each day, billions of tons of seawater flow through the Bay of Fundy, driven by the bay’s powerful tides. Tracking sea life, particularly swift-moving fish, in that mess of churning water is a challenge, including for tidal power developers who must monitor the environmental impact of their technologies in the bay.

“Right now they’re relying heavily on sonar for detecting fish,” says Marc Skinner, a researcher and Stantec’s marine ecology technical leader for Canada.

In March 2018, Skinner began developing genetics tools to more efficiently conduct that environmental monitoring, to augment the traditional—and not entirely successful—use of video and sonar.

That research is one of roughly 20 projects connected with Genome Atlantic, a not-for-profit corporation that aims to link companies with researchers in the genomics field, which combines biology, genetics and computer science. And though the organization boasts some successes, it is also limited in its ability to grow by a need for more money and research brainpower.

Skinner’s genomics project turned to eDNA, an environmental monitoring tool that identifies species’ DNA from their genetic material (such as scales, fur, feces) collected, in this case, from water samples.

Skinner says testing at Dalhousie University proved successful in tracking the presence of striped bass: eDNA signals from the fish could be detected from water samples, confirming the presence of striped bass, as well as a sense of their density, within a 24- to 48-hour period. Basically the test could say definitively if striped bass had been present within that period.

“The end result was that the tool worked,” Skinner said in an interview. “So if we pair this new eDNA approach with the traditional methods, we get a new resolution to say: ‘Yes, there are fish here. Yes, it is this species.’”

Skinner’s research, which took about a year to complete and was undertaken for the Offshore Energy Research Association of Nova Scotia, represented the project’s first phase. Phase Two will involve testing the technology in the Bay of Fundy. If proven in the open ocean, it could provide a better monitoring tool for use in regulatory approvals, in the tidal power and oil and gas sectors. It would also provide evidence of Genome Atlantic’s value.

Formed in 2000, Genome Atlantic works to match companies (and their specific operations quandaries) to researchers who could potentially solve the problem using genomics research.

“We try and help company CEOs get a better night sleep by solving what’s making them toss and turn at night,” says Steven Armstrong, Genome Atlantic’s president and chief executive. “It’s trying to connect genetic code with function. It’s highly-applied, company-driven (research).”

According to Armstrong, a successful example of such pairings involved a $4.9-million project that aided New Brunswick’s Cooke Aquaculture. The aim was to use genomics in Atlantic salmon aquaculture, to boost their growth rate, and to improve the survival of eggs and juveniles, flesh quality, and disease and parasite resistance. The salmon’s genetic blueprint was used to identify fast-growing fish and the result was a five-per cent increase in annual production, and a forecasted boost in sales.

“The same kinds of principles apply whether it’s potato agriculture, wine grapes, or solving a challenge in a forestry sector,” says Armstrong, who holds a PhD in pharmacology, during an interview at his Halifax office. “In each and every case, it’s how does the genetic blueprint of what I’m interested in control a function that I’d like to manage?”

All current Genome Atlantic projects involve “genetic optimization”, not “genetic change”. But Armstrong acknowledges that projects involving genetic modification could be pursued.

He also notes that some of Genome Atlantic’s current projects involve problems that don’t appear to be obvious candidates for genetics solutions. One involves microbes that feed on oil seeps on the ocean floor. Finding those microbes can help locate oil reserves and de-risk exploration efforts by oil and gas companies.

“That’s not the first thing that comes to mind when people think about genetics—they’re not thinking about applications in the oil and gas sector,” Armstrong says. “In fact there are very prominent applications there.”

Genome Atlantic does not seek to generate scientific publications based on its associated research. Instead, the organization measures success in terms of employment, research dollars, and economic impact. Since its inception, Genome Atlantic has facilitated $120-million worth of applied research projects, Armstrong says.

The organization only has a staff of seven and all research associated with the organization is conducted at outside locations, such as university labs and private sector facilities. “We’re the connector, the enabler, the funder, the manager, but the hard-core science is done elsewhere,” Armstrong says.

There are typically 20 active projects spanning the four Atlantic provinces, with another 30 at early stages of planning. And though Armstrong is quick to cite successful projects, he acknowledges there are challenges that limit expansion of Genome Atlantic’s work.

One is funding. “I can’t candy-coat that one,” he says.

The organization runs on an annual operations budget of roughly $1.3 million, which is drawn from a combination of federal and provincial government sources, including the Atlantic Canada Opportunities Agency, a major East Coast funding agency that doles out an average of $323 million annually. (ACOA and the provincial governments have committed approximately $1.5 million over three years to support Genome Atlantic’s business and proposal development efforts).

In a given year, roughly $10 million is also spent across Genome Atlantic’s 20 or so active research projects, which draw funding from public sources (such as ACOA and provincial governments) and the private companies involved. (Companies typically put in 25-30 per cent of their respective project costs).

Genome Atlantic is an independent entity but part of the Genome Canada Enterprise. Armstrong notes that Genome Atlantic’s sister centre in Vancouver (Genome BC) has an annual operations budget of approximately $8 million, and a strategic plan for 2015-2020 that included $85 million from the Government of British Columbia.

“This reality allows Genome BC to have much more robust operational and strategic plans and it puts their project proposals in a more competitive position,” he notes. “This serves as a catalyst for us to keep challenging Atlantic stakeholders in the private and public sectors to invest more aggressively in Genome Atlantic.”

Brainpower is also a limiting issue. Simply put, more scientific talent is needed.

“I think we’re doing a decent job in Atlantic Canada but we can do better and need to do better,” Armstrong says. “To get there we have to bring in some more high-end talent to the region. We’ve got some great stars here but we need some strategic recruitment to go hand-pick some folks at MIT and Harvard and Cambridge.”

(Marc Skinner has felt the pinch in his own work. “Like everybody we struggle to attract talent to the region,” he says.)

For Armstrong, increased funding is essential for Atlantic Canada to capitalize on the global growth of genomics technologies. “If we don’t invest aggressively in this space we’re going to be left behind,” he says.

Eric Cook, the chief executive of RPC, a New Brunswick Crown corporation, puts it another way. RPC does fee-for-service research, mainly for businesses, and has been involved in a couple of Genome Atlantic research projects. One involved using bacteria to help extract sought-after minerals from ore, to avoid using potentially harmful chemicals, such as cyanide.

Cook, a former chair of Genome Atlantic (and a current Genome Canada board member) argues that genomics is part of a significant new “wave” of innovation, along with artificial intelligence and digital health.

“It’s particularly important for Atlantic Canada because this plays into our hands nicely. We have the oceans. We have the forests. We have a big aquaculture industry. Biotech applies to all those sectors,” he said in an interview.

In other words, he argues, Atlantic Canada is positioned to benefit from biotech and genomics because of its natural resource economy.

“That’s what excites me most,” Cook added. “Instead of playing catch up, as we sometimes do, we’re actually out in front of this one. And I think that’s really promising.” •

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