Canada-U.S. scientists to hunt for genetic clues to help struggling North Atlantic right whales rebound

Are clues to improved conservation of the critically endangered North Atlantic right whales lurking in their genes?

Genome Atlantic and Saint Mary’s University, Halifax, together with the New England Aquarium’s Anderson Cabot Center for Ocean Life, Boston, are teaming up on a $6 million, four-year study to find out. The Large-Scale Applied Research Project, funded by Genome Canada and managed by Genome Atlantic, is expected to get under way between July and September this year. (read the press release here)

It is hoped the project’s findings will help conservation efforts become “more effective and efficient,” said Dr. Tim Frasier, one of the project’s two co-leads. A specialist in genetic analyses and marine mammal behaviour, he is an Associate Professor in the Department of Biology, Saint Mary’s University.

“Our work is focused on using genomic data to quantify the impact of inbreeding on reproductive success and species recovery, and to identify if there are long-term negative consequences of non-lethal entanglements in fishing gear,” he said. Genetic implications of non-deadly vessel strikes will also be investigated.

Given current failures to stop or reverse the right whale’s continuing decline, it is anticipated insights from the project could prove critical.

The North Atlantic right whale has been on endangered species’ lists in Canada and the United States for years. Yet today there are estimated to be less than 400 left, of which fewer than 100 are breeding females. In addition to having a high mortality rate from entanglement in fishing gear and vessel strikes, the species’ reproductive rate is also compromised. It is about three times lower than their known potential. A relatively high percentage of females have either never given birth or have had only one calf. Those females with multiple calves reproduce on average every six-to-10 years, as opposed to the expected three-year cycle.

With this low reproductive rate comes greater risk of the species’ extinction. Dr. Frasier’s project counterpart, Philip Hamilton, a leading expert on right whale biology and Senior Scientist at the Anderson Cabot Center for Ocean Life, New England Aquarium, wouldn’t hazard a guess at how long that scenario might take to play out on the current trajectory. However, he said, the North Atlantic right whale, though long-lived, could become “functionally extinct” sooner than later, “because reproductive females are killed at a faster rate.”

“The important point, is that this species can survive and potentially thrive again, if we stop wounding and killing them with ropes and vessels,” he said. Encounters with fishing gear and vessels, coupled with declining reproduction rates, constitute a triple threat to North Atlantic right whale survival.

The genomic probe into these phenomena will benefit from complementary databases. Dr. Frasier’s lab maintains the archival tissue and DNA bank for the species, while Mr. Hamilton curates a photo database that contains all data on right whale health and reproduction.

Philip Hamilton, the New England Aquarium’s Senior Scientist, Kraus Marine Mammal Conservation Program, Anderson Cabot Center for Ocean Life, takes a quiet moment to watch an endangered North Atlantic right whale as it disappears beneath the ocean’s surface. (Photo: New England Aquarium)

Dr. Moira Brown, Senior Scientist at the Canadian Whale Institute, Welshpool, N.B., and a member of the project team, has noted big strides in molecular analysis of these mammals over her 40-year career. For her PhD thesis in 1988, she said, “I started the skin biopsy sampling program in the Bay of Fundy. Using a small stainless tip attached to a bolt launched from a crossbow, I sampled 25 whales that first year. The initial goal was to be able to identify males from females and to determine the sex ratio of the population using DNA analyses. Fast-forward three decades. Scientists have since learned a great deal about right whales from molecular analyses.”

Today, she said, 80 per cent of the whale population has been sampled, equipping researchers to address “the burning question: what, if any, is the impact of inbreeding on reproduction and how does that affect species recovery?” It is a question shipping and fishing industry representatives repeatedly ask her, and she hopes soon to have the answer.

The North Atlantic right whale research community is “extremely collaborative,” and has been so for decades, said Dr. Frasier. That factor made it easy, he said, to recruit researchers to this international project. He pointed out that the North Atlantic Right Whale Consortium – a data- and research-sharing group dedicated to the recovery of the species – has been active, since 1986, bringing together Canadian and American researchers, policy makers, fishing and shipping industry representatives and educators in an effort to conserve the species.

On another level, though, Mr. Hamilton pointed out right whales’ international movements between American and Canadian waters have complicated their plight. “Ideally,” he said, “right whales would be equally protected in both countries–a goal that is complicated by the two countries’ very different regulatory frameworks.”

Consequently, the research team is hoping to produce persuasive, actionable, scientific data for the Department of Fisheries and Oceans in Canada and the National Marine Fisheries Service in the U.S. to better manage North Atlantic right whale conservation in their respective jurisdictions. Researchers also hope their study’s findings can promote changes in fishing and shipping industry perceptions and behaviours to help the struggling right whale population rebound.

To ensure the project’s conclusions resonate in those circles, Dr. Randle Hart, a specialist in the sociology of science and, more particularly, in the way scientific information is chosen for incorporation in policy development, has been recruited to the research team from Saint Mary’s University.

Dr. Frasier described Dr. Hart’s role as “key to the success of this project.” He explained, “understanding how best to use the data available to result in the most effective and efficient conservation actions is a social science, and this is the work that Randy will be conducting.”

At the data-gathering end, the scientific team will measure the impact of inbreeding on reproduction and species recovery and attempt to fill a major knowledge gap on the role of genetic factors in wildlife conservation. Also, on the agenda are assessment of the long-term genetic impacts on whales that have had non-lethal encounters with vessels and fishing gear, and an evaluation of the team’s findings for North Atlantic right whale conservation.

Apart from the multi-million-dollar whale watching industry that has grown around them, whales play a vital role in stabilizing marine ecosystems by helping to regulate a wide spectrum of marine organisms with their presence. Their nitrogen-laden fecal matter, released when they rise to the ocean’s surface to defecate, for instance, is known to stimulate plankton growth and other microorganisms that form the foundation of the oceanic food chain, critical to the existence of marine life and for the maintenance of the fishing industry.

For seasoned right whale researchers, such as Mr. Hamilton, with more than 30 years in the field, these gigantic creatures remain endlessly fascinating.

Having studied these animals so long, he says he knows “almost every individual” and he has followed some of them “consistently year-to-year and habitat-to-habitat,” and yet, he said, so many questions are unanswered: “How do they locate their patches of prey? What do the loud, percussive ‘gunshot’ sounds they make signify? And how do they produce the sounds? Why do some whales make such long-range explorations, like Mogul, and how do they decide where to go?”

He added, “this species has been the underdog for most of my career. For the first two decades, the general public didn’t even know the species existed. People thought I was saying ‘white whale’ not ‘right whale.’ They had heard of belugas. Fighting for the underdog feels instinctive to me.

“Finally, every birth, every death, every injury has a face and a story behind it. Many of the whales alive today, I saw as calves. To watch them weather the many hardships of living in an urban ocean is heartbreaking. They can’t advocate for themselves. It’s up to those of us who know and care about them to speak for them.”

Others on the Frasier-Hamilton team besides Dr. Brown, all keenly committed to right whale welfare, include Dr. Angelia Vanderlaan, Research Scientist, Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, N.S.; Dr. Linda Rutledge, a bioinformatics expert and Assistant Professor in the Biology Department, Trent University, Peterborough, Ont.; Dr. Michael Asaro, Economist, NOAA (National Oceanic and Atmospheric Administration) Northeast Fisheries Science Center, Woods Hole, Mass; Dr. Robert Schick, Independent Research Scientist, Marine Geospatial Ecology Lab, Nicolas School of Environment, Duke University, Durham, S.C.; and R. Clay George, Senior Wildlife Biologist, Georgia Department of Natural Resources, Nongame Conservation Section, Brunswick, Ga.

Besides Genome Canada funding, the project is being supported by Fisheries and Oceans Canada and Research Nova Scotia in Canada, and by the Georgia Department of Natural Resources, the US National Marine Fisheries Service, and the New England Aquarium in the United States.

Canada-U.S. team looks to genomics to guide North Atlantic right whale conservation

For immediate release

Canada-U.S. team looks to genomics
to guide North Atlantic right whale conservation

July 22, 2021- Halifax, N.S.

The number of critically endangered North Atlantic right whales continues to be buffeted by high mortality rates from vessel strikes, fishing gear entanglements, and by a low rate of reproduction. There is now estimated to be fewer than 400 individuals left, including less than 100 breeding females. With inbreeding suspected as a major factor in the species’ low birth rate, a Canadian-U.S. team of scientists is launching a research project to assess how genetic factors are hampering the right whale’s recovery.

Conservation Genomics of the Endangered North Atlantic Right Whale is a $6 million, four-year international collaboration with Genome Atlantic and Saint Mary’s University, in Halifax, N.S., and with the New England Aquarium in Boston, Mass. Other collaborators include Fisheries and Oceans Canada and the Canadian Whale Institute in Canada, along with the Georgia Department of Natural Resources, Duke University, and the National Oceanographic and Atmospheric Administration, all in the United States.

This landmark project was one of eight announced today by the Honourable François-Philippe Champagne, Minister of Innovation, Science and Industry. The projects are the latest to attain funding through Genome Canada’s Large-Scale Applied Research Project (LSARP) Competition.

Managed by Genome Atlantic, the project is co-led by Dr. Timothy Frasier, Saint Mary’s University, who has been doing genetic analysis of the right whale for more than 20 years; and by Philip Hamilton, a leading expert on right whale biology and Senior Scientist at the Anderson Cabot Center for Ocean Life, New England Aquarium in Boston.

The Genome Atlantic project will look at genetic factors that could explain why the reproductive rate of North Atlantic right whales is three times lower than their known potential. The team also plans to assess if, and to what degree, non-lethal encounters with vessels and fishing gear change the expression of genes in a manner that lowers the long-term health and reproduction of individuals, and to evaluate the ramifications for conservation of the species. The team will combine genomics– the study of genes and their functions–with long-term field data on North Atlantic right whales and their reproductive histories.

Recommendations, based on the project findings, will be made to the Department of Fisheries and Oceans in Canada and to the National Marine Fisheries Service (also known as NOAA Fisheries, an office of the National Oceanic and Atmospheric Administration) in the U.S. on right whale-related recovery expectations, goals and conservation priorities. The results could have implications for marine management policies, practices and conservation plans. The two government entities are charged with managing and conserving the North Atlantic right whale population within their respective jurisdictions. Seasonal migrations, which send a portion of the right whale population through Canadian and American waters, have made recovery of the species a joint concern.

Apart from the multi-million-dollar whale watching industry that has grown around them, whales play a vital role in stabilizing marine ecosystems by helping to regulate a wide spectrum of marine organisms with their presence. The nitrogen-laden fecal matter they release when they rise to the ocean’s surface to defecate, for instance, is known to stimulate plankton growth and other microorganisms that form the foundation of the oceanic food chain, critical to the existence of marine life and for the maintenance of the fishing industry.

Besides Genome Canada funding, the international research project will receive support from Fisheries and Oceans Canada and Research Nova Scotia in Canada, and from the Georgia Department of Natural Resources, the US National Marine Fisheries Service, and the New England Aquarium in the United States.

The project is expected to start between July and September this year.

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QUOTES:

The endangered North Atlantic right whale plays an important role in our marine ecosystem, and conserving this species is of vital importance and urgency. By identifying to what degree genetic factors are influencing the whales’ recovery, this project will aid conservation efforts and help us monitor their population. Conserving endangered marine wildlife benefits our environment, our economy and our communities.”

—Dr. Steve Armstrong, president, Genome Atlantic, the Canadian non-profit corporation managing the project.


“Although inbreeding has been an important topic in population biology for over a century, our understanding of its impact in the wild, and in endangered species in particular, is still in its infancy due to a lack of good case studies. This study, where we have the ability to combine 40 years of field data with genomic data for such a high percentage of individuals, will allow us to not only quantify the impacts of inbreeding on the recovery potential of this species, but will also greatly improve our understanding of the impacts of inbreeding on wildlife populations and the subsequent implications for conservation.”

—Dr. Timothy Frasier, project co-lead and Associate Professor, Department of Biology, Saint Mary’s University, Halifax, N.S.

“Since 2015, this species has experienced a precipitous decline that is unprecedented in 40 years of study. We know many are dying from vessel strikes and entanglements; We don’t know the impacts of non-lethal wounds caused by humans, or the impacts of their reduced breeding pool. We need to make bold changes to how we use the oceans and to do so, we need as much understanding of the problem and cultural support for those changes.”

—Philip Hamilton, project co-lead and Senior Scientist, Kraus Marine Mammal Conservation Program, Anderson Cabot Center for Ocean Life, New England Aquarium, Boston, Mass.

“We now have individual genetic profiles for over 80 per cent of the whale population that has enabled researchers to identify paternity and construct family trees. We can now address the burning question: what, if any, is the impact of inbreeding on reproduction and how does that affect species recovery? In my dealings with representatives of the shipping and fishing industries, I often get asked that very question. The results of the DNA analyses will be shared with mariners to help them understand the importance of measures to reduce entanglements and ship strikes, in order to avoid further narrowing the genetic diversity of the species. Additionally, this will enable researchers to identify paternity, and therefore help reveal the family tree of these incredible creatures.”

—Dr. Moira Brown, Senior Scientist, Canadian Whale Institute, Welshpool, N.B.

MEDIA:


Genome Atlantic is a not-for-profit corporation with a mission to help Atlantic Canada reap the economic and social benefits of genomics technologies. Since its inception in 2000, the corporation has worked with a range of private and public-sector partners to enable more than $125 million in new genomics R&D.

Saint Mary’s University is one of Canada’s top primary undergraduate universities–known for its international collaborations, leadership in entrepreneurship, and research that benefits local and global communities. Our programs in Arts, Science, Graduate Studies and the Sobey School of Business are among Canada’s best and feature professors who are committed to the success of their students. Saint Mary’s provides our 7,000 students with a place that fosters possibility, excellent research opportunities, and distinguished graduate and professional programs combined with a caring community. Nestled in the heart of Halifax, Nova Scotia, on Canada’s east coast, Saint Mary’s University is marked by iconic buildings, green spaces and fresh ocean air. The Saint Mary’s University community is committed to a prosperous future for the world—a world without limits.

The New England Aquarium is a global leader in marine science and conservation, working to safeguard ocean animals and habitats. With more than 1.3 million visitors a year, the Aquarium is one of the premier visitor attractions in Boston and a major public education resource for the region. The Aquarium’s research and rescue efforts build on the institution’s 50-year legacy of protecting the blue planet and advocating for vital and vibrant oceans. In the Anderson Cabot Center for Ocean Life, scientists conduct applied marine research that informs ocean management, policy, and industry practices, and contributes to the innovation of new technologies. Through its Sea Turtle Rescue Program, the Aquarium helps protect critically endangered and threatened sea turtle populations through rescue, rehabilitation, and release efforts.

Conservation Genomics of the Endangered North Atlantic Right Whale

Media Note: Through any of the contact persons listed below, interviews are available with Britta Fiander, Director of Innovation Programs, Genome Atlantic; Dr. Tim Frasier, project co-lead and Associate Professor, Department of Biology, Saint Mary’s University and Philip Hamilton, project co-lead and Senior Scientist, Kraus Marine Mammal Conservation Program, Anderson Cabot Center for Ocean Life, New England Aquarium.

Contact:

Charmaine Gaudet, Director of External Relations
Genome Atlantic
Halifax, N.S.
Cell: 902-488-7837
Email: cgaudet@genomeatlantic.ca

Megan Harris, Communications
Genome Atlantic
Halifax, N.S.
Cell: 604-417-9020
Email: harrismeganc@gmail.com

Cale Loney, Communications Manager
Saint Mary’s University
Halifax, N.S.
Cell: 902-579-0967
Email: cale.loney@smu.ca

Danielle Boudreau, Communications Officer
Saint Mary’s University
Halifax, N.S.
Cell: 902-999-2744
Email: Danielle.Boudreau@smu.ca

Pam Bechtold Snyder, Director of Communications
New England Aquarium
Boston. Mass.
Cell: 617-686-5068
Email: psnyder@neaq.org

Diana Brown McCloy, Communications
For the New England Aquarium
Boston, Mass.
Cell: 978-697-9414
Email: diana@teakmedia.com

Hannah Miller, Communications
For the New England Aquarium
Boston, Mass.
Cell: 413-717-7759
Email: Hannah@teakmedia.com


Employment Opportunity: Director of Finance

Note: The application deadline for this position has been extended to May 2, 2021.

Genomics is a powerful combination of genetics, biology and computer science. It provides us with the unprecedented ability to better understand all living things, leading to a host of opportunities across a variety of sectors. Genome Atlantic is a not-for-profit corporation with a mission to develop and lead a program of genomics R&D that delivers tangible economic, social and environmental benefits to Atlantic Canada.

We connect ideas and people across public and private sectors to find new uses for genomics, invest in large-scale science and technology to fuel innovation, and translate discoveries into solutions across key sectors of national importance. Key sectors include health, agriculture and agri-food, forestry, fisheries and aquaculture, the environment, energy, and mining. Together with our many partners, we have enabled over $120 million in strategic R&D since our inception in 2000.

Reporting to the President & CEO and acting as a department of one within a small, energetic and talented team, the Director of Finance will provide leadership in all areas of Accounting, Finance, and Administration.  Your duties will span a broad spectrum of activities, including the maintenance of a full set of accounting records, budgeting, payroll administration, financial reporting, funding requests and claims, and financial support for the various research projects that we manage.  You will be the primary company liaison with bankers, auditors, institutional Research Services Offices, and our lead funder, Genome Canada, on all financial matters.  You will provide support and direct reporting to the company’s Finance & Audit Committee and Board of Directors.

Demonstrated expertise in the following areas will be assumed:

  • Quick Books accounting program
  • MS Excel and other Microsoft programs
  • Payroll administration, including group benefits
  • Accounting for not-profit organizations

You are an accredited CPA with at least 5 years of relevant experience.  You are an independent, organized worker, a flexible and open-minded team player with a ‘customer-service’ orientation, an excellent communicator, and are comfortable responding to a variety of needs in a fast-paced environment.

Experience in the bioscience sector and an interest in science will be considered assets.

A full job description can be made available upon request.

Genome Atlantic offers an attractive total compensation package encompassing a competitive salary, health and dental benefits, paid parking and work schedule flexibility.    This position is based out of our Halifax, NS office and will require occasional travel throughout Atlantic Canada or other parts of Canada (once pandemic restrictions are relaxed).  

How to Apply

Please indicate your interest by sending a cover letter and résumé (as one integrated pdf) to ndentremont@genomeatlantic.ca by May 2, 2021 and please insert “Director of Finance”  in the subject line.  Please entitle all attachments to include your first and last name. Your cover letter should articulate why you believe you are a fit for this position, key career accomplishments relevant to this opportunity, and how you see yourself contributing to our team dynamic.

Genome Atlantic is committed to creating an inclusive environment and building a team that represents a variety of backgrounds, perspectives, and skills. We value diversity and recognize that experience comes in many forms and skills are transferable. Please view this description as a general overview, but not a mandatory comprehensive list. If you feel passionate about our efforts and believe that you have the skills to contribute and lead in this role, apply! 

We thank all interested parties; however, only those applicants under consideration will be contacted.

N.S. gains COVID early warning system via wastewater sampling

Dr. Crystal Sweeney, Dalhousie University-based Project Manager for the Nova Scotia-wide wastewater surveillance project.

Nova Scotia’s low incidence of COVID-19 has endowed a short-term, province-wide wastewater surveillance project with the ability to act as an early warning system for clinical caseload surges.

That capability sets the Nova Scotia program apart from other wastewater sampling initiatives across the country, monitoring for the virus that causes the disease, according to Dr. Graham Gagnon, who co-leads the surveillance project with Dr. Amina Stoddart, both from Dalhousie University’s Faculty of Engineering.

Dr. Gagnon, who is also the University Research Professor and Director of the Centre for Water Resources Studies, explained, “in regions of high caseloads, the viral signal is expected to be seen in the wastewater and can be monitored for increasing or decreasing trends.

“What’s interesting about our program is that while we expect the viral signal in wastewater to be low when cases are few, a notable increase in the signal could indicate the presence of the virus before new cases are reported.

“When used in this way, our research has the potential to provide us with an early warning signal for the re-occurrence of COVID-19 in our communities.”

As talk of a third pandemic wave grows, advance warning could give Nova Scotia Public Health officials a distinct advantage to take mitigating measures ahead of a viral outbreak and reduce its potential impact.

“Another notable feature of our program,” said Dr. Gagnon, “is that in addition to wastewater testing, we are incorporating primary solids testing, as well as passive sampling in targeted locations for a more comprehensive monitoring strategy.”

Wastewater surveillance exploits a quirk of SARS-CoV-2, the virus that causes COVID-19. Its genetic material survives longer in the gastrointestinal tract than in the respiratory system where it causes most of its havoc. That factor makes it possible to detect the virus, via its RNA, when excreted in human waste by individuals who may be asymptomatic, pre-symptomatic or symptomatic.

With the mass vaccination program against COVID-19 under way, Public Health worries have shifted to the infiltration of variants of concern and their potential to show resistance to the antibodies generated by the new vaccines and the natural immunity acquired from having had COVID-19. In some cases, variants first detected in the U.K., Brazil and South Africa seem to be more transmissible and, to cause more serious disease, than the wild form of the virus – the non-mutated form we are more familiar with.

Responding to these developments, Project Manager, Dr. Crystal Sweeney, noted the Nova Scotia team’s detection method targets the N2 gene on the viral RNA to identify the presence of SARS-CoV-2 in wastewater samples.

“Since the mutations identified in the variants of concern do not involve the N2 gene,” she said, “our method is able to detect the variants, if present, but we cannot identify whether the viral signal is from the wild-type SARS-CoV-2 or a variant.

“However, we are working with a laboratory here at Dalhousie University to sequence RNA extracted from our wastewater samples to determine whether variants of concern are present in the environmental samples.”

Dr. Sweeney is confident RNA fragments from SARS-CoV-2 cannot easily elude the sensitivity of the team’s testing method. “Through strategic and targeted monitoring, along with innovative method advances, we have demonstrated the ability to detect the viral signal in wastewater when there were only nine active cases in the entire province,” she said.

Data collection and assembly have been organized for fast, accurate retrieval and distribution, with a dashboard that displays the latest sample collection and analysis data. Dr. Sweeney said, “We have also prepared consolidated reports for wastewater testing results at each sampling site so that a complete sampling and data history can be provided for any site at any time.”

Wastewater sampling for pathogens is not new to public health. It was widely used in the past to uncover Poliovirus 1, for instance.  Many countries, most of them in the context of research, are using wastewater sampling for SARS-CoV-2 detection, and Dr. Gagnon said, “We view our work as a research program that builds upon the active body of research that is happening in the field of wastewater surveillance across the globe.”

The current Dalhousie-led project is the successor to a Genome Atlantic-funded pilot in which Dr. Gagnon’s team succeeded in finding evidence of SARS-CoV-2 in Wolfville’s municipal wastewater system, last year. The province’s Public Health officials responded by expanding capacity at the town’s primary COVID-19 assessment centre and opening pop-up rapid testing sites in the community. It was a demonstration of how wastewater surveillance and Public Health officials can work together to mitigate the spread of COVID-19.

Dr. Gagnon recounted, “Genome Atlantic’s support allowed us to get some small laboratory equipment and to bridge a research assistant into this much larger project.” The funding helped finalize some lab testing and demonstrated the potential of the wastewater sampling method on environmental specimens.

The current $852,000 wastewater surveillance project, sponsored by Research Nova Scotia, has more than 15 wastewater sampling sites around the province. Weekly sentinel sampling for sustained monitoring in vulnerable locations is done at wastewater treatment facilities in the Halifax Regional Municipality, Sydney, Antigonish and Wolfville. Specimens are also collected up to three times a week from targeted sewersheds in surrounding areas designated for intense and frequent monitoring.  

The research team’s affiliation with a wastewater research program initiated with Halifax Water and NSERC, said Dr. Gagnon, facilitated sample collection, access to sewersheds and the ability to build the sampling programs critical to the project.

Samples are analysed by the 18-member project team within three to four hours of arrival at a lab. The team uses the new internationally deployed rapid and direct SARS-CoV-2 RNA extraction method, recently developed by Dr. Gagnon and his research group, in partnership with LuminUltra Technologies, an international biotech company based in Fredericton, N.B.  

The company is a key partner in the program along with Halifax Water, which is a co-investigator in the project along with Acadia University, Cape Breton University and St. Francis Xavier University.

It is worth pointing out that although detection of the SARS-CoV-2 signal involves the amplification of RNA fragments, Dr. Sweeney said, “the virus itself may not be in the infectious state.” She added, “although no cases of transmission through contact with sewage or contaminated water have been reported to our knowledge, and studies conducted with these matrices have not detected infectious viruses, it is important to apply the precautionary principle when handling samples.”

The surveillance program is expected to continue until July, with a final report due in November.

Newly formed AtlanTIC prepares to fight climate change with genomics-based tree improvement




Second generation white spruce growing in the Parkindale Seed Orchard, owned by J.D. Irving Limited. The orchard is used to produce high quality seed for reforestation. Photo Courtesy of J.D. Irving Limited.
 

Genome Atlantic is helping the newly formed Atlantic Tree Improvement Council, known as AtlanTIC, get up and running with an initial $6 million, five-year regional tree improvement program for long-term forest sustainability.

Among AtlanTIC’s “big objectives,” said Stefan Richard, Executive Director of the new regional non-profit, is to leverage “the genetic gains we get from tree improvement to fight and adapt to a changing climate – to make sure we’re planting the right kind of trees now for harvest in 35-50 years.” To do that AtlanTIC intends to facilitate and coordinate the region’s tree improvement breeding programs in order to respond to threats to commercial woodlands.

“For example,” said Mr. Richard, “if areas of New Brunswick are predicted to warm more due to climate change, perhaps some of the trees from the southern part of Nova Scotia will become more important, because genetically they evolved to grow in warmer temperatures.”

Genomics is set to have a starring role in the organization’s selective tree breeding program. Dr. Richard Donald, an Associate with Genome Atlantic’s business development team who has been closely involved in AtlanTIC’s gestation, cited program activities such as collecting germplasm, the seeds or living tissue from which new plants can be grown; conducting field trials in selected locations with different tree species; and doing data collection and analysis.

For Atlantic Canada’s forest industry, genomics offers new possibilities for developing commercial species with better growth rates, pest resistance, climate resilience and wood quality. That means more sustainable woodland, greater plantation productivity, and a competitive advantage for the industry.

Where conventional tree breeding methods take up to 30 years to verify the inherited traits in a new generation, Dr. Donald pointed out, genomic selection methods require only a few years. Traits can be confirmed in the genetic composition of the tree seeds, making the genomic route to commercial breeding faster, cheaper and more effective.  

The first regional tree development program undertaken by AtlanTIC will expand coordinated progeny testing throughout Atlantic Canada. Data will figure prominently in the initiative and the plan is to develop a database ontology in which relationships among collected data are described. Data collection methods will be standardized, and the latest big data statistical methods region-wide will be used. Also, on the agenda is integrating genomics technologies to improve tree breeding program outcomes, improving training and development of regional expertise, and ensuring knowledge transfers are made to AtlanTIC’s membership.

An estimated $4.7 million will be raised for AtlanTIC’s planned tree improvement activities through member contributions. The Nova Scotia Forestry Innovation Transition Trust recently awarded $315,000 to Genome Atlantic for AtlanTIC’s planned tree improvement work in Nova Scotia. Applications to other funding agencies are being considered.  

As an added bonus, Dr. Donald said the program aligns with Nova Scotia’s Lahey report, a 2018 review of the province’s forest practices that called for designated high-production forestry areas and allowing for biodiversity and more sustainable forests. Mr. Richard explained the program will improve commercial woodland productivity and boost genetic diversity by “bringing together sources of genetic material from across all four Atlantic provinces.”

AtlanTIC’s founding was facilitated by Genome Atlantic, through the work of Dr. Donald and Britta Fiander, Director, Innovation Programs, Genome Atlantic. The organization was propelled into the convener role by its region-wide connections with government and the forestry industry, and by its genomic expertise.

Dr. Donald said Genome Atlantic’s role involved “bringing people together, figuring out how this group is going to work, developing the bylaws, developing the mission statement, hiring the executive director, coming up with the initial budget and writing funding applications.”

The recent Genome Quebec-managed and Genome Atlantic-supported FastTRAC project, which focused on genomic selection for white and red spruce in New Brunswick and Quebec, helped validate the central role of genomics in AtlanTIC’s broad-based regional program. That project, funded through the Genomic Applications Partnership Program, involved J.D. Irving Limited, Laval University and the provincial governments of Quebec and New Brunswick.

AtlanTIC’s charter members from the forest industry are J.D. Irving Limited, Northern Pulp, and Port Hawkesbury Paper, but other companies in the region are expected to join and Mr. Richard said expanding the list is a priority.

The charter group also includes Genome Atlantic as well as government forestry departments: the federal government’s Canadian Forestry Service, Natural Resources Canada; Nova Scotia’s Department of Lands and Forestry; Newfoundland and Labrador’s Department of Fisheries, Forestry and Agriculture; New Brunswick’s Department of Natural Resources and Crown Lands; and Prince Edward Island’s Department of Agriculture, Natural Resources and Industry.

Dr. Donald said membership will also be extended to universities in the region with the research capacity to engage in AtlanTIC’s tree improvement program. 

The reason for AtlanTIC’s formation lies in new and growing challenges facing the region’s forestry industry. There are increasing pressures to modernize facilities and methods, compete with off-shore competitors that have faster growing tree stock, adapt to changing social values associated with woodland, combat the harmful effects of climate change, and deal with the influx of invasive non-native pests.

Meanwhile, a consensus has grown that the region’s forestry players need to work together for shared solutions, which they cannot achieve alone or through their provincial organizations.

Mr. Richard said working together “increases the efficiency in this type of work. Whether it’s funding of research development projects, developing datasets that we require, or accessing different genetics, different species, that we need, we are much stronger as a group than we are as individual members.

 “And you get a multiplying effect,” he added. “So, for every research dollar that our members put in, we can multiply that – we can make the impact greater because we are a group working together towards the same goals.”

$4.7 Million Atlantic Salmon Gill Health Initiative announced

Dr. Kathleen Frisch, Cermaq, Complex Gill Health Initiative Co-Lead
Dr. Mark Fast, UPEI, Complex Gill Health Initiative Co-Lead

In March, the Government of Canada announced research support for a $4.7 Million Complex Gill Health Initiative that will focus on Complex Gill Disease (CGD), a growing health challenge for salmon farming operations in both the Pacific and North Atlantic.  This project, co-led by Genome Atlantic and Genome BC, will validate biomarkers of healthy and compromised gills of Atlantic salmon and use these to develop an early warning system for the development of gill disease on Atlantic salmon production sites across Canada. The resulting genomics-enabled tools for fish health will guide the management and intervention strategies for complex gill disease in Atlantic salmon.

Genome Atlantic congratulates the coast-to-coast research team and acknowledge the generous support of project funders the Government of Canada through Genome Canada, the federal Department of Fisheries and Oceans, Genome BC, Mitacs Canada, Memorial University, the University of Prince Edward Island, the BC Salmon Farmers Association, and industry partners Cermaq Canada, Grieg Seafood, and Cargill. 

A bold new business model for drug discovery

Dr. Aled Edwards

In a world of skyrocketing drug costs, a revolutionary new business model is being trialed in Canada that promises to spur the pace of drug development and price the results within reach.

The concept will form the basis of Dr. Aled Edwards’ virtual presentation, Open Drug Discovery – A Business Model that can Discover New Medicines and Price Them Affordably, 12 p.m. April 7. The talk is part of the Centre for Genomics Enhanced Medicine (CGEM) Seminar Series, of which Genome Atlantic is a sponsor.

Dr. Edwards, a protein biochemist, based at the University of Toronto, is a leading thinker in the field of chemical biology and drug discovery. He is best known as the founding and current CEO of the Structural Genomics Consortium, or SGC, a charitable open science research organization with university-based sites in Canada, the United Kingdom, Brazil, Sweden, United States and Germany.

Essentially, SGC is a public-private partnership intent on using open science, sharing data and materials fast and publicly, unencumbered by the peer review publishing process, to speed up discoveries of new therapeutic drugs. SGC’s pre-competitive research in structural biology and medicinal chemistry is funded by a range of large pharmaceutical companies, governments, charities, and Genome Canada.  

In addition, Dr. Edwards is a director of Toronto-based M4K Pharma, which also uses open science principles to partner with organizations that contribute their scientific expertise and research services.

In this case, the focus is on developing a cure for DIPG–diffuse intrinsic pontine glioma–an aggressive form of pediatric brain cancer for which there is no effective therapy for the small population of children affected by the disease. 

What makes M4K Pharma so radically different is it combines open science with reliance on regulatory exclusivity as its primary intellectual property and commercial asset instead of patents.

This new business model is attracting interest from government, foundations and individual funders that have different expectations compared with biotech, pharmaceutical companies or venture capitalists, when it comes to return on investment. Because of this difference, Dr. Edwards is convinced that therapeutics commercialized on the basis of open science and regulatory exclusivity mean discoveries can be speeded up, and the resulting drugs can be affordably priced.

Regulatory exclusivity refers to incentives awarded under many governments’ drug approval regimes. These inducements aim to stimulate the discovery of new drugs by shielding the developers from competition.

On the list is data protection for drugs with new active ingredients. This form of regulatory exclusivity effectively blocks competition from generic drug manufacturers. Some governments give regulatory exclusivity to orphan drugs developed for rare diseases, whether or not they contain new active ingredients and there are other forms of regulatory exclusivity as well.

The argument is that these forms of market protection compare quite well with the average length of patent protection, which, unlike regulatory exclusivity measures, can be costly for companies to obtain, defend and extend.

Dr. Edwards and others associated with M4K Pharma expect its success will reinforce their conclusions about the benefits of open science and regulatory exclusivity for quicker development of new affordable drugs.

M4K Pharma has been making headway dealing with DIPG, now the leading cause of death among pediatric patients with brain tumours. The company stepped in to try and come up with a drug therapy because the market for those who need it is too small and unprofitable for conventional pharmaceutical companies to direct research to the problem.

Using open science, M4K Pharma’s collaborators have already identified the ALK2 kinase receptor as a key pathway along with a potential therapeutic approach to exploit it with precision medicine.

Toronto’s Krembil Foundation has already given the given the open science – no patents approach its seal of approval with a $1.5 million donation to set up Medicines 4 Neurodegenerative Diseases, known as M4ND Pharma. The new company’s brief highlights their plan to pursue new genetic drug targets for Parkinson’s disease and Amyotrophic Lateral Sclerosis or ALS modelled on the M4K concept.

The number of attendees at Dr. Edwards’ April 7 virtual presentation is limited. Register here.

[https://www.eventbrite.com/e/virtual-cgem-seminar-series-april-7th-dr-aled-edwards-tickets-142934229127.] Dr. Edwards is a professor at the University of Toronto, and Adjunct Professor at the University of Oxford and McGill University.

On the path to understanding bipolar disorder

Dr. Martin Alda

When he entered medical school at Charles University, in Prague, Martin Alda, knew without a doubt, his specialty would be psychiatry. He “never had second thoughts,” he said.

“For me, it represented ‘the royal road’ to a better understanding of the human mind and brain, and their mutual relationship.“  He noted, “Psychiatry is among the most complex and yet less developed areas of medicine, and there is still much work to do.”

Today, Dr. Alda is one of the world’s leading experts in mood disorders and psychiatric genetics.

In Halifax, he holds the Killam Chair in Mood Disorders at Dalhousie University, a position he has filled since 2007, and heads of the clinical Mood Disorders Program at the Queen Elizabeth II Health Sciences Centre, while maintaining adjunct professorships at McGill University, the University of Pittsburgh, and his alma mater in Prague.

Last year he picked up the Colvin Prize for Outstanding Achievement in Mood Disorders Research and the Heinz Lehmann Award for outstanding contributions to the field of Canadian neuropsychopharmacology research – awards relegated to the top scientists in those fields.

In a career largely devoted to studying and treating the highly inheritable conditions of bipolar disorder (formerly known as manic depression), schizophrenia and depression, Dr. Alda has pushed to close psychiatry’s knowledge gaps about these maladies through three lines of inquiry: mapping genes for these conditions, linking the genetic predisposition to the treatment response, and examining how genetic risk manifests in the behavioural and clinical features of the illnesses. He uses methods that run the gamut from clinical, molecular-genetic and biochemical to brain-imaging and neuropsychological techniques to study the disorders in patients and their families.

In recent years the growing possibilities of genomics to unravel the mysteries of bipolar disorder have commanded his attention.

One current project along those lines, and supported by Genome Atlantic, is Early Detection of Bipolar Disorder and Optimized Selection of Long-Term Treatment. The three-year $975,000 study, begun in 2019 by Dr. Alda and his Dalhousie psychiatry colleague, Dr. Rudolf Uher, the Canada Research Chair in Early Intervention, is exploring genetic factors in bipolar disorder which they believe could provide new clinical tools to speed up diagnosis considerably.

He describes the diagnostic tool they have in mind as “a guide for conducting a focused clinical assessment, using the information gleaned from our analyses of clinical factors and family history, together with a panel of genetic markers that can be readily combined into the risk score.”

One of the most significant advances in thinking about bipolar disorder, said Dr. Alda, has come from “a recognition that bipolar disorder starts years before the first manifestation of mania.” This realization has switched the attention of researchers and clinicians to prevention and early intervention. Faster diagnosis and treatment could substantially improve outcomes because the condition responds better to therapies when the disorder is in its early stages.

Now midway through the project, Dr. Alda said, “we have completed analyses of the clinical and genomic predictors of response to long-term lithium treatment and we are now comparing the lithium data with those on other mood stabilizers.” The results could be important.

Currently, lithium is the standard clinical mood stabilizer most often prescribed to treat bipolar disorder. With the right drug treatment, the illness’s manic and depressive episodes are preventable. However, all patients with bipolar disorder do not respond in the same way to the same treatments, and genetic predisposition appears to play a role in determining what therapies work best.

 “As well, we are collecting the largest sample of children of people with bipolar disorder and their DNA samples, most of which are now genotyped,” he said. “This cohort comes not only from our group in Halifax, but also from collaborators worldwide, and includes now over 2,000 such individuals. We expect this will allow us to differentiate, based on genetic data, which of these children are at a higher or lower risk of developing the illness in the future.”

Bipolar disorder ranks as one of the top 10 causes of death worldwide.

“Indeed, over the last several decades the rate of suicide in bipolar disorder and in psychiatric illness in general has not decreased,” said Dr. Alda. “The factors responsible are probably several. One of them is the fact that suicide risk is especially high in early stages of the illness.

“People with bipolar disorder often seek help after several years of struggle with their symptoms. They can be misdiagnosed early on, and then it takes time before their clinicians come up with the right treatment. These factors are also among those Dr. Uher and I hope to improve with our research – that is, to be able to diagnose the illness accurately and early, and shorten the time to find the effective treatment. Another factor is the societal stigma around mental illness.”

The conundrum of bipolar disorder is compounded by the fact that genetics is determinative for the condition about 80 per cent of the time, leaving environmental factors responsible for the remaining 20 per cent.  “In simple terms,” said Dr. Alda, “this amounts to an equation with two unknowns – the genes and the environment.” He is hopeful that, “Once we know the role of the genes, it will be easier to understand the contribution of the environment.”

What sparks his continuing clinical and research interest in bipolar disorder, considered one the most serious in psychiatry?  His response is surprisingly upbeat. Dr. Alda said it’s a combination of the full recoveries he has witnessed in successfully treated patients, their pleadings for a scientific look at the genetics of treatment response, and the talented and gifted nature of many of the patients themselves. This last point has been well documented and he mentioned Kay R. Jamieson’s book, Touched with Fire, as an example.

Being a psychiatric geneticist also suggests genomics may be part of what keeps him so engaged too. These days, it fuels and facilitates many of his investigations along “the royal road” he has chosen to better understand the mind-brain relationship in bipolar disorder.

New applied genomics research investments announced

News release –

Tuesday, March 9, 2021
Ottawa, ON
$8.6 million in federal funding to support healthier Canadians and a resilient food supply  Genomics is on a mission to develop new knowledge, tools and technologies to improve Canadians’ lives.  

Today, on behalf of the Honourable François-Philippe Champagne, Minister of Innovation, Science and Industry, William Amos, Parliamentary Secretary to Minister of Innovation, Science and Industry (Science), announced $8.6 million in federal support through Genome Canada to five applied genomics research projects that will improve the well-being of Canadians. Working in collaboration with industry, health-care players, as well as provincial and other federal partners—with co-funding valued at $17.8 million—this represents a total investment of $26.4 million in projects that will deliver tangible benefits.

Today’s announcement will support research on early detection and better treatment for atrial fibrillation. This disease affects 25% of Canadians aged 70 and over, increasing their risk of strokes, heart failure and other complications. The funding will support research by Peter Liu at the University of Ottawa Heart Institute, in collaboration with Roche Diagnostics, to improve disease diagnosis, risk prediction, and patient care and outcomes, while also reducing health-care costs. 

This investment also includes funding for a profiling tool to better understand the unique progression of breast cancer in individuals. Working with Thermo Fisher Scientific, John Bartlett of the Ontario Institute for Cancer Research is investigating the effect of ethnicity on the progression of the disease to improve the delivery of targeted breast cancer treatment to Black and Asian women.

In addition, this funding will support a new project in our All for One initiative. Cheryl Rockman-Greenberg, at University of Manitoba, is collaborating with Shared Health to deliver genomics-based precision health services to children in the Prairies with inherited metabolism issues. All for One is a pan-Canadian network of health-care facilities that apply genomics-based tools to rapidly diagnose patients with rare genetic conditions, improving their care, outcomes and family wellness. This lays an equitable foundation for precision health across British Columbia, Alberta, Quebec, the Atlantic provinces—and now the Prairies.

The other two projects funded are in the area of climate-adaptive food production, with a focus on using genomics to breed better soybeans, the third most important crop in Canada, and on developing an early warning system for identifying complex gill disease in salmon farms in the Pacific and North Atlantic.

Demand-driven genomics collaborations like those announced today harness the power of bio-innovation to create healthier, more sustainable and prosperous communities across Canada.

Quotes “Investing in genomics research with a line of sight to application is critical for the health and well-being of Canadians. Genome Canada is proud to work with the Government of Canada to fuel demand-driven genomics research and innovation collaborations among academic, industry, health-care and other partners to shape a better, healthier future for Canadians.” – Dr. Rob Annan, President and CEO, Genome Canada

“Genomics has enormous potential to improve Canadians’ lives and to advance post-pandemic economic recovery. Investments, like the one we are making today in genomics research, help keep Canadians healthy and help keep our industries productive, sustainable and competitive globally.” The Honourable François-Philippe Champagne, Minister of Innovation, Science and Industry

“Genomics research is driving innovation across a range of sectors and generating exciting results that will benefit all Canadians – from more sustainable agricultural practices to treatments for rare diseases. Our Government is proud to support these investments through Genome Canada to fund critical and high impact research.” – William Amos, Parliamentary Secretary to Minister of Innovation, Science and Industry (Science)

Quick Facts
Today’s announcement is for $8.6 million in federal funding for genomic research and an additional $17.8 million in co-funding from provincial governments, businesses and research partners across Canada.

This funding will support five new projects within Genome Canada’s Genomic Applications Partnership Program (GAPP).

Today’s funding announcement includes a $2.1 million federal funding for the fifth regional All for One precision health partnership. This pan-Canadian initiative now spans British Columbia, Alberta, Saskatchewan, Manitoba, Quebec, New Brunswick, Nova Scotia, Prince Edward Island and Newfoundland and Labrador.

Since 2000, Genome Canada has leveraged $1.6 billion in federal investment into a total investment of $3.9 billion in R&D including co-funding, supported over 5,000 talented research trainees and spun-out more than 80 new Canadian companies.

Genome Canada has identified and allocated considerable resources to COVID-19-related work, including leading on the Canadian COVID Genomics Network (CanCOGeN), the COVID-19 Regional Genomics Initiative, as well as partnerships with CIHR on the Canadian 2019 Novel Coronavirus Rapid Research Funding Opportunity and with CIFAR on the AI and COVID-19 Catalyst Grants Initiative.

Learn more about the five projects announced today:
Canadian Prairie Metabolic Network (Health)
In partnership with Genome Prairie and Genome Alberta
Cardiovascular Biomarker Translation Team 2 – Atrial Fibrillation (Health)
In partnership with Ontario Genomics
Complex Gill Disease Initiative (Fisheries)
In partnership with Genome Atlantic and Genome BC
Development and Implementation of a Toolkit for Genomics-Assisted Breeding in Soybean (Agriculture)
In partnership with Génome Québec
Development of an Epigenomic Profiling Tool to Facilitate Precision Medicine in Early Breast Cancer (Health)
In partnership with Ontario Genomics

Related links Backgrounder: Five Genomic Applications Partnership Program Projects Funded

Media contact
Nicola Katz
Director, Communications
Genome Canada
Cell: 613-297-0267
nkatz@genomecanada.ca

Forestry Innovation Transition Trust approves Genome Atlantic project

News release – Feb 4, 2021

The Forestry Innovation Transition Trust is helping to bring innovation to the forefront of the Nova Scotia forestry sector.

The Trust announced three more projects today, Feb 4, that allows businesses focused on new ecological forestry practices to tap into additional expertise to get their products ready for market.

The Innovation Hub of Nova Scotia Inc. will receive $921,000 to support forestry related bioeconomy clients at the pre-commercial stage to overcome technical and business hurdles in their development. The Hub and its partners are working to transform Nova Scotia’s renewable resources and underused waste streams into economic opportunities for the province by producing sustainable, renewable and recyclable products.

The Verschuren Centre for Sustainability in Energy and the Environment (VC Inc.) at Cape Breton University is receiving $672,500 over the next six months to support the development of a Bio-technology Acceleration Centre to help advance key forestry and biomass sector innovative technology companies towards commercialization.

Genome Atlantic will receive $315,500 over four years to support The Atlantic Tree Improvement Council (AtlanTIC) in producing more resilient, commercially important tree species in Nova Scotia.

It will include collaborative breeding, field testing, and new tree improvement technologies such as genomics, which have been shown to shorten breeding cycles and increase growth rate, wood quality, pest resistance and adaptation to climate change.

The projects open up new opportunities within the Nova Scotia forestry sector, advance environmental, social and economic objectives and support the adoption of new ecological forestry practices.

The Trust is also entering into a partnership with Research Nova Scotia to develop a strategic forestry research agenda that is focused on accelerating the production, use and sustainability of forestry and biological resources.

The Trust is in the process of seeking vendors to facilitate sessions with forestry sector organizations who have expressed an interest in advancing sustainable forestry practices in Nova Scotia.

The $50 million trust was announced in February 2020 and may be used by companies, organizations or post-secondary institutions to bring innovation to the forestry and biological resources sector.

Quotes:

Nova Scotia’s forestry sector has an opportunity to be a leader in the bioeconomy and these projects advance the overall purpose of the trust and support both innovation and transition for this vital industry.”

Sandra McKenzie, chair, Forestry Innovation Transition Trust Board

This funding will enable the Verschuren Centre to help companies advance forestry biomass clean tech scale up and commercialization, thereby bringing new innovation to market and building diversification into the forestry sector.

Dr. Beth Mason, president, The Verschuren Centre

Working with our partners, we are committed to building a bioeconomy in Nova Scotia that is responsible, sustainable, and clean.

Rod Badcock, executive director, Nova Scotia Innovation Hub

Genome Atlantic is pleased to partner with the Atlantic Tree Improvement Council (AtlanTIC) in order help the forestry industry realize the economic and environmental benefits of tree improvement technologies. Genomics has recently become a key tool in tree improvement and has been successfully used in many other jurisdictions, and now, through the generous support of the Nova Scotia Forestry Innovation Trust, these tools will be widely available to benefit Nova Scotia producers.

Dr. Richard Donald, Genome Atlantic

Quick Facts:

  • 12 applications were received during the second intake round. One project was approved, Genome Atlantic, and three others are under consideration.
  • the trust will issue three calls for proposals in the 2021-22 fiscal year and the next round opens on April 1
  • the fund will be available until March 31, 2025 or when the funds have been spent
  • trustees are chair Sandra McKenzie, Douglas Hall and David Saxton

Additional Resources:

Government’s forestry sector support website is at: https://novascotia.ca/forestry-sector-support/

More information about the Nova Scotia Forestry Innovation Trust is available at: https://novascotia.ca/forestry-trust/