In this issue of sequence
International team to meet in Halifax next month
The international research team, assembled to explore the potential role of genetic factors in the problematic recovery of the North Atlantic right whale, is meeting in Halifax in January to discuss their approach.
Saint Mary’s University and the New England Aquarium are collaborating on a $6 million research study announced in July by Genome Atlantic.
They are using extensive data about whale health and reproduction collected in Canada, the United States and elsewhere to further their research. The team’s findings could have implications for marine management, policies, practices and conservation plans.
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Initiative sets its sights on complex gill disease in farmed salmon
For reasons unknown, farmed east coast Atlantic salmon have so far escaped the costly rise in complex gill disease (CGD) experienced in net pens on the west coast and as far away as Norway and Scotland.
“CGD does occur in the North Atlantic, and in quite severe cases in European salmon aquaculture operations, but it has not had the same severity in Atlantic Canada,” confirms Dr. Mark Fast, Professor of Fish Health and Immunology at the Atlantic Veterinary College, University of Prince Edward Island (UPEI).
Whether the east coast can remain largely unaffected by the disease is also an open question. However, a new research initiative, begun in August, is aimed at checking CGD nationally and sparing the east coast salmon industry the scale of the west coast problem.
As the academic project leader, Dr. Fast, and his long-time research collaborator, Dr. Matthew Rise, at the Department of Ocean Sciences, Memorial University, have joined forces with British Columbia-based industry, government and academic scientists on a three-year, $3.6 million Complex Gill Disease Initiative (CGDI) under the Genomic Applications Partnership Program of Genome Canada. The initiative is managed by Genome Atlantic, in partnership with Genome British Columbia.
Together the researchers are developing genomic tools to pinpoint the risk factors for CGD and help aquaculturists spot and manage it for better outcomes. At the moment there are no vaccines or therapeutics for CGD available.
Dr. Fast readily admits there is plenty of scientific mystery here to investigate. CGD is found only in farmed fish and shows up as “a range of gross and microscopic lesions” he said.
These lesions are associated with various environmental conditions as well as some fish attributes among other factors. Yet linking cause and effect remains murky. Dr. Fast says CGD is more of a syndrome than a disease, but whatever the label, costs are staggering, even though salmon with CGD is considered safe for human consumption.
Overall, sea mortalities, slowed fish growth, and delayed harvests due to CGD are estimated to be costing the Canadian industry at least 12,500 tonnes in lost annual production, valued at $130 million. Factoring in indirect losses, the figure rises to $250 million.
As for costs to this region’s salmon producers, Dr. Fast said, “There has been some impact on Atlantic Canada but we have not estimated this since it has been a greater concern in British Columbia for a longer period of time.”
Given the revenue at stake, Cermaq Canada, with salmon farms on the east and west coasts of Vancouver Island and Grieg Seafood, with British Columbia salmon operations and a site in development in Placentia Bay, N.L. are leading the charge on the CGDI. Cermaq Canada’s Fish Health Director, Dr. Kathleen Frisch, is the industry lead on the CGDI, while Grieg Seafood’s Director, Fish Health and R&D, Tim Hewison, is the co-lead. Cargill Canada is involved too as an industry partner.
Also on board are Dr. Colin Brauner from the University of British Columbia and Dr. Simon Jones from the federal Department of Fisheries and Oceans.
Dr. Fast expects,” the genomic tools developed in the CGDI will assist in our understanding of gill health in general and could be applied to any gill issue of salmon and potentially other species.” Once risk factors for the disease are better known, he says, the disease will become easier to control, leading to fewer incidents of CGD and measures to prevent outbreaks.
He is optimistic too that “there are likely different therapies and or strategies that already exist to mitigate CGD impacts. For instance, identifying farm practices that contribute to the disease may allow these to be altered to reduce their contribution and there are gill health diets on the market, some of which we will be testing to determine their ability to help heal or resolve CGD.”
Before mitigation work can go ahead, though, Dr. Fast says, the team needs to chart the acute to chronic phases of the syndrome, in order to test various relief strategies throughout the course of the disease for efficacy.
The key aim of the initiative is to validate biomarkers to indicate when Atlantic salmon gills are healthy or compromised. Dr. Fast explains, “First we will be conducting a series of controlled lab experiments at U.B.C. and U.P.E.I. to develop histological and molecular markers associated with a number of different gill trauma events… Once we have found these robust markers from the lab we will test these same markers out in the field during CGD events on multiple farms in B.C. to validate their use during the different states of CGD in the field.”
Markers assigned to different stages of CGD will allow veterinarians to diagnose the syndrome and determine how far advanced it is. Once developed, the cellular and molecular markers can be tested for the proteins they produce when different fish feeds, developed for gill health, are trialed. Knowing the proteins being expressed, enables assessment of how well the feeds are working to treat the condition.
While European salmon producers have had an earlier start on trying to solve their CGD problem, their results are not necessarily transferrable. Dr. Fast said “while they have made some progress toward identifying contributing factors to CGD, they are still working on intervention strategies. The issue we have in Canada is that we do not know that we have the same contributing factors to CGD here, and we cannot treat it without knowing what is causing it.”
He added that it’s possible some European mitigation strategies may work in Canada. That possibility, he said, “is also why we are collaborating with Dr. Sam Martin, at the University of Aberdeen, and others to determine synergies to help the industry as a whole. It’s also possible that some of these strategies may be proprietary…so we will need to develop agreements to use and test these.”
Meanwhile, the initiative will also be building genomics research capacity for aquaculture at the Atlantic Veterinary College. Dr. Fast said the college has been able to purchase a multi-slide scanner to associate histological lesions, the hallmark of CGD, with biomarkers. The link will be made via high throughput image scanning and analysis, sharable with CGDI collaborators and others. A fish pathology resident has been hired under the initiative who will add new expertise to the university. Moreover, the sequencing pipelines and genomics collaborations developed with Memorial University during a previous GAPP-funded project are now being expanded to take on gill transcriptomes. Three post-doctoral fellows and student trainees hired for the initiative are expected to strengthen UPEI’s relationship with MUN and forge new ones with the University of British Columbia, the University of Connecticut and various universities in the United Kingdom.
Other key investigators for the CGDI are Dr. Rachel Balder, a Senior Scientist and Manager for the Nutrition Sciences group at Cargill Animal Nutrition, Elk River, MN; Dr. Simon Jones, Research Scientist, leader of the Marine Parasitology Program in Nanaimo, B.C. for the Department of Fisheries and Oceans; and Dr. Sonja Saksida, an aquatic epidemiologist at the Atlantic Veterinary College, UPEI.
Besides Cermaq, Grieg Seafood and Genome Canada, the CGDI collaborators include the Department of Fisheries and Oceans, Cargill, and MITACS.
SEQUENCE #7: Looking to genomics for hope and solutions
“There is hope”.
This is how Dr. Martin Alda summed up the promise of genomics as a potential game-changer for diagnosing and treating bipolar disorder (BD). Clinicians have known for some time that BD tends to run in families, and Dr. Alda and his colleague Dr. Rudolf Uher are at the forefront of new research that is using genetics to diagnose BD more quickly in high-risk individuals and to predict which treatment will work best for which people.
Drs. Alda and Uher, psychiatrists and researchers with Dalhousie University and the Nova Scotia Health Authority, were speaking at a recent panel discussion on genomics and bipolar disorder co-hosted by Genome Atlantic and Genome Canada. The event opened up with some exciting news: Genome Atlantic and Genome Canada were joined by the Nova Scotia Health Authority, Dalhousie Medical Research Foundation, Research Nova Scotia Trust, and the Dalhousie Department of Psychiatry in announcing $975,000 in funding for a new research project co-led by Drs. Alda and Uher, which aims to develop new clinical screening tools to better diagnose and treat BD. Also read our interview with Dr. Alda.
It was a big week. A few days earlier, Genome Atlantic celebrated the announcement of a $1.4 million project co-led by Dr. Rob Beiko of Dalhousie University, that will develop new genomic tools to fight superbugs. These tools, consisting of bioinformatics algorithms and software, will track genes that contribute to antimicrobial resistance (AMR) – a huge problem for the agri-food industry and the health of Canadians.
The mental health and superbugs projects are on the cutting edge of health innovation. The work led by Drs. Alda and Uher has the potential to improve lives through speedier, personalized medicine-based treatments. Dr. Beiko and his team are leading the charge in developing tools that will allow us for the first time ever, to track AMR as a dynamic phenomenon involving the transfer of genes among AMR-resistant bacteria.
Genomics is the impact driver in the innovation toolkit. But not just in health. In November, we launched a $1.1 million New Brunswick-based project to advance cannabis research and increase productivity – and we’ll soon have some exciting project news on the aquaculture and environment fronts too. All the above projects are supported by Genome Atlantic, with funding from Genome Canada and other public and private partners.
Recently, Genome Atlantic took part in an important announcement for the Maritime apple industry: the launch of the National Apple Breeding Consortium which brings together Canadian researchers, breeders and marketers with the aim to streamline apple development and boost returns to the industry. Genome Atlantic and Dalhousie University apple researcher Dr. Sean Myles were instrumental in getting the Consortium off the ground, and we hope to pursue future research through the Consortium, using genomics to improve and accelerate the development of successful new Maritime apple varieties.
The ability to recruit and keep top talent is critical for Atlantic Canada. And so, we’re pleased to share with you the stories of three talented scientists working in Prince Edward Island, Nova Scotia and New Brunswick, and a doctoral student at Memorial University in Newfoundland – all living and working here in part because of Genome Atlantic projects.
Finally, a big thanks to Invest Nova Scotia who recently announced funding of $325,000 over three years to support Genome Atlantic’s business development activities in Nova Scotia. Genome Atlantic’s strategy is driven by the needs of end-users, and this investment will help us to meet the rapidly-growing demands for genomic solutions across health and resource sectors.
Sequence #12: Wastewater surveillance acquiring a place in COVID detection
Recent news, rife with reports of an approaching third pandemic wave that could delay economic recovery plans, underline how crucial genomics has become as a navigational aid in the continuing storm. Virus detection through sequencing has proven invaluable to public health efforts to contain the pandemic, and to employers and workers to keep the country’s economic engines turning.
One of the newer additions to the virus detection arsenal is wastewater surveillance technology. A project in this vein, worth keeping an eye on, is led by Dalhousie University. With sampling sites across Nova Scotia, this project has the capacity to serve as an early warning system for surges of clinical COVID‑19; caseloads. In that respect, the project appears to be unique in the country and it should give Nova Scotia a potential extra buffer against a third wave. We have a story on the project in this issue of Sequence.
Elsewhere, in this edition, you’ll learn genomics is about to help Atlantic Canada’s forestry sector forge ahead collectively with a tree improvement program to safeguard the industry against climate change and other threats.
We also have hot off the press news on a major gill health improvement initiative, which has just been greenlighted with funding by Genome Canada. The project will keep researchers at the University of Prince Edward Island busy validating biomarkers of healthy and compromised gills of Atlantic salmon to use in early detection of developing gill disease in this commercially important farmed fish.
On the human health side, you may be surprised to learn the region is home to one of the world’s leading experts in mood disorders, Dr. Martin Alda. One of his projects is using genomics to better understand bipolar disorder, one of the top 10 causes of death worldwide.
To keep your diary filled, we offer a heads up for an April 7 virtual seminar, presented by the Centre for Genomics Enhanced Medicine and featuring Dr. Aled Edwards, a leading thinker in the field of chemical biology and drug discovery. He will be discussing a formula being trialed in Toronto to speed up new drug development and keep the results affordably priced.
Finally, we send a shout-out to Dr. Stefanie Colombo, the aquatic nutritionist at the Truro Agricultural Campus, Dalhousie University, who is focused on improving the nutrition of farmed fish. Featured in our last edition as a scientist to watch, Dr. Colombo has just been announced as one of this year’s Science Meets Parliament delegates by the federal Science Policy Centre and the Office of the Chief Science Advisor. Way to go, Stefanie!
Also In This Issue….
Nova Scotia Gains COVID Early Warning System Via Wastewater Sampling
Key Forestry Players Fight Climate Change with Tree Improvement
A Leading Thinker to Discuss Open Drug Discovery
$4.7 Million to Improve Gill Health In Salmon
Understanding Bipolar Disorder: a pre-eminent expert describes his pursuit
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Sequence #11: A path to economic recovery
As this unforgettable year nears its close, we have upbeat news to report in this issue from the health care and oceans sectors.
Despite the COVID-19 pandemic, Genome Atlantic has never been busier. Our current portfolio has 23 active, funded projects worth nearly $50 million, encompassing 25 companies and 15 university partners.
These projects span all four Atlantic provinces and represent a broad range of sectors including human health, oceans (aquaculture and energy), environment, agriculture, forestry and mining.
Significantly, our portfolio includes an ever-increasing amount of private sector investment, which has grown from eight per cent in 2008 to between 20-30% in recent years.
As we track the beneficial, unfolding effects of the projects on our list, we continue to pilot new opportunities through our business development pipeline.
Based on our activity, genomics is poised to be a driving force in our region’s economic recovery.
At this time, we want to acknowledge the tremendous support of our many partners in government, academia, and industry throughout this unprecedented period. They have been a pleasure to work with.
To you, our subscribers, we extend our seasonal best wishes and the hope that you’ll find inspiration for the year ahead in the people and applied genomics projects highlighted in this issue.
We all know recovery won’t be instant or easy, and that it will be more important than ever for Atlantic Canada to back innovations with a proven track record of impact. Genomics is one of these technologies, delivering impressive ROI across a range of sectors strategic to Atlantic Canada’s health and prosperity and attracting high levels of private sector investment.
Our sleeves are rolled up and the path to our region’s greater prosperity lies ahead.
In This Issue….
Climate proofing P.E.I.’s blue mussels
Early diagnosis of rare genetic disorders in children
Initial findings on track in offshore energy project
One to watch: Dr. Stephanie Colombo
One genomic discovery leads to many more
Cleaner fish for salmon farming
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Sequence #10: Pandemic response & economic renewal go hand in hand
The last few months have been unprecedented as we have all struggled to respond to a global pandemic. We hope that through it all, you and your families have stayed healthy. Even as restrictions ease and the economy re-opens, we are mindful of the need for continuing vigilance to ensure that we can all move forward, propelled by cautious optimism and a shared commitment to renewal.
Despite the challenges, this has been an especially productive time for Genome Atlantic as we have actively advanced an array of initiatives on two independent tracks: those focused on COVID-19 surveillance and the genetic determinants of disease severity, in parallel with ongoing efforts to continue to strengthen the bioeconomy of Atlantic Canada. Both are necessary for our region’s economic recovery and well-being. In this issue of Sequence, we share some exciting examples of each, including some great new video content.
We recently announced funding to Dalhousie University researchers to support important COVID-19 genomics projects. One, led by Drs. David and Alyson Kelvin, aims to find COVID-19 biomarkers that will help doctors triage patients and inform patient care protocols in settings like long-term care facilities, emergency rooms, hospitals, and ICUs. The second project, led by Drs. Nikhil Thomas, John Archibald and Morgan Langille, is piloting a surveillance tool to quickly identify early trends in transmission in high-risk settings like long-term care facilities, food processing plants or fishing vessels.
Genomics is a vital tool in our battle against COVID-19. Watch our short, animated videos “On the Trail of Covid-19” and “The Race for a Vaccine” to find out why.
On the economic development front, find out how forestry giant JD Irving Ltd. is using genomic selection to significantly improve forestry tree breeding practices and increase production. Take a deeper dive into the headline-making New Brunswick oyster breeding project through an engaging project video and a Q/A (Scroll down) with L’Étang Ruisseau Bar’s Dr. Martin Mallet and Laval University’s Dr. Louis Bernatchez. And hear from Dr. Kurt Gamperl at Memorial University and Dr. Mark Fast at UPEI for an update on their work addressing the adverse effects of climate change on farmed Atlantic salmon.
To round out this issue, medical research innovator Dr. Janessa Laskin of the BC Cancer Agency tells us why genomics could be the future of cancer treatment. And we profile our long-time industry collaborator Dr. Richard Taylor, recently retired from a long career with EWOS and Cargill, who shares some tips on forging successful industry-academic partnerships.
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SEQUENCE # 9: De-risking investments through genomics R&D
Recently we visited the Research and Productivity Council (RPC) in New Brunswick to film how they use genomics in testing, developing and improving products and processes. RPC is a global leader in material and environmental testing, work that puts them in daily contact with innovation at every stage of technology and market readiness. For many years, Genome Atlantic has collaborated with RPC – for example, working with RPC scientists like extractive metallurgist Neri Botha to improve the efficiency of bioleaching for mining clients. (See link to our story and video below.)
RPC’s Executive Director Eric Cook believes that genomics is a critical biotechnology for driving innovation and he credits Genome Atlantic for helping to de-risk business investment in genomics projects. Genome Atlantic does this by providing advice and guidance at every step – from assessing the feasibility of a genomic solution, to helping with proposal development, to securing funding, to project management – to ensure that projects deliver maximum benefit to our business and public-sector clients. And because all our projects are industry-led, we’re committed to finding practical solutions and delivering maximum benefit for our business and public-sector clients – whether we’re using genomics to help de-risk offshore oil and gas exploration decisions, develop novel clinical aquaculture feeds, or find new treatments for Atlantic Canadians with genetic diseases.
The fact that private sector investment makes up almost 30% of our portfolio speaks to the high level of confidence Atlantic Canadian businesses have in genomic technologies and in Genome Atlantic’s ability to maximize and de-risk their investment.
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In this issue of Sequence we zero in on three innovative examples of genomics applications relevant to Atlantic Canada. Three years ago, Genome Canada and Genome Atlantic launched a large-scale R&D project aimed at tackling Microbiologically Influenced Corrosion (MIC), which is a multi-million-dollar problem for our oil and gas energy sector. We caught up with project co-lead Dr. Lisa Gieg to find out what she and her team have learned so far and how this information could be used to help predict and manage MIC. At RPC, we met up with Neri Botha to see how using naturally occurring bacteria to extract metal could be a viable and environmentally friendly solution for the mining industry. And we talk with two plant geneticists who are passionate about helping the region’s apple industry shine – Dr. Sean Myles dishes on apple breeding (and cannabis traceability) and Dr. Zoë Migicovsky tells us why her love of apples drew her to Nova Scotia (watch our video profile and story on Zoë.).
SEQUENCE # 8: New technologies, real solutions
There’s no denying genomics is cool. The study of genes and their functions is adding to our understanding of every living thing. But there’s more to genomics than the wow factor. Genomic technologies are driving solutions for our resource industries, human health, and the environment.
One of the most promising new genomic technologies is eDNA, an environmental monitoring tool that identifies species’ DNA from their genetic material (scales, fur, feces, etc.) collected in water or land samples. It’s non-invasive, accurate and relatively inexpensive. In Atlantic Canada, Parks Canada is using eDNA to track invasive chain pickerel in Nova Scotia’s Kejimkujik National Park. EDNA led scientists at New Brunswick’s Canadian Rivers Institute to a unique population of Saint John River striped bass thought to be lost forever. And in St. John’s, NL, The Centre for Environmental Applications (CEGA) is using eDNA to conduct environmental monitoring around the province’s offshore oil and gas platforms.
But how effective is eDNA in extreme turbulent marine conditions? Could it, for example, be used to monitor marine species-at-risk in a place like the Bay of Fundy’s Minas Passage where 160 billion tons of seawater flow through twice a day driven by the world’s highest tides? That’s what Stantec’s Dr. Marc Skinner wanted to find out when we partnered with him, the Offshore Energy Research Association of NS (OERA), the University of Guelph and Dalhousie University on a unique eDNA test using Dalhousie’s Aquatron. The results so far are promising. Check out the article and our two new videos with Marc! (Scroll down the article for the second video.)
Another environmental use for genomics is in remediating contaminated industrial sites like abandoned mines. Saint Mary’s University’s Dr. Linda Campbell, world-renowned researcher in the field of environmental contamination, is partnering with Genome Atlantic (with support from the NS Department of Energy and Mines) to explore biological solutions to the age-old problem of remediating toxic arsenic and mercury in tailings from legacy gold mining sites.
In human health, genomics contributes to improved diagnosis and treatment of cancers and inherited and infectious diseases. Sequence Bio, a biotechnology company based in St. John’s, NL, is launching its NL Genome Project this summer to study the unique genetic makeup of Newfoundland and Labrador – with the ultimate aim of improving treatments and health outcomes. Genome Atlantic recently caught up with Sequence Bio CEO and co-founder Chris Gardner for an update on the company’s ambitious plans and goals.
We also take a closer look at how genomics is being used to track genes that contribute to antimicrobial resistance (AMR), a big problem for the agri-food industry and the health of Canadians. Dalhousie University’s Dr. Rob Beiko is at the forefront of this new science, and he shares with us some of the cutting-edge tools that he’s developing to combat AMR.
In the last issue of Sequence, we told you how apple researchers across Canada are pooling their information and innovations to bring new apples to market more quickly. It’s all about developing new varieties that grow best in local conditions, says Dalhousie University’s Dr. Sean Myles. Find out how scientists like Myles are using genomic selection to develop varieties more quickly and how this could help Maritime apple producers.
Lastly, Genome Atlantic is hosting the 7th International Symposium on Applied Microbiology and Molecular Systems (ISMOS-7) from June 18-21 in Halifax. ISMOS is the world’s leading conference on microbiology and molecular biology in the oil and gas industry, and a forum where delegates from industry and academia come together to discuss how emerging microbial and molecular tools can help solve some of the industry’s biggest challenges like biocorrosion and sustainable oil extraction.
Registration is still open (editor’s note: registration is now closed) but it’s filling up fast so don’t miss out. Hope you can join us for a great program and a fun time!
Sequence #1: So What’s Up With The Microbiome?
The microbiome is a hot topic these days, embraced by research scientists and the media alike. The microbiome refers to all the microorganisms and their collective genetic material that reside in human beings and other animals, plants, soil, and water. These communities of ‘microbial flora’ have always been with us but we’re just beginning to understand the role they play in everything from human health to mining and agriculture.
We know, for example, that not all microbes are equal. Some are harmful, some benign and some essential for the health of their hosts. Microbes can boost our immune systems and our natural resources – but maintaining a healthy microbiome is a balancing act that can be thrown out of whack by factors like diet(in humans) and chemicals (in soil and water).
This issue of Sequence explores the new frontier of the microbiome. We’ll go behind the scenes with scientists on the cutting edge of human microbiome research, meet a hard-working sequencing facility that’s a hit with genetic researchers near and far, and see why microbes are the Midas touch for gold extraction, a better tool for cleaning oil spills, and the magic in making better wines.