Young scientist profile: Dr. Zoë Migicovsky

A passion for apples and grapes

Apples and grapes, two of Nova Scotia’s most important crops, are opening research doors at home and in the United States for Dr. Zoë Migicovsky, a bright postdoc geneticist with a self-confessed passion for Nova Scotia.

Genome Atlantic can take some credit for helping to pry those doors open early on. As a doctoral student, she worked with Dr. Sean Myles, Dalhousie’s Research Chair in Agricultural Genetic Diversity and a leading apple breeding expert, on a research project called “Exploiting the Full Potential of the Next Generation DNA Sequencing for Crop Improvement”. It was a Genome Canada project, supported by Genome Atlantic. Dr. Migicovsky also worked with Dr. Daniel Money from the University of Cambridge, and Dr. Kyle Gardner, with Agriculture and Agri-Food Canada, on the project, which produced “two papers and associated software to help researchers get more genetic information out of their sequencing data.”

Now as a postdoctoral fellow, Dr. Migicovsky is busy with another of Dr. Myles’s genomics projects, this one funded by National Sciences and Engineering Research Council of Canada with continuing support from Genome Atlantic. The research is part of his ongoing efforts – and hers – to use genomics to accelerate the traditionally painstaking work of apple breeding.

The work centers on more than 1,000 different apple varieties known as the Apple Biodiversity Collection (http://www.cultivatingdiversity.org/) in Kentville. Working with collaborators at Agriculture and Agri-Food Canada in Kentville, she is helping to comprehensively record a diverse array of traits, or phenotypes, across the apple varieties. By linking together this phenotype information with genetic data to perform genetic mapping, she says, the resulting work will “allow breeders to screen seedlings using genetic markers in order to predict if they possess a trait of interest.”

This approach should help reduce the lengthy and costly process of cross-breeding that requires apple trees to be grown from seedlings to confirm the selection of specific traits. The outcome would be known in advance, based on the genomic evidence in the seedlings – the tool kit of genetic markers Dr. Migicovsky is helping to develop. While apple breeders would still have to evaluate the remaining trees, new commercial cultivar development would become both faster and cheaper.

Dr. Migicovsky is especially interested in pinpointing the sources of variations in fruit for characteristics that fuel consumer appetites, such as colour, shape and flavour. This area of investigation relies heavily on bioinformatics and other data analytic techniques to process vast quantities of phenomic and genomic data generated by the research.

Her abilities have been duly noticed. Fresh from doctoral studies, she was tapped to join a $4.6 million, five-year, multi-institutional American research project, funded by National Science Foundation Plant Genome Research Program 1546869 and led by Dr. Allison Miller (Saint Louis University/Donald Danforth Plant Science Center). The project, “Adapting Perennial Crops for Climate Change: Graft Transmissible Effects of Rootstocks on Grapevine Shoots”, aims to help the U.S. wine industry weather the impacts of climate change with more resilient and adaptable grape vines. She heads a team assigned to assess the status of grafted grapevines planted in three vineyards across a transect of California, while other teams examine experimental vineyards planted in areas of Missouri, South Dakota and New York state.

Ordinarily, she would have been expected to relocate to the U.S for this work. Instead, she chose to maintain Kentville, the Dalhousie Faculty of Agriculture and the lab of Dr. Sean Myles, one of her doctoral thesis advisors – as home base. She gratefully points out that her American project advisor, Dr. Dan Chitwood, a plant morphologist who uses mathematical models to analyze morphological data from x-ray CT scans at Michigan State University, was among those who championed her cause. As a result, for most of the year she works remotely on the project and she is the only Canadian on the team.

“I love Nova Scotia,” she explains, “and as long as I can do work here, I’d really like to stay in the province.” A native Montrealer, she admits she fell hard for Nova Scotia as an Acadia University undergraduate. The lure was so strong that after graduate studies at the University of Lethbridge, she opted to return to the province for her doctorate.

These days she resides in the Annapolis valley, near Kentville. Outside the lab, she describes herself as a voracious reader with eclectic tastes that range from poetry to thrillers and non-fiction; someone who “loves to write” and enjoys the exploratory side of travel.

On the job, to satisfy the American project, she spends June, July and part of August sampling across three vineyards in the Californian Central Valley. “I work with a team of students to measure traits including physiology, mineral composition, leaf morphology, and gene expression in grafted grapevines,” she said.

The plan, she explains, is to link the data to weather information and learn how the environment, root systems and shoots interact. These are all critical elements in understanding how grapevines respond to the environment around them.

The rest of the time, she is in Kentville analyzing the huge data sets produced by her California team and working on apples.

She is confident that some of the data from the large American project will be transferrable to this province’s wine industry since some of the examined areas have climates relatively similar to Nova Scotia’s.

As fate would have it, the U.S. project focuses on a long-held interest in climate change, a subject she once thought she would be examining through a very different lens. Initially she went to Acadia determined to become an environmental lawyer. That was until a serendipitous biology course got in the way, and so captivated her interest that law school lost its lustre and she set her cap on advanced biology instead.

The switch has proved so inspiring that Dr. Migicovsky now has many fans in the local science and genomics community all watching her career with great interest and hoping that Nova Scotia and Atlantic Canada can hang on to her burgeoning talent.

Digging into Mic

Corrosion-causing bacteria account for approximately 20 percent of corrosion failures in oil and gas pipelines, and billions of dollars of damage each year. Yet, relatively little is known about how this phenomenon, known as Microbiologically Influenced Corrosion (MIC), occurs.

In 2016, a $7.8 million collaborative research project involving four universities in Alberta and Atlantic Canada was launched with the aim of filling in some of our knowledge gaps about MIC. Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production (“geno-Mic” for short) uses genomics to better predict how, where and why MIC occurs and how to mitigate it. Ultimately, a better understanding of MIC could improve infrastructure integrity, reduce the potential of oil spills, and improve worker safety – potentially reducing operating costs and saving Canada’s oil and gas industry $300-500 million over 10 to 20 years.

The project is funded by the federal government under Genome Canada’s Large-Scale Applied Research Project Competition (LSARP) with additional support from multiple university and industry partners, and is co-managed by Genome Alberta and Genome Atlantic.

Dr. Lisa Gieg, University of Calgary, is a co-lead on the project. Dr. Gieg was in Halifax recently for a project meeting and to present at ISMOS-7, an international scientific conference on microbiology and molecular biology in the oil and gas industry. We caught up with her for an update on the project three years in and to find out how project scientists are filling some of those knowledge gaps.

An interview with Dr. Lisa Gieg


Genome Atlantic: Why do we know so relatively little about MIC – and how is this project trying to change that?

A:MIC is one of the several ways by which corrosion of materials can occur – and one of the challenges with understanding and diagnosing MIC is that it is not an isolated mechanism. That is, while microorganisms play a key role in the corrosion, their metabolism is affected by the chemical environment surrounding them (e.g., kinds of carbon, such as fatty acids or hydrocarbon; or electron acceptors, like oxygen, nitrate, or sulfate, pH) and the surrounding physical conditions, such as temperature and pressure. MIC is very complicated because many factors can affect whether microorganisms will thrive and metabolize in such a way that leads to corrosion. Thus, it’s difficult to pinpoint that corrosion is solely due to the action of microorganisms. Put another way, microorganisms are everywhere, but whether their activity leads to corrosion can be difficult to sort out because of other corrosion that may occur due to the chemical and physical environment.

Based on studies with pure cultures of microorganisms such as sulfate-reducing microorganisms (SRM), a lot is already known about specific mechanisms of MIC, but less is known about other types of microorganisms, and how communities of microorganisms can work together in a way that leads to corrosion. Also, MIC has often been studied in ‘isolation’ – e.g., by microbiologists, or chemists, or engineers. Rarely have all these disciplines come together to tackle the MIC problem.

The geno-MIC project is unique in that it has researchers in many different disciplines such as these working together towards a better understanding of MIC. We are approaching an understanding of MIC from a holistic point of view. We are using genomics to identify key microorganisms present in different environments for which we know the physical conditions (or operating conditions – temperature, pressure, fluid flow rates, etc.), and the chemical conditions (pH, chemical composition, etc.), and determining corrosion rates under these different conditions. In this way, we start to look for trends as to which kinds of microorganisms are most actively contributing to corrosion under different oil and gas operating conditions (e.g., in different kinds of pipelines, processing facilities, produced waters, etc.). When we identify the key microorganisms and the conditions most conducive to promoting MIC, we will know which organisms to target to better monitor and mitigate MIC.

Does MIC manifest itself differently in onshore and offshore pipelines?

A: Microbial corrosion can occur in both environments, but differences in the mechanisms of MIC are due to the chemical environment surrounding the microbial communities. Offshore, because seawater is used in many of the operations, sulfate is present in relatively high concentrations (20-30 mM) which readily stimulates sulfate-reducing microorganisms (SRM). This microbial metabolic process yields hydrogen sulfide which reacts with iron in carbon steel infrastructure to form FeS (iron sulfide) which is highly corrosive.

Onshore, sulfate may be present in some systems, but not always, so other microorganisms are likely playing more important roles. For example, we recently studied a sample collected from a leaking pipeline, and while all indications strongly pointed to MIC as the major mechanism of corrosion, neither sulfate nor SRM were present in substantial amounts – many other kinds of microorganisms were more abundant and were most likely the key players in the corrosion scenario. We are still in the process of identifying exactly how these other kinds of microorganisms are behaving in order to corrode metal. In almost all cases of MIC, microorganisms attached to pipe surfaces are the most detrimental, but we still have a lot to discover in terms of the many ways and the kinds of microorganisms that may be contributing to metal corrosion.

Three years in, what are some of the main things you’ve found out? And what are the next steps?

A: The major objective of our project is to gain a better understanding of MIC under different conditions in order to better detect and manage this important yet poorly understood mechanism of corrosion. Our project has 4 major activities (1) Knowledge – where we aim to identify the different kinds of microbes and activities associated with MIC and are building a MIC database in order to do this; (2) Devices & Assays – where we aim to develop tools for MIC monitoring/detection; (3) Models – where we aim to better predict MIC; and (4) Translation – where we aim to better understand the gaps between academic research and industry uptake, to incorporate research findings into industry standards, and to help industry consider MIC as part of corrosion management strategies.

To date, the project has developed several predictive and risk-based models and we are in the process of validating these with field data from our industry partners. For the translation piece, our team has been hosting stakeholder workshops and conference forums/workshops on the topic of MIC and are actively involved in either creating new standards (on the topic of using molecular microbiological methods for MIC) or updating industry standards related to MIC (e.g., through NACE International, and DNV-GL).

For the Knowledge and Devices/Assays activities, we have been analyzing many field samples from different kinds of oil and gas operations (offshore and onshore, collected from infrastructure operated under different physical conditions such as temperature/pressure) by characterizing microbial communities, chemistry, and corrosion rates. This data is being entered into a new database also being developed by the project that we will ultimately use to discern trends in the data – again – for the purpose of identifying which microbial players are most corrosive under different conditions so that we can better detect (through devices and assays), monitor for, and mitigate MIC.

When will the project wrap up?

A: We officially wrap up in October 2020 but are applying for a no-cost extension so hope to continue the project until October 2021. We will be looking for opportunities to continue some aspects of the project beyond that date, either through another LSARP, GAPP (Genome Canada’s Large-Scale Applied Research Project and Genomic Applications Partnership Program), or another funding avenue.

How will the project results be integrated into industry practices or operations?

A: Our project team is actively involved in meeting with our industry partners on an ongoing basis. We host workshops and forums on MIC a few times a year, bringing together academic researchers and industry stakeholders (oil and gas operators, service companies, chemical suppliers, consultants) so that we can learn from each other and have an ongoing dialog about the challenges and the tools that can be used/developed to determine whether MIC will be a problem in a given system.

We are also involved in preparing industry standards related to the topic of MIC that a lot of industry stakeholders look to for guidance on dealing with corrosion detection and management. For example, several team members (academic and industry partners) are in the process of developing a new NACE International standard on Molecular Microbiological Methods – essentially outlining the best practices towards using genomics for identifying microorganisms in oil and gas samples. Finally, predictive or risk-based models developed in the geno-MIC project are being reviewed by our industry partners who are also providing field data for their validation. Thus, our geno-MIC team is doing research in close conjunction with industry, which will help immensely with the uptake/use of our research findings by them.

Why Bioleaching is primed for prime time

Using rock’s naturally occurring bacteria to extract metal from ore isn’t nearly as experimental or futuristic as some people might think. Neri Botha, an extractive metallurgist with the Research Productivity Council (RPC) in Fredericton, N.B., says the technique, known as bioleaching, is primed to be ready for prime time in the mining industry.

Using naturally occurring microbes instead of toxic chemicals to extract metal from ores could soon be the environmentally-friendly preferred choice of the mining industry.

“The technology is ready,” she says, “but the commercialization is lagging behind. What is needed is the right opportunity where the obstacles necessitate the process, making it worth taking on any perceived risk, due to the process being relatively novel. Government support for the environmentally friendlier process could also help,” she adds.

Bioleaching has been around at least since 1000 BC when the Romans and Phoenicians utilized the process to recover copper from streams passing through ore bodies. It was first used commercially in a South African gold mine in 1986. As a South African-trained professional engineer, Botha has kept a close watch on developments in this area since her days at the University of Pretoria, where a course in hydrometallurgy first sparked her interest in this novel process.

Bioleaching works, Botha explains, “by utilizing certain microorganisms to accelerate the rate of dissolution of sulfide minerals using their enzymes. These microorganisms, known as mesophiles or moderate thermophiles, could be isolated from mine water, or from ores, or from sulphur-bearing hot springs etc.”

Genomics plays a critical role in helping sort out the identities of the microorganisms, and Botha has been researching genomics applications for the mining industry for many years, with ongoing support from Genome Atlantic.

She explains that in the mining industry, bioleaching’s economic and environmental advantages – particularly in gold mining, but also in nickel, cobalt and copper mining – are spurring intense interest.

The reason for this is the depletion of conventional high-grade reserves. The situation, she says, has created a need to treat lower grade ores as well as re-treat old tailing sites to extract residual metals. Bioleaching makes those propositions not only doable but economically feasible. For tailing sites, bioleaching presents opportunities to unlock their value as well as to remediate them with the added bonus of producing no atmospheric pollution. The technique also boasts low capital and operating costs.

RPC, New Brunswick’s provincial research institution where Botha has worked since 2012, is considered an important centre of bioleaching expertise in the world’s scientific community. That expertise has developed in conjunction with the institution’s mandate to engage in industry-driven applied research. RPC has been involved in various types and phases of bioleaching projects in over 30 countries since 1989.

Currently, RPC is assisting on a primary copper bioleaching project now under development with an Ontario based engineering firm. In addition, the institution is working on a chalcopyrite bioleaching project in Zambia and on a cobalt research project in the United Kingdom (CoG3). Other research projects in progress, Botha says, concern “the gold extraction process for Newfoundland ores and we are also involved with Rare Earth Element Research.”

The U.K. project, CoG3, is particularly prestigious. The focus is on safeguarding the supply of cobalt, a metal critical to advanced technology, for such things as batteries and superalloys. The project, led by the National History Museum in the U.K., involves a research consortium of six universities, three research institutes and eight industrial partners. RPC is part of the technical advisory committee.

Bioleaching is a “proven technology,” says Botha, “especially in the gold industry and for secondary copper minerals as well as other metals.” When it comes to gold, she says bioleaching is “uniquely situated to assist in the extraction of problematic ores containing locked gold.” The metal can be locked for physical or chemical reasons or it can be trapped in the ore’s sulphide lattice. Bioleaching could potentially unlock it.

“Certain minerals still present challenges though, such as chalcopyrite,” she pointed out. Chalcopyrite is the brassy yellow mineral in which copper is commonly found. It tends to form passivating or unreactive layers of oxides on its surface,” she said, “These layers limit the recovery of copper at temperatures and redox conditions suitable for microbial culturing.” She adds, “significant research has thus gone into this and the world’s first primary copper bioleaching plant is currently being built, incorporating RCP findings.”

Once this new plant is running, she foresees bioleaching becoming standard for copper extraction within a few years. As secondary copper minerals and high-grade ores continue to deplete, she says, the bulk of the world’s unexploited copper reserves are becoming increasingly less economic to mine by conventional means.

In many cases, bioleaching, with some help from genomics, presents an irresistible solution, which Botha expects will make it a mainstream mining technology very soon.

The future of personalized health & human performance

In today’s data revolution, genomics is emerging as a potential game changer for medicine and human performance, fuelled, in part, by pioneering work in precision personalized data underway on Canada’s east and west coasts. This exciting development was examined in a recent panel discussion hosted and emceed by Genome Atlantic on “The Future of Personalized Health & Human Performance” during BioPort Atlantic 2019.

Dr. Steve Armstrong, Genome Atlantic’s President and CEO and the panel’s emcee, teed up the discussion by posing the following questions: 

“If you were diagnosed with cancer today, wouldn’t you want a treatment plan that is custom designed for you, your genetic blueprint and your specific cancer?  If your son or daughter had an unexplained illness and you were bouncing from specialist to specialist for years on end, wouldn’t you want to bring this diagnostic odyssey to an end?  Or if you were the owner of the Pittsburgh Penguins, home of our local hero Sydney Crosby, wouldn’t you want to ensure that Sid and the team were performing at their best?  In all three examples, what kind of data would you need to make that happen?”

To answer these questions, the panel tapped three well known trailblazers who use data every day in their quest to improve human health and well-being: Dr. Janessa Laskin, a BC Cancer medical oncologist and the clinical leader of the Personalized Oncogenomics (POG) initiative in Vancouver; Dr. Christopher McMaster, Scientific Director of the CIHR Institute of Genetics and Director of the Scientific and Clinical Hub for Orphan Drug Development (formerly IGNITE), both based at Dalhousie University in Halifax; and Dr. Travis McDonough, founder and CEO of Kinduct, a Halifax-based athlete management and monitoring company with professional sports team clients from around the world.

POG is the world’s only cancer research project that uses whole genome sequencing, including transcriptomic (RNA) data to search for personalized treatments for patients with metastatic cancer, a malady Dr. Laskin characterizes as “a disease of the genome.”  Dr. Chris McMaster and his group have uncovered a potential therapy for congenital sideroblastic anemia, a condition in which the bone marrow fails to produce enough healthy red blood cells, and are developing treatments for inherited Parkinson’s disease and for familial exudative vitreoretinopathy, a hereditary disorder that can cause vision loss. Meanwhile, Kinduct collects, sifts and aggregates a vast array of data, including genomic information, on individual athletes to come up with comprehensive regimes to improve athletic performance.

Dr. Janessa Laskin

Dr. Laskin said one of the challenges of using genomics to find and then target the drivers of an individual’s cancer is the realization that “we have been extremely siloed in the way we think about cancer and how we think about drugs. But now we have technology that tells us that a particular drug might be very useful in multiple different kinds of cancers and genome technology is helping us figure that out.”

What we are learning, she said, is that drugs not normally used for cancer or for a particular type of cancer can be strong therapeutic possibilities to attack drivers of a particular cancer based on its genomic analysis. Drugs normally used for hypertension, for instance, have been selected for use in some POG cancer treatments, as well as drugs conventionally deployed in different types of cancer. For example, based on an individual’s genomic data, a drug approved for lung cancer might be appropriate for a particular case of pancreatic cancer.

These findings have potential disruptive consequences, she said: “We have to think about how regulatory authorities are approving drugs and funding drugs, so they aren’t just siloed in particular applications in one particular tumour type.”

Dr. Christopher McMaster

The growing role for genomics in human health and other fields is largely due to the plummeting cost of creating the data, said Dr. McMaster. “The human genome was sequenced in 2003,” he said, adding, “It took a decade and it cost over $1 billion. In 2019 we can sequence the human genome in a few weeks for about a thousand dollars.” No technology, he said, has accelerated at such a pace.

Dr. McMaster’s research lab uses genomic data to uncover therapies for orphan diseases, most of which are currently untreatable. For orphan diseases which used to take five-seven years and up to $30,000 of tests to detect with certainty, Dr. McMaster said advances in genomics mean “we can now diagnose these cases by sequencing the [patients’] genomes in a matter of weeks. It’s speeding up a diagnosis without increasing costs to the health care system.”

Sometimes called “rare diseases,” orphan diseases are not rare at all when viewed as a category. More than 7,000 diseases fall into this grouping. In Canada, it has been estimated, one in 40 children are born with an orphan disease and because it is often life-limiting, 35 per cent of them fail to reach their fifth birthday.

“The nice thing about inherited diseases is, it’s a single gene in which a mutation is causing a disease,” said Dr. McMaster, so there is “an immediate cause to an effect.” With the help of Genome Canada, Genome Atlantic and other partners, he is now involved in a “scientific-clinical hub to come up with treatments.”

For most inherited disease there is no current treatment. “So, this hub is looking to lead Canada in terms of bringing medicines into the clinic and into the market for treating cases with inherited diseases,” he said. Helping advance this ambition, the Food and Drug Administration in the U.S. offers Rare Pediatric Disease Priority Review Vouchers which help companies move qualifying drugs to the front of the review line in the approval process. The express provision brings cost savings to drug developers, ranging from $100 million to $250,000.

Dr. Travis McDonough

The software company, Kinduct, grew out of Mr. McDonough’s experience in the healthcare industry where 3-D medical examinations and rehabilitation programming generate a slew of compartmentalized data. Elite sports do the same thing with even more varied types of data – all sorts of player monitoring and player tracking, for instance. Kinduct figured out how to put it all together and draw helpful conclusions to optimize performance and wellness in professional sport.

“Essentially we create better athletes,” said Dr. McDonough. The goals, he said, are to create “vigorous, stronger, faster athletes,” mitigate costs associated with soft tissue injuries, identify “the next great athlete out there,” and capitalize on the new markets starting to appear for monetization.

Kinduct aggregates reams of data, including DNA, and with the help of AI engines, the company contextualizes and analyzes it. Detected trends can then lead to recommendations or interventions for the athlete – from nutrition to training programs and playing strategies. Kinduct is now considered a world leader in Athlete Management Systems and many professional sports teams, including in the NHL, have jumped aboard. Kinduct, he said, is now also starting to work with player associations.

“It’s been a crazy journey for us,” Dr. McDonough admitted.  While focused on elite professional sport, he said, opportunities to move into related areas with Kinduct’s methodology of data collection and analysis seem boundless – from sports medicine to horses in equestrian sports.

“We hope that the people who attended were inspired”

“The panelists are recognized leaders in clinical care, orphan disease research and human performance and each brought to the table information on the incredible advancements they’re pioneering,” said Dr. Steve Armstrong. “We heard about a revolutionary new approach to cancer therapy, the progress being made in treating rare diseases in children at the IWK, and how a Halifax-based company is helping professional sports teams get the most of their athletes. These seemingly disparate topics are linked together by the ability to custom-tailor treatments and optimize performance thanks to personalized data.”   

“We hope that the people who attended were inspired and that they left feeling optimistic about a future made brighter by the transformative power of personalized data and genomics.”

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!

$3.8 million project puts NB company at forefront of oyster breeding technology

Baby oysters – Photo Credit ERB

Please note: French Version follows

Halifax, NS – The oyster industry in Eastern Canada is expanding rapidly, registering revenues near $31 million in 2017, a 25% increase from 2016.  However, this growth cannot be sustained by relying solely on wild-caught oyster spat.  L’Étang Ruisseau Bar Ltée (ERB), the main oyster hatchery seed supplier located in Shippagan, New Brunswick is teaming up with Université Laval scientists, Genome Atlantic and Génome Québec on a transformative, $3.8 million project using genomics to produce the first selectively bred Canadian strain of Eastern oyster. 

Genomics for Developing the first Canadian production ready strain of selectively bred Eastern Oyster is one of 20 Genome Canada funding projects announced today by the Honourable Kirsty Duncan, Minister of Science and Sport. The project is led by Dr. Louis Bernatchez of Université Laval and Dr. André Mallet of ERB, Eastern Canada’s largest oyster seed producer.

The project will use genomic tools like high-density SNP chips to create a breeding program that will select for traits such as improved growth, better flesh quality and resistance to disease -traits that are difficult to improve using wild stocks and conventional methods. The end goal is to increase the profitability of oyster farms.

“Genomic tools offer the potential to greatly improve selective breeding of molluscs but unfortunately, the availability of genomic tools to enhance aquaculture production of the Eastern oyster has been lagging behind, compared to other oysters,” said Dr. Louis Bernatchez, Université Laval. “This project, involving the collaboration of Université Laval and University of Chile, will allow our partners from ERB to substantially accelerate progress toward developing the first Canadian domesticated strain of eastern oyster with improved performance in growth and survival.”

‘’L’Étang Ruisseau Bar Ltd looks forward to collaborating with our partners in developing genomic selection tools for the Eastern oyster,” said Dr. André Mallet.  “By combining our expertise in oyster genetics and hatchery operation with our partners’ extensive experience in genomics, we will be able to produce high performance seed which will improve farm profitability and help us respond to a changing environment. This project will make a significant contribution towards ensuring the future of the Atlantic Canadian oyster industry, and we wish to thank the many funding partners that have made this project possible. ‘’

“This ambitious project has the potential to accelerate the growth and profitability trajectories of the oyster industry, an opportunity that is both exciting and timely given the growing global market demand for this delicious product”, says Steve Armstrong, President and CEO of Genome Atlantic.  “We extend our congratulations to this talented project team and our sincere thanks to the many funding partners.”

The project is enabled through Genome Canada’s Genomic Applications Partnership Program (GAPP) with additional funding provided by L’Étang Ruisseau Bar Ltée; ministère de l’Économie et de l’innovation du Québec; Atlantic Fisheries Fund; University of Chile; and Mitacs Canada. The project will be managed by Genome Atlantic in partnership with Génome Québec.

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 $100 million in new genomics R&D.

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Contact:  Charmaine Gaudet, Director of External Relations, 902-488-7837 / cgaudet@genomeatlantic.ca

POUR DIFFUSION IMMÉDIATE – 23 JUILLET 2019

Un projet de 3,8 millions de dollars place une entreprise du Nouveau-Brunswick à l’avant-garde de la technologie ostréicole

Halifax (Nouvelle-Écosse) – L’industrie ostréicole dans l’Est du Canada croît rapidement, récoltant des revenus de près de 31 millions de dollars en 2017, une hausse de 25 % par rapport à 2016. Toutefois, cette croissance ne peut être assurée en se reposant uniquement sur les naissains d’huîtres sauvages. L’Étang Ruisseau Bar Ltée (ERB), le plus important fournisseur de naissains d’huîtres en écloserie, situé à Shippagan au Nouveau-Brunswick s’associe aux scientifiques de l’Université Laval, à Génome Atlantique et à Génome Québec pour la réalisation d’un projet transformateur de 3,8 millions de dollars, utilisant la génomique dans le développement de la première souche canadienne d’huîtres de l’est reproduite de façon sélective.

La génomique dans le développement de la première souche canadienne d’huîtres de l’est reproduite de façon sélective et prête à la production constitue l’un des 20 projets de financement de Génome Canada, a annoncé aujourd’hui la ministre des Sciences et des Sports, Kirsty Duncan. Le projet est dirigé par Louis Bernatchez de l’Université Laval et André Mallet d’ERB, le plus important fournisseur de naissains d’huîtres de l’est du Canada.

Le projet développera et utilisera des outils génomiques, notamment les puces SNP à haute densité pour créer un programme de sélection basée sur la génomique tel que l’amélioration de la croissance, une meilleure qualité de la chair et la résistance aux maladies, caractéristiques qui sont difficiles à améliorer en utilisant les stocks sauvages et les méthodes conventionnelles. L’objectif final est d’accroître la rentabilité des fermes ostréicoles.

«Les outils génomiques offrent la possibilité d’améliorer grandement l’élevage sélectif de mollusques mais malheureusement, la disponibilité des outils génomiques pour améliorer la production aquacole des huîtres de l’est affiche un net retard par rapport à celle des autres huîtres,» affirme Louis Bernatchez de l’Université Laval. «Ce projet, impliquant la collaboration de l’Université Laval et de l’Université du Chili, permettra à nos partenaires d’ERB d’accélérer considérablement le développement de la première souche domestique d’huîtres de l’est en améliorant les performances de croissance et de survie.»

«L’Étang Ruisseau Bar Ltée se réjouit à la perspective de collaborer avec nos partenaires afin d’élaborer des outils de sélection génomique pour l’huître de l’est,» a déclaré André Mallet. «En combinant notre expertise en génétique de l’huître et d’exploitation d’écloserie avec la vaste expérience de nos partenaires dans le domaine de la génomique, nous serons en mesure de produire des naissains de haut rendement, ce qui permettra d’améliorer la rentabilité des fermes ostréicoles et nous aidera à répondre à l’évolution constante de l’environnement. Ce projet permettra d’apporter une contribution importante en vue d’assurer l’avenir de l’industrie ostréicole du Canada atlantique, et nous tenons à remercier les nombreux partenaires financiers qui ont rendu ce projet possible.»

«Ce projet ambitieux a le potentiel d’accélérer la trajectoire de la croissance et de la rentabilité de l’industrie ostréicole, une occasion qui est à la fois passionnante et opportune étant donné la croissance de la demande sur le marché mondial pour ce délicieux produit,», explique Steve Armstrong, président-directeur général de Génome Atlantique. «Nous adressons nos félicitations à cette talentueuse équipe de projet et nos sincères remerciements aux nombreux partenaires financiers.»

Le projet est rendu possible par l’entremise du Programme de partenariats pour les applications de la génomique (PPAG) de Génome Canada, et des fonds supplémentaires provenant de L’Étang Ruisseau Bar Ltée, du ministère de l’Économie et de l’Innovation du Québec, du Fonds des pêches de l’Atlantique, de l’Université du Chili et de Mitacs Canada. Le projet sera géré par Génome Atlantique en partenariat avec Génome Québec.

Génome Atlantique est une société sans but lucratif qui a pour mission d’aider le Canada atlantique à profiter des avantages économiques et sociaux des technologies de la génomique. Depuis sa création en 2000, la société a travaillé avec un éventail de partenaires des secteurs privé et public afin de permettre l’investissement de plus de 100 millions de dollars en recherche et développement dans le domaine de la génomique.

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Personne-ressource: Charmaine Gaudet, Directrice des relations extérieures, 902-488-7837 / cgaudet@genomeatlantic.ca

‘Omics project takes de-risking NS’s offshore to next phase

Adam MacDonald, NS Department of Energy & Mines, examines a core sample taken during an offshore coring cruise

For Immediate Release – July 24, 2019

Halifax, NS – A major new initiative that adds genomics technologies to traditional geoscience aims to reduce the risk for oil exploration in Nova Scotia’s offshore. 

The $6.5 million project, Validation and Integration of Genomics Solutions for Offshore Oil Exploration in Nova Scotia and Beyond, was announced today by the Honourable Kirsty Duncan, Minister of Science and Sport, as one of 20 projects across Canada awarded through Genome Canada’s Genomic Applications Partnership Program (GAPP).  Other major project partners include the Nova Scotia Department of Energy and Mines; the Geological Survey of Canada, Natural Resources Canada; Research Nova Scotia; Nova Scotia Offshore Energy Research Association (OERA); Mitacs Canada; Applied Petroleum Technology (APT); the University of Calgary; and Saint Mary’s University.

The initiative builds on the work of a previous GAPP project in which genomics data and results were compared with petroleum geochemistry data to paint the clearest picture yet of petroleum deposits in areas of Nova Scotia’s offshore. The project announced today, involving the same team, will take that work to the next level by delivering high resolution tools and maps developed with the help of autonomous underwater vehicles (AUVs), advanced ‘omics technologies and machine learning.

“The idea of using genomic (DNA-based) tools to help de-risk offshore oil and gas exploration efforts has transitioned from a ‘what if’ idea not that long ago into a compelling opportunity that has earned the support of this project’s many partners,” said Steve Armstrong, President and CEO of Genome Atlantic. “We are extremely pleased to have the opportunity to work with such a dedicated and talented group committed to establishing Nova Scotia as a leader within this globally competitive sector.”

The Province of Nova Scotia’s commitment to the project is part of its $12 million investment in offshore R&D over the next four years.  “For generations, the offshore has paid off for Nova Scotians and it still holds tremendous potential to grow our economy and create jobs across the province, especially in rural areas,” said Nova Scotia Energy and Mines Minister Derek Mombourquette. “By continuing to invest in leading-edge research we will find cleaner and safer ways to look for resources and attract international investment to our shores.”

The project is co-led by Dr. Casey Hubert (University of Calgary), Dr. Todd Ventura (Saint Mary’s University) and Adam MacDonald (NS Department of Energy and Mines) and is managed by Genome Atlantic in partnership with Genome Alberta.

 “This new project will allow us to explore sites that preliminary testing revealed as particularly promising, this time using AUV mapping, ROV (Remotely-Operated underwater Vehicle) video-guided sampling, and higher density sediment coring,” said Dr. Hubert.  “We will integrate a broader slate of ‘omics technologies, including rapid DNA sequencing using hand-held devices that will enable genomics to guide daily sampling decisions on the ship out at sea.  This work will combine various cutting-edge technologies to map petroleum potential while simultaneously generating environmental baseline data on seabed biodiversity.”

“This GAPP is expanding on the microbiological toolkit with the addition of lipidomics,” said Dr. Todd Ventura, Saint Mary’s University.  “This allows us, for the first time, to detect ancient, deep water seeps that, while no longer active or infrequently active, nevertheless paint a more comprehensive picture of a dynamic petroleum system. Additionally, speed is everything – and with the development of a lab on a ship and AI-based data mining, we hope to greatly improve the turnaround time between sample acquisition, processing and data analysis – all of which will help exploration companies in their decisions.”

“De-risking our offshore for exploration is critical for Nova Scotia to remain competitive in a global market,” said Adam MacDonald, NS Department of Energy and Mines. “Adding new tools and building innovative and integrated projects such as this collaboration with the University of Calgary and Saint Mary’s University gains recognition and attention to our quality and capacity to compete. Not only do we de-risk exploration but this project provides environmental baseline information on the benthic life and communities that may be dependent on natural occurrences of hydrocarbon on the seafloor.”

“The advanced sampling and seafloor profiling techniques being used in the project will deliver rapid, high resolution tools and maps to reduce offshore exploration risk,” said Alisdair McLean, Executive Director of OERA. “The hope is to engage local companies with advanced technologies, which will build business opportunities in a global industry.”

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 $100 million in new genomics R&D. Please visit genomeatlantic.ca for more information.

Genome Alberta is a publicly funded not-for profit corporation which invests primarily in large-scale genome sciences research projects and technology platforms focused on areas of strategic importance to the province including, forestry, plant and animal agriculture, energy, environment, and human health.  To date, the organization has managed a research portfolio with approved budgets of over $228 million.  Please visit GenomeAlberta.ca for more information.

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Media Contact:  Charmaine Gaudet, 902-488-7837, cgaudet@genomeatlantic.ca