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

ISMOS-7 comes to Halifax

FOR IMMEDIATE RELEASE June 11, 2019

HALIFAX, NS – The 7th International Symposium on Applied Microbiology and Molecular Biology in Oil Systems (ISMOS-7) is coming to Halifax, Nova Scotia from June 18-21, 2019. Hosted by Genome Atlantic, ISMOS-7 will bring together the world’s top scientists from the oil and gas industry and from academia to discuss the latest molecular methods for tackling major industry challenges.

“Bacteria and other microbes can cause problems like pipeline corrosion and reservoir souring, but they can also enhance oil recovery, de-risk exploration and help clean up oil spills. Studying these microbes and how we can best apply them is an emerging focus for the industry,” said Dr. Torben Lund Skovhus, VIA University College in Denmark and ISMOS conference planning co-chair. “Conferences such as ISMOS provide an excellent opportunity to explore recent applications of emerging molecular tools through presentations, workshops and poster sessions.”

Genomics, a science that studies the DNA of living organisms, is key to understanding these microbes and how they interact with their environment, explained Genome Atlantic President & CEO, Dr. Steve Armstrong.  “For example, some microbes eat oil and congregate near oil seeps.  Tracking them can help to de-risk companies’ decisions on where to drill, thereby potentially increasing their chances of success and reducing the environmental impact of unnecessary drilling.” Armstrong added that “ISMOS-7 offers a tremendous opportunity to showcase leading research from around the world, including innovative microbial genomics work taking place in Atlantic Canada.”

Conference topics include hydrocarbon degradation; subsurface and reservoir biochemical processes; deep oilfield microbiology; reservoir geophysics and geology; microbiologically-influenced corrosion and souring; microbial enhanced oil recovery; microbiology and modelling in the oil and gas sector;  integrity management in oil, gas and fuel systems; and microbial energy and molecular biology in the oil and gas sector.

ISMOS-7 will take place in the Halifax Convention Centre. For more information, including a full list of topics and speakers, consult the conference website (http://www.ismos-7.org/

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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FOR MEDIA:

Members of the media are welcome to attend sessions of interest and are asked to contact Charmaine Gaudet (cgaudet@genomeatlantic.ca / 902-488-7837) for a press pass. 

Highlights:

  • For an overview of how research in the oil and gas industry moves from the lab into the field, consider attending the mini-workshop “Science-based oilfield management – from the lab to field” on Tuesday, June 18 from 3:00-5:30 p.m.
  • Dr. Kenneth Lee, National Senior Scientific Advisor with Fisheries and Oceans Canada and a leading expert in oil spill countermeasures, will give the keynote presentation (Friday, June 21, 3:05 p.m. in Convention Hall C2-C3).  
  • The plenary talk (Wednesday, June 19, 9:20 a.m., Convention Hall C2-C3) will focus on how Nova Scotia is combining traditional geoscience and new genomics technologies to paint a clearer picture of offshore petroleum deposits.  Presenters TBA.
  • The Hon. Derek Mombourquette, Nova Scotia Minister of Energy and Mines, will provide remarks at the Welcome Reception (Tuesday, June 18, 6:00 p.m., Room 605).  

Speakers/experts available for media interviews include:

  • Dr. Kenneth Lee (Fisheries and Oceans Canada) is a world-renowned expert on research, development and application of emerging technologies in ocean sciences, including in the oil and gas sector. He will give the Keynote Presentation on Friday, June 21, 3:05-3:50 p.m.
  • Dr. Torben Lund Skovhus (VIA University College, Denmark) and Dr. Corinne Whitby (University of Essex) are Co-Chairs of the ISMOS Planning Committee and co-authors of Oilfield Microbiology, considered a definitive text on the impact of microorganisms in the oil and gas industry. They are available to speak about the ISMOS-7 conference as well as their specialties.
  • Dr. Lisa Gieg (University of Calgary) will speak on “Assessing MIC (Microbiologically-influenced Corrosion) in the petroleum Industry – a holistic approach” on Tuesday, June 18, 3:20-3:40 p.m.  Dr. Gieg’s specialties include microbial corrosion, bioremediation and microbial enhanced oil recovery. She is a co-lead on a major R&D project focused of reducing pipeline corrosion on Canada’s offshore and onshore oil production.
  • Dr. Casey Hubert (University of Calgary) is an expert on offshore prospecting, souring and corrosion, and oil spill bioremediation. He is a co-lead in the “De-Risking Offshore Oil and Gas Exploration in Nova Scotia” project that combines geoscience and genomics to build a clearer picture of petroleum depositis in Nova Scotia’s offshore.
  • Dr. Rick Eckert (DNV GL, North American Oil and Gas)is an oil and gas industry internal corrosion management specialist and co-chair of the June 18 Workshop on “Science-based oilfield management – from lab to the field” workshop.
  • Dr. Geert van der Kraan (R&D Specialist at DuPont Microbial Control) will be giving a presentation titled, “Phylogenomic and Metagenomic analyses of oilfield microbial communities shows they genetically differ and align with the differences in the chemical engineering parameters of top side asset elements” on Thursday, June 20, 4:30-4:50 p.m.. in Convention Hall C2-C3.
  • Dr. Joe Moore (Technical Service Specialist at DuPont Microbial Control) will be on site to discuss poster 151 – “Highly Resolved Sampling and Analysis of a Hydraulic Fracturing Pad Reveal Insights into Effective Microbial Control”, which he co-authored.
  • Mr. Andrew Stone (Genome Atlantic) is available to talk about the importance of bringing ISMOS-7 to Halifax and Atlantic Canada.

Media Contact:

Charmaine Gaudet, Genome Atlantic, 902-421-5683 / 902-488-7837 / cgaudet@genomeatlantic.ca

Could microbes help remediate abandoned gold mines?

Photo: Saint Mary’s University

Mines operating in Canada today adhere to rigorous environmental regulations and strive to minimize the impact of their operations on the environment.  But in the 1800s, before such legislation was in place, valuable minerals were extracted from ore using chemicals or concentrations of those chemicals that would not be permitted today.  For example, in Nova Scotia as elsewhere, liquid mercury was historically used to separate gold particles from the crushed ore.   The leftover material, called tailings, can contain mercury and arsenic that exceed acceptable standards.

The Government of Nova Scotia may undertake remediation efforts on some of the province’s legacy (abandoned) gold mines in the future.  A potential new tool may be added to the remediation efforts: genomics.

Genome Atlantic is partnering with Saint Mary’s University researcher Dr. Linda Campbell to study biological alternatives to the age-old problem of remediating legacy gold mine tailings.

Dr. Campbell, a noted environmental containment specialist, will explore whether microbes found in and around the lakes and wetlands impacted by 100-year old tailings could be the key to reducing toxic levels of mercury and arsenic. (The idea being that some microbes are natural remediation (clean-up) specialists in that they can detoxify heavy metals like arsenic and mercury.) This summer she and her team are undertaking a proof of concept pilot-scale investigation through Genome Atlantic’s Genomics Opportunity Review Program (GORP), with additional support from the Nova Scotia Department of Energy and Mines.

“In order to be able to develop effective, feasible and cost-manageable remediation approaches for freshwater sites, we need information and data to support the decision-making process,” said Dr. Campbell.

She explained that while extensive work has been done to develop a variety of ways to remediate ground and saltwater contamination, the impact of historical gold mine tailings on freshwater ecosystems is not as well understood.

Principally occurring in eastern mainland Nova Scotia, there are around 360 historic, abandoned mine sites that were established between the late 1860s and the 1940s.

Due to a combination of the province’s naturally occurring arsenic-laced geology along with historic gold processing practices that used mercury, levels of these toxic substances can be high in tailings.

Dr. Campbell explained, “freshwater sites have key chemical and biological differences, which means a remediation approach which works for terrestrial settings cannot be applied to freshwater settings.”

She predicted, “Our work investigating the metagenomic makeup of microbial communities in aquatic freshwater sediments will go a long way towards bridging this problematic data gap and supporting the necessary evidence-based decision making.”

The Nova Scotia government commissioned site characterization work this fiscal year at two large legacy gold mine tailing sites: at Montague, a rural community near Dartmouth, and at Goldenville near Sherbrooke. Based on the results, the province may soon be hunting for innovative remediation strategies.

Dr. Campbell’s inter-disciplinary team – Landon Getz, a PhD candidate with Dalhousie University’s Department of Microbiology and Immunology, who is studying bacterial genomics, and Dr. Josh Kurek, a Mount Allison University scientist who reconstructs past environments from physical, chemical, and biological evidence contained in lake sediments – are testing whether sediment metagenomics can provide needed information to help formulate a new remediation approach.

Metagenomics is the genetic analysis of genomes in an environmental sample that enables identification of the microbes or bacteria within. Campbell’s team will use this technique to analyze the surface sediment in specific contaminated and non-contaminated sites to find out what microbes are there and assess what their presence indicates about the state of the freshwater environments they inhabit.

It is known that some microbial communities can help reduce arsenic and mercury levels in their surroundings. Dr. Campbell explained, “some types of bacteria, especially iron and sulfur reducing species, can increase the bioavailability of arsenic and mercury to biological organisms, while other types can limit bioavailability. As a result, microbial approaches hold much promise for managing and limiting contaminant transfer to living organisms, including humans and wildlife. Before we can develop remediation strategies and remediation frameworks using those approaches, we need to better understand the microbiomes existing in those sites.”

Equally important, she said, is understanding “the makeup of microbial communities in healthy, unimpacted wetland sites to provide us with an approximate benchmark to consider while developing future remediation strategy frameworks.”

Consequently, environmental samples will be taken from three freshwater sites directly impacted by contaminated historical tailing materials from legacy gold mine sites plus two reference sites which have not been impacted by gold mine tailings. Those are all in the Halifax Regional Municipality, enabling rapid sampling and processing of the samples in the laboratory.

If all goes to plan, the resulting dataset this summer will pave the way for further and more long-term research into this relatively unexplored route to remediation.

“The province is always interested in pioneering new and innovative solutions that can be applied here, and around the world,” said Nova Scotia Energy and Mines Hydrogeologist Gavin Kennedy. “The work of Genome Atlantic and Saint Mary’s University is exciting and has the potential to change the way legacy gold mine sites are managed in the future.”

A Q/A with Chris Gardner, Sequence Bio

Photo Credit: Dave Howells

The founder population of Newfoundland and Labrador make it an ideal place to conduct studies linking certain genetic markers with diseases prevalent in the province.  Sequence Bio, a private St. John’s-based biotech company, recently cleared a provincial regulatory hurdle to allow it to launch the NL Genome Project this summer to study the unique genetic makeup of Newfoundland and Labrador. The company’s hope is that the data will lead to improved treatments and health outcomes. We caught up with Sequence Bio CEO and co-founder Chris Gardner recently to talk about his vision for the company, the project, and what gets him excited to go to work every morning. 

What inspired you to co-found Sequence Bio in 2013? What was your vision for the company?

I have always been excited by the biggest and most important challenges. And healthcare is up there – it has such a wide, and significant, impact on all of our lives, but innovation has traditionally been slow. Now we are at this exciting crossroad because of rapid advances in genomics, personalized medicine and sequencing technologies. And for me, this presented an incredible opportunity to accelerate innovation and help deepen our understanding of disease and improve patient outcomes.

But what makes this opportunity truly special and inspired me to start Sequence Bio is that we believe the right place to make change happen is Newfoundland and Labrador. And even better, we can do it in a way that ensures that communities, families and participants in Newfoundland and Labrador benefit for generations to come. Innovation that brings everyone along and leaves no one behind is my vision for Sequence Bio.

What makes Newfoundland a good place to study genetics sequencing?

Modern drug discovery relies on the right kind of information. This information isn’t found everywhere, but it is found in Newfoundland and Labrador. And it all starts with our unique history. As a founder population, it’s estimated that over 90% of our province’s residents are descendants of approximately 25,000 English and Irish settlers from the 1700’s. Founder populations like ours are rare, and can identify genetic changes from tens or hundreds of people instead of thousands or millions in other admixed populations. Coupled with our province’s high disease rates and comprehensive longitudinal health records, we believe Newfoundland and Labrador is the best unexplored cohort for human data to discover novel variants and potential drug targets.

Sequence Bio’s main focus has been to lead a large-scale genetic research project in Newfoundland and Labrador.  Now that the company has cleared the provincial regulator hurdle, where does that project stand? What are the short-term and long-term goals?

We’re incredibly excited to share that the pilot phase of the NL Genome Project is launching this summer! This pilot phase will recruit 2,500 Newfoundlanders and Labradorians through participating physician’s offices. We’ll combine genetic information from a simple saliva sample, with medical records, to deeply characterize the population and help design a larger research project in Newfoundland and Labrador with tens of thousands of individuals. All with the long-term goal to produce novel, validated drug targets no one else can find.

How do you access the patients in these studies? And what is done with the data you collect?

Sequence Bio is working with local, dedicated family physicians who see the value of integrating genomics into their own practice and the ability to positively influence the care of their patients. For the NL Genome Project, participating physicians will introduce the study to interested participants, who can then enroll with a research nurse at the clinic.

There is no greater priority to Sequence Bio than protecting participant data. Sequence Bio’s security program is built to align with ISO 27001/2 standards. All data is handled with extreme care and is immediately encrypted using AES 256 bit encryption and protected with the latest military-grade security measures. We know that if we want to be trusted with people’s most personal information, we have to earn that trust.

You are a recognized innovation leader. You’ve been named a Change Agent by Canadian Business and you’ve been asked to sit on the federal government’s Health/Bio-Science Economic Strategy Table.  You’ve said that Canada is sometimes slow to embrace change. What’s slowing us down and how can we as a country and a society do more to nurture innovation?

Canada’s regulatory processes present significant hurdles for the rapid adoption of innovation – reducing patient access to leading-edge therapeutic products and harming the international competitiveness of Canadian health and biosciences firms. This is why modernizing Canada’s regulatory processes is something I am so passionate about.

An effective regulatory environment ensures patient safety and well-being while encouraging the development and adoption of innovative products and services. Innovation and improved patient care are not mutually exclusive – in fact, it’s quite the opposite, they go hand in hand! A high performing regulatory system should be predictable, efficient, consistent and transparent, while ensuring patient safety and encouraging innovation. It’s been done in other jurisdictions and it’s time for Canada to do the same.

Things move quickly in the biotech world.  But six years after you launched your company, and even after a number of setbacks, Sequence Bio remains proudly Newfoundland.  What does this province mean to you, and what do you hope to accomplish that will benefit the people of this province?

We believe that to be successful we have to build a company that makes the entire province proud. That’s why the model for our population genetics project ensures that the people who contribute to research also benefit from that research. We’ll share discoveries with local researchers, policy makers, and doctors across the province. Plus, all participants can choose to receive findings about their genetic makeup, including information on medically actionable genes and carrier status information.

Our genetic founder population has the opportunity to meaningfully contribute to health research, and we can ensure research participants benefit at the same time we build a great company.  We have the chance, right here in Newfoundland and Labrador, to change lives by coming together and being part of ground-breaking research.

What role does Government play in projects like yours?

Initiatives like ours have the potential to reap social, economic and health benefits, but there are still incredible associated costs and risks – from sequencing to storage to infrastructure. Through job grants, SRED credits, subsidies, or non-dilutive funding, Government plays a critical role in helping with the underlying costs and risk management for those willing to innovate. And the return on investment benefits us all as we create the next generation of companies that will drive economic and regional growth. Our country has the opportunity to be leaders in genomics, but the only way we can do this is if we continue to support public and private research and work together along the way.

Finally, can you tell me a little bit about Sequence Bio? What about the company culture & philosophy gets you and your team excited to go to work every morning?  

We have a committed team in Newfoundland and Labrador and with teammates across Canada. We all come to work for our own reasons, but I can say with confidence that it all comes back to a shared desire to make this province a better place for us all – through improved healthcare, growing the biotech sector, and tackling the diseases that impact this province the most. We know what we’re trying to do is ambitious. But whether it’s our leaders in science, technology or research, we all believe it is possible. And I think in the end, it’s that drive, passion and commitment to the province that makes this such an incredible company.

Detecting marine species at risk with eDNA

Environmental DNA (eDNA) is a promising new tool for environmentally monitoring living organisms in water and on land. It works by analyzing DNA found in expelled skin samples, feces, etc. collected from environmental samples (e.g. of seawater, soil and even air) to determine what species are present. eDNA is non-invasive and can be done at considerably lower sampling effort and cost and has been shown to be an effective monitoring tool in many environments.


Jump To Video #2: Full FAQ interview with Dr. Marc Skinner

But how effective is eDNA for monitoring marine species at risk in turbulent marine conditions like the Minas Passage in the Bay of Fundy where more than 160 billion tons of seawater flow through twice a day driven by the world’s highest tides? In partnership with Genome Atlantic, the Offshore Energy Research Association of Nova Scotia (OERA), the University of Guelph, and Dalhousie University, Stantec’s Dr. Marc Skinner is trying to answer this question.

The Minas Basin is home to several marine species at risk such as striped bass, Bay of Fundy salmon and Atlantic sturgeon that are important to First Nations and inshore fisherman. It’s also the site of planned tidal power development. Maintaining the health of marine species and monitoring the environmental effects of tidal development sites on these species will require a science-based approach and the best tools of the trade. Dr. Skinner, Stantec’s Marine Ecology Technical Leader for Canada, believes that eDNA could be a promising option in this regard.

“Traditional sonar and fisheries methods weren’t able to adequately capture the diversity and richness of species, including species at risk, in the Minas Basin, so we were asked by OERA if eDNA had a role to play in helping do that, in a more objective fashion.”

To find out, Dr. Skinner is carrying out a laboratory-based study conducted at Dalhousie University’s Aquatron facility in Halifax, which can simulate multiple marine conditions. The project, which is supported by a Genome Atlantic Genomics Opportunity Review Program grant, is using striped bass as the sample species. Dr. Skinner and his team hope to develop a ‘proof of concept’ for eDNA’s effectiveness and reliability as an environmental monitoring tool in high flow marine conditions – ultimately, providing reliable data for monitoring the environmental impact of developments such as tidal turbine projects on marine species.

The study has answered several critical questions. The first is whether the technology can detect the striped bass DNA at different levels of the water column – the answer being a resounding yes. (The Aquatron marine simulation tanks are as deep as a two-storey building is tall.) Secondly, Dr. Skinner wanted to determine how long the DNA signal is detectable after the fish leave an area. He discovered that DNA is readable for up to 24 to 48 hours, after which it starts to break down. Thirdly, he was able to demonstrate that eDNA can be used to measure relative abundance of certain species in an area, such as how many striped bass were present in an area over a two-week period.

Having tested the technology in both benign and turbulent simulations in the Aquatron, Dr. Skinner will soon take the equipment into the field, testing it in the Minas Basin. Given the results so far, he is hopeful that eDNA will prove to be a useful environmental monitoring tool in challenging marine conditions.

“EDNA can certainly be an effective tool for species detections and quantifications like we’re using in this project for species at risk,” he said. “But overall, the potential application of eDNA and genomics in the ocean space is virtually unlimited – for example, for biodiversity assessments, tracking pathogens and invasive species, ocean exploration for resource development, prospecting for oil and gas seeps, asset integrity, infrastructure development….the list goes on.”

Genome Atlantic will provide an update on this and other eDNA projects in the near future. Stay tuned for some exciting innovations in the ocean space!


FAQ With Dr. Marc Skinner

Using EDNA in Marine Conservation

ISMOS-7 is coming to Halifax

In June 2019, Genome Atlantic is hosting the world’s leading conference on microbiology and molecular biology in the oil and gas industry. Join us for ISMOS-7 (the International Symposium on Applied Microbiology and Molecular Biology in Oil Systems), June 18-21 in Halifax, Nova Scotia.

ISMOS brings together professionals in the oil & gas industry and in academia to explore how emerging microbial and molecular tools can help solve key challenges facing the industry – including biocorrosion, souring, and conducting energy extraction in a sustainable manner.

Register today.

Helping Maritime apple growers with Genomics

Photo Courtesy of Scotian Gold Cooperative Ltd.

With its fertile soil and mild temperatures, Nova Scotia’s Annapolis Valley has long been famous for its apple harvest. Now, thanks to a recently-announced National Apple Breeding Consortium that  Genome Atlantic helped co-found, apple researchers, growers and marketers will share data that will allow them to bring new varieties to market more quickly – including varieties that grow best in local conditions.

It’s all about genomics. Genomics is a key technology for breeding apples with commercially desirable traits – increasing the likelihood of success in breeding better apple varieties. Genomics reduces the time it takes to develop a new apple variety by allowing breeders to predict what apples will taste like before the trees are fully mature. 

The National Apple Breeding Consortium grew, in part, out of a vision of Dalhousie apple researcher Dr. Sean Myles and a project he led supported by Genome Atlantic. Myles’ vision was simple:  One day, every novel apple tree developed by a breeder will be screened at the seedling stage to determine whether it is a potential winner in one of Canada’s growing regions.  In this manner, apple growers across Canada will end up planting only new varieties anticipated (or predicted) to thrive in their unique growing conditions.  

Over the years, Dr. Myles has collected an enormous amount of genomic data and planted more than 1,000 varieties of apples together with collaborators at Agriculture and Agri-Food Canada’s Kentville Research and Development Centre.  It is no small task to manage, analyze and interpret all the information necessary to determine desirable genetic profiles of new varieties. So, Dr. Myles’ team received support from Genome Atlantic and Genome Canada to develop new user-friendly software, now licensed, to enable desirable DNA profiles to be easily identified, removing the guesswork and increasing productivity of apple breeding. 

Imagine if apple researchers across Canada pooled their information and innovations. Enter the National Apple Breeding Consortium, which brings together Canadian researchers, breeders and marketers.  Genome Atlantic and Dr. Myles were instrumental in getting the Consortium off the ground.  (The Consortium co-founders include Genome Atlantic, Genome BC, Ontario Genomics and Agriculture and Agri-Food Canada.)

“How do we measure what the consumer really wants and then rapidly breed it using genomics? The National Apple Breeding Consortium is particularly well-equipped to tackle this, and it is precisely in this area of “fruit quality genomics” where we feel Nova Scotia and Canada can lead internationally,” says Dr. Myles.

The Consortium aims to streamline apple development in Canada and boost returns to the industry, while increasing consumer satisfaction.  It will also help growers by providing them with  new apple varieties uniquely suited to their growing regions.  

Developing new varieties is important. Witness the success of the Honeycrisp apple which grows well in Nova Scotia.  The big, crisp variety can bring in five times more money for Nova Scotia growers than more traditional varieties grown here and as a result, it has helped to reinvigorate the province’s once-dwindling apple industry.

Continued success for Nova Scotia growers depends on being able to develop the next big apple variety and get it to market quickly.

Scotian Gold Cooperative Ltd., a member of the National Apple Breeding Consortium, believes that finding the right variety for the local growing environment is key.  “It is about finding a variety that is best suited for our unique climate that will allow Nova Scotia growers to produce a superior product,” says Joan Hebb, Tree Fruit Coordinator for Scotian Gold.

Genome Atlantic, in partnership with the National Apple Breeding Consortium, wants to help Maritime apple growers get a head start developing the next generation of successful signature varieties.  Currently, Genome Atlantic is helping the Consortium seek funding for a project led by Dr. Myles, using genomics to improve variety development.