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.

Using genomics to combat superbugs: Q/A with Dr. Rob Beiko

Recently, the Government of Canada announced funding for 37 Genome Canada projects including $1.4 million for Antimicrobial Resistance: Emergence, Transmission, and Ecology (ARETE), a project co-led by Dalhousie University’s Dr. Robert Beiko and Dr. Fiona Brinkman of Simon Fraser University.  ARETE aims to develop new surveillance tools to help identify and track the genes that contribute to antimicrobial resistance (AMR), a huge problem for the agri-food industry and the health of Canadians.

Backed by his lab team at Dalhousie University, Dr. Beiko has earned a place on the front line of bioinformatics research, probing the mysteries of AMR in bacteria. It’s an area of pressing worldwide concern for human health, agriculture and the food industry, as the effectiveness of antibiotics declines and antimicrobial resistance grows.

A biologist and expert in computational biology, he applies the power of algorithms, machine-learning and biological data visualization to microbial research. His focus has been on gaining a better understanding of the genes that make bacteria resistant to antibiotics and how they spread.

Genomics has a central role in this research field.  Unfortunately, current analysis tools lack the needed software to predict antimicrobial resistance profiles in the huge datasets generated from genetic profiling of microbial communities (metagenomics). Software is needed to separate the wheat from the chaff. Dr. Beiko, alongside Drs. Andrew McArthur of McMaster University and Fiona Brinkman of Simon Fraser University, has been working on a software solution, enabled by Genome Canada’s Bioinformatics and Computational Biology funding program, with support from Genome Atlantic.  

Through ARETE, Drs. Beiko, Brinkman and their fellow researchers will take a closer look at lateral gene transfer (LGT), the process by which bacteria share genes with each other. Disease-resistant bacteria can move between habitats, such as soil and animals, but science has yet to learn the most important points of transmission – this information is vital for monitoring and regulating the process.

Dr. Beiko has led or been involved in numerous large-scale research projects funded by Genome Canada, Genome Atlantic and other regional Genome Centres, the Natural Sciences and Engineering Council of Canada, and other major national and international granting agencies.

How close are you to developing software that will open up microbe research for better genomics analysis?

It’s an ongoing process. You can draw a clear line from the tools developed in the 1980s, which were developed before genome sequencing really took off, to the ones we use today. Each technological revolution brings new challenges, and we were asking very different questions in 2000 when the first microbial genomes came out than we are now. Where once we had maybe one or two genomes of important species, we’re now looking at tens of thousands of genomes of E. coli or Salmonella alone. These rich datasets offer great opportunities for us to map out the fine points of the emergence and evolution of pathogens, and AMR in particular. But as you can probably guess, dealing with 100,000 genomes at a time opens up some new and very exciting challenges from a bioinformatics standpoint.

ARETE is built on a foundation of existing tools, including large databases of AMR genes and mutations, methods to identify regions of microbial genomes that pose a high risk for carrying and transmitting AMR, and software that can identify the transmission of genes between potentially very distantly-related bacteria. A key challenge in ARETE is getting these tools working together properly and to scale up the absurd number of genomes that are coming down the pipe. Consequently, and coming back to the original question, many pieces of the puzzle are in place, which makes us very optimistic about delivering a unified toolkit over the three years of the project.

What practical advantages do you envision for microbe research from this kind of software?

A key aspect of the ARETE project is the close involvement of researchers in the Public Health Agency of Canada. DNA sequencing has become the gold standard for mapping epidemics, which has resulted in a huge effort to sequence the genome of every pathogen that comes across our desk. But what are the benefits of having all this information? There are lots of practical outcomes of this research, but the key driver of ARETE and the wider umbrella of genomic epidemiology projects is the ability to study the transmission pathways of both AMR genes and the bacteria that contain them. If you see the exact same gene in chicken X and patient Y, in farm soil, sewage, or what have you, that can give you a pretty clear view of what is being transferred, where it is happening, and by whom. This knowledge can then drive efforts to contain the spread of AMR.

What intrigues you most about lateral gene transfer – the process of gene sharing among bacteria?  Why?

The realization that LGT is a defining aspect of microbial evolution broke most people’s preconceived notions about how bacteria evolve. When we think about inheritance, we almost invariably picture an unbroken line of transmission from parent to offspring. In a lot of cases this is not true of microorganisms. Although researchers always knew that some transmission was happening, the central role of LGT could only be appreciated when people started to sequence genomes en masse. We now know that when one microorganism has a good idea, evolutionarily speaking, it might not be long before its neighbours pick it up. While the life-or-death (for the bacterium) situation of AMR is a particularly acute driver, we see strong evidence for a central role of LGT in the evolution of everything from adaptation to extreme temperatures (in some cases, above the boiling point of water) to the breakdown of new compounds that humans have introduced into the environment.

Eight Questions with GE3LS Researchers – Dr. Matthew Schnurr

Content provided by Genome Canada

Dr. Matthew Schnurr, Ph.D.

GE3LS research looks at the important ethical, environmental, economic, legal or social issues of where genomics and society intersect.  Genome Canada kicks off a series on GE3LS researchers with this profile of Matthew Schnurr, Ph.D., Associate Professor, International Development Studies, Dalhousie University.

Where did you grow up?  Toronto.

Apart from your present one, what’s the best job you ever had?  Swim Instructor.

What’s your academic/research background? How did it lead you to GE3LS research? I started off as a student in the natural sciences studying agricultural biotechnology, then got interested in examining the political and social implications of these new tools.   

How would you describe your research to a group of Canadian students? Why is your work important to them?   My work explores the potential for genome-enhancing agricultural technologies to alleviate poverty and hunger for small-scale African farmers.  These questions should resonate with anyone concerned about issues of global poverty and inequity.

What kind of response has there been to your research? What impact have you seen?  My work seeks to amplify the voices of farmers within these debates.  The response from policy makers and development donors in Africa has been positive as most stakeholders agree that for a technology to be widely adopted it must reflect the priorities of the end user. 

What’s the most unusual or unexpected thing about your work as a GE3LS researcher?  The debate over new biotechnology is politicized and polarizing.  I’ve been surprised by how fervent people are on both sides of the ideological divide. 

What do you think is the biggest issue facing genomics in the next decade?  In my view it’s the new suite of gene editing technologies that make genomic manipulation more accessible and more available than ever before, In particular, I believe there is an urgent need for social scientific research into the social, political and ethical impacts of this transformational technology. 

Finally, we’re all going out later for karaoke. What song do you sing and why?  Toto’s Africa – it’s my place and my song!

Invest NS announces support for Genome Atlantic

Press Release – Feb. 15, 2019

The Invest Nova Scotia Fund is helping entrepreneurs and researchers across the province use genomics to innovate and solve problems.

Genomics is the science of understanding, interpreting and harnessing DNA code to solve problems in new ways.

The fund’s independent board of directors announced today, Feb. 15, an investment of $325,000 in Genome Atlantic, a Halifax business organization specializing in DNA-based solutions.

Genome Atlantic will work with entrepreneurs and researchers to advance 25 DNA projects over the next three years. The organization will also focus on initiatives that drive growth in key sectors, like oceans, aquaculture and fisheries, agri-food, forestry, oil and gas and sustainable energy.

“Invest Nova Scotia’s support will help us advance more projects,” said Steve Armstrong, president and CEO of Genome Atlantic. “We are excited to introduce genomics to more entrepreneurs and researchers and have greater impact across the province.” Apple growers are already benefitting from working with Genome Atlantic. The organization is helping producers in the Annapolis Valley perfect varieties like the Honeycrisp apple and boost sales through a national project called the Apple Breeding Consortium. “

We are thrilled to be working with Genome Atlantic and Nova Scotia scientists on perfecting our products,” said Joan Hebb, horticulturalist at Scotian Gold Cooperative Ltd. in the Annapolis Valley. “Finding the right variety of apples for our unique climate is key, as we continue to strive for excellence and compete in the marketplace.”

“Invest Nova Scotia is funding smart, innovative projects that strengthen whole regions and sectors of our economy,” said Invest Nova Scotia chair Kenneth Deveau. “Now, Genome Atlantic will be able to work with more entrepreneurs and researchers, increasing our capacity for innovation and strengthening our economy, particularly in rural Nova Scotia.”

Invest Nova Scotia was established in 2014 as an independent fund for granting economic incentives. Projects must spark innovation, be collaborative, measurable and sustainable and advance the strategic goals of the ONE Nova Scotia Coalition.

For more information on Invest Nova Scotia, visit http://www.novascotia.ca/business/invest/. For more information on Genome Atlantic, visit http://www.genomeatlantic.ca/ .

Interview with Dr. Martin Alda: How genomics can lead to better outcomes for those with bipolar disorder

Interview with Dr. Martin Alda: 

How genomics can lead to better outcomes for those with bipolar disorder

Dr. Martin Alda (R) and Dr. Rudolf Uher Photo Credit: David Grandy

Two psychiatrists at Dalhousie University and the Nova Scotia Health Authority (NSHA) have plans to apply genomics to the development of some much-needed clinical tools for the early detection and treatment of bipolar disorder. Success could bring significant improvement to the lives of those with the condition.

Dr. Martin Alda, the Killam Chair in Mood Disorders at Dalhousie, and Dr. Rudolf Uher, Dalhousie’s Canada Research Chair in Early Intervention in Psychiatry have received $975,000 to pursue their goal in a three-year research study, which started in early 2019.  The two psychiatrists also run successful research programs with NSHA.

Their project, Early Detection of Bipolar Disorder and Optimized Selection of Long-term Treatment, will take a personalized approach, using genomics to develop new screening tools and fast-track treatment for individual patients. Led by Genome Atlantic, the project has the support of a wide-range of financial backers, including Genome Canada, the Research Nova Scotia Trust, the Nova Scotia Health Authority, the Dalhousie Department of Psychiatry and the Dalhousie Medical Research Foundation. The number and diversity of their sponsors indicate the importance being placed on their work.

Nova Scotia has one of the highest rates of psychiatric disease in the country. In the world of mental illness, bipolar disorder is rated one of the top 10 causes of disability.

Current methods of diagnosis and finding the right individualized response, which usually involves long-term medication, are time-consuming. Delays can impair results, which are known to improve with early detection and treatment.

Drs. Alda and Uher hope to overcome those hurdles to achieve better outcomes by leveraging the role genetics plays in some key features of bipolar disorder, including causation, the risk of suicide and the response to long-term treatment. Using this knowledge, the plan is to achieve better patient results by developing clinical tools for early diagnosis and treatment. They anticipate their work could shorten the time from diagnosis to effective treatment by at least 12 months.

Genome Atlantic spoke with Dr. Alda recently to shed more light on their project:  

Genome Atlantic: What exactly is bipolar disorder and how debilitating is this condition?

Dr.Martin Alda: Bipolar disorder is a serious psychiatric illness, previously known as manic-depressive disorder. It typically affects young people and runs a lifelong course characterized by episodes of mania and depression. Bipolar disorder is often disabling, ranking among the top ten causes of morbidity worldwide. People with bipolar disorder are at risk of increased mortality due to suicide but also from various physical causes such as heart disease or diabetes. The manic and depressive episodes can be prevented by suitable long- term treatment, but not all people respond to the same treatments and choosing the right medication by trial and error is a lengthy and frustrating process.

Genome Atlantic: How common is bipolar disorder in Nova Scotia?  In Canada?

Dr. Martin Alda: Bipolar disorder affects about 2 per cent of all adults in Canada (and Nova Scotia).

Genome Atlantic: How is the condition commonly diagnosed now, and what are the drawbacks with this process?

Dr. Martin Alda: Bipolar disorder is typically diagnosed based on clinical symptoms. In the early stages, the illness is often difficult to differentiate from other psychiatric conditions such as major depression or schizophrenia. This uncertainty of diagnosis means that many patients are diagnosed properly only after a delay of several years. It is during this early stage of illness when timely treatment can make the most difference in the illness outcome.

Genome Atlantic: What are the genetic links to bipolar disorder and how long have we known about them?  What are the odds that people with these genes will go on to develop bipolar disorder?

Dr. Martin Alda: A number of studies have established that bipolar disorder is heritable and that the genetic factors account for up to 80-85 per cent of the overall risk of the illness. Several genes have been discovered that increase the odds of developing bipolar disorder, but more work is needed to clarify how these genes in combination with non-genetic factors predispose people to develop bipolar disorder.

Genome Atlantic: Since this project will be breaking new scientific ground, perhaps you could explain what made you think of using these genetic links to try and develop methods for earlier detection and better treatment for bipolar disorder?  Was there a Eureka moment when you came up with this project?

Dr. Martin Alda: From work of several research groups including our own work, we know that genetic factors play a role in the risk of bipolar disorder and that they are an important factor in determining who responds to what kind of long-term treatment. Thus, it is a logical step to start looking at the risk genes and their combinations to come up with a set of factors that will guide clinical decisions.

Genome Atlantic: Can you describe the new clinical tools you aim to develop?

Dr. Martin Alda: We plan to use a combination of clinical measures and genetic information from the entire human genome. Ultimately the tool should provide a guide to clinical features relevant to the risk of illness and/or the likelihood of responding to a particular medication and combine these with the genetic factors.

Genome Atlantic: How do you foresee these new clinical tools changing diagnosis and treatment of bipolar disorder?

Dr. Martin Alda: Our proposal falls under the now much-talked-about concept of precision medicine. Most areas of medicine including cancer treatment or cardiology are moving towards tailored treatments based on individual patient characteristics rather than one prescription fitting all.

Genome Atlantic: What benefits would they bring to patients and their families?

Dr. Martin Alda: Our hope is that the improved treatment will reduce the risk of the illness and will shorten the time to an effective treatment selected to fit the patient’s clinical and genetic profile.

Genome Atlantic: This project is a three-year endeavor so can you briefly outline what you intend to do over that period?

Dr. Martin Alda: Most of the work is to be done here at Dalhousie and in the Nova Scotia Health Authority. Exactly speaking, it is not a three-phase project, but some parts of it will take a full three years (and possibly longer). Our proposal has several aspects and some are closer to clinical applications than others. We expect that any new discoveries and decision tools will need to be further tested before being implemented in clinical practice.

Genome Atlantic: If you succeed in developing these new genomic diagnostic tools, how soon could Nova Scotians expect to see them adopted for general clinical use?

Dr. Martin Alda: We expect that at least some of the tools will be ready by the end of the project; some may take longer.

Genome Atlantic: Are there other psychiatric disorders where you think genomics could provide the keys to better diagnosis and earlier or better treatment?

Dr. Martin Alda: Not only bipolar disorder but other forms of severe mental illness such as schizophrenia or depressive disorder.