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.

Forging careers in Atlantic Canada, thanks to genomics

Forging careers in Atlantic Canada, thanks to genomics

Three highly trained scientists, one from Brazil and two from Canada, attribute their ability to forge careers in Atlantic Canada partly to their experiences as doctoral students or as postdocs working on Genome Atlantic-supported projects.

“Well, the CGP quite literally changed my life,” said Dr. Tiago Hori, recently appointed Director of Innovation at Atlantic AquaFarms in Orwell, PEI.  He joined the CGP – shorthand for the Atlantic Cod Genomics and Broodstock Development Project – as a Memorial University doctoral student from Brazil and helped build genomic data for Atlantic cod. He also used these resources to conduct functional genomics analysis of cod’s molecular response to stress.

The $18.4 million project, developed in partnership with Genome Atlantic and roughly half-financed by Genome Canada with matching funds from other sources, worked closely with aquaculture companies to find cod genes related to economically-relevant traits such as increased growth rates, disease resistance and stress tolerance. The aim was to reduce production costs to the point that cod aquaculture could become commercially viable in Atlantic Canada.

 “For one thing, I would not have come to Canada,” said Hori, without the project’s associated stipend, most of which came from Genome Canada. “Perhaps, more interestingly, it also almost completely changed my career.”

He explained, “When I first joined CGP, my role was supposed to be centered on the generation of physiological data and the use of a few molecular tools to characterize the stress response of cod. In 2006, I was supposed to spend six months in Newfoundland at Memorial University doing one of my own physiology experiments. However, the tanks that CGP had ordered for me burnt down alongside the factory that made them. I kid you not!”

In the aftermath, he was redeployed to work on a heat shock experiment to help Dr. Matthew Rise at Memorial, a principal investigator doing stress tolerance research for the CGP. “That’s when I started doing genomics, and I really never went back,” Hori says.

Hori completed his PhD in Biology during the highly successful $6.1 million camelina project, funded through the Atlantic Canada Opportunity Agency’s Atlantic Innovation Fund, and supported by Genome Atlantic. His role there was to provide training and secondary supervision, including assisting graduate and doctoral students with their analyses and sample collection.

The study found camelina to be an excellent match to the fatty acid composition required in the diets of farmed fish, and ultimately resulted in government approval of camelina as a feed ingredient for farmed salmon and trout.

Dr. Stefanie Colombo, Assistant Professor and Canada Research Chair in Aquaculture Nutrition, Dalhousie University, is another camelina project veteran. She offered an unqualified “yes” too, when asked if the experience helped her research career.

As a Memorial University doctoral student, she recalled her part in the study provided unusually well-defined deliverables for a PhD project. That factor enabled her not only to work more purposefully, but also to develop the creative freedom to pick up on what she had learned on each round of experimentation and figure out how to apply it to the next.

“My part of the project,” Colombo said, “was to evaluate the lipid biochemistry and growth of Atlantic salmon, rainbow trout and Atlantic cod that were fed diets containing camelina oil and meal.”

She added, “I was allowed and encouraged to publish my results, which was motivating for me to produce data. The project provided this established framework which gave me a roadmap and stability to excel in my studies.”

A native of Brantford, Ontario, Colombo did her undergraduate degree at the University of Guelph in marine and freshwater biology. Later, scouting for a job, she landed one at Scotian Halibut Ltd., Clark’s Harbour, Nova Scotia, her first encounter with Atlantic Canada. The company’s collaborations with the National Research Council in fish nutrition inspired her to do graduate study at Dalhousie, and then a chance meeting, during an annual conference of the Aquaculture Association of Nova Scotia, introduced her to Genome Atlantic and the prospect of a PhD project with Dr. Chris Parrish within the camelina undertaking.

Her PhD completed, she took up a postdoc position at Ryerson University, Toronto, but kept an eye on Atlantic Canada for future opportunities. One arrived in familiar territory. During the camelina project, she spent time with Dr. Derek Anderson and his lab in the Dalhousie Faculty of Agriculture. The experience, she believed, proved an asset when a faculty position there opened.

Today, she is a marine biologist specializing in aquatic nutrition. She uses genomics “as a tool to help answer questions related to nutrition in aquaculture. My work explores the area of nutrigenomics.”

Dr. Kyle Gardner, a research scientist with Agriculture and Agri-Food Canada, Fredericton, New Brunswick, maintains that his work on a Genome Canada project “was an important component in keeping me in the Atlantic region and fostering collaborations with local researchers from academia and government.”

A Cape Breton native he is now a quantitative geneticist with expertise in bioinformatics. As a postdoc research associate, he worked with Dr. Sean Myles at Dalhousie between 2012 and 2015 on a project that explored how new genomics technologies can help make traditional crop breeding more efficient, cost-effective and accurate. The project, Exploiting the Full Potential of the Next Generation DNA Sequencing for Crop Improvement, was led by Myles, funded by Genome Canada and supported by Genome Atlantic.

“The Genome Canada project I was involved with aligned well with my interests in bioinformatics and complemented the other work that was going on in the Myles lab, such as developing high throughput genetic markers for future tree fruit – apple –improvement,” Gardner explained.

“With the Genome Canada award, we were able to put together a team to develop some novel tools to efficiently generate more complete DNA marker data from low coverage DNA sequencing in non-model organisms, such as apples,” he said. “Essentially the method that was developed, in conjunction with Dr. Daniel Money (University of Cambridge) and Dr. Myles, allows you to get more DNA marker information out of the same DNA sequence dataset at no extra cost. This method, and associated software, has now been used in many different species study systems from wheat, corn, and grapes to house sparrows and corals.”

Fast forward to today

Today, Hori’s and Colombo ‘s expertise is focused on bettering aquaculture, while Gardner’s know-how targets improvements in potato breeding.

As a bioinformatician, Hori worked on harnessing functional genomics and structural genomic tools for the aquaculture industry, in his previous role as the Director of Genomics at the Centre for Aquaculture Technologies (CAT).  “My main role was to  figure out how genomic technologies can be applied to aquaculture in an economically feasible way,” he said. “That means testing many different approaches and algorithms and being up-to-date with technologies like sequencing and microarray. I also share the load of the bioinformatics analysis for clients.” More recently, he was appointed Director of Aquaculture Innovation with Atlantic AquaFarms, where he will focus on actively driving the application of genome-based and other innovations to improve aquaculture production and sustainability.

His participation in Genome Atlantic-supported projects has played a role in keeping him in the region. “I could have gone west,” he said, “because I worked quite a lot with salmon, but my wife is from Newfoundland, and the people I know and work with are in the Atlantic region.” Hori still works closely with many of the people he encountered on the CGP and camelina projects, especially Dr. Rise and Dr. Kurt Gamperl, professors, Ocean Sciences, Memorial University, and Dr. Mark Fast, Associate Professor of Fish Health, Atlantic Veterinary College, University of Prince Edward Island.          

Colombo’s current research at Dalhousie’s Truro, NS campus, aims to discover sustainable new ways to improve nutrition and aquaculture production.  Specifically, she is interested in developing sustainable sources of omega-3s in diets for farmed fish and discovering new ways to boost their nutrition and metabolism. The goal is to produce healthy farmed fish that supply consumers with omega-3s in ways that effectively use ocean resources. “I use genomics as a tool to help answer these nutritional questions,” she said. “It allows us to dig deeper into the synthesis and storage of these important fatty acids.” 

She now has graduate students working in her lab, and she also teaches fish nutrition as part of the B.Sc. Agriculture (Aquaculture) program.

At Agriculture and Agri-Food Canada, Gardner says he uses “genomics tools, like DNA sequence-based genotyping, in the potato breeding program, based in Fredericton, New Brunswick.” It takes 10-12 years to develop a new potato variety, he says, “so we are keen to use emerging technologies to make the variety selection process more efficient and cost effective. “

It is clear that Hori, Colombo and Gardner are applying their knowledge to help the Atlantic region prosper. For Hori especially, the journey has been an eye-opener. As a student at the Federal University of Sao Carlos, Brazil when the CGP project emerged on his radar, Atlantic Canada was well off the beaten path. “Never heard of it,” he said. Now Atlantic Canada is home.

Young Scientist Profile: Nicole Smith, doctoral student

Nicole Smith, doctoral student.

Young Scientist Profile:  Nicole Smith, doctoral student

Hails from St. John’s, where she is currently pursuing doctoral studies at Memorial University in Newfoundland. Her MSc in biochemistry and BSc (Hons) in Biochemistry and Neuroscience are also from Memorial.

Field: marine biology, specializing in fish immunology.

I work with Dr. Matthew Rise’s group (Department of Ocean Sciences) and am co-supervised by Dr. Sherri Christian (Department of Biochemistry). I met Matt, the Canada Research Chair in Marine Biotechnology, when I received a Research Assistant II position in 2014 at the Cold-Ocean Deep-Sea Research Facility (CDRF) located at the Ocean Sciences Center, Memorial University. I worked full-time as a research assistant (RA) for 1.5 years, and then decided I would like to complete a PhD with Matt and Sherri, designing a project that uses some of the techniques and equipment that I run at the CDRF (flow cytometry to analyze various cell characteristics including cell size, cell count, cell surface proteins; confocal microscopy for high resolution optical imaging, and scanning electron microscopy equipment). I still hold a part-time position as an RA at the CDRF while completing my PhD.

Current Projects:

• Natural Sciences and Engineering Research Council of Canada (NSERC): Characterization of Atlantic Salmon Macrophage Differentiation. Sept 2015-May 2019

• Genome Atlantic: The Effect of Functional Feed Ingredients on Atlantic Salmon Macrophages. January 2016-January 2018

The Challenges: Part of my project, which is funded by the National Sciences and Engineering Research Council of Canada, involves characterizing macrophage differentiation in Atlantic salmon. Macrophages are important cells in the immune system, and while they have been well characterized in mammals, they have not been in fish.

In addition to characterizing macrophage differentiation, another part of my project, which was funded through Genome Atlantic, involves testing various functional feed ingredients (FFI) on Atlantic salmon macrophages to determine if the FFI have immune modifying properties. 

The Objectives:  As fish in aquaculture are prone to infection, having both financial and environmental effects, it is important to fully clarify the markers and mechanisms behind macrophage differentiation, especially in economically important fish such as the Atlantic salmon, so that we can better understand how these immune cells work.

In the Genome Atlantic-funded project we want to find out if various functional feed ingredients (FFIs) have immune modifying properties in Atlantic salmon macrophages and whether these FFIs could potentially be used as a safe and natural feed additive in aquaculture.

The Projects’ importance: By better understanding the fish immune system, we can help fight and prevent disease in farmed fish. Advances in this field will improve the sustainability of aquaculture world-wide.

The Exciting Part: This project calls for me to use many different techniques including genomic techniques such as microarray and RT-qPCR, flow cytometry, confocal microscopy and in vitro cell culture. Coming from a mammalian background (Master of Science in Biochemistry) it excites me to apply techniques and methods used in the mammalian world to fish research, which is a relatively new concept.

Project’s significance for Your Career Path:  I hope to become a senior scientist in industry or government, whether that be in mammalian or fish research. The wide variety of methods and equipment I am using in these two projects, as well as in my position as a RA, are expanding my skills to equip me for greater roles in future research investigations. In the immediate term these experiences are also helping with my doctoral studies.

New mental health project will explore the DNA of bipolar disorder

Check out our brief “Genomics Can Help” videos of Dr. Alda and Dr. Uher:

HALIFAX, NS – A team of Nova Scotia mental health researchers are set to explore the genetic factors that play a role in bipolar disorder (BD).  Led by Dr. Martin Alda and Dr. Rudolf Uher, the three-year, $975,000 research project could lead to new clinical tools to better diagnose and treat this disorder.

Early detection of bipolar disorder and optimized selection of long-term treatment will take a personalized medicine approach, using genomics to develop new screening tools for early detection and identify optimal long-term treatment for individual patients.  Ultimately, Drs. Alda and Uher hope to engage clinicians and patients in the personalized management of BD, based on new treatment guidelines informed by this work.

“Treating BD with long-term medication can be effective,” said Dr. Alda, chair in mood disorders at Dalhousie University and a clinical psychiatrist and researcher with the Nova Scotia Health Authority (NSHA).  “However, no two individuals are alike and choosing which treatments work best for individuals can take months and even years of trial and error.  With the right genetic screening tools, we can more accurately predict which treatments are most likely to work for certain individuals, allowing us to prescribe the right treatment more quickly.”

Bipolar disorder (BD) is a serious, chronic psychiatric illness that affects young people in their early 20s and recurs throughout their lifetime. BD affects an estimated 500,000 Canadians and is one of the top 10 causes of disability and mortality worldwide. Genetic factors influence who is at risk from BD and how individuals respond to long-term treatment.

The risk of suicide in individuals with BD is highest in the first years of illness ­– precisely the time when most treatment delays occur.  A key component of the research will be to identify the key risk factors that predict who might get the disease.


How Genomics Can Help

Check out our brief “Genomics Can Help” videos of Dr. Alda and Dr. Uher:


“By identifying susceptible individuals, we can implement preventive strategies before the onset of symptoms,” said Dr. Uher, Canada Research Chair in early intervention in psychiatry at Dalhousie University and a clinical psychiatrist and researcher with the Nova Scotia Health Authority.

“Timely diagnosis is critical for decreasing morbidity and mortality.”

Dr. Rudolph Uder

Early detection of bipolar disorder and optimized selection of long-term treatment is supported by Genome Atlantic with funding from Genome Canada’s Regional Priorities Partnership Program (RP3), Research Nova Scotia Trust, Nova Scotia Health Authority, the Dalhousie University Department of Psychiatry and Dalhousie Medical Research Foundation.


Partner Quotes

The partnership that came together to support this project speaks to its critical importance. Genomics technologies hold great promise for a personalized medicine approach to diagnosing and treating mental illness, and the ground-breaking work done by Drs. Alda and Uher could significantly reduce the impact of bipolar disorder on the lives of patients and their families.”

Dr. Steve Armstrong, PhD; President and CEO, Genome Atlantic

“We know more today than we ever have about the diagnosis and treatment of mental illness – but there is still much to learn. Government is pleased to support research projects like this one that increase our collective understanding of mental illness while also improving outcomes for those living with bipolar disorder.”

Hon. Randy Delorey, Minister of Health and Wellness  

One in five Canadians are affected by mental illness and addiction each year, which includes those affected by bipolar disorder. Early detection and genetic screening could radically alter the effect this illness has on lives. The achievements of Drs. Alda and Uher in clinical work, in research, in leadership, and in mentorship, are exceptional and we are fortunate to have them working in our department and on this very critical project.”

Dr. Michael Teehan, head of the Department of Psychiatry, Dalhousie University, and Chief,

Department of Psychiatry, NSHA Central Zone

“Thanks to the generosity and vision of our donors, DMRF is able to support world-renowned researchers like Drs. Uher and Alda. Innovative medical research has the power to strengthen the ability to identify, diagnose, treat and ultimately prevent severe mental illness. Health is key to an improved quality of life. This, and the critical role our donors play as agents of change, underscores the necessity to continue supporting advances in health research.”

Brian Thompson, CEO, Dalhousie Medical Research Foundation

“Innovative health research is a priority area for the Research Nova Scotia Trust, and we are proud to support this work. This research will drive solutions to mental health care for Nova Scotians.”

Dr. Colin Dodds, PhD, Trustee of the Research Nova Scotia Trust

Media Contacts:

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

Carla Adams, NSHA Media Relations, 1-844-483-3344; Carla.adams@nshealth.ca

News Release: Developing new genetic tools to fight superbugs

Halifax, NS – Bacteria are becoming increasingly resistant to antibiotics, posing an enormous risk to the agri-food industry and to the health of Canadians. To better understand antimicrobial resistance (AMR), we need to know which genes contribute to resistance and how they spread.

A team of researchers at Dalhousie University, Simon Fraser University, McMaster University and the Public Health Agency of Canada will work to develop new surveillance tools to help identify and track these problem genes. Their $1.4 million research project, Antimicrobial Resistance: Emergence, Transmission, and Ecology (ARETE), was one of 37 Genome Canada projects announced today by federal Minister of Science and Sport, the Honourable Kirsty Duncan.

The research team led by Dr. Robert Beiko of Dalhousie University and Dr. Fiona Brinkman of Simon Fraser University are seeking to determine which genes are being shared, which bacteria are sharing genes, and how bacteria are moving between habitats. “Resistance genes can be shared by pathogenic bacteria, and these resistant bacteria also move between habitats, such as agricultural soil and farm animals,” said Dr. Beiko. “To track this process, we will develop informatics algorithms and software that will shift how we look at AMR from a static “snapshot” to a dynamic view of AMR transmission.”

Once the tools are developed, they will be rigorously tested, said Dr. Brinkman. “We will validate them using thousands of genomes of Salmonella, E. coli, and other pathogenic bacteria collected by partners in the Public Health Agency of Canada and Agriculture and Agri-Food Canada.”

Ultimately, the project aims to minimize the risks posed by resistance and foster a national framework to apply genomics and bioinformatics to the “farm to fork” continuum of AMR. The integrated software modules developed through the project will be open-sourced and freely available.

ARETE is enabled through Genome Canada’s Bioinformatics and Computational Biology funding program with additional funding from The Public Health Agency of Canada, The Research Nova Scotia Trust, Simon Fraser University, McMaster University, and Compute Canada. The project is led by Genome Atlantic and supported by Genome BC.

Genome Atlantic is a not-for-profit corporation with a mission to help Atlantic Canada reap the economic and social benefits of genomics and associated technologies. Since 2000, the corporation has worked with a range of partners to enable more than $100 million in genomics R&D to benefit the region.

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

Sequence #1: So What’s Up With The Microbiome?

The microbiome is a hot topic these days, embraced by research scientists and the media alike.  The microbiome refers to all the microorganisms and their collective genetic material that reside in human beings and other animals, plants, soil, and water.  These communities of ‘microbial flora’ have always been with us but we’re just beginning to understand the role they play in everything from human health to mining and agriculture. 

We know, for example, that not all microbes are equal.  Some are harmful, some benign and some essential for the health of their hosts.  Microbes can boost our immune systems and our natural resources – but maintaining a healthy microbiome is a balancing act that can be thrown out of whack by factors like diet(in humans) and chemicals (in soil and water). 

This issue of Sequence explores the new frontier of the microbiome. We’ll go behind the scenes with scientists on the cutting edge of human microbiome research, meet a hard-working sequencing facility that’s a hit with genetic researchers near and far, and see why microbes are the Midas touch for gold extraction, a better tool for cleaning oil spills, and the magic in making better wines. 

Invitation: Announcement & panel discussion on genomics & bipolar disorder – Feb. 7th, 2019

Genetics plays a big role in diagnosing and treating bipolar disorder (BD). Please join us for an announcement about an exciting new research project that could improve early detection and treatment of BD – followed by a panel discussion with Nova Scotia Health Authority/Dalhousie University mental health researchers Dr. Martin Alda and Dr. Rudolf Uher (moderated by Cynthia Maillet, former radio producer/host for Radio Canada & CBC) on new genetic approaches to diagnosing and treating BD.

Date & Time: Thursday, February 7, 2019, 6:00 p.m. (Reception at 5:30 p.m.)

Location: Atrium, Life Sciences Research Institute, 1344 Summer Street, Halifax, NS

Hosted by Genome Atlantic with support from Genome Canada and in partnership with the Research Nova Scotia Trust, Nova Scotia Health Authority, the Dalhousie University Department of Psychiatry and the Dalhousie Medical Research Foundation.

All welcome, please register at: http://genomeatlantic.eventbrite.ca