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GEN-FISH: Genomic Network for Fish Identification, Stress and Health (2018)

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Overview

Freshwater fish resources contribute to Canada’s economy both directly and indirectly. Thriving  freshwater fish resources are the lifeblood of many rural, northern and Indigenous communities and are central to the social and cultural lives of millions of Canadians. Yet, freshwater fish stocks are under threat. Canadian freshwater fish stocks need science-based monitoring and management. The logistical difficulties of monitoring fish stocks in Canada’s 2+ million lakes and countless rivers are compounded by the limitations of conventional sampling methods, which provide only a snapshot. The project will use genomic approaches to develop a Fish Survey Toolkit based on environmental DNA from water samples and a Fish Health Toolkit that will provide quantitative assessments of the health of fish and the stressors they face. Collectively, these toolkits will enable a complete and accurate assessment of the status of Canada’s freshwater fish resources and save millions of dollars for government, NGOs, fish culture facilities, and environmental consultants in fish survey costs, and will result in additional indirect savings through more effective and directed management actions. Furthermore, and most importantly, the project will ensure sustainability of Canada’s freshwater fish resources for generations to come.

BeeCSI: ‘omic tools for assessing bee health (2018)

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Overview

Honey bees are crucial to Canada’s agriculture and contribute up to $5.5 billion a year to our economy by pollinating valuable Canadian crops. However, the health of honey bees has been declining over the past decade, with Canadian beekeepers losing more than a quarter of their colonies each winter since 2006-07. The causes of bee declines are complex, variable over space and time, and often difficult to identify. This project aims to use genomic tools to develop BeeCSI – a new health assessment and diagnosis platform powered by stressor-specific markers. Working with beekeepers, industry technology-transfer teams, and diagnostic labs, in consultation with federal and provincial regulatory entities to ensure that the tools are implemented and accessible to the beekeeping industry by the end of the project.

TRIA-FoR: Transformative Risk Assessment and Forest Resilience Using Genomic Tools for the Mountain Pine Beetle Outbreak (2020)

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Overview

The current mountain pine beetle (MPB) epidemic has killed approximately 20 million hectares of mainly lodgepole pine forests in British Columbia and Alberta. Climate change and forest management practices have contributed to unprecedented range expansion of MPB. From its historic range in central British Columbia, MPB has spread through novel habitats in Alberta, establishing in a new host, the jack pine. Jack pine is a boreal forest species with a range that extends to the Atlantic Ocean, raising the spectre of continued eastward spread of MPB. Given the importance of lodgepole and jack pine to the forest industry, their central role in providing ecosystem services and their cultural importance, there is an urgent need to enhance resiliency of forests replacing MPB-killed stands, and to quantify eastward spread risk potential of MPB.

In TRIA-FoR, we will adopt a state-of-the-art multidisciplinary and integrative approach to develop genomics-informed knowledge, tools and application frameworks that mitigate risk for the present MPB epidemic and improve resiliency in future epidemics. Risk and resiliency will be investigated in the context of MPB-pine-climate interactions that affect MPB population dynamics, human dimensions in forest resource management, and impacts on diverse communities connected to forests at risk.

TRIA-FoR research encompasses three overarching goals. (1) Enhance lodgepole pine genetic resiliency to MPB. We will identify gene-based markers that predict MPB resiliency in lodgepole pine and identify traits that contribute to MPB resiliency. To understand how genetic resiliency translates into forest resiliency, we will model the impact of planting MPB-resilient lodgepole pine on outbreaking MPB populations. (2) Improve risk assessment efficacy for MPB northern and eastern spread into the boreal forest by examining MPB – pine host – climate interactions. We will test whether jack pine forests east of Alberta can support MPB populations, or whether expanding populations require immigration from the lodgepole x jack pine hybrid zone. In tandem, we will determine how overwintering temperatures and pine host characteristics in these marginal habitats affect MPB success. (3) Develop a social sciences framework of risk management planning and resilience building that can facilitate adoption of genomics-informed practices or technologies. We will investigate geographic, sociological, economic and policy aspects of risk related to the MPB epidemic, identifying factors that influence stakeholder willingness to adopt genomics-informed applications. This collaborative cross-scale research will enable a genomics-informed total risk and resilience management approach that can enhance forest health in the face of present and future MPB epidemics.

Optimizing a Microbial Platform to Break Down and Valorize Waste Plastic (2020)

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Overview

In Canada, 29,000 tonnes of plastic leak into the environment and oceans every year, creating severe environmental problems. Waste plastic kills 100,000 marine mammals annually, including whales, dolphins, seals, and sea lions, either through ingestion of plastic debris or entanglement in fishing gear. Another 2.8 million tonnes of plastic are sent to Canadian landfills, which creates a latent problem for future generations. Only 9% of plastic is recycled.

Despite the waste and environmental impact, plastic production is increasing in Canada, with an additional 4.8 million tonnes produced per year. Demand for plastic continues to grow because it is cheap to produce and has many important benefits. However, with a growing awareness of the environmental impacts of plastic, governments and manufacturers are working towards a zero-plastic waste future. Under this paradigm, plastics will be made with recycled or biodegradable components. For this change in paradigm to succeed, government, the public, and industry will all need to play a role.
In this project a Canadian-led team consisting of multiple universities, municipal governments, and industries will drive a shift to a zero-plastic waste future by harnessing genomics technologies to create a circular economy for plastics. Our goal is to identify and engineer bacteria and enzymes that can break down plastics into recyclable components or into valuable fine chemicals more effectively than chemical conversion-based technologies. On a second front our team will conduct a holistic investigation into the impact of these new plastic biotechnologies on society, the economy, and the environment. Preliminary estimates indicate that if 90% of plastic is diverted to recycling instead of landfill, Canada could avoid $500 million per year in costs, and create 42,000 jobs in new industries. The market for recovered waste plastic in the textiles sector alone is up to $600 million per year. We could also save 1.8 million tonnes of CO2 equivalents per year in greenhouse gas emissions. Globally, stopping plastics from leaking into the environment would avoid up to $13 billion per year in damage to marine ecosystems. Ultimately, we envision a future where plastics continue to contribute to the economy in a positive way, but without the concomitant negative impact on the environment.

This project is affiliated with the Contaminants of Emerging Concern Research Excellence Network (CEC-REN) at Queen’s University, which is an interdisciplinary research and innovation initiative. CEC-REN is focused on the detection and treatment of emerging contaminants in the natural and built environment that pose environmental and human health risks.

BIOSCAN–Canada (2020)

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Overview

The Global Risks Report 2020 from the World Economic Forum ranked biodiversity loss as one of the top five threats confronting humanity. Stemming this loss requires understanding how species interact and respond to changes in their environment, but this is impossible to accomplish with traditional morphological methods. DNA barcoding first emerged 15 years ago as a rapid, accurate way to discriminate species based on the sequence characterization of short segments of DNA. The International Barcode of Life Consortium, led by the Centre for Biodiversity Genomics at Guelph, involves research organizations in 40 nations which share the goal of cataloging all species and establishing a global biosurveillance system before mid-century.

Its current research program, BIOSCAN, is harnessing new technologies to make DNA barcoding faster and less expensive, advances that will broaden its application. Importantly, the technologies normally used to sequence whole genomes can be employed to gather DNA barcodes from thousands of specimens at a time. BIOSCAN–Canada is a core component of this global effort; its work will increase the cost effectiveness of DNA-based identification systems while also providing new biodiversity data with direct relevance to Canadians. For example, new species will be revealed from under-explored regions such as the Arctic and the ocean floor off British Columbia. DNA barcoding will also be used to illuminate interactions among species, such as which flowers a bee visited, and to track the shifting distributions of species in response to environmental change at previously impossible scales. Through community engagement, BIOSCAN–Canada will incorporate Indigenous ways of knowing into an accounting method for “natural capital” that extends beyond conventional economic metrics like the GDP.
By combining genomics-based biodiversity data with this accounting system, it will enable effective, timely environmental impact assessments and policymaking for the forestry, mining, and agricultural sectors as well as for conservation planning. Through such action, BIOSCAN–Canada will slow biodiversity loss, improve Indigenous relations through consultation, increase the sustainability of our agricultural and forestry sectors, and strengthen Canada’s leadership in global conservation efforts.

Genomics for a competitive greenhouse vegetable industry

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Overview

Tomatoes, peppers and cucumbers generate more than $1 billion in annual sales for the Canadian greenhouse vegetable industry. These plants are susceptible to a number of diseases, which threaten crops and decrease profits for producers. In order to maintain a competitive edge, create growth and ensure future success, Canada’s greenhouse vegetable industry needs plant varieties that are resistant to disease. To address this challenge, Vineland Research and Innovation Centre will partner with Dr. Keiko Yoshioka, a leading academic from the University of Toronto, who has discovered a key gene involved in plant disease resistance. By using proven gene technologies to enhance disease resistance in greenhouse vegetables, this project aims to develop new commercial traits and varieties for Canada’s vegetable industry. These technologies will benefit Canada’s greenhouse vegetable industry by adding value to Canadian greenhouse vegetables, and fostering economic growth, increased exports, reducing competition from imports.

Development of low cost diagnostic platform for infectious disease testing

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Overview

Conventional lab testing for infectious diseases such as Hepatitis C, malaria and tuberculosis is inefficient and not cost-effective, particularly in developing countries. The development of fast and accurate point-of-care testing for these infections would significantly improve the clinical management of infectious diseases. For this research, Xagenic will partner with Dr. Shana Kelley, a leading academic from the University of Toronto, to leverage expertise in viral assay development, sensor technology and plastic chip fabrication. This project will lead to a single affordable and accurate genotyping test to screen for infectious pathogens, and will provide a new solution for rapid disease diagnosis. The low-cost, disposable, battery-powered testing device will identify pathogens in human blood in minutes, which could reduce infectious disease in Canada and around the world, and dramatically improve disease management. The launch of this new product line by Xagenic will result in increased revenues and significant job creation within the company.

Clinical utility and enhancements of a pharmacogenomic decision support Tool for Mental Health Patients

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Overview

One in five Canadians will experience some form of mental illness in their lifetime. Treatments are available but each person responds differently to them, in part because of their genes. A clinically proven genetic test, called GeneSight, analyzes an individual’s genes and recommends the optimal drugs for that person along with dose adjustments among the 33 most commonly prescribed antidepressant and antipsychotic drugs. Clinical testing in the United States has shown that GeneSight doubles the odds of a patient responding to antidepressant medication. More than 100,000 patients have received GeneSight tests in the United States. Now, Assurex Health, the company that developed GeneSight, is partnering with scientists at Toronto’s Centre for Addiction and Mental Health (CAMH) to develop the Enhanced GeneSight (E-GeneSight) genomic test. E-GeneSight will incorporate new genomic markers that scientists at CAMH have identified and characterized for their association with patient responses to psychiatric medications. Assurex Canada and CAMH will together validate these markers for their ability to predict efficacy and side effects of psychiatric medications; the most predictive markers will be integrated into E-GeneSight. E-GeneSight, when launched in 2017, is anticipated to reduce the need for “trial-and-error” approaches to prescribing and increase the likelihood that people will respond optimally to the medications prescribed for them, while reducing side effects. This will increase the proportion of patients who stay on their medications and improve their quality of life. It will also save the Canadian healthcare system $4,000 per year per treatment-resistant patient and will generate royalty revenues for CAMH as E-GeneSight is marketed internationally.

SIRPaFc: Translating genomics research into a novel cancer immunotherapy

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Overview

Nearly all (96 per cent) people aged 65 or older diagnosed with acute myeloid leukemia (AML) die within five years, as do two-thirds of younger patients. Because it primarily affects older people, the incidence of this aggressive cancer is expected to rise in coming years as the population ages. Chemotherapy regimens for AML have remained essentially unchanged since the 1970s. With standard treatment, many patients can achieve remission, but most will relapse; following relapse two-thirds of patients will die within 3 years. One of the reasons for the high rate of relapse in AML is that standard chemotherapy does not kill leukemia stem cells, leaving them to grow and mature into new leukemia cells. Leukemia stem cells express high levels of a protein called CD47. This protein sends a “do not eat” signal that stops white blood cells of the immune system called macrophages from surrounding and “eating” cancer cells. With previous support from Genome Canada and Trillium Therapeutics Inc. (TTI), a publicly traded biotech company in Toronto, Canada, Dr. Jean Wang and team at the Princess Margaret Cancer Centre, University Health Network, and Dr. Jayne Danska and team at SickKids have developed SIRPaFc, a novel therapeutic that blocks the “do not eat” signal, freeing the immune system to attack leukemia stem cells. TTI is completing formal preclinical studies and will carry out clinical trials aimed at demonstrating SIRPaFc’s safety and efficacy. The collaboration between Drs. Wang and Danska and TTI will assist in realizing the commercial potential of this promising discovery.

Scale-up of bioaugmentation cultures and development of delivery strategies and monitoring tools for anaerobic benzene and alkylbenzene bioremediation

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Overview

BTEX compounds – benzene, toluene, ethylbenzene and xylenes – are natural components of crude oil and petroleum and are used in the synthesis of a wide range of useful materials and chemicals. They are also toxic, and benzene in particular is a known human carcinogen. As a result of extraction, transportation and refining processes, as well as accidental spills and leaks, BTEX compounds frequently pollute groundwater in all industrialized regions of the globe. In Canada and elsewhere, remediation of contaminated sites is difficult and costly. When possible, affected soils are dug up and treated or disposed of offsite. Dr. Elizabeth Edwards of the University of Toronto is working with SiREM, a Canadian leader in bioremediation, to scale up and commercialize anaerobic bioaugmentation cultures for in situ BTEX remediation. These cultures were developed in Dr. Edwards’ lab where genomic knowledge was used to identify novel benzene-depleting microbial strains. Bioaugmentation, or the injection of specific microbes into contaminated sites, could significantly accelerate the rate of biodegradation, leading to the cleanup of these sites. How well the cultures perform this biodegradation should be understood in 1-3 years, leading to a cost-effective approach for cleanup of BTEX-contaminated sites. If successful, this project would be the first commercial application of bioaugmentation for anaerobic BTEX degradation. It would lead to more widespread cleanup of contaminated sites where currently technologies are not feasible or too expensive. It will enable remediation of soils in-place, as opposed to excavation and removal. There are also significant economic benefits, as the global bioremediation market was conservatively estimated at $1.5 billion in 2009 and is now probably greater than $10 billion and continuing to grow.