Projects by department

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Agriculture and Agri-Food Canada

Camelina sativa as a 21st century Clean Energy crop for Canada

Funding period: 2017-2019
Lead: Dwayne Hegedus
Total GRDI funding: $370,000

Camelina is being aggressively marketed as a bio-diesel and aviation fuel feedstock. It is a close relative of canola and mustard and is, therefore, amenable to conventional production practices. It grows in marginal soils that are not well-suited for food crops, thus avoiding food vs fuel concerns. This project will explore camelina genetic variation and apply genomic solutions to address limitations in agronomic characteristics, seed and product quality, and undertake studies to provide a clear understanding of the economic opportunity for this emerging clean energy crop. This project is part of a cluster of initiatives aimed at developing camelina for energy purposes. The collective work involves stakeholders at several levels (producers, private sector breeders, seed suppliers, bio-products & bio-fuel suppliers, and rural communities).

Targeting resistance and susceptibility genes and dissecting infection mechanisms through genomics for durable Fusarium and rust resistance in cereals

Funding period: 2017-2019
Lead: Linda Harris
Total GRDI funding: $1,144,509

The sustainability of the Canadian cereal crop sector depends on high yielding, high quality grain with minimal pathogen and mycotoxin contamination. Fusarium head blight and rust continue to be top priority threats for Canadian cereal producers. Resistant cereals are required to prevent devastating losses as seen recently in Western Canada. Through AAFC's established multidisciplinary network (breeding, genetics, genomics, proteomics, pathology, tissue culture, metabolomics and mycotoxin chemistry), we are mapping novel sources of fusarium and rust resistance, and are investigating fusarium infection mechanisms, regulation of mycotoxin production and fusarium species interactions. The goal is to develop durable fungal resistance in cereal crops to sustain the profitability of Canada's agriculture.

Gene-for-Gene Mediated Resistance to Midge in Canola and Wheat

Funding period: 2017-2019
Lead: Martin Erlandson
Total GRDI funding: $211,000

Billions of dollars are removed from the Canadian economy by insects that damage field and vegetable crops. Recent advances in the understanding of host plant-pest interactions and insect genomics has led to the development of exciting new alternatives to chemical insecticides, including crop plant resistance genes and genomic-based approaches that specifically target vital pest genes. The swede midge is a serious pest of brassica vegetables and canola in Ontario and Quebec and the orange blossom wheat midge is a serious threat to Canadian wheat production. The objective of this project is to develop a genomics database for both pests and to investigate their interaction with host crop plants at the molecular level. The long term goal of this project is to develop resistant crop varieties.

Advanced genomics strategies to capture novel genetic diversity for oilseed crop improvement

Funding period: 2017-2019
Lead: Kevin Rozwadowski
Total GRDI funding: $1,073,510

Exploiting genetic variation is the central tenet of plant breeders in their efforts to optimise germplasm for yield, quality traits and sustainable production in the face of biotic and abiotic stresses. However, there is a lack of variation in the current germplasm that limits the ability of breeders to effectively address new production challenges. To accelerate genetic improvement of canola there is a strategic need to define the genomic nature of available variations, identify favourable alleles, and enable marker-based selection of desirable traits. By overcoming barriers that inhibit genetic recombination, targeted gene modification can be facilitated to enable the recovery of desired traits. With an understanding of genetic variations and the tools to enable them, genetic improvement will be faster and will secure the sustainable production and profitability of canola crops.

Genetic and epigenetic variants of Canadian cereal crops for breeding and functional analysis

Funding period: 2017-2019
Lead: Nick Tinker
Total GRDI funding: $1,072,000

Soybean is the third largest field crop in Canada with 5.5 million acres planted in 2016. Ontario, Manitoba and Quebec are the major producers. Biotic stresses caused by the pathogens Phytophthora sojae, Sclerotinia sclerotiorum, soybean mosaic virus, and soybean cyst nematode are among the major disease risks and result in losses to productivity and income. AAFC is addressing these issues through a multidisciplinary approach by building on previous AAFC-GRDI funded projects using the latest technologies in genomics, metabolite and transcript profiling, and gene editing (e.g. CRISPR/CAS technology).

Canadian Food Inspection Agency

Application of whole genome sequencing for molecular epidemiological investigations of bovine tuberculosis in Canada and for the high throughput discovery of novel diagnostic antigens for Mycobacterium bovis and Brucella abortus

Funding period: 2014-2019
Lead: Olga Andrievskaia
Total GRDI funding: $350,000

The recent development of new genomics methods and whole genome sequencing has supported the CFIA's response capacity for the detection of pathogens threatening wildlife reservoirs. This project supports the harmonization of molecular epidemiology approaches applied in bovine tuberculosis outbreak and incident investigations with the US Department of Agriculture. It develops models of Mycobacterium bovistransmission in Canadian bovine tuberculosis wildlife reservoirs and livestock population. This research enables the CFIA to acquire new information on the evolution of Mycobacterium bovisstrains, which will serve to better protect wildlife reservoirs in various Canadian and North American geographical areas.

Detection and identification of plant pests and plants with novel traits using next generation sequencing

Funding period: 2014-2019
Lead: Guillaume Bilodeau
Total GRDI funding: $1,000,000

The CFIA is developing capacity for DNA barcoding and next generation sequencing to enhance CFIA regulatory plant health responsibilities in the areas of detection and identification of invasive plants, regulated plant pests and pathogens and plants with novel traits. Researchers have acquired materials and bioinformatics tools are being used to create sequencing data repositories. New tools, field protocols, genotyping of target organisms, and pipelines for genome assembly support the detection of viruses, insects and plants with novel traits. This work advances innovative regulatory science to support the CFIA regulation for plant protection.

Development of diagnostic sequencing methods to monitor, detect and characterize RNA viruses of food, animals and plants, following viral contamination or infection

Funding period: 2014-2019
Lead: Mike Rott
Total GRDI funding: $350,000

The Canadian Food Inspection Agency's list of regulated pests includes many RNA viruses responsible for infection of plants and animals. Some of these viruses also present significant risks to human health. This project proposes to use novel RNA Sequencing genomic technologies to detect, identify and characterize at the molecular level the RNA viruses found in various matrices such as plants, animal tissues or a variety of foods. This project will facilitate a joint effort by scientists in all three of CFIA's business lines, to develop, improve, adapt and harmonize next generation sequencing methods and pipelines for the identification and characterization of known or unknown RNA viruses. The genomic tools will be integrated into the Agency's diagnostic arsenal.

Development of infrastructure and bioinformatics tools to support genomics activities in CFIA's food, plant and animal business lines

Funding period: 2014-2019
Lead: Catherine Carrillo
Total GRDI funding: $200,000

Recent developments in the field of genomics have led to the increased application of these technologies to CFIA's regulatory science activities. A number of methods and applications have been developed in parallel in the food, plant and animal business lines. This project is working to harmonize genomics activities, including method development, bioinformatic analysis of genomic data and the provision of training on the use of bioinformatic tools in all three of CFIA's mandated protection areas: food safety, animal health and plant protection. It builds on existing collaborations with other federal laboratories and to enhance the agency-wide access to tools. The use of common platforms for genomics/bioinformatics work will ensure that efforts are not duplicated and that resources can be re-allocated to increase the integration of emerging genomics technologies into CFIA's mandated activities.

Enhancing the CFIA's genomic capabilities for detection and characterization of high consequence known and unknown/unexpected animal viruses and their vectors/reservoirs

Funding period: 2014-2019
Lead: John Pasick
Total GRDI funding: $650,000

This project enhances the CFIA's capacity to detect and characterize high priority animal viruses. Research efforts support the development of methods and protocols for the sequencing of viral isolates and implementation of next generation sequencing as a complement to routine diagnostics. This research supports the National Centre for Foreign Animal Disease's ability to respond to avian influenza and Seneca Valley virus field sample diagnostics. Significant progress has been made to enhance and develop new protocols for a number of foreign animal disease viruses (Bluetonque virus, Seneca valley virus, foot and mouth disease virus, avian paramyxovirus-1 virus, and classical swine fever virus), and the genomes of many isolates of these high priority viruses were generated to increase diagnostic capacity.

Whole genome sequencing technologies as tools for the detection, isolation, identification and characterization of pathogens in support of Canadian food inspection objectives

Funding period: 2014-2019
Lead: Burton Blais
Total GRDI funding: $1,000,000

This project develops genomics databases of known pathogens that will allow the CFIA to deliver a highly responsive, risk-based food inspection system. In this project, CFIA scientists are working to create a database of food borne pathogens and new tools for the enhanced detection of microbial hazards in the food supply system. Thousands of pathogens including strains of Salmonella, Listeria, Escherichia coli, Shigella, Staphylococcus and infectious bacteria related to food-borne illnesses have been fully sequenced and added to the regulatory genomic database. This database will be instrumental to mitigate public health risks associated with the food supply system.

Environment and Climate Change Canada

Application of genomics to assess the impact of harvest and other mortality sources on vulnerable populations of North Atlantic murre

Funding period: 2016-2019
Lead: Greg Robertson
Total GRDI funding: $60,272

Murres are a common seabird breeding throughout the northern hemisphere, and face many pressures from human activities, including legal harvests in Canada and Greenland. Many, but not all, breeding colonies across the North Atlantic are declining, so understanding if certain populations are preferentially affected by hunting is required to ensure harvest levels are sustainable. We use generation DNA sequencing to identify the source colonies of harvested murres from both Canada and Greenland. Our results will directly inform, and if necessary adjust, harvesting practices in both countries to avoid placing undue pressure on declining populations.

Development and validation of metabolomic techniques to evaluate impacts of large-scale environmental changes on stress responses in wildlife

Funding period:2016-2019
Lead: Catherine Soos
Total GRDI funding: $149,477

Understanding the causes and consequences of stress in wildlife is increasingly important, given that large-scale environmental changes are occurring at a rapid rate and result in multiple concurrent stressors that threaten wildlife and human health. Non-invasive and cutting-edge tools are required to help us understand and mitigate impacts of stress on wildlife, and potentially identify populations at risk. In this project we are developing and validating the use of novel metabolomics tools for evaluating stress in wildlife, and applying these tools to investigate responses to large-scale changes such as climate change and oil sands development.

Development of next-generation genomic tools to investigate cumulative effects of urban pollution and pathogens in two sentinel fish species

Funding period:2016-2019
Leads: Magali Houde and David Marcogliese
Total GRDI funding: $262,109

Municipal effluents are major sources of pollution for the aquatic environment. This project aims to investigate the cumulative impacts of anthropogenic (chemical exposure) and natural (parasites) stressors on the health of two wild fish species from the St. Lawrence River environmentally exposed to a major primary urban effluent. The use of state-of-the-art tools will help us identify biological systems that may be impacted by the exposure to the complex man-made cocktail. Complementary long-term laboratory exposure using juvenile rainbow trout will also allow us to look at more specific effects of a metal and a natural stressor (water temperature or oxygen level) in fish and better understand possible impacts of cumulative effects in aquatic organisms.

Environmental DNA - improving inference through validation studies

Funding period: 2016-2019
Lead: Kirsty Gurney
Total GRDI funding: $170,019

Scientists are increasingly using genetic material found in the natural environment (environmental DNA) to monitor biodiversity; to determine where endangered, elusive, or invasive species are located; or to study diet in free-ranging animals. There are, however, knowledge gaps concerning the efficient recovery of genetic material from environmental samples. To help fill these gaps and improve the reliability of studies that include use of environmental DNA, we are conducting both field studies and laboratory-based feeding experiments. By validating an emerging technology, our research will benefit programs in environmental monitoring, wildlife conservation, and risk assessment.

Hybrid data generation from traditional and DNA-based biomonitoring

Funding period: 2016-2019
Lead: Donald Baird
Total GRDI funding: $276,963

Environment and Climate Change Canada's Canadian Aquatic Biomonitoring Network (CABIN) studies the biological composition of river ecosystems to understand how human impacts are influencing aquatic ecosystem health. Working directly with the CABIN team and network partners, this project explores the use of high-throughput DNA sequencing methods to obtain quantitative information on the composition of wetland communities from threatened sites in Atlantic Canada and the Alberta Oil Sands region. Results generated from this study are improving the quality and quantity of data available for uptake and use in environmental assessments.

Measuring Genome Health in Wildlife Populations

Funding period: 2016-2019
Lead: Jason O'Brien
Total GRDI funding: $156,454

Pollution and habitat disruption from human activity can negatively affect the genomes of wildlife. Compromises to genome health, such as DNA damage, DNA mutations, or impaired genome regulation (epigenetics) may have heritable consequences that could impact entire populations. This STAGE project applies modern genomics and high-throughput technologies to measure markers of genome heath in wildlife populations exposed to a variety of environmental stresses caused by Canadian resource development. Result from this study will improve our understanding of the impact of human activity on the genomes of Canadian wildlife populations and provide important information that will support responsible resource development.

Metabolomics for predicting the mode of action of chemicals of concern in aquatic organisms

Funding period: 2016-2019
Lead: Vimal Balakrishnan
Total GRDI funding: $184,976

Metabolomics is a new type of approach for assessing and predicting the effects of chemicals of concern in aquatic organisms and ecosystems. To better understand the adverse outcome pathways, we are developing the "in-house" capacity to investigate the genomic responses for organisms (including the wavy-rayed lampmussel, a species at risk) exposed to priority contaminants targeted under the Chemicals Management Plan. The new techniques will support chemical substances risk assessment and future regulatory decision-making process by providing new DNA based information.

eDNA profiling of river water quality for pollution source tracking and watershed protection

Funding period: 2016-2019
Lead: Tom Edge
Total GRDI funding: $124,784

Fecal pollution and excessive nutrients are widespread water quality problems in rivers across Canada. Such pollution can lead to outbreaks of waterborne disease, closures of beaches and shellfish areas, algal blooms, and adverse impacts on human health, ecosystem health, and local economies. This STAGE project is applying next generation sequencing techniques to characterize environmental DNA (eDNA) in rivers to detect cells shed by host animals (e.g. human, cow, wildlife species…). These techniques are being investigated alongside conventional microbial source tracking techniques to improve identification of sources of nutrient and fecal pollution, and correct targeting of remediation actions.

Population genetic structuring in a widely-distributed Pacific coast seabird

Funding period: 2017-2019
Lead: Mark Hipfner
Total GRDI funding: $51,256

The Rhinoceros Auklet is a widely-distributed Pacific seabird for which ECCC has primary global stewardship responsibility. The species is vulnerable to mortality from oil pollution, fisheries bycatch, toxic blooms, and food-web perturbations attributable to ocean warming. However, ECCC's conservation efforts are hampered by a lack of information on population genetic structuring in this and other species. The aim of this project is to support these conservation efforts (e.g., Marine Emergency Response, the creation of Marine Protected Areas, Environmental Assessments) by completing a range-wide assessment of structuring in Rhinoceros Auklets in order to identify population management units across the North Pacific.

Rapid assessment of algal community composition and harmful blooms using DNA barcoding and remote sensing

Funding period: 2016-2019
Lead: Jérôme Comte
Total GRDI funding: $169,651

Declining plankton biodiversity and outbreaks of harmful algal blooms are increasingly reported across Canada's freshwaters, with adverse effects on the health and resilience of aquatic food-webs and many negative socioeconomic impacts. The main goal of this project is to develop a multidisciplinary rapid assessment screening for important indicators of toxic cyanobacteria and algae. To this end, we apply DNA barcoding and high resolution satellite imagery to build a reference DNA barcode and spectral imagery database from cyanobacteria and algae isolated from the Great Lakes and other waterbodies, and will apply this to samples from Lake Erie and other waterbodies and link these data with remote imagery. This work directly contributes to expand Canada's capacity for detection, long-term monitoring and sustainable management of this water quality issue.

Toxicogenomic solutions for assessing exposure and effects of environmental contaminants in wildlife

Funding period: 2016-2019
Lead: Doug Crump
Total GRDI funding: $179,278

The "toxicogenomic solutions for assessing impacts of environmental contaminants in wildlife" project aligns with ECCC science strategies including reducing contaminant impacts on the environment, environmental monitoring, supporting policies and regulations, and environmental technology innovation. We use novel genomics approaches to characterize the effects of priority chemicals and mixtures of relevance to the Canadian environment using avian species. Project outcomes include toxicological characterization of mixtures from the Great Lakes and oil sands areas, developing genomic tools for avian wildlife, and contributing to screening assessment reports for evaluating high priority toxic chemicals and the development of adverse outcome pathways.

Transcriptomic analysis of the ecotoxicological effects of nanomaterials on microorganisms

Funding period: 2016-2019
Lead: John Lawrence
Total GRDI funding: $152,667

Production of nanomaterials and their use in a wide range of industrial and consumer products requires assessment of their risks to the environment. High throughput sequencing and bioinformatics analyses (genomics) are being used to assess effects of manufactured nanomaterials on the expression of specific genes, gene categories or metabolic pathways in aquatic microorganisms that are important in ecosystem functioning. The goal is to provide an experimental approach and methods of analyses that facilitate efficient, effective environmental assessment of the potential risks associated with these nanomaterials.

Viable pathogen identification using DNA sequencing technology in microbial risk assessment

Funding period: 2016-2019
Lead: Lee Beaudette
Total GRDI funding: $177,726

There is a requirement for Environment and Climate Change Canada to have sound science-based methods to assess the safety of commercially available microbial-based environmental products used in bioremediation, septic tanks, pet stain removers, etc. With the advancement of methods that use genetic material from microorganisms to identify all of the microorganisms in these products, there is a further need to be able to distinguish the viable (alive) from the non-viable (dead) microorganisms. The ability to fully characterize microbial-based environmental products will result in sound screening-level risk assessments under the New Substance Notification Regulations for living organisms.

Fisheries and Oceans Canada

Detecting aquatic organisms 'In the Field' using environmental DNA methods

Funding period: 2017-2019
Lead: Rob Bajno
Total GRDI funding: $187,200

Scientists use newly developed, easy to use, portable qPCR instruments for environmental DNA analysis to detect in the field and in real-time, aquatic invasive, species-at-risk, or species important for fisheries. Scientists are developing methodologies for zebra mussel, a recent invasive in Manitoba, and will then test the transferability of these methods to other aquatic organisms (e.g., freshwater finfish). The work will have applications for programs with monitoring requirements in remote areas or other 'point-of-need' locations (e.g., shipping ports, inspection sites), providing the capacity for community-based approaches to facilitate government monitoring and managing of important aquatic organisms.

Parentage-based tagging (PBT) of Chinook salmon in British Columbia

Funding period: 2017-2019
Lead: Terry Beacham
Total GRDI funding: $360,000

Scientists collaborate with Salmon Enhancement programs to develop a genomics-based alternative to the expensive and impractical coded-wire-tag program that is currently used to monitor hatchery contributions to Chinook salmon stocks. By genetically identifying all individuals used as hatchery broodstock, the age, origin, and parents of hatchery-born fish returning from their marine migration can be identified. This non-invasive technique will provide much more information than the current program in an easier and less costly manner, to provide science advice for salmon enhancement and conservation management.

Genomic analysis of spatial stock structure of Arctic Charr in Labrador

Funding period: 2017-2019
Lead: Ian Bradbury
Total GRDI funding: $481,400

Arctic charr is a freshwater and anadromous Arctic salmonid with a long history of commercial and subsistence fisheries. However, little is known to inform management decisions related to commercial and First Nations fisheries. Scientists and collaborators characterize Arctic Charr population structures using genome-wide scans and genetic markers. These investigations will provide an unprecedented understanding of population structure to inform decisions related to the exploitation of this valuable arctic species.

Rapid and sensitive environmental DNA methods for early detection and mitigation of aquatic invasive species and monitoring of aquatic species at risk

Funding period: 2017-2019
Lead: Nellie Gagné and Francis LeBlanc
Total GRDI funding: $207,800

The detection of species using environmental DNA in water samples can support traditional field surveys for the management and conservation of aquatic species, particularly for hard-to-find cryptic species. This project develops, evaluates and optimizes environmental DNA-based tests for over twenty species aquatic invasive species, as well as the species at risk Brook Floater. This will provide a new tool to monitor important aquatic species, and to create distribution maps for the Brook Floater and for ecologically and economically damaging invasive species, leading to more efficient management and conservation strategies.

Investigating population structure and connectivity of Atlantic cod in the western Atlantic using next generation sequencing

Funding period: 2017-2019
Lead: Geneviève Parent and Yanjun Wang
Total GRDI funding: $216,700

Understanding stock structure is essential to successful fisheries management. Atlantic cod fisheries had enormous commercial value historically, but despite management efforts populations have not recovered. This project aims to solve management issues by identifying factors involved in stock recovery. Atlantic cod populations are genetically characterized through a comprehensive sampling of spawning areas in Canada and US. Population structures and connectivity are assessed at the Canada-US border and the northern Gulf of St. Lawrence. This project will validate existing management units, or help design alternate units to improve fishery management in both Canadian and US waters.

Health Canada

An integrated systems biology approach to investigate immunopotentiation induced by Respiratory Syncytial Virus vaccines

Funding period: 2014-2019
Lead: Sean Li
Total GRDI funding: $1,192,000

Respiratory Syncytial Virus is a common and highly contagious virus that infects the respiratory tract of infants, young children and seniors, and is the most common cause of bronchitis. At this time, there is no vaccine available for the prevention of diseases induced by this virus. This is largely due to a lack of understanding of the virus's disease processes and relevant evaluation tools for vaccine assessments. In this project, Health Canada's researchers are using a genomics approach to better understand the vaccine-induced toxicity and establish regulatory tools to ultimately assess the safety of this vaccine.

Development of a genomics biomarker to provide mechanistic context and data in support of human relevance for chemicals inducing cellular stress responses

Funding period: 2014-2019
Lead: Carole Yauk
Total GRDI funding: $1,075,000

Health Canada evaluates the health effects of thousands of chemicals found in the Canadian marketplace. Traditional tools used to evaluate toxicity are time consuming and expensive. Regulators need less expensive and faster approaches to help meet their regulatory responsibilities. In this project, scientists are developing and validating timesaving and more effective risk assessment methods to predict whether a chemical causes DNA damage or other adverse genetic effects. The team has published several peer review papers and reports, including a book chapter, which describe how this research has been applied to the risk assessment context. Data from this research contributed to a submission to the US Food and Drug Administration's biomarker qualification program to validate these genomic tools.

Identification of biomarkers for the standardization and risk assessment analysis of mesenchymal stem cell based health products

Funding period: 2014-2019
Lead: Michael Rosu-Myles
Total GRDI funding: $1,316,000

Stem cells have tremendous potential to treat diseases for which there are currently no cures but their use is not without risk. In this project, scientists are developing diagnostic tools to enable a thorough evaluation of the risks and benefits associated with the therapeutic use of human mesenchymal stem cells, a type of adult stem cell. This research has led to the development of a Health Canada guidance document, which is helping industry and health care professionals comply with regulatory requirements. The team has identified two new biomarkers that could be useful for evaluating the capacity of human mesenchymal stem cells for treating diabetes. It has also generated a list of potential biomarkers identifying mesenchymal stem cells that are both safe and effective for treating immune disorders. These biomarkers will be used in the evaluation of stem cell-based health products.

MicroRNA profiling of serum and milk from toxicological studies of natural and anthropogenic chemicals as an endpoint for comparative assessment with apical endpoints within the benchmark dosing framework

Funding period: 2014-2019
Lead: Ivan Curran
Total GRDI funding: $455,000

Health Canada evaluates the health effects of thousands of chemicals, pharmaceuticals, biologics, food constituents, nutrients, natural health products and natural toxins, which may be present in health products and foods. Genomics approaches allow an examination of the whole genome response to chemical or toxin exposure, a field known as toxicogenomics. Past research has identified microRNA molecules that regulate gene expression. In this project, scientists are identifying and characterizing miRNA in serum and milk associated with dietary exposure to fungal toxins and chemical contaminants detected in foods. This work will generate toxicogenomics data that will enhance Health Canada's ability to ensure the safety of food consumed by Canadians.

Safety of prebiotics in infants

Funding period: 2014-2019
Lead: Steve Brooks
Total GRDI funding: $474,000

Breast milk contains a wide variety of carbohydrates that serve as nutrients for the developing infant gut bacterial community. Some infant formulas contain fermentable carbohydrates to mimic this function. In Canada, three types of fermentable carbohydrates have been added to infant formula. Some of these have been linked to increased inflammation in infants' guts. In this project, scientists are assessing the impact of these carbohydrates on infant gut bacterial communities during weaning and over the long term in rats. This research informs Health Canada regulators of potential impacts associated with fermentable materials, especially in infant formula.

Systems biology informed structure-activity-relationships to predict pulmonary pathology induced by nanomaterials

Funding period:2014-2019
Lead: Sabina Halappanavar
Total GRDI funding: $1,017,000

Nanotechnology involves the manipulation of matter at a very small scale, the nanoscale, where one nanometre equals one billionth of a metre (human hair is about 75,000 nanometres wide). At the nanoscale, matter exhibits chemical and physical properties that differ from the properties of bulk materials and might present risks to human health. In the first study of its kind, scientists are using toxicogenomics methods and computational tools to analyze the effects of different classes of nanomaterials on cells and tissues. This research is helping Health Canada regulators to screen for potential toxicities of novel nanomaterials of concern in Canada and to establish standards for human health risk assessment.

The coming revolution: next generation sequencing detection of de novo mutations in the offspring to identify germ cell hazards

Funding period: 2014-2019
Lead: Francesco Marchetti
Total GRDI funding: $1,469,000

Mutations are increasingly recognized as contributing to a wide range of human diseases. Evidence suggests that many environmental agents cause DNA damage that increase the risk of inherited mutations and genetic diseases. In this project, scientists are using genomics technologies to analyze how benzo(a)pyrene, a common pollutant from cigarette smoke, barbecued food and vehicle emissions, increases the number of mutations that are passed onto future generations. This project is helping Health Canada regulators to analyze the inherited mutations in humans exposed to benzo(a)pyrene to protect future generations from inherited mutations.

National Research Council

Biologics and Biomanufacturing: development of support technology

Funding period: 2014-2019
Lead: Bernard Massie
Total GRDI funding: $4,440,000

The GRDI supports the Biologics and Biomanufacturing program, which covers all aspects of development from discovery up to pre-clinical testing in collaboration with industrial partners. Using genomic, proteomic and bioinformatic approaches, promising targets are identified based on their cancer-associated profiles. Hundreds of antibodies are then made against these targets and screened for specificity and function. NRC scientists are adapting this pipeline to immunotherapy using antibody-drug conjugates. These are revolutionizing the field of cancer chemotherapy by combining the targeting specificity of antibodies with the killing potential of cellular toxins for high efficacy and low toxicity.

Wheat improvement flagship (enhancing fusarium and rust tolerance; genomics-assisted breeding; abiotic stress; seed development)

Funding period: 2014-2019
Lead: Alison Ferrie
Total GRDI funding: $17,760,000

The Canadian Wheat Improvement flagship program, funded in part by the GRDI, is NRC's contribution to a large-scale research alliance established to improve the yield, sustainability, and profitability of Canadian wheat for the benefits of Canadian farmers and the economy. This will be achieved by improving breeding efficiency and reducing losses from drought, heat, cold and diseases, and improving nutrient use efficiency. The Canadian Wheat Alliance includes major contributions by NRC, AAFC, the University of Saskatchewan, and the Government of Saskatchewan.

Natural Resources Canada

Accelerating the discovery of insect volatile attractant molecules with genomics

Funding period: 2015-2019
Lead: Daniel Doucet
Total GRDI funding: $217,598

Trapping insects is a reliable means of obtaining information on insect population levels. To maximize effectiveness, traps use pheromone lures specific to the target insect. Unfortunately, the identification of the insects' pheromone is a time intensive process dependant on many variables including insect biology, a hindrance when addressing rapidly evolving insect outbreaks. This project develops a method to identify the active compounds that beetle species respond to. Genomic tools are used to examine the beetles' sensory receptors, and match the appropriate attractant compound(s). We also create a reference library of the beetles' sensory receptors for future research and use.

An early detection tool for Emerald Ash Borer and ash resource protection

Funding period: 2015-2019
Lead: Armand Seguin
Total GRDI funding: $334,270

The Emerald Ash Borer is an invasive non-native insect species that has killed millions of infested ash trees across eastern North America. It is likely to continue its spread across the continent. Unfortunately few options are available to control Emerald Ash Borer in Canada. This project seeks to develop knowledge that can be used to help slow the spread of this insect. In an effort to improve detection, we identify genomic signatures indicating the presence of Emerald Ash Borer before symptoms can be detected. The project also examines substances produced by Emerald Ash Borer that trigger a defensive response in ash trees.

Applied genomics for tree breeding and forest health

Funding period: 2014-2019
Lead: Nathalie Isabel
Total GRDI funding: $612,161

Traditional tree improvement is time consuming and approximately 15 years of growth are required before a tree can be assessed for desired traits. This project applies genomic methods to test one year old seedlings for key traits such as height and wood density, saving considerable time. It also produces a library of genetic traits that correspond to other desired characteristics such as drought and pest resistance. Finally, this project assesses the Canadian Forest Service's capacity to perform genomic "fingerprinting" to identify Canadian spruce species. This technique can be used to detect mislabeled tree species and address imports of illegally logged timber products.

Developing molecular and environmental genomic approaches for microbial and invertebrate communities to assess ecosystem integrity in forest management

Funding period: 2015-2019
Lead: Lisa Venier
Total GRDI funding: $470,162

Canada's forest industry faces increasing pressure to demonstrate the sustainability of its harvesting practices, and many producers use forest certification processes to validate their management practices. This project seeks to develop a genomics-based method to assess the effect of various silvicultural practices on key soil microbes and invertebrates. The method is intended to be used by forest managers to identify sustainable practices that support forest certification. Additionally, the project seeks to identify profiles of aquatic and terrestrial microbes and invertebrates under various forest management practices to gauge the impact of different harvesting processes.

Developing the next generation biosurveillance tools for tracking and preventing forest pest invasions

Funding period: 2015-2019
Lead: Philippe Tanguay
Total GRDI funding: $653,007

Monitoring for potential pests (native or exotic) can be a difficult and expensive task. This project arose from a request by the Canadian Food Inspection Agency (CFIA) for more information on a particular group of problem species to support their monitoring efforts. The project generates a reference database of outbreak maps, DNA barcodes and genomic data to support the CFIA. In addition, project members are developing a proof of concept portable detection system for Phytophthora ramorum, the pathogen that causes Sudden Oak Death. Such a portable detection system would eliminate the need for costly laboratory detection.

Development of metagenomic and bioinformatics tools to facilitate processing of trap captures

Funding period: 2015-2019
Lead: Jeremy Allison
Total GRDI funding: $252,283

Trapping and identifying insects is a long, expensive process due to the time required to manually sort and identify the insects caught in a trap. Also, the number of personnel qualified to complete this work is declining. Trap capture data are critical for forest pest management decisions. To address the loss of taxonomic expertise and the high costs associated with processing trap captures, this project aims to develop metagenomic tools to identify captured insects as a cheaper alternative. Furthermore, the project will begin compiling a reference library of beetle DNA for identification of future genomic material.

Genomics-assisted tree breeding for improving remediation of disturbed forest ecosystems

Funding period: 2015-2019
Lead: Jun-Jun Liu
Total GRDI funding: $313,738

Forest managers, governments and conservation agencies have been searching for White Pine Blister Rust resistant pines to restore pine species at risk on the landscape. This project uses genomics tools to identify and understand resistance mechanisms in the following species: western white pine, limber pine, whitebark pine, and eastern white pine. The goal is to identify individuals that are fully resistant or partially resistant to White Pine Blister Rust for breeding and planting.

Innovative land reclamation approaches following oil sand mining: Improving phytoremediation tree-soil microbe interactions

Funding period: 2014-2019
Lead: Armand Seguin
Total GRDI funding: $542,378

Oil sands companies in Alberta have committed to restore land to a functioning ecosystem after oil extraction is complete. Restoration is an expensive process, and will likely influence social acceptance of oil sands operations. The goal of this project is to improve the remediation process for oil sand soils, focusing on the relationship between soil microbes and different varieties of aspen trees planted on three site types: oil sands, disturbed forests and natural forests. We will develop a method to monitor tree-microbe interactions, and will evaluate aspen varieties based on associated microbes that are best suited for sustainable tree growth.

Spruce Budworm eco-genomics: from population dynamics to population suppression

Funding period: 2014-2019
Lead: Michel Cusson
Total GRDI funding: $295,832

Spruce Budworm is a significant defoliator in the forests of Canada, impacting the growth of commercial tree species on a cyclical basis. A Spruce Budworm outbreak is currently underway in Quebec, spreading towards Ontario and New Brunswick. This project uses molecular markers to characterize the genetic structure of spruce budworm populations in Ontario. Scientists will use this information to help forecast outbreak trajectories and model current and future outbreaks. This information will assist managers of Ontario forests in making spruce budworm management decisions.

Tools for enhanced molecular detection of Asian Gypsy Moth and identification of their geographic origins

Funding period: 2015-2019
Lead: Michel Cusson
Total GRDI funding: $328,500

Exotic species represent a significant concern to trade, forest industries and forest health. The Canadian Food Inspection Agency (CFIA) monitors Asian Gypsy Moth at Canadian ports. This insect has the potential to become established in Canada's forests, to cause extensive defoliation, and to restrict Canadian exports. The project will examine the genome of Asian Gypsy Moth species to identify markers relating to their geographic origin. The ability to identify the origin of Asian Gypsy Moth increases the efficiency of the CFIA's monitoring program and will assist in trade discussions to prevent future invasive species.

Public Health Agency of Canada

BioTools for the predictive genomics of priority foodborne pathogens

Funding period: 2014-2019
Lead: Vic Gannon
Total GRDI funding: $722,255

Predictive genomics assessed phenotypes from raw genome sequence data. We build on the pilot platform that we developed for Escherichia coliand add modules for Salmonella entericaand Campylobacter jejuni. The platform facilitates the upload of sequences from public or private users and integrates sequence data and analysis tools for all publicly available genomes. Specific analyses include the identification of virulence and antimicrobial resistance determinants, epidemiological associations, clade-specific genome markers in bacterial populations, and in silico molecular types. These near real-time analyses of thousands of genome sequences provide results that are understandable and useful to a wide community, including those in the fields of clinical medicine, epidemiology, ecology, and evolution.

Bridging the Genomic Epidemiological Gap for priority Salmonella serovars through genomic characterization and nomenclature development

Funding period: 2017-2019
Lead: Roger Johnson
Total GRDI funding: $200,000

Nearly 60% of human Salmonellosis cases in Canada can be attributed to four Salmonella enterica serovars. The high rate of human infection with these serovars makes them highly significant targets for developing more effective subtyping methods and comprehensive information on the population structure that will enhance capacity for outbreak detection and source attribution. Before we can analyse the Canadian population structure of these serovars, new whole genome sequence (WGS) data are needed to provide the necessary Canadian context to understand the circulating populations. This project will then analyse the new and existing WGS data to develop a nomenclature for precise subtyping.

Field deployable genomic sequencing for pathogen identification using the MinION

Funding period: 2018-2019
Lead: Stephanie Booth and Darwyn Kobasa
Total GRDI funding: $100,000

Rapid identification of genome sequences from clinical samples is crucial for characterizing rare or novel pathogens, clarifying patterns of pathogen evolution, monitoring the validity of diagnostic assays, and investigating zoonotic transmission chains. This project focuses on the development of portable and reliable devices for pathogen sequencing that can be rapidly deployed in the field. These are of great importance for clinical diagnosis, tracking spread of infection and real-time implementation of interventions to protect public health.

Implementation of genome-based analyses to "One Health" surveillance of enteric disease

Funding period: 2014-2019
Lead: Eduardo Taboada
Total GRDI funding: $375,000

This project applies genomic epidemiology approaches to food safety through: 1) analysis of attribution of the likely sources of exposure to foodborne illness; 2) assessment of the relative risk associated with different pathogen subtypes; and 3) analysis of their transmission dynamics along the food chain. The over-arching goal is to support public health decision-making and program development for improved public health interventions related to foodborne pathogens and antimicrobial resistance.

Improving surveillance of non-enteric bacterial pathogens by whole genome sequencing

Funding period: 2017-2019
Lead: George Golding
Total GRDI funding: $603,000

Non-enteric bacterial pathogens cause a variety of illness from mild infections to severe disease. This project conducts genomics-based studies on Streptococcus pneumoniae and Haemophilus influenzae, which can cause severe invasive infections of the blood (septicemia) or brain (meningitis), and two other high priority organisms: Neisseria gonorrhoeae, which causes sexually transmitted gonorrheal infections and Clostridium difficile, which causes life-threatening diarrhea. Whole genome sequencing has the potential to address gaps in surveillance of antimicrobial resistance, virulence and transmission of these pathogens.

Mass Spectrometry Technology Development

Funding period: 2017-2019
Lead: Patrick Chong
Total GRDI funding: $250,000

The project is comprised of two independent sub-projects that employ two distinct mass spectrometry-based technologies, both aimed at improving diagnostics in microbiology laboratories: National MALDI database development using matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF MS) and targeted proteomics toxin assay development using multiple reaction monitoring and triple quadrupole mass spectrometry.

PulseNet Canada: Model framework development for genomic technology delivery in a laboratory network

Funding period: 2015-2019
Lead: Celine Nadon
Total GRDI funding: $285,000

PulseNet Canada is the national molecular subtyping network for foodborne disease surveillance. This program provides real-time information that enables the detection of outbreaks and their source at the earliest possible stage. To date, PulseNet Canada has relied almost exclusively on a single test method: pulsed field gel electrophoresis, considered the international gold standard for nearly two decades. In 2013 the PulseNet Canada steering committee drafted a plan for the development and implementation of genomics within its network. Most PulseNet Canada partners (comprising microbiologists, epidemiologists, managers, and regulators) will require education in genomics before it can be adopted network-wide. The primary objective of this project is to design and develop a translation framework encompassing all aspects of genomics in the context of PulseNet Canada. Knowledge translation will ensure that the transition of national surveillance to genomics technology occurs smoothly.

Revolutionizing molecular viral characterization strategies in support of enhanced viral disease outbreak investigation and surveillance in the next generation sequencing era

Funding period: 2017-2019
Lead: Ji Hezhao
Total GRDI funding: $637,606

This project aims to implement Next Generation Sequencing and sophisticated bioinformatics technologies for more robust surveillance and outbreak investigation on a group of viruses recognized as global public health threats: human immunodeficiency virus (HIV), hepatitis viruses A, B and C (HAV, HBV and HCV), influenza virus (IFV) and measles virus (MeV). NGS protocols for partial and/or whole-genome sequencing of the targeted viruses are developed and validated. In addition, new NGS data analysis tools are created for in-depth viral characterization that will enhance our surveillance capacity, strengthen transmission and outbreak investigations, and enable the prediction of drug resistance. These new analysis pipelines will be operationalized by their incorporation into Canada's Integrated Rapid Infectious Disease Analysis (IRIDA) platform. The outcome of this project will significantly boost PHAC's capacity to respond quickly and effectively to viral diseases.

Single nucleotide variant subtyping of Salmonella Enteritidis and Salmonella Heidelberg

Funding period: 2014-2019
Lead: Roger Johnson
Total GRDI funding: $452,534

Salmonellosis is a very common foodborne illness, with Salmonella serovars Enteritidis (SE) and Heidelberg (SH) among the most frequent causes in Canada. Reliable subtyping methods are required for outbreak detection, tracking, and source attribution. Current subtyping methods, including the gold standard (Pulsed Field Gel Electrophoresis) lack the high resolution needed to accurately subtype these two highly clonal serovars. This project aims to develop and validate a simple Single Nucleotide Variants analysis platform for end users in public health laboratories. Importantly, the identified variants for both serovars can be integrated into future analysis of whole-genome sequences, enhancing federal and provincial public health responses to SE and SH infections.

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