Looking for answers in tiny strands of genetic material
» The science of food and beverage ISSUE 2 • 2022 Putting Genetics on the table Looking for answers to climate change and food security THE CIRCULAR ECONOMY OF PLASTICS Hidden Treasure in Waste 12 GETTING TO THE ROOT OF THE TREE OF LIFE BioGenome Project aims to map complete plant and animal genomes 3 inside standard SUZUKI MATTERS 5 CANADIAN NEWS 7 WORLDWIDE NEWS 8 LABWARE 24 MOMENTS IN TIME 44 Feature SPECIAL GUEST EDITORIAL TACKLING TODAY’S BIG CHALLENGES Genome Canada’s Chief Scientific Officer shares insights FEATURE CANADA’S GENOMICS MACHINE A sampler of 10 initiatives to watch NEWSMAKER A CANADIAN FIRST UBC scientists 3D print human sperm LAB PROFILE PLANT GENE RESOURCES OF CANADA More than Noah’s Ark COMPANY PROFILE OCEAN SUPERCLUSTER TEAMS UP WITH EDNATEC To bridge the biodiversity knowledge gap APPLICATION NOTE SENSING BIODIVERSITY One researcher sucks mammal DNA out of the air 6 14 16 20 22 9 LOOK INSIDE FOR YOUR COPY OF
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GENES AND THE BIG BANG
Publisher of BioLab Business Magazine
Printed in Canada
epic tale of scientific discovery recently added a new chapter with the launch of the James Webb telescope, an optical and technical marvel that lets researchers peer across light-years to grasp a deeper understanding of the origins of the universe and the miraculous dance that created our planet and its inhabitants.
While there are many theories about what exactly was in that primordial soup from which life emerged, scientists believe it contained amino acid and proteins that created the progenitor gene, a primitive form of single-stranded ribonucleic acid (RNA). These were simple RNA molecules that found a way to replicate and evolve.
Flash forward to early 2020, and RNA has proven invaluable in the fight against SARS-CoV-2 virus with the development of mRNA vaccines. Given the contributions made by genomics to human health even before the pandemic, as well as its role in environmental sciences and agriculture, the editorial team felt that a closer look at Canada’s contributions to this exponentially growing field was timely.
Our search for content for this issue of BioLab Business began with Genome Canada, which leads Canada’s genomics ecosystem and coordinates a network of six genome centres across the country. In this issue, Genome Canada’s Chief Scientific Officer, Catalina Lopez-Correa, shares how her organization’s storehouse of knowledge contributes to the future of health, agriculture, natural resources and environmental sustainability.
Highlighting some of the work of Canadian researchers in the field of genomics, we curated a sampler of game-changing initiatives. Among them, you’ll find Canada’s largest human genome sequencing project; the discovery of gene mutations that may trigger breast cancer in some individuals; and the power of artificial intelligence in helping advance genomic research.
And while there is excitement over the recent publication of the first complete, gapless sequence of a human genome, we took another route, shining a light on the Canadian BioGenome Project which aims to map the genomes of all plants, animals, fungi and other microbial life in Canada.
In this issue, we also tour an unusual library: the Plant Gene Resources of Canada, which houses the seeds, tubers, and cuttings of Canadian agriculture reaching back to the 1960s.
Works like these have helped build plant resiliency, created life-saving drugs and vaccines, and introduced personalized medicines to combat disease.
And it all began with a “big bang.”
Forbes PUBLISHER & CEO
EDITOR’S NOTE 4 BIOLAB BUSINESS VOLUME 37, ISSUE
Dr. David Suzuki is a scientist, broadcaster, author and co-founder of the David Suzuki Foundation.
Learn more at davidsuzuki.org.
BY DAVID SUZUKI
CITIZEN SCIENCE AND GENETIC TESTING YIELD POSITIVE RESULTS
Since I started working as a geneticist in the early 1960s, the field has changed considerably. James Watson, Francis Crick and Maurice Wilkins won the 1962 Nobel Prize in physiology or medicine for their discovery of the double helix structure of DNA. Researchers then “cracked” the genetic code, which held promise for fields like health and medicine. It was an exciting time to be working in the lab.
More than 40 years later, in 2003, an international group of scientists sequenced the entire human genetic code. Researchers can now find a gene suspected to cause a disease in a matter of days, a process that took years before the Human Genome Project. As of 2013, more than 2,000 genetic tests were available for human conditions. Forty years ago, I never dreamed scientists would have the knowledge and manipulative capabilities that have become standard practice today.
In a couple of decades, genetics has allowed for systematic inventorying of the world’s biodiversity. Canada’s Centre for Biodiversity Genomics at the University of Guelph has the genomes of more than 265,000 named species identified with barcodes in its database. The cost to analyze a sample against this free public database is about $10. Cost reductions and digital communication allow citizen scientists to utilize an enormous storehouse of information.
Young citizen scientists in San Diego were recently able to help compile information about the area’s biodiversity through their local libraries. Kids signed out genetic testing kits — which included sampling vials, tweezers and a return bag — through Catalog of Life @ the Library. They then uploaded photos and locations of their finds using a LifeScanner or website. It’s part of an effort to collect 4,000 samples of local
bug life. After returning kits to the library, the young scientists could go online to see and compare the genetic barcodes of their discoveries.
According to the library, “Only an estimated 20 percent of species on earth have been identified by their DNA barcode.” The San Diego program is part of Barcode of Life, which has the ambitious goal of identifying all life on Earth to help researchers “understand the diversity of species, monitor the health of the environment and the impacts of climate change.” Canada’s Centre for Biodiversity Genomics is doing the genetic sequencing.
People in Canada can also help identify seafood fraud with the LifeScanner service. Genetic testing helps consumers identify the species and possibly origin of fish they buy — important for people who care about sustainability and health and nutrition.
Identifying and tracing seafood has long been a challenge, especially because about 40% of wildcaught seafood is traded internationally — and labelling is often inadequate. Once fish are skinned, cleaned and packaged, it’s not always easy to tell what they are. If you buy something labelled “rockfish” in Canada, it could be one of more than 100 species. Often, labels don’t indicate whether the fish were caught or processed sustainably. Although the European Union and U.S. require more information on seafood labels than Canada, one study found 41% of U.S. seafood is mislabelled.
A European study found stronger policies combined with public information led to less mislabelling. People in Canada have demanded better legislation to trace seafood products. More than 12,000 people recently sent letters to government asking for better labelling.
SeaChoice (the David Suzuki Foundation is a member) is working with LifeScanner to register 300 people in Canada to test seafood, in part to determine whether labels are accurate. Participants will get testing kits, buy seafood, collect data and images, and return samples in a provided envelope. Samples will be analyzed and coded, with results posted online.
With the help of citizen scientists, genetic testing can offer a powerful approach to righting environmental wrongs. Combining crowdsourced scientific data, public policy reform and consumer activism is already showing positive results. The same approach could work in areas such as testing for antibiotics, pesticide and mercury residues, and more.
DNA Day is celebrated in Canada on April 21 and in the U.S. on April 25 to commemorate completion of the Human Genome Project in 2003 and the discovery of DNA’s double helix in 1953. We’ve come a long way since then, but we still have much to learn. Citizen scientists are helping!
BIOLABMAG.COM 5 SUZUKI MATTERS
Researchers can now find a gene suspected to cause a disease in a matter of days, a process that took years before the Human Genome Project.
BY CATALINA LOPEZ-CORREA, MD, PHD, CHIEF SCIENTIFIC OFFICER, GENOME CANADA
NEW INVESTMENT MODEL KEY TO GENOME CANADA’S LEADERSHIP IN TACKLING BIG CHALLENGES, INCLUDING AGRICULTURE’S CARBON FOOTPRINT
including pandemic preparedness.
In leading Canada’s genomics response to COVID-19, we mobilized a pan-Canadian network of cross-sectoral academic and public health teams in record time and broke longstanding barriers to healthcare data-sharing in the country – significant changes that are here to stay, with the promise of benefits across sectors. We saw genomics viral surveillance and analysis inform public health policy and decision-making in ways we’ve never seen before. We saw Canada’s pandemic response draw genomics out of the lab and into everyday vernacular.
Keeping pace with what the world needs from genomics sometimes means changing how we invest in finding solutions. Genome Canada’s unique federated model, with provincial/regional, industry and end user partners involved with nearly every project has evolved over the years to meet these changing needs. A big step in this evolution came this spring with the launch of a Climate-Smart Agriculture and Food Systems initiative, which will invest $30 million in cutting-edge genomic research and innovation to reduce the carbon footprint of Canada’s food production systems and contribute to a more sustainable industry. Co-funding from partners will bring the funding total to more than $60 million.
big problems—like climate change and emerging threats to human health—demands an ambitious and strategic response. That’s what drives the work of Genome Canada. Together with the pan-Canadian network of Genome Centres and partners in the private, public, and government community and research sectors, we mobilize Canada’s genomics ecosystem—its resources, capacity and diverse talent—to generate solutions to today’s biggest challenges.
We’ve been leading Canada’s genomics revolution for more than 20 years, helping chart the future of health, agriculture, natural resources and environmental sustainability. From breakthroughs in precision health and playing a leading role in Canada’s COVID-19 response, to recently launching a new challenge to reduce the carbon footprint of Canada’s agricultural industry, Genome Canada is about connecting, convening and coordinating interdisciplinary research teams with end users for maximum impact.
It’s ecosystem-leading work that aligns with the Government of Canada’s commitment to mobilizing cutting edge science, innovation and technologies in service of major public policy priorities like climate action, food security and strong public health,
This new initiative will fund a portfolio of interdisciplinary genomics research and innovation projects connected by cross-cutting data and knowledge mobilization programs. A portfolio approach allows benefits from one solution to translate into other food systems or supply chains and cascade impact throughout the broader agriculture and food systems.
Canada’s genomics ecosystem has proven its ability— with strategic leadership and shared purpose—to mobilize and generate solutions to pressing challenges. The ClimateSmart Agriculture and Food Systems initiative will continue that tradition, with its new portfolio funding model setting a new standard for excellence and impact in bringing the right teams together to get the results Canada and the world need from genomics.
What do smart ag and food systems look like?
Net-zero carbon agriculture and food systems: Reducing greenhouse gas emissions and the carbon footprints of food production and inputs manufacturing
Scalable biologybased solutions: Developing novel, nature-based solutions and processes that can replace traditional consumptive production processes with sustainable and circular solutions for the environment and economy
Biological carbon sequestration: Enhancing carbon sequestration to improve performance, mitigate climate impacts and support healthy ecosystems
Resilient and sustainable food systems: Building resilient, sustainable food systems that reduce environmental impacts and greenhouse gas emissions
6 GUEST EDITORIAL BIOLAB BUSINESS VOLUME 37, ISSUE 2 • 2022
QUANTUM IMAGING LEADS TO UNDERSTANDING DISEASE BETTER
U of T researchers use machine learning to speed up counting of microplastics
To gain a deeper understanding of the extent of plastic in our world, researchers at the University of Toronto are using machine learning to quantify environmental microplastics in a faster, more affordable way.
Microplastics in the environment are not unexpected , but the standards for how to quantify their levels and how to compare different samples are still emerging. The team established a prediction model that uses trained algorithms to estimate microplastic counts. The approach lets researchers manually process only a fraction of their collected samples and predict the quantity of the rest by applying an algorithm. The researchers say it is less costly and faster than manual counting.
NEW NATIONAL OCCUPATIONAL
New research out of the University of Waterloo is taking Magnetic Resonance Imaging (MRI) technology to new highs — or more accurately, new lows — down to the atomic scale to help improve image clarity. “At a high level, this work could be used to develop quantum technologies to study protein structure and dynamics,” says lead investigator Raffi Budakian, a member of the Institute for Quantum Computing.
MRI works on the millimetre scale. To gain an even clearer image, Budakian’s Nanoscale Magnetic Resonance Imaging Lab takes it down to the angstrom scale, a metric unit of length that is 10 million times smaller than a millimetre. Using quantum sensors, Budakian’s team generated magnetic fields on nanometre light scales for imaging and controlling nuclear spins.
What happens to an industry when it faces a major talent shortage? Progress slows and growth stalls. That’s the reality for Canada’s bioeconomy if trends continue and hiring practices remain the same, according to BioTalent Canada CEO Rob Henderson.
“The talent pipeline should be overflowing, but it’s not,” says Henderson. “Right now, in most sub-sectors of the bio-economy, there will be an average of at least two job openings for every potential candidate. By 2029, that ratio could grow to 4:1.”
To support employers in Canada’s bio-economy, BioTalent Canada has launched its 45 National Occupational Standards (NOS) for Canada’s bio-economy. The tool for bio-economy employers took three years to develop and is expected to aid in fulfilling talent shortages in the industry. More than 40 key roles were analyzed and optimized with the help of partners and industry experts. Companies can use the standards for more effective recruitment, professional development, succession planning, and other HR activities.
According to data from BioTalent Canada’s recently released national labour market information (LMI) study, the bio-economy is forecasted to need an additional 65,000 workers by 2029.
“The NOS will benefit employers, candidates, and the bio-economy as a whole,” says Henderson. “They will help employers recruit effectively for key people within their organization. Having the right people in the right roles will limit turnover and help ease the talent shortage.”
One of these things is not like the others
A special fish found in deep Canadian lakes has caught the attention of University of Toronto biologist Nathan Lovejoy. What makes the sculpin special is that it evolved into similar varieties—deepwater sculpin, freshwater forms of fourhorn sculpin, and marine fourhorn sculpin—which has led to misidentifications and muddled taxonomy. Lovejoy is leading a project looking to sequence the deepwater sculpin’s entire genome, which will help add clarity. His project is supported by CanSeq150, a sequence-based genomics research initiative led by CGen and its partners. Launched in 2014, CGen is a federally funded national platform for genome sequencing and analysis. CanSeq150 commemorates Canada’s sesquicentennial and aims to enable future research in biodiversity and conservation, applications in breeding and biomedicine, as well as technology development, across Canada.
CANADIAN NEWS BIOLABMAG.COM 7
Photo by Shuyao Tan
FIRST GAPLESS SEQUENCE OF A HUMAN GENOME COMPLETED
Scientists have published the first complete, gapless sequence of a human genome two decades after the Human Genome Project produced the first draft human genome sequence.
The complete sequence, reported this April by the Telomere-to-Telomere (T2T) consortium, includes more than 3 billion base pairs across 23 chromosomes. The T2T consortium further used this newly completed genome sequence as a reference to discover more than 2 million additional genomic variants, opening doors to a comprehensive view of how human genomes vary, as well as for investigating how these newly discovered variants influence health and disease.
The T2T consortium includes leadership from researchers at the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health; University of California, Santa Cruz; and University of Washington, Seattle. NHGRI was the primary funder for the study.
“Generating a truly complete human genome sequence represents an incredible scientific achievement, providing the first comprehensive view of our DNA blueprint,” said NHGRI director Eric Green, M.D., Ph.D.
The full sequencing adds to the Human Genome Project, which mapped about 92% of the genome. That last 8% includes numerous genes and repetitive DNA, comparable in size to an entire chromosome. Researchers generated the complete genome sequence using a human cell line with only one copy of each chromosome, unlike most human cells, which carry two copies of each chromosome. The researchers noted that most of the newly added DNA sequences were near the repetitive telomeres (long, trailing ends of each chromosome) and centromeres (dense middle sections of each chromosome).
The cost of sequencing a human genome using “shortread” technologies, which provide several hundred bases of DNA sequence at a time, is only a few hundred dollars, having fallen significantly since the end of the Human Genome Project. However, using these short-read methods alone still leaves some gaps in assembled genome sequences. The massive drop in DNA sequencing costs comes hand-inhand with increased investments in new DNA sequencing technologies to generate longer DNA sequence reads without compromising the accuracy.
Over the past decade, two new DNA sequencing technologies emerged that produced much longer sequence reads. The Oxford Nanopore DNA sequencing method can read up to 1 million DNA letters in a single read with modest accuracy, while the PacBio HiFi DNA sequencing method can read about 20,000 letters with nearly perfect accuracy. Researchers in the T2T consortium used both DNA sequencing methods to generate the complete human genome sequence.
‘Snipping’ out disease
New research from the University of California San Francisco has shown that a genomic variant in DNA linked with physical differences between sexes also points to disease risk. Some physical traits that differ between sexes are known to be linked to certain single nucleotide polymorphisms (SNPs) in chromosomes other than the X and Y chromosomes, with each SNP representing a difference in a certain DNA building block in a particular stretch of DNA. The researchers previously found that SNPs associated with certain differences in physical traits between men and women—such as waist-hip ratio and basal metabolic rate—may also affect the biology of autism spectrum disorder and other complex diseases. Now, they have built on that work, leveraging two publicly available genome-wide statistical datasets to identify an updated list of 2,320 sex-heterogeneous SNPs.
STUDY FINDS CELLS TAKE OUT THE TRASH BEFORE THEY DIVIDE
MIT researchers have discovered that before cells start to divide, they do a little clean-up by tossing out molecules they may to need anymore. Using a new method they developed for measuring the dry mass of cells, the researchers found that cells lose about 4% of their mass as they enter cell division. The researchers believe this emptying of trash helps cells to give their offspring a fresh start without the accumulated junk of the parent cell.
Measuring the dry mass of a cell—the weight of its contents not including the water—is commonly done using a microscopy technique called quantitative phase microscopy. This technique can measure cell growth, but it does not reveal information about the molecular content of the dry mass, and it is difficult to use with cells that grow in suspension. To overcome the challenges, the researchers relied on a technique that measures the cells’ buoyancy as they float in normal water and then in heavy water. But because heavy water is toxic to cells, they designed a system in which cells could be measured repeatedly with minimal exposure to heavy water. The approach enabled them for the first time to track not just the dry mass of a cell, which is what others do using microscopic methods, but also the density of the dry mass, which gives information on the cell’s biomolecular composition. In the study, the team measured three types of cancer cells, which are easier to observe because they divide more frequently than healthy cells.
To their surprise, the researchers found that the dry mass of cells actually decreases when they enter the cell division. Additional experiments revealed that as cells enter mitosis, they ramp up the activity of a process called lysosomal exocytosis. Lysosomes are cell organelles that break down or recycle cellular waste products, and exocytosis is the process they use to jettison any molecules that aren’t needed anymore.
WORLDWIDE NEWS 8 BIOLAB BUSINESS VOLUME 37, ISSUE 2 • 2022
REVVING THE ENGINES OF CANADA’S GENOMIC MACHINE
A sampler of 10 Canadian genomic initiatives to watch
BY JANA MANOLAKOS
Despite a slower pace than other countries, Canada’s genomic research landscape is expanding, powering up Canada’s contributions to genetics and biotechnology in health, agriculture and the environment.
From precision health, which harnesses the potency of genome sequencing to diagnose and determine treatment of genetic conditions, to the barcoding of species, public and private sector organizations are pushing new horizons in genomics often as partners, unravelling the complexities of an organism’s genes in an effort to discover new therapies and applications.
Among these, Genome Canada, a government agency launched in 2000, spearheads a national strategy along with a network of six regional centres on the West Coast (Genome BC), the Prairies (Genome Alberta and Genome Prairie), central Canada (Ontario
Genomics and Génome Québec), and the Maritimes (Genome Atlantic). Then there’s CGEn, a federally funded national platform for genome sequencing and analysis with nodes in Toronto (The Centre for Applied Genomics at The Hospital for Sick Children), Montréal (McGill Genome Centre at McGill University), and Vancouver (Canada’s Michael Smith Genome Sciences Centre).
Private sector start-ups have also staked their claim. Take Deep Genomics, which applies artificial intelligence in searching for life-saving genetic therapies; Precision Nanosystem, which is focused on gene function in neurons and glia cells; and DalCor Pharmaceuticals, which is genetically targeting patients that will benefit from precision treatments for cardiovascular disease.
Among an impressive array of genomic initiatives, here are 10 game changers working to put Canada on the map.
BIOLABMAG.COM 9 FEATURE STORY
CANADA’S LARGEST HUMAN GENOME SEQUENCING INITIATIVE
Led by CGEn, the HostSeq databank will include the full set of DNA of 10,000 Canadians, with the goal of understanding how their genetics influenced their individual responses to COVID-19. The HostSeq databank also includes linked standardized clinical information collected at multiple clinical sites across Canada over the past two years of the pandemic. “The need for a national genomics databank grew very quickly early on in the pandemic,” explains Dr. Naveed Aziz, chair of the HostSeq Implementation Committee and Chief Executive Officer, CGEn. “As soon as we started to observe differences of disease manifestation and symptoms in people infected with SARS-CoV-2 virus, we realized that there was an urgent need to collect and analyze populationwide host genetic data.” The initiative, funded through Genome Canada’s Canadian COVID-19 Genomics Network (CanCOGeN), is accessible to Canadian and international researchers.
GENE MUTATIONS MAY HOLD THE KEY TO OVARIAN CANCER
Ovarian cancer affects about 3,000 women every year in Canada. Although most cases are sporadic, there are hereditary forms of ovarian cancer that are largely attributed to mutations in the BRCA1 and BRCA2 genes, which are also involved in breast cancer. However, some families with no known cancerpredisposing genes develop multiple cases of ovarian cancer, suggesting that mutations in unknown genes remain to be discovered.
With this in mind, scientists at the Research Institute of the McGill University Health Centre (RI-MUHC) set out to investigate new genes that could be associated with a risk of ovarian cancer. Their findings show that a mutation in a specific protein gene known as FANCI (FA Complementation Group I) is more common in ovarian cancer patients with a family history of ovarian cancer than in cancer-free people, suggesting that it may influence the risk of developing that cancer. Dr. Patricia Tonin, principal investigator of the study and senior scientist in the Cancer Research Program at the RI-MUHC, explains: “This study emphasizes the importance of pursuing variants during the gene discovery phase, especially when plausible gene candidates are revealed by analyses of defined cancer families.”
The researchers performed genetic testing on two sisters who had ovarian cancer and a family history of ovarian cancer. Next-generation sequencing showed that both subjects carried a mutation in the FANCI gene. The researchers then sequenced familial cases of ovarian cancer and compared variant frequencies in people with and without ovarian cancer in a population pool of French Canadians from Québec. This population has a unique genetic landscape inherited from common ancestors that arrived in Québec from Western Europe as early as the 1600s.
The study authors also point out that other genetic,
environmental or host factors could affect the risk of ovarian cancer in carriers of FANCI variants. Replication studies are needed to confirm these results in larger groups worldwide. In addition, studies to clarify the cancer risk conferred by FANCI variants are required to inform medical genetic screening practices for managing risk and ovarian cancer.
NEW NATIONAL PLATFORM ADVANCES CLINICAL GENOMIC TESTING
Canadians struggling to get a diagnosis will now have access to state-of-the-art genome-wide sequencing thanks to a new pan-Canadian All for One precision health partnership led by Genome Canada. Already deployed across six implementation projects serving nine provinces, the $39-million All for One initiative includes $13 million in federal investment through Genome Canada and $26 million in co-funding from industry, health-care organizations, provincial governments, and other partners brought in through six regional Genome Centres.
To commemorate Canada’s sesquicentennial in 2017, CGEn and its partners embarked on the Canada 150 Sequencing Initiative (CanSeq150) aimed at sequencing 150 new genomes to support sequence-based genomics research in Canada in biodiversity and conservation, applications in breeding and biomedicine, and technology development. More than 100 species were selected for sequencing through the CanSeq150 program, providing a platform for biologists, ecologists, population geneticists and other scientists to work with genomic scientists. CanSeq150 has now joined the Canadian arm of the Earth BioGenome project (featured in the spring issue of BioLab Business), which will identify an additional 400 species important to Canadian wildlife conservation, recovery and monitoring.
BRIDGING THE GENOMIC DIVIDE FOR INDIGENOUS CHILDREN
Although the rapid development of genomic technologies is advancing precision medicine, it is also widening the health inequity gap for Indigenous populations that often have little or no access to genomic technologies and the research that drives them. This prevents accurate diagnosis because of the absence of the reference data needed for precise genetic diagnosis. Working with Genome BC, Genome Canada last year launched Silent Genomes, a partnership with First Nations, Inuit and Métis peoples to enable access to diagnosis and treatment of genetic disease for their children. The project will establish processes for Indigenous governance of biological samples and genomic data, lead to policy guidelines and best practice models for bringing genomic testing to Indigenous children, and develop an Indigenous Background Variant Library of genetic variation from a diverse group of First Nations.
BIOLAB BUSINESS VOLUME 37, ISSUE 2 • 2022
FEATURE STORY 10
NEW NON-HUMAN GENETIC DATA BANK LEVERAGES ARTIFICIAL INTELLIGENCE
This past April, Génome Québec and Université Laval launched Genovalia, the first centre in Québec dedicated to the production, processing, and application of non-human genomic data in agri-food, forestry and environmental sciences. Bolstered by Université Laval’s artificial intelligence experts, Genovalia aims to contribute to standardization in data collection, increase information sharing, grow computational capacity and develop better analytical tools.
KEEPING FEEDER FISH AND THE SALMON INDUSTRY HEALTHY
Sea lice, which feed on the skin of living salmons, are a big problem for Canada’s commercial Atlantic salmon industry, costing producers $18 million last year alone in lost stock. To mitigate the problem, feeder fish like lumpfish are introduced to salmon tanks to eat the tiny crustaceans. However, lumpfish are highly susceptible to Vibrio anguillarum, a bacterial pathogen which causes haemorrhagic septicaemic disease in the fish. Keeping them healthy is the focus of genomic research at Memorial University’s Ocean Science Centre (OSC) in St. John’s, Nfld., where a research team, led by Javier Santander, a marine microbiologist and Associate Professor in the Department of Ocean Sciences at Memorial, has been sequencing lumpfish and cunner genomes. Santander believes the team is close to solving the lumpfish’s high susceptibility to the pathogen. “We have an effective vaccine that has been tested several times and soon will be evaluated in the field,” he said. His research group is now processing the data for transcriptomic profiling of the lumpfish response to the effective immunization.
FOUR GENOMICS AND ENGINEERING BIOLOGY TEAMS WIN FUNDING FOR CELLULAR AGRICULTURE INITIATIVES
Cellular agriculture encompasses several innovative approaches that use cell cultures, tissue-engineering, or precision fermentation-based techniques that push beyond conventional production. This past May, four genomics and engineering biology projects won more than $900K in funding from AcCELLerate-ON, Canada’s first regional cellular agriculture competition in support of food innovation in Ontario. Ardra Inc. was named for its development of fermentation-based production of heme, a natural flavour ingredient that mimics the taste of meat. Cell Ag Tech won for scaling up the manufacturing of fish muscle stem cells from a 2D to 3D culture system with proteomic assessments of the cells. The third recipient,
Evolved, won for creating cultivated pork belly that is identical to conventional pork belly. The University of Toronto’s Dr. Michael Garton, in collaboration with MyoPalate, shared in the prize for establishing the foundational tools for cultivated pork production. The funding comes from Ontario Genomics and the Canadian Food Innovation Network.
KEEPING AHEAD OF GLOBAL COMPETITORS WITH SPECIALIZED LENTILS
Canada grows more than 3 million tonnes of lentils annually, more than half of the world’s total supply. Nearly all (about 95%) of Canada’s lentil crops, which produced almost $3 billion in export revenue in 2021, are grown in Saskatchewan. But global competition is heating up, so researchers working on the EVOLVES (Enhancing the Value of Lentil Variation for Ecosystem Survival) project at the University of Saskatchewan are looking at growing specialized lentils. A significant part of the project is improving the genetic variability, phenotyping and gene sequencing of both cultivated and wild lentils. EVOLVES also takes an ‘omics (combining genomics and phenomics) approach so traits that are prized by exporters like greater nutritional content, flavour and climate resistance can be zeroed in on to produce specific varieties. Field trials will begin this summer in Saskatchewan and southern Italy. The initiative is supported by Genome Prairie, Saskatchewan Pulse Growers, Western Grains Research Foundation, and Agriculture and Agri-Food Canada.
GENOMIC TOOLS WILL HELP SUPPORT BETTER MITE RESISTANCE
Honey bee colony collapse is a significant problem for both Canada and the world because of the insect’s vital importance to pollination and food production. Unfortunately, the mite Varroa destructor feeds on bees at adult and juvenile stages, weakening them and transmitting deadly viral infections that can lead to colony collapse. Recently, a new acaricide that is poisonous to mites like the Varroa but does not harm bees and vertebrates was introduced to the industry. A Genome BC-funded project aims to discover the efficacy of this new compound. Researchers are using proteomics tools to identify the molecular target and determine how, when and where the compound can be used. The project will run until September 2023 so that early learnings can be applied to the next cycle of field testing.
BIOLABMAG.COM 11 FEATURE STORY
Canada grows more than 3 million tonnes of lentils annually, more than half of the world’s total supply.
GETTING TO THE ROOT OF THE TREE OF LIFE
The Canadian BioGenome Project is an ambitious undertaking that aims to map the complete genome of plants and animals
BY SEAN TARRY
When it comes to scientific pursuits, there aren’t many that match the ambition, breadth or significance of the Canadian BioGenome Project. Established as part of the larger Earth BioGenome Project, it’s an undertaking that aims to map the genomes of all plants, animals, fungi and other microbial life — an effort to, in effect, catalogue the complete genetic diversity of Canada's plants and animals through genomic sequencing.
The sheer magnitude of the project is not lost on Steven Jones, Co-Director of Vancouver’s Genome Sciences Centre and CoLead Investigator for the Canada BioGenome Project. However, he says equal to the amount of work that will be required to complete this endeavour is its importance to our ability to further our collective understanding of life on Earth.
“What we’ve just started in our attempt to sequence the genomes of Canada’s plants and animals presents an enormous challenge, which will require a great deal of work,” he says. “It will also require a tremendous amount of collaboration between individuals within the science community in order for us to achieve our objective. It’s a massive project that poses huge potential benefits in the way of enhancing our understanding of the evolution of life and uncovering fundamental genetic principles of health and disease that will help populations everywhere.”
Beginning as a consortium of sequencing laboratories across the country, which includes the Genome Sciences Centre in Vancouver, Toronto’s Hospital for Sick Children, and McGill University in Montréal, the project has grown to rely on a host of experts whose insights have been sought in order to guide and direct the research and work being conducted. There are just over an estimated 80,000 species of plants and animals that are known to inhabit Canada from coast to coast to coast. Jones and the Genome Project are starting with the sequencing of between 400 and 800 species.
Experts, Jones says, are helping to narrow the project’s focus.
FEATURE STORY 12
“We’ve got a group of a few hundred or so scientists located right across the country who are all experts concerning very specific types of animals and plants, like conifers or crustaceans,” he says.
“They’re helping us to identify the species that are high priority for sequencing. We can’t possibly sequence every species of plant and animal across the entire country right away. So, we’ve got to choose wisely to start. It really comes down to understanding and being aware of the parts of the tree of life that are underexplored, identifying the plants and animals for which no genetic understanding exists and prioritizing them as such.”
Jones goes on to explain that in addition to filling out the tree of life, there are also other factors considered when prioritizing the sequencing of species, including scientifically interesting plants or animals that may interact with humans and possess unique properties, as well as species that have become endangered as a result of climate change.
In addition, he suggests that it may also be just as important to sequence and study the prey of the endangered species to further understand why the numbers of some predators are diminishing. In fact, there is a whole web of criteria that inform decisions made by scientists feeding into the Canada BioGenome Project. Supporting much of the human effort, Jones explains, is cutting-edge technology that is serving to elevate and improve the work being conducted.
“The major type of technology that we use is obviously related to DNA sequencing,” he says. “It’s recently become a much more critical and useful tool. Its potency and power have increased, and the prices have come down significantly since the first human genome was sequenced at the turn of the century. It is rapidly improved technology that is now much more accessible for this type of work, allowing us to do more, quicker, faster, cheaper and more efficiently.”
THE POWER OF ARTIFICIAL INTELLIGENCE
It is estimated that the sequencing of the first human genome took in excess of 15 years and cost somewhere in the range of US$2.7 billion. Today, Jones and his team of scientists can routinely sequence genomes in a matter of days for a little more than CDN$1,000. And, in addition to the vastly improved technology, advancements related to artificial intelligence are going a long way toward supporting efficiencies and breakthroughs within the study and research of genomics and
the sequencing of species.
In particular, Jones points to the recent introduction of AlphaFold, an artificial intelligence program developed by Google which, informed by deep learning, presents the ability to perform predictions concerning protein structure, among other things.
“One of the greatest advancements over the course of the past 24 months or so is the AI that’s coming out of Google’s AlphaFold project,” he asserts.
“If we can sequence the genes, Google’s AI will then predict the threedimensional structure of the protein that the gene creates. It represents a huge step forward, allowing us to, for instance, sequence the genome of a bee, and with a couple weeks of computation will be able to produce the three-dimensional structure of every protein in that bee. It helps us better understand things like how the bee is interfacing with its environment and perhaps design a new insecticide that doesn’t impact the bee population. It’s quite incredible that we are now, through sequencing, able to generate a parts list of each plant and animal, and through Google’s technology can understand the precise shape of each part. It’s going to continue to be a key technology that we use going forward.”
OPEN DATA ECOSYSTEM
Google’s technology will also be key in helping Jones and his team of scientists fulfill one of the mandates of the Earth BioGenome Project, which is to freely share with the public all of the data and information that’s generated through sequencing. To do this, data is submitted to collaborators in Europe who annotate it in a way that’s consistent with all of the other genomes being created around the world as part of the project. It is an approach that allows everyone involved to operate within an open data ecosystem, enabling its full access and use to anyone on the planet, posing a multitude of potential future benefits. It is one of the core concepts of the project, says Jones, and one of its aspects that makes it such an exciting one to work on.
“It really is quite an incredible project to be a part of. And only a few months in, our work is only now beginning in earnest. The initial phase of the project is scheduled to be a duration of four years. We’re hoping that in that time we’re able to, through our work, show significant progress in our sequencing efforts. In addition, over this time, we’re anticipating further technological advances that will make the use of these tools even more accessible and financially viable, allowing us to continue deepening our understanding of the vast Canadian ecosystem.”
BIOLABMAG.COM 13 FEATURE STORY
This poses huge potential benefits in the way of enhancing our understanding of the evolution of life and uncovering fundamental genetic principles of health and disease.
In a Canadian first, UBC scientists 3D print human sperm
Sciencehas come a long way since the first blood vessels were bioprinted in 2010, successfully printing cartilage, bone, cardiac, nervous, liver, and vascular tissues. Recently, scientists at the University of British Columbia added to that list with 3D bioprinted human testicular cells, a Canadian first that offers hope for men with a severe form of infertility known as non-obstructive azoospermia (NOA).
According to UBC, the scientists, led by UBC urology assistant professor Dr. Ryan Flannigan, suggest that the technique may one day offer a solution for people living with currently untreatable forms of male infertility.
“Infertility affects 15% of couples, and male factors are a contributing cause in at least half of those cases,” said Dr. Flannigan, whose lab is based at the Vancouver Prostate Centre at Vancouver General Hospital.
“We’re 3D printing these cells into a very specific structure that mimics human anatomy, which we think is our best shot at stimulating sperm production. If successful, this could open the door to new fertility treatments for couples who currently
have no other options.”
Within human testicles, sperm is produced by tiny tubes known as seminiferous tubules. In NOA, no sperm is found in ejaculate due to diminished sperm production within these structures.
While in some cases doctors can help NOA patients by performing surgery to find extremely rare sperm, Dr. Flannigan says this procedure is only successful about half the time. “Unfortunately, for the other half of these individuals, they don’t have any options because we can’t find sperm for them.”
Those are the patients Dr. Flannigan’s team is hoping to help.
For the recent study, the researchers performed a biopsy to collect stem cells from the testicles of a patient living with NOA. The cells were then grown and 3D printed onto a petri dish inside a hollow tubular structure that resembles the sperm-producing seminiferous tubules.
“3D bioprinting is a highly customizable platform that gave us control on the largest number of variables to facilitate
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favourable cell-cell interactions and recapitulate in vivo cytoarchitecture like we see naturally in the human body,” explains Dr. Flannigan.
The team used a 3D printer manufactured by Aspect Biosystems, which also supplied the proprietary bioink in which the cells were mixed. To determine the precise amount of biomaterial for the ink, as a starting point they relied on previously published data on cell density required for 3D bioprinting, explains Dr. Flannigan, and “then performed several series of optimization experiments of cell concentration, and printing parameters to achieve the structure achieved in this publication.”
To shape the 3D printed cells, they used a coaxial needle that consisted of a sacrificial core material (polyvinyl alcohol–PVA 6%) with cells situated in AGC10 bioink in the outer shell to achieve the tubular structure.
Twelve days after printing, the team found that the cells had survived. Not only that, they had also matured into several of the specialized cells involved in sperm production, and they were showing a significant improvement in spermatogonial stem cell maintenance — both early signs of sperm-producing capabilities. The results of the study were recently published in Fertility and Sterility Science
“It’s a huge milestone, seeing these cells survive and begin to differentiate. There’s a long road ahead, but this makes our team very hopeful,” said Dr. Flannigan.
The team is now working to “coach” the printed cells into producing sperm. To do this, they’ll expose the cells to different nutrients and growth factors, and fine-tune the
structural arrangement to facilitate cell-to-cell interaction.
If they can get the cells to produce sperm, those sperm could potentially be used to fertilize an egg by in vitro fertilization, providing a new fertility treatment option for couples.
Dr. Flannigan’s research program has also been shedding new light on the genetic and molecular mechanisms that contribute to NOA. They’ve been using various single-cell sequencing techniques to understand the gene expression and characteristics of each individual cell, then applying computational modelling of this data to better understand the root causes of the condition and to identify new treatment options. The work has been highly collaborative, involving UBC researchers across computer science, mathematics and engineering, as well as international collaborations.
“Increasingly, we’re learning that there are likely many different causes of infertility and that each case is very patient-specific,” said Dr. Flannigan. “With that in mind, we’re taking a personalized, precision medicine approach. We take cells from a patient, try to understand what abnormalities are unique to them, and then 3D print and support the cells in ways that overcome those original deficiencies.”
This research is supported by Michael Smith Health Research BC, the Canada Foundation for Innovation, Canadian Institute of Health Research, Vancouver Coastal Health Research Institute, American Society of Reproductive Medicine, Canadian Urologic Association Scholarship Foundation and the Vancouver Prostate Centre.
Dr. Ryan Flannigan and research assistant Meghan Robinson with the bioprinter they’re using to 3D print copies of a patient’s testicular cells.
Photo Courtesy: University of British Columbia
MORE THAN NOAH’S ARK
BY ROBERT PRICE
Diederichsen has a scientist’s sense of humour. A research scientist and curator at Plant Gene Resources of Canada (PGRC), he recalls one of the more thrilling moments in his career. While studying cultivated flax, a plant only known to have blue flowers, he found a wild relative with white flowers. “Botanists can get excited about these things,” he laughs.
As a curator at PGRC—a government agency tasked with
preserving and enhancing “the genetic diversity of cultivated plants of importance for Canadian agriculture and their wild relatives”—Diederichsen stays close to the excitement found in watching the grass grow.
It’s quiet work. It’s also enormous importantly work. As a repository for the seeds, tubers and cuttings of Canadian agriculture reaching back to the 1960s, the PGRC might look a bit like Noah’s Ark—a life raft carrying the sum of genetic
PLANT GENE RESOURCES OF
A LIVING LIBRARY
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diversity produced by farmers. But such a comparison wouldn’t capture the whole story. As Diederichsen explains, the PGRC is “more than Noah’s Ark.”
It is, in fact, more like Borge’s magical library that collects every sequence of words ever written. Instead of words, PGRC catalogues plant genetics. PGRC is, Diederichsen says, a place “where you find exotic things”—all of it packed in tens of thousands of envelopes and waiting to be brought to bloom.
A living library
PGRC, a part of Agriculture and Agri-Food Canada, operates three genebanks. A bank in Saskatoon stores seeds and grains; a bank in Fredericton collects tubers for potato farming; and a bank in Harrow, Ont., houses materials needed to help Canada’s orchards and fruit patches thrive. In each location, scientists house and study seeds, cultivars of landraces (crops that have been improved through farming), obsolete cultivars and wild relatives of seed relevant for agricultural production. The scientists at PGRC regenerate plants, describe the basic botanical features of the seeds they have on file, and make these seeds available for research, breeding and education through online databases, publications and work the organization does with agricultural scientists.
PGRC has close to 114,000 accessions—plant material collected from a single location—with a strong focus on cereals, a key component of Canadian agriculture. Around 80% of the collection comes from cereals, including 40,000 different barleys (both cultivated and wild species) and 48,000 samples of oats. The genebank seeks to capture a complete portrait of cultivars bred in Canada and solicits donations from breeders who retire or give up all or part of their agricultural programs. “They have working collections with interesting material, some of it very difficult to find,” says Diederichsen.
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Plant breeders actually said we need living genebank collections [to preserve information] because even if it’s not suited today, it may carry traits we need for doing something.
The donations will eventually find their way back to Canadian farms. Successful agriculture relies on genetic diversity—a value that must be constantly renewed since it’s so easy to lose. Three hundred years ago, for example, villages across Europe farmed different types of wheat, barley, or oat, each type adapted to local conditions. Over time, farmers singled out the most successful grains, and soon all farmers were cultivating these grains.
“So we lose the reservoir of diversity we depend on,” says Diederichsen.
PGRC works to buffer against this loss of diversity, by ensuring a diverse set of genetic diversity remains accessible to farmers and scientists, even if particular seeds aren’t currently used for agricultural purposes—and haven’t been planted in decades.
Genetic diversity is a strength
Genebanks have a long history. Medieval monasteries cultivated and collected cereals and medicinal plants, and in the 16th century Italian botanical gardens cultivated and traded exotic
Images provided by Plant Gene Resources of Canada (PGRC), ©Her Majesty The Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food, licensed under the Open Government Licence – Canada
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Medieval monasteries cultivated and collected cereals and medicinal plants, and in the 16th century Italian botanical gardens cultivated and traded exotic plants.
plants. With the advent of modern plant breeding some 150 years ago, plant breeders quickly learned that if they wanted to create something new, they needed a diverse collection of seeds to breed and crossbreed. But, as Diederichsen recounts, as breeders became successful at creating new cultivars that produced higher yields, the older, locally adapted crops that farmers had used for hundreds of years started disappearing.
Plant breeders knew what the extinction of older crops meant: the loss of information and a loss of crop vitality.
“Plant breeders actually said we need living genebank collections [to preserve information],” Diederichsen says, “because even if it’s not suited today, it may carry traits we need for doing something.”
Genebanks like PGRC serve an important role in preserving—in living form—the genetic heritage of each crop. The genebank ensures the genetic integrity of each sample in the library—the material remains frozen in time, preserved in the state it was when it was collected. Unlike traditional farming that relied on a farmer’s experience with a crop, today’s geneticists can scour the genetic histories of individual crops— moving backwards in time, so to speak— to find older generations of a particular crop that might have resistance to specific diseases.
Nicolas Tinker, a senior research scientist at Agriculture and Agri-Food Canada who uses the collections at PGRC as part of his bioinformatics research, describes this ability to search the family trees of different plants as a primary driver for seed libraries that might, to uncreative minds, seem like esoteric lines on a balance sheet.
“In oat, in particular, there’s a disease called crown rust that sweeps through and defeats the genes that we have, and if we don’t keep going back to the genebank and finding new sources of resistance to that disease, we lose the crop,” says Tinker.
“We keep genebanks going because we don’t know what we’re going to get
out of them in the future, and that’s the conundrum.”
Browsing other libraries
To extend the diversity of crops around the world, PGRC works with genebanks in other countries on international initiatives geared to preserving diversity in cultivated plants. These genebanks exist all over the world, each with a different focus. Norway’s Svalbard Global Seed Vault, for instance, holds more than 1 million seed samples of some 5,400 species in an underground storage facility. The International Rice Genebank in the Philippines, which is the largest bank of rice genetics in the world, holds more than 132,000 rice accessions.
Like PGRC, these genebanks push data about plant genetics into the public realm. PGRC has a sizeable database that allows clients to see what material the bank has available to the scientific community nationally and internationally. Scientists inside and outside the genebank research the PGRC’s holdings for certain traits and publish their findings, and with climate change threatening crops, study of the molecular composition of the collection intensifies as breeders look to adapt crops to changing environments. Currently, a research team is studying 30,000 accessions of PGRC’s genebank and will describe the genetic makeup of these individual accessions using the sequencing technologies.
Safety against the future
As the climate changes and food producing nations feel the pinch of inflation, fertilizer shortages, and political unrest, the cultural and political environment seem ripe for longer and deeper discussions of how organizations like PGRC can diversify agriculture and ensure crops remains resilient and plentiful.
“Ultimately, our food security nationally but also globally depends on having access to this diversity,” Diederichsen says.
BIOLABMAG.COM 19 LAB PROFILE
With climate change threatening crops, study of the molecular composition of the collection intensifies as breeders look to adapt crops to changing environments.
New DNA insights will transform Arctic marine biodiversity and fisheries management
BY BRIAN BURKE, NUNAVUT FISHERIES ASSOCIATION & CARON HAWCO, EDNATEC
Indigenous fishing enterprises are playing a key role in the application of genetics research to support the commercial fishery of Canada’s North. This has the potential to address the significant knowledge gaps that currently exist relating to Canada’s biodiversity in the North. Traditional environmental programs have typically been limited due to the challenges of operating in remote and harsh Arctic conditions.
The Nunavut Fisheries Association (NFA) and environmental genomics specialists at eDNAtec have partnered
to bridge this knowledge gap. The focus is to build on their Canada’s Ocean Supercluster project, OceanDNA System, integrating Indigenous knowledge with eDNA research to transform commercial fisheries research by involving Indigenous fishers directly in the research process.
In September 2020, eDNAtec, working with the NFA, Petroleum Research Newfoundland and Labrador (now Energy Research and Innovation Newfoundland and Labrador), and the federal Department of Fisheries and Oceans (DFO) launched the
OceanDNA System project to assess, monitor and characterize the ocean. It was financed by Canada’s Ocean Supercluster to the tune of $2.2 million with additional funding of $2.7 million from the project partners.
All organisms shed environmental DNA (eDNA) into their surroundings. The eDNA in one water sample can reveal an abundance of data about the variety and number of organisms present in an ecosystem and can be completed in a fraction of the time required for conventional field sampling.
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Through the OceanDNA System project, eDNA sample collection tools can now be easily deployed on operating fishing vessels where crews are trained to collect samples from marine ecosystems, which are then analyzed with eDNA sequencing systems.
“We have been building capacity using environmental DNA (eDNA) water sampling techniques on our commercial and research vessels,” said NFA Executive Director Brian Burke. “This research, which is taking place in the harsh conditions of Canada’s Eastern Arctic, is being incorporated into NFA’s annual fisheries research and tracking programs to improve understanding of the marine environment and management of fishery resources.”
Expected to be completed by the end of 2022, the OceanDNA System project developed eDNA workflows and procedures that supported the integration of eDNA technology with conventional biodiversity assays and Indigenous knowledge, providing an improved understanding of Northern ocean biodiversity through the following advancements:
1. Development of field protocols that are straightforward and easy to learn, with equipment that works reliably without requiring technical expertise, particularly when collecting water samples without introducing other contaminants, such as human DNA, which can complicate lab analysis.
2. Identification of targeted commercial species and bycatch so their DNA is pre-identified, making for a quicker and more efficient analysis of samples. Target species included Greenland Halibut, Greenland Shark, Arctic Skate, Arctic Cod, Narwhal, two species of Northern Shrimp, two types of Redfish, and two types of Grenadier.
3. Abundance of target species. This research is based on work conducted in related fields, including medical genetics, to conclude not just what species are present, but the relative abundance of each species present.
4. Understanding genetic diversity within species. Related to stock assessment, determining if populations of certain stocks are one distinct population that can be managed as one entity, or if there are discrete populations
that are separate and don't intermix. For example, Greenland Halibut is currently considered to be one population that has a very broad geographic distribution. We are now using environmental genomics to determine if this species is actually represented by two or more distinct populations.
5. Ecosystem modeling. All the information is brought together, layered and applied to define species extent and density across the entire ecosystem area. This model provides a better understanding of how various factors, such as water depth, temperature and nearby structures affect the populations of target species.
According to eDNAtec CEO Steve Barrett, eDNA sampling can now be easily done by non-scientists in remote communities and is proving to be safer, faster and less expensive than ever before. “This technology also aligns with Inuit philosophy that ecosystems must be viewed as a whole versus by individual species,” he added. “By improving ecosystem knowledge, northern communities can be more involved in directing the environmental stewardship of their coasts, including Marine Protected Areas.”
“We are integrating Indigenous knowledge with eDNA to improve stock management, invasive species detection and biodiversity assessments,” said Burke. “This will build on our existing research and is not only important for NFA’s offshore fishery but also for assessing inshore fishery potential for communities in the Qikiqtani region and across Inuit Nunangat.”
The Nunavut Fisheries Association NFA is a non-profit organization established to provide a unified industry voice for Nunavut’s fishing industry. NFA represents four Inuit-owned quota holders, including the Arctic Fishery Alliance, Baffin Fisheries, Qikiqtaaluk Corporation and the Pangnirtung Fisheries/Cumberland Sound Fisheries Partnership.
Specialists in environmental genomics, eDNAtec is transforming how to assess, monitor, and characterize ecosystems through DNA sequencing, which enhances environmental stewardship of our planet’s marine and terrestrial biodiversity. eDNAtec works closely with the world’s ocean industries and organizations with an interest in them, including energy, fisheries, and the Government of Canada.
COMPANY PROFILE BIOLABMAG.COM 21
By improving ecosystem knowledge, Northern communities can be more involved in directing the environmental stewardship of their coasts, including Marine Protected Areas.
SENSING BIODIVERSITY: VACUUMING MAMMAL DNA FROM THE AIR
A geneticist uses a simple pump to filter microscopic genetic samples from air. The approach is a novel way to monitor biodiversity, identify species interactions and assess changes in the ecosystem.
BY REHANA BEGG
a deep breath. Now consider the air you’ve inhaled…
Along with the oxygen, air contains nitrogen and carbon dioxide, as well as ozone, smoke, dust and pollen. A lesser-known fact is that air molecules could also contain trace amounts of animal DNA.
That’s according to Dr. Elizabeth Clare, geneticist and assistant professor at Toronto’s York University, who recently published a proof-of-concept study outlining a method for detecting the presence of animal DNA in air several hundred meters from the source.
Her research is not only a step toward validating the presence of hard-to-detect mammals but has the added benefit of being non-invasive — an essential factor when dealing with endangered species. “There is a risk associated with interfering with endangered populations or, if I catch one of them, it’s a stressful experience for both them and me,” says Clare.
Environmental DNA (eDNA) is any DNA not taken directly from an animal or a plant. This method for collecting DNA samples is growing, says Clare, who previously sequenced eDNA to monitor fish, iDNA in leeches to monitor invertebrates, and DNA in feces to
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work out predator-prey and seed dispersal relationships. “We’re gradually moving away from catching the animals to capturing the thing that touches the animals and moving to going directly to the environment.”
For the “airDNA” study, 72 samples were collected at targeted locations at the Hamerton Zoo Park, a 25-acre conservation zoo in Huntingdonshire, UK. “We were even able to collect airDNA from animals that were hundreds of metres away from where we were testing without a significant drop in the concentration, and even from outside sealed buildings,” says Clare. “The animals were inside, but their DNA was escaping.”
After analyzing the samples, the team identified 25 species of mammals and birds. Seventeen were known species. Squirrels, ducks, and hedgehogs from the surrounding rural area were also detected in the count. The range of species detected, notes Clare, validates the potential use of airborne eDNA in detecting and monitoring biodiversity.
If there’s a downside to environmental sampling, then it has to be that one cannot collect a clean sample. “There’s lots of DNA in my sample, and we’re still working on how to do it with air,” explains Clare.
Samples in the experiments were also dispersed (as opposed to concentrated) and could not provide detail beyond identifying individual species. Exposure to ultraviolet light (such as that from the sun), temperature changes and age of the animal can cause degradation of the DNA.
Still, for Clare, the objective is largely to detect the diversity of species in a given ecosystem, rather than detecting a single species.
Current sample collection methods are anything but foolproof and Clare’s team continues to work on perfecting a method to filter the DNA from the air. “We’re trying different things, but mostly, we suck air through very fine filters,” she says. “It’s a bit like filtering coffee. We’re trying to pull air through a filter and track particles, such as dead skin cells and bits of hair and free-floating DNA from the air sample.”
To collect airDNA samples, Clare uses a Geotech peristaltic pump, which moves air through a flexible tube. Air drawn from the outside moves through Sterivex-HV filters (Merck Millipore) at the intake end of the tube before moving into the hose. The soiled filters are then placed in sterile bags and frozen until DNA extraction. The samples are lysed overnight and centrifuged for extraction.
Once the DNA is extracted, a technique called polymerase chain reaction (PCR) is used to inspect the DNA sequences and compare the results to DNA databases. The raw DNA amplicon data is then deposited at the NCBI Sequence Read Archive, a large, publicly available repository of highthroughput sequencing data.
“This is just a natural process that we have co-opted in a lab, so that we can target and make copies of something very specific,” explains Clare. “I can design a test for elephant DNA and I can just assay for elephants. I can’t really distinguish which elephant, but I can probably design something that will amplify elephant DNA and nothing else.”
Rather than use a vacuum pump to collect the air samples, Clare uses a suction pump to siphon water through a filter. “Vacuums are loud and we were constrained by the noise,” explains Clare. “We were trying to be non-disturbing to the animals. Our pump was almost silent. It was not efficient, but it worked. All we were trying to show is that it was possible.”
Clare is currently testing more powerful vacuum systems. Since she carries her gear into rugged terrain, the pumps need to be lightweight, portable, battery-powered and affordable. One company offered her a commercial sampler at the cost of $15,000, she says. Given the prohibitive cost, Clare decided to engineer her own air-pumping device. “I’ve got seven different prototypes that I’m going to test,” she says. “I’m simply trying to make something that students and I can haul out in the middle of nowhere and fix when it goes wrong.”
As with most research, Clare’s team has a few unanswered questions. How far does it travel? How quickly does it accumulate? How quickly does it degrade?
Plans to address these questions are in the offing, as is finding better technology solutions. “We do have an engineering problem, which is trying to figure out how to sample large amounts of air efficiently,” muses Clare. “We haven’t gotten to that yet. This is very early in this type of technology.”
At the same time Clare was conducting the airDNA research, a second research team in Copenhagen was working on an identical question. Rather than run the risk of scooping each other, the teams co-ordinated their research and published the findings simultaneously. “We purposely didn’t talk about what we’re doing; we only talked about the process,” says Clare. The upshot, she says, is that the work was twice validated.
BIOLABMAG.COM 23 APPLICATION NOTE
Getting a closer look at molecular structures
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Pinpointing variants and gaining actionable insights from next-generation sequencing (NGS) data can be time-consuming and drain resources. The SOPHiA DDM platform sifts through extremely large, complex, and noisy datasets for analysis. It uses machine learning with patented algorithms to efficiently call, annotate and pre-classify variants from raw NGS data. User-friendly features streamline prioritization, simplify interpretation and expedite reporting. High-throughput genomic analysis is possible in any laboratory, with end-to-end workflows tailored to different experimental settings. www.sophiagenetics.com
Laboratories are high-risk environments, presenting a unique set of dangers for workers. Medicom offers a full range of protective gloves for those who are exposed to these occupational hazards every day. The SafeTouch Advanced Form ultra-slim nitrile gloves are ideal for high-precision procedures, are powder-free, and come in a range of sizes. These all-purpose, mid-level thickness gloves conform to hands to provide an optimal balance between protection and tactile sensitivity. Textured fingertips ensure a secure grip, even when wet. www.medicom.com
Unique fluorescent dye
Bio-Rad Laboratories offers the StarBright UltraViolet 400 Dye, the first in its range of unique fluorescent nanoparticles designed for use with a UV laser in flow cytometry applications. The dye offers exceptional brightness with narrow excitation and emission profiles, making it suitable for use in multicolor flow cytometry panels. Bio-Rad's range of StarBright Dyes are conjugated to highly validated flow antibodies and are compatible with most flow cytometers and experimental protocols. It provides researchers with greater choice and flexibility when designing flow cytometry experiments.
A simple-to-use, automated tan gential flow filtration system
The Mobius FlexReady Solution for tangential flow filtration (TFF) comes pre-assembled and pre-tested, integrating easily into any process. The flexible system provides maximum adaptability to your changing process needs, such as varying volume levels. The retentate recycle tank is specifically designed for efficient concentration and diafiltration of proteins. The fully automated system eliminates carryover from previous batches and enables use with single-use tangential flow filtration devices.
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cpdn.ca Bio Talent
Putting Genetics on the table
Looking for answers to climate change and food security
ISSUE 2 • 2022
» The science of food and beverage
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GENES AND THE BIG BANG
As the planet’s population grows, scientists are scrambling to find better ways to produce enough food. With more than 7.753 billion mouths to feed, researchers are managing to move the needle on food production, but their efforts are being hampered by climate change which has upped the ante. Catastrophic flooding and drought, diseased livestock and stressed crops, a loss of arable land, higher carbon dioxide levels and hotter temperatures have made feeding the world a problem of colossal proportions.
For some Canadian food producers, genomics may offer hope. Manipulating the genes of crops and livestock to build their resiliency and yield will play an increasingly important role in bolstering global and local food system.
In Canada, genetically modified organisms (GMOs) are carefully monitored and must meet stringent requirements; to date, Canada has approved 15 GM foods including four that are grown in Canada (canola, soybeans, corn and sugar beets) as well as GM foods that have been imported from other countries (alfalfa, cotton, papaya and squash).
In this issue of Canadian Food Business, we look at how GMO foods contribute to the food supply in the age of climate change and we feature an expert on managing plastics through a circular economy. We also learn how to make the most of waste produce and hear how a leading genomics technology company has introduced a mobile testing device aimed at improving the detection of foodborne pathogenic bacteria like listeria and salmonella.
The solution to the world’s food supply may very well live in a tiny sequence of genetic material.
Finally, don’t miss our fall issue of Canadian Food Business which dives into the world of functional foods with the latest research into phytochemicals, bio-oils, developments of new products with health benefits, and enhancement of food antioxidant capacity.
Jana Manolakos EDITOR
In 2022 the Canadian Institute of Food Science & Technology (CIFST) and Canadian Food Business magazine launched a partnership to create a platform for leading experts, innovators and scientists to showcase the latest trends, knowledge and developments that are changing the face of Canada’s food industry today. For further information contact email@example.com
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Engineering solutions to Food Security
By Pierre Petelle, President & CEO, CropLife Canada
The past few years have seen considerable public discourse about the challenges facing our planet. While the COVID-19 pandemic garnered most of the attention, concerns around food security are increasing and we are faced with an important question: how will we feed a growing global population amidst a warming climate? Technology and innovation are essential parts of the equation. One set of tools in particular, plant breeding innovations, presents incredible opportunities to enhance the sustainability and resiliency of agricultural production around the world.
Scientific tools with significant impact
Humans have been breeding plants for more than 10,000 years, selecting varieties of crops that performed well or had desirable characteristics (e.g. tasted better, larger kernels, etc.). Traditional plant breeding results in a random crossing of genetic material between the two parent plants in hopes that some of the offspring will be successful, however there is little control over the result. Over time, the processes for making tweaks to improve crops have improved and diversified with new science and technology.
There are now a number of plant breeding innovations that scientists and plant breeders can access. The most commonly discussed type is genetic engineering, which produces genetically modified organisms (GMOs). Genetic engineering
GUEST EDITORIAL CANADIAN FOOD BUSINESS VOLUME 37, ISSUE 2 • 2022 28
is the process of very precisely moving favourable genes from one organism to another. Regulatory agencies and other groups around the world, including Health Canada, the World Health Organization and the United Nations Food and Agriculture Organization all consider crops developed through genetic modification to be as safe as traditional crops.
Now there is a newer plant breeding technology called gene editing, which includes techniques like CRISPR (clustered regularly interspaced short palindromic repeats). CRISPR allows researchers to cut or edit out certain pieces of a plant’s own DNA in order to add, remove or enhance a desired characteristic. It holds such potential that its developers were awarded the 2020 Nobel Prize in Chemistry.
Both genetic modification and gene editing present incredible opportunities to benefit people and the planet. Farmers in Canada first started using GMOs in 1996. Since then, these farmers have benefited from growing GMOs such as corn, canola and soybeans that are resistant to insects and herbicides. Consequently, farmers can keep their plants healthier and improve the yield of their crops. These GMO crops have reduced the need for tillage as a form of weed control on tens of millions of acres of land, resulting in improved soil quality, significantly increased carbon sequestration and reduced greenhouse gas emissions from machinery.
Increasing resiliency in unpredictable conditions
As the real effects of climate change create challenging growing conditions, plant breeding innovations are driving the development of more resilient crops. Scientists have developed varieties of plants that are better able to survive and thrive under flood or drought, or to resist disease. Such developments help to provide a more predictable harvest to feed a growing population. Recently in Canada, we’ve seen devastating droughts, floods and extreme weather events that have significantly impacted farmers’ ability to grow food. Outside of Canada’s borders, we see the same kinds of challenges that make agricultural production more unpredictable than ever. While weather is a variable outside of anyone’s control, what we do have some control over is embracing innovations that lead to heartier crops, helping protect our food supply in the face of challenging weather conditions.
Improved nutrition for a growing population
According to the United Nations, almost 9% of the world’s population (approximately 690 million people) are
experiencing food insecurity (FAO, 2022). That number could swell to 840 million by 2030 if current trends continue. Technologies like GMOs and gene editing will be crucial in moving toward the UN Sustainable Development Goal of Zero Hunger.
Numerous examples of plants developed for improved nutrition already exist. Genetic modification created the vitamin A-enhanced golden rice and omega-3 soybeans. Scientists are using gene editing to develop heart-healthy tomatoes, high-fibre wheat and nutrient-dense lettuce. The precision with which these nutrition-related traits can be harnessed presents opportunities to address the widespread global issue of malnutrition. But perhaps most exciting is that tools like gene editing can accomplish the research and development for these crops in a fraction of the time needed for traditional breeding. Given that our population is expected to increase by another 2 billion people by 2050, there is no time to waste.
It is also important to note that GMOs and gene-edited crops can play a role in reducing food waste. The Food and Agriculture Organization estimates that one-third of all the food produced globally is lost or wasted each year, contributing to 6% of global greenhouse gas emissions. Plant breeding innovations can help decrease those numbers, and also reduce the cost implications along the supply chain. For example, potatoes that are resistant to browning and bruising can lessen the estimated 400 million pounds of potatoes that are thrown away every year.
Enabling a path forward for innovation
The agriculture and food system in Canada is innovative, productive and responsive, and access to tools like genetic modification and gene editing can help our country play a leading role in a bright future for our planet. But in order to truly unleash the potential of these kinds of innovations, we need to ensure Canada’s regulatory system continues its robust protection for human and environmental health, while also relying on science to deliver policies that enable this kind of much needed innovation to come to the market in Canada. With global food security at the forefront like never before, we need to be embracing these technologies now to deliver important benefits for tomorrow.
Pierre Petelle is the president and CEO of CropLife Canada, the trade association that represents the Canadian manufacturers, developers and distributors of pest control products and plants with novel traits. Pierre joined CropLife Canada in 2008 and is now responsible for the strategic direction and leadership of the association.
Genetic engineering is the process of very precisely moving favourable genes from one organism to another.
Ocean Brands adds to its sustainability portfolio
With more voices calling for better sustainability standards in the seafood industry, Ocean Brands recently announced its Ocean’s Skipjack Tuna is now 100% Marine Stewardship Council-certified sustainable. With this addition, Ocean Brands has now increased the MSC-certified segment of its Ocean’s portfolio from 11% in 2021 to 70%, a move that has pushed it into the lead for MSC-certified products in Canada’s canned seafood category.
Data shows the planet could provide protein for 72 million additional people if oceans were fished sustainably on the whole. That’s according to the MSC, an international non-profit organization that works closely with experts to uphold the seafood industry’s highest standards of sustainability. Consumers can easily identify certified sustainable seafood by looking for the MSC blue fish label, which signals that it has met the council’s strict criteria.
“There is still so much work to do when it comes to managing our fisheries. As we take from our natural environment, we also have an obligation and a commitment to ensure the vitality of our oceans for years to come,” says Ian Ricketts, President of Ocean Brands.
“Our long-standing partnership with MSC and the certification of our Ocean’s Skipjack Tuna are a testament to how we are investing back into the management of the fisheries that are depended upon by so many nations. We applaud those who have taken these steps towards sustainability before us, and we look forward to other brands making this same commitment. Our collective efforts are needed to secure the future of our oceans.”
The MSC represents the industry’s highest standard of sustainability. It meets globally recognized best practice standards and its ecolabel has the highest rate of recognition among consumers. Purchasers of MSC-labelled seafood can rest assured that it was sustainably wild-caught and fully verified to come from a certified fishery. By choosing products with this label, consumers are directly supporting fisheries and companies that take care of our oceans.
Funding solutions that mitigate the effects of climate change
Genome Canada recently launched a $24-million funding opportunity to support the development of genomic solutions to climate change challenges faced by agriculture and food production systems. The Climate Action Genomics Initiative funding involves teams of researchers from different disciplines and users working together to resolve issues related to the carbon footprint and greenhouse gas emissions of Canada’s agriculture and food systems. As part of the initiative portfolio, the teams will work toward broader national impacts that deliver value beyond each individual project. The teams will provide genomic solutions for agriculture and food production systems that are climateresilient, socially responsible, economically viable and environmentally sustainable, and that contribute to the mitigation of climate change impacts.
Consumers remain confident in Canada's agriculture and food sectors
Foodbanks Canada and Grassroots Public Affairs teamed up for an online survey that measured public opinion about Canada’s agri-food sector. The survey found that as the country emerges from the pandemic, almost half of Canadians believe very strongly in the sector’s ability to drive the Canadian economy. While Canadians remain extremely confident (92%) in food grown or produced at home, recent price increases are driving some interesting shifts in consumer habits and attitudes. 71% of Canadians are opting for discounted or lower-cost items, up by one-third since 2020. More than eight in 10 (84%) see hunger and food insecurity in Canada as a serious problem, a 25% increase since 2021. Half of them (51%) noted that animal proteins are "significantly" more expensive this year, and yet red meat consumption is slowly on the rise, a 2% increase since 2021. The Canadawide survey was conducted via an online panel of 1,007 Canadians aged 18 and over. Fieldwork for the survey took place March 25-31, and the survey was offered in English and French.
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Black energy drink
Known for its bright colours, Gatorade has launched a new Canadian sports beverage called Gatorade Black Ice. It features a new, limited-time flavor in a dramatic black drink. Launched in South America earlier this year, the beverage is making its North American debut exclusively in Canada for a limited time this summer. It was made available at most major convenience stores across Canada starting the week of April 25. “Gatorade’s mission of fuelling excellence in sport continues through innovations like Gatorade Black Ice, providing competitive athletes with new and exciting flavours and colours that stand out in the hydration category,” said Lourdes Seminario, Senior Marketing Director, Hydration at PepsiCo Beverages Canada.
Cascades expands its eco-friendly packaging
Cascades recently introduced a 100% recycled polyethylene terephthalate (PET) tray that is also recyclable. As an alternative to hard-torecycle food packaging like traditional styrofoam trays, Cascade’s innovative design allows it to be compatible with the packaging equipment already used by food processors and retailers. It took three years of research to develop its unique design that allows for minimal use of materials while ensuring optimal rigidity. Its rolled edges reduce the risk of tearing when using shrink-wrap, helping to prevent food waste. The tray is manufactured in Québec at the Cascades Inopak plant, which has benefited from an investment program of more than $30 million aimed at supporting the development of packaging made from 100% recycled PET flakes.
Taylor Farms opens Toronto production facility
Canobi AgTech teams up with AgriTech for food security across Canada’s North
Canobi AgTech has teamed with AgriTech North to solve the food security crisis in 600 rural and remote communities across Canada's North through local indoor agriculture. AgriTech North is a wholesale-scale, year-round grower of fresh produce in Northwestern Ontario. They are validating a stack of technologies to resolve economic viability issues surrounding the production of food crops in the North.
“Due to our very challenging environment, we need capabilities that growing systems don't have natively,” says AgriTech North CEO Benjamin Feagin, Jr. The AgriTech North facility in Dryden, Ont., will become a centre of excellence for indoor farming technology innovation in Northwestern Ontario, producing up to 450 kg of leafy greens, culinary herbs and small fruiting crops every week.
Canobi AgTech installed a nutrient dosing system, control system, sensors and monitoring system in AgriTech’s pilot indoor vertical farm. “Because Canobi’s innovative technologies are system-agnostic, they can work with any hardware and plug into any system,” explained Canobi CEO Robin Vincent.
As AgriTech North expands to serve more rural communities, they will use Canobi’s platform to monitor their remote sites and help keep their energy and resource usage down. Canobi’s systems will help reduce the farm's water usage to 10% of that required in conventional farming.
“We need to find ways to grow food where people need it, using less energy and fewer inputs,” says Robin Vincent. “Canobi’s technology can help any farm do that by supplying the data to pinpoint problems and providing innovative solutions to solve them.”
Taylor Farms, a North American producer of salads, fresh-cut vegetables and healthy prepared fresh foods has opened a new facility in Toronto. With production focused on the retail product portfolio, Canadian customers will now have access to an array of the fresh products like Taylor Farms Chopped Salad Kits and Earthbound Farm Organic Salads. “We have seen explosive growth in Canada over the last five years, and with this new location we’re able to address that demand by producing and delivering the freshest and most flavorful foods to our customers,” said Kevin Silver, General Manager of Taylor Farms Canada.
2022 FCC Food Industry Report:
Growth amid inflationary pressures
The annual FCC Food Report reviews last year’s economic environment and highlights opportunities and risks for Canadian food manufacturers for 2022. This includes an annual sales forecast, grocery sales performance and a new gross margin index.
Industries featured in the report are:
• Grain and oilseed milling
• Sugar and confectionery products
• Fruit, vegetable and specialty food
• Dairy products
• Meat products
• Seafood preparation
• Bakery and tortilla products
Beverage manufacturers, we didn’t forget about you. We will be releasing a separate beverage report later this year.
Several external factors impacted Canadian food industries in 2021, which have resulted in higher input costs, amplified labour shortages and upended food consumption patterns. In early 2021, there was hope that the pandemic could soon be behind us; however, new variants provoked more disruptions, restrictions and uncertainty. Despite these challenges, food manufacturers’ performance proved to be strong.
Three key observations from this year’s report:
1. Industry gross margins bounced back in 2021 but remain below historical levels
Gross margins as a percent of sales in food manufacturing increased in 2021 YoY but remain below historical levels and below 2019 (Figure 1). Manufacturers have struggled to fully pass on higher labour and material costs for almost a decade. But margins improved slightly in 2021. At the individual industry level, results widely differ, which we dive into in the report.
Figure 1: Gross margins grew in 2021 but remain below historical levels
Source: Statistics Canada, FCC Economics
2. Food manufacturing sector to outperform the overall economy
Food manufacturing sales increased 14.8% YoY to $125 billion in 2021 (Table 1). This is the strongest YoY sales growth in recorded history (starting in 1992). Increased foodservice volumes and higher selling prices offset volume declines at grocery stores.
Food manufacturing sales are projected to increase 7.4% in 2022, driven by:
• Historically strong disposable income and accumulated savings in 2021
• Food prices remaining elevated
• Robust export markets with food exports representing an estimated 36.8% of overall sales
2020 2019 2018 2017 2016 2015 2014 2013 2021 90.2 93.6 95.0
88 90 92 94 96 98 10 0 102
9 5.4 99.4 10 0.0
Table 1: Manufacturing sales and exports grew in 2021
All figures in million $ 2021 YoY% change 2020 YoY% change
Food manufacturing sales 125,226 14.8 109,104 2.1
Food exports 46,063 16.9 39,417 5.1
Food imports 31,828 3.4 30,786 5.5
Food trade balance 14,234 64.9 8,631 3.7
Grocery & specialty food retail sales 116,650 0.4 116,134 10.9
Restaurant retail sales 26,609 23.6 21,525 -37.2
Fast food retail sales 33,397 15.6 28,902 -14.3
Specialty food service sales 3,921 19.1 3,292 -47.8
Total estimated food retail sales 180,342 6.2 169,853 -5.4
Source: Statistics Canada
3. Consumption of Canadian manufactured food climbed in 2021
The total share of domestically manufactured food consumed in Canada increased an estimated 1.9% after declining for two straight years. The combination of ‘buy local’ trends and domestic investments boosted Canadian sales.
The share of imports relative to consumption as opposed to the share of exports relative to manufacturing sales within an industry provides information about the domestic vs foreign emphasis of manufacturers (Figure 2).
Sales within the dairy manufacturing industry almost entirely occur within Canada. Under 10% of the value of dairy manufacturing sales are exported, and under 10% of Canadian consumption is of imported products. On the other end of the spectrum, seafood is more of a global industry. Over 90% of the sales value were exported, and the percent of imported product consumed was also over 90%. Overall, there’s a lot of two-way trade in the Canadian food industry. For example, nearly 50% of sales in fruit, vegetable and specialty food manufacturing is exported while an equivalent share of domestic consumption is imported.
Figure 2: Most manufactured food consumed in Canada is made in Canada
Fruit/Vegetable and speciality
Grain and oilseed milling Meat Other
The bottom line
Economic conditions are evolving rapidly. The labour market continues to be a challenge, and inflationary pressures continue to climb. War in Eastern Europe and economic sanctions also pose a risk to global economic growth, creating food shortages in many countries that depend on commodities from this region, potentially causing a food crisis for millions.
Stronger disposable income and higher savings in 2021 will support 2022 domestic food consumption growth, although inflation is diminishing many households’ purchasing power. Margin growth will depend on several factors, the biggest being the COVID pandemic’s evolution and how businesses adapt to interest rates increases and input costs.
Read the full report at fcc.ca/FoodReport
Kyle Burak, Senior Economist
Sugar/confection 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 Exports percent of manufacturing sales
Imports percent of domestic consumption
THE CIRCULAR ECONOMY OF PLASTICS
By Carol Zweep
Plastic waste is a global issue. When plastic is released into the environment outside a managed waste stream, it becomes pollution. Plastic pollution found in waterways and oceans causes harm to wildlife. According to Plastic Oceans, more than 10 million tonnes of plastic is dumped into oceans every year and 1 million marine animals die every year when they become entangled in plastic or mistake it for food.
Plastics have many desirable properties as a packaging material: they are durable, strong, lightweight, waterresistant, and relatively easy and inexpensive to manufacture. Unfortunately, plastics in the environment degrade very slowly.
Although excessive use of plastic packaging is concerning, some form of packaging is often necessary to maintain the hygiene or freshness of food or to maintain the integrity of a product during storage and distribution. Finding alternatives to plastic that combines all the desirable properties the material offers can be challenging.
In Canada, over 3 million tonnes of plastic waste are thrown away every year. With only 9% of plastic waste being recycled, most of the plastic ends up in landfills. Up to 15 billion plastic bags are used every year and close to 57 million straws are used daily.
A LOOK AT MANAGING PLASTICS IN THE FOOD INDUSTRY THROUGH INNOVATION CANADIAN FOOD BUSINESS VOLUME 37, ISSUE 2 • 2022 34
The Canada-Wide Strategy on Zero Plastic Waste was introduced by the Canadian Council of Ministers of the Environment (CCME) in November 2018. This strategy was built on the Ocean Plastics Charter and takes a circular economy approach to plastics, providing a framework for action. Currently, plastic material flows are largely linear. The circular economy aims to keep products and materials in use for as long as possible and closes the loop in the use of natural resources by reducing, reusing, repairing, remanufacturing, recycling and composting materials, and by recovering energy at end-of-life.
To support the Zero Plastic Waste Strategy and promote the circular economy, the Government of Canada published the Single-Use Plastics Prohibition Regulations on June 22, 2022. The regulation prohibits the manufacture, import and sale of single-use plastic checkout bags, cutlery, foodservice ware made from or containing problematic plastics, ring carriers, stir sticks and straws. Single-use plastics are found in the environment and often not recycled, but viable alternatives are available.
On February 12, 2022, the Government of Canada published a Notice of Intent and a technical issues paper on the development of proposed regulations that would set minimum recycled content requirements for certain plastic manufactured items. As part of Canada’s plan to achieve zero plastic waste by 2030, the Government of Canada will require all plastic packaging in Canada to contains at least 50% recycled content.
TIPS FOR MAKING THE MOST OF PLASTIC PACKAGING
Packages should be designed to eliminate problematic or unnecessary plastic packaging. The materials and components (e.g. labels, closures, sleeve, etc.) should be selected to ensure packages can be reused, recycled or composted. The Golden Design Rules developed by the Consumer Goods Forum provide guidelines on which plastics should be primarily used for packaging and address specific design elements. The purpose is to maximize recovery of recyclable materials and increase the value of plastics in the marketplace.
Development and investment are required in collection systems to enable convenient and necessary recovery of waste. Rural and remote communities, residential buildings and businesses pose collection challenges. Extended producer responsibility (EPR) programs are recognized as one of the most effective mechanisms to support the creation of a circular economy. EPR is a strategy to make the producer (i.e., brand owners, first importers or manufacturers) responsible for the waste management costs of their packaging and shift it away from municipalities and taxpayers. EPR programs also incentivize producers to change packaging design to support waste reduction, reuse and recycling activities.
As part of Canada’s plan to achieve zero plastic waste by 2030, the Government of Canada will require all plastic packaging in Canada to contains at least 50% recycled content.
PARTICIPATION AND ENGAGEMENT
Two key ways of increasing the capture of recyclables are raising consumer awareness and inspiring participation in sustainable practices, including behavioral changes around recycling. Other means to improve engagement include the education of youth by providing information on plastics to teachers to incorporate into school programs. Leading initiatives and encouraging good waste management practices at businesses, organizations and institutions will also improve recyclable material capture.
Technology is used to sort and maximize the capture of recyclable plastics in an efficient manner. Advances in technology include robotic recycling sorting that uses artificial intelligence and robotics to sort plastics.
The expansion of facilities for easy-to-recycle products and capacity to deal with plastics not currently recycled in Canada is required. Scaling solutions of advanced recovery and recycling methods, including both mechanical and chemical recycling, is also needed.
Seeking opportunities and markets for commonly recycled plastics as well as contaminated and hard-to-recycle plastics will drive the recycling business. Challenges include virgin resins that are available at lower prices than recycled resins. Diverse measures are needed to increase the supply, demand and quality of recycled plastics.
There are, however, a few important considerations. New packaging will need to meet municipalities’ infrastructure for recyclability and composability, which varies from region to region across the country. This requires food and beverage companies to consider how the change in materials or design of the package will affect their product. Specifically:
• If new materials are used, they will need assurance of safety for food contact.
• Change in material should not impart taste and odor to the product or appreciably affect its shelf life.
• The redesigned package will need to withstand applicable thermal processing conditions and the rigors of handling, transportation and storage.
• Lastly, presentation — and ensuring consumer-friendly use and acceptance of the new package — is critical for its success.
Carol Zweep is Manager of Consulting and Technical Services
NSF Canada. Contact her at firstname.lastname@example.org.
Plastic packaging GAME CHANGERS & BARRIER BREAKERS
In recent years, several solutions have been introduced to address the challenges presented by plastic waste.
Edible and biodegradable packaging: Ooho is made from brown seaweed, a renewable natural resource. It is safe for consumption and can replace plastic single-use beverage bottles, cups, and condiment sachets.
Elimination of plastic packaging: Apeel is a plant-derived coating for fruit and vegetables that slows water loss and oxidation. It extends shelflife without the need for plastic packaging, such as shrink-wrap on fruit and vegetables.
Reusable Takeout Container: Friendlier has designed a system with the circular economy in mind. After use, its entire takeout container can be returned to Friendlier collection bins, where the package is picked up, washed, sanitized and redistributed to create a closed loop system. At the end of its life, the polypropylene container can be recycled.
Recyclable Meat Tray: Klockner Pentaplast has developed a unique design for the bottom of the meat tray. This tray traps and retains liquid and keeps it away from the meat at any angle. This feature eliminates the use of an absorbent pad and improves the quality of the product while also providing clear product visibility. The PET (polyethylene terephthalate) tray has recycled content and is recyclable.
Compostable Packaging: Given the challenging nature of recycling single-use plasticbased coffee pods, composting is a preferred
CANADIAN FOOD BUSINESS VOLUME 37, ISSUE 2 • 2022 36
alternative and one recently explored by Nabob and Maxwell House brands, which developed a zero-waste solution for the entire package. All of the pod components, including the lids, rings and filter, along with the used coffee grounds, are compostable. The pods successfully break down real world-tested in a variety of composting conditions and processes. Additionally, the bag that holds the coffee pods is also compostable and the carton is recyclable.
Increasing recycling rate:
A relatively new innovation on the scene is digital watermarking technology, which enables a much higher sorting and recycling capture rate for packaging and helps reduce waste. Digimarc technology works by modifying the pixels of the packaging to carry an imperceptible code that is undetectable to the consumer but can be picked up by cameras, such as one installed on a sorting line at a waste management facility. Digimarc has been used for Procter & Gamble’s Lenor Fabric Softener but has applications for food packaging as well.
Processing of Recycled Plastic:
Ice River is a bottled water company that uses post-consumer PET from bottles and thermoform clamshell packaging to make new food
containers and water bottles. The material is collected from municipal recycling facilities across Canada and the Northern U.S. Post-consumer material is often contaminated and requires rigorous purification to make food grade recycled plastic.
Companies are diverting hard-torecycle plastics into other non-food products. For example, the recycling service company Firstar Fiber Corporation (Firstar) is working to transform hard-to-recycle plastic waste into value-added products, such as plastic lumber for use in decking and furniture. Also, CRDC Global announced scale solutions for converting hard-to-recycle plastic waste into a concrete additive for building and construction applications.
Innovative packaging solutions will require development activities, pilot evaluations and scale-up exercises at each step within the supply chain and at the end of life. Expanding citizen awareness, increasing collection and diversion of plastic waste are also key elements of the circular economy. The Zero-Plastic Waste action plan is ambitious. Collaborative efforts and support from government, industry and citizens are critical to achieving a circular economy that keeps plastic out of the environment.
C M Y CM MY CY CMY K
New report finds hidden treasure in waste produce
By Nathalie Dreifelds
In Leamington, Ont., the greenhouse capital of North America, approximately 6.8 million kg pounds of edible tomatoes and 5.4 million kg of cucumber grade-outs are discarded annually.
It’s just one example in a new report by the Lincoln, Ont.-based Vineland Research and Innovation Centre that suggests fruits and vegetables are missing out on the valueadd of waste produce, not the least of which is the impact on the environment.
“The greenhouse tomato and cucumber sector, along with fruit and vegetable processing, have ample volumes of underutilized streams,” says the study’s lead, Alexandra Grygorczyk, Vineland’s Research Scientist, Sensory & Consumer Services. “These have potential, when managed differently, to help organizations reach environmental sustainability targets and generate better returns from valueadded products.”
Approximately one-third of the food produced in the world for human consumption is wasted. Among these, fruits and vegetables have the highest wastage rates with 40% to 50% of products produced being thrown away, according to the United Nations’ Food and Agricultural Organization.
In Canada, approximately 74% of produce is wasted
before it reaches consumers, a total of nearly six million metric tonnes of fruit and vegetable waste. Two-thirds of this waste is categorized as avoidable waste, the result of operational or market factors such as a breakdown in sellerbuyer relationships, an oversupply, or excess food that wasn’t donated due to a vendor agreement.
One-third of that total, considered unavoidable because of current processing and grading standards, generates expenses for producers and processors who must dispose of it in landfills, ship it to neighbouring livestock farms or allow it to decompose on unused plots of land.
The report, titled Underutilized byproduct streams from the Canadian horticulture value chain, suggests that these massive amounts of wasted yet potentially edible products could be reduced or eliminated by changing management practices to retain value in the byproducts streams and transform the waste products into new products or divert them to industries better suited to transforming them.
Besides the economic factor, changing local regulations and an increasing focus on environmental sustainability are driving interest in finding new solutions to managing byproduct streams.
To tackle this issue and help increase the industry’s
CANADIAN FOOD BUSINESS VOLUME 37, ISSUE 2 • 2022 38
environmental sustainability, Vineland examined underutilized waste streams for the top seven Canadian produce crops (potatoes, apples, field tomatoes, greenhouse tomatoes, greenhouse cucumbers, onions and carrots) and identified the range of opportunities for managing these.
“We interviewed over 40 companies across the horticulture and food value chain to identify underutilized byproducts, better understand trends driving product formulation, and find gaps in the ingredient market that could be filled through the transformation of waste,” says Grygorczyk. “We found not all sectors have similar levels of waste ,although those producing the most waste are actively looking for the right solutions.”
Fresh market field crops including apples, carrots, potatoes, onions and tomatoes result in limited waste as nearly all edible seconds are sold for further processing.
Although the waste is limited, many growers are interested in more profitable options for their byproducts. For example, a lot of apple growers sell their lowest grades of apples to processing for break-even prices just to not lose money. But if they could divert those apples elsewhere for better returns— just as some already are by producing apple chips—they would be happy to do that.
However, since no processing market exists for greenhouse tomatoes and cucumbers, edible products with any amount of discoloration or other cosmetic defect are either landfilled or allowed to decompose near the greenhouse.
The processing sector generates a substantial volume of unavoidable waste when potatoes, apples, field tomatoes, carrots, and onions are processed into products that are chopped, sliced, frozen, fried, juiced or pureed.
The study also offers solutions to managing diversion. Established popular solutions involve the direct use of raw material for boosting soil nutrients, or shipping to livestock farms or biodigesters. These produce minimal or negative returns but are simple to execute, carry minimal risk and
do not require a great deal of capital investment. For those producers and processors seeking higher returns and willing to invest in processing, there are many other options to consider.
Fruit and vegetable streams are rich in nutritional and functional compounds that may be of interest to the food industry (e.g., pectin/starch, antioxidants, colours, enzymes) or agricultural industry (e.g., organic matter and minerals). The byproduct streams have the potential to be converted by various means including drying and milling to produce powders, dehydration to produce concentrates, extrusion to produce dried pellets or snacks, and extraction of valuable components, among others.
Clean label, which is the reformulation of food products to have fewer and more easily recognizable ingredients with fewer allergens or additives, is a major trend driving current food product reformulations. Fruit and vegetable-derived food ingredients have the potential to bring many different functionalities to products (e.g., shelf-life extension, natural colour, thickening, sweetening) while fitting within clean label constraints.
Alternatively, these streams may be converted for use in the cosmetics industry (e.g., skin creams), materials engineering (e.g., car tires, packaging films) and for agricultural applications (e.g., compost, substrate mixes, biofertilizer).
Fruit and vegetable byproduct streams have a great deal of potential to not only be managed differently to help organizations reach environmental sustainability targets, but also to produce value-added products that bring better returns to Canadian producers and processors.
The report, co-written by Grygorczyk and Amy Blake, can be downloaded here. Their research was supported by the Canadian Agricultural Strategic Priorities Program (Agriculture and Agri-Food Canada), Martin’s Family Fruit Farms and the Canadian Agricultural Partnership (the Partnership), a five-year initiative.
More than 15 million pounds of greenhouse tomatoes with minor cosmetic defects are landfilled annually
PROOF THAT DIET SODA ACTUALLY LEADS TO REDUCED CALORIE COUNTS IN A MEAL
Some consumers go to fast food outlets and order high-calorie meals like cheeseburgers and fries before choosing a diet soda to go with their meal. But are they really saving on calories? Or do those low-cal drinks encourage them to buy more fattening foods?
Some studies suggest that people may experience the “Big Mac and Diet Coke effect” where they justify ordering bigger burgers, larger fries, or a dessert because they consider some part of their meal healthier. Meanwhile, others have shown that ordering diet pop can encourage better habits, or at least reduce the overall caloric load.
According to a new study from the University of British Columbia’s Sauder School of Business, on average those diet drinks really do result in a significantly lower calorie count.
For the study titled “Do Consumers Order More Calories in a Meal with a Diet or Regular Soft Drink? An Empirical Investigation Using LargeScale Field Data,” researchers used data from Canada-wide consumer surveys conducted between 2000 and 2007 that included peoples’ “food away from home” meal consumption.
Because McDonald’s makes its
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nutritional information (including calorie counts) widely available, and because its offerings are consistent across the country, the team homed in on the consumer data involving McDonald’s meals specifically, then merged it with the fast food chain’s calorie information.
In total, they examined roughly 9,000 McDonald’s meals involving more than 2,000 people. Of those, roughly 64% of those surveyed ordered regular soft drinks, 20% ordered diet pop, and the remaining 16% went back and forth between the two. The researchers also focused on more calorie-rich meals (lunches and dinners) and on larger drinks (medium or large) because they would more clearly demonstrate the caloric gulf between those who ordered diet and those who chose sugary sodas. Because the data spanned seven years, they could also see patterns in buying behaviours.
“For a particular person, we might see five, six, seven occasions, and we could see what their individual patterns were,” says UBC Sauder Professor Emeritus Charles Weinberg, who co-authored the study with Amazon Inc. Research Scientist Sina Ghotbi and University of Guelph Associate Professor Tirtha Dhar. “So, we could control for individual effects.”
After crunching the numbers, the researchers found no evidence that consumers use diet drinks to justify other indulgences. In fact, after controlling for drink size and consumer demographics, they found that people who bought diet drinks had significantly lower overall calorie counts: 298 fewer calories for those who ordered a large diet drink — or 18 fewer tsp. of sugar — and 156 fewer calories for those ordering a medium (about 10 tsp.). What’s more, the total food calories they ordered did not go up when they ordered a diet drink.
The research marks the first field study to examine whether “Big Mac and Diet Coke” behaviour leads to greater calorie
consumption. “We’re looking at the actual behaviour, not why people engage in it,” says Weinberg. “So, we’re focused on what people actually do.”
At first blush, the question might seem lighthearted, but in reality it’s serious business, especially given that the obesity crisis in the United States has worsened dramatically — from 12% of U.S. adults in 1990-1991 to 42.4% in 2017-2018 — and the consumption of sugary, high-calorie sodas is considered to be a major factor. What’s more, 85 million Americans — or 37% of the population — dine at a fast food restaurant per day.
Weinberg emphasizes that from a health perspective, drinking water with a meal is still the healthiest option, but for consumers who are set on soda, diet pop might represent a healthier alternative than sugary drinks.
As a result, Weinberg says health authorities may want to rethink their advice on soft drinks. It’s not that they should necessarily advise people to drink diet sodas, but they may not want to caution against it — and making diet soft drinks more available could form part of an effective harm-reduction strategy.
“People like going to fast food restaurants, and in the obesity crisis one of the main culprits is people having added sugars in their meals,” says Weinberg. “If you’re a person who likes to have carbonated soft drinks and you’re not willing to switch to water, this seems to be an intermediate step you can take.”
In the meantime, he says consumers should understand the impact of their decisions.
“People make choices. There are going to be people who say, ‘I prefer the taste of regular soda and I want to enjoy it,’” says Weinberg. “It’s not like you have to give up every pleasure. But you should know in terms of calories what that pleasure is, and what it’s costing you, then make the choice.”
Health authorities may want to rethink their advice on soft drinks. It’s not that they should necessarily advise people to drink diet sodas, but they may not want to caution against it
FOOD DETECTION IN THE PALM OF YOUR HAND
Genomics industry expert Precision Biomonitoring is developing a rapid, highly sensitive and mobile testing device aimed at improving the detection of foodborne pathogenic bacteria like listeria and salmonella, particularly in leafy greens.
With a grant from the Canadian Food Inspection Agency (CFIA) through the Innovative Solutions Canada Program, Project Bistro aims to offer technology that is even more sensitive than what is currently on the market to food producers, farming and agriculture operations, distribution centres and large-scale grocers.
"As foodborne illnesses rise, it will be important that Canada is equipped with the innovative tools and resources that will enable bacteria detection before products reach stores and consumers," says Precision Biomonitoring CEO Mario Thomas. "We are looking forward to being able to potentially
improve foodborne illness detection that will ensure the health and safety of Canadians."
Project Bistro is an ultra-portable, low-cost platform that uses onsite sample preparation tools to extract nucleic acids from various contaminated sample types. Using highly sensitive amplification coupled with digital lateral flow devices, the device will be able to deliver reliable detection results in less than two hours. Project Bistro is an adaptation of Precision Biomonitoring’s TripleLock device, which was approved by Health Canada for rapid testing of COVID-19.
"If successful, a portable tool like this could help reduce the risk in the food supply by detecting foodborne pathogens throughout the farm-to-fork continuum," says Tammy Switucha, Chief Food Safety Officer for Canada and Executive Director, Food Safety and Consumer Protection Directorate, CFIA.
A TASTE OF...
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Award-winning plate reader
3M Food Safety was named a 2022 Edison Awards gold winner in the Commercial Technology category for its 3M Petrifilm Plate Reader Advanced. The device is an enhancement of previous technology that allows food safety professionals to enumerate micro-organisms quickly and accurately. The equipment includes a small peripheral device containing a five-megapixel camera, versatile bar code reader and fixed artificial intelligence that expedites result interpretation in six seconds or less. www.3m.com
GloCyte automated cerebrospinal fluid cell counter
GloCyte is an automated cell counter that delivers accurate and precise total nucleated cell (TNC) and red blood cell (RBC) results at clinically relevant low levels, reducing valuable time spent counting those more difficult specimens. Using a novel combination of fluorescence technology, highly specific reagents and an intelligent counting algorithm, GloCyte can handle all of the cerebrospinal fluid specimens (CSF) that enter your laboratory. www.aicompanies.com
Midea offers a heavy-duty, large commercial microwave with a userfriendly touchpad that includes braille navigation. The 2100W Push Button Heavy Duty Commercial Microwave can be programmed, features five power levels and three cooking stages, and can be stacked with same-style ovens. The large-capacity 1.2 cubic ft. (34 L) cavity accommodates a 14-in. (356 mm) platter or several tall pans. www.midea.com
Modular filling machine evolves with business needs
Synerlink recently launched Versatech, an innovative filling machine for food and dairy processors with a modular design that evolves to meet customer business needs, outlasting the standard 20- to 30-year life cycle. Starting with a compact 2.5 m. by 4 m. frame, it can be quickly and inexpensively reconfigured, and it is expandable with standard-increment modules that come in lengths of 440, 880 or 1,320 mm. A centralized cabling network offers plugand-play functionality. www.synerlink.com
Grabbing customers’ attention with new eco-friendly plastic packaging
Keeping food fresh in a sustainable way
Calgary-based Hempalta’s Hemp-Fresco Organic Food Pads are a natural produce saver shown to extend the life of fresh fruits and vegetables. Made from 100% renewable and eco-friendly Canadian hemp fiber, the chemical-free pads slow spoilage and decrease food waste by absorbing liquids, gases and moisture to avoid premature spoiling. Effective odor control extends freshness, keeping food smelling, tasting and looking fresh for days longer. They’re also safe to compost after use. www.hempalta.com
Printex Transparent Packaging has introduced its new Eco-PET 100 series clear folding boxes, made from 100% recycled post-consumer recycled polyethylene terephthalate (PET). Up until now, North American PET sheet and film producers have only offered up to 25% and 50% post-consumer recycled content plastic for box grade packaging, making it difficult to find a clear and untinted PET in 100% PCR. www.ptpackaging.com
CFI CELEBRATES 25 YEARS with a forward-looking survey of youth
Tomark its 25th anniversary, the Canada Foundation for Innovation (CFI) launched a survey last year to ask 18- to 24-year-olds about their attitudes toward science. Among the findings released last fall, the survey revealed that many of the participants felt science was too intellectually demanding.
“This significant and meaningful survey rings notes of hope and caution as we look to the future and to the next generation,” said Roseann O’Reilly Runte, President and CEO, Canada Foundation for Innovation.
“Their impressive overall support for science and their concern for the environment, for example, are promising. Their need for the basic tools to discern and understand truth and for the mathematical skills required to do so require immediate attention. This survey is a call for action and an indication of the path to follow.”
When it comes to forming attitudes and opinions on issues ranging from COVID-19 vaccines to environmental sustainability, the majority of young adults in Canada use scientific information to guide their actions. Some cohorts, however, either question or ignore science, which affects their attitudes about those science-based issues.
The survey, developed together with Acfas and Ipsos, revealed that science matters for young adult Canadians. 70% of respondents agreed that science can be relied upon because it is based on facts and not opinion, and 77% think science is a good field for people in their age group to pursue as a career.
Ipsos surveyed 1,500 young people across the country on questions around the sources of information they access and which sources have the greatest influence on their attitudes toward four science-related issues: COVID-19 vaccine safety, environmental sustainability, climate change and the importance of science, technology, engineering and math (STEM) education for the future.
Overall, the survey made clear that young adults are navigating an extremely complex and diverse information
ecosystem where they are inevitably exposed to fake news and anti-science information. This presents an increasingly difficult challenge for science communicators and educators: how to effectively reach those who do not have the tools or the interest to fully understand science-related issues and fight misinformation. Policy-makers, ministries of education and economic development organizations also have a role to play in taking up this challenge in order to build a stronger scienceliterate society.
The survey also revealed that this age group holds opinions consistent with the scientific evidence. About 68% agreed COVID-19 vaccines approved for use in Canada are safe; 63% agreed that single-use plastics should be banned; 55% agreed that curbing the use of fossil fuels will help reduce the impacts of climate change; and 57% agreed it is critical for Canadian politicians and governments to rely on science when making policy decisions for the benefits of Canadians on issues including health, well-being and the economy.
As part of the research, Canadian youth were divided into five segments that represent general mindsets that span a spectrum of attitudes towards science, from pro-science to science-hesitant.
The survey revealed some areas of concern including a shortfall in mathematics, skepticism and the ability to determine real news from fake news; for instance, 84% believe they are not good in math. While their opinions generally align with science, they are more likely to say science is too intellectually demanding and that they don’t feel equipped to distinguish valid science from pseudoscience. Among those who question science, the majority use intuition to make personal decisions related to health and don’t believe scientific proof equals truth. Social media influencers holding anti-science views are prevalent and pervasive, with 73% of respondents reporting they follow at least one social media influencer that has expressed anti-science views.
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