Genomics of the spruce budworm and its viral pathogens

July 20, 2001

Canada is a custodian of approximately 10% of the world’s total forests. Occupying nearly 35% of our land mass, they are an enormous renewable resource of importance for recreation, the environment and the economy. Forests contribute approximately $30 billion dollars annually to Canada; about 10% of all the jobs in Canada are forestry-related. Basil Arif of the Great Lakes Forestry Centre, and Arthur Retnakaran of the Government of Canada used genomics to study one of the most devastating forest-insect pests, the spruce budworm. Their project developed a large body of knowledge about the genomics of spruce budworm and many of its naturally occurring viruses in addition to environmentally friendly methods that use insect viruses to control spruce budworm, and a way to produce large amounts of viral proteins that can be used for further development by the pharmaceutical industry, and veterinary and agricultural agencies.

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Mapping the genes influencing Cystic Fibrosis

July 20, 2001

Due to the pioneering work in the 1980s of researchers at the Hospital for Sick Children, it is known that all Cystic Fibrosis patients are defective in a gene called CFTR, which instructs the cell to make a protein that moves ordinary chlorine ions into and out of cells. Yet, even in patients with the identical genetic change in CFTR, the severity of Cystic Fibrosis can be very different – pointing to other genes interacting with CFTR to alter the course of the disease. Peter Durie of The Hospital for Sick Children and Lap¬Chee Tsui of the University of Hong Kong used the most up-to-date genomic methods to find these other genes. This project created the world’s largest repository of family-based cell lines for clinical-genetic studies, and further identified genes that potentially affect the severity of Cystic Fibrosis.

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Proteomics and functional genomics

July 20, 2001

Brenda Andrews and Cheryl Arrowsmith of the University of Toronto used functional and chemical genomic approaches to establish a comprehensive description of the biology of the budding yeast Saccharomyces cerevisiae. They used a variety of cutting-edge functional genomics approaches to define gene function and to probe the mechanistic basis for drug action and the characterization of novel, unknown and microbial proteins. They then identified the biochemical function of these proteins and made hypotheses about their cellular role in microbial cells. This new information has greatly extended fundamental knowledge about microbial biology and created an experimental basis for the development of novel anti-microbial drugs and biotechnological processes by Canadian biotech industry.

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Genetic determinants of human health and disease

July 20, 2001

Katherine Siminovitch of The Lunenfeld-Tanenbaum Research Institute explored gene variants causing and/or modulating a number of common multigenic disorders, including Alzheimer’s, inflammatory bowel disease, cancer (breast, endometrial, prostate, ovarian, melanoma) and osteoporosis. In addition to knowledge relevant to the diagnosis and treatment of specific diseases, this program has provided new information and methods to improve technical platforms for genotyping, gene expression profiling and the computational management and statistical analyses of clinical and genetic datasets. Such tools are key to the exploitation of the human genome sequence for the purposes of disease gene discovery and, ultimately, for translation of genomic information to clinical and therapeutic applications.

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Functional genomic analysis of soil micro-organisms

July 20, 2001

One of the most important groups of bacteria in the world is also one of the least known by many people—microbes that cause the formation of nodules on the roots of many plants. Inside these nodules specialized bacteria convert atmospheric nitrogen into a chemically useful form, which is essential for plant growth and thus ultimately for life on Earth. Using complex genetic methods, Turlough Finan and Brian Golding of McMaster University created a body of knowledge about S. meliloti – a bacterium which fixes nitrogen in the roots of plants, an essential process for plant growth- by using genomic methods to study how its genes direct nitrogen fixation and other important biochemical reactions. This deeper understanding of S. meliloti growth will lead to better and more environmentally friendly methods of nitrogen fixation for the food and agricultural industries in Canada and the world.

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Functional genomics of Type 1 Diabetes

July 20, 2001

Type 1 Diabetes (T1D) is a complex, autoimmune-mediated disease caused by multiple genetic risk factors and currently unknown environmental factors. Canada has the third highest rate of T1D in the world, costing ~$13 billion annually in T1D-related health care, disability, lost work, and premature deaths. Jayne Danska, of SickKids, led a project to identify key genes conferring T1D risk to humans, and gain insight into the biological pathways that confer early stages in disease progression. Progress made under this project was essential to the formation of an expanded $15M, 4 year T1D research effort that recently began funding with support from Genome Canada/Ontario Genomics Institute, the National Institutes of Health, Celera Diagnostics, Inc., and several European funding agencies.

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Functional genomics of Arabidopsis

July 20, 2001

In the current competitive world, agricultural and forestry industries must rely on genetic improvements to important kinds of plants to maintain an international lead. Arabidopsis is an organism which has been studied, genetically, and has many similarities to important crops such as rice, wheat, corn and canola. John Coleman, Nick Provart, and Peter McCourt of the University of Toronto created a worldwide resource for plant genomic research, setting up some of the basic tools that will enable genetic research on Arabidopsis. This will lead to a deep understanding of many aspects of plant growth that will be important for genetic improvements such as salt- and drought-tolerance, pest resistance, increased productivity, and enhanced protein content. They have made these three experimental tools available to plant researchers all over the world, speeding up research and putting Canada on the map for plant researchers everywhere to appreciate.

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Fiber Optic Nucleic Acid (FONA) biosensor based gene profiling

July 20, 2001

DNA and its close relative, RNA, carry the code of life in all of nature’s creatures, and their study enables scientists to learn a great deal about human genetic diseases, and disease-causing viruses and micro-organisms. For all of these studies, scientists need to measure very accurately the amount of nucleic acids in a sample, however, previous methods were defective, with major limitations. The goal of Alex MacKenzie, Paul Piunno and Ulrich Krull’s project was to develop a new kind of nucleic acid sensor (a “biosensor”) that is reusable, sturdy, rapid, accurate, selective, sensitive and cheap. The value of this new instrument was demonstrated by evaluating DNA associated with Spinal Muscular Atrophy, a very severe childhood genetic condition.

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Development and applications of functional genomics technologies

July 20, 2001

The Human Genome Project documents the complete DNA sequence, not only of humans, but of over 300 other organisms, with more to come. The next step is to turn this wealth of information into useful knowledge so that it can be applied to medical and biological advances. This kind of research is called “functional genomics” and it seeks to learn how genetic information coded in DNA directs all the workings of a living organism.
Jim Woodgett, of Mount Sinai Hospital, developed new techniques and measuring instruments for functional genomics, and applied them to basic research and clinical studies. The work developed better array design through the use of computational algorithms, more efficient storage and recovery of data from DNA microarray experiments, and better ways to compare our data with other researchers in the world. Additionally, one of the team’s robot designs is now sold commercially.

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Bridging the emerging genomics divide

July 20, 2001

Peter Singer and Abdallah Daar, of the University of Toronto examined the ethical, environmental, legal and social implications of advances in biotechnology and genomics. They studied ethical questions faced by biotechnology companies and how they deal with them with the aim of encouraging companies to adopt suitable ethical policies. They also led in writing a proposal for the Canadian government to guide its strategy for development of genomics and biotechnology, and were a major contributor to the Genomics and Nanotechnology Working Group of the United Nations Science and Technology Task Force; this report was distributed all over the world.

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