It's All in the Genes

By Andrew Vowles

Prof. David Evans uses the genomics and microarray facility to study how poxviruses infect host cells.

Photo by Martin Schwalbe

For a look at U of G's role in the growing field of genomics research, take a peek at the rather unprepossessing equipment in a laboratory just down the hall from the Axelrod Building office of Prof. David Evans, chair of the Department of Molecular Biology and Genetics.

Unprepossessing, yes, but it packs a wallop when it comes to offering state-of-the-art technology for campus researchers investigating the genetic makeup of everything from the bane of the Canadian forestry industry to boar taint in pigs.

Last fall saw the delivery of the last of four main pieces of equipment, worth a total of about $500,000, to the recently established genomics and microarray facility, which is located in two labs in Evans's department.

The instruments sequence DNA, process DNA samples, prepare DNA slides and scan microarrays to analyse patterns of gene expression. Operated by technicians Margaret Howes and Jason Ho, the equipment serves the needs of customers from four colleges - CBS, CPES, OVC and OAC - as well as researchers from the Food System Biotechnology Centre.

"It's becoming a very common discovery tool," says Evans, referring to slides or microarrays that let him and other researchers study patterns of gene expression. About 12 faculty members or groups are now using the facility's DNA array technology to study expression of thousands of genes in certain plants and animals, as well as in other organisms such as viruses and yeast. Among their goals: learning how genes control development, what goes wrong during disease, how pathogens infect their hosts and how to develop useful new drugs.

Those goals are fuelling interest in genomics research at labs in Guelph and across Canada, says Evans. He and five other U of G researchers were among the Canadian scientists who received a total of more than $300 million this month for national genome research projects from Genome Canada and other organizations.

Evans studies how poxviruses infect host cells, including what virus genes are turned on and off during infection and how that process is regulated.

"I'm interested in seeing whether chip technology can identify the genes expressed throughout different stages in the process of virus infections," he says.

He is also a participant in a Genome Canada-funded project on spruce budworm with Prof. Peter Krell, Microbiology, and Basil Arif of the Canadian Forest Service. This project will use gene sequencing to study genes involved in the development of the spruce budworm, a major pest in the forest industry.

Having access to facilities in the Axelrod Building makes this work cheaper and easier than sending samples to other Ontario research institutions, Krell says.

Botany professor Barbara Mable uses the microarray facility to study molecular changes in yeast cells, such as those used in the fermentation industry.

She's especially interested in how gene expression in yeast changes when an entire genome is duplicated, a process called polyploidization.

Mable also expects to use the equipment to study genome duplication in plants.

"Polyploidy is very common in plants, but may have significant effects on the breeding system, ecology and demography of plants in which it arises," she says. "The microarray facility will enable us to compare changes in gene expression across a vast number of genes, something that wasn't possible using previous methods."

In the Department of Animal and Poultry Science, Prof. Jim Squires and graduate student Jennifer Stewart use the scanner to examine slides spotted with thousands of different samples of DNA, to identify pig genes that cause boar taint, a problem in meat quality from uncastrated males.

Squires uses arrays containing up to 1,700 human genes obtained from the Ontario Cancer Institute.

"No porcine chips are available," he explains, adding that genetic and biochemical similarities between humans and pigs make this kind of cross-hybridization between human and pig DNA sequences possible. "We're using humans as a model for pigs, which is kind of an interesting twist. You can learn a lot by looking at what's known in one species and seeing whether it applies to others."

Having identified several key genes using microarrays and other methods, he plans to investigate which genes are most important in boar taint and identify genetic markers for animals without the problem. He says the pork industry is interested in his work for breeding programs for pigs that would grow leaner without the need for castration. Although castration prevents boar taint, it also reduces lean meat yield and feed efficiency.

Identifying promising breeding lines through genomics would allow producers to sidestep these problems, he says. "You're improving productivity, but also improving animal welfare at the same time. It's kind of rare."

Squires has also worked on microarrays with OVC faculty in the Department of Pathobiology and the Department of Biomedical Sciences.

"I've been hoping that, as part of this process, we would put together a users' group for microarray technology," he says. "If you come up with a new way of improving sensitivity or reliability of methods for data handling, then it could be shared around the group."

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