Powerful new processor helps unlock the secrets of an iron-eating bacteria known as Desulfovibrio vulgaris

Oct 6 2004

Gerrit Voordouw, PhD, a microbiologist at the University of Calgary, has spent the past 20 years trying to unlock the secrets of an iron-eating bacteria known as Desulfovibrio vulgaris.

This potent microbe, found in oil and gas reservoirs, can eat its way through a pipeline in just a few months. “We wanted to understand why D. vulgaris is so corrosive to pipelines and oilfield equipment,” says Voordouw. “ And we knew that the key was to sequence its 3,394 genes.”

That’s when he approached Christoph Sensen, PhD, about using the Faculty of Medicine’s immensely powerful computer processor, Paracel Genematcher 2.

“We asked Dr. Sensen and his colleagues to design the gene chip for us on a Wednesday, and by Thursday, it was done,” says Voordouw. “That kind of genetic probe design would normally take months to accomplish. I am thrilled to have such a powerful research tool at my fingertips.”

“When scientists are doing genetic research, the volume of information is so large, it quickly becomes unmanageable,” says Sensen, director, Sun Center of Excellence for Visual Genomics at U of C’s Faculty of Medicine. “That’s why we installed this highly specialized processor – a kind of über-calculator for genetic scientists.”

The Genematcher 2 has 28,800 specialized processors that search multiple databases, including all of the public genomes in GenBank. It is the first system of this magnitude in the world available to research scientists via the Internet. Researchers input their genomic data into the processor, which takes their specific genetic strain and compares it against genomic databases world-wide.

• Genetic research tries to answer three fundamental questions:
  • where is a gene located within the entire blueprint?
  • which proteins are produced and what do they do?
  • how active is the gene?

“It’s as if you know all of the addresses and phone numbers for everyone in Calgary, and what you really need to know is, who the people are, and what they do for a living,” says Sensen. The Genematcher 2 generates a report telling scientists where the genes are and what they do. Sensen’s team then produces a gene chip that researchers use in follow-up experiments.

“I now have a detailed genetic blueprint of D. vulgaris. This map is guiding our new project - how to harness the bacteria’s natural ability to reduce toxic metals, such as uranium or chromium at abandoned mining sites,” says Voordouw.

Genomic researchers at the University of Calgary and across Canada are using Genematcher 2 to investigate viruses, cancer cell lines, funguses and the entire human genome.