MARCH 2018 NEWSLETTER
MARCH 2018 NEWSLETTER
When I was a kid, I wanted to go out to the seas in ships. I grew up in a small town about the same size as Gloucester, only landlocked in the Ural Mountains which divided Europe and Asia. The largest body of water was a small river that a chicken could safely cross. I read books about distant ports, great adventures, and dangerous expeditions, which led me to study sails and navigation, geography, and biology.
One day, I took a train to Novosibirsk University, one of the most prominent centers of learning and research of modern Biology. Alas, my new college was even farther from any sea. In fact, almost as far as you can get: nearing the center of the largest landmass on this planet -- Asia.
After graduation, I started a research career and went to visit distant lands. Each time, I took a plane or drove a car. I lost my connection to the ocean, but the ocean seemed to have a different idea. It started chasing me. Time after time, when I looked for a new job, I found it near the ocean. When I moved to higher ground in Colorado, the ocean came to me in a test tube. One of the projects I worked on was dealing with the molecular physiology of Antarctic seals adapting to deep diving. It had surprising parallels to altitude hypoxia, for which the Rocky Mountains are famous.
This work intrigued me and I began looking into genomes of marine critters more often. Now, at GMGI, this is all that I do. As a computational biologist, I assemble and interpret genomes from small pieces of DNA sequences. Each genome tells a long fascinating story of its origin, relatives, ages of struggle, adaptations, and wins over perils of disease and extinction. Our best sequencing machines can read one DNA word or phrase at a time. Sometimes the machine reads one DNA word a thousand times over and misses the next sentence completely. My job is to piece the stories together by matching words and letters in DNA code.
Have you noticed that a huge, old lobster tastes as good as small one? The reason might be that the lobster doesn’t show any sign of senescence on the cellular level. They live over a hundred years and die from infections (if not in the kitchen) but never get senile or have cancer. Perhaps we could pick up a trick or two if we knew how to read the story.
GMGI is the place where we learn to ask the right questions and comprehend the answers that the ocean gives us. We don’t go out to the sea in ships -- at least not very often yet. However, we are at the water’s edge with the tools to harvest information from beneath the waves, just like the generations before us.
Today, we bring home knowledge of marine life, and it is that knowledge which moves the economy much like cod, clams, and lobsters did before. But we still tell tall tales about sea monsters just like old salts. If you ask.
Director of Bioinformatics,
Andrey Ptitsyn, PhD
Andrey’s original home, in the Ural Mountains of Russia
Novosibirsk University in Novosibirsk, Russia
Assembling the pieces of a genome
A selfie with GMGI’s Auxiliary Server for NGS data and gargantuan monitor
417 Main Street
Gloucester, MA 01930
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