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RIT scientists decode 3 bacterial strains common to grapevines and sugarcane
Date:12/17/2012

Hudson and Savka collaborated with alumnus and lead author on all three manuscripts Han Ming Gan '08 (biotechnology), Sean McGroty '11 (bioinformatics) and Larry Buckley, professor in RIT's Thomas H. Gosnell School of Life Sciences. Ming's collaborators include professors Teong Han Chew from Universiti Teknologi Malaysia and Kok Gan Chan from University of Malaya.

Gan, Savka's former student, is a research scientist at ScienceVision SB in Selangor, Malaysia, with access to the high-through put sequencing and data management technology necessary to sequence and annotate nucleotides. Each bacterium they have studied consists of approximately 5 million to 6 million nucleotides.

The sequencing process breaks an organism down into its basic genetic component and lays the parts side-by-side for scientists to interpret and make useful.

"It's like having a book with no spaces in between the words and you have to find where the words begin and end," says Savka, professor of biological sciences at RIT. "That's what it's like to annotate a genome."

Advancements in sequencing technology helps Gan, Savka and Hudson connect the dots to understand host-bacteria interactions.

"We assembled millions of short DNA sequences into long sequences and made biological sense out of them," Gan says. "Having the near complete genetic information from a bacteria will bring us to a new level of research."

"We can tease out information based on the genome of the organism that live inside the plant," Hudson adds. "The question is, why are these bacteria living in the plants? Are they destroying the plants or are they providing a benefit? Are they providing nutrients that are helping the plant grow, like plant hormones, phosphorous or nitrogen? Is it a mutualistic relationship where the plant and bacteria are both benefiting?"

To answer these questions, the team scoured the nucleotides for proteinschains of amino acids that replic
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Contact: Susan Gawlowicz
smguns@rit.edu
585-475-5061
Rochester Institute of Technology
Source:Eurekalert

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