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How now, inside the cow: Nearly 30,000 novel enzymes for biofuel production improvements
Date:1/27/2011

bial symbionts located in the foregut perform their magic. To better control the process, Hess and his colleagues at the University of Illinois worked with the fistulated cow model that, for scientific research purposes, allows direct access through a tube into the foregut, which can be considered as a fermentation chamber in which oxygen is absent. Instead of feeding the grasses directly to the cows, the switchgrass samples were placed in nylon bags and then inserted into the cow rumen, where they were left to be digested. After 72 hours, the bags were removed, and the DNAs from the microbes involved in digesting the material that were adherent to the switchgrass were isolated and then sequenced.

The amount of data generated for this study of rumen microbes, 270 billion letters of the DNA code, was enormous; about 100-fold greater than the number of letters in the entire human genome. Generating the data was not the most challenging part of this project, Hess noted. "The real challenge was to analyze the vast amount of data for which no reference genome was available and to identify and produce full-size functional enzymes based solely on information obtained from billions and billions of short snippets of DNA sequences," he said.

To analyze the information, the researchers developed a genome assembly strategy that could handle the vast amount of data while making sure to avoid misassemblies that would have led to chimeras artificial genes not present in the microbial community. "Imagine someone mixing hundreds of jigsaw puzzles with millions of pieces each into a big pile," said Sczyrba. "We tried to put as many of these back together, making as few mistakes as possible. It is not an easy problem. You need a good strategy and a lot of computational resources to solve this problem.

By employing different filters Sczyrba whittled down the number of the more than two million predicted genes to 27,755 candidate genes that encoded a spe
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Contact: David Gilbert
degilbert@lbl.gov
925-296-5643
DOE/Joint Genome Institute
Source:Eurekalert  

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How now, inside the cow: Nearly 30,000 novel enzymes for biofuel production improvements
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