SITE VISIT: Munching on Strange Chemicals

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Science  02 Jun 2000:
Vol. 288, Issue 5471, pp. 1543
DOI: 10.1126/science.288.5471.1543c

Microbes that devour or otherwise help break down exotic chemicals are cleaning up the environment, spawning new technologies, and deepening our understanding of microbial life. While biodegradation and biocatalysis are young fields, much of what is known can be found in the University of Minnesota Biocatalysis/Biodegradation Database.

The site provides detailed explanations of 99 “pathways”—chains of reactions that break down various chemicals —as well as data on hundreds of individual reactions, compounds, enzymes, and microorganisms. The site focuses on the reactions that begin to break down compounds not commonly found in nature, for example, those involving naphthalene, the stuff of mothballs. For information on the more common metabolic pathways that complete the breakdown, the site links to databases such as the Kyoto Encyclopedia of Genes and Genomes. All data display their pedigrees, and a guided tour helps first-time visitors find their way around.

The site lacks only for style. Hyperlinked graphics accompany most pages of data; however, by default, reactions and pathways are rendered in old-fashioned diagrams made with text and keyboard symbols. “We made a conscious design decision to use text as much as possible,” says computational biologist and site co-director Lynda Ellis, “and to have the graphics a click away for those whose computers are fast enough to use them.”

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