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Novel experiment documents evolution of genome in near-real time

A team led by bioengineering researchers at UC San Diego report in the November issue of Nature Genetics rapid evolutionary changes in a bacterial genome, observed in near-real time over a few days. Scientists have previously published static "snapshots" of the genome sequences of more than 100 bacterial species, from the harmless to those that cause plague, but this new report shows how these genomes are moving targets.

"Paleontologists look at the fossil record to study how evolution of dinosaurs and other animals occurred over millions of years, but in the case of the E. coli bacterium, new technology has given us the ability to observe evolution as it is occurring over a matter of days," said Bernhard . Palsson, the senior author of the study and professor of bioengineering at UCSD. "The published genomic sequences of bacteria are like a fossil record and our experiments confirm that these genomes can change quickly as bacteria adapt to new conditions."

Because of past technical limitations, biologists have historically made inferences about rapid bacterial evolution by carefully observing changes in a handful of genes at a time or by monitoring the visible characteristics, or phenotypes, as the organisms adapt. Palsson's team used comparative genome sequencing technology developed by NimbleGen Systems Inc., a Madison, WI-based biotech firm, to identify changes that occurred during the experiment in the bacterium's complete set of genes.

In a paper scheduled for online publication Nov. 5 on Nature Genetics's Website, the researchers report that they grew E. coli in an environment that favored the emergence of mutants: the organism was fed a poorly metabolized carbon and energy source called glycerol. The researchers removed samples of cells from the culture and sequenced their entire genomes as a way to find mutations that enabled faster growth.

After six days of growth, mutations appeared in the gene for an enzyme that initiates the proc
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Contact: Rex Graham
ragraham@ucsd.edu
858-822-3075
University of California - San Diego
5-Nov-2006


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