A genetic sleight-of-wing
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Ecologists have come to rely on a tiny fly called the midge as an environmental sentinel--an entomological canary-in-a-coal-mine for rivers. They have learned that a variety of midge species thrive in healthy streams, whereas in polluted water, like that near a lead mine, midge species can dwindle to nothing. So by skimming the skins that pupating midges shed as they enter adulthood, ecologists can attain a cheap snapshot of a stream's living conditions.
Raw numbers, though, reveal nothing about changes in progress that portend environmental peril. What if stream life is on its way downhill, but the effects of a pollutant cannot yet be seen in the destruction of a species? What if you could trade that snapshot for a movie--catch stream degradation in the act and take corrective action before it is too late for the bio-indicator organism and other creatures living in the stream?
Charles Brandt, staff scientist and manager of Pacific Northwest National Laboratory's ecology group, wondered if he could produce this movie cheaply, with off-the-shelf technology. Knowing that cells under environmental stress will express proteins differently from healthy cells, Brandt supposed pollutants could be quickly identified by using the midge genome to scan for cell damage. One hitch: There is no midge genome map, and nobody was about to commission one.
Undaunted, Brandt cleverly substituted that of a distant relative: the thoroughly mapped fruit fly Drosophila. To test his idea, he assembled a team that included PNNL's Jack Small, Amoret Bunn and Matt Bleich as well as the Environmental Protection Agency's Ann Miracle, who exposed midges to various chemicals and extracted their RNA.
The researchers found that a chip containing the midge-cousin's genetic material will bind to protein-precursor RNA from ground-up midge larvae and yield a pattern specific to heavy metals, radionuclides, hormone analogues and pesticides to which the midges were exposed. "We also exposed midge larvae to strontium-90 so we could get RNA from a rad-exposed midge to test using the microarray," Brandt said.
At first, they needed 10 times the midge genetic material required to run the same test on a fruit fly. After tweaking the system, "we got the sensitivity to where we need only twice the amount," Brandt said. The researchers will continue refining the tests so that they can catalog the expression patterns that match all major classes of pollutants.