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Researching Microarrays for Bioremediation, Team Unearths Bonus Discovery

NEW YORK, Feb. 6 - Three years ago, a group of researchers in Washington state developed a microarray that could detect and monitor microbes in environmental samples. Their goal, to make a chip that can be used in the field for  bioremediation projects, happened to lead them to another discovery: a cheap and no-fuss way to make low-density microarrays.

 

The team's initial plan was to adapt biochips to perform during real-time field observations of environmental microorganisms in bioremediation efforts. The technology interests the US Department of Energy. Keen on improving environmental decontamination projects, the DOE could use the chips to detect sulfate- or metal-reducing microbes and observe these bugs' activity in response to nutrients and contaminants.

 

But the technical challenges in adapting microarray technology to bioremediation projects are substantial, said microbiologist Darrell Chandler, technical group leader of the project at DOE's Pacific Northwest National Laboratory.

 

For one thing, getting contaminant-clogged sediment or soil samples into microarray-ready condition is no simple feat. Plus, the researchers wanted to develop a detector that doesn't rely on PCR, in order to get an accurate quantitative picture of the diversity and the activity of the microbial communities.

 

As a result, much of the team's research has focused on working out the kinks in sample preparation and figuring out how the best methods for nucleic-acid extraction and cleanup.

 

The team has already developed a chip that can be used in the lab to analyze  samples that the DOE is interested in.  "We're coming along pretty well," said Chandler. "We can take an extract from soil or sediment or other filthy things like that and put it straight on the chip, and detect what we want to detect without the dirt or other things getting in the way of the signal." But his ultimate goal-to create a field-ready microarray-may take a few more years.

 

Chandler and his colleagues are also interested in developing the same techniques for on-the-spot detection of biowarfare agents, and has a cryptosporidium detection project for the US Environmental Protection Agency.

 

The team's work also led to a surprising discovery. Chandler's partner at Washington State University, Douglas Call, stumbled upon a crucial shortcut. He found that the researchers could slash their manufacturing costs by affixing unmodified DNA directly to the surface of the glass.

 

"We were trying to optimize chemistry for printing, and we found we didn't need to use it," Chandler says. "People know that DNA sticks to glass. But nobody connected that with keeping it immobilized for microarrays."

 

With this shortcut, the group is able to produce 100 to 200 spot arrays at a cost of 25 cents to 50 cents each.

 

Chandler says that since the US Patent and Trade Office rejected their patent application for the technique--DNA's tendency to stick to glass is too well-known--the team instead published its discovery in the hopes of encouraging other researchers to work with the technology.

 

"We're very interested in working with other people to adapt and develop array technologies for the purpose of environmental monitoring and other applications," he said. "Hopefully, the average investigator can use this technique, so as not to let the cost of array technology inhibit them."

 

The microarray work is public-domain research, said Chandler, but he is looking for commercial partners to work on perfecting their sample preparation technology in order to develop a field-ready chip.

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