VICKSBURG, Miss.-Federal scientists here at the Army Corps of Engineers' Waterways Experiment Station (WES) are developing a landmark process that would use so-called DNA chips to provide much more accurate assessments of the ecological harm caused by contaminated sites-a development that could prove especially useful for the military and other federal agencies coping with toxic locations.
Though the project will require both technical refinement as well as approval from such entities as the Environmental Protection Agency (EPA), scientists involved say the new technique promises quicker and more useful information than current methods of contaminated-site testing provide. In turn, this detailed information could enable agencies like the Defense Department to use triage to determine which sites are the most ecologically harmful, thereby reducing their remediation costs and finishing off their cleanup backlog more quickly.
"The Army has 32,000 sites to clean up, and they will never get there at their current cleanup rate," says Edward J. Perkins, a WES research scientist working on the DNA chip project. "We could use this process as a screening tool, to rule out certain sites."
Along with researchers at the Oak Ridge National Laboratory in Tennessee, the WES scientists are hitching their project to DNA chips, a once-futuristic technology that's come into its own during the past year or two. Some biotech companies are already producing DNA chips commercially, with the most common format using silicon chips covered with strands of DNA-strands that are mirror images of gene sequences that scientists want to detect. The way the strands are attached to the chip has led some to dub the strips "hairy."
Scientists douse these DNA chips with a specially prepared sample taken from blood or other biological liquids. The exposed DNA strands from the sample naturally attach themselves to their mirror-image strands on the chip, as if they were opposing strips of Velcro. By building in a detectable signal that goes off once the strand-to-strand connection is made-often some sort of laser-induced fluorescence-the researchers can quickly tell what kinds of matches the chip has made.
The WES scientists are using an analogous process designed by Oak Ridge scientist Ken Beattie to test samples from environmentally contaminated soils. The glass substrate for their chip, developed by Ron Tonnucci of the Naval Research Laboratory, starts as a finger-sized amount of both etchable and non-etchable glass. Tonnucci stretches the glass to ever-thinner widths, over and over again, packing them together tightly each time.
When the glass strands have become thin enough and packed together tightly enough, Tonnucci eats away the etchable material with acid, leaving a honeycomb-shaped square run through with tube-shaped "microchannels" that reach all the way from the top of the chip to the bottom.
The WES scientists then adhere thousands of identical genetic sequences to each microchannel. In WES's case, the scientists label each different microchannel with a different gene sequence. Each of the gene sequences they attach to the microchannels indicates some harm to organisms, such as codings for environmental stress, cancerous activity, damaged metabolic pathways or genetic mutations. Some of these suspect gene sequences can be found easily on the World Wide Web. Once the sequences are attached to the chip, they flood the preparation back and forth with a solution taken from a contaminated site.
The project's scientists say the benefits of the WES approach are multiple. Compared to the "hairy" chip model, the microchannel structure leaves more surface area available for attaching gene sequences. In addition, the WES scientists have set up their system so the intensity of the emitted fluorescence correlates directly with the prevalence of a particular genetic sequence in the sample.
More importantly, the process can take as little as a day to complete-far quicker than current tests mandated by the Environmental Protection Agency, which require researchers to grow complete generations of organisms (say, a worm or an insect) that are deemed to be indicators of a contaminated site's ecological health. Growing these generations can take 10 to 28 days and be dauntingly expensive, the WES scientists say.
"There are easier ways to analyze a sample, but the power of the array is that it can look for 1,000 things at the same time," Perkins says. "It's a shotgun approach."
Moreover, discovering mutations on the genomes of a wide variety of local organisms could prove especially valuable to environmental policymakers. Current tests require so many educated guesses that the EPA builds in a multiplier-a fudge factor, essentially-to err on the side of caution where human health is at risk. By contrast, WES' DNA chips might be able to detect ongoing genetic damage that's unnoticeable by scientists carrying out today's whole-organism studies.
Scientists will also be able to use the new technology in innovative ways. "You can monitor how well the environment would clean itself up without human intervention," Perkins says. "If the conditions are right, bacteria can degrade the contaminant themselves if you let them sit there for a while. You can use our process to look for genes that are known to define enzymes involved in degrading that contaminant."
Scientists might also determine exactly which genetic sequences are damaged by exposure to TNT and other military-related compounds. Such findings could help design a better-targeted generation of DNA chips.
But above all, the most important factor to federal policymakers may be that the WES tests' quick turnaround time makes it economically feasible to sample many locations within one cleanup zone. That makes it possible to pinpoint exactly where contamination is occurring-and where it is not occurring-so that remediation projects can be targeted precisely, with savings in cost, time and human resources.
"If you have a PCB spill on a wetland, you have an area that has certain hotspots of contaminated sediments," says WES scientist Herb Frederickson, another project member. "But 98 percent has much less contamination. The critical thing when you're looking at a cost-analysis is that you can go into a small area and clean it up rather cheaply. But if you have to do the other 98 percent too, it drives up the cost enormously."
The WES project, which began a year ago, is being funded by the Army Corps of Engineers' Environmental Quality and Technology Program and the federal Strategic Environmental Research and Development Program. The WES group has completed the first of three years worth of federal grants they've been allocated.
Tonnucci has a patent on the honeycomb array, while Gene Logic Inc., a Gaithersburg, Md., biotech company, has licensed portions of the system. Whether the EPA accepts the project remains to be seen, however. "The EPA is under no obligation to believe in our system, but we're hoping to involve them. We've been trying to get the EPA on board from the get-go," Tonnucci says.
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