RNA extraction
Labeling/ hybridization
Scanning
Analysis
(bioinformatics)
3’AAAA
DNA “chip”
The sources of technical variation that can occur during a cDNA microarray experiment are shown above.
using the same platform. To better understand what is causing the data variations, NIEHS’s Microarray Center joined forces with five academic centers that have expertise in toxicology and gene expression research to form the Toxicogenomics Research Consortium (TRC) in 2001. One of TRC’s primary goals is to standardize how gene expression data are generated. Currently, TRC is investigating the technical variations in gene expression profiling, which include things like how RNA is extracted from animal tissue, how it is stored, and how the complementary DNA is amplified, labeled, and bound to the microchip. The consortium also plans to address variations in data analysis that arise from using different software and statistics programs, as well as differences in gene nomenclature. Eventually, the consortium hopes to examine biological variations, or genetic differences among animals of the same species, which could explain some of the intralaboratory variations. Although standards for microarray data have been developed and
adopted by an international organization called the Microarray Gene Expression Data (MGED) Society, those standards, which are referred to as the Minimum Information About a Microarray Experiment (MIAME), do not specify a protocol to follow. Rather, MIAME outlines what information about an experiment must be reported. MIAME provides a means for sharing information, so that you can get a full data set and annotation in a form you can use from a public database, says Chris Stoeckert of the University of Pennsylvania’s Center for Bioinformatics. “Although we have MGED standards, independent source variation is unknown, and the impact of variation on data interpretation is unknown,” says Weis. Nearly everyone agrees that it is important to create a common language for toxicology, but some members of the NRC committee feel that too much time is being spent discussing variations in gene expression data, and not enough time is being devoted to other important issues. “Let’s get the information and give it to the statis-
Corps, EPA pull back from wetlands regulation Two years after a U.S. Supreme Court decision questioned to what extent the Clean Water Act (CWA) applies to isolated wetlands, the Army Corps of Engineers (Corps) and EPA have issued guidance withdrawing federal protections from 20% of the nation’s wetlands. In concert with the guidance, the agencies issued an advance notice
of proposed rulemaking on January 15 that solicits comments on how to better define federal jurisdiction over isolated wetlands (Fed. Regist. 2003, 68, 1991–1998). The action has alarmed environmentalists, who believe it will lead to the loss of federal regulations of industrial discharges, while the regulated community, mainly builders, wel-
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ticians. It will be solved,” says committee member Timothy Zacharewski of Michigan State University. Still others, such as Dow Chemical’s James Bus, believe “we will need to give more thought to biological variability.” One important area in which the committee hopes to spend more time is addressing the impacts and limitations of using toxicogenomics data in risk assessment and environmental decision making. The technology could help identify subpopulations that are more susceptible to health effects from a particular chemical exposure, as well as identify common mechanisms in humans and other species, so that traditional toxicity data can be better extrapolated from laboratory animals to humans, says Linda Greer, director of public health at the Natural Resources Defense Council. Another area is chemical mixtures. The National Institutes of Health is already funding toxicogenomics research to investigate mixtures, and according to Kenneth Olden, director of NIEHS, “they are producing good data.” —BRITT E. ERICKSON
comes the opportunity to refine a muddy definition. “The guidance helps clarify how to apply federal authority since a 2001 Supreme Court case struck down the use of migratory birds as the sole basis for the Corps to assert CWA jurisdiction over isolated, non-navigable intrastate wetlands,” explains John Millett, press officer for EPA. The CWA allows the Corps to issue permits for the discharge of
NIEHS
Environmental▼News
Twenty percent of U.S. wetlands would no longer be protected under recently proposed federal rules.
Now, only three other factors, including whether the water body is used for interstate recreation, fishing, or industrial purposes, may still be used to establish jurisdiction over isolated wetlands, according to the guidance. But if a permit writer from the Corps or EPA cites one of these criteria, they must now consult with their headquarters for approval, a step not required before this new guidance was issued, Millett says. “This guidance changes an interpretation of the CWA that has been in place for 30 years, and goes way beyond what the Supreme Court decided,” charges Julie Sibbing, a wetlands specialist with the National Wildlife Federation. The Supreme Court only struck down the use of migratory birds, but the guidance effectively drops the other three factors—use for interstate recreation, fishing, or industrial purposes—as a reason for jurisdiction over isolated wetlands, she says. The guidance could withdraw CWA protection from 20% of the nation’s wetlands, including prairie potholes and playa lakes, Sibbing says. She and other environmental groups believe these ac-
tions are a warning that the Bush administration might encourage Congress to change the CWA. “The loss of federal jurisdiction over isolated wetlands doesn’t just apply to Corps permits for draining and filling water bodies but to all CWA programs, such as national pollutant discharge permits,” says Jeanne Christie, executive director of the Association of State Wetland Managers. This is because the Supreme Court decision focused on the validity of all federal jurisdictions over isolated wetlands, not just the Corps role. Only 17 of the 50 states have strong wetland laws to take the place of the federal oversight eliminated by the new guidance, she adds. How far might the decision extend? “Aside from isolated wetlands, it is important to note that all navigable waters, their tributaries, and adjacent wetlands are still governed by the CWA,” Christie says. But the questions asked by the proposed rulemaking—how broadly should the term “isolated waters” be defined and what kind of hydrologic connections are needed to claim a wetland is adjacent to navigable waters—could eliminate CWA protections from more water bodies, she warns. The CWA applies to navigable waters, yet does not precisely define what that means. Today, wetlands adjacent to navigable waters are covered by the CWA, but what sort of hydrologic connections— groundwater flow or surface ditches—will the new rules count as valid for establishing connectivity, Christie asks. If the new rules were to say that navigable waters are just the main stems of rivers and their tributaries, it would make no sense in terms of achieving the goals of the CWA, she says. The proposed rulemaking is the beginning of a very important process to ask the public what kind of rules should be proposed and how many wetland acres should be regulated at the federal level, says Bob Szabo, executive director of the National Wetlands Coalition, an industry group. Comments on the proposed rulemaking were due March 3. —JANET PELLEY
News Briefs Cleaning and greening electronics recycling A group of 15 U.S. electronics recycling companies have pledged to prevent hazardous waste from entering municipal incinerators and landfills or be exported to developing countries, according to the Silicon Valley Toxics Coalition (SVTC), a nonprofit organization that helped broker the agreement. “We are frustrated by the failure of the federal government and electronics manufacturers to … deal with the current e-waste crisis,” explains Bobby Farris of Resource Concepts Inc., Carrollton, Texas. SVTC has alleged that 50–80% of electronic waste collected for recycling in North America is actually sent to developing countries such as China, India, and Pakistan, and the mercury, chlorine and bromine in electronic products can leach into groundwater from landfills or be released by incinerator emissions or ash. For more information, go to www.svtc.org.
Finding alternative fueling stations California drivers of alternative fuel cars can locate fuel stations thanks to a website run by WestStart-CALSTART, a consortium of transportation companies and organizations in California. The Clean Car Maps site locates stations that provide compressed natural gas, liquefied natural and petroleum gas, ethanol, methanol, hydrogen, and electric fueling. The locator service is supported by the South Coast Air Quality Management District, the Federal Transit Administration, the California Air Resources Board and the California Energy Commission, and is available at www.cleancarmaps.com.
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PHOTODISC
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fill material into “waters of the U.S.,” which include navigable waters, their tributaries, and adjacent waters. But in order to issue permits for isolated, non-navigable intrastate waters, the Corps must invoke the Interstate Commerce Clause, which allows federal agencies to become involved in activities affecting commerce between states. Because migratory birds cross state lines, their use of isolated intrastate waters had been cited by the Corps as a trigger for the Commerce Clause, extending the Corps’ authority over these waters.
