U.S. environmental genomics gets big boost - Environmental Science

U.S. environmental genomics gets big boost. Kellyn Betts, and Catherine M. Cooney. Environ. Sci. Technol. , 2002, 36 (19), pp 372A–373A. DOI: 10.102...
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portant microbes whose genomes have already been fully mapped. S. oneidensis is being investigated as an aid in DOE cleanups because of its potential for sequestering metals in contaminated soil. The PHOTO BY DAVID HANSON, C&EN

Over the past few months, both the U.S. Department of Energy (DOE) and the U.S. EPA have significantly expanded their investment in genomics as a means to solve environmental problems. New programs promise to throw significant funds into genomics-related research, but officials remain cautious about using the new technology in regulatory schemes. Genomics allows scientists to analyze changes in gene expression at the gene or organism level (Environ. Sci. Technol. 2001, 35, 364A–370A). With most of the human genome mapped, many researchers refer to the current focus as “postgenomic.” “This is the next big step in biology, putting the genome to work,” says Michelle Buchanan, director of Oak Ridge National Laboratory’s (ORNL) Chemical Sciences Division, who has been named head of DOE’s new Genomes to Life Center for Molecular and Cellular Systems headquartered at ORNL. The ORNL center is but one of the recipients of the $103 million that DOE Secretary Spencer Abraham announced in July will be spent over the next five years to support postgenomic research in new technologies for generating energy from biological sources, sequestering carbon, and cleaning up the environment. Six DOE labs, together with 16 universities and research hospitals and 4 private research institutes, will receive funding from the Genomes to Life program, Abraham says. These DOE projects go beyond the DNA sequences to systematically tackle questions about the mechanisms of how organisms develop, survive, reproduce, and carry out their normal functions under a wide variety of environmental conditions. For example, at ORNL’s Genomes to Life Center for Molecular and Cellular Systems, researchers are taking on a $23.4 million project to identify and characterize all of the protein complexes associated with Shewanella oneidensis and Rhodopseudomonas palustris—two im-

The U.S. EPA’s first science adviser, Paul Gilman, leads the agency’s foray into genomics.

ORNL researchers are focusing on R. palustris due to the important role it plays in the earth’s carbon cycle, while other DOE researchers are investigating its potential for producing hydrogen and degrading organic pollutants. Similarly, because computational models are considered a key component of postgenomic research, the new center headquartered at the Lawrence Berkeley National Laboratory is receiving $36.6 million to develop models for predicting how microbial gene regulatory networks respond to the environmental conditions associated with metal and radionuclide waste sites. In the next three to five years, DOE hopes that Genomes to Life will grow into a multihundredmillion dollar program, says David Thomassen, program coordinator for DOE’s Office of Biological and Environmental Research. He notes that the U.S. Senate appropriated $10 million more than DOE requested for 2003. The use of genomics at EPA also received a boost in June when Administrator Christie Whitman


appointed Paul Gilman—a former executive with Celera Genomics, Inc., a company that helped map the human genome—to be the agency’s first science adviser. Shortly thereafter, Gilman announced an interim policy designed to guide EPA’s research and regulatory projects related to genomics. It is an area of research Gilman has enthusiastically supported at EPA; the proposed EPA budget includes $3.2 million for the National Computational Toxicology Project, which if approved by Congress, would bring the total funding to $8 million. The program, which began in late 2001, uses gene arrays to identify how selected genes respond to toxic exposure. During a briefing in July, Gilman, who is also the assistant administrator of EPA’s Office of Research and Development, noted that the information gleaned from genomics research wouldn’t by itself guide any regulatory decisions. Instead, this data will be considered on a case-by-case basis. The four-page policy indicates the agency’s commitment to using genomics mostly in risk and health assessments. The report argues that genomics will “ultimately improve” the quality of information used in the assessment process, because it can identify an individual’s genetic variability and susceptibility to environmental agents. Genomics might also provide a better understanding of the mechanism, or mode of action, of a toxin, helping scientists screen for these chemicals or other stressors, and design monitoring and exposure studies, the policy states. And it might be used to evaluate how factors such as genetic diversity and health status affect the cumulative response to multiple exposures. EPA has several genomic research projects under way specifically related to developing screening tools to identify whether certain industrial chemicals affect the human endocrine system. For example, researchers at the MidContinent Ecology and Gulf Ecology Divisions have a collaborative effort under way to study en-

col for these arrays nor a testing protocol, Henry says. Another hurdle is overcoming the many social, legal, and ethical issues that are bound to arise from genomics, including the potential for genetic discrimination. Nevertheless, the ACC supports EPA’s interim policy focused on research rather than regulation. “One of our fears was that the government would be unprepared for this technology,” Henry says. “Gilman’s policy indicates that EPA is going to be prepared.” —CATHERINE M. COONEY and KELLYN BETTS

Humic substances have regular structural patterns Researchers at Florida State University (FSU) recently published evidence that humic substances called fulvic acids have regularly repeating molecular groups in their structures (Anal. Chem. 2002, 74, 4397–4409). Although soil scientists have speculated about the polymeric nature of humic substances for years, William Cooper says his group is the first to positively identify functional groups and “polymeric themes”, such as numbers of CH2 groups, in fulvic acids. Elucidating the structure of these notoriously complex compounds could help researchers understand critical interactions between humic substances and pollutants. Found in soil and natural waters, humic substances are important degraded organic materials that can affect drinking water quality and the bioavailability of chemicals, such as pesticides, in soils. They are generally classified as humic acid, fulvic acid, and humin on the basis of solubility, but their structures are hard to further characterize with analytical methods because they are mixtures that appear to be fragments and condensation products of large biomolecules. Cooper says his group used an “unconventional” mass spectral technique and made a key modification to the instrument that helped to resolve the charged particles in fulvic acids from the Suwannee River, a standard source of “black water”

that flows from Georgia through Florida. After successfully isolating fulvic acids, they used Fourier-transform ion cyclotron resonance mass spectrometry to analyze fulvic acid ions in the National High Magnetic Laboratory at FSU. This sophisticated method uses strong magnetic fields that induce ions to travel at a frequency that is related to their mass-to-charge ratio. “You can measure frequency with greater precision than any other physical parameter,” Cooper says. Using a high strength field helped distinguish these ratios in mass spectral data, thus making it possible to characterize patterns and structures. Adding a device called a quadrupole filter that introduces only a few molecules into the mass spectrometer maximized the effect of the field. Cooper Langford, a researcher at the University of Calgary in Canada, who has characterized humic substances, described Cooper et al.’s paper as “a beautifully careful and complete study.” After hearing Cooper speak at the International Society of Humic Sciences meeting in August, Langford was “impressed [that] they could sort out the homologous series and reduce the 4600 components of the fulvic acid to 260 molecular families.” Other researchers remain skeptical because, as Langford says, “there may be more big pieces hiding” that would alter the interpretation. —RACHEL PETKEWICH

News Briefs Clean-energy technologies and pollution prevention processes will grow substantially over the next two years, according to projections by Environmental Business International, Inc. (EBI), a consulting and publishing firm that regularly surveys the environmental industry. EBI calculates that the environmental industry as a whole is growing at a modest 2.1% rate, but it projects that technologies for producing clean energy, such as solar, wind, and fuel cells, will grow 16.5% from 2001’s $9.96 billion by 2004. Equipment and technology for preventing pollution (as opposed to end-ofpipe controls) and waste treatment and recovery are expected to grow 8.0% during the same period, from their 2001 level of $1.26 billion. For more information, go to www. ebiusa.com.


docrine disrupters in sheep head minnows using DNA arrays. They are also using arrays to monitor the expression patterns of genes within the thyroid of developing tadpoles. But these projects are in the beginning stages, EPA scientists say. While the scientific tools are being developed, the government faces a slew of technical issues, notes Carol Henry, vice president for science and research at the American Chemistry Council (ACC), an industry trade group. For example, there is neither an agreed-upon manufacturing proto-

Four research centers in the northwest United States have joined together to create a new institute dedicated to the development of technologies that convert agricultural and food wastes into energy and industrial products, such as solvents and fibers. Under the agreement, researchers at two of the Department of Energy’s national laboratories—Pacific Northwest National Laboratory and Idaho National Engineering and Environmental Laboratory—will work closely with researchers at two land-grant universities— Washington State University and the University of Idaho—to develop a research and development program, with input from industry and grower organizations. Ultimately, the Northwest Bioproducts Research Institute expects to transfer more environmentally sustainable processes and technologies to the agricultural community.


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