Sea-Level Rise Threatens Coastal Species Habitats

Habitats of threatened and endangered birds, turtles, alligators, and fish in South Carolina may be vulnerable to a rise in sea level that could result from global warming, according to ORNL research.

Tammy White and Richard Daniels, both of the Environmental Sciences Division, identified nine species whose habitats are at risk to a sea-level rise that could result from glacial melting.

"The habitat of the nationally endangered Bachman's warbler will be most affected by sea-level rise," White says. "This finding is significant because the species is near extinction in South Carolina.

"The continued existence of nesting habitat is essential for the survival and reestablishment of these species. The threat to the species of a potential climate warming is not considered by the Endangered Species Act of 1973. This act, which defines methods for identifying and protecting threatened and endangered species, assumes that the climate remains stable."

In this analysis, White and Daniels considered geophysical factors such as elevation, land erodibility and subsidence, shoreline retreat, and the energies of high waves and tides. They correlated a coastal vulnerability index--calculated values indicating the relative vulnerabilities of coastlines to inundation and erosion as a result of sea-level rise--with the habitats of the threatened and endangered species.

The species and percent of habitat at risk were found to be Bachman's warbler, 67%; red-cockaded woodpecker, brown pelican, and bald eagle, 50%; loggerhead sea turtle and wood stork, 40%; American alligator and piping plover, 35%; and shortnose sturgeon, 14%. Except for the shortnose sturgeon, these species nest along the coastline.--Carolyn Krause


Informatics and the Human Genome

Even in this age of information, "informatics" is not a household word. Nevertheless, it is the linchpin of what may prove to be one of science's greatest feats--deciphering the human genome.

Individual laboratories at ORNL are microcosms of global efforts now under way to understand the estimated 100,000 human genes that make up the genome and encode our very beings. As the mystery unravels, reams of data with many loose ends will have to be dealt with.

Informatics is an emerging field that will help tie it all together," Ed Uberbacher, informatics group leader in ORNL's Engineering Physics and Math Division, said. "It's an area that has combined biological and computer sciences to support many of the research activities of the Human Genome Project," he said. In part, the ORNL informatics effort will allow researchers studying animal chromosomes, such as mouse chromosomes, to quickly access and identify corresponding pieces of human DNA. Often, gene abnormalities in mice are strikingly similar to those in humans.

Uberbacher shares responsibility for development of informatics in ORNL's human genome program with the Biology Division's Richard Mural, who says a vigorous fusion of computational and biological sciences is critical to genome work.

"A tremendous volume of biological data is being generated in hundreds of labs, all of which work a little differently. They each tend to log information in a somewhat customized manner," Mural said.

To benefit mutually, he explained, researchers need to be able to create, access, and exchange research data across the country or around the world. Facilitating this information flow is the essence of informatics.

The final outcome of genome data is a message composed of four letters--A, T, C, and G--that represent the individual chemical bases that form strands of DNA. Their order along the DNA strand defines the genes that encode life's essential proteins.

But this four-base code's apparent simplicity can be deceiving; spanning the entire genome, it is roughly three billion characters long. That's enough to fill a 200,000-page telephone directory. To recite it completely would require some 26 years of round-the-clock oration.

"A primary goal of the Human Genome Project is to chart the genome in its entirety. This makes for an immense cataloging task, even by today's high-tech standards," Mural said. And the goal of informatics is not simply to catalog and compare this sequence but to apply computer-based methods to learn about its function and importance in human terms.

The ORNL informatics team has three immediate priorities, Uberbacher said. First, it will provide genome scientists an "electronic laboratory notebook" that will keep track of laboratory data that are generated daily and that will ease data entry, tracking, and information exchange. Second, it will construct and make available to the worldwide genome community an accessible, comprehensive data base for ORNL's gene-mapping efforts (in which scientists determine the location of specific genes along strands of DNA). And third, it will implement a variety of analytical "tools" to help researchers access gene-mapping data bases and sequence data to query about a specific base sequence, gene location, or other information about genome function.--Wayne Scarbrough


Miniplant Helps Evaluate Wastewater Treatment Methods

In recent years, DOE has strengthened its efforts to clean up hazardous waste resulting from past operations and to greatly reduce the amount of new waste produced at its facilities nationwide.

As part of the efforts, chemical engineers at ORNL have designed a unique facility to monitor and evaluate methods of treating wastewater. The work is being funded by DOE's Office of Environmental Restoration and Waste Management.

Called the Wastewater Treatment Test Facility (WTTF), it was designed to be a scaled-down, combined version of two elaborate wastewater treatment systems at ORNL--the Process Waste Treatment Plant and the Nonradiological Wastewater Treatment Plant.

"It was made to simulate, on a small scale, the operations at both plants," said Cliff Brown, a section head in ORNL's Chemical Technology Division.

The test facility is an aluminum trailer that has been outfitted as a high-tech laboratory. Inside, small stainless-steel tanks and tall plastic columns filled with carbon chips and purifying resins treat samples of wastewater to remove contaminants.

The first phase of treatment in the laboratory simulates the Process Waste Treatment Plant. In the small stainless-steel tanks, calcium, magnesium, and other minerals are separated out to soften the water, and any radioactive contaminants, such as cesium-137 and strontium-90, are removed by a purifying resin.

Then begins a second round of purification, imitating operations at the Nonradiological Wastewater Treatment Plant.

In a process called air stripping, wastewater is pumped to the top of clear plastic columns and allowed to trickle down through about 3 meters (10 feet) of packing material that resembles chips of seashells. This approach increases the water's surface area, making it easier for organics, such as toluene and xylene, to move out of the water and into a flow of air that is continually pumped up through the columns, which reach from floor to ceiling. The air, which carries and disperses the chemicals in a more environmentally safe manner than does water, is then siphoned away through an exhaust system. (If large amounts of contaminants were being stripped, the air from the columns would undergo additional treatment before being discharged to the outside.) To further ensure purification, the water is filtered again, this time through a column filled with chips of activated carbon. Such filtration removes large organic molecules and any mercury that may be present.

The step-by-step treatment precisely mimics the operations in the two full-scale facilities. "But because of its operating scale, the pilot-plant testing is much less expensive and greatly reduces risks to the environment," Brown said.

The wastewater most recently tested at the pilot plant came from ORNL's Solid Waste Storage Area Number 6 (SWSA-6), which is scheduled to be closed by Martin Marietta Energy Systems' Environmental Restoration organization. During closure, full-scale wastewater treatment will be necessary, and plans are to use the Process and Nonradiological plants for that purpose.

"The pilot plant worked just great in testing the SWSA-6 samples," said Tim Kent, principal investigator at the test facility. He said the tests answered one of the most important questions about closure of the storage area: whether the two full-scale plants could treat the wastewater without producing mixed waste, a combination of wastes that are regulated individually as "hazardous" or "radioactive."

"Mixed waste poses the biggest challenge, both from a regulatory and a disposal standpoint," Kent said. "We were really pleased to find that treating the SWSA-6 wastewater with our existing methods did not produce any mixed waste."

The new test facility is transportable and has a system design that can be altered for various studies without a major expenditure. Thus, it could be useful to other sites involved with waste treatment. It will be used extensively in the future to evaluate treatment of other cleanup-related waste streams and to perform process improvement studies for the ORNL liquid-waste treatment plants.--Wayne Scarbrough


Lasers Accelerate DNA Sequencing

Among the keys to unraveling the mysteries of the human genome is developing a fast and accurate method of sequencing the chemical bases that make up segments of DNA. With this in mind, C. H. Chen and his co-workers in the Health Science Research Division's (HSRD's) Photophysics Group have succeeded in using laser mass spectrometry to measure the masses of DNA molecules up to 130 bases long. They have also been able to measure 130-base-long positively and negatively charged ions of DNA molecules using a similar laser technique.

In this procedure, DNA bases are added to a small molecule, known as a primer, which is labeled with an organometallic compound. Then new DNA segments that terminate at each occurrence of a particular DNA base (A, G, C, or T) are built up on the primer using the original DNA as a template. When the masses of these progressively longer segments are measured, the sequence of their DNA bases can be determined.

In the course of their research, the HSRD research team found that some of the ions they created were stable for as little as 100 microseconds. To analyze these ions before they became unstable, HSRD researchers employed a time-of-flight (TOF) mass spectrometer. Unlike Fourier transform mass spectrometers, which require samples to be confined in a magnetic field for several milliseconds, TOF mass spectrometers can accommodate shorter-lived, "metastable" ion samples, resulting in more complete and accurate data. Also, while traditional mass spectrometry techniques can detect only ionized DNA molecules (those with positive or negative charges) the TOF method can also detect neutral, or chargeless, molecules.

Using this high-speed analysis system, the HASRD team hopes to develop a fast-sequencing laser spectrometry system within the next three years.

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