Johns Hopkins Magazine -- November 1998
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S C I E N C E    &    T E C H N O L O G Y

Ecologists take a slice of life... the inner workings of the mitochondria... a leap into the wireless realm at Public Health

Grace Brush with (from l to r) Dan Bain, Kristen Holt, and Steve Kenworthy.
Photo by Jay Van Rennselaer
History in the dirt

A visitor to south Baltimore's Smith Cove along the Patapsco River sees a striking juxtaposition of the pristine and the prosaic. In the foreground, glittering water, leisure boats docked at a marina, the occasional duck, and the lyrical buzz of insects; in the background, a freeway, a decaying factory, and the drone of cars and trucks. At water's edge, a lush expanse of marsh grasses obscures an astounding collection of liquor bottles, broken toys, and fast-food wrappers.

Both the natural and the man-made stuff interest Hopkins paleoecologist Grace Brush. She and three graduate students have come to a clearing in this urban marsh to do field work for an ecological study that has a unique twist: It focuses on a metropolis.

The Hopkins team and scores of researchers from other institutions are participating in "Human Settlements as Ecosystems: Metropolitan Baltimore from 1797 to 2100," as the project is called. The study is funded by the National Science Foundation and is led by the Institute of Ecosystem Studies, in Millbrook, New York. A second team of researchers, also funded by NSF, will conduct a parallel study of Phoenix.

"For a long, long time, ecology taught as though humans were not part of the system," says Brush, a professor of geography and environmental engineering at the Whiting School of Engineering. NSF began funding long-term ecological studies about two decades ago, she says, but all of those projects focused on "pristine" regions such as Antarctica. Other scientists who did include people in the equation generally studied narrow slices of the ecosystem, such as the effects a sewage system has on a river. "Now, humans are included as a species in an ecosystem. So we are looking at the relationship of a dominant species in the ecological process," Brush says.

The goal this sweltering September day is to extract a four-foot tube of dirt from the land beneath the litter-strewn marsh. The sediment core, as such samples are called, could encapsulate an amazing amount of history. Depending on the sedimentation rate in the region, one centimeter's depth can represent one year or 200 years. Brush has collected hundreds of sediment cores during her tenure at Hopkins. Using the cores, she has created a paleoecological record of the greater Chesapeake Bay and its tributaries.

Graduate student Steve Kenworthy inserts a clear plastic tube inside a four-foot-long stainless steel tube called an augur. Grad student Dan Bain places the bottom, serrated end of the augur on the ground, and then hammers on its top until the entire tube is sunk into the ground.

"The cores give us an opportunity to compare, hopefully, what the area was like when no people were here [to what it is like now]," says Brush. At one time, Swan's Cove and all of greater Baltimore was forested. European settlers then farmed the land, and over the centuries Baltimore gradually was transformed into an urban/suburban landscape. By analyzing the contents of each layer of a sediment core, Brush can learn, for example, how deforestation affected the nitrogen content of the soil.

Using a special jack, Bain, with assistance from Kenworthy and graduate student Kristen Holt, yanks out the augur. Brush pulls out the clear tube, and voilà her prize. "We've definitely got an interesting transect," declares Kenworthy.

The top six inches are a rich black organic material. Previous experience has taught Brush that such sediment probably contains ragweed pollen. Ragweed is an excellent marker of previously tilled land, says Brush. "It grows very well on plowed-up land and produces a great deal of pollen." Beneath that are several inches of brown earth, possibly deposited before the introduction of agriculture. And beneath that is about a foot of gray stuff. "This looks like fill to me," says Kenworthy. And this is the amazing thing. The gray stuff--what paleoecologists call "fill"-- could be compacted remains of refuse discarded by people who lived here hundreds of years ago. Sediment cores the researchers have taken from less developed regions of Baltimore have not contained the gray fill.

Brush and her students will take the core back to the lab, slice it into one-centimeter-thick sections, and examine each one under the microscope. Seeds, pollen grains, carbon, nitrogen, phosphorous, beetles, midges, diatoms--each is a clue to the amount and type of living that went on. For example, the amount of carbon, nitrogen, and phosphorous indicates how much fertilizer farmers used at various times. The researchers plan to collect hundreds of sediment cores from throughout greater Baltimore.

Their findings will then dovetail with other components of the Baltimore project undertaken by other researchers. These include efforts to trace the pathway of fertilizers and pesticides, to determine which nutrients that runoff leaches from the soil, and to find how ozone affects various tree species. The general idea is to look at the flow and cycling of energy and materials, just as ecologists have done when examining pristine areas. Together, all the pieces of the NSF study will be fed into a model. "It's an attempt to get the big picture," says Brush.

These results can then be used to predict the long-term consequences of present-day changes on the Baltimore ecosystem, and to help communities plan and revitalize neighborhoods with an eye toward improving the environment.

Brush also plans to investigate a theory that could bring the big picture of urban ecology down to the level of a single animal: the humble beaver. "I have a feeling that the whole landscape here was influenced by the beaver population," she says. "The beaver was probably the most dominant species at one time." The flooding caused by their dams, she suggests, created soils that were extremely marshy and nutrient-rich. But within only about 50 years, fur traders virtually wiped out the entire beaver population in the U.S. And with the beavers went the wealth of nutrients found in the soil. If Brush is right, then the tale of the beaver will be told through the dirt. --Melissa Hendricks

Inside the body's energy factory

Life could not exist without ATP. It is the vital fuel for all activities ranging from the growth of a leaf to the winking of an eye. Now Hopkins biochemists Peter Pedersen and Mario Amzel provide detailed atomic images of the enzyme that produces ATP.

Every high school biology student learns that the compounds ADP and phosphate combine to form ATP. This reaction takes place within a bean-shaped organelle called a mitochondrion, and is catalyzed by the enzyme ATP synthase. But simply knowing the key ingredients of this reaction is like looking at a power plant from the outside. What goes on inside the plant? Amzel and Pedersen now give a glimpse of the inner mechanism.

"It's a unique molecular machine," says Pedersen. He and Amzel began crystalizing ATP synthase molecules 20 years ago and examining their structure through a technique called X-ray crystallography.

Each ATP synthase molecule is shaped like a mushroom, complete with a "cap" and "stem," says Pedersen. The stem (the yellow ribbons in the image below) acts like a rotor that spins inside the cap (the white and blue ribbons).

Last year, Paul Boyer, of UCLA, received the Nobel Prize for proposing that this rotorlike motion enables the synthase molecule to produce ATP. John Walker, of the Medical Research Council Laboratory, in Cambridge, England, shared the prize for deciphering the structure of the enzyme "cap" during one stage of this process.

Pedersen and Amzel now report that rotation of the enzyme stem causes a shift in the shape of the enzyme cap. Each conformational change enables a different phase of ATP production, they report in the September issue of the Proceedings of the National Accademy of Sciences.

At the beginning of a production cycle, ADP and phosphate rest in two separate regions of the synthase cap. The rotor stem turns, which causes a shift in the cap, which brings ADP and phosphate together. Another turn of the rotor releases the ATP molecule from the enzyme cap.

Chemicals called free radicals, which have been shown to cause mutations and damage to skin, may also attack ATP synthase molecules, says Pedersen. Such long-term assaults on the body's energy factories may be one reason we run out of steam more easily as we age. --MH

Public Health goes wireless

Grab a cup of coffee in the cafeteria, tap a few keys on your laptop computer, and you can check e-mail, finish a statistical analysis project using the Internet, or print a document--all via wireless radio transmissions. Sound too cool for school?

Computing at the School of Public Health has taken the next technological leap into the wireless realm. About 300 of more than 1,500 students can now work modem-free on their laptop computers in one of 40 classrooms, two cafeterias, and throughout the school's libraries, lounges, and conference rooms.

Under the technology provided by Bay Networks Inc., wireless access transmitters installed at various points in the building's ceilings emit radio waves with a range of up to 150 feet. Students insert cards in their laptops--cards that pick up the transmissions by acting as Internet antennas.

The system, which is used by only a handful of universities, costs less to install than other computer-oriented upgrades, including a proposed rewiring of Public Health's 80-year-old building. "That was estimated to cost $18,000 per classroom, and the wireless cost us $3,000 per classroom. It's a huge difference for us," says Ross McKenzie, director of information systems for the school.

The system is free to students and is limited mostly to campus use. The wireless project is the latest in the school's push to get students computing. Public Health also offers rebates and discounts for students who buy computers, and administrators plan to require that all students own laptops.

"The analytical power you have with laptops is essential to public health," McKenzie says. "So much of the research is Internet-centered." --Joanne P. Cavanaugh