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New Recruits Advance Plant Science

by Randy Weckman

The Research Challenge Trust Fund (RCTF), commonly called "Bucks for Brains," provides support for ongoing efforts to attract and retain renowned faculty and researchers.

"In the UK College of Agriculture, RCTF funds have been used to hire four young researchers, shining stars in the field of plant sciences," says Scott Smith, dean of the University of Kentucky College of Agriculture. "Their research findings will not only advance the knowledge of science, but will also benefit Kentucky farmers almost immediately."

Helping Plant Viruses Self-Destruct
Peter Nagy loves to help plants make mistakes.

"The idea goes something like this," he explains. "Viruses invade their host, set up housekeeping, then start copying themselves, like a super-powered Xerox machine, at a frenetic pace. But because the virus copies itself so fast, it makes mistakes." These mistakes, he adds, aren't all small and inconsequential. "Luckily for us, the virus makes some pretty serious mistakes that can lead to its own eradication."

Photo of Peter NagyPeter Nagy is working to turn viruses against themselves with the goal of protecting plants from harm. [photo by Matt Barton]

Those self-destructing mistakes—and how they can be used to protect plants from viral harm—are the subject of Nagy's research. A plant virologist, Nagy arrived at the UK College of Agriculture two years ago from the University of Massachusetts, where he completed postdoctoral training.

Viruses, which are much too small to be seen without the use of a special microscope, come in a variety of sizes, shapes, and structures. (Several hundred thousand of them could fit into the period at the end of this sentence.) Some of these tiny entities copy themselves using DNA, as animals do, and some replicate using only RNA, because that's all they contain.

RNA-type viruses are the most abundant types; those that cause the human cold, encephalitis, and flu are all examples of this type. These viruses make many more mistakes in replicating than do the DNA types. During the copying process, bits and pieces of the genetic code are written erroneously, with letters left out, so to speak. These mistakes sometimes become full-fledged "superparasites" that attack the virus (the "mother parasite") from which they came.

Nagy's research is focused on how to help the RNA-viruses make mistakes more quickly and more often so that molecular superparasites developed from the virus can out-compete—and either minimize or eliminate—the parent virus before it has debilitated or killed the plant.

In his laboratory, Nagy has been able to cause mistakes in a destructive virus that is widely found in wild tobacco, cucumber, and tomato. He does this by simply rubbing a bit of the genetically modified "mistake" virus on a leaf of wild tobacco, previously infected with the "parent" virus; then he waits for two days.

"The new superparasite out-competes its parent virus and the plant recovers in a few days and can then thrive," Nagy says.

He is optimistic that his technique can be refined and used to help farmers protect their crops. "Conceivably, the skilled plant breeder will be able to breed into seed the mistake virus so that the plant will be protected from the time it germinates."

Creating Wetlands for Cleaner Water
Ecologists sometimes call marshes, bogs and swamps the "kidneys of the landscape," because through a slew of physical and chemical processes they remove pesticides, nutrients and metals contained in water. Mother Nature's water-treatment plants, these wetlands cleanse water entering lakes and streams, and support a wide range of wildlife, from frogs to birds and other animals.

Photo of Elisa D'AngeloElisa D'Angelo is focusing her work on how to make constructed wetlands more efficient.

In Kentucky, 80 percent of natural wetlands have been lost, due mostly to the encroachments of farming and coal mining. But Kentucky is actually increasing its wetland acreage, thanks in large part to federal rules that require developers who disturb natural wetlands to replace them with man-made wetlands on an acre-for-acre basis, and in some cases even more.

But are these constructed wetlands the real deal? How well do they purify water compared with natural wetlands that are centuries old?

These questions are at the core of plant scientist Elisa D'Angelo's research. Her work focuses on the nutrient storage and transforming capabilities of man-made wetlands (called mitigated wetlands by scientists). Specifically, she's monitoring, at the site and in the laboratory, several key biochemical processes that occur in wetland soils and that are responsible for water-quality improvement at more than a dozen man-made and natural wetlands in western Kentucky.

Wetland soils, compared with upland and aquatic soils, says D'Angelo, who came from the University of Florida in May 1999, are unique in that they harbor microorganisms that biochemically purify water that flows through them. "The science of creating man-made wetlands, on the other hand, is still in its infancy. And without accurate knowledge, we can only guess at where and how man-made ones need to be built."

That guesswork can lead to costly or inefficient use of constructed wetlands.

"If the constructed wetland works only half as well as a natural one, we would need to use twice as much land to achieve the same results, since the federal government may require as much as 10 acres to replace the five that have been developed," she explains. "Obviously, this 'two-for-one' rule can be very expensive."

To try to determine the efficiency of wetlands, D'Angelo takes a unique, biogeochemical approach: she measures physical, chemical and biological processes inside the wetland rather than simply measuring only what goes into the wetland area and what comes out. This influx-outflux approach has been the standard technique for many years.

"We know the big-picture processes responsible for water purification in wetlands such as deposition of nutrient-enriched sediments and plant detritus, the decomposition of organic matter by bacteria, how nitrates are processed and the like. How efficient these processes are depends on environmental conditions and microbial communities in the wetlands, which are likely different in man-made sites compared with pristine ones," she says.

How nitrogen and phosphorus work in the wetlands is the focus of her research; both elements, she says, are responsible for the algal blooms and aquatic plant-clogged waterways. Besides causing off-flavors in drinking water and being a nuisance to boaters and fishermen, decomposition of dead algal cells and plants in lakes and streams leads to lower levels of dissolved oxygen, a condition that kills fish.

"In looking at the two kinds of wetlands, we expect that there will be significant differences in rates at which water impurities are processed and also differences in microbial communities that process them," D'Angelo says. "We hope our results will provide scientists and engineers the necessary tools to assess whether an engineered ecosystem is following the correct track, so that actions can be taken to correct a failing system."

Gaining Insight into Seeds
How smart are plant cells?

Sharyn Perry, in the Department of Agronomy, is trying to find out. Her goal is to understand how plant cells "know" how to develop as seed tissue that eventually grows into a new plant.

Photo of Sharyn PerrySharyn Perry's research is focused on the process of how plant cells develop from seeds. [photo by Matt Barton]

"It's really molecular biology with an agronomic purpose," says Perry, who earned a doctorate in molecular biology from the University of Wisconsin. Her research focuses on something called AGL-15, which is short for AGAMOUS-like 15, a protein involved in gene expression. AGL-15 sets in motion what scientists call transcription machinery—enzymes that glide down the DNA and turn genes on or off. If the gene is turned on, the plant develops a certain way; if it is turned off, the plant develops quite differently. AGL-15 is a necessary "light switch" which directs genes that eventually command cells to develop into seed.

To gain insight into this process, Perry first mechanically pulverizes plant embryos of Arabidopsis, a weed of the mustard family. The resulting dust is treated with an antibody developed from rabbits that binds to AGL-15, which is, in turn, bound to the DNA.

Tiny beads of agarose (a compound used in a variety of applications, including making ice cream) are added to the mixture and bind to the antibody. Then, after the mixture is whirled a bit in the centrifuge, a device that revolves so fast that heavier parts of a solution are pushed outward, the agarose beads, now with the antibody, DNA, and protein clinging to them, are heated.

The heating process separates the DNA pieces from the protein. The "cleaned" DNA pieces are then compared with the known Arabidopsis genome map to see exactly where the AGL-15 is positioned.

"By comparing the DNA fragments with the known genome map, we can find out exactly which genes are turned on or turned off by AGL-15," Perry says.

So far, her research has isolated and identified genes that are regulated by AGL-15, but many more tests are needed to fully understand how the regulated genes function in seed development.

"Finding out what genes AGL-15 controls will help us understand how this particular protein functions during plant development," Perry says. "Because this protein is a member of a protein family believed to be involved in critical developmental decisions of fungi and animals, as well as plants, I am hopeful this research can help our understanding of the cell differentiation process in many organisms."

So how does all this work relate to the average citizen, the non-scientist?

"If you think about it, seeds are really very important to human beings," Perry says. "Most of what we eat is from seeds—wheat, corn, and rice. Beans are important, too. It's been estimated that 70 percent of the human diet comes directly from seeds, and the rest is all from animals that feed on grains—seeds—and crops propagated by seed."

Hi-Tech Farming
The focus of soil scientist Tom Mueller's current research can be summed up, he says, in three words: precision agriculture technology. He is using and assessing various technologies that can benefit Kentucky farmers, including yield-monitoring sensors that record how much grain is harvested in each small section of a field, and global positioning systems (commonly known as GPS), which can locate precisely where a tractor is in a field by using triangulating signals from space. GPS is analogous to time-tested systems mariners use to keep tabs on the whereabouts of their ship in the ocean.

Photo of Tom MuellerTom Mueller has made a major contribution in soil conductivity research. Measuring how well soil conducts electricity gives an indication of yield potential.

Yield monitors, soil sensors, GPS, and remote sensing devices can work in tandem to gather and record information that farmers can use to make better crop decisions, says Mueller, who received his doctorate from Michigan State University.

"Many farmers in Kentucky are already using yield-monitoring devices to map grain yield each second as they traverse their fields," Mueller says. "This allows them to identify low or marginally productive areas that may respond to site-specific management."

And while farmers have been using the technologies of precision agriculture for a few years now, Mueller's research could make high-tech farming even more precise. His work is multifaceted, and he is quick to point out that he routinely teams up with colleagues in agronomy, agricultural economics, agricultural engineering, and other plant sciences.

One of the areas where he has made a major contribution is in soil conductivity research. Mueller and one of his graduate students, Than Hartsock, have shown that the electrical conductivity of soils is related to topsoil depth and depth of fragipan, a hard layer often found in soils that thwarts root growth and limits crop-available water. Measuring how well soil conducts electricity in a field gives some indication of yield potential.

In recent work, Mueller and Hartsock measured soil conductivity in a field at different times during a year-and-a-half period using special devices called coulters. Coulters, which look like buzzsaws without teeth, spin and slice through the soil as they are pulled through a field behind a slow-moving tractor. Soil conductivity is determined by comparing the intensities of electrical charge from one coulter to another.

"What we found is that conductivity varies over time and is dependent on environmental conditions such as soil moisture," Mueller says. "But even though absolute soil conductivity values are moisture dependent, the relative patterns in the field are pretty stable during a large range of moisture conditions.

"Precision technologies are here to stay. I hope my work will help Kentucky farmers make better use of their resources and improve the profitability of agriculture in Kentucky," Mueller says.