Shaping the Future of Plant Science

By Randy Weckman

The UK College of Agriculture has hired four plant scientists through
funds generated from the Kentucky General Assembly’s Research Challenge Trust Fund (RCTF). Popularly known as “Bucks for Brains,” this program matches donations to the university dollar-for-dollar.

The scientists’ research illustrates both the breadth and depth of studies that have the potential to improve farming and the environment. The studies range from very basic research at the molecular level to more applied research where the results can be put to practical use almost immediately. Their research is described here.

Better Wetlands, Cleaner Water

Marshes, bogs, and swamps are sometimes called the “kidneys of the landscape,” because they remove pesticides, nutrients, and metals contained in water through a slew of physical and chemical processes. In so doing, these wetlands cleanse the water entering into lakes and streams. On top of that, wetlands support a wide range of wildlife, from frogs to birds and other mammals.

In Kentucky, 80 percent of the state’s natural wetlands have been lost due mostly to farming and coal mining. But Kentucky is one of the few states that is actually increasing its amount of wetland acreage, in large part because of federal rules that require developers who disturb natural wetlands to replace them with man-made wetlands on at least an acre-for-acre, and sometimes more, basis.

But are these new, constructed wetlands the real deal? How well do they purify water compared with the natural ones that are centuries old? Those are some questions that soil biochemist Elisa D’Angelo is asking. Her research compares the nutrient storage and transforming capacities of man-made wetlands (called mitigated wetlands) with the real thing, natural wetland areas next to rivers that have been around for eons of time.

Specifically, she’s monitoring several key biochemical processes in wetland soils responsible for water quality improvement at more than a dozen man-made and natural wetlands in western Kentucky. The man-made wetlands range in age from one year to more than a decade.

Wetland soils, compared with upland and aquatic soils, she explained, are unique in that they harbor microorganisms that biochemically purify water that flows through them. They are truly Mother Nature’s water treatment plant.
“The science of creating man-made wetlands is in still in its infancy. And without accurate knowledge, we can only guess at where and how man-made ones need to be built,” she said.

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; if it works as well as or better than naturally occurring wetlands, then a two-for-one rule that is sometimes applied is highly expensive,” she said.

D’Angelo’s approach is unique: it’s a biogeochemical approach, which implies measuring physical, chemical, and biological processes inside the wetland, rather than measuring only inputs and outputs, which has been the standard technique so far.

“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 aerobic and anaerobic bacteria, nitrification and denitrification, sorption and precipitation reactions. 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 said.

Nitrogen and phosphorus are the main elements of concern in her research, as they are largely responsible for the algal blooms and aquatic plant-clogged waterways. Besides causing off-flavors in drinking water and being a nuisance to boaters and fisherman, aerobic decomposition of dead algal cells and plants in lakes and streams leads to lower levels of dissolved oxygen and fish kills.
A well-known example is “the Dead Zone”— a tract in the Gulf of Mexico the size of New Jersey— in which all manner of aquatic life perishes for several months each year as a result of low dissolved oxygen caused by algal decay and overabundance of nutrients emanating from the Mississippi River. Losses of wetland areas adjacent to the Mississippi have been linked to this phenomenon.
“We expect that there will be significant changes in rates at which water impurities are processed and also in microbial communities that process them between the mitigated and pristine wetlands. 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,” she said.

Protecting Plants from Viruses

Peter Nagy speaks with a decided accent. And he should. The plant virologist is from Hungary. He arrived at the UK College of Agriculture two years ago via the University of Massachusetts, where he completed post-doctorate training.
Nagy’s work involves plant viruses and even with an accent, he can mesmerize you with the details of their lives and their mistakes.

Mistakes? Yes, indeed.
In fact, viral mistakes are Nagy’s stock in trade as a plant virologist.
The idea goes something like this. Viruses invade their host— for Nagy this is a plant, but animals can be hosts, too, as we all know. The virus sets up housekeeping and starts copying itself at a frenetic pace.

Just think about when you have a virus, such as a cold. When the virus has made enough copies of itself, you start to feel sick, and as the number of copies gets larger and larger, you feel worse and worse. But because the virus is making copies of itself so fast, it makes mistakes— not just little meaningless ones but serious mistakes that can lead to its own self-destruction. Those self-destructing mistakes— and how they can be promoted and used to protect plants from viral harm— are the subject of Nagy’s research.

Now the specifics. Viruses, which are much too small to be seen without the use of special microscopes, come in a variety of sizes and shapes and structures. (Several hundred thousand of them could fit into the period at the end of this sentence.) Further compounding their mystique is the fact that some copy themselves using DNA, like animals, 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 RNA viruses. RNA viruses make many more mistakes in replicating than do the DNA types. That’s why it seems that each year the world is warned of a new flu or new cold, with names such as Spanish flu, Hong Kong flu, Swine flu and the like— they are mutations of earlier versions.

Nagy’s research is focused on how to cause the RNA-viruses to make mistakes more often. Without help they make mistakes in replication one out of 10 times, which means a great number of mistakes considering they can make millions of copies of themselves in a day.

More specifically, it is during the copying that bits and pieces of the genetic code are written backward— or with letters left out— so to speak. These mistakes sometimes become parasites that attack the virus (which also is a parasite) from which they came. Now, that’s gratitude for you.

Nagy is researching ways to understand this process and force the viruses to make mistakes happen more quickly and more often so that molecular parasites developed from the virus can out-compete (and minimize or eliminate) the parent virus before it has killed or debilitated the plant.

In his laboratory, Nagy has been able to cause mistakes in a virus that is widely found— and destructive— in wild tobacco and tomato. These “mistakes” compete with the original virus and weaken its ability to destroy the plant, but it doesn’t live very well even with the virus having been weakened.

Nagy has genetically modified these “mistake” viruses, so that they can out-compete the parent virus so well that they can eliminate the parent virus from the plant. And because the modified “mistake” virus causes no harm to the plant, the plant thrives.

How does the new, molecular parasite work? Nagy rubs a bit of the new, genetically modified “mistake”virus on a leaf of wild tobacco, previously infected with the “parent” virus. The new parasite out-competes its parent virus and the plant recovers.

Nagy is enthusiastic that his technique can be refined and used to help farmers protect their crops. “Conceivably, farmers could spray crops with genetically modified ‘mistake’ viruses to protect their crops. But more likely, skilled plant breeders will be able to breed into seed the ‘mistake’ virus so that the plant will be protected from the time it germinates,” he said.

How does the scientist with so much enthusiasm stop thinking about his research when he goes home? He doesn’t.
“I tell my 9-year-old about the value and power of science and how we can protect plants, animals, and humans,” Nagy said.

Proteins That Tell Genes What to Do

Think about what you ate yesterday. Try to name something you ate that doesn’t have any connection with seeds, either directly or indirectly. You probably can’t.

That’s why plant scientist Sharyn Perry’s very basic research has such importance. Her goal is to find out how plant cells “know” how to develop into seed tissue that eventually grows into a new plant or is eaten for food for humans or other animals, some of which in turn are consumed by people.
It’s really molecular biology with an agronomic purpose. She’s investigating things that you can’t see with a naked eye that are both complex and simple at the same time. They’re complex because she can’t see what’s really happening at the molecular level; they’re simple because the process is likely straightforward enough once she understands it.

Her goal is to understand better something called AGL-15, which is shorthand for Agamous-like 15, a protein that is involved in gene expression. AGL-15 sets in motion what scientists call transcription machinery— enzymes that glide up or down the DNA and turn genes on or off. If the gene is turned on, it is expressed and the plant develops a certain way; if it is turned off, it’s not expressed and the plant develops quite differently. As such, then, AGL-15 is necessary for switching on or switching off genes that eventually lead cells to develop into seed.

How can a researcher investigate things that she can’t really see? That’s complicated.
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, which binds to AGL-15, which is bound to the DNA. Tiny beads that are so small that you’d have to have many of them to be able to detect them are added to the mixture, where they bind to the antibody. Then, after the mixture is whirled a bit in the centrifuge, the beads— now with the antibody, DNA, and protein together clinging to them— are removed and heated. Heating separates the DNA pieces from the protein. The “cleaned” DNA is replicated (so that she has more of it to work with) and then compared with the known Arabidopsis genome map to see exactly where the AGL-15 was positioned. (Even though Arabidopsis is a weed, researchers have determined its entire 5-chromosome genome map.) By comparing the DNA fragments with the known genome map, she will be able to ascertain just which genes are turned on or turned off by AGL-15.

Already, her research has isolated genes that have passed many of the tests to show that they 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 regulates will help us understand how this particular protein functions during plant development. Because this protein is a member of a protein family believed to be involved in critical development decisions of fungi and animals, as well as plants, I am hopeful this research can help our understanding of the entire cell differentiation process in many organisms,” Perry said.

Sharyn Perry

Precise Maps, More Precise Farming

Soil scientist Tom Mueller is refining techniques that Cro-Magnon hunters developed about 35,000 years ago: making maps of productivity. The early hunters used bits of charcoal to draw on cave walls pictures of animals they hunted along with track lines and tallies to show the animals’ migration routes, presumably to help the hunters become more successful on their next hunt.
But instead of a lump of charcoal, Mueller uses high technology equipment, some of it situated several miles in the sky, to make productivity maps. And instead of noting the migration of wild animals, Mueller’s focus is yield potential in fields. Mueller is using cutting-edge technology to improve the precision of farming.
“Somebody once said that precision farming allows farmers to do the right thing, at the right time, in the right way. Mapping where a field’s fertility is good and where it could benefit from fertilizer helps farmers improve yields while cutting costs,” he said.

And while farmers have been using the technologies of precision agriculture for a few years now, it could be even more precise. And that’s exactly what Mueller’s research is doing. He is using space-age machines and concepts, including global positioning systems (that locate exactly where the tractor is in the field), yield monitors (that record how much grain is harvested within a few square feet of the field), and geographic information systems (that record and map key field factors), as well as soil sensors and remote sensing devices to improve the information farmers have from which to make decisions.

Some of Mueller’s work has shown that the electrical conductivity of soils is related to topsoil depth and depth of fragipan (a hard layer in soils that reduces root growth). Measuring how well a field’s soil conducts electricity gives some indication of yield potential. And registering a field’s conductivity with a global positioning system (GPS) allows farmers to make precise decisions about particular parts of a field. However, electric conductivity varies over time, depending on environmental conditions such as soil moisture.

To understand better whether this variability is important, Mueller checked soil conductivity within fields several times over the course of a year. Using a special device that sent an electrical charge from one coulter (which looks a great deal like a circular knife you use to cut pizza) to another coulter, both of which were slicing through the soil, he measured soil conductivity at the same points at different times during the summer. The amount of electricity that the second coulter picked up was compared with the amount sent to determine the soil’s conductivity.

Although the electrical conductivity values at every point changed throughout the growing season, the pattern within the field remained relatively constant, suggesting that farmers using electrical conductivity as part of their precision agriculture strategy may want to take into consideration that values at any point are contingent upon soil moisture and other factors that vary throughout the season.

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