Rick Spinrad, Vice President for Research, Oregon State University

When land grant universities were created 150 years ago, science was already an international activity. Well before the signing of the Morrill Act in 1862, American scientists aboard six U.S. Navy vessels had circumnavigated the globe, collected thousands of plant and animal specimens and mapped parts of the Pacific Ocean from the Columbia River to Antarctica. In 1859, Charles Darwin published his theory of evolution partly on the basis of a worldwide voyage aboard the HMS Beagle. The world’s first international scientific conference was held in 1860, two years before President Abraham Lincoln set the land grant research and education engine in motion.

These universities — the people’s colleges as they were called then — are a singular American innovation. They put a college education and the world’s collected knowledge within the reach of everyday people and focused their energies on such practical endeavors as agriculture and engineering. And they have made global impacts (think the Green Revolution or the computer). They have also made global opportunities available to the sons and daughters of every state, regardless of income or social class.

My own career as a scientist, begun through connections made at Oregon State, has taken me to South America, Africa, the Mediterranean and more than a few unlikely places, such as a cattle-hauling freighter in the Congo River. By its very nature, oceanography is an international endeavor. Ocean currents and ecosystems have no respect for political boundaries.

In one of the Earth's most active fault zones, OSU geoscientist John Nabelek and colleagues are defining the forces that created Mt. Everest and threaten millions of people. (Photo courtesy of John Nabelek)

While we are committed to this state — its people, governments and businesses — international collaborations are also crucial to our mission. Our researchers, faculty members and students alike, work on transdisciplinary projects on every continent. In Terra, you can read about students studying wildlife management in Africa, deep-sea methane near South Korea and sea urchins in Ireland. Our anthropologists and agronomists are at work in India and China. Our geologists are studying the Himalayas and the Andes. Our chemists work with colleagues in Scandinavia, Germany and France. Water resources scientists advise the United Nations and national governments. Public health researchers work in Africa, Mexico and Taiwan.

In the OSU Research Office, we regularly review proposals from faculty members who are being recruited for international projects, but their work pays off for Oregon. It gives them a rich perspective on the world and enables them to train our students with the latest knowledge. And our graduates help Oregon businesses (farmers, equipment manufacturers, apparel design companies) compete in the global marketplace.

There are still important challenges to address in managing this far-flung enterprise. The volatility of the global economy means that three-month-old financial agreements might need to be renegotiated. Concerns about protecting national commercial interests raise regulatory compliance issues, which dictate careful, sometimes complicated considerations about access to equipment and materials. And, despite translation apps and cultural competency training, the Tower of Babel is still standing (How do you say “earned value management principles” in Farsi?).

Just as technology links the world economy and events echo within minutes across the globe, researchers collaborate across international boundaries in ways unimaginable only a generation ago.

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For more information about education abroad opportunities for OSU students, contact the International Degree & Education Abroad (IDEA) office at 541-737-3006.

Reported in this week’s issue of the journal Science, the findings could lead to new understandings about the molecules that drive processes in biology, medical diagnostics, nanotechnology and other fields.

X-ray reflections between the black and green lines hold useful information but are typically discarded. (Image courtesy of Andy Karplus)

Like dentists who use X-rays to find tooth decay, scientists use X-rays to reveal the shape and structure of DNA, proteins, minerals and other molecules. As X-rays pass through the lattice of atoms, they reflect distinctive patterns, and scientists use those patterns to determine what atoms are present and how atoms are bonded to each other. However, some data are typically discarded because of concerns over quality. In particular, data derived from edge regions of the pattern — although very important for understanding the details of structure — are often overwhelmed by the random errors associated with measuring a weak signal in the midst of a lot of background noise.

Oregon State University biophysicist Andy Karplus and his colleague Kay Diederichs at the University of Konstanz in Germany have now proven that useful information can be gleaned from data that have up to about five times the noise levels that have previously been considered acceptable. “The criteria that have been used in the past are way too conservative,” said Karplus. “These data that people have been throwing out are actually good.”

The bottom line for crystallographers is the accuracy of their molecular models, those physical representations of the arrangement of atoms. The better the model, the better it will predict the pattern created by X-rays passing through a molecule, and the better it will be for guiding the development of new drugs and nanotechnologies that operate at the molecular scale. Although the first X-ray diffraction pattern was recorded 100 years ago and the first protein structures were determined 50 years ago, scientists have struggled to find statistical methods to connect data quality and the accuracy of their models.

This chart offers proof that data at the edges of X-ray reflection patterns contribute to model accuracy. (Image courtesy of Andy Karplus)

The new method may be the most important conceptual advance in the past 20 years in how these data are used in modeling, the scientists said. In 1992, statistics were developed to ensure that models were not biased by randomness or “noise.” The new method carries that further by showing how data from parts of the measurement where noise becomes stronger can still provide information that makes the model more accurate. It also allows scientists to see directly where the model is limited by noise in the data and where the model is a better estimate of molecular structure than experimental data.

“The question is, ‘Where do we cut it off?’” said Karplus, whose research focuses on protein structure and stability. By adding data at incremental steps and showing how the model improved, Karplus and Diederichs showed that scientists had been cutting off their analyses too soon and discarding data that could sharpen their view of molecular structure.

“The big impact on the field will be that every structure determined from here on out will be a little more accurate because people won’t throw away data that are OK. If you have a crummy image of the protein, it will get a little sharper. If you have a good image of the protein, it will also get a little sharper,” added Karplus.

For example, he noted, some enzymes work in concert with water molecules embedded within their structure. However, it takes data at a certain level of detail (about 2.6 angstroms) to discern exactly where water molecules are suspended between the atoms of an enzyme. If X-ray data at that scale were being discarded, it could mean that the scientists are not able to conclusively demonstrate the presence of water and thus cannot properly understand how the enzyme works.

While the method will be an important step for X-ray crystallographers, Karplus and Diederichs think that other physical sciences may also find ways to benefit from this type of data quality analysis. They also discovered that one branch of science has been using this type of statistical analysis for many years. The field of psychometrics — the analysis of data from psychological tests — has used a similar technique called the “Spearman-Brown prophecy formula” to determine the minimum length of such tests.

Andy Karplus

Kay Diederichs

Karplus and Diederichs have worked together off and on since 1985 when Karplus was an Alexander von Humboldt post-doctoral fellow in Germany. In 1997, they published a paper demonstrating that certain statistics used in analyzing X-ray crystallography data were misleading, but few crystallographers have adjusted their practices since that time. In 2011 during a sabbatical leave, Karplus visited with Diederichs in Germany to develop the new method. “Now that we know that very noisy data are useful, this will presumably enable still further improvements as it stimulates new software development to do a better job of handling such weak data,” said Karplus.

The paper is also the subject of a Perspectives piece in the same issue of Science by Phil Evans of the MRC Laboratory of Molecular Biology in Cambridge, England. The research was supported by grants from the National Institutes of Health and the Alexander von Humboldt Foundation.

(Photo: Karl Maasdam)

“A lot of people think you have to look like this to be a scientist!” says Professor Sujaya Rao, pointing at Einstein. A giggle ripples through the room.

Professor Rao is here to dispel that stereotype. An entomologist (bug scientist) who studies pollinators, like bumble bees and honey bees, as well as pests that damage crops, Rao wants young girls to know that science is wide open to them. That’s why she and other women at Oregon State University, students as well as professors, are devoting their Saturday to being role models and encouraging girls to consider careers in science and engineering.

About 120 girls from all over the state of Oregon participated in the annual science workshop for girls, Discovering the Scientist Within. “We collected information on schools and towns where they came from,” Rao reports. “Some came from Burns and Hines and Jewell and places I had never heard of!”

The discovery began with an engineering challenge: build a catapult. After teams of five or six girls had finished fashioning their catapults from wood and rubber bands, they tested their inventions by launching cotton balls as far as they could fly.

After that, the girls headed across campus to visit labs of their choice. At one lab, students learned about amphibians in the Northwest from graduate students Lindsey Thurman and Jennifer Rowe, a duo that calls itself “Women of Wildlife.”

First they gave a presentation about all sorts of frogs, newts and salamanders — including a weird video in which a bullfrog eats a poisonous newt and dies instantly from the poison, after which the newt triumphantly emerges from the dead bullfrog and walks away. Then the girls got to handle and feed the live amphibians living in lab.

(Photo: Karl Maasdam)

At another lab, the girls built and tested blades for a model wind turbine. They generated wind with a big fan, and then measured the voltage produced by their blades. Kari van Zee, who was leading the lab, helped them rethink their designs to produce more electricity.

Discovering the Scientist Within is sponsored by the OSU Provost’s Office, the SMILE Program, STEM Academy (formerly Saturday Academy), Scientists and Teachers in Education Partnerships, 4-H Youth Development, the Women’s Center, and Pre-college Programs.

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Read a story and see photos from the Discovering the Scientist Within workshop in the Corvallis Gazette-Times.

“People ask ‘why?’” says Johnson. “I just say, ‘because it’s interesting to me.’ It’s so simple,” he adds, as though he were taking snapshots at the beach, “but you get a lot of information out of it about the molecules.”

Ken Hedberg advises undergraduates Robert Johnson, right, and Luke Costello. (Photo: Karl Maasdam)

For Johnson and Costello, there’s more to it than personal interest and curiosity. They’re solving problems — troubleshooting equipment, puzzling over data with Hedberg, running numbers, reporting results — on their way to bachelor’s degrees in chemistry at Oregon State University. They both plan to attend graduate school and to pursue research full time, Johnson in chemistry and Costello in material science.

Every good coach, whether in baseball or chemistry, focuses on the fundamentals. Hedberg shows his students how to transform solid materials into gasses, generate and guide an intense electron beam the width of a human hair through the gas, record the resulting “diffraction pattern” and use the results to calculate the distances between atoms that define the size and shape of the molecule. To get on base, Costello and Johnson run samples to make sure the machinery is working properly. Convincing evidence of the shape of a complex molecule is a home run.

Hedberg, an OSU alumnus (Chemistry, ’43) and emeritus professor, explains further: “The energy of the electron beam we use is so great that it passes right through the atoms, looks at the nucleus and gets bent around the nucleus. And as these electron waves pass through, they interfere with each other and create a diffraction pattern. That diffraction pattern is what we analyze to determine the structures of the molecules in the gas phase.”

Since he came to OSU in 1956, Hedberg and his students have explored a library of compounds — halides and butadienes, diboranes and cyclohexanes. Unless you’re a chemist, you probably wouldn’t know a halide from an oxide, but in 1993, he and his team were the first to confirm and publish the structure of a newly discovered soccer-ball shaped molecule that had made the headlines: carbon 60, aka the “buckeyball.” Hedberg’s analysis of carbon 60 in the gas phase turned out to be more accurate than studies of its solid form.

In past generations, you would have been hard pressed to find undergrads doing this kind of work. Original research — studies that push the edge of current theory and practice and contribute new knowledge — used to be the domain of graduate students, post-doctoral researchers and the faculty. Undergrads had to get through the basics before they were admitted to the inner sanctum of the lab.

At OSU, as at colleges and universities around the country, Johnson and Costello are part of a movement, undergrads who conduct independent research and original creative work as part of their academic programs. It’s not learning by listen and repeat-after-me. It’s about jumping in with both feet, curiosity-based inquiry under the guidance of people who have been there and remember the thrill of creating something new. In the process, students learn about themselves — their skills, personal goals and career interests — as much as about atoms, the arts, the environment, human health, technology and other fields.

“Independent research teaches you how to work things out yourself and not have somebody hold your hand the whole way,” says Costello, who nevertheless appreciates the supportive, close-knit atmosphere he’s found in the OSU chemistry department. “I have friends who are in big labs elsewhere and end up watching other people’s experiments or doing total grunt work. They’re not doing the actual experimental work.”

Knowing how molecules are shaped, says OSU emeritus professor Ken Hedberg, leads to understanding how they function. (Photo: Karl Maasdam)

And besides, he says, “Ken Hedberg’s a great guy to work for.”

Independence and ownership — what Susie Brubaker-Cole, associate provost for academic success and engagement, calls “a feeling of agency” — define this activity. So does mentorship. In teams or one-on-one, faculty members instruct and guide undergrads through the process of asking questions, designing experiments, analyzing data and creating presentations. This “learning community” of undergraduate and graduate students, post-doctoral researchers and faculty members can become a student’s family away from home, adds Brubaker-Cole. And the faculty link today’s students to academic traditions and culture. In Hedberg’s case, that legacy includes another stellar OSU alumnus, Linus Pauling.

Job on the Home Front

Hedberg grew up in southern Oregon and graduated from Medford High School. In 1943. with an OSU chemistry degree in hand, he went to work for the research arm of the Shell Oil Co. in California on aviation gasoline, synthetic rubber and penicillin extraction, projects deemed crucial to the war effort.

After earning his Ph.D. in physical chemistry and working as a post-doctoral researcher at Caltech, Hedberg came to OSU with strong encouragement from Pauling. OSU Chemistry Professor Earl Gilbert had made a second job offer to Hedberg that spring (Hedberg turned him down the first time), and the young chemist sought Pauling’s advice. One evening, on the veranda of Pauling’s Pasadena home, the Nobel Prize winner urged Hedberg, already an expert in the analysis of molecules by electron diffraction, to accept.

After he came to OSU, Hedberg maintained his friendship with Pauling, and with nearly continuous National Science Foundation support for his research since 1962, he depended largely on graduate students to help him with studies in molecular structure. Although he retired in 1987 and turned 91 in February, the emeritus professor of chemistry continues to work nearly every day in his office and plays an occasional game of tennis. “My wife Lise says she is retired and knows it and that I am retired and don’t know it,” says Hedberg.

Meanwhile, his NSF grants have shifted to support for undergraduates like Costello and Johnson. “They are doing much the same kind of work that my graduate students used to do. It’s lots of fun. These kids are bright, and for the most part, they have been quite interested and productive,” he says.

His goal, he wrote in a 50-year retrospective published in the journal Structural Chemistry, is always to answer a simple question: “Why are things the way they are?” In 2005, after more than five decades of seeking answers through chemical structure, Hedberg traveled to Ulm University in Germany to receive one of the highest honors in his field: the International Barbara Mez-Starck Prize, given to scientists who have made outstanding contributions to structural chemistry.

In addition to his achievements, Hedberg brings something else to his role as a student mentor. Virginia Cross, a 1972 OSU chemistry alumna, recalls that Ken and his wife Lise, a chemist and computer programmer who wrote analytical software for the lab, made students feel welcome. “It was a little family down there in the basement in the chemistry building,” she says. “He respected you to the point of saying ‘what do you think about this?’ He would ask for your opinion even if he could have just told you what he thought. And he was interested in your life, not just the science.”

Cross was a forerunner of today’s trend in undergraduate research. With support from NSF, she spent the summer of her junior year in Hedberg’s lab analyzing sulfuryl fluoride (a pesticide). Success in determining its structure helped her get into graduate school at MIT and led to a paper in the Journal of Molecular Structure on which she was co-author with Norwegian chemist Kolbjørn Hagen and Hedberg.

Currently a resident of Houston, Cross grew up on a dairy farm near Hillsboro, Oregon, and worked in the chemical industry and, until her retirement in 2010, with Richard Smalley, discoverer of the “buckeyball” molecule and a Nobel Prize winner. She has stayed in touch with Hedberg over the years.

National Imperative

Three years before Cross graduated from OSU, MIT created the country’s first campus-wide undergraduate research program. Over the next two decades, Caltech followed suit, the NSF spurred new opportunities with a Research Experience for Undergraduates program and a national conference for undergraduates got under way. That annual event continues to attract student presenters from the sciences, engineering, the humanities and the arts.

At OSU, student opportunities have grown along with the university’s research portfolio, which has more than doubled in the last decade. Little university-wide data is available (monitoring student participation is left to each faculty member, department and college), but personal discoveries are shaping today’s undergraduates in ways their parents could have hardly imagined.

The experiment is taking place at Oregon State University in a special laboratory equipped with huge wave machines. When a strong earthquake shakes the Earth beneath the ocean, it can cause a giant wave called a tsunami. These giant waves can travel for hundreds of miles across the ocean.

An undersea earthquake triggers a tsunami.

When a powerful tsunami reaches the shore, it can wash away anything in its path. Boats, cars, roads, bridges and buildings can get picked up and carried off.

To help people prepare for these destructive waves, scientists at OSU are studying their incredible strength. If scientists like Professor Harry Yeh can discover how much force the waves carry when they come ashore and crash into buildings, they can help builders, engineers and architects to design stronger offices, stores and houses.

“Strong buildings can stand up to a tsunami,” says Professor Yeh, who is one of the world’s top experts on tsunamis. “We have to figure out the best way to do it.”

The scientists conduct their experiments in OSU’s Hinsdale Wave Research Laboratory, one of the largest wave labs in the world. In the lab, there is a very long, narrow tank made out of cement. The tank, which holds 300,000 gallons of water, is kind of like a flume at a water park. Scientists can create waves in the tank and then calculate the strength of the waves.

Simulated tsunamis crash into scale model buildings at OSU's O.H. Hinsdale Wave Research Lab, the nation's largest tsunami test facility. Engineers have run tests with the Oregon coastal communities of Seaside and Cannon Beach (Photo: Frank Miller)

“Tsunamis are very difficult to measure in the real world because they don’t happen very often and when they do, they happen very fast,” says Alicia Lyman-Holt, who organizes tours of the wave lab for students and other visitors. “That’s why scientists use models to study them. Models are a substitute for direct observation.” These experiments will help make people safer the next time a tsunami happens.
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Arrange for school tours of the Hinsdale Wave Research Lab here.

See tsunami wave tests in action at OSU’s Hinsdale Wave Research Lab in a video produced by the National Science Foundation.

Simulated tsunamis crash into scale model buildings at OSU's O.H. Hinsdale Wave Research Lab, the nation's largest tsunami test facility. Engineers have run tests with the Oregon coastal communities of Seaside and Cannon Beach (Photo: Frank Miller)

It may come like it did the last time, in the middle of a cold and blustery January night. Suddenly the ground will begin to shake, windows will shatter, bridges collapse, the electricity will go out and parents will frantically try to find a flashlight and dig sleepy kids out of bed, ignore everything else and run – because they know they only have minutes before the water arrives.

Even worse, it may come on a warm and breezy summer afternoon in July, when tens of thousands of visitors fly kites, build sand castles and play fetch with their dogs on one of the most beautiful stretches of coastline in the world. The rumble and shaking on the crowded beaches will quickly be replaced by a receding shoreline as the water eerily slides away, and people will start to run, anywhere they can, to get to higher ground – because they know the water will soon be coming back.

It will be scary, it will be destructive, and it’s going to happen, reasonably soon. People will talk for generations to come about the great subduction zone earthquake and tsunami of ____. Fill in the blank with a date; science can provide some guidance, but no one knows for certain when it will be.

Pat Corcoran, a coastal hazards outreach specialist with Oregon Sea Grant, is mindful of these risks and calls the disaster that’s waiting to happen “arguably the greatest recurring natural hazard in the lowest 48 states.” That’s about right. Subduction zones – like the Cascadia Subduction Zone that lurks just off the coast of the Pacific Northwest – produce the most massive earthquakes in the world. And their “up and down” ground motion triggers tsunamis, one of the most deadly ocean wave events in the world.

Like Clockwork

The problem is, at least in the United States, these events don’t happen very often. In fact, until the mid-1980s, scientists didn’t think great earthquakes and tsunamis were caused by Pacific Northwest fault zones. Then some pioneering research by the U.S. Geological Survey, Oregon State University and others began to unravel some ancient mysteries. Scientists found that not only do they happen here, they occur pretty regularly, about every 300 to 500 years on one part or all of the Cascadia Subduction Zone, which runs 700 miles from Cape Mendocino in California to Vancouver Island in Canada. The last event was pinpointed because the enormous tsunami it created raced all the way across the Pacific Ocean to Japan, where written records were kept. It occurred here about 9 p.m. on Jan. 26, 1700.

“The Native Americans at the time of the last subduction zone earthquake in 1700 had a rich oral history surrounding earthquakes and tsunamis,” Corcoran says. “One tradition encouraged people to weave long ropes. That way, the saying went, following the earthquake a person could tie one end of the long rope around a tree and the other onto their canoe in order to ride out the tsunami waves.”

It’s now 2010, more than three centuries later. The newest studies produced by Chris Goldfinger, an OSU marine geologist and one of the world’s leading experts on the Cascadia Subduction Zone, indicate that there’s a 37 percent chance of a partial rupture of the zone within the next 50 years, an event that could be similar in magnitude to the earthquake just experienced in Chile.

“Perhaps more striking than the probability numbers is that we have already gone longer without an earthquake than 75 percent of the known times between earthquakes in the last 10,000 years,” Goldfinger says. “And 50 years from now, that number will rise to 85 percent.”

So it’s coming soon, possibly tomorrow. Possibly in 10 years. A better than one in three chance within the next 50 years. But no one knows for sure, and that isn’t going to change. With existing science, earthquakes cannot be predicted with precision; we can only prepare.

But Are We Prepared?

A few years ago, local residents in Cannon Beach, Oregon, were pondering that question, as they followed the developing science on subduction zone earthquakes and worked with officials from the Oregon Department of Geology and Mineral Industries on evacuation maps for the anticipated tsunami.

Preparation for a tsunami, in this context, would be defined as people knowing what to do, where to go, getting to high ground and having the time to do it. Jay Raskin, a longtime resident, community leader and local architect, didn’t like what he was hearing.

“Around then, the scientists were describing and updating the potential risks for an earthquake and tsunami caused by the Cascadia Subduction Zone,” Raskin says. “We talked about the distances we needed to go, how high the water might get, where high enough ground was, the bridges that probably would be destroyed.

“And then we’re thinking, oh darn, this strategy of getting to high ground might not work for everyone,” he says. “For some people there just might not be enough time. We needed another option.”

Then Hurricane Katrina struck, and another lesson was offered to the Cannon Beach residents. In the aftermath of the storm, not only had the devastation of coastal communities been enormous, but there was no functioning city government, no working facility to help rebuild.

A Sunny Day at the Beach

Cannon Beach is a small coastal community a little south of Seaside, Oregon. It’s butted up against coastal headlands and stretches for several lovely miles along the Pacific Ocean coast. Most of its 1,700 residents live within a few blocks of the beach, and about half of them, and 75 percent of the businesses, reside within a tsunami inundation zone. But it could be much worse. On a peak summer day, up to 12,000 people may crowd the beaches around Cannon Beach. The city presents a microcosm of an issue that affects a vulnerable shoreline about 900 miles long.

Tsunami Evacuation Building

In addition to a tsunami response plan, the city needed a new city hall. So Raskin and others had an idea. Why not build a structure that could survive a tsunami, stand above the incoming water, give local residents and visitors a safe place they could run to on short notice, save many lives, and also serve as a base of operations after the disaster to help the city recover and get back up and running?

It was the comparatively new concept of “vertical evacuation” to escape a tsunami, and it was a good idea. Two problems: No structure of that type had ever been built in the United States, and in the few places in the world where such structures had been built, such as Japan, none had yet experienced a tsunami. So as an engineering challenge, this was literally uncharted water. Also, it would cost more. A design has now been created for a new 10,000-square-foot structure, and it’s estimated to cost around $4 million, about double the cost for a more conventional building.

But the issues are real, and the Cannon Beach residents knew it. They had watched the devastation from the Sumatra earthquake and tsunami in 2004, where 230,000 people died, most of them not from the earthquake, but rather the tsunami. The geology of that region is nearly identical to the Cascadia Subduction Zone.

“After the Sumatra earthquake, I saw on television this scientist from Thailand, who had tried years before to convince local authorities to put in warning buoys, but no one did anything,” Raskin says. “He was in tears, he considered it a personal failure.”

“That struck me hard,” he says. “I was a city councilor at the time, I knew we faced the same issues, and I didn’t want that to happen here, to have to say years later that we knew all about this but didn’t do anything.”

For a nearby subduction zone earthquake like the one expected on Cascadia, warning buoys are not really the point. The earthquake itself will give any informed person all the warning they need, and only minutes will be available to get to high ground before the water starts rising and just keeps coming – an event Raskin likens to “a sneaker wave on steroids.”

The Real Enemies: Time and Transportation

So last May, at the Hinsdale Wave Research Laboratory at OSU, a small model of the proposed new city hall building at Cannon Beach was being hit by simulated tsunamis repeatedly, to help address some of the questions. It’s not fancy, essentially a square structure on stilts, but very strong and with a sturdy foundation. But how strong is strong enough? What will be the effect of debris, such as floating cars, slamming into the pillars? OSU was helping Cannon Beach to answer those questions, in research supported by the National Science Foundation.

“We have to know just how strong this building has to be, so the community can build something that will work, but at the same time keep costs as low as possible,” says Dan Cox, an OSU professor of coastal and ocean engineering. “Some buildings may slow the force of the waves before they hit, for instance, and other debris may cause additional impacts.

“In engineering, this is new territory. We’re just scratching the surface of everything we need to know, but these studies should give us a higher degree of confidence in what we build, and in the process our students are learning how to build structures of this type for the future.”

Other work to aid Cannon Beach is also under way at OSU. Harry Yeh, the Edwards Professor of Coastal and Ocean Engineering, one of the world’s leading experts on tsunamis, has been involved with the community for years to help it address concerns, design the new structure. He is now working on an evacuation plan.

“We know we can build a structure that will survive an earthquake and tsunami, and could serve as an emergency shelter,” Yeh says. “Strong, reinforced concrete buildings can stand up to that, we saw that in Indonesia in 2004. And pretty much everyone agrees this structure would be good to have. But it will cost more, so to make this feasible, we have to figure out the best way to balance cost and function.”

The initiative in Cannon Beach is unique, and if implemented, will be the nation’s first structure designed specifically to survive an earthquake, resist the forces of a tsunami, and hopefully save lives. OSU has worked closely with state and federal agencies, as well as private companies, to make this happen. The result could form a model, both physically and inspirationally, for many other coastal communities that face similar concerns. And community support so far, Raskin says, has been reasonably strong. People have raised some fair and intelligent questions, but almost no one is advocating the status quo. Funding support may ultimately be sought from both local, state and federal levels and the private sector.

But Cannon Beach is one small town, on one short section of beach. The earthquake on the Cascadia Subduction Zone, when it happens, could be one of the great geologic events in world history, affecting three states, some of British Columbia, major cities and many millions of people. That’s a big problem, which goes well beyond the issue of the expected tsunami.

Living in the Quake Zone

Are we prepared?

OSU researchers are doing what they can. Earthquake and tsunami simulation modeling is being done in several Oregon sites. A course has been created and is being taught on “living with earthquakes.” OSU researchers have worked with the Oregon Department of Transportation to simulate tsunami loads on coastal bridges. Scientists have gone to Sumatra, to American Samoa, to Chile, to the sites of all the recent major subduction zone earthquakes and tsunamis in recent years to learn whatever might help.

To further explore these questions, Scott Ashford and Solomon Yim from OSU were part of a group supported by the National Science Foundation who went to Chile this past spring after the February 8.8 magnitude earthquake — also on a subduction zone similar to that of the Pacific Northwest. Yim, a professor of civil engineering, led a team of tsunami, structural and geotechnical engineers and surveyed damages to ports, coastal buildings and bridges. Ashford, professor and head of the School of Civil and Construction Engineering at OSU, said the group wanted to learn as much as possible about what had happened, what worked and what didn’t.

Chile, even more than the United States, has experience with subduction zone earthquakes. They happen with more frequency there, and a massive 9.5 event in 1960 was the largest earthquake ever recorded. Because of that, they have modern and aggressive building codes, as good or better than those in the Pacific Northwest, and much better than those used when many of the urban structures in Oregon and Washington were built 30 or more years ago.

“Part of what was striking about the Chile earthquake was the geographic extent of the damage. It was spread out over an area essentially from Seattle to Medford here in the U.S., and from I-5 to the coast,” Ashford says. “The damage itself, as you often see with earthquakes, was variable. Some areas were very hard hit, others much less.”

Chile, Japan and New Zealand – like the U.S., all situated on the notorious “ring of fire” around the Pacific Ocean – have some of the best seismic design standards in the world, Ashford adds. Engineers in Chile were able to observe certain types of architecture, often square, unimaginative buildings, that tended to resist damage much better than more innovative and irregular designs. But it still wasn’t good enough.

“In Concepcion, all the bridges from the south were collapsed or out of commission; people were cut off,” Ashford says. “You would see people living in tents, staring at the building they used to live in but afraid to enter it even for a few minutes to get their belongings, fearing it would collapse. And of course in the areas hit by the tsunami, the damage was just devastating; it was really heartbreaking.”

Engineer for Resilience

Oregon and Washington, Ashford says, face even greater devastation in the future. “We’re going to get hit worse than Chile did; I suspect much worse. We have many large buildings in our cities that were built in the 50s, 60s and 70s that will not do well in the earthquake.”

A prime lesson Ashford says he took away from the recent Chilean experience is to preserve the lifelines: electricity, gas, water, communication and transportation, as well as critical facilities like hospitals, fire stations and schools.

“What we need here is resiliency, to provide the infrastructure for rescue, relief, and recovery efforts that will enable Oregon to bounce back from such a disaster,” Ashford says. “Like the proposed city hall at Cannon Beach, that will save lives and give you something to build around.”

Ashford sees OSU as the logical institution to lead that effort. Working with the Oregon Department of Transportation, the National Oceanic and Atmospheric Administration, utility companies, cities, and other agencies, OSU has the engineering and scientific and management expertise to help coordinate preparation for a major disaster, to build in that resilience that can literally mean the difference between life and death after a major disaster.

Fortunately, there may still be time to accomplish a great deal. Oregon Sea Grant’s Pat Corcoran noted that “we are the first modern generation to intellectually understand that we will experience great earthquakes and tsunamis.” The next event could happen tomorrow, but it also might not be for 30, 50 or 100 years. If so, that could offer a pretty good window of opportunity for public education and outreach for both local residents and tourists, community preparations, new and better building designs, sustained research programs, replacement of aging and dangerous structures. All of that is possible and many of these issues can be addressed if everyone involved — government, universities, agencies, people — work together to create a safer future.

But there’s a lot to do and only a limited time available to do it. Because a massive earthquake is coming that will destroy homes, buildings, roads, bridges and infrastructure across the Pacific Northwest. And a massive tsunami is coming with waters that will sweep ashore with deadly force. They are coming. We know that.

Are we prepared?

No.
________________________________________
See a, April 2012 video about tsunami preparedness by Tom Bearden, National Public Radio.

Watch Risky Business in the Northwest on PBS. See more from PBS NewsHour.

For information about supporting research and teaching through faculty endowments, contact the Oregon State University Foundation, 1-800-354-7281 or visit CampaignforOSU.org.

In his quest to discover new antibiotics and cancer-fighting drugs, Taifo Mahmud is studying bacteria that originated in black-water ecosystems on the other side of the world. Click on the link above to listen to a podcast. (Photo: Karl Maasdam)

Taifo Mahmud opens the incubator and, picking up the stacked petri dishes one by one, raises them to the light. Each round, lidded container displays a colorful pattern pocked or sprayed across the agar. The researcher points with pride to the branching abstractions of yellows and rusts, oranges and greens, the visible etchings of billions of microscopic bacteria multiplying in his Oregon State University lab.

In these microbial colonies collected from the rich, dark soils of Indonesia’s equatorial rainforests, he foresees nothing less than a healthier future for humankind. From them he has isolated compounds that could become the basis for new antibiotics and drugs to fight cancer.

“Microorganisms have yielded most of the therapeutic agents that have revolutionized modern medicine,” says Mahmud, a medicinal chemist in the College of Pharmacy who specializes in natural products. “Since the 1940s when soil bacteria were first identified as producers of antibiotic substances, over 10,000 biologically active compounds have been isolated from these organisms, including over 3,000 antibiotics.”

Their waters stained by tannins from peaty soils, "black-water" rivers like this one meeting a muddy tributary on the island of Borneo are rich sources of novel medicinal compounds. (Photo: Don Lyon)

The microbes in OSU’s Pharmaceutical Science lab, which are undergoing tests or “assays” that will determine their power to heal, originated halfway around the world in one of Earth’s biodiversity hotspots, the Indonesian archipelago curving between the Indian and Pacific oceans. In the steamy jungles of Borneo, Sumatra, Papua and hundreds of the nation’s smaller islands, there are unique ecosystems alive with undiscovered organisms: “black-water” rivers. Black water, not to be confused with muddy water, is transparent but tinted, like tea, by tannins leached from peaty soils. Its acid level is like vinegar’s.

A native of Indonesia, Mahmud was eager to investigate the pharmaceutical promise of black-water ecosystems. So he reached out to Dwi Andreas Santosa, director of the Indonesian Center for Biodiversity and Biotechnology, in pursuit of samples. Santosa dove in – literally. On Kalimantan (the Indonesian part of Borneo), home of the rare Kalimantan orangutan, Santosa and his research team donned swimsuits to collect soil from the beds of the Pangkoh Lima and Sungai Kala black-water rivers.

Since the 750 microorganism samples were delivered to OSU in 2005, Mahmud and his colleagues Mark Zabriskie and Phil Proteau have turned up a number of compounds with the power to fight infections and shrink tumors. As a result, diseases ranging from malaria to melanoma are a little bit closer to being scourges of the past.

Germ to Germ

It seems paradoxical, fighting bacteria with bacteria. Yet scientists have long known that these ubiquitous, single-celled microbes have the power to heal as well as to infect. Their curative properties reside in substances they produce in their natural environment to ward off threats or to communicate with each other. Researchers call these substances “secondary metabolites,” meaning they’re not essential to maintaining life but instead serve secondary functions.

Isolating these substances, analyzing their chemical structures and identifying which ones are “bioactive” – potent against infections such as tuberculosis (TB) and malaria or even against cancer – is Mahmud’s life’s work. As a child in Sumatra, Mahmud loved hanging around the clinic where his father practiced medicine. He got to know the TB patients with their hunched postures and rail-thin frames. The dispensary with its bottles of sulfa and tetracycline was as familiar to him as his mother’s kitchen. When time came to choose a career, health care seemed an easy fit. It was his father who steered him toward drug discovery.

“As a doctor, my father worked very hard but could only help 30 people a day, maximum,” Mahmud recalls. “He told me, ‘If you do pharmaceutical research and develop drugs, you can help millions of people every day.’”

Medicine from Dirt

Here’s another puzzle: Can soil really be a source of health? But making “medicine from dirt,” as one website puts it, isn’t really so outlandish when you remember that penicillin was derived from a fungus. Plants, too, have long been known to have medicinal properties. The hunt for herbal curatives was the focus of Mahmud’s doctoral work at Japan’s Osaka University, where he isolated compounds from potentially bioactive species identified by shamans in rural villages. But plants are bulky. Many pounds of leaves, bark and roots must be collected, dried and transported for laboratory research. Marine invertebrates such as sponges and tunicates are another source of healing compounds. But they, too, are unwieldy. Microbes, in contrast, can fit into minuscule spaces by the millions (a quarter-teaspoon of soil contains about 40 million bacteria).

Mahmud likes the practicality of using bacteria. But the work is no less laborious just because the organisms are microscopic. As a practical matter, the lofty quest for a viable drug requires a long, painstaking slog in the lab.

To the outsider, Mahmud’s lab is a bewildering jumble of scientific gear. It’s a place where mysterious, multihued liquids in test tubes and flasks are furiously agitated in orbital shakers. Where shelves are jammed with jars of culture media (the agar ingredients on which the bacteria grow) labeled with the names of such familiar nutrients as soy, potato, yeast and malt. Where microbial strains with unpronounceable names are subjected to technical procedures like spectrometry and chromatography.

It’s on the posters festooning the laboratory walls where the essence of the research starts to become evident. Diagrams of the microbes’ molecular structures, their honeycombed hexagonal cores and trailing side chains of smaller molecules, are the graphic representations of the lab’s findings. As the isolation and manipulation of these complex chemical structures advances, Mahmud and his colleagues move another step closer to lifesaving breakthroughs.

“The original extract contains hundreds of compounds,” says Mahmud. “It’s like when you make a cup of cappuccino – you have sugar, you have lactose, you have caffeine, you have everything in there. If you want to isolate one compound, like the caffeine, you have to separate it from everything else. We split the extract into fractions and keep narrowing down the target until we get a pure compound.”

Once a promising anti-infective compound has been isolated, the researchers clone its genetic “backbone” – its structural blueprint – and then manipulate the genes to create improved versions. They also send samples of the compound to the Oregon Translational Research and Drug Development Institute, a public-private signature research center, for more tests. Anti-tumor compounds are sent to the National Cancer Institute for further study. The compound’s chemical properties and structure are also entered into the Natural Products Library, a searchable database.

“Scientists have sequenced nearly 1,000 bacterial genomes,” Mahmud says. “One bacterium has the capacity, based on its blueprint, to produce 10 to 20 or even more different compounds. In the lab, we try to push them to produce at the highest capacity.”

Novel Compounds

A number of brand-new compounds have turned up in Mahmud’s black-water samples. Among them are six novel metabolites, which the OSU researchers have named “panglimycins” after the river Pangkoh Lima where they were collected. Seven additional new compounds called “limazepines,” a growing group of antitumor antibiotics isolated from soil bacteria, were recently found as well.

As described in the Journal of Natural Products and the Journal of Antibiotics, each of the new compounds takes a different form in lab tests – from colorless crystals to yellowish powders, oils or “needles.” Outward color and texture sometimes give clues to underlying molecular structure.

Finding novel compounds such as these is just the first step on a long journey to a viable drug – a journey that can take decades.

“Even if we find a bioactive molecule, the pharmaceutical companies have to do a lot of testing and clinical trials before they can market it,” says Mahmud. “We’re basically at the beginning of the whole process. The compound we isolate today may not become a drug for 20 years. We’re realistic enough not to get frustrated.”

To support the search for new life-saving drugs in the College of Pharmacy, contact theOSU Foundation.

Swainson's thrush is a common visitor to the H.J. Andrews Experimental Forest where Matt Betts and his students are recording birdsong. You can listen to its call here. (Photo: Greg Lavaty)

Recording the subtle syllables, notes and motifs that distinguish one bird species from another requires some pretty sophisticated gear. But for OSU researchers, collecting audio data in an old-growth forest last summer was a walk in the park compared with analyzing it. “It’s a lot of data,” reports Jed Irvine, a faculty research assistant in the OSU Bioacoustics and Machine Learning group.

Confronted with a terabyte of digital sound from the H.J. Andrews Experimental Forest, Irvine and a team of students in the College of Engineering are building a website that will let them borrow the ears of experienced birders to identify avian singers. These IDs will then be used to “teach” computers how to distinguish a robin from a Swainson’s thrush or a tree swallow for a study being led by forest ecologist Matt Betts.

The terabyte gets its name from the Greek word tera, meaning “monster.” The etymology is apt. Trying to grasp the size of a terabyte – a trillion bytes of computer data – is like trying to wrap your mind around the number of water drops in Crater Lake or sand grains on Cannon Beach. Besides their monstrous size, these audio files may contain all sorts of extra sounds, from streams to airplanes to distant highway traffic. Also complicating the task of automatically recognizing bird sounds is the fact that birds can sing in regional “dialects,” and some even mimic other species.

Where the Birds Are

“The bioacoustic team is developing software that will automatically identify bird species – perhaps even individual birds – so that we can assess population distribution on an ongoing basis,” Irvine explains. Then, without a hint of irony, he adds, “It’s a lofty idea.”

An amateur birder himself, Irvine came up with the idea of creating a website that would allow birders to upload bird images and audio for annotation and discussion. The bioacoustics and machine learning problem being worked on by professors Xiaoli Fern and Raviv Raich was a perfect task for the Web, Irvine says. Once the website was ready for the first round of user testing, he asked local birders to test-drive the site by listening to sound clips online and then posting species IDs for each clip. By the end of June, he had gotten 85 identifications from about a dozen volunteers.

In the next phase of website development, he hopes to make the experience of using the site as close to the experience of “birding by ear” as possible. Each online session will be designed as a “birding trip” into the forest, where volunteer birders can employ their knowledge of birdsong to further the goals of science.

“The next iteration will be more interesting,” says Irvine, who started birding with his dad as a kid in New Jersey. “We want to make the site addictively fun for birders, so that we can get as many bird sound snippets identified as possible.”

Visit the site at http://web.engr.oregonstate.edu/bird.

“The surge in obesity in this country is nothing short of a public health crisis, and it’s threatening our children, it’s threatening our families, and more importantly it’s threatening the future of this nation.”
— First Lady Michelle Obama

Romping in the backyard at Cozy Corners family childcare home, Avery and Lauryn are boosting their health by doing what kids do naturally - running, jumping and playing. (Photo: Nancy Froelich)

When the doorbell chimes, the toddlers instantly forget about the movie flickering on the giant TV screen. Scrambling over the plush sofa and scooting past the coffee table, the five preschoolers at Cozy Corners family childcare home cluster curiously by the door to see who’s here.

These pintsized Albany residents have, after all, seen Beverly Hills Chihuahua before. What they haven’t seen are the mysterious high-tech gadgets Oregon State University doctoral student Kelly Rice starts unloading from her backpack soon after childcare provider Michelle Hoyt ushers her in.

“What are they, what are they?” the kids clamor, crowding around.

“They’re called accelerometers,” Rice tells the wide-eyed boys and girls, who range in age from 2 to 5. “They tell us how much activity you guys are getting while you’re here. Who wants to be first?”

“Me! Me!” Riley yells.

“OK, Riley, come on over here.” She wraps a black elastic belt around Riley’s waist and cinches up the Velcro. “We need to make it nice and snug because the last thing we need is a floppy accelerometer,” she tells him.

The matchbook-sized electronic monitor on his left hip will keep track of activity levels (sedentary, light, moderate, vigorous) by recording the frequency and magnitude of movement. Riley and his playmates will wear the accelerometers for a week during Phase One of an OSU study led by Associate Professor Stewart Trost. This initial activity data will form a baseline, along with each child’s body mass index (the ratio of height to weight, used to estimate the proportion of fat to lean tissue), for gauging progress at the study’s end.

Listen to .mp3 audio of Stewart Trost

Stewart Trost

Cozy Corners is one of 60 Oregon childcare homes in seven economically diverse counties along the I-5 corridor that are participating in the Healthy Home Child Care Project. Half of the homes will use the obesity-combating techniques devised by Trost and his team. The other half will serve as a “control” group for comparison, as well as receive training in food allergies.

The program’s premise: You don’t need fancy jungle gyms or pricey cuisine to make kids healthy and keep them that way. Rather, ordinary household items like card tables and couch cushions can get kids moving, and small changes like switching to skim milk can add up to big benefits.

“We’re making the intervention as simple as possible,” says Rice, who is coordinating the study. “We’re looking for really little things that can make a huge difference, things like giving kids balls and bats to play with, adding a couple of veggies to the lunch menu — teeny little steps.”

Essentially, the program will plug into kids’ innate love of running and jumping and introduce fun, fresh foods like fruit pizza to compete with the “bubblegum-flavored cereal” and “Hot Pockets” children see every day on TV, says Trost.

“Just like puppies and lambs and kittens, kids have a natural inclination to play,” he says. “Active play is inherent to normal development. Yet our studies have shown that kids in family childcare settings are getting only about five minutes of physical activity per hour, on average.”

Designer Diabetes Gear

The statistics are alarming. Nearly 30 percent of American kids are overweight or obese. Their parents are even heavier, with two-thirds tipping the scales at excessive numbers. If trends continue, fully 50 percent of kids born this year will end up with Type 2 diabetes in their lifetimes. Just imagine: Half of Americans soon could be tucking a diabetes testing meter (these days, they come in designer colors like “Tickled Pink” and “Purple Fusion”) into their purse or pocket along with their iPod and cell phone.

It was these startling trends — along with her pediatrician’s warnings about her own daughters’ marginal BMIs — that inspired First Lady Michelle Obama to plant an organic garden at the White House and to launch a national campaign to curb childhood obesity. She has gone so far as to demonstrate how easy exercise can be by hula-hooping on the South Lawn. The changes she made in her own household — a ban on weekday TV, smaller portions, low-fat milk, water bottles and apple slices in lunchboxes, grapes on the breakfast table, brightly colored veggies for dinner — she described to USA Today as “very minor stuff.” But the payoff was surprisingly big. “These small changes resulted in some really significant improvements,” Obama reported.

These are just the kinds of practical strategies Trost and his graduate students are using in their program, which is built around the theme “Journey to Healthy Child Care Home.” Kids will map their make-believe travels and send postcards to friends and family along the way. The program is funded by the National Institute for Food and Agriculture.

Participating childcare homes in Benton, Linn, Lane, Yamhill, Polk, Marion and Washington counties were identified through local “resource and referral” agencies (“R&Rs,” which train providers and help parents find quality facilities). Assistant Professor Kathy Gunter is leading the program design and will train OSU county Extension faculty to use it. They, in turn, will train the providers.

“It’s a train-the-trainers, capacity-building approach,” says Trost. “Our goal is to translate research into practice in a sustainable, community-based way.”

With these kinds of novel approaches, Trost has rocketed to prominence in his field. “Stewart has rapidly become one of world’s foremost researchers of issues related to physical activity in children and youth,” notes Professor Russell Pate of the University of South Carolina. “He has developed an international reputation for his work on measurement and promotion of physical activity in kids.”

In the tropics of Costa Rica, this violet sabrewing hummingbird is helping researchers understand the effects of forest fragmentation on ecosystems.

A thrush’s melody, warbler’s trill and sparrow’s chip-chip-chip form the musical backdrop for a hike in the woods. When birds sharing a forest patch all sing at the same time, the cacophony suggests the jumbled chatter of a human social gathering, with competing tones and pitches. In the din, distinguishing among species of warblers, for instance, or tracking individual chickadees is tricky. Scientists who study birdsong call this the “cocktail party” problem. Further muddying the forest sound-scape is background noise: rushing wind, splattering rain, crashing branches, foraging animals. Making sense of this audio hodgepodge can test a biologist’s mettle.

Matthew Betts is not deterred.

The OSU researcher is taking an innovative approach to recording birdsong in old-growth and second-growth forests. About a dozen microphones recently installed in Oregon’s H.J. Andrews Experimental Forest are capturing the calls of bird communities from high in the canopy to low in the understory. A parallel study is under way in New Hampshire’s experimental forest, Hubbard Brook.

Concerned with widespread reports of declines in bird populations, Betts is developing new ways to analyze trends in biodiversity. “We’re looking at the distribution of 40 or 50 species across the entire elevation gradient at each experimental forest,” explains the assistant professor of forest landscape ecology. “We want to know why species live where they do. Why do some species cut off at 1,200 meters yet others persist higher? Is it competition among species? Is it vegetation that’s driving that relationship? Is it climatic? It’s basic research, but it has big implications for how we predict the effect of climate change on animals.”

Matt Betts

Birds by Bytes

Gathering acoustic data digitally, he says, has big advantages over the current practice: putting people in the woods to count birds, song by song. Still another technological advance – artificial intelligence – will streamline the analysis of the electronic data. By employing smart computers that can “learn” to sort ambient noise from distinct species sounds, a team of computer scientists in OSU’s Ecosystem Informatics Program is translating the recordings into signals that can be read by computers. Betts and his collaborators hope to push forest ecology to a new level of efficiency and sophistication.

“We spend an immense amount of time and money every year surveying birds with technicians,” Betts says. “The overall idea of setting up microphones in the forest was, wouldn’t it be cool if we could have cheap, long-term data?”

But Betts’s investigations don’t stop there.  His research program, which has taken him and his graduate students all over Central and North America – from pollination experiments in Costa Rica to molecular studies of migratory birds in New Brunswick, Canada – has chalked up a lot of firsts: first to influence warblers’ nesting choices with recorded sound. First to put radio transmitters on tropical hummingbirds. First to test continental-scale geographic-dispersal patterns in the chemistry of feathers.

Each study launched from the Betts Forest Landscape Ecology Lab, no matter how far-flung geographically or out-front technologically, has one overarching goal: to isolate the effects of habitat loss, landscape fragmentation and climate change on biodiversity and species persistence (survival over time).

Betts cites a 2010 report from the International Union for the Conservation of Nature showing that steep declines in populations of birds, mammals, amphibians, plants and invertebrates are continuing across the planet, despite some successful efforts at conservation.

“Habitat loss and fragmentation are known to be the primary cause of species extinctions worldwide,” he notes. “With thousands of species verging on extinction, discovering how animals respond to habitat degradation and disruption is urgent if we hope to reverse the trends.”

By opening all sorts of new windows onto avian behavior – such as using LiDAR (Light Detection and Ranging) technology in a recent habitat study with Woods Hole Research Center – Betts has become a noted innovator in the field of landscape ecology.

“Matt’s research on the response of bird populations to forest fragmentation has served as a critical guide for many young and aspiring ecologists,” says Benjamin Zuckerberg, a research associate with the Citizen Science Program at the Cornell Lab of Ornithology.  “Using advanced statistical approaches, he has made significant contributions to the study of ecological thresholds and breeding-site selection in forest birds. Land managers and policymakers, as well as graduate students, appreciate his ease in communicating complex scientific concepts.

“Most importantly,” Zuckerberg concludes, “the results of Matt’s research emphasize the role of landscape ecology in natural resource conservation.”

Lab-Rat Bird

In the hardwood forests of New Hampshire’s White Mountains lives the black-throated blue warbler. Nesting in low-growing shrubs, this abundant warbler is easy to find and count, making it a favorite subject for East Coast ornithologists.

“The black-throated blue warbler is the lab rat of eastern avian demography,” jokes Betts, who first studied the species as a post-doctoral fellow at Dartmouth College.

These handy birds have given Betts surprising new insights into the purposes and powers of song. Wondering how birds choose nesting sites, Betts and a team of researchers from Wellesley College and from Queen’s University and Trent University in Ontario, Canada, recently ran an experiment to see whether, in essence, they could “trick” the warblers into picking poor places by making them think other warblers favored those spots. The scientists played electronic warbler songs at 54 White Mountain locations – scrubby areas with scant cover that warblers normally would bypass. But having heard their species’ songs broadcast as they flew over in the late summer, many returning warblers chose the sub-par nesting sites the following spring. In fact, more than 80 percent of first-time breeding males settled in the bad habitat, Betts and his colleagues reported in the Proceedings of the Royal Society B: Biological Sciences.

“We were very surprised,” Betts told Science magazine’s blog, ScienceNOW. “It was almost as if we’d attracted a spotted owl (secretive old-growth dwellers) to a parking lot.”

Taking cues from fellow warblers is a shortcut to scoping out optimal breeding grounds, Betts explains. It’s a behavior that can aid the species’ adaptability to rapidly changing landscapes.

“The approach this bird uses can be very efficient in allowing individuals to find new habitat quickly when old habitat has been lost or degraded,” he says. “We’re developing a library of species that use this nest-site selection strategy, which may make them less sensitive to environmental changes than species that are poor at finding new habitat.”

Flight Paths

The green hermit hummingbird of Central America weighs over three-tenths of an ounce – approximately the heft of a good-sized chickadee. By hummingbird standards, that’s huge. (In contrast, the Pacific Northwest’s ubiquitous rufous hummingbird tips the scale at just one-tenth of an ounce.) The green hermit’s heavyweight status makes it a prime candidate for tracking by radio transmitter because although the transmitter weighs less than one-hundredth of an ounce, it’s too heavy for the tiny rufous to carry on its back.

Betts and Ph.D. student Adam Hadley wanted to investigate hummingbirds’ travels through the rainforests of Costa Rica to help explain why pollination levels around the world appear to be dropping. In particular, they wondered how fragmented forests – patches of trees left stranded amidst areas cleared for roads, crops or timber – affect the flight patterns of the iridescent, curved-billed pollinators.

“Recently, people have started realizing that landscape configuration, especially fragmentation – how habitat is distributed – can be quite important for some species,” Betts explains.
So in the winter of 2008, the researchers glued miniature transmitters to 19 green hermits with false-eyelash adhesive and then monitored the birds’ movements for several weeks until new feather growth made the transmitters fall off. In the journal Biology Letters, the scientists reported that the birds adhered closely to  forested corridors in the landscape, clinging to treed areas while avoiding open patches devoid of cover – even when that meant flying longer distances. Not only are the longer distances potential stressors for the birds, but the avoided patches may miss being pollinated, thus losing plant diversity over time.

“We don’t yet know for sure if pollen dynamics are being disrupted by forest fragmentation, but we think so,” says Betts. “Our hummingbird research suggests that maintaining riparian corridors of forest between patches could be quite important for pollination dynamics.”

Heroic Triumvirate

Betts’ heroes – three titans of biology, Edward O. Wilson, Ernst Mayr and Paul Ehrlich – all began their careers studying animals (ants, birds and butterflies, respectively). But over time, they extended their inquiries to such sweeping scientific questions as the mechanisms of evolution, Earth’s ecological thresholds and the origins of human nature. All became active in the political sphere, advocating on behalf of the planet’s long-term survival.

While not presuming to share the lofty status of these science superstars, Betts imagines his career taking a similar beyond-the-lab trajectory. For him, however, public-policy work will be a homecoming of sorts. As an undergraduate – motivated by his childhood wanderings among the woods of New Brunswick – he aspired to conserve the forests where so many mysteries were secreted. So he studied political science. He soon realized, however, that if he hoped to influence policy, he first needed grounding in the fine and complex details of ecosystems – in what he calls the “micro” sphere of forest management and conservation. So he went back to study biology and ecology.

Still, it’s at the policy level where discoveries give rise to action. Betts sees himself looping back more strongly to the macro sphere as time goes by. “It can get very frustrating doing science when you’re just pumping out scientific papers and nobody’s paying any attention to it,” says Betts, who serves as OSU’s representative on Oregon’s State Forest Advisory Committee, which provides input to the Oregon Department of Forestry on forest management issues. “That’s what drew me to the College of Forestry, actually. There’s this potential link between basic research and applied work, and then translation into some kind of action.”

If science can, for instance, reveal how fragmentation affects animals – as opposed to simple habitat loss – the findings can guide decision-makers in tangible ways.

“We have the power to design landscapes in different ways,” Betts notes. “Losing the same amount of habitat, developers or foresters could decide to leave wildlife corridors, or they could decide to leave a single big patch instead of making four little ones. It becomes pretty important when thinking about the persistence of species.”

Still, he says, doing science – even stopping for a minute to enjoy a warbler’s stirring call – can be a satisfying refuge from the contentious political arena.

“Basic research is nice because it doesn’t depend on people that much,” he admits. “So if I’m depressed about the rate at which my findings get turned into policy, at least I’m finding out some interesting things about nature. That’s good in itself.”

To support forest ecology research in the OSU College of Forestry, contact the OSU Foundation.

OSU forestry student Steve Ashley has spent six summers fighting forest fires in Central Oregon. (Photo courtesy of Steve Ashley)

Which of Oregon’s abundant tree species can provide not only logs for your vacation cabin but scented oil for your afternoon massage and flavor for your evening cocktail? Juniperus occidentalis, western juniper. This hardy species – which is endemic to the dry, rocky grasslands east of the Cascades – has heartwood that is both beautiful and enduring, fragrance that is coveted for soaps and lotions, and berry-like cones that give gin its characteristic taste (indeed, the word “gin” is derived from the Dutch word for “juniper,” genever or jenever).

Despite its potential market value, this high-desert native is viewed mainly as a worrisome invader across much of Oregon’s rangeland. Its dense roots suck up gallons of water, stealing scarce moisture from sagebrush, grasses and streams. Habitat for wildlife and forage for livestock are becoming lost or degraded. Ranchers are fighting back, downing the trees with chainsaws and tractors. Much of the wood remains where it falls, unused.

From Logs to Lotions

Transforming juniper from problem to profitability is the vision of OSU forestry student Steve Ashley. Cultivating new markets for juniper products could benefit not just Oregon’s ranchers but also its mills, builders, landscapers, furniture makers, garden centers, retailers and enterprises in specialty niches such as essential oils, craft distilleries and animal bedding, he says. And then there’s the growing demand for sustainable energy. Juniper is a vast source of biomass just waiting to be tapped, Ashley asserts.

So what’s getting in the way? That’s the question Ashley explored for his senior thesis in the Wood Science and Technology program with guidance from his adviser, Scott Leavengood, director of OSU’s Wood Innovation Center. For the young man from Albany who spent boyhood summers working on the 700-acre Prineville farm where his grandfather grew mint, alfalfa and sugar beets, it’s more than just an academic question. He is constantly drawn back to the sage and rimrock and dry, desert winds of Central and Eastern Oregon. For the past six fire seasons, he’s been back out among the junipered hills battling wildfires with the U.S. Forest Service.

“Since I was a kid helping out on my grandpa’s ranch, I’ve seen the juniper grow up and take over,” Ashley says.

Reviving Ecosystems

An estimated 6.5 million acres of private and government lands in Oregon are classified as juniper savanna or juniper forest. That’s up from just 1.5 million in the 1930s. Suppression of wildfires on rangelands has allowed young seedlings to survive and flourish in recent decades. Yet despite the abundance – and landowners’ eagerness to be rid of it – juniper occupies a very small place in Oregon’s wood-products industry. Typically a short, limby tree that tapers sharply and has a swirling grain pattern, juniper is not ideal for mills, which are geared for long, straight-grained, knot-free logs, Ashley says. With only one large-scale juniper mill in the state – the nonprofit REACH (Rehabilitation, Employment and Community Housing) mill in Klamath Falls – transportation costs and logistics hinder large-scale logging.

Harvesting presents its own set of hurdles. Scattered widely and randomly across the landscape, juniper doesn’t lend itself to efficient logging like dense stands of, say, Douglas fir or ponderosa pine, Ashley explains.

But none of these impediments is impossible to overcome, according to Ashley. In his study, he makes recommendations for expediting the western juniper market, including using alternative harvesting methods such as mule or horse logging and creating a “value-added” product such as wood chips right on the harvesting site.

His vision for juniper in Oregon centers on its “green” assets.

“The ecological effects of removing western juniper have yielded great results in increasing stream flows and native grasses,” Ashley says. The ranchers he interviewed have seen “drastic ecological changes” after cutting juniper on their land. In fact, one of those ranchers, Bill McCormack of Brothers, told Ashley that “the grasses seem to grow overnight” as soon as the juniper is cut down.

Besides reviving ecosystems, harvested juniper can be used in all sorts of green products, from long-lived fence posts and landscape timbers that don’t need to be treated with chemicals to pellets for woodstoves to biofuels for energy generation.

Down to Business

For the juniper market to take off in Oregon, however, landowners, mill operators and government agents need to reach a meeting of the minds on how to move it forward, Ashley says. This “communication triangle,” he insists, must collaborate more closely to benefit all stakeholders. In the meantime, he plans to seek investment capital for a start-up company where he can put his extensive juniper knowledge to work.

“The public needs to be re-educated about western juniper,” he says. “They may be very interested in juniper products because the harvest restores ecosystems and yields ‘green’ products. Anything green is selling these days.”

To support student scholarships, contact the OSU Foundation.

Marsha Lampi brings the discipline of a long-distance runner to her research in bioengineering as well as to OSU cross-country and track. (Photo: Jan Sonnenmair)

By Nick Houtman and Darryl Lai

Marsha Lampi runs for distance – 5,000 or 10,000 meters in track, 5,000 or 6,000 meters in cross-country. The former Lincoln High School student from Portland enjoys pacing herself but is always looking to improve. “I usually think, if only I had done this or that differently, I could have run a little bit faster,” she says.

This summer will take the Oregon State University athlete, a junior in bioengineering and the University Honors College, further than she has ever gone, at a pace that surprises even her. She is one of two-dozen students from around the world who have been accepted into an eight-week internship at the Swiss Federal Institute of Technology (known as the EPFL) in Lausanne, Switzerland.

Lampi will work in the Hubell Laboratory, which specializes in research on biomaterials, drug delivery and tissue engineering. It’s a great fit for a student who is setting her sights on med school or biomedical research.

Lampi’s laboratory experience at OSU has prepared her for the challenge. Last summer, she worked in OSU’s Howard Hughes Medical Institute undergraduate research program on a subject of great interest to runners: the fluid that lubricates knees, hips and other joints. Under guidance from Willie “Skip” Rochefort, associate professor of chemical engineering, Lampi looked at how proteins in this so-called synovial fluid affect its ability to help joints absorb shock.

She credits Rochefort and the College of Engineering for giving her the opportunities and academic support she needed to qualify for the Swiss program. “Dr. Skip has been there every step of the way to help me,” she says. “He made me think about the big picture.” As a result, she developed the confidence to apply to internship programs (Berkeley, Stanford, MIT and EPFL) that she didn’t think would accept her. No worries: She got into each one.

“I chose to do research at the EPFL because of the international opportunity of working with people from around the world,” she says. Although she speaks fluent Spanish, she is looking forward to learning new languages and the by-ways of an unfamiliar country.

Rochefort says that Lampi is one of the best students that he has mentored at OSU. “She has the talent to go a long way and the desires to make an impact on people’s lives, both with her research and as a role model in both her professional and personal lives. She is possibly the most disciplined and organized student, with a huge capacity for work, that I have met in my 17 years at OSU!”

Lampi has served as a mentor for other students in high school and at OSU. In her own family, she looks to her older brother (an engineer) and sister (in med school) for inspiration. “They showed me I can do whatever I want,” she says.

Despite her new surroundings, Lampi will continue to work on her running in preparation for the fall cross-country season. And she’ll have additional support through her coach, Kelly Sullivan, and the OSU Athletics Department, which has arranged for friends to meet her in Switzerland.

To support student scholarships and the University Honors College, contact the OSU Foundation.

Experience Oregon’s beauty and bounty through OSU research

Take a hike! Summer may have arrived a bit late in the Pacific Northwest, but you can make up for lost time by exploring public demonstration gardens, old-growth forests, wetlands, agricultural field days and an archaeological dig through OSU’s Summer of Science Google map. Each listing on the map includes directions and a description of what you’ll find.

View Oregon State University Summer of Science in a larger map

Illustration by Scott Laumann

Bi-Mart seems an unlikely springboard for social change. Yet tucked away in a corner of a store on the edge of Springfield, pharmacist Kathy Hahn is waging a militant campaign against pain.

“I’m kind of an activist,” she says, leaning close to her listener and whispering the word “activist” as if confiding a dark secret. “When I see something that’s wrong all day every day, I’m the type that says, ‘I’m going to do everything in my power to change that.’”

What she’s changing is the way chronic pain is managed in Oregon. In her 20 years as Bi-Mart pharmacy manager, she has seen legions of patients — combat veterans, fibromyalgia sufferers, accident victims, people with auto-immune disorders and degenerative diseases — who suffer needlessly because their pain is poorly controlled. The twin fears of patient addiction and illegal drug trafficking scare doctors away from prescribing opium-based medications for many of the 76 million Americans living with chronic pain, Hahn explains. And pharmacists often behave judgmentally when patients come to the counter with high-dose prescriptions for opioids.

“Many pharmacists think people who use Vicodin or Percocet are all potential addicts, and they treat them horribly — horribly! — whispering to the technician, looking at the patient with suspicion,” she says. “A pharmacy that does not understand pain management can be the biggest barrier in the health-care chain.”

Far from being content with just filling “scrips,” Hahn teaches in OSU’s College of Pharmacy as an affiliate faculty member, chairs the Oregon Pain Management Commission (the first of its kind in the United States) and serves as Oregon co-leader for the American Pain Foundation. She also is active in Death with Dignity, Oregon’s first-in-the-nation assisted suicide law.

Listening to Patients

From a curtained consultation room overlooking the Bi-Mart pharmacy counter, Hahn keeps a sharp eye out for patients who might need her expertise or just a cheerful “hello.” When Vietnam vet Richard Ketter shuffles up, bent low over a shopping cart, his hat decorated with buttons and pins — including a purple heart — Hahn calls out to him.

“Hi, Mr. Ketter, how are you today?”

“Good. Gettin’ ready to go prospectin’ for gold out in Arizona.”

The news is nothing short of miraculous. Injuries suffered during a helicopter crash in Vietnam left the 65-year-old Ketter with a painfully damaged leg. Unable to get the meds he needed through Veteran’s Affairs, he searched online for a new doctor and was steered to Hahn. She in turn referred him to Dr. Martin Klos, who accepts patients like Ketter whom “no one else will touch.”

“Kathy and Dr. Klos saved my life,” says Ketter, who admits to nearly giving up on life before finding help. “They’re the only people who seem to care.”

Passing the Torch

As the chair of the 17-member Oregon Pain Management Commission, Hahn helps set policies and guidelines to improve the lives of patients. One controversial issue is medical marijuana.

“The commission understands that marijuana can have tremendous medical value,” she says. “It is a travesty that more money has not gone into investigating and developing it. I believe that its niche is going to be neuropathic pain, and neuropathic pain — if you look at the whole spectrum of pain — is the monster. It is the one that is most difficult to treat.”

As a teacher and mentor, Hahn is passing the torch to a new generation of pharmacists, raising awareness and providing guidance during students’ six-week rotations at Bi-Mart. “What the students have to learn is that it takes a village to take care of a pain patient,” she says. “I want them to do a paradigm shift before they leave here. I want them to become advocates.”

— Lee Sherman

To support OSU pharmaceutical research, contact the OSU Foundation, 800-354-7281.

The Fibromyalgia Challenge: Q&A with Kathy Hahn

Fibromyalgia: Fibromyalgia makes you feel tired and causes muscle pain and “tender points.” Tender points are places on the neck, shoulders, back, hips, arms or legs that hurt when touched. People with fibromyalgia may have other symptoms, such as trouble sleeping, morning stiffness, headaches, and problems with thinking and memory, sometimes called “fibro fog.” (National Institutes of Health)

Terra: Who are some of the most vulnerable patients dealing with chronic pain?

Kathy Hahn: Probably my best examples are middle-aged women with fibromyalgia. I try to champion these women, because there are still so many people who still don’t believe that fibromyalgia exists. There are so many things we don’t know about the disorder and how to treat it. We have some patients who are on some pretty heavy medication, and they often are discriminated against.

Terra: In what ways are they discriminated against?

Hahn: I had one patient in her 40s who had been going to another pharmacy that was being very judgmental. They weren’t keeping her medication in stock, not doing any of the things they needed to do to facilitate a smooth treatment and make sure she didn’t run out. A pharmacy can either be a help or a hindrance. For example, if you’ve got a patient saying, “My insurance company won’t pay for this medication,” the pharmacy can jump through the right hoops, work with the doctor and be a facilitator in getting the medication through the insurance process. The pharmacy has to be a big partner in helping patients with chronic pain. They are the gatekeepers of the medications. If they become judgmental, everything falls apart.

Terra: Part of your mission is to encourage patients to advocate strongly for what they need, right?

Hahn: Yes, and that can be very difficult, especially for the fibromyalgia patient who is isolated and alone. You get these women who’ve had more and more trouble and pain and can’t get out of bed, and they lose everything – they lose their job, they lose their spouse, they lose their family, they lose their home – and trying to teach them how to advocate for themselves is tough. You’re trying to pull them back in. You’re trying to teach them: “You’re not alone. You are not alone!” We teach them how to access resources, encourage them to get a computer and find online communities for discussion and information. We have to stop them from every day just curling up on the couch and thinking, “Should I continue breathing today, or not?”

nvestigating the link between human and animal health is a critical focus for Cyril Clarke, dean of OSU’s College of Veterinary Medicine, as he leads the college in a new era of veterinary research. (Photo: Karl Maasdam)

Veterinarians, as everyone knows, care for dogs, cats and livestock. Less well-known is their role in safeguarding human health.

“It’s important to point out the strengths and critical assets that veterinarians bring to public health,” observes Cyril Clarke, Lois Bates Acheson Dean of Veterinary Medicine.

Clarke ticks off the key intersections of animal-human health one by one. First, the vast majority of emerging infectious diseases worldwide — swine flu, avian flu, HIV-AIDs and Ebola, to name a few — have animal origins. Next, 80 percent of pathogens that pose a national-security threat — infectious agents like anthrax, for instance — are transferred to humans from animals. And food-borne illnesses such as salmonellosis and E-coli infection, which sicken thousands of Americans each year, typically are traced to livestock.

“Veterinarians really are the guardians of a safe food supply,” says Clarke, who grew up in South Africa and began eyeing a veterinary career during summers at his grandparents’ farm near Kruger National Park. “They are responsible for investigating the causes of diseases linked to contaminated foods and for maintaining a healthy food supply.”

Too, animal studies can reveal the causes of and cures for human illnesses. Researchers have developed well over 400 animal models of human disease, Clarke says. Studies with mice, for instance, have resulted in new understandings of tumor progression in lung cancer, as well as suggesting new diagnostic methods and therapies. Golden retrievers, which can carry spontaneous mutations in the dystrophin gene that causes a condition similar to Duchenne’s muscular dystrophy, have shed light on this lethal childhood disease.

Clarke’s own research program at Oklahoma State University, in fact, was funded in part by the National Institutes of Health and other agencies that support human health studies. That’s because his investigations of microbial pathogens in bovine respiratory disease — studies spurred by his initial professional interest in agriculture and livestock — illuminated principles of immune response and antimicrobial resistance that have applications in human health.

It is at this nexus of human-animal health where Clarke and his OSU colleagues in the human health sciences are laying the groundwork for a signature program that they hope will gain recognition nationally and internationally — what he calls an “area of critical mass and excellence.” Clarke is working closely with fellow deans Tammy Bray (College of Health and Human Sciences) and Wayne Kradjan (College of Pharmacy) to design a multidisciplinary research and graduate program that will blend together and build upon OSU’s strengths in the health sciences. Under the university’s realignment plan, the three colleges are being folded into an overarching Division of Health Sciences.

“As we look to the future, the College of Vet Med will have a much larger research program — one that is overlaid and undergirded by an inter-departmental, cross-disciplinary graduate program in comparative (cross-species) health sciences,” says Clarke. “We will also be enhancing our opportunities for outreach so that we can extend new knowledge to our stakeholders and constituents.”

To support the College of Veterinary Medicine at OSU, contact the Oregon State University Foundation.

Rural landowners depend on access roads to move livestock and farm equipment. (Photo: Jesse Abrams)

Beautiful landscapes may inspire us, but it takes more than scenery to create community vitality. Wallowa County and rural communities across the country struggle with economic development, a future for their youth and the cultural tensions that arise from changing land ownership. For more than a decade, such issues in Wallowa have been addressed by Wallowa Resources, one of the nation’s leading nonprofit natural resources organizations.

“Wallowa Resources shows us what is possible. There are few places you can go in the country to get this range of innovative thinking about rural communities,” says Oregon State University forestry professor John Bliss.

So it was natural for Bliss and Associate Professor Kate MacTavish in Human Development and Family Sciences to partner with Nils Christoffersen, Wallowa Resources executive director, in the creation of an experiential learning course for OSU graduate students. Since 2005, students have spent 10 September days living with families and meeting with community leaders from Garibaldi on to the coast, to the Warm Springs Indian Reservation in Central Oregon, to Wallowa County in the northeast corner of the state.

For students, the experience has been unforgettable. Caitlin Bell, who participated in 2008, had this to say on her final exam: “I was faced repeatedly with the formidable and humbling task of dismantling my assumptions and preconceptions and rebuilding knowledge from scratch. I learned, among many things, that rural residents are innovative, entrepreneurial, and warmly hospitable people who value community, simple living, and hard work.” Wallowa Resources reprinted her remarks in a 2009 newsletter.

The Communities and Natural Resources course has spawned student projects that arm local decision-makers with useful information about trends in education, land use, forests and other topics, adds Christoffersen. For example, two students working with MacTavish – Devora Shamah and Brooke Dolenc – surveyed Wallowa County high school students and graduates to find out what drives their aspirations. They discovered that while about a third of high school students wanted to live in Wallowa County as adults, about one quarter of graduates were actually doing so. Dolenc’s and Shamah’s reports are available online in the OSU Scholar’s Archive.

OSU’s relationship with Wallowa County is just one example of the close partnerships between the university and rural communities through Extension and agricultural experiment stations. In addition, the OSU Rural Studies Program has established formal agreements to do research in Wallowa and Tillamook counties and has been active in Lake, Coos and other counties as well.

A signature effort has been the development of “community indicators” of vitality. OSU students and faculty have collaborated with local citizens to identify markers that allow leaders to prioritize goals and evaluate progress in reaching them. Wallowa County was the focus of a recent effort led by Lena Etuk, a social demographer with OSU Extension and the College of Health and Human Sciences. With funding from the Ford Institute for Community Building, she worked with Wallowa Resources and a team of volunteers to outline 26 indicators of vitality in social, economic and environmental health and community capacity.

Reports for Oregon counties, including Tillamook and Wallowa, are available online here.

Related story: The Mythbuster

To support OSU Extension or the Rural Studies Program, contact the OSU Foundation, 800-354-7281.

Tiny fruit fly gives a giant headache to Oregon's berry and tree fruit growers.

It’s a pest not much bigger than the head of a pin. But for Oregon farmers, the tiny fruit fly has the potential to take a giant bite out of yields — and profits.

The spotted wing Drosophila has made its way to Oregon from its native Southeast Asia, turning up first in wine grapes late last summer and then invading berries, cherries, plums, peaches and other fruit crops across 13 counties. Willamette Valley growers lost up to 20 percent of their blueberries and raspberries and as much as 80 percent of their late-season peaches.

“This is an insect that, up to last year, had never been seen in the continental United States,” says OSU research entomologist Amy Dreves.

In February, to help head off a crisis in the state’s $500 million tree-fruit and berry industry, the Legislature gave $225,000 to a team of researchers from OSU and the state and national departments of agriculture for monitoring and controlling the fly. Among the team’s tasks are sampling fruits to detect infestations, mapping outbreaks, testing traps, developing natural baits, doing outreach and training growers.

“It is crucial to find infestations of this pest as early as possible, when they can still be treated effectively,” warns Dreves.

People who want to monitor the spotted wing Drosophila in their home gardens can learn how to make a trap and identify the insects through a series of videos produced by Dreves and Tiffany Woods of Extension and Experiment Station Communications.

To support OSU research on crop production, contact the OSU Foundation, 800-354-7281.

March 15, 2010: “The Bridge Team’s goal for today was to determine the geographical extent of bridge damage from the Chilean earthquakes. We did this by driving nearly 450 miles south along Route 5 (the Pan American Highway) from Santiago to Temuco, keeping along the outer edge of the zone of strong shaking (about 50 miles or so inland). To put this into Pacific Northwest context, it would be very similar to driving from Seattle to southern Oregon along I-5 after a Cascadia Subduction Zone earthquake off the Oregon/Washington coast.”
— Blog post from OSU civil and construction engineer Scott Ashford

Ashford visited Chile as a member of the international Chile Earthquake Reconnaissance Team sponsored by the Earthquake Engineering Research Institute. The quakes that have devastated Chile and Haiti in recent months, he notes, are reminders that Oregon, too, sits poised for heavy shaking. The Cascadia Subduction Zone shifts abruptly every 300 to 400 years or so, and the next time it does, experts predict destruction and dislocation from the Pacific shoreline inland to Portland and the Willamette Valley. A tsunami could follow in the earthquake’s wake.

To help Oregonians prepare, Oregon Sea Grant outreach specialist Patrick Corcoran is working with coastal communities. “We may have as little as 15 minutes’ warning for a potential tsunami, and the damage from an earthquake could be immediate,” says Corcoran, who coordinates the Coastal Storms Program at OSU. “We all need to be prepared to help ourselves.”

Ashford and Corcoran are among more than a dozen OSU faculty who are sharing their expertise in engineering, geology, communications and marine sciences with Chilean colleagues.

More information on tsunami preparedness is available at OSU Extension.

Pankaj Jaiswal is a co-creator of the new Gramene database that helps plant breeders develop new crop varieties (Photo: Truen Pence)

To find the genes that enable a crop — ryegrass or wheat, for example — to resist disease or tolerate drought can mean endless searching, not through one haystack but through many. And success is only the beginning of time-consuming breeding trials. Now scientists, farmers and plant breeders who feed the world have a new scientific resource at their disposal to help them cut through the DNA clutter.

An online gold mine known as the Gramene database is really a library of datasets, says one of its creators, Pankaj Jaiswal, assistant professor in Oregon State University’s Department of Botany and Plant Pathology and a faculty member in the Center for Genome Research and Biocomputing. While a post-doctoral scientist at Cornell University, Jaiswal helped to create the database, research tools and educational information that are revolutionizing the application of genomics to crop development. He continues to be one of Gramene’s principal investigators with colleagues at Cornell and the Cold Spring Harbor Laboratory in New York.

Supported by grants from the U.S. Department of Agriculture (USDA) and the National Science Foundation (NSF), Gramene focuses on grasses (family name: Gramineae), including wheat, corn and rice, which collectively provide about half of the world’s calories.

“What’s unique about Gramene,” says Jaiswal, “is that it builds relationships between scientists who work from a purely genetics and breeding perspective and the people who work from the molecular and biochemical perspective. It tries to bridge the gap between these two.” To develop crops with desirable characteristics, crop breeders can identify genes that are associated with specific traits, such as cold hardiness, disease resistance or flowering time.

And by providing genetic information about multiple species, the database bridges genomes that have been fully sequenced and are relatively well described, such as corn and rice, and those that are less well known, such as wheat and ryegrass. Commonalities between different genomes can generate important clues for breeders of new plant varieties.

Scientists use Gramene for basic science — understanding evolutionary relationships among difference species, for example — as well as for studies that seek innovations in plants for biofuel production or disease resistance. In 2008, USDA and university scientists, including Reed Barker of the Agricultural Research Service in Corvallis, used Gramene to identify likely candidates for disease resistance genes in perennial ryegrass, a mainstay of Oregon’s grass seed industry. The close similarities with disease resistance genes in rice, which had been studied and described in detail, led them to suggest that the ryegrass genes might have the same function.

Judging by the traffic on its website, Gramene has been a global hit. In the last year alone, its data files have been downloaded or viewed in more than 140 countries by about 220,000 visitors. Scientists have cited it as a model for an emerging plant knowledge system, says OSU plant geneticist Todd Mockler. Mockler’s lab participated in the recently completed sequencing of a small grass plant, Brachypodium, whose genome is now stored on Gramene. Brachypodium is a promising model for grass genomics studies.

Jaiswal, an acknowledged leader in developing standardized vocabularies (what scientists call “ontologies”) for the rapidly expanding plant genome sciences, also trains breeders and farmers to use Gramene. “We try to avoid too many scientific terms,” he says with a nod to the technical language of his profession, “but we can’t do that all the time.”

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To support OSU research in biotechnology, contact the OSU Foundation, 800-354-7281.

OSU news release, Dec. 26, 2010. Pankaj Jaiswal contributed to the compete genome sequence of the woodland strawberry, a relative of commercially bred strawberry varieties. The plant shares genes with other fruit crops, including peaches, apples, cherries and plums.