Fermentation Education

As the one and only enologist, or wine scientist, on the UW–Madison campus, a large part of Nick Smith’s job is guiding a group of hopeful undergraduates through Food Science 552 — and toward their futures in winemaking and other jobs in the fermented food and beverage industries.

Students who took Smith’s fall 2017 course, “The Science of Wine,” emerged with a solid understanding of the chemistry and microbiology behind the winemaking process. But they also went beyond lecture-style learning to get a real taste for the process of fermentation.

“A key element of the class is to teach the production process,” Smith says. “How does the chemistry impact the final product?”

During the semester, students took two trips to Wollersheim Winery in Prairie du Sac, Wisconsin, where they learned about production procedures and bottling. Back on campus, students broke into small groups, each tasked with creating one of three different wine styles — sparkling, red, or white.

Philippe Coquard, who owns Wollersheim Winery with his wife, Julie, displays a bottle of the freshly pressed grape juice that will become the next small-batch wine, called Campus Craft, to be developed with involvement from students in the Science of Fermented Food and Beverages certificate program. Photo by Ben Vincent.

“[The course gave] me a greater appreciation for winemaking, and I found it very interesting to compare the winemaking and beer-making processes, as they have a lot in common,” says Miles Gillette BSx’18, a senior majoring in food science. He was first inspired to select his major after dabbling in homebrewing of beer, a process he calls “hands-on microbiology.”

Food Science 552 is just one component of the UW–Madison’s new Science of Fermented Food and Beverages certificate program, which was made available to undergraduate students for the first time in the 2017-18 academic year.

The certificate is an option for students pursuing various science majors — food science, microbiology, biochemistry, and others — who want to delve deeper into fermentation. As they progress through the program, students learn about the various scientific aspects involved in fermentation.

Food Science 410, for example, teaches them about the chemical components of food constituents like proteins, lipids, carbohydrates, and enzymes. They also learn about the latest techniques and technology used to produce fermented beverages such as wine, beer, and cider, as well as fermented foods like cheese, bread, and pickles. The hope is that such a comprehensive suite of courses will give graduates a competitive edge in the field.

“The dream is to make UW–Madison the top college when it comes to the fermentation sciences,” says David Ryder, former vice president of brewing and research at MillerCoors and an expert on fermentation and yeast physiology. Ryder was instrumental in coordinating the donation of pilot-scale beer brewing equipment from MillerCoors to UW–Madison in 2008, and he has been a steadfast advocate for the development of the university’s fermentation sciences program, including the new certificate.

Long viewed as a major national center for the beer and cheese industries, Wisconsin is also home to other major manufacturers of fermented goods. The state boasts a growing wine industry, with around a dozen new wineries opening each year. Every bottle of Kikkoman Soy Sauce sold in North America is brewed and bottled at the company’s factory in Walworth. GLK Foods, headquartered in Appleton, is the largest producer of sauerkraut in the world. The scope of the industry in the state is only likely to expand. And that requires trained workers, specialists, and experts in the field.

“With the prominence of all the fermented food and beverage industries we have, we [aim to] start filling the niches and educational needs,” says Smith.

Smith arrived at UW–Madison in March 2015 after spending eight years as an experimental winemaker at the University of Minnesota. The initial funding for his position was secured through a Specialty Crop Block Grant from the Wisconsin Department of Agriculture, Trade and Consumer Protection with the support of the state’s key wine organizations. Beyond his teaching duties on campus, Smith works directly with winemakers to assess and improve their wines, helping to troubleshoot problems, as needed.

Students observe as red grapes harvested from the Wollersheim Winery vineyard are sorted prior to crushing and destemming. Photo by Ben Vincent.

This hands-on experience is also a boon for Smith’s students, who participate in the development of various fermented products while earning their certificates. Students in Food Science 551 participate in a beer design and brewing competition offered in collaboration with the Wisconsin Brewing Company (WBC) of Verona, Wisconsin. This partnership has yielded a new WBC beer in each of the last three years. The collaboration’s 2017 brew, Red Arrow, proved so popular that the initial batch sold out in a matter of weeks.

Wollersheim Winery is also a partner in the fermentation sciences program. The company sends grapes to campus for students to make into small batch wines and hosts students so they can observe what’s involved in full-scale wine production.

With the new certificate program, UW–Madison is better positioned to be a wellspring of talent, research, and creativity to support the state’s fermentation-related companies, according to program coordinator Monica Theis MS’88.

“Our vision is that Wisconsin is the place to go to learn about the science of fermentation and that our graduates leave here with a competitive edge,” she says.

Corn Conundrum

When in place, plants have no choice but to adapt to their environments, responding to stresses like drought or pests by changing how they grow. On a broader scale, crop breeders need to be able to develop new varieties that are adapted to a new location or changing growing conditions in the same area.

Both types of adaptation rely on a pool of possibilities, the combinations from which one can choose. For the individual plant, those possibilities depend on the genome it was born with. For breeders, that pool of possibilities is the whole range of genomes of cultivated crops, which they can blend together to create new varieties.

CALS researchers wanted to know whether the last 100 years of selecting for corn that is acclimated to particular locations has changed its ability to adapt to new or stressful environments. By measuring populations of corn plants sown across North America, they could test how the corn genomes responded to different growing conditions. What they found is that artificial selection by crop breeders has constricted the pool of possibilities for North American corn varieties.

A drone’s eye view of research plots for an experimental field maize hybrid grain trial at UW-Madison’s West Madison Agricultural Research Station. Photo by Dustin Eilert

In a recent issue of Nature Communications, agronomy professor Natalia de Leon MS’00 PhD’02, her student Joe Gage PhDx’19, and colleagues at several institutions concluded that the existing corn varieties are strong and stable, but they are less flexible in their ability to respond to various stresses. At the same time, these corn populations might have a reduced ability to contribute to breeding programs that seek to create new varieties adapted to novel environments.

“Over the last 100 years, people have definitely improved cultivars,” explains de Leon, the senior author of the report. “What we were trying to do in this study is to measure whether by doing that we have also limited the ability of the genotypes to respond to environments when they change.”

By intensively breeding for high yield — in Wisconsin, for example — those plants might lose the flexibility to respond to environments that are very different from Wisconsin growing conditions. To test this idea, de Leon and her colleagues at 12 agricultural universities in the U.S. and Canada devised a large field trial with more than 850 unique corn varieties growing in 21 locations across North America. There were more than 12,000 total field plots where researchers measured traits like yield and plant height while recording weather conditions.

The massive experiment is possible only because of a collaboration called Genomes to Fields, which is led by de Leon, UW–Madison agronomy professor Shawn Kaeppler BS’87, and others. The project stretches across 20 states and parts of Canada. This provides precisely the range of various field conditions required to tease apart the different contributions of the genomes and of the environments to the final traits of the corn.

De Leon and her collaborators found that the regions of the corn genome that have undergone a high degree of selection — for example, gene regions that contribute to high yield in a particular location — were associated with a reduced capacity of corn to respond to variable environments compared to genomic regions that weren’t directly acted on by breeders. The upshot is that the modern corn varieties are very productive in the environments they are grown in, but they might have a harder time handling changes in those environments.

“The data seem to point to the idea that by selecting genotypes that are better suited to be more productive, we are eroding variability that might be important as we move into a world where climate might be more erratic and where we might need to move cultivars into places where they haven’t been grown before,” de Leon says.

Yet this loss of flexibility is an inherent trade-off for highly productive cultivars of corn, she says.

“When you try to adapt cultivars to many different environments, you end up with plants that are not great anywhere,” de Leon says. “The cost of maintaining this plasticity is to the detriment of maximum productivity.”

“So we have to strike the right balance in the long term,” she says.

Saving an American Icon in England

On a mild spring day in 1980, a handful of men gathered on the sprawling lawn of England’s Windsor Castle, there to do a little landscaping. But these chaps wore suits, and one of them brought a silver-plated shovel.

The ornate spade cleared a hole for a new tree as any other would, but the laborer just happened to be Prince Philip, husband of Queen Elizabeth II. And the tree that would take root in British soil just happened to be a hybrid elm from America. This simple act was part of a broader campaign to save the species from widespread annihilation.

Accompanying Prince Philip that day was Eugene Smalley, a professor of plant pathology at UW–Madison who had been tasked with fighting the spread of Dutch elm disease (DED) more than two decades earlier. First identified in the Netherlands in 1919, DED quickly spread through Europe via elm bark beetles before arriving in the United States in 1930. Since then, more than 50 million American elm trees have been felled. The towering Ulmus americana once stood as an elegant staple in communities across much of the United States.

“The American elm tree has had a unique niche in American life,” Smalley told The New York Times in 1989. “Before the disease, you could find streets lined with elms in almost every American town.”

Ray Guries, a professor emeritus in the Department of Forest and Wildlife Ecology and a former associate of Smalley’s, called the rapid decline of the American elm a “traumatic experience” for residents of urban areas. “When they disappeared, it was as though an icon had been lost.”

Early efforts to halt the spread of Dutch elm disease were ineffective. Smalley was hired in 1957 as part of a state initiative, and he immediately went to work planting elm seedlings at the Arlington Agricultural Research Station north of Madison. This stand became known as “Smalley’s Elms,” and many can still be seen today as one drives north- bound on State Highway 51.

Smalley theorized that hybrid species with natural pest resistance — not pesticides — offered the best defense against the beetles. Through 20 years of research, he and his colleagues produced several hybrids — Regal, American Liberty, New Horizon, and Cathedral — that proved to be hardy against the cold and generally resistant to DED.

Another promising hybrid was Sapporo Autumn Gold. When Prince Philip set one in the ground at Windsor Castle, he also planted the seeds of hope. That elm still stands today and has since propagated more than 100 others on the property.

Smalley died in 2002, but his legacy lives on. His disease-resistant elms have served as replacements all over the world. Even the embattled American elm may be bouncing back. Guries has spotted them being planted once again in Madison. Although it’s unlikely ever to reclaim its former status, the tree and its hybrid cousins serve as reminders that Smalley’s work will continue for decades.

“In developing the right tree, we don’t deal in years,” Smalley once told the Wisconsin State Journal. “We deal in generations.”

Catching a ‘Silent’ Cow Killer

Mitch Breunig BS’92 has been around dairy cows long enough — all his life, to be exact — to suspect something was amiss with two of his Holsteins.

And he’s been around the Department of Dairy Science long enough — considering he’s an alumnus and his 450-cow farm in Roxbury, Wisconsin, is practically a field research station for the department — to suspect ketosis.

This “silent killer” is caused by excessive toxic particles released by the liver, usually when a cow starts to produce milk after giving birth. So it was fortuitous that Heather White, an assistant professor of dairy science and one of the world’s experts on detecting ketosis, was visiting Breunig’s Mystic Valley Dairy, within sight of the St. Norbert’s church steeple in northwestern Dane County, on that day in March.

The start of lactation is the moment of maximum metabolic stress for a dairy cow, when her overworked liver can crank out molecules called ketones that provide energy to other tissues in the body. But if ketones reach excessive levels, they can reduce milk output, set the stage for disease, and even cause the cow to be culled from the herd.

Milk output from the cows in question had dropped, which could have had many causes. Ketosis, however, appears in 40 to 60 percent of lactating American dairy cows.

Even though ketosis costs farmers an average of $290 per cow, it’s often undiagnosed because the blood tests are laborious and expensive. Far better would be a test for telltale molecules in the milk, which is exactly what White has been working on, in collaboration with dairy science department chair Kent Weigel MS’92 PhD’92 and Gary Oetzel, a professor of medical sciences at the UW–Madison School of Veterinary Medicine.

The result of their labor, called KetoMonitor, is now incorporated in the AgSource system used by dairy farmers across the state to track their herds and milk output. AgSource relies on a sophisticated spectrometer to look for two milk-borne compounds that signal ketosis and then refines the prediction through an advanced computer analysis.

When Ryan Pralle BS’15 and Rafael Caputo Oliveira, both graduate students who work with White, sampled blood from the two cows, Breunig’s hunch proved correct. The cows had a silent, or “subclinical,” ketosis. Armed with that knowledge, Breunig began corrective measures that usually tame ketosis, such as dietary supplements.

Blood tests are the old-fashioned but still gold standard method for detecting ketosis. But KetoMonitor’s milk tests and computation have become the first line of defense.

By testing milk from “fresh” cows every week or so, KetoMonitor first estimates the prevalence of ketosis in the fresh cows. Then, by analyzing the data on milk production, reproductive history, and other matters on each fresh cow, it identifies cows that might need a blood test for ketosis.

KetoMonitor already catches 85 percent of cows with the condition, which is almost enough to avoid blood tests entirely. Once they reach 90 percent accuracy, blood tests for every fresh cow would no longer make economic sense, White says.

To reach that magic number, Pralle is using a computational tactic called “machine learning” (think digital self-help class). When the software makes a mistake, it combs through the data, looking to do better next time around. The accuracy is improving, he says. “When we compare it to some other non-blood tests, I think our tools are very competitive.”

White and her collaborators began tackling the problem about 10 years ago. “We recognized there is a lot of money lost in subclinical ketosis,” she says. “A cow is having negative outcomes — she’s making less milk and is not going to rebreed as easily, but she can’t walk up and tell you she’s sick.”

Due to the efforts of White and others at UW– Madison and beyond, that has changed. “Ketosis has become something that producers really want to manage because they recognize the cost of the disorder,” says Pralle.

None of this is lost on Breunig, who sees a future with more constraints as a prime reason to focus on efficiency. “We will be in a position where we will need to grow more food on less land with fewer cows.”

KetoMonitor can help in unexpected ways, Breunig says. “When we adapted to the market by eliminating BST [the hormone bovine somatotropin], we had to change nutrition and management, and we used KetoMonitor to assess the impact of those changes.”

“Advances like KetoMonitor help us keep the herd healthy and allow us to stay competitive,” he says. “That’s the kind of help we really need.”

Clean Tubers, from Test Tube to Plate

Years before that french fry landed on your plate, the plant that would eventually give rise to the spud your fry was cut from was sealed away deep in a secureaccess building, growing slowly in a test tube inside a locked growth chamber.

At least, that’s the case if it was the product of the Wisconsin Seed Potato Certification Program (WSPCP), a 104-year-old CALS program dedicated to supplying Wisconsin seed potato farmers with quality, disease-free tubers.

All that security helps keep these important plants clean, and clean is a big deal for potatoes. Because they are grown from the eyes of tubers, or seed potatoes, rather than from true seeds, potatoes can easily carry bacterial and viral diseases in their starchy flesh from generation to generation. The solution is exacting cleanliness and rigorous testing at every stage of potato propagation.

WSPCP supplies 70 percent of the seed potatoes for Wisconsin’s 9,000 acres of farmland dedicated to propagating seed potatoes. The program certifies 200 million pounds of seed potatoes every year, enough to plant roughly 90,000 acres for commercial growing. Those spuds are then sold to commercial potato growers in Wisconsin, in other states, and around the world to be turned into farm-fresh potatoes, chips, and fries.

Each one of those potatoes’ progenitors once passed through the hands of two plant pathology researchers at UW–Madison, Andy Witherell and Brooke Babler BS’06 MS’10. In about three months, they can turn a handful of small potato plants growing in test tubes into hundreds. Multiply that by dozens of different varieties of potatoes — Caribou Russet, Magic Molly, German Butterball — and together Witherell and Babler produce tens of thousands of potato plantlets every year.

The two scientists work out of the Biotron, a facility on the UW–Madison campus designed to replicate any climate needed for research. The building’s secure access and clean protocols help them scrub the potato plants of any diseases and propagate them in sterile environments until they’re ready to plant in soil.

“This is a good place to grow plants because we’ve got a system that’s really clean,” Witherell says. “The Biotron air is filtered, and we have a clean room to work with.”

The researchers start by sterilizing an eye of a tuber and then inducing it to grow in a sterile container full of a jelly-like growth medium containing bacteria- and virus-inhibiting chemicals. As the spud sprouts into a small plant, they ramp up the heat to try to kill off any viruses. Then they clip off a portion of the shoot and replant it in a clean test tube of growth medium.

Brooke Babler and Andy Witherell check on micropropagated potato plants housed in test tubes at the Biotron Laboratory. (Photo by Bryce Richter)

Babler and Witherell can keep their plantlets in stasis in cold storage until the call comes in — 308 plantlets of Dark Red Norland are needed by July. Babler pulls out a box with several plantlets and takes them to the clean room, a space about the size of a parking space. On a sterile work surface, she takes out a scalpel and slices the plants into several pieces before replanting them in a new box. Just a small portion of one plant’s stem will grow an entirely new plant under the right conditions.

In this way, eight potato plants become 30. Four weeks later, those 30 become 80; then 80 become 310. They are all genetically identical clones of one another, and they are all still clean.

Thousands of plantlets of different varieties are shipped to the program’s farm in Rhinelander, Wisconsin, where they are grown hydroponically or in pots to begin producing tubers. Over several generations, one plant gives rise to many spuds, which in turn are replanted to make even more potatoes. In a few growing seasons, what once was handled by Witherell and Babler in the Biotron now weighs hundreds of millions of pounds and requires the work of two dozen independent, certified farms to manage.

Along their journey, the potatoes are screened for diseases that might have crept in. After Babler and Witherell leave the Biotron for the day (they only enter the facility once per day to better avoid bringing in pathogens from outside), they work in Russell Laboratories, where they help run diagnostic tests on potatoes to screen for viral and bacterial infections.

“Part of the certification process is to walk the fields and visually assess plants for the disease,” says Babler, a native of Viroqua, Wisconsin, who earned her UW–Madison degrees in both plant pathology and horticulture. “You can visually assess plants, but sometimes you can’t tell exactly what the disease is. So the inspectors ship the plants back to us, and we do diagnostics throughout the growing season.”

As part of her research, Babler is developing an improved test for a relatively new potato disease, Dickeya. The bacteria can spoil up to a quarter of a farmer’s yield under the right conditions and has recently taken hold in North America. Seed potato programs like the WSPCP are designed to detect and restrict the spread of new diseases like Dickeya, which spread primarily through infected seed potatoes.

Only those potatoes with a healthy pedigree get the WSPCP seal of approval. A portion of the sale of each bag of potatoes that commercial growers buy, certified to be as clean as possible, supports this years-long, labor-intensive process.

It’s a certification well worth the price — ensuring that Wisconsin potato growers continue to succeed, helping keep the state one of the top producers of potatoes in the country.

New Clues to Healthy Bones for People with PKU

Individuals with the metabolic disorder phenylketonuria, or PKU, cannot metabolize the amino acid phenylalanine. Without careful dietary management, it can accumulate at high levels in their blood, leading to cognitive impairment, seizures, and other serious health problems.

There is no cure for PKU, and patients must adhere to a lifelong diet of medical foods that contain protein but are low in phenylalanine. Traditionally, these medical foods have been made using synthetic protein substitutes derived from mixtures of amino acids. But these amino acid- based medical foods could be contributing to the skeletal fragility seen in many PKU patients, according to a new study led by nutritional sciences professor Denise Ney and Bridget Stroup PhD’17.

The researchers also discovered that an alternative medical food, developed by Ney from a protein called glycomacropeptide (GMP) — a natural byproduct found in the whey extracted during cheese production — could allow PKU patients to manage their diets without compromising their bone health. This study represents the first human clinical trial comparing how different PKU-specific diets affect the bone health of people living with the disease.

Ney helped develop GMP-based foods for PKU patients just over a decade ago. In subsequent studies, she has shown that mice fed GMP-based diets have larger and stronger bones than mice on amino acid based diets. “It was a vital clue that there could be a link between amino acid medical foods and the skeletal fragility seen in many PKU patients,” says Ney, a researcher at UW–Madison’s Waisman Center.

For the current study, Ney and her research team assigned eight individuals with PKU to a diet of amino acid-based medical foods before switching them to GMP-based foods with a low dietary acid load. The researchers found that PKU patients had higher amounts of calcium and magnesium in their urine while on the amino acid based diet, a sign of bone breakdown, which can impair bone health.

“The amino acid medical foods have high acid loads, which can change the overall acid-base balance within the body,” Stroup says. Bones are able to buffer high acid loads in the body, but over time this leads to a breakdown and release of minerals. On the other hand, Glytactin (the trademarked brand name for the formulation used in the study) GMP medical foods do not have high acid loads.

Although the researchers did not directly measure bone breakdown and density in this study, other studies have found that reducing the acid content of diets leads to lower urine-calcium excretion and increased bone density.

These findings, Ney says, could also help patients with other kinds of metabolic disorders, like maple syrup urine disease. And although the sample size of the study was relatively small, it is typical of investigations into rare diseases; Ney hopes to secure additional funding for further study.

Ney is working on a larger clinical trial to study the metabolism of calcium and other minerals in PKU patients consuming amino acid or GMP medical foods. “We will be looking at bone health and also other physiological aspects, such as the gut microbiota,” she says.

Class Act: Caroline Hanson and the ‘Patio Tomato Project’

For sophomore genetics major Caroline Hanson, growing tomatoes goes beyond community gardens and farms. It could be the key to healthier lifestyles.

With that in mind, she teamed up with campus and community partners in summer 2017 to distribute free patio tomato plants to low-income families, introducing them to easy, low-maintenance gardening that yields health benefits and encourages long-term healthy practices.

Hanson’s interest in food security began to take root after completing a First-Year Interest Group seminar in plant pathology with professor Jeri Barak-Cunningham. The course inspired her to secure a Wisconsin Idea Fellowship from UW–Madison’s Morgridge Center for Public Service to help pay for the materials for her project. As a part of the grant, she proposed teaming up with the River Food Pantry on Madison’s north side to distribute the tomato plants. Hanson and her team of fellow CALS students grew the project’s cherry tomatoes in two campus locations and then transplanted them into donated five-gallon buckets that act as inexpensive patio pots.

When distributing the plants during workshops at the pantry and community centers on Madison’s north side, the team provides tomato care instructions, recipes, and arts and crafts for kids. They also offer free samples of dishes that incorporate cherry tomatoes — cheddar tomato cobbler, tomato risotto, parmesan tomato chips — many of which can be made for $4 or less. The workshops get families involved in working with vegetables and understanding more about healthy lifestyles.

“The health benefits are obvious, and you see kids become passionate about something they can do on their own and is good for them and is good for their community,” Hanson says.

The project was initially slated for a single summer, but Hanson is working with different organizations to secure funding for another year and eventually make it an official student organization. With possible expansion, Hanson is determined to keep the project simple and rooted in helping people.

“What we love about this project is, even if you can’t start a community garden, it’s focused on container gardening,” Hanson says. “You don’t need a fancy gardening system. You can just get a bucket and some dirt, and you can get to work.”

Bridging the Gap

International support: Food science major Hannah Fenton (bottom left) carrying BRIDGE partner Kanokwan Duangkunarat, of Thailand; and Jenny Falt, from Sweden (bottom right), carrying her fellow landscape architecture student Sherry Yang.

International support: Food science major Hannah Fenton (bottom left) carrying BRIDGE partner Kanokwan Duangkunarat, of Thailand; and Jenny Falt, from Sweden (bottom right), carrying her fellow landscape architecture student Sherry Yang.

Food science major Hannah Fenton gratefully recalls the kindness shown to her during the three years she and her family spent in Thailand. “I know what it’s like to live in a foreign place and to feel lonely and in need of a friend,” she says.

That’s why Fenton joined BRIDGE—short for “Building Relationships in Diverse Global Environments”—a campus program that matches U.S.-born Badgers with students from around the world. “I wanted to give international students the love, support and guidance that I had when I was in Thailand,” says Fenton.

Last fall Fenton was paired with Bangkok native Kanokwan “Kim” Duangkunarat, who credits BRIDGE with helping her make the most of her five months in Madison. “Before I came here, I thought that the international students would be treated differently,” Duangkunarat says. “However, I was wrong.”

The feeling of “fitting in” she describes is at the heart of BRIDGE’s mission. Offered through International Student Services (ISS), BRIDGE seeks to ease the transition of foreign students to campus while giving U.S. students the opportunity to connect as cultural ambassadors. Each semester an interview process matches international and domestic students according to their interests and gathers these pairs into teams of 14 to 20 students.

To cultivate participants’ leadership and cross-cultural communication skills, each BRIDGE team is assigned to design and host a special event for the others. Past activities have included tours of research labs, visits to a traditional Wisconsin farm, a trip to a corn maze, and even a tailgate party at Miller Park.

After a focus group of CALS undergraduates revealed that many students appreciated the diverse origins of their peers in the classroom but were unsure how to connect socially, CALS administrators reached out to ISS to sponsor a college-specific BRIDGE team.

Now in its fourth semester, the CALS team has attracted students from all corners of the globe, including Germany, Brazil, Malaysia, Singapore and China. Participants have included majors in biochemistry, animal sciences, microbiology, and community and environmental sociology, though the program welcomes international students from non-CALS majors as well. Inspired by CALS’ success, two other colleges on campus are sponsoring college-specific teams this year.

“Now I have many good friends from different countries,” says Duangkunarat. “I have learned that UW–Madison is a really great place to study and live.”

Meanwhile, Fenton has enjoyed seeing her campus through the eyes of students for whom their time here is study abroad. “My favorite question to ask them is, ‘How do you like Madison?’” she says. “I enjoy showing them my favorite things and hearing about their new adventures as well.”

Making It Personal

It was one of the strangest homework assignments Erin Syverson had ever had. The senior genetics major was asked to open a small vial and start spitting.

“I would much rather have gotten my blood drawn, but it’s a simple, effective way to collect DNA at home without a medical professional,” notes Syverson, who submitted her saliva to 23andMe, a private company that analyzes a person’s DNA—all 23 pairs of chromosomes, hence the name—for $99.

Syverson underwent the analysis as part of Genetics 677, Genomic and Proteomic Analysis. While DNA testing is not required for the course, professor Ahna Skop encourages her students to undergo it. Students may use their own results as the basis of their individual semester-long class project, which requires doing in-depth research about a particular genetic disease or disorder and presenting findings in class and on a website the student creates.

“Because they have a vested interest in their project, they are emotionally engaged and seek out answers from me, their classmates and beyond the classroom—for example, from doctors and their families,” says Skop. “The payoff I see in my course is deeper, longer-lasting learning due to this emotional investment.”

Those benefits are being cited all around the nation as more and more college genetics courses encourage students to get tested. They were confirmed by a recent study in the journal PLOS One showing that 70 percent of students who underwent personal genome testing self-reported a better understanding of human genetics on the basis of having undergone testing. They also demonstrated an average 31 percent increase in pre- to post-course scores on knowledge questions, which was significantly higher than students who did not undergo testing.

Syverson didn’t end up basing her research project on her own results, but she still found the testing worthwhile. “Through learning to interpret my own results and scrutinize them, I have learned a lot about not only the diseases they tested me for, but also how to think critically about genetic results,” she says. “I’ve also learned a lot about the state of the field and how to explain it to others, which will be very helpful for my future career as a genetic counselor.”

The course will be offered again next spring. Student presentations are posted at
http://gen677.weebly.com/projects.html.

Wisconsin’s “Brown Gold” Rush

Earth’s petroleum stores are dwindling, but a Wisconsin project aims to produce energy from a resource that’s in little danger of running low: cow manure, or “brown gold.”

The University of Wisconsin–Madison and several state companies, funded by a $7 million grant from the USDA Biomass Research and Development Initiative (BRDI), have partnered to pilot the conversion of dairy farm manure into useful product streams—a project that is expected to have significant environmental and economic benefits.

The Accelerated Renewable Energy (ARE) project is in progress at the 5,000-cow Maple Leaf Dairy in Manitowoc County, where animal waste is separated into different streams, or fractions, of processed manure.

After small plant fibers in the manure are separated and anaerobically digested to biogas, liquids from the digestion process are used to fertilize crops, while solids can be converted into useful chemicals and bio-plastics. Larger plant fibers make great animal bedding and mulch, not to mention a starting material for ethanol fermentation.

Meanwhile, at the new Wisconsin Energy Institute at UW–Madison, project co-investigator Troy Runge, a CALS professor of biological systems engineering, is analyzing the ARE project’s separation techniques to improve their efficiency. “We are performing many of the same separations that occur on the farm, but in the controlled environment of
the lab to both measure and optimize the system,” says Runge.

Tom Cox, a project collaborator and a CALS professor of agricultural economics, sees great potential for the initiative. “This is a triple-win situation; we would like to make money by doing the right thing by the environment and society,” he says.

Aicardo Roa-Espinosa MS’85 PhD’89, president of partner SoilNet LLC and an adjunct faculty member in biological systems engineering, developed the manure separation technology behind the project. Roa-Espinosa and Runge will monitor the quality, quantity and composition of biogas produced and analyze processed manure streams to identify chemical constituents. Student researchers will conduct life cycle assessments to evaluate the project’s environmental impact.

The goal for the four-year grant, researchers say, is to improve these manure separation technologies until their sustainability benefits can be realized on a broader commercial scale.

Runge notes that the public-private, multidisciplinary project exemplifies what the university hopes to do with the Wisconsin Energy Institute. “It’s also an example of a project that’s important to Wisconsin,” he says.

Indeed, the project may help farmers manage manure with benefits for both the environment and human health. A 5,000-cow dairy farm like Maple Leaf produces approximately 25 tons of manure per day, which require millions of gallons of water to manage. Although some manure may be used as fertilizer, nutrient imbalances and runoff can create environmental problems. However, manure processed using SoilNet’s technology yields concentrated, homogenized fertilizer that can be applied with greater control over nutrient content.

In addition to its environmental benefits, the cellulosic—or non-food—plant biomass derived from dairy manure avoids the conflict of “food versus fuel.”

That’s a promising basis for exciting innovations at dairy farms. For ARE project leaders, farms are not only the heart of agriculture. They also have the potential to serve as foundations for cellulosic biorefineries that could prove key in supporting a local green economy and a sustainable energy system throughout the region.

Getting to the heart of a problem

When Marion Greaser set out to study titin, the largest natural protein known to man, his goal was to answer some basic questions about its role in the body. A major protein of skeletal muscle that’s also found in heart tissue, titin gives muscle its elasticity and is known for its massive size, which ranges from around 27,000 to 33,000 amino acid residues in length.

“Initially we were just going to look at whether titin was related to muscle growth in animals,” says Greaser, a CALS professor of animal sciences.

Working in rats, his team looked at changes in the size of the titin protein over the course of animal development—and immediately came across something strange. In most cases the titin protein shifted from a larger form to a smaller form during development due to natural changes in protein processing known as alternative splicing. But in some rats the titin didn’t change. It stayed big.

The team wondered if they’d mixed up the samples. “But we’d kept good track of things and, in fact, all of the weird samples were from the same litter of rats,” says Greaser. “Then the light bulb went off: There must be some genetic reason why these samples are different. These rats had a genetic mutation affecting the alternative splicing of the titin.”

But where was the mutation? They first checked the titin gene itself, but it was fine. With hard work, they were able to pinpoint the mutation to a little-studied gene called RBM20, which had been previously linked to dilated cardiomyopathy and sudden death in humans.

Dilated cardiomyopathy affects approximately one in 2,500 people. Sufferers have enlarged hearts, with thin walls, that don’t pump blood very well. People with the RBM20 mutation need heart transplants and, without them, tend to die quite early: between ages 25 and 30.

Scientists first linked RBM20 to hereditary dilated cardiomyopathy in 2009, but they hadn’t yet figured out how a faulty RBM20 gene worked—or didn’t work—to cause disease inside the body.

Greaser’s accidental discovery, as described in Nature Medicine, filled in the blank. In healthy individuals, the RBM20 protein is involved in the alternative splicing that helps trim titin down to its smaller, adult form. Without it, titin doesn’t get processed correctly, and the presence of extra-large titin in heart tissue leads to disease.

“Now doctors can analyze people showing symptoms of dilated cardiomyopathy, see if they’re carrying this mutation and factor this information into their treatments,” says Greaser. That treatment would probably start with careful monitoring to catch any further deterioration of the heart condition, Greaser notes.

Better Fishing and Hunting

When his grandfather would complain to him about the difficulty of fishing on choppy days out on Green Bay, biological systems engineering student Justin Vannieuwenhoven did more than listen. He came up with a solution.

His invention, a boat-mounted holder for fishing rods that self-adjusts to keep bait steady relative to the bottom of the water, won the top prize and $10,000 in this year’s Innovation Days competition, held by the College of Engineering for undergraduates to showcase their creative and marketable ideas.

And in a separate Innovation Days contest, another BSE student took the top prize of $2,500 for a device that improves safety for hunters. Luke Stedman teamed with mechanical engineering senior Steve Burbach to create TreeREX, a portable tree stand equipped with steel “jaws” that clamp around a tree trunk and use the hunter’s weight to secure the clamp. The heavier the hunter, the firmer the grip on the tree.

Both avid hunters, the students said they were interested in addressing safety because falls from tree stands are the leading cause of death during Wisconsin’s gun deer season. (Stedman once took a bruising 20-foot fall from a tree stand himself.)

As for fishing, Vannieuwenhoven says his device, which he calls the CFS Holder, works so well because keeping bait steady makes it look more natural to the fish. In addition—unlike other fishing rod holders on the market—its construction makes rods less likely to pull out when a fish bites, and allows fishers to quickly change bait after a catch. Also unlike other holders, the CFS Holder also can be used on ice or land.

Vannieuwenhoven tested his invention with several experienced anglers who reported higher success rates during rough weather. He has filed a provisional patent application for his design and is launching a business called 3 in 1 Holders. Meanwhile, he continues to gather feedback for further improvements.

At least one target market is already satisfied. “My grandpa has six to eight on his boat at all times,” Vannieuwenhoven says. “He’s in love with it.”