Gina Lewin studies the power of ants to break down cellulose

For many college students, summer provides a chance to test-drive future career paths. When Gina Lewin took advantage of such an opportunity, her test drive hit the jackpot.

In the summer of 2009, Lewin participated in a National Science Foundation-funded program called Research Experience for Undergraduates (REU), which invites college juniors and seniors to join research projects around the country.

At the Great Lakes Bioenergy Research Center (GLBRC) at the University of Wisconsin–Madison, Lewin worked in the lab of chemical and biological engineering professor Brian Pfleger. She was tasked with coaxing a bacterium to produce diesel fuel compounds.

As summer progressed, Lewin’s interest in bioenergy and microbiology grew, but she also found herself falling in love with the big research campus of UW–Madison and the city that surrounds it.

“The REU was my first time doing microbiology research,” Lewin says. “I had been thinking about going to graduate school since the end of my freshman year, but being here definitely cemented that interest.”

She applied for graduate school and joined UW–Madison’s microbiology doctoral training program in the fall of 2010.

Lewin, the daughter of two lawyers, grew up in a semi-rural part of central New Jersey. One of her favorite childhood memories is attending summer nature camps at a nearby environmental education center where she learned to identify the bugs she caught in the woods and streams.

After graduating from high school in 2006, Lewin moved across the country to Pomona College, some thirty miles east of Los Angeles, where she was drawn to science and majored in molecular biology.

But it was not until her REU at UW–Madison that Lewin discovered a connection between her childhood interest in bugs and bioenergy research.

In the lab of GLBRC researcher Cameron Currie, Lewin now studies how insects use microbes to break down cellulose, the sugars found in the cell walls of woody plants, in order to procure nutrient-enriched food. Understanding the insects’ process for breaking down cellulose could ultimately inform GLBRC’s own efforts to convert biomass to ethanol and other biofuels.

Lewin’s particular focus is on the insects’ powerful ability to partner with a community of microbes.

“Scientists have long studied how a single microbe in a flask degrades cellulose,” Lewin says. “But in the environment, organisms don’t exist in isolation; they have evolved to be part of a community. Our goal is to apply the power of these symbiotic relationships to biofuel production.”

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Gina Lewin and thesis advisor Cameron Currie present their research to then-Secretary of Energy Steven Chu. Photo: Matthew Wisniewski

Leaf-cutter ants found in tropical rainforests are a particularly impressive example of these mutually beneficial relationships.

Living as a highly organized society in colonies that can grow large enough to be visible from space, the vast majority of leaf-cutter ants work to support their queen. In return, the queen maintains the colony by laying up to 20,000 eggs a day for up to twenty years in the lab.

What is perhaps most remarkable, however, is that the leaf-cutter ants are miniature farmers who have perfected their agricultural activities — deconstructing biomass and cultivating a fungus — over the course of ten million years. Humans, in contrast, have spent a mere 12,000 years developing and fine-tuning their agricultural expertise.

Leaf-cutter ants collect and degrade large amounts of fresh leaves that the fungus converts to food.

“The fungus makes a fuzzy pearl-like structure that contains the nutrients the ants need,” Lewin says. “The larvae and the queen only eat these fungal structures, while the adult workers also feed on leaf sap and fruits.” Some species of leaf-cutter ants even grow a bacterium on their body that protects the fungus from pathogens.

Each colony’s fungus farm consists of a garden, where the plant material is first deposited and partially degraded, and a dump, a dedicated waste management site that may be located under- or aboveground, depending on the ant species.

“Seventy percent of the leaves’ cellulose is carried to the dump for final degradation. It turns out that the dump’s microbial community is much more efficient at degrading cellulose than any individual strain we have studied thus far,” Lewin summarizes her dissertation findings.

Currie, Lewin’s advisor, is as pleased with these results as with Lewin’s success in obtaining external funding for her work.

“I teased Gina that the offer letter for the National Science Foundation’s predoctoral fellowship [dated around April 1, 2012] was probably an April Fool’s joke,” Currie recalls. “These fellowships are incredibly competitive. I’ve never even heard of anyone getting one in their second year.”

Graduate school clearly suits Lewin well, whether she peers through the microscope, gathers fungal samples in Costa Rica, or applies for a research fellowship.

“In college, I had to choose between ecology and molecular biology,” Lewin remembers. “When I decided to major in molecular biology, I was a little sad to leave behind the outdoor activities we did in the ecology classes. But graduate school has allowed me to bring those two interests back together. “

Last but not least, Lewin has also contributed significantly to GLBRC’s education and outreach efforts.

In the summer of 2011, Lewin worked with high school science teacher Craig Kohn from Waterford, Wis., who participated in GLBRC’s Research Experience for Teachers (RET) program. Together they designed a classroom activity that adapted Lewin’s lab assay for demonstrating the breakdown of cellulose for a high school level.

“We figured out that Craig could make a cheap growth medium for microbes by mixing Miracle Gro fertilizer from a garden center with tap water,” Lewin explains.

To see if an environmental sample, such as a scoop of cow manure, contains microbes capable of growing on a piece of cellulosic filter paper, Kohn’s high school students put the sample, the paper, and the fertilizer in a test tube. The students then quantified cellulose degradation by counting the days until a complete tear was observed in the paper.

The following two summers, Lewin and John Greenler, director of GLBRC’s education and outreach program, presented the activity to teachers attending the Bioenergy Institute for Educators. And in the fall of 2014, the activity was expanded for UW–Madison freshmen and used in a First-Year Interest Group (FIG) course in bioenergy.

“In today’s world, just being a great researcher and doing teaching assistant duty for one semester is no longer enough to become a successful faculty member. Gina is a poster child for the importance of translating her research into engaging classroom material,” Greenler says.

“In the six years since her REU, Gina has grown into a real spokesperson for GLBRC,” Greenler adds.

The GLBRC is one of three Department of Energy Bioenergy Research Centers created to make transformational breakthroughs and build the foundation of new cellulosic biofuels technology. For more information on the GLBRC, visit www.glbrc.org.

Unpuzzling diabetes: Alan Attie tracks the internal mechanisms behind a fast-growing disease

The body makes it seem so simple.

You take a bite of supper, and the black-box machinery of metabolism hums into life, transforming food into fuel and building materials. It’s the most primal biology: Every living thing must find energy, and must regulate its consumption.

But for an alarming and ever-increasing number of people, the machinery breaks down. The diagnosis? Diabetes.

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Alan Attie; Banner photo above: This pancreatic islet contains healthy beta cells (stained red for insulin). It also contains a high number of cells producing glucagon (stained green), which raise the concentration of glucose in the bloodstream—indicating diabetes.

Alan Attie, a CALS professor of biochemistry, has been peering into the black box for two decades now, trying to identify the pathways in our bodies by which the disease is formed. “You can’t find a better excuse to study metabolic processes than diabetes,” he says. “It’s very, very rich.

Type 2 diabetes, caused by an inability to produce enough insulin to keep the body’s blood glucose at normal levels, is a global health crisis that has accelerated at a frightening speed over the last 20 years—roughly the same time Attie has been studying it.

It’s an enormously complex disease driven by both genetics and the environment. A DNA glitch here, an external variable there, and the body slides irretrievably out of balance. But only sometimes. Most people who develop type 2 diabetes are obese, yet most people who are obese don’t actually wind up diabetic.

Tracking this riddle has led Attie and his lab to several major discoveries, chief among them identifying two genes associated with diabetes: Sorcs1 and Tomosyn-2. Through years of elaborate experimentation, Attie and his team teased them from the genetic haystack and then relentlessly deciphered their role in metabolic malfunction.

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Why do some mice become diabetic when they are obese—like the mouse on the left—and others not? This pair carries a mutation in determining genes, such as Tomosyn-2 and Sorcs1, which Attie’s lab identified.

Science has uncovered more than 140 genes that play a role in diabetes, yet genetic screening still has little value for patients. As with any part of a large and complicated puzzle, it’s hard to see precisely how Sorcs1 and Tomosyn-2 fit in until we have more pieces. The biology of diabetes is so complex that we can’t be certain what the discoveries may ultimately mean. But both genes have shed light on critical stages in metabolism and offer intriguing targets for potential drugs.

Attie need not look far to replenish his motivation. His own mother suffers from diabetes, and she used to quiz him weekly about when he would cure her. “The painful answer is that translation of basic research into cures takes a long time,” Attie once told the American Diabetes Association. “The most important clues that can lead to cures do not necessarily come from targeted research or research initially thought to be relevant to the disease.”

Continue reading this story in the Spring 2015 issue of Grow magazine

Chris Hittinger names newly discovered yeast for Bucky Badger

When you discover a new organism, you get to name it — but not for yourself. There are rules to the naming business in biology. You can, however, name it for the sponsor of your research. When Chris Hittinger and his group of yeast researchers at the University of Wisconsin-Madison found a rather aggressive yeast, it was natural to name it for the fierce carnivore that is the mascot of his home institution: Bucky Badger.

And so Blastobotrys buckinghamii emerged from the soil of Michigan’s Upper Peninsula to become one of approximately 1,500 known species of yeast. “It was the most aggressive of the eight new species we found,” Hittinger says, “and we thought it was appropriate to name it for Bucky Badger, as it reminded us of Bucky charging down the field.”

Bucky yeast Sylvester

Kayla Sylvester was first author of a new study that identified Blastobotrys buckinghamii, a yeast named for the UW-Madison mascot Bucky Badger. As an undergraduate, Sylvester was instrumental to a survey that retrieved more than 80 species of yeasts, including eight unknown ones, for identification. Banner photo: Yeast cultures being grown in the Hittinger lab; both photos: David Tenenbaum

The badger became UW-Madison’s football mascot in 1889 but went nameless until about 1950, when a contest christened him Buckingham U. Badger. As best as can be determined, B. buckinghamii is the first organism named in Bucky’s honor, says Cindy Van Matre, trademark licensing director at UW-Madison.

Finding eight new species in one project was a fine haul, says Hittinger, an assistant professor of genetics, noting that this represents about one-half percent of all known yeast species. His new study is now online in the journal FEMS Yeast Research. (For more on Hittinger’s yeast work, see the cover story in the Spring 2015 issue of Grow magazine.)

Although it was lab manager Amanda Hulfachor who retrieved B. buckinghamii, Hittinger credits Kayla Sylvester, who started working in his lab as an undergraduate, as “our most prolific wild yeast hunter. She’s really gotten excited about pushing the boundary of what we know about yeasts in the wild, and has been exceptional in setting up and taking over the wild yeast sampling program.”

Sylvester, a native of Sussex, Wisconsin, admits she “didn’t give much thought to where yeasts came from until I came here. It’s hard to tell people you work with yeasts. They think of beer, bread or a yeast infection. They don’t think it would be found outside, but where else could yeasts come from?”

Avid collectors are only the first necessity for finding new yeasts, Hittinger adds. “Specialized enrichment and high-speed genetic sequencing were also key.” Enrichment starts by excluding other organisms, then growing pure colonies of the remaining yeast. Genetic sequencing solves a longstanding problem: yeasts vary little in appearance, even when they have radically different genes.

The lab work can be tedious, Sylvester admits, “but if you’re passionate, it’s very easy. If you are not passionate, it’s very hard. I am very passionate about what I am doing, making my job very enjoyable.”

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Chris Hittinger

Like the other fungi, yeasts specialize in decay, so yeast prospectors tend to sample dirt, rotting wood and bark. “A lot of early yeast collectors looked for fermenting sap,” says Hittinger, “but with appropriate enrichment, yeasts can be isolated directly from soil and rotting wood, without directly observing yeasts in the field.”

Yeasts are creative chemists. Hittinger notes that a single subphylum called Saccharomycotina contains more genetic diversity than all the vertebrate animals. That diversity gives them the ability to do more chemical transformations on the materials they consume.

The Saccharomyces yeasts metabolize sugar into alcohol, a compound that is poisonous to competing microbes. The alcohol makes wine, beer and the biofuel ethanol, while the carbon dioxide released raises bread.

Other yeasts have their own useful chemical tricks. “Some yeasts can accumulate half of their dry weight in oil, and that has more potential as a more advanced biofuel than ethanol,” Hittinger says.

Sylvester, who has graduated and is working in the Hittinger lab until she starts graduate school, says her experience has unleashed her curiosity. “Discovering eight new species is pretty cool. Everywhere you go, you sample. You start to develop all these questions: Does it matter what kind of tree you’re searching under? Does it matter if it’s close to a lake?”

Aside from Saccharomyces, most yeasts are poorly understood, Sylvester says. “You do the sequencing and get the genetic information. What makes this yeast species interesting? Once we get a big enough database, we can look for associations. Pattern-finding is fun; you can ask endless questions. That’s what I like. You can’t stop asking questions.”

This story was originally published on the UW-Madison News website.

 

Top beer from student competition to be sold at Terrace this spring

Spring is on the way, and so is a new UW-Madison student-designed beer that will be sold at the Memorial Union Terrace.

The beer—a red lager that will be called “Inaugural Red”—was selected this past Thursday during a competition held in food science professor Jim Steele’s fermented foods and beverages laboratory class. Six student teams participated in the contest, each presenting a red lager beer of their design to an expert panel of judges.

The top honor went to “team #3,” composed of Andrew Lefeber, Sean Hinds and Elizabeth Wolff. And it’s quite an honor indeed. The team’s beer will now go into full-scale production at the Wisconsin Brewing Company (WBC), which partnered with the UW-Madison food science department to create this unique, hands-on learning experience for students.

“We couldn’t imagine a better way to inspire new generations than combining our brewing experience, expertise and facilities with the exceptional minds and laboratories of the UW,” said WBC president Carl Nolan in a news release about the partnership. “It’s a win-win for students, CALS, WBC—and future generations of Wisconsin beer-drinkers.”

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Kirby Nelson sits with the judging panel and addresses the students before judging begins. From L to R: Rob LoBreglio, Kirby Nelson, David Ryder, Lance Baldus and Rob Gretzlock.

Steele’s students were informed about the competition early in the semester and given a clear charge: to create a red lager with less than 5.5 percent alcohol by volume. How exactly to do that, however, was less straightforward. Students were free to be creative and add different kinds and amounts of malt and hops to make a drinkable, enjoyable beer.

After weeks of experimentation, the teams presented their “final draft” beers last Thursday to an impressive panel of experts, including Kirby Nelson, vice president and brewmaster of WBC; David Ryder, vice president of brewing and research at MillerCoors and adjunct professor in the Department of Food Science; Rob LoBreglio, co-owner and brewmaster at the Great Dane Pub & Brewing Company; Rob Gretzlock, manager of Memorial Union Terrace; and Lance Baldus, associate director of restaurant operations at Memorial Union.

One by one, the beers were introduced by a student brewer and presented to the judges. After smelling, swirling and tasting each one, the judges deliberated and discussed their favorites.

“I want to congratulate all of you because these beers were good,” said Ryder, after tasting all six beers. “You took risks using different types of hops and malts, and we like to see that.”

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The judges deliberate after tasting the beers.

At the end of a close competition, team #3 came out on top. Their beer will go into production at WBC starting on March 15, and all of the students in Steele’s class will have the opportunity to see and help with the full-scale production. “Inaugural Red” will be available at the Memorial Union Terrace starting in May and then at other locations after that.

In an unexpected twist, another team—Nate Elliot, Adam Bartling and Katherine Habbel—will have the opportunity to see their beer produced. LoBreglio was so intrigued by the beer made by team #5, his personal runner-up, that he offered to brew the beer at the Great Dane.

The competition is part of an ongoing effort to develop a fermentation sciences program at UW-Madison, which is being moved forward with the support of both on- and off-campus partners.

“The dream is to make UW-Madison the top college when it comes to the fermentation sciences,” said Ryder, who helped facilitate MillerCoors’ donation in 2008 of the pilot-scale brewing system used in Steele’s class.

That key donation has enabled many good things already—the new student-made “Inaugural Red” beer the most recent among them—and there’s more to come.

“This beautiful little brewery is capable of making something great – small batches of beer that you can really learn something from and then scale up,” said Nelson, who will oversee the production of “Inaugural Red” at WBC.

UW-Madison helps train aspiring farmers enrolled in ‘the MBA of dairy’

Considering the average age of a Wisconsin farmer is upwards of 56 years old and the state has been losing around 500 dairy farms per year in recent years, experts say it’s important to prepare young people to step into farm roles to help keep the state’s $88 billion agricultural economy strong into the future.

But making the transition into dairy farming is complicated, and aspiring farmers often don’t have the capital — or the experience — to take over an established operation.

The Dairy Grazing Apprenticeship (DGA) program is working to address the issue by providing support for young people interested in becoming dairy farmers. Started in 2010, the first-of-its-kind program is administered by the Wisconsin-based non-profit GrassWorks, Inc., with the University of Wisconsin-Madison as a key partner.

Earlier this month, DGA received $750,000 from the U.S. Department of Agriculture’s Beginning Farmer and Rancher Development Program. The funding will enable organizers to improve and expand the program in Wisconsin, as well as explore the possibility of rolling it out to other dairy states.

“It’s a meat-and-potatoes program that really takes people up to the level where they can own and operate their own dairy,” says DGA director Joe Tomandl. “It’s the MBA of dairy.”

DGA participants complete 4,000 hours of paid training over two years, most of it alongside experienced dairy farmers, and work their way up from apprentices to Journey Dairy Graziers and Master Dairy Graziers. While the majority of hours are spent in on-the-job training, there’s also a significant requirement for related instruction. That’s where UW-Madison comes in.

As part of the program, apprentices attend a seminar about pasture-based dairy and livestock through the UW-Madison School for Beginning Dairy and Livestock Farmers (WSBDF), which is co-sponsored by the university’s Center for Integrated Agricultural Systems and the Farm and Industry Short Course. The seminar involves a 32-hour commitment, which is generally fulfilled in a distance education setting.

“We believe in the Wisconsin Idea and want to make sure our classes are accessible to people who want more education, but preferably close to where they live and work,” says Nadia Alber, an outreach coordinator for WSBDF, who helps organize the seminar and also serves on the DGA board.

In 2009, GrassWorks, Inc. turned to WSBDF director Dick Cates for guidance and access to well-respected educational curriculum to help get the DGA up and running, and the WSBDF team has been involved ever since.

“We were just this little non-profit with this very small budget trying to compete for a big federal grant,” says Tomandl. “For us, it was important to have UW as a strategic partner.”

As part of the most recent round of funding, DGA’s UW-Madison partners will lead an effort to quantify the broader impacts of the program.

“They have already proven that participants are moving along to their own farms after the apprenticeship, so they have an established track record that way,” says Alber. “This new study will look at some of the program’s other impacts, including economic, environmental and social.”

The DGA program is a formal apprenticeship program approved by the Wisconsin Department of Workforce Development — Bureau of Apprenticeship Standards.

For more information about the program, visit: http://www.dairygrazingapprenticeship.org/.

Spring lambing season at Arlington ARS

UW-Madison is home to two distinct flocks of sheep, both of which are used to enhance the research, teaching and outreach missions of the college. The flock located at the Spooner Agricultural Research Station is composed of dairy sheep, the types that Wisconsin farmers raise for milk production. The other flock, kept at the Arlington Agricultural Research Station, includes breeds that play a more traditional role in the production of wool, meat and breeding stock.

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Todd Taylor holds a new member of the flock.

CALS photographer and reporter Sevie Kenyon recently paid a visit to the Arlington flock to take some photos and record a podCALS episode with shepherd Todd Taylor. Taylor explained that the Arlington flock is about 300 ewes (female sheep), three-fourths of which will give birth to two, three and sometimes four lambs each during the spring lambing season. “The ewes are made to take care of two lambs and some of them will care for three,” says Taylor. “Lambs the ewes can’t care for get milk replacer.”

Spring lambing starts as early as January, peaks in late February and early March, and is over in April. Lambs arrive in a cold, well-bedded barn and are moved into a nursery shortly after being born. Once Taylor and the staff are certain everything is fine, the lambs and ewes are moved to group housing in a larger barn nearby. Four breeds make up the Arlington flock: Hampshire, Polypay, Rambouillet and Targhee.

16557599936_3adc8c46f1_k“While we do some research, we’re geared a lot toward teaching and extension work,” explains Taylor. “We furnish sheep for numerous classes across the animal science department, and vet students come out and use us quite extensively as well.”

UW-Madison sheep are well known on the show circuit. In fact, everything that goes into showing sheep on a professional show circuit is turned into opportunities for UW-Madison students to get hands-on experience. The presence of the flock also works as a recruitment tool for the Department of Animal Sciences and for UW-Madison around the country.

For more, listen to the podCALS episode featuring Taylor and check out these adorable photos.

 

Dave Nelson helps found—and fill—the new Madison Science Museum

Generally it’s a bad thing to be called a “hoarder.” In Dave Nelson’s case, however, his pack rat tendencies are for a good cause—and will soon come to a very good end.

Nelson, an emeritus professor of biochemistry and defacto CALS historian, has been collecting old scientific instruments, books, papers and other scientific artifacts from the UW-Madison and around Wisconsin for the past 45 years. He has amassed a collection that now fills three rooms on campus—two in the Biochemical Sciences Building and one in the Old Dairy Barn. Soon, however, many of these items will be sent to the home of the new Madison Science Museum, a non-profit museum that Nelson helped found and hopes to see open this coming fall.

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David Nelson with a cast iron Babcock centrifuge and an aluminum one, two of over 100 instruments in his collection.

“The reason I’ve saved my collection all these years is exactly this,” says Nelson. “I want it to be where people can see it and touch it and maybe even use it.”

The museum will occupy the sixth floor of the Madison Area Technical College’s downtown facility, just a stone’s throw from the Madison Children’s Museum, the Wisconsin Veterans Museum and the Wisconsin Historical Museum.

“The museum will pull together in one place much of the exciting science and engineering that’s been done around here in the last century,” says Nelson. “Wisconsin has a wonderful history of research, and it desperately needs to be told.”

When Nelson joined the UW-Madison faculty in 1971, he took over the laboratory space previously occupied by biochemistry professor Marv Johnson. It was the perfect spot.

“Marv had kept all of his old instruments, protecting them so they didn’t get thrown away, so I walked into a lab that was already full of 50-year old instruments,” says Nelson, who hung on to everything—and soon started adding his own pieces to the collection.

“When somebody had an instrument they didn’t need anymore, I grabbed it, and I began to watch for these things at SWAP,” he says. “And then when eBay opened up, I began to get really serious about buying instruments. Usually they’re not very expensive. For instance, a Babcock centrifuge costs maybe $50 or $75, which seems like a good deal for a real piece of history.”

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Nelson with an early apparatus to separate RNA molecules.

Over the decades, Nelson’s collection grew to fill one room, then two, then a third. It features a lot of turn-of-the-century pieces, including early instruments to measure weight, quantities of light, hemoglobin in blood, and blood glucose levels for diabetics. Highlights include the ultraviolet light that Harry Steenbock used in his experiments with rickets and vitamin D; the analytical balance that Karl Paul Link used in his studies of warfarin; and the light microscope that Joshua Lederberg used in his Nobel Prize-winning work on bacteria.

Now these instruments—and the stories that go along with them—will have the opportunity to be shared with the public at the Madison Science Museum. Exhibits, which will be geared toward middle schoolers, high schoolers and adult learners, will highlight early scientific discoveries. They will also show how those initial findings led to important subsequent discoveries, medical and/or technological advances and commercial applications.

“There are more than 150 biotech spinoffs in the Madison area, and some of them are multi-million dollar businesses. We want to show these accomplishments, too, and really all of the aspects of the state’s science and engineering enterprise,” says Nelson.

Exhibits will rotate, giving museum visitors a reason to come back again and again. One of the first exhibits will explore imaging technologies of all kinds—from microscopes to CAT scans to weather satellites.

Nelson, along with UW-Madison Biotechnology Center outreach director Tom Zinnen and others, spent many years searching for a home for the science museum. Initially the goal was to site the museum on the UW-Madison campus, but Nelson came around to the MATC location after considering the many benefits. There are plenty of parking spaces, bus routes and museum-goers in the area.

Nelson’s goal is to open the museum, which will operate 10 a.m. – 9 p.m. Tuesday through Saturday, in time to be a part of this fall’s Wisconsin Science Festival.

While the museum has some funding secured, more is still needed. To encourage emeritus faculty from UW-Madison to donate, Madison Science Museum board member Thomas “Rock” Mackie, an emeritus professor of biomedical engineering, has established a matching grant program that will match 100% of donations from emeritus faculty up to a grand total of $50,000.

For more information about the museum, visit the Madison Science Museum website, download this MSM_two_pager vision document and/or read this madison.com article.

On a related note: The newly-formed CALS History Work Group invites all emeritus and active faculty and staff of the college to a meeting on Monday, February 23 to discuss ways that CALS’ rich history can be preserved and celebrated. The meeting will be held at the UW Credit Union (3500 University Avenue) at 2:00 pm on Monday February 23. David Null from UW Archives will talk about ways the Archives can help in this effort.

Tim Donohue on President Obama’s Precision Medicine Initiative

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Tim Donohue (right) with Jo Handelsman (left) and New York University’s Martin Blaser at the Precision Medicine Initiative launch.

On Jan. 30, CALS bacteriology professor Tim Donohue attended the launch of President Obama’s Precision Medicine Initiative at the invitation of Jo Handelsman, associate director for science at the White House. The goal of the initiative, which is funded to the tune of $215 million in the president’s 2016 budget proposal, is to develop medical treatments and preventive strategies that take into account individual differences in people’s genes, environments and lifestyles. eCALS caught up with Donohue after the event to ask a few questions about the initiative, the launch and his role in the effort.

eCALS: What is the Precision Medicine Initiative, in a nutshell?

Donohue: This is a large inter-agency program to collect genomic and other data on a large patient cohort of one million volunteers. Current medical treatments are often based on how the average patient responds. The goal of this program is to generate sufficient data to tailor treatments to individual patients when possible. If successful, this will revolutionize methods to prevent and treat disease, help keep patients healthy and promote longevity.

eCALS: How did you get involved?

Donohue: The scientific experts who are planning this initiative recognize that the microbiology community is going to be a key player in the success of this approach. I was invited to the initiative launch by Jo Handelsman due to my role as president of the American Society for Microbiology (ASM), the largest microbiology professional society in the world. While a lot of leg work had already happened before I got involved, I and others in ASM have been tracking this initiative for awhile and we have been brought in on an as-need basis to educate, consult and share our expertise.

eCALS: How does microbiology fit into this initiative?

Donohue: There are more microbial cells in your body than human cells, and they have a huge influence on human health. We need to know which are the good ones that we should leave alone or promote their growth–and which ones are the bad ones to isolate and take out. We still have a lot to learn about the body’s microbial communities, and this initiative will help generate knowledge that help us bring microbes out from behind the shadows.

eCALS: What was the launch event like?

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Donohue snapped this photo of Obama speaking at the launch event.

Donohue: It was a stimulating experience, just to be in the White House for such an event. It was also reassuring to see representatives from both political parties in the audience as a sign of potential bipartisan support for the basic science research needed to promote human health. Finally, it was inspiring to see young people who are doing research in this field and to meet some people who have already benefitted from early-phase precision medicine.

Kareem Abdul Jabar was in attendance. He had a very rare form of cancer. Genetic testing revealed he was a good candidate for a brand new drug, and he took it and it worked. There was another man there who was diagnosed with cystic fibrosis as a child and given a life expectancy of 20 years. Now he’s 27 and his disease is under control and he’s a third year medical student. These examples, which show the potential of this approach, put tingles in your spine.

Learning lessons by following Madison’s foxes and coyotes

Photos and accompanying slideshow by Jeff Miller/UW-Madison.

Last year, a family of foxes — complete with roly-poly kits — took up residence on the University of Wisconsin-Madison campus and made the city its playground.

With winter in full swing, the foxes and their larger dog-like counterparts, coyotes, are out there again, roaming the wilder (and often not so wild) parts of the city and campus. This year, David Drake, a UW-Madison associate professor of forest and wildlife ecology, is welcoming the public to join him and his research team as they go out and radio collar the animals in an effort to track and better understand these urban canids.

“There’s so much interest in these animals in Madison, I think this is a great outreach opportunity to talk to people about why these animals are moving into the city,” says Drake, also a UW-Extension wildlife specialist.

For the next several weeks, Drake, graduate student Marcus Mueller and undergraduates like wildlife ecology junior Cody Lane will be on campus and off, humanely trapping foxes and coyotes and fitting them with small radio collars so their whereabouts may be tracked. The public and campus community can arrange a time to join them by emailing uwurbancanidproject@gmail.com or finding them on Facebook. Though as with all things wild, there is no guarantee the team will catch an animal on any given day.

Photo: David Drake

David Drake

“We want to tell people about their behavior, what to do if you see one in your neighborhood, what not to do, and also talk to them about best management practices, as well,” says Drake.

Amid the hustle and bustle of daily life, the urban foxes and coyotes serve as a powerful reminder that nature is yet all around us. Even as cars and buses and bikes zoom past, as we duck our heads against blustering winds or find distraction in the digital glow of smartphone screens, these relatives of man’s best friend are also there among us.

It was an unusually warm January morning when Drake and Mueller met up for the graduate student’s first hand at trapping the fox and coyote. Mueller, a 2012 UW-Steven’s Point graduate in wildlife ecology, has spent the last couple of years working for the Wisconsin Department of Natural Resources Deer Project, and also has experience working in wildlife rehabilitation in Milwaukee. Despite this, on this morning, he was quiet, contemplative, readying himself for the work ahead.

In all, there were 20 traps to be checked, six set for fox and 14 for coyote (Drake pronounces the word kai-yote, a variation on another common pronunciation, kai-yo-tee). Today would prove to be a fruitless one. No fox, no coyote.

The traps themselves are unremarkable. They were made for Drake and his team by expert Wisconsin trapper Mike Schmelling — who by Drake’s account has helped make the state a national leader in best management trapping practices — and Schmelling helped the team place the cable restraints in discrete, mostly sheltered locations around campus, where these animals are likely to be found.

Made according to regulation, the restraints are similar to a small, thin choke collar many people use for their dogs. The cable is looped on a swivel and anchored into the frozen ground. The loop is set according to the specifications for each animal and as a fox or coyote passes through it — usually in search of food or along a travel corridor — the loop hits its shoulders and impedes its progress. As the animal tries to back out, the loop tightens until it hits the animal’s fur, or until it hits the stopper that prevents choking.

There, the animal waits, for no more than 12 hours by Drake’s research protocol (and generally far less), before the scientists remove them from the restraints and set about their work. Legally, traps must be checked at least once every 24 hours.

Marcus Mueller and Cody Lane

Marcus Mueller and Cody Lane

The next morning — a frigid, windy one — crows murmured overhead and a bright, young red fox sat among a thicket of reeds, caught up in his hunt for a snack. The day before, a bald eagle had visited, keeping watch on this area of prime real estate. Tracks in the snow gave away the presence of canids, as did a small pile of scat nearby.

Drake and Mueller called Mike Maroney, senior program veterinarian for the UW-Madison Research Animal Resources Center, for his assistance in handling and caring for the animal, who was soon to be sedated using a common veterinary anesthetic.

Working swiftly with confident yet gentle hands, Mueller laid the still animal on a tarp and towel to keep him warm while the researchers monitored and recorded his temperature, breath and heart rate. Maroney and Mueller collected a blood sample from the young male and used cotton rods to swab his nose and rectal area.

From a large orange bucket of supplies, fit with organizing pockets, Mueller drew out a brown collar and a mouse-brown sack containing a blue box with digital screen. Keeping a space of two fingers between the fox’s neck and the collar, Mueller bolted it closed. He and Lane tested the collar to make sure it registered on the blipping blue box. Collar number 11463.

The team wants to learn where Madison’s foxes and coyotes are traveling. From data collected last year, Drake knows the coyotes are roaming from Madison to Middleton to Maple Bluff and everywhere in between. Are the animals visiting the city’s ample backyard chicken coops and gardens, complete with berries and small mammals? How close do they get to people, and how do they and the humans respond? How are the coyotes and foxes — a predator and its prey — interacting with one another, and are the animals picking up diseases like parvovirus and canine distemper from people’s unvaccinated pet dogs, or vice versa?

That the study involves trapping is an element Drake would like the public to see, because people often get the wrong idea. His team has done all it can to ensure its actions are humane and safe, not just for the foxes and coyotes, but for dogs and other animals, too. The restraints are out of the way, yet easy to release. Still, he urges people to keep their dogs on leash in areas where signs announce the presence of traps, such as near the Lakeshore Preserve on campus.

“We’re trying to understand these foxes and coyotes a little more so we can make sure we’re managing for these animals in this urban environment … ” David Drake

It’s also against the law to tamper with legally set traps and anyone caught doing so is subject to fines and even imprisonment.

“We just aren’t a society that’s outdoors and enjoying wildlife as much as we used to — whether its hunting or photographing or watching them — so there is that disconnect between nature and humans, and I don’t think people quite understand what this is all about,” Drake says. “We’re trying to understand these foxes and coyotes a little more so we can make sure we’re managing for these animals in this urban environment as much as we can, and also trying to tell people: ‘Here’s what these animals are doing,’ so we can be proactive and try head off any conflicts that might occur.”

As the team wrapped up its work, the fox was weighed — a large, healthy 13.5 pounds — and his brilliant, sharp white teeth and pink gums were examined as a measure of his health. He was given a reversal drug to help arouse him from his twilight, and the researchers moved him to a safe area, out of the wind. They waited and watched to ensure he didn’t put himself in harm’s way upon waking.

With a start, the nimble creature bolted up, dashing back into the reeds. The biologists waited several minutes until he was out of sight before heading back to the truck.

What’s left now is to keep tabs on this animal — a team of five or six students will check in every so often on him and the others yet to be found, venturing out into the urban wild, matching the blips on the blue box to their collars, registering their movements and keeping track of their overall well-being.

Now that this task was over, working on his very first fox, the quiet and reserved Mueller seemed to spring to life, almost drunken with elation over the morning’s seamless — even breathtaking — events.

“Nothing could be better than that,” he said. “That was perfect.”

To the ends of the earth

In April 2011, James Bockheim led a small team of researchers to a rocky spit of land called Cierva Point, a habitat protected by the Antarctic Treaty as a “site of special scientific interest.” Home to breeding colonies of bird species like Gentoo penguins, as well as a remarkably verdant cover of maritime plants, Cierva Point is also one of the most rapidly warming places on Earth.

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James Bockheim (left) in Antarctica with former graduate student Adam Beilke MS’11. They are drilling a shallow borehole in which to install instruments for measuring temperatures of “active layer” soil, which thaws and freezes.

Bockheim and his crew were beginning another field season on the Antarctic Peninsula, the long finger of rock and ice that snakes past Palmer Station, the United States’ northernmost Antarctic research station, and curls out in the Southern Ocean (see map, page 25). They’d been deposited onshore, along with their gear, by the Laurence M. Gould, a research vessel that wouldn’t return until late May. As the ship sailed back into the frigid sea, Bockheim turned his attention not to penguins or polar grasses, but to the ground beneath his feet.

Every year there was more and more of that ground as glaciers drained into the Southern Ocean, revealing soils and bedrock that had been covered in ice for millennia. Bockheim wanted to know what was going on underneath the newly exposed surface and had brought along a soil and bedrock coring tool, a device that looks like a cartoonishly oversized power drill, to get to the bottom of it.

His crew fitted the drill with its two-meter-long impact hammer bit. Graduate student Kelly Wilhelm pointed the drill at the ground and pulled the trigger.

It wouldn’t be the first time that Antarctica caught Bockheim by surprise. Bockheim, a CALS professor of soil science, has spent his career studying polar and alpine soils. From field sites north of the Arctic Circle to mountain passes in the Andes and the dry valleys of Antarctica, Bockheim has worked to classify and understand how soils are formed in the Earth’s coldest climates.

Bockheim first set foot on Antarctic soil in 1969 as a Ph.D. candidate at the University of Washington. Although his dissertation was on alpine soils in the Cascades, his advising professor had a project in Antarctica and invited him to come along.

“And that was it,” Bockheim recalls. “It just got in my blood.” Startled by the “peace, solitude and stark beauty,” he knew he would have to return.

Six years after that first trip, Bockheim got his chance. He had recently accepted a position at the University of Wisconsin–Madison when a call came in asking if he’d like to join a glacial geologist from the University of Maine on a multiyear research project in Antarctica’s dry valleys. Bockheim’s reply was succinct: “Absolutely.”

To continue reading this story, go to the Fall 2014 issue of Grow magazine