The Island of Giant Mice

Two thousand miles east of the coast of Argentina, Gough Island rises out of the Atlantic Ocean in an awesome display of ancient volcanic activity. A green carpet of windswept mosses and grasses covers 35 square miles of jagged peaks and steeply sloping valleys. Waterfalls spill out of craggy cliffs and fall hundreds of feet to the sea, which runs uninterrupted for another 1,700 miles before crashing into the tip of South Africa. It is one of the most remote places on our planet.

Four miles west of the University of Wisconsin– Madison campus, the Charmany Instructional Facility is a low-slung labyrinth of concrete hallways lined by bright fluorescent lights and permeated with a smell that is equal parts animal and antiseptic. Part of the UW School of Veterinary Medicine, Charmany is nearly half a world away from Gough Island (pronounced “Goff ”). Yet the two locations share a common trait— they both are home to the largest mice on Earth.

In terms of body size and weight, Gough Island mice are twice the size of their mainland cousins, notes Bret Payseur, a geneticist with a joint appointment in CALS and the School of Medicine and Public Health. “The amazing thing about them being twice the size is that they’ve only been on the island a couple of hundred years,” he says. The island’s early rodent settlers were a more moderate-sized strain of Mus musculus, house mice stowaways in the holds of sealing ships from Western Europe. But somewhere along the line, Gough Island mice outgrew that ancestry—doubling in size over the course of only a few hundred generations. “That’s incredibly rapid evolutionary change,” Payseur says. “It’s some of the most rapid that I know about.”

In the canon of origin stories, however, this tale reads more like a mystery. How did the Gough Island mice get so big so quickly? It could be that a genetic mutation proved so advantageous that huge mice became the norm. Or maybe conditions on the island favored preexisting genetic traits that had lain dormant until the mice became castaways. For the time being, however, the Gough mouse story is transcribed only in A’s, T’s, C’s and G’s—the nucleic acids that write genetic code. Payseur hopes to translate that text. What he finds could not only shed light on evolution in action. It could also help illuminate the genetic mechanisms underlying human metabolic diseases like obesity and diabetes.

The Island Rule

While Gough Island mice are unusually large, it isn’t unusual for small animals on islands to grow bigger than their mainland counterparts. The phenomenon is often referred to as the “island rule,” which states that, in general, small animals tend to get bigger and large animals tend to get smaller once they’ve been island castaways for some period of time. There are, of course, exceptions. But from giant Komodo dragons to extinct pygmy mammoths, examples of the island rule run throughout the animal kingdom.

The gigantism effect of this rule seems to be especially pronounced in rodents. Human history is full of daring adventure on the high seas involving fearless mariners and the obligatory stowaways—mice and rats. As a result, the world’s islands are full of transplanted rodents. Biologist J. Bristol Foster first posited the island rule in a 1964 paper in the journal Nature, titled “The Evolution of Mammals on Islands.” In his study, Foster looked at 69 populations of island mice off the coasts of Western Europe and North America. The mice in 60 of those populations were measurably larger than their mainland cousins. Since that study, time and again, scientists find mice and rats on islands that are markedly bigger than genetically similar mainland populations.

This is notable because, in evolution, random genetic mutations or suddenly shifting environmental conditions can lead a species down a certain path. Which means that chance plays a big role in charting a species’ history. “If you ‘run the tape’ once and go back and run it again,” Payseur says, “you would expect different outcomes because of that role of chance.” When patterns like the island rule appear in evolution, he says, “People get very excited. It suggests that what underlies the patterns is a common mechanism that would tell us something important about how evolution works.”

Payseur’s scientific background is anchored in evolutionary biology, and the natural history of species on islands has fascinated him throughout his career. After early work with primates in Madagascar, Payseur realized that, while there is a lot one can do in primate research, keeping captive colonies of lemurs in a lab and breeding the thousands of crosses needed to actually get at answers wasn’t one of them. So he turned his attention to mice.

“The great thing about house mice—and I know most people don’t think house mice are great—is that the strains or lines of mice that people study in the lab are descended from wild house mice, including the wild mice that often inhabit islands,” Payseur says. “So they’re kind of cousins evolutionarily and share a lot of the same traits. That means we can use the genetic tools developed for the lab strains of mice to understand what’s happening in wild mice.”

He’s looking to these small creatures to answer some very big questions. “In the very long term, what I would like to answer with this research is, ‘What types of genetic changes are responsible for the extreme body size on islands?” Payseur says. “Are they the same on different islands? Do we see the same genes popping up over and over again, or do organisms take different paths to get big?”

Knowing that he would have the time, money and resources to deal with only a single strain of island mouse at a time, Payseur decided to start with the most extreme example of the island rule that he could find. He turned to colleagues who studied house mice in the field—and every one of them pointed him to Gough Island.

An Incredible Journey

Most researchers simply order mice via catalog, usually from what Payseur calls “the world center for mouse genetics,” the Jackson Laboratory in Maine. A copy of their glossy catalog lets researchers pick trait-specific lines of mice, from body size and coat color to preassigned conditions like immunodeficiency. Then, simply place an order and wait a few days for the mail to arrive. Gough Island mice aren’t in that catalog. Which means that Payseur had to figure out a way to get mice from an incredibly remote island with a grand total of six to eight full-time human residents, all of whom were busy with their year-long stint staffing the South African National Antarctic Programme’s weather station.

The solution came in the form of an unusual and macabre adaptation of behavior in Gough Island mice. In addition to developing bigger bodies in their few hundred years on the island, they have also developed an appetite for bigger food—the chicks of nesting seabirds, which they, quite literally, nibble to death. Luckily for Payseur, there are quite a few people concerned about those seabirds.

Gough Island is officially a possession of Britain and part of the Dependency of Tristan de Cunha. It is also listed as a World Heritage Site by the United Nations Educational, Scientific and Cultural Organization, which recognizes Gough as a pristine, primarily untouched ecosystem. Its towering cliffs, according to the UNESCO description of the island, “host some of the most important seabird colonies in the world,” from the endangered Tristan albatross to the Atlantic petrel to the Northern Rockhopper penguin. Under such circumstances, a population of non-native, quick-breeding, bird-eating mice is of grave concern—especially to the governments and scientists tasked with preserving the island’s biodiversity.

Peter Ryan, director of the Percy FitzPatrick Institute of African Ornithology at the University of Cape Town, South Africa, says that, especially where petrels and albatrosses are concerned, Gough Island mice are a threat to breeding populations. Ryan has been an honorary conservation officer in the Tristan de Cunha islands since 1989 and has witnessed the decline in seabirds firsthand. When Payseur reached out to him in 2008, Ryan was working with Richard Cuthbert, a scientist at the Royal Society for the Protection of Birds, on a census of sorts to help the British government plan an intervention—or, rather, an eradication.

The mice “were easy enough to catch,” Ryan wrote in an email recalling Payseur’s request. “They occur at very high densities and we’d been live-catching lots of mice to estimate their movements and densities and to conduct poison trials to ensure that all were susceptible to the poison bait.” Ironically, in order to study how best to kill them, the researchers had the live traps, food, bedding and other paraphernalia needed to keep the mice alive for study.

The “big issue” Ryan recalls, was shipping them. Eventually, the crew of the S.A. Agulhas, a South African Antarctic research vessel, agreed to give the mice a lift, but “Even this was a bit tricky, because we had to convince them that the mice wouldn’t be able to escape.” In the fall of 2008, 50 Gough Island mice boarded a boat and took the return trip to the mainland, specifically Cape Town, South Africa. After a lot of paperwork they were sent to Johannesburg, with inspections and quarantines and mountains of paperwork piling up as they made their way by plane to Europe, then to Chicago and, in a final car ride, to the campus of the University of Wisconsin–Madison, where postdoctoral researcher Melissa Gray was waiting.

That September, Gray had just begun her stint in Payseur’s lab. The idea of working with mice excited her, since, as with Payseur’s initial study of primates in Madagascar, the Channel Island foxes she had been working on promised to be a difficult study organism. When a mentor suggested she reach out to Payseur, Gray says, “It was a perfect connection.” She had a background working on island populations and the genetics of size and “Bret already had this project and nobody to work on it.” Plus, she wouldn’t have to wait long to get going. “I started in Bret’s lab in September,” Gray recalls, “and the mice arrived in late October.”

Immediately upon their arrival, the Gough Island mice alleviated any concerns about their suitability as a study subject. “Basically it was a cardboard box with some breathing holes and food stuffed inside,” Gray recalls. But when she opened the box, “It was amazing,” she recalls. Ryan had sent 50 mice off to Wisconsin. Forty-five survived the trip and, even better, they’d managed to produce a couple of litters along the way. They hadn’t even begun their experiment, and already the Payseur Lab was growing a colony of Gough mice. “In a way, we ended up with more than we started with, which is crazy with the amount of stress they were under,” Gray says.

After that initial excitement wore off, the real work began. First, Gray had to randomly breed several sets of mice to ensure that their large size was genetic and not the result of conditions on the island. When those lines came out as big as the wild-born mice, she could turn her attention to creating the first lab-raised line of Gough Island mice, inbreeding some promising strains of mice to create lines that were genetically identical, which makes gene mapping much easier. These mice would then serve as the lab’s breeding colony, slated as mates for lab mice with a mainland heritage.

One way to think about the process—to borrow a metaphor from Mark Nolte, a current postdoctoral researcher in the Payseur Lab—is to imagine two decks of playing cards, one red and the other blue, where each card is a gene. Each deck represents a chromosome, a long strand of DNA wrapped around proteins that carries genetic instructions from a parent to its offspring. When sexual reproduction occurs, each parent contributes a copy of one of their two chromosomes to their offspring.

Imagine the Gough Island mice as having two blue decks of cards—one deck for each chromosome—and the mainland mice as having two red decks. Their initial mating yields what’s called a “filial generation one,” or an F1 baby mouse with two distinct chromosomes, one with all blue cards and the other with all red cards. But when an F1 mouse mates with another F1 mouse, those decks get shuffled. These “filial generation 2,” or F2 mice, hold the first key to untangling the riddle of the evolution of Gough Island’s giant mice.

Breaking the Code

In a small, windowless room at the Charmany Instructional Facility, doctoral candidate Michelle Parmenter lifts two wriggling brown mice out of separate plastic cages by the base of their tails. One is from a line of laboratory mouse with a lineage that runs, if one looks far enough back, to a population of U.S. house mouse. The other is also a strain of laboratory mouse, although it’s of the lab’s own creation—its Gough Island heritage evident in the way it dwarfs its companion when nestled side by side in Parmenter’s hand.

Parmenter, Nolte and a half-dozen Payseur Lab undergrads spend a large portion of their time taking measurements, plopping each of the 480 mice in the room—increasingly inbred descendants of the original Gough mice—one by one into an empty container of French onion dip and putting it on a scale.

Parmenter has slipped on tough blue “bite gloves” before handling the mice— and one mouse’s attempted nibbles remind her why she needs them. “Okay, you’re trying to bite me,” she announces, putting the critter down. “These bite gloves are good, but they’re only so good.”

A smaller mouse, on the other hand, sits meekly in her palm. Parmenter and Nolte say there are a lot of anecdotal differences in behavior between the Gough line of mice and their mainland counterparts. Gough mice scrabble at the corners of their clear plastic cages and frantically scale the grates near their water bottles like monkey bars. The mainland mice spend more time quietly nestled in the shredded paper bedding provided for burrows. When working with the mice, Parmenter and Nolte put them in deep plastic basins, since the Gough mice seem to be strong jumpers and more aggressive. In comparison, says Nolte, “I could work with classical laboratory strains of mice on a level surface and they wouldn’t go anywhere. They wouldn’t even try to escape.”

While they enjoy discussing the potential evolutionary drivers behind some of this observed behavior, what is really exciting to Parmenter and Nolte is what these mice are now telling them at a genetic level.

By crossing mice from Gough and the mainland strain, the Payseur Lab has produced about 1,400 F2 mice. They’ve extracted DNA from each one, sent those samples to a lab for analysis and, in return, received a genomic portrait of each mouse’s DNA. Combing through all of that is a slow process, says Parmenter, but already they are finding hints of the genetic code responsible for their remarkable size.

“Imagine I take the two decks of cards—or ‘chromosomes’—and spread them out, and I can go down each row and say, ‘Oh, there’s a mainland chunk of DNA,’ or ‘Hey, that one came from Gough,’” Nolte says. When you do this enough, patterns begin to appear. “If you take your largest mice and spread their decks, you notice that at the same position on the chromosome they all share the same Gough DNA.” When a big enough percentage of large mice show the same chunk of genes at the same position on the genome, Nolte says, it indicates that, somewhere in the region, there is a gene responsible for size.

That strong association, however, isn’t exactly a smoking gun. When the project began, says Payseur, a prevailing thought was that the rapid evolution in Gough Island mice would be the result of mutations in just a couple of key genes. But in a September 2015 paper in the journal Genetics, the lab published its first genetic mapping results from the F2 crosses, reporting that 19 different sections of the genome appear to play some role in the rapid and extreme size evolution of Gough Island mice. Each of those 19 sections is comprised of anywhere from 400 to 1,400 genes, which means there is much more work to do.

Right now, the process “is not getting at a specific gene,” says Gray, who was the lead author of the Genetics paper. “It’s saying, ‘Okay, this chunk of genome right here somehow corresponds to body size.’ So if you want to tease that apart more, you have to shuffle the deck again. And then shuffle it again.” Keeping your eye on the right card gets difficult. “You really need a lot of samples to get past the noise,” she says, “and that’s a challenge about a project like this. You need a lot of individuals, and that means a lot of money and a lot of time and a lot of mice.”

The Search for a New Island

As the “giant mice” experiment currently stands, the Payseur Lab will, eventually, uncover specific genes that are responsible for the Gough Island mouse’s astounding size, work that could have implications for research on things like human metabolic diseases or even breeding livestock.

“When you look at domesticated animals, size is one of the most important traits because it’s correlated with characteristics like productivity,” Payseur explains. “There’s a lot of interest in CALS in understanding the genetic basis of size variation—in that context it would help select for increased body size and know what genes confer the response. Maybe there’s a more efficient way to ‘build the animal.’”

But if Payseur is to truly unravel the evolutionary mystery of the island rule, he’s going to not only need more time, money and mice—he’s going to need a new island.

The idea is to run the same experiment with another population of large island mice and see if evolutionary patterns emerge. Do some of the same 19 genetic regions his lab has identified show up in those mice, or did they get bigger through a completely different mechanism?

“It would be nice to choose an island because it has similar ecological conditions to Gough that might have driven the same kind of body size increase,” Payseur muses. “But another consideration is, it would be nice to choose an island where the mice have come from a different part of the world. I’m in the throes of figuring that out right now.”

Either way, it’s not a decision that will be made quickly. And the project, which is funded in part by the National Institutes of Health, is slated to run for several more years, meaning that large mice will be calling a UW–Madison lab home for a while.

Gray has already moved on from the project, taking a job as a research scientist at Exact Sciences, a Madisonbased biotech company. Both Nolte and Parmenter realize that they’ll also head elsewhere in their careers before the full story of the Gough Island mice can be translated. But they admit to hoping that they’re still around when the next cardboard box full of large, wild mice arrives in the lab.

“Just knowing that Bret is pursuing a new island population makes us all giddy,” Nolte says.

Payseur shares their excitement, but he knew when he launched the study that he was signing on for what could end up being a career-long project.

“I think that genetics is the most powerful way to answer evolutionary questions,” he says. But getting at answers can be “more complicated than one might imagine,” Payseur admits. “It would be nice to have a simple explanation, but I tend to be attracted to more complicated projects.”

In one respect at least, things might be finally getting a little less complicated for the Payseur Lab: Wherever they turn next for a population of giant mice, the island in question will be a little less remote than Gough. And the mice involved will be a little smaller. And, just maybe, writing the next chapter of this story will be a little bit easier—aided by a key created from the genome of the largest mice on Earth.

 

To Market, to Market

If you’re familiar with the College of Agricultural and Life Sciences (CALS), you no doubt know all about Stephen Babcock and his test that more than 100 years ago revolutionized the dairy industry by providing an inexpensive, easy way to determine the fat content of milk (thus preventing dishonest farmers from watering it down). What you might not know is that his great discovery went unpatented. The only money Babcock received for his invention was $5,000 as part of a Capper Award—given for distinguished service to agriculture—in 1930.

Just years before Babcock received that award, another entrepreneur was hard at work in his lab—and his discovery would break ground not only in science, but also in direct remuneration for the university.

In 1923, Harry Steenbock discovered that irradiating food increased its vitamin D content, thus treating rickets, a disease caused by vitamin D deficiency. After using $300 of his own money to patent his irradiation technique, Steenbock recognized the value of such patents to the university. He became influential in the formation in 1925 of the Wisconsin Alumni Research Foundation (WARF), a technology transfer office that patents UW–Madison innovations and returns the proceeds back to the university.

Discoveries have continued flowing from CALS, and WARF plays a vital role for researchers wanting to patent and license their ideas. But today’s innovators and entrepreneurs have some added help: a new program called Discovery to Product, or D2P for short.

Established in 2013, and co-funded by UW–Madison and WARF, D2P has two main goals: to bring ideas to market through the formation of startup companies, and to serve as an on-campus portal for entrepreneurs looking for help. Together, WARF and D2P form a solid support for researchers looking to move their ideas to market. That was the intent of then-UW provost Paul DeLuca and WARF managing director Carl Gulbrandsen in conceiving of the program.

“The idea of D2P is to make available a set of skills and expertise that was previously unavailable to coach people with entrepreneurial interests,” explains Leigh Cagan, WARF’s chief technology commercialization officer and a D2P board member. “There needed to be a function like that inside the university, and it would be hard for WARF to do that from the outside as a separate entity, which it is.”

D2P gained steam after its initial conception under former UW–Madison chancellor David Ward, and the arrival of Rebecca Blank as chancellor sealed the deal.

“Chancellor Blank, former secretary of the U.S. Department of Commerce, was interested in business and entrepreneurship. D2P really started to move forward when she was hired,” says Mark Cook, a CALS professor of animal sciences. Cook, who holds more than 40 patented technologies, launched the D2P plan and served as interim D2P director and board chair.

With the light green and operational funds from WARF and the University secured, D2P was on its way. But for the program to delve into one of its goals— helping entrepreneurs bring their ideas to market—additional funding was needed.

For that money, Cook and DeLuca put together a proposal for an economic development grant from the University of Wisconsin System. They were awarded $2.4 million, and the Igniter Fund was born. Because the grant was good only for two years, the search for projects to support with the new funds started right away.

By mid-2014, veteran entrepreneur John Biondi was on board as director, project proposals were coming in and D2P was in business. To date, 25 projects have gone through the Igniter program, which provides funding and guidance for projects at what Biondi calls the technical proof of concept stage. Much of the guidance comes from mentors-in-residence, experienced entrepreneurs that walk new innovators down the path to commercialization.

“For Igniter projects, they need to demonstrate that their innovation works, that they’re not just at an early idea stage,” explains Biondi. “Our commitment to those projects is to stay with them from initial engagement until one of three things happen: they become a startup company; they get licensed or we hand them over to WARF for licensing; or we determine this project might not be commercial after all.”

For projects that may not be destined for startup or that need some additional development before going to market, the collaboration between WARF and D2P becomes invaluable. WARF can patent and license discoveries that may not be a good fit for a startup company. They also provide money, called Accelerator funding, for projects that need some more proof of concept. Innovations that may not be ready for Igniter funds, but that are of potential interest to WARF, can apply for these funds to help them move through the earlier stages toward market.

“Some projects receive both Accelerator and Igniter funding,” says Cagan. “Some get funding from one and not the other. But we work together closely and the programs are being administered with a similar set of goals. We’re delighted by anything that helps grow entrepreneurial skills, companies and employment in this area.”

With support and funding from both WARF and D2P, entrepreneurship on campus is flourishing. While the first batch of Igniter funding has been allocated, Biondi is currently working to secure more funds for the future. In the meantime, he and others involved in the program make it clear that the other aspect of D2P—its mission to become a portal and resource for entrepreneurs on campus—is going strong.

“We want to be the go-to place where entrepreneurs come to ask questions on campus, the starting point for their quest down the entrepreneurial path,” says Biondi.

It’s a tall order, but it’s a goal that all those associated with D2P feel strongly about. Brian Fox, professor and chair of biochemistry at CALS and a D2P advisory board member, echoes Biondi’s thoughts.

“D2P was created to fill an important role on campus,” Fox says. “That is to serve as a hub, a knowledge base for all the types of entrepreneurship that might occur on campus and to provide expertise to help people think about moving from the lab to the market. That’s a key value of D2P.”

Over the past two years, D2P, in collaboration with WARF, has served as precisely that for the 25 Igniter projects and numerous other entrepreneurs looking for help, expertise and inspiration on their paths from innovation to market. The stories of these four CALS researchers serve to illustrate the program’s value.

Reducing Antibiotics in Food Animals

Animal sciences professor Mark Cook, in addition to helping establish D2P, has a long record of innovation and entrepreneurship. His latest endeavor, a product that has the potential to do away with antibiotics in animals used for food, could have huge implications for the animal industry. And as he explains it, the entire innovation was unintentional.

“It was kind of a mistake,” he says with a laugh. “We were trying to make an antibody”—a protein used by the immune system to neutralize pathogens—“that would cause gut inflammation in chickens and be a model for Crohn’s disease or inflammatory bowel disease.”

To do this, Cook’s team vaccinated hens so they would produce a particular antibody that could then be sprayed on feed of other chickens. That antibody is supposed to cause inflammation in the chickens that eat the food. The researchers’ model didn’t appear to work. Maybe they had to spark inflammation, give it a little push, they thought. So they infected the birds with a common protozoan disease called coccidia.

“Jordan Sand, who was doing this work, came to me with the results of that experiment and again said, ‘It didn’t work,’” explains Cook. “When I looked at the data, I saw it was just the opposite of what we expected. The antibody had protected the animals against coccidia, the main reason we feed antibiotics to poultry. We knew right away this was big.”

The possibilities of such an innovation—an antibiotic-free method for controlling disease—are huge as consumers demand antibiotic-free food and companies look for ways to accommodate those demands. With that potential in hand, things moved quickly for Cook and Sand. They filed patents through WARF, collaborated with faculty colleagues and conducted experiments to test other animals and determine the best treatment methods. More research was funded through the WARF Accelerator program, and it became clear that this technology could provide the basis for a startup company.

While Cook didn’t receive funds from D2P to bring the product to market, he and Sand used D2P’s consulting services throughout their work—and continue to do so. Between WARF funding and help from D2P, Cook says starting the current company, Ab E Discovery, has been dramatically different from his previous startup experiences.

“D2P is a game changer,” says Cook. “In other cases, there was no structure on campus to help. When you had a technology that wasn’t going to be licensed, you had to figure out where to get the money to start a company. There were no resources available, so you did what you could, through trial and error, and hoped. Now with WARF and D2P working together, there’s both technical de-risking and market de-risking.”

The combination of WARF and D2P has certainly paid off for Cook and Sand. They have a team and a CEO, and are now producing product. Interest in the product is immense, Cook says. He’d like to see the company grow and expand—and stay in Wisconsin.

“It’s been a dream of mine to make Wisconsin a centerpiece in this technology,” Cook says. “I’d like to see the structure strong here in Wisconsin, so that even when it’s taken over, it’ll be a Wisconsin company. That’s my hope.”

Better Corn for Biofuel

Corn is a common sight in Wisconsin and the upper Midwest, but it’s actually more of a tropical species. As the growing regions for corn move farther north, a corn hybrid has to flower and mature more quickly to produce crop within a shorter growing season. That flowering time is determined by the genetics of the corn hybrid.

Conversely, delayed flowering is beneficial for other uses of corn. For example, when flowering is delayed, corn can produce more biomass instead of food, and that biomass can then be used as raw material to make biofuel.

The genetics of different hybrids controls their flowering time and, therefore, how useful they are for given purposes or growing regions. Shawn Kaeppler, a professor of agronomy, is working to better understand those genes and how various hybrids can best fit a desired function. Much of his work is done in collaboration with fellow agronomy professor Natalia de Leon.

“We look across different populations and cross plants to produce progeny with different flowering times,” Kaeppler explains. “Then we use genetic mapping strategies to understand which genes are important for those traits.”

Throughout his work with plant genetics, Kaeppler has taken full advantage of resources for entreprenuers on campus. He has patents filed or pending, and he has also received Accelerator funds through WARF. For his project looking at the genetics behind flowering time, Kaeppler and graduate student Brett Burdo received Igniter funds from D2P as well. The Igniter program has proven invaluable for Kaeppler and Burdo as they try to place their innovation in the best position for success.

“I found the Igniter program very useful, to go through the process of understanding what it takes to get a product to market,” says Kaeppler. “It also includes funding for some of the steps in the research and for some of the time that’s spent. I can’t fund my graduate student off a federal grant to participate in something like this, so the Igniter funding allowed for correct portioning of funding.”

The end goal of Kaeppler’s project is to develop a transgenic plant as a research model and license the technology, not develop a startup company. His team is currently testing transgenic plants to work up a full package of information that interested companies would use to decide if they should license the technology. For Kaeppler, licensing is the best option since they can avoid trying to compete with big agricultural companies, and the technology will still get out to the market where it’s needed to create change.

“In this area of technology transfer, it is important not only to bring resources back to UW but also to participate in meeting the challenges the world is facing with increasing populations,” says Kaeppler. “Programs like D2P and WARF are critical at this point in time to see the potential of these discoveries realized.”

A Diet to Treat Disease

Around the world, about 60,000 people are estimated to have phenylketonuria, or PKU. Those with the inherited disorder are unable to process phenylalanine, a compound found in most foods. Treatment used to consist of a limited diet difficult to stomach. Then, about 13 years ago, nutritional sciences professor Denise Ney was approached to help improve that course of treatment.

Dietitians at UW–Madison’s Waisman Center wanted someone to research use of a protein isolated from cheese whey—called glycomacropeptide, or GMP—as a dietary option for people living with PKU. Ney took on the challenge, and with the help of a multidisciplinary team, a new diet composition for PKU patients was patented and licensed.

“Mine is not a typical story,” says Ney, who also serves as a D2P advisory board member. “Things happened quickly and I can’t tell you why, other than hard work, a good idea and the right group of people. We’ve had help from many people—including our statistician Murray Clayton, a professor of plant pathology and statistics, and the Center for Dairy Research—which helped with development of the foods and with sensory analysis.”

Being at the right place at the right time had a lot to do with her success thus far, Ney notes. “I’m not sure this could have happened many places in the world other than on this campus because we have all the needed components—the Waisman Center for care of patients with PKU, the Wisconsin Center for Dairy Research, the clinical research unit at University of Wisconsin Hospitals and Clinics, and faculty with expertise in nutritional sciences and food science,” she says.

Ney is currently wrapping up a major clinical trial of the food formulations, referred to as GMP medical foods, that she and her team developed. In addition to those efforts, the new diet has also shown surprising promise in two other, seemingly unrelated, areas: weight loss and osteoporosis prevention.

“My hypothesis, which has been borne out with the research, is that GMP will improve bone strength and help prevent fractures, which are complications of PKU,” explains Ney. “I have a comprehensive study where I do analysis of bone structure and biomechanical performance, and I also get information about body fat. I observed that all of the mice that were fed GMP, whether they had PKU or not, had less body fat and the bones were bigger and stronger.” Interestingly, the response was greater in female compared with male mice.

To support further research on this new aspect of the project, Ney received Accelerator funds from WARF for a second patent issued in 2015 titled “Use of GMP to Improve Women’s Health.” Ney and her team, including nutritional sciences professor Eric Yen, are excited about the possibilities of food products made with GMP that may help combat obesity and also promote bone health in women.

“There is a huge market for such products,” says Ney. “We go from a considerably small group of PKU patients who can benefit from this to a huge market of women if this pans out. It’s interesting, because I think I’m kind of an unexpected success, an illustration of the untapped potential we have here on campus.”

Fewer Antibiotics in Ethanol Plants

Bacteria and the antibiotics used to kill them can cause significant problems in everything from food sources to biofuel. In biofuel production plants, bacteria that produce lactic acid compete with the wanted microbes producing ethanol. At low levels, these bacteria decrease ethanol production. At high levels, they can produce so much lactic acid that it stops fermentation and ethanol production altogether.

The most obvious solution for stopping these lactic acid bacteria would be antibiotics. But as in other industries, antibiotics can cause problems. First, they can be expensive for ethanol producers to purchase and add to their workflow. The second issue is even more problematic.

“A by-product of the ethanol industry is feed,” explains James Steele, a professor of food science. “Most of the corn kernel goes toward ethanol and what remains goes to feed. And it’s excellent animal feed.”

But if antibiotics are introduced into the ethanol plant, that animal feed byproduct can’t truly be called antibioticfree. That’s a problem as more and more consumers demand antibiotic-free food sources. But Steele and his colleagues have a solution—a way to block the negative effects of lactic acid bacteria without adding antibiotics.

“We’ve taken the bacteria that produce lactic acid and re-engineered it to produce ethanol,” says Steele. “These new bacteria, then, compete with the lactic acid bacteria and increase ethanol production. Ethanol plants can avoid the use of antibiotics, eliminating that cost and increasing the value of their animal feed by-product.”

The bacteria that Steele and his team have genetically engineered can play an enormous role in reducing antibiotic use. But that benefit of their innovation didn’t immediately become their selling point. Rather, their marketing message was developed through help from D2P and the Igniter program.

“Learning through D2P completely changed how we position our product and how we interact with the industry,” says Steele. And through that work with D2P, Steele plans to later this year incorporate a company called Lactic Solutions. “D2P has helped us with the finance, the organization, the science, everything. Every aspect of starting a business has been dealt with.”

Steele and his collaborators are now working to refine their innovation and ideas for commercialization using Accelerator funds from WARF. Steele’s work, supported by both WARF and D2P, is a perfect example of how the entities are working together to successfully bring lab work to the market.

“There is no doubt in my mind that we would not be where we are today without D2P,” says Steele. “On top of that you add WARF, and the two together is what really makes it so special. There’s nothing else like it at other campuses.”

With such a strong partnership campaigning for and supporting entrepreneurship at UW–Madison, CALS’ strong history of innovation is poised to endure far into the future, continuing to bring innovations from campus to the world. And that is the embodiment of the Wisconsin Idea.

 

Breeding for Flavor

On a sticky weekday morning in August, a new restaurant called Estrellón (“big star” in Spanish) is humming with advanced prep and wine deliveries. All wood and tile and Mediterranean white behind a glass exterior, the Spanish-style eatery is the fourth venture of Madison culinary star Tory Miller. Opening is just three days away, and everything is crisp and shiny and poised.

But in the dining room, the culinary focus is already years beyond this marquee event. This morning is largely about creating the perfect tomato. Graduate students from UW–Madison working on a new program called the Seed to Kitchen Collaborative have set the table with large sheets of white paper and pens. At each place setting are a dozen small plastic cups of tomatoes, diced as if for a taco bar. Each container is coded.

Chef Miller takes a seat with colleagues Jonny Hunter of the Underground Food Collective and Dan Bonanno of A Pig in a Fur Coat. The chefs are here to lend their highend taste buds to science, and they start to banter about tomato flavor. What are the key elements? How important are they relative to each other?

Despite their intense culinary dedication, these men rarely just sit down and eat tomatoes with a critical frame of mind. “I learned a lot about taste through this project,” says Hunter. “I really started thinking about how I defined flavor in my own head and how I experience it.”

This particular tasting was held last summer. And there have been many others like it over the past few years with Miller, Hunter, Bonanno and Eric Benedict BS’04, of Café Hollander.

The sessions are organized by Julie Dawson, a CALS/UW–Extension professor of horticulture who heads the Seed to Kitchen Collaborative (formerly called the Chef–Farmer–Plant Breeder Collaborative). Her plant breeding team from CALS will note the flavors and characteristics most valuable to the chefs. Triangulating this with feedback from select farmers, plant breeders will get one step closer to the perfect tomato. But not just any tomato: One bred for Upper Midwest organic growing conditions, with flavor vetted by some of our most discerning palates.

“We wanted to finally find a good red, round slicer, and tomatoes that look and taste like heirlooms but aren’t as finicky to grow,” says Dawson at the August tasting, referring to the tomato of her dreams. “We’re still not at the point where we have, for this environment, really exceptional flavor and optimal production characteristics.”

Nationwide, the tomato has played a symbolic role in a widespread reevaluation of our food system. The pale, hard supermarket tomatoes of January have been exhibit A in discussions about low-wage labor and food miles. Seasonally grown heirloom tomatoes have helped us understand how good food can be with a little attention to detail.

But that’s just the tip of the market basket, because Dawson’s project seeks to strengthen a middle ground—an Upper Midwest ground, actually—in the food system. With chefs, farmers and breeders working together, your organic vegetables should get tastier, hardier, more abundant and more local where these collaborations exist.

Julie Dawson decided she wanted to be a farmer at age 8. By her senior year in high school she was hooked on plant breeding and working in the Cornell University lab of Molly Jahn—now a professor of agronomy at CALS—on a project developing heat tolerance in beans. Dawson stayed at Cornell for college and continued to work for Jahn and Margaret Smith, a corn breeder who was working with the Iroquois to resurrect traditional breeds. By the time she finished college, Dawson had a strong background in both plant breeding and participatory research. During her graduate education at Washington State University she began breeding wheat for organic systems. As a postdoc in France, she started working on participatory breeding with bakers and farmers, focusing on organic and artisanal grains.

In September of 2013, barely unpacked in Madison, Dawson found herself traveling with CALS horticulture professor and department chair Irwin Goldman PhD’91 to a conference at the Stone Barns Center for Food & Agriculture north of New York City.

Organized by food impresario Dan Barber, author of The Third Plate: Field Notes on the Future of Food, the conference gathered chefs and breeders from across the country to talk about flavor. Barber knew what could happen when chefs and breeders talked because he was already working with Dawson’s graduate advisor at Washington State, wheat breeder Stephen S. Jones.

In the 1950s, as grocery stores replaced corner markets and California’s Central Valley replaced truck gardens, the vegetable market began to value sizes and shapes that were more easily processed and packed. That a tomato could be picked early in Florida and ripen during the boxcar ride to Illinois was more important than how it tasted. Pesticides and fertilizers also became more common, buffering differences between farms and providing a more uniform environment. Packing houses and national wholesalers dominated the market, and vegetable breeding followed.

Breeders have at their disposal a huge variety of natural traits—things like color, sugar content and hardiness. Over the course of decades they can enhance or inhibit these traits. But the more traits they try to control, the more complex the breeding. And flavor has been neglected over the last few decades in favor of traits that benefit what has become our conventional food system. “Breeders were targeting a different kind of agricultural system,” explains Dawson.

Barber wanted to reverse that trend, to connect farmers and plant breeders and chefs. It appealed to Dawson’s sense of where food should be going. “Breeding for standard shapes and sizes and shipping ability doesn’t mean that breeders aren’t interested in flavor,” she says. “It just means that the market doesn’t make it a priority.”

New to Madison, Dawson hadn’t met Tory Miller, but they connected at the Stone Barns Center, and together realized Madison was the perfect place to pursue this focus on flavor: A strong local food movement supporting a dynamic and growing number of farms, world-class chefs, and—through CALS’ Plant Breeding and Plant Genetics Program—one of the highest concentrations of public plant breeders in the world.

They decided to get started in the summer of 2014 by growing a collective palette of many varieties of the most common vegetables. Dawson approached the breeders, Miller rallied the chefs, and both reached out to their network of farmers. “The main idea of the project is to get more informal collaboration between farmers and plant breeders and chefs—to get the conversation started,” says Dawson. “We can really focus on flavor.”

When the chefs are done tasting tomatoes, they wander over to a table of corn and cucumber. They are magnetized by the different kinds of corn: an Iroquois variety, another type that is curiously blue, and large kernels of a corn called choclo, which is very popular in the Andes.

These are just a few jewels from the collection amassed over four decades by CALS corn breeder Bill Tracy, who works in both conventional and organic sweet corn. Tracy leads the world’s largest research program focused on the breeding and genetics of organic sweet corn, with five organically focused cultivars currently on the market. He was recently named the nation’s first endowed chair for organic plant breeding, with a $1 million endowment from Organic Valley and Clif Bar & Company and a matching $1 million gift from UW alumni John and Tashia Morgridge.

The support gives Tracy more room to get creative, and Dawson is helping to develop potential new markets for his breeds. Despite his focus on sweet corn, Tracy has always suspected there might be interest in corn with more flavor and less sugar. “We know from sweet corn that there are all sorts of flavors and tendencies,” Tracy says. From soups to the traditional meat and potato meal, he thinks savory corn deserves a place.

And building from deep Mexican and South American traditions of elotes and choclo corns, Tracy sees vast potential for new varieties. “Corn is one of the most variable species,” he says. “For every trait that we work with in corn there is an incredible range of variation.”

The chefs went crazy last year when Tracy introduced them to some of the Andean varieties. “Amazing,” says Bonanno of A Pig in a Fur Coat. “I want to make a dish like a risotto or a pasta dish or some type of salad. I don’t want the sweet on sweet on sweet. I just want the corn flavor. I want savory.”

Tracy’s modest sampler inspired chefs Hunter and Miller as well, and they started brainstorming potential growers for 2016. If the experiment takes off, the corn could start infiltrating Wisconsin restaurants this summer.

With so much genetic potential, the chefs help focus the breeding process. “Breeding is a craft,” Tracy says. “The great chefs—and we have some great ones in Madison—are truly artists. They are fine artists at the same level as a fine arts painter or musician. The creativity is just mind-boggling.”

And there is little question that they understand flavor. “They are able to articulate things that we can’t. We might be able to taste the differences, but we can’t say why they are different or why one is better than the other. The chefs are able to do that,” says Dawson. “And that’s useful for the whole food system.”

A food system has so many pieces— chefs, farmers, retailers, processors, consumers—but perhaps the most fundamental unit is the seed. After decades of consolidation in the seed industry and a significant decline in public breeding programs at land grant universities, many sectors of the food movement are turning their attention to seed.

One fortunate consequence of the industry concentration has been to create a market opening for smaller regional and organic seed companies. They, along with a few public breeders, still serve gardeners and market farmers. One goal of the Seed to Kitchen Collaborative is to systematically support breeding for traits that are important for local food systems.

These small companies develop their own breeds, but also adopt interesting varieties from public breeding programs. They have the capacity to target regional seed needs, and are usually okay with seed saving. “It’s almost like working with nonprofits because they are really interested in working with the community,” says Dawson.

After Adrienne Shelton MS’12 completed her PhD in 2014—she studied sweet corn breeding under Bill Tracy— she moved to Vitalis Organic Seeds, where she works with growers to find cultivars best suited for the Northeast. As a graduate student in CALS’ Plant Breeding and Plant Genetics program, Shelton was a leader in establishing the Student Organic Seed Symposium, an annual national gathering to offer information and support to young researchers focusing on breeding organic varieties.

“Getting farmers’ feedback is critical,” says Shelton of the opportunity to work with the Seed to Kitchen Collaborative. “The more locations, the better, especially in organic systems where there is more variation.”

The organic movement deserves a lot of credit for the trajectory of new food movements. “Organic growers often have a higher bar for the eating quality of produce because that’s what their customers are demanding,” Shelton says. “Putting a spotlight not just on the farmers but all the way back to the breeding is helping the eater to recognize that all these pieces have to be in place for you to get this delicious tomato that you’re putting on your summer salad.”

These kinds of seed companies will also help make local and regional food systems more resilient to climate change. “It’s fairly easy to breed for gradual climate change if you are selecting in the target environment, because things change over time,” says Dawson. “The most important thing is to have regional testing and regional selection.”

Overall, a more vigorous relationship between breeders and farmers promises a larger potential for varieties going forward, Dawson notes. The ultimate goal is to make plant breeding more of a community effort. When chefs and farmers and consumers participate in the selection process, says Dawson, “The varieties that are developed are going to be more relevant for them.”

Amy Wallner BS’10, a CALS graduate in horticulture and soil sciences, has worked behind both the knife and the tiller. While farming full-time, she spent six months working nights at a Milwaukee farm-to-table restaurant called c. 1880. Now she’s the proprietor of Amy’s Acre—actually, an acre and a half this year—on the margins of a commercial composting operation in Caledonia, Wisc., south of Milwaukee.

She sells to a co-op and a North Side farmers market, but her restaurant clients—c. 1880, Morel and Braise RSA (also part of the Seed to Kitchen Collaborative)—are integral to her business. Before she orders seed for the next growing season, she’ll drop off her catalogs for the chefs to study, returning later for in-depth conversation. “Chefs who want to buy local foods want to have a greater understanding of the whole process,” Wallner says. “I just like to sit down and talk about produce with somebody who uses it just as much as I do.”

Knowing the ingredients they covet, and what kinds of flavors intrigue them, helps Wallner narrow her crop list. Joining the Seed to Kitchen Collaborative took it further. As a student Wallner had worked in the trial gardens at the West Madison Agricultural Research Station, and now she can truly appreciate the farm value of that research. “I wanted to stay connected to UW,” she says.

This will be Wallner’s third season as part of the group’s trials. In her excitement, the first year she grew more than she could handle. Last year she trialed beets, carrots and tomatoes alongside radicchio and endives. “I took on a smaller number of crops because I wanted to be able to collect more extensive observations,” she says.

Wallner hopes getting the breeders involved may lead to strengthening the hardiness of early- and late-season crops. “In the Upper Midwest, that’s when you’re doing the most gambling with your crops. If we can continue to find things that can push those limits out a little bit …”

Eric Elderbrock, of Elderberry Hill Farm near Madison, has similar practical concerns: With the region’s incredibly variable climate, he’s always looking for something that isn’t going to require the most perfect growing conditions and is also resistant to disease and insects: “For it to be a realistic thing for me to be able to grow, it has to meet these demands.”

When he was growing up, Elderbrock didn’t pay much attention to where his food came from. It wasn’t until he spent a college semester in Madagascar that he began to realize the relationship between the food and the land around him. For him, the collaboration is a form of continuing education.

“It’s helpful to me as a farmer to have a sense of what’s possible as far as the breeding side,” says Elderbrock. “I love seeing all of the different colors and flavors and textures. It helps keep farming interesting.”

As picturesque as these relationships are, the business has to work. High-end cuisine doesn’t reflect most daily eating, but these chefs are very committed to helping Wisconsin farmers stay in business and make a good living.

“The chefs always seem to be a couple of years ahead,” Elderbrock notes. This year he is continuing to experiment with artichokes, a crop typically associated with dry Mediterranean climates like Spain and California. Chef Dan Bonanno is encouraging the research in part because of his Italian heritage and culinary training, which included a year in Italy. He would be thrilled to find Wisconsin variations on some traditional Italian ingredients like the artichoke.

And sourcing locally also leads to a robust cuisine. “Italy has 20 regions and each region has its own cuisine because they source locally,” notes Bonanno.

This past February, a few weeks before growers would start their seedlings, the Seed to Kitchen Collaborative gathered to tweak plans for this year’s trials.

At L’Etoile, Chef Tory Miller’s flagship establishment in Madison, beautiful prints of vegetables adorn the wall. But the tables that day were rearranged in a horseshoe. The distinctive conference seating suppresses the normally refined air. Only the curvature of the bar and its adjacent great wall of bourbon suggested a more sensual approach to food.

After introductions and a quick review of last year’s progress, Dawson opens the floor to feedback. The ensuing conversation distills into savory glimpses of market baskets and menu flourishes to come.

They’ve been talking about running a trial for tomato “terroir”—drawing from the wine enthusiasts’ notion that differences in soil can have subtle and profound impacts on flavor. Dawson is a little concerned about logistics, but Miller is persistent: “I think it would be a mistake to not include terroir.”

They discuss what they can do for unsung vegetables like rutabaga and parsnip—produce particularly suited for the Wisconsin climate, but generally unloved. They learn about a new trial focusing on geosmin, which produces the earthy flavor of beets. The chefs wonder aloud if it’s possible to preserve the beautiful purple hues of some heirlooms. Dawson regrets to inform them that changing the physical chemistry involved—the pigments are water soluble, and flush easily from the plants—is a little beyond their powers.

They talk about what makes perfect pepper for kitchen processing. Is seedless possible? Dawson smiles wryly and reminds them of the intrinsic challenge of a seedless pepper.

The conversation gets very detailed over potatoes. Researcher Ruth Genger from the UW’s Organic Potato Project has about 40 heirloom varieties of potato from the Seed Savers Exchange that will be grown out over the next few years. Chef Bonanno asks a technical question about starch content for gnocchi, and then Chef Miller goes off on French fries.

“I’ve been working on trying to break the consumers’ McDonald’s mentality on what a French fry should be,” Miller says. The sheer volume is a perfect example of how hard it can be to assemble the pieces of a sustainable and local food system. “We’re talking about thousands of pounds of French fries,” he says, the other chefs nodding in agreement. “You want to have a local French fry, but at a certain point it’s not sustainable or feasible. Or yummy.” One recent hitch: a harvest of local spuds were afflicted by hollow heart disease.

Genger’s heirloom potato trials have focused on specialty varieties—yellows, reds and blues—but Genger has an alternative: “We have some white potatoes that are pretty good producers organically, but what I tend to hear is that most people don’t like white potatoes.” The chefs don’t seem worried about the difference. “There are some good, white varieties from back in the days when that was what a potato was,” Genger continues, making a note. Knowing that the interest is there, she can make sure farmers and chefs have a chance to evaluate some white heirloom potatoes.

It’s a short conversation, really, but shows the potential value of having everybody at the table. If the breeder has the right plant, the farmers have a good growing experience and the chefs approve, perhaps in another couple of years there could be thousands of pounds of locally sourced organic white French-fried potatoes ferrying salt and mayonnaise and ketchup to the taste buds of Wisconsin diners.

“We try to make the project practical,” says Dawson. “The food system is so complicated. It feels like this is something we can make a difference with. This can help some farmers now, and in 10 years hopefully it will be helping them even more.”

Bill Tracy puts the program in an even bigger context.

“The decisions we make today create the future,” Tracy says. “The choices we make about what crops to work in and what traits to work in literally will create the future of agriculture.”

Farmers, gardeners and chefs are welcome to join the Seed to Kitchen Collaborative. You can learn more about project events at http://go.wisc.edu/seed2kitchen or email Julie Dawson at dawson@hort.wisc.edu.

A Jolt to the System

As a linebacker for the UW–Madison Badgers, Chris Borland made a name for himself as a hard-hitting tackler. His senior year, he was selected as a first-team All-American as well as the top linebacker and defensive player in the Big Ten Conference.

A third-round draft pick, Borland seemed destined for a headline career in the National Football League. But during a full-contact practice at the San Francisco 49ers summer training camp in August 2014, Borland got his “bell rung” by a 290-pound fullback during a routine exercise. Though Borland felt dazed, he played through—as he’d done dozens of times before.

Like many football players, Borland had endured his share of hard hits, including two diagnosed concussions. This particular hit, however, got him thinking seriously about the future, and about the negative effects that repeated collisions could have on his long-term physical and cognitive health. Even so, he went on to play a dynamite rookie year.

Then, after the season was over, Borland quit.

The announcement shocked the sports world. Borland was 24 years old and healthy, yet chose to walk away from a $2.3 million, four-year contract.

“I just honestly want to do what’s best for my health,” Borland explained on ESPN’s Outside the Lines. “From what I’ve researched and what I’ve experienced, I don’t think it’s worth the risk.”

With their repeated hits, football players—along with boxers—are at increased risk of developing chronic traumatic encephalopathy (CTE), a degenerative brain disease marked by memory loss, depression, suicidal thoughts, aggression and dementia. Of 91 brains donated to science by former NFL players, 87 have tested positive for CTE. It’s seen as a likely contributing factor to nine suicides by current and retired football players over the past decade.

Borland didn’t want to share that fate.

“To me, Chris Borland is a hero. He walked away before he made the big bucks and he was very explicit about why he quit—that it was not worth it to him,” says CALS genetics professor Barry Ganetzky, whose findings about the central nervous system in fruit flies are shedding light on what hard hits do to humans.

Ganetzky isn’t a sports guy, but he started paying attention to football-related brain injuries after the 2012 suicide of New England Patriots linebacker Junior Seau, intrigued by the biological processes driving this tragic phenomenon.

“I started wondering, what’s the link between a blow to the head and neurodegeneration 10 or 20 years down the line? When I started digging into the scientific literature, it became clear that we know very little,” says Ganetzky, who held the Steenbock Chair for Biological Sciences for 20 years. “And my usual response is, well, if we don’t understand something about the brain, then we should be studying it in flies.”

Fruit flies, officially known as Drosophila melanogaster, are a widely studied model organism, with a vast arsenal of genetic and molecular tools available to support that work. Flies reproduce rapidly and are easy to work with, enabling swift research progress. They are well suited for brain research because they have nerve cells, neural circuitry and a hard skull-like cuticle remarkably similar to our own, allowing scientists to conduct probing experiments that would be difficult in rodent models—and impossible in human subjects.

Fly models already exist to study Alzheimer’s, Parkinson’s and a number of other neurological diseases. Why not concussion? But there wasn’t a model available.

Then Ganetzky remembered work he’d done decades earlier.

“It occurred to me that I knew how to make flies have a concussion, and I had done it 40 years ago as a post-doc,” says Ganetzky. “I thought, ‘That’s it!’”

It was a simple thing: As a post-doctoral researcher at the California Institute of Technology, Ganetzky decided to see if any of his flies happened to be bang-sensitive mutants, flies that display seizures and paralysis after given a high-powered swirl on a vortex machine. But he didn’t have a vortex nearby, so he decided to just bang the vials against his hand.

“After a couple of sharp whacks, some of the flies were hanging out at the bottom of the vial, stunned. Others were on their backs, obviously knocked out. And after a few minutes, they all got up and started walking around again,” recalls Ganetzky.

He immediately knew the flies weren’t bang-sensitive—it’s an extremely rare mutation—but Seau’s death helped Ganetzky realize they had displayed symptoms “very similar in many respects to the empirical definition of a concussion.”

After developing and validating the new fly model, Ganetzky and UW genetics professor David Wassarman have been able to charge forward with brain injury research. The model has already been used to reveal key genes involved in the body’s response to brain injury. It’s also poised to help unlock medical applications, including a genetic test for high-risk individuals and an assortment of promising drugs and treatments.

In addition to helping athletes in contact sports, these advances will benefit the millions of Americans each year who experience traumatic brain injury due to falls, car accidents and violent assaults.

“At the most fundamental level, we just want to understand how traumatic brain injury works,” explains Ganetzky. “However, this is a major medical problem for which there are not many good—or any good—treatments or therapies or preventives, and so that is part of our motivation. If we can learn the genes and the molecules and the pathways, can we come up with interventions?”

Ganetzky was raised in a working-class neighborhood in Chicago by a candy salesman father and a homemaker mother. Growing up, he had an abundance of natural curiosity and asked a lot of tough questions—and often questioned the answers he received. While this trait caused him some problems as a youth, it came to serve him well in science.

At the University of Illinois in Chicago, he figured he’d become a chemist for the good career prospects. He ended up switching to the biological sciences, however, after a 10-week honors biology research experience in a Drosophila lab that expanded into a two-year project. From that point forward he stuck with flies, earning his doctoral degree at the University of Washington and then doing his post-doc work at Caltech.

In 1979, Ganetzky joined the University of Wisconsin–Madison, where he chose to focus his research program on exploring temperature-sensitive paralytic mutants, flies that behave normally at room temperature, but then start to tremble and twitch—or pass out—when things heat up. For each mutant he identified, he sought to uncover the faulty gene involved, and thus better understand how brain cells work.

Over the decades, this approach enabled Ganetzky’s team to discover a number of critical genes and molecular pathways involved in brain cell signaling, including those required for the release of neurotransmitters. That body of work established Ganetzky as one of the foremost leaders in neurogenetics. Some of his findings shed light on human genetic diseases and led to a test that’s now routinely used to assess the safety of new pharmaceutical drugs. For his contributions, Ganetzky was elected in 2006 to the National Academy of Sciences, the nation’s preeminent scientific society.

After Ganetzky’s “eureka moment” about fly concussions in spring 2012, he immediately reached out to colleague David Wassarman, a genetics professor in the UW–Madison School of Medicine and Public Health. Wassarman, who studies human neuronal disorders using fruit flies, had already been attending Ganetzky’s lab meetings for a few years after some of their research findings linking the innate immune response and neurodegeneration dovetailed.

“I did a demonstration of fruit fly concussion for David, and I remember his response very well,” says Ganetzky. “His jaw kind of dropped, and he said, ‘If you’re not going to study that, then I want to.’”

It was exactly the response that Ganetzky had been hoping for. With retirement looming on the horizon, Ganetzky needed a trusted and enthusiastic collaborator to help pursue the work—someone who would be willing to take on more and more as time went on. Wassarman was game.

“I wanted to put both feet in,” says Wassarman. “I said, ‘If we’re going to do it, let’s do it.’”

As a first order of business, Wassarman developed a tool capable of delivering a consistent “dose” of brain injury to flies. The result, known as the High-Impact Trauma (HIT) device, utilizes a metal spring to slam a vial of flies against a firm foam surface. In this setup, it’s important to note, the brain injury the flies experience is caused by the rapid acceleration and deacceleration of their bodies; it’s not necessarily about a direct hit to the head.

“Quite often, as with football players, it can happen because they are running fast and then meet an immovable object. The concussion is caused by a kind of whiplash, where the brain is ricocheting off the inside the skull, and that’s what’s causing the damage,” says Ganetzky. “That’s what we’re doing here with the flies.”

Ganetzky and Wassarman found that flies injured using the HIT device exhibit many of the classic symptoms of traumatic brain injury (TBI) seen in humans. As they reported in the Proceedings of the National Academies of Science in 2013, flies show temporary incapacitation and loss of coordination immediately after injury. Those that survive severe injury go on to develop long-term symptoms: activation of the innate immune response, neurodegeneration and early death.

These TBI flies have the potential to reveal much-needed insights—and medical interventions—for the millions of Americans who experience traumatic brain injury each year. According to the U.S. Centers for Disease Control and Prevention, TBIs cause around 2.5 million emergency room visits, 283,600 hospitalizations and 52,800 deaths each year. Top causes are falls, motor vehicle accidents, and blows or jolts to the head or body, including sports-related concussions. Bomb blasts can cause brain trauma in soldiers in combat zones. Across the country, as many as 6.5 million people are believed to be struggling with the consequences of TBI, and the total economic cost of this health issue is estimated to be $76 billion per year.

In a demonstration of the power of the TBI model, Rebeccah Katzenberger, a senior research specialist in Wassarman’s lab, subjected 179 genetically unique strains of flies to four strikes of the HIT device—meant to simulate a series of severe brain injuries—and then monitored them for death at 24 hours post-injury, a data point that serves as an easy-to-measure proxy for the various negative events unfolding inside the body.

The results revealed a huge diversity of responses, underscoring the fact that genotypes matter when it comes to TBI response. Some strains were particularly susceptible to death, losing as many as 57 percent of the flies in those first 24 hours, while others were much more resilient, losing just 7 percent. The team then identified the genes that possibly made a difference, publishing their findings in eLife in March 2015.

“Now we have these 100 genes, and scientists can start looking at them in more detail,” says Wassarman. “A lot of them are genes that had never really been implicated in traumatic brain injury before. I think this is going to be one of our big contributions.”

These findings, the researchers note, may help explain why people respond so differently to similar brain injury events, and may help lead to a genetic test to identify high-risk individuals.
“Once we understand those genetic links, we’ll be able to test people and tell them, ‘Look, you probably shouldn’t play football. You should play non-contact sports,’” explains Ganetzky.

After identifying the TBI genes, Ganetzky and Wassarman immediately noticed a handful of genes involved in tissue barrier regulation. Tissue barriers—such as the intestinal barrier and the blood-brain barrier—function as biological blockades keeping “bad” things out while allowing “good” things to pass through.

To explore the connection between brain injury and tissue barriers, the duo had Katzenberger conduct a simple, colorful experiment that involves adding bright blue dye to the flies’ food. Under normal conditions, when flies eat the blue-colored food, it stays in the gut, something that is readily observable through the fly exoskeleton. However, after exposure to brain injury—via the HIT device or by having their heads pinched with a forceps—they found that the dye leaks out of the gut and turns the entire body blue, a phenomenon called “smurfing” (after the blue Smurf cartoon characters).

Leaky tissue barriers have previously been observed in rodent models of brain injury as well as in human medical cases. “Somehow this injury to the brain is triggering a series of events that leads to the breakdown of the intestinal barrier,” notes Ganetzky. “So there’s some sort of cross-talk going on between the brain and the intestine, but we don’t fully understand it yet.”

Upon further exploration, Ganetzky and Wassarman were able to confirm that—along with the blue dye—glucose and bacteria were also crossing the intestinal barrier into the fly’s circulatory system, or hemolymph, after brain injury. Homing in on glucose, they found that it plays a causative role in fly death after TBI. “By simply withholding sugar, we were able to keep some of these flies alive, and by a substantial margin,” says Wassarman.

If the findings hold up in rodent models and in human trials, he notes, athletes may one day find themselves advised to avoid certain foods after experiencing concussion.

The bacteria that cross the intestinal barrier appear to be playing more of a long game. Ganetzky and Wassarman believe they are the culprits triggering the innate immune response observed in TBI flies. The innate immune response, also known as the inflammatory response, is the body’s natural reaction to microbial invasion and other stressors. If properly controlled—turned on and off at the right time—it protects the body. If left on, however, it can cause collateral damage throughout the body, including damaging brain cells.

“Here’s what we think is happening: Traumatic brain injury is causing increased intestinal permeability. That causes the bacteria to leak out, which turns on the innate immune response, and that is possibly leading to neurodegeneration down the line,” explains Wassarman.

Ganetzky and Wassarman are intrigued by a concept that is emerging from their work and related studies: that TBI accelerates aging. Some of the key physical outcomes of brain injury—problems with tissue barriers and increased inflammation—are also hallmarks of the natural aging process. More support for this idea came in summer 2015, with the release of a report describing signs of early aging in the brains of war veterans exposed to bomb blasts in Iraq and Afghanistan.

“Somehow a blow to the head is activating all of these pathways related to aging and speeding them all up. Biologically, I think that this is maybe one of the most fascinating things about the whole project,” says Ganetzky, noting that TBI flies are a great model for further exploration.

Even at this early stage, without fully understanding the basic scientific mechanisms involved, the model is already revealing some promising medical applications. As soon as Ganetzky and Wassarman realized that the inflammatory response might lead to neurodegeneration, a treatment suggested itself: Could a simple anti-inflammatory help? They tried giving TBI-injured flies some aspirin mixed in their food. It helped.

“Our studies show that there appears to be a window of time after brain injury when the flies are particularly susceptible to dying. And if we can prevent certain events from happening during this time, then we can prevent death,” says Wassarman. “That’s what we think aspirin is doing—by lowering the innate immune response.”

The next step is to look for drug candidates that work even better than aspirin. Ganetzky and Wassarman are in the process of screening a set of 2,400 compounds, and they’ve already found a handful of very promising ones that can now be tested in rodent models and, ultimately, in human clinical trials.

“It would be wonderful if someday it were possible to offer a simple intervention beyond surgery to help individuals who have suffered a severe traumatic brain injury,” says Wassarman.

There’s a lot left to learn, and Ganetzky and Wassarman are eager to pursue all that the model can tell them. With Ganetzky’s retirement set for early 2016, the work of securing the project’s first federal grant and conducting experiments will largely fall to Wassarman.

But Ganetzky won’t be out of the picture. He continues to keep up on brain injury medical cases and scientific discoveries, and is encouraged by the national conversation about sports and brain injuries that’s starting to gain traction—and by the NFL’s commitment to scientific research in this area.

Some of these advances can be attributed, in part, to Chris Borland, whose post-NFL journey has led him deeper into the world of sports-related brain injury. Borland has submitted to numerous brain scans to support research, and has also become a sought-after speaker, touring the country to raise awareness about the risks of concussion.

It’s that kind of dedication to public service on the part of Borland and many other athletes, along with the excitement of discovery, that’s keeping Ganetzky in the game. Despite his retirement, Ganetzky plans to keep a scaled-back version of his lab running for at least a few more years.

For the Birds

Slipping into a patch of woods in western Dane County, Jim Berkelman ignores the swarming mosquitoes and strains to sort through the early- morning chatter of warblers, robins and vireos and the nearby drum of a pileated woodpecker. “I’m hearing something I wouldn’t expect to hear,” says Berkelman, a lecturer in the Department of Forest and Wildlife Ecology at CALS and a volunteer contributor to the Wisconsin Breeding Bird Atlas II, a comprehensive, volunteer-powered survey of birds that nest in Wisconsin.

Experienced birders use their ears as much as their eyes to identify species, and Berkelman thinks he hears a northern parula, a small warbler that doesn’t typically nest this far south. Finding a bird, Berkelman explains, is only the start. The point of the Atlas, he notes, is to identify and map where birds in Wisconsin are courting, nesting, breeding and raising their broods.

To be sure of that, “atlasers,” as volunteer observers like Berkelman are called, must find tangible evidence that a species has actually taken up residence. A nest, of course, is the most obvious clue. But most birds are assiduously covert in their nesting and only conspicuous players like robins, herons, orioles, house wrens and bluebirds construct their nests in ways that make them easy to find and identify.

Other definitive hallmarks of breeding birds include observations of birds carrying nesting material or food for nestlings; distraction displays where birds seek to draw animals, other birds or humans away from a nest; and, of course, fledglings. Some bird species are fastidious as well and carry fecal matter away from occupied nests. Such an observation is also a telltale sign of breeding and can be used by an atlaser to confirm breeding activity and provide a new data point that science can ultimately draw on.

Following a rising wooded path to the top of a hill, Berkelman’s rounds on this warm June day encompass two different types of ecosystems: forest, and open fields and prairie. His block is designated as a “priority block,” a specified block within a six-block “quad” on a grid of more than 7,000 three-mile-by-three-mile blocks that covers Wisconsin. Within that grid are 1,175 priority blocks, each of which requires at least a year’s documentation of breeding birds within a five-year period to ensure that the state is uniformly surveyed for the new Atlas. In addition, there are 153 “specialty blocks” that have unique habitat, are of high conservation value or are of particular interest to ornithologists.

Today, Berkelman is recording his data the old-fashioned way: with pen and notebook. Later, he can plug his observations into Atlas eBird, an online checklist program that is a direct conduit to the database that is the bedrock of the Wisconsin Breeding Bird Atlas.

Data, of course, are the raw material of science. Astronomers gather it by measuring and parsing starlight. Molecular biologists get data by plumbing the sequence of the chemical base pairs that make up a gene or genome. Meteorologists numerically dissect the many variables of weather—temperature, precipitation, wind, clouds.

To be sure, most data collection is a laborious and numbing process—the antithesis of the eureka moment. Harvesting data can be very expensive, too, as the tools of modern science have become bigger, more complex and more powerful in their ability to see farther or smaller, drill deeper, or accelerate particles to higher energies. Indeed, much of what we hear about modern scientific discovery rests on the pillars of sophisticated technology. Think of the Hubble Space Telescope, the Large Hadron Collider, the IceCube Neutrino Observatory and the Human Genome Project as just a few examples.

But while technology is taking science to new heights, it’s also giving a boost to the age-old methods of data gathering like the ones Berkelman uses in his efforts to document the presence of breeding birds. The Internet and personal computing technology are being used like never before to crowd-source traditional observational data collected by a growing cadre of citizen scientists. Groups of people or individuals armed with laptops and app-laden smartphones are collectively logging everything from trash in the ocean and flying ants to cosmic rays and precipitation, giving working scientists access to oceans of new data and the revelations that come from subsequent analysis and interpretation.

In the realm of ecology, citizen science has gained a new standing as researchers have tapped into the potential of an interested public. Citizen science projects, mapping things like the presence and behaviors of bumblebees, manta rays, butterflies and bats, have fueled dozens of published studies.

It’s proven to be a powerful resource for Ben Zuckerberg, a professor of forest and wildlife ecology at CALS. North American birds and their distribution on a changing landscape are a primary focus of his research, a significant portion of which depends on data gathered by volunteer observers.

For instance, Zuckerberg and post-doctoral fellow Karine Princé drew on citizen science data to tell us that the cast of characters we see at our bird feeders in the winter is shifting, most likely due to climate change. Their study of wintering songbirds shows that some species, once rare during the Wisconsin winter, are shifting their ranges north, remaking the resident communities of birds that visit our backyard feeders.

The conclusions of the study rested on two decades of data gathered by thousands of citizen scientists through the Cornell University Laboratory of Ornithology’s Project Feederwatch.

“Birds have always been important environmental indicators,” Zuckerberg explains. Rapidly declining songbird populations in the 1950s and 1960s, he notes, were used to help ascertain the consequences of widespread use of the chemical insecticide DDT, which was subsequently banned, first in Wisconsin and then nationally.

The DDT story was famously informed by the unintended involvement of ordinary citizens who gathered baseline data in the form of bird eggs. In the 19th century, collecting bird eggs was a widespread hobby, an artifact of the Victorian obsession with the natural world. Many collections ended up in museums where, decades later, CALS ornithologist Joseph Hickey and his students used them to document the thinning of eggshells subsequent to the widespread introduction of DDT into the environment in the 1940s and ’50s.

Today the contributions of citizen scientists tend to be more directed, and the advent of personal computers and smartphones, in particular, are making participation easier, more immediate and more effective. And a prime example of that trend is the Wisconsin Breeding Bird Atlas, a collaborative project by the Wisconsin Department of Natural Resources (DNR), the Wisconsin Society for Ornithology, the Wisconsin Bird Conservation Initiative and the Western Great Lakes Bird and Bat Observatory.

This year, the group launched a second iteration of the Atlas. Zuckerberg and other scientists are working with Atlas coordinators and waiting in anticipation of a flood of new data from the project, which recruits volunteers statewide to survey thousands of designated blocks over a five-year period for evidence of breeding birds.

The first Wisconsin Breeding Bird Atlas featured data collected by nearly 1,600 volunteers between 1995 and 2000. As its name implies, the Atlas is a survey that documents the distribution and abundance of birds breeding in Wisconsin. It provides critical baseline information about bird species that live in our state and is an important benchmark in terms of assessing potential changes in bird populations over time due to things like habitat loss and climate change. It also helps document avian diversity, the state of endangered and rare bird species, and habitat needs in Wisconsin.

Such data, explains Zuckerberg, help scientists make sense of a world that involves players ranging from microbes to plants and animals, including birds. There are so many moving parts that capturing a wide snapshot of what exists where at a given point in time can give scientists insightful information about the dynamics, nuances and health of an ecosystem.

“Ecology is necessarily a messy endeavor,” Zuckerberg observes. “But at certain scales, it all becomes very clear.”

Drawing on things like Breeding Bird Atlas data, Zuckerberg and other scientists can get at the scales that matter: geography and time. As the Wisconsin Breeding Bird Atlas II effort gets under way, ecologists are laying the groundwork for analyzing the data by formulating hypotheses and ideas about what the data might show and how it will compare to data in the first iteration of the Atlas, which, according to the Wisconsin Society of Ornithology, “represented the largest coordinated field effort in the history of Wisconsin ornithology.”

Data collection for the Wisconsin Breeding Bird Atlas II began in 2015 and runs through 2019. In September the DNR released findings for the first Atlas season. Volunteers submitted nearly 24,000 checklists documenting the location and breeding activity of 229 species of birds. These early data show that wild turkeys are on the move, now populating nearly every corner of our state. And eight species of birds new to the Wisconsin breeding landscape since the last survey—including the iconic whooping crane—have cropped up in the new Atlas data.

“The stories that come out of the data are so robust,” Zuckerberg says. “We go in with our ideas of what we’re going to uncover, and some of the patterns just jump out at us.”

The major advantage of the Wisconsin Breeding Bird Atlas, according to noted ornithologist Stan Temple, a CALS emeritus professor in forest and wildlife ecology, is that it documents the relationship between birds and the places they require to successfully reproduce. “Habitat affinity is where the Atlas works best,” Temple explains.

Temple cites other long-standing citizen science efforts to document birds. The North American Breeding Bird Survey was officially launched in 1966. Conducted during the breeding season, volunteers traverse by car more than 3,700 randomly selected 24.5-mile road transects in the United States and Canada. Stopping every half-mile, volunteers document every bird seen or heard in a three-minute span before moving to the next observing station. The North American Breeding Bird Survey, Temple argues, is the gold standard for measuring population trends among birds.

A more recent citizen science effort—one that capitalizes on personal computing technology and helps inform the Wisconsin Breeding Bird Atlas—is the aforementioned eBird. Taking old-fashioned pen and paper checklists into the digital age, eBird is an online checklist linked to a central database. Used by amateur and professional birders, eBird logs millions of bird observations worldwide in any given month through a simple and intuitive web interface. The Wisconsin Breeding Bird Atlas II is the first state Atlas effort to employ it.

“We’re in the information age now,” explains Nick Anich, the Wisconsin DNR Breeding Bird Atlas coordinator. “We have eBird. We’re excited to use this new system. The developers have put an awful lot of effort into the checklist input, and they just launched the maps function. And the data update at least every 24 hours, so we can see things in real time.”

But can the information gathered by armies of citizen scientists be trusted? Can it help researchers predict the future of Wisconsin’s environment? How is it validated? Can scientists get over any qualms they might have about data collected beyond the strict parameters of controlled experiments and expert observation?

Zuckerberg, who has published on the use and value of crowd-sourced data, believes that many scientists are coming around to the idea that the data indeed represent an accurate picture of the natural world. “There has always been some skepticism about it in ecology. But studies show it is valuable data that are relatively accurate for picking up ecological patterns and processes,” Zuckerberg says.

“There are entire subfields of ecology dependent on these data. Theories in macroecology and how species respond to widespread environmental changes, such as pollution or climate change, for example,” Zuckerberg observes, referencing the study of relationships between living organisms and their environments at large spatial scales. “We wouldn’t be able to do anything like that without citizen science.”

That kind of insight is essential, Zuckerberg stresses, as broad-scale environmental change due to pollution, deforestation, reforestation and climate change will have significant and possibly lasting effects on birds in many different types of ecosystems.

According to Temple, the power of citizen science lies in the sheer numbers of observers. As a new CALS faculty member in 1976, Temple launched the Wisconsin Checklist Project. “The Wisconsin Checklist Project did in the predigital age what eBird does now,” Temple explains. “It is a rigorous way of engaging lots of bird-watchers in a very systematic way.”

For the most part, Temple says, the data are trustworthy. “Bird-watchers are used to keeping records, so you’re not asking them to do anything that already isn’t part of the culture. Mistakes in observing and recording happen, but it is safe to say those few errors become insignificant noise in comparison to the strength of the signal: the overwhelming number of accurate observations.”

For atlasers like Florence Edwards-Miller, a 31-year-old communications specialist from Madison, the chance to go into the field and gather data blends neatly with her deep-felt appreciation of the natural world.

Trekking through the prime birding habitat of Madison’s Nine Springs E-way on a rainy midsummer morning, Edwards-Miller is on a mission. An experienced birder, she knows she can confirm any number of breeding birds that use the settling ponds of Madison’s Metropolitan Sewerage District to raise their broods. And she is eager to contribute those little bits of data to the Wisconsin Breeding Bird Atlas effort.

“You can’t make good decisions unless you know what’s out there,” says Edwards-Miller. “I believe in science. I believe in the importance of the data.”

In a little more than an hour, she confirms the presence of breeding mallards, Canada geese and red-winged blackbirds—all pedestrian wetland species—by noting offspring and, in the case of the blackbirds, a cantankerous distraction display.

It takes a little longer to find the killdeer fledglings, but at the end of our circuit around the pond, there they are: little puffballs on stilts trailing behind their foraging parents. It’s a beautiful sight. And another valuable data point for the Wisconsin Breeding Bird Atlas.

Age-Old Traditions, New Media

There is no better place to begin this story than on an August morning in the remote reaches of the Bad River Ojibwe Reservation, afloat on Lake Superior’s shining Chequamegon Bay beneath an expansive, cloud-filled sky.

Several flat-bottomed boats are lined up gunwale-to-gunwale, bobbing in the gentle waves. They’re filled with students—a mix of UW–Madison undergraduates and tribal youth—on a field project run through UW–Madison’s Global Health Institute. They are listening to Dana Jackson and Edith Leoso, Bad River tribal members and elders, talk about wild rice and the windswept, watery landscape around them, the sloughs and the tamarack stands, the distant islands and the shimmering headlands.

It is all ancestral home to the Ojibwe, and Jackson and Leoso bring it to life with their words. They tell the Ojibwe creation story of how their tribal forebears came to the land so many years ago from the east, seeking, as they had been told in visions, a place where “the food grows on top of the water.” They speak of the chiefs who signed treaties to protect this homeland and of the warriors who fought to protect it and of the threats that come with modern times.

The students, armed with video cameras and recorders, soak it all up. The land seems to take on new depth and meaning, peopled now with the ghosts and the place names and shrouded in the mystery and the magic of the old stories.

It’s an ideal classroom for the CALS professor who is the guiding hand behind this floating, open-air lecture session.

Patty Loew, a professor of life sciences communication, has brought these students here to share with them the lives and the culture of a people she knows well.

Loew is a tribal member of the Bad River Ojibwe. She can trace her family back to ancestors who were among the tribal leaders signing the tribe’s historic treaties in the 1800s. When she looks out upon the waters of Lake Superior and the winding sloughs of the reservation, she sees her own family’s history. These places are as special to her as to any other member of the Bad River community.

Two years ago, in a column in the Wisconsin State Journal about the importance of this place to the Ojibwe, Loew wrote, “You won’t see any stained glass or church spires in the Bad River or Kakagon Sloughs, but those wetlands are as holy to us as any temple or cathedral.”

A noted television journalist and the author of several acclaimed books on Wisconsin’s Native Americans as well as an accomplished scholar, Loew could easily be resting on her many successes.

Instead, she is deeply involved in a number of teaching and media projects that are not only bringing the stories of Wisconsin’s Native Americans to life, but also are providing new ways for those stories to be shared by tribal members themselves. Since 2007, she has led efforts to teach tribal teenagers digital storytelling and technology skills. Working with colleagues as well as tribal leaders, she has helped young people create documentaries sharing Native American issues and culture. In a 2012 project, for example, eight St. Croix Ojibwe students created a tribal history told through the life stories of five St. Croix elders.

In this work Loew has also partnered with the UW–Madison Global Health Institute. She’s currently in the midst of a project—the one that has us floating on Chequamegon Bay—in which global health students from a wide range of majors work alongside tribal youth to bring the power of digital media to bear on reservation health issues such as nutrition and childhood obesity. The Bad River reservation has some of the highest diabetes and cardiovascular disease rates in the United States, according to a 2008 Wisconsin Nutrition and Growth Study.

Loew’s projects can already boast some impressive successes. In 2013, three 14-year-old Bad River participants in her tribal youth media workshops produced a documentary, Protect Our Future, that detailed the potential environmental threats posed by a proposed iron mine in the Penokee Range above the Bad River reservation.

The video was an award-winning hit. It played to large audiences at film festivals throughout the Great Lakes region and was screened at the Arizona State University Human Rights Festival. The teens were on hand to introduce their film, which they also shared at the nearby Salt River Tribal High School.

The project followed a unique blueprint developed by Loew that melds traditional knowledge from tribal elders and leaders with the use of digital media skills now being deployed by tribal youth.
It is, in effect, an artful and sensitive blending of the old and new. Loew, not one to think small, says she sees the work in the context of a larger and more powerful dream. Oblivious to the breeze and splashing water from Lake Superior, she speaks from her seat in one of the boats as it motors through the reservation’s famed Kakagon Sloughs. In between her answers to questions, she patiently works with students as they learn how to use video cameras. She helps one of them frame a shot and assists another who is figuring out how to program a video card.

“My ultimate goal,” Loew says as she works, “is to help Bad River become the media center for Indian Country. We want to combine really strong media skills with a really strong sense of culture.”

Loew’s work has drawn praise from many quarters, from tribal leaders to academic colleagues.

Joe Rose is an elder with the Bad River Ojibwe and has watched young tribal members embrace Loew’s teachings. He describes the pride that the video Protect Our Future brought to the reservation.
“We were fighting against the mine then,” Rose recalls. “That was a very serious threat to us. We were very concerned about our wild rice. That was exceptional work that Patty did with the young people. She taught them how to use the media, how to do the photography and the interviewing. They even did the music. And it was all done by students, only 14 or 15 years old.”

Don Stanley, a CALS faculty associate in the Department of Life Sciences Communication who specializes in social media, has worked alongside Loew on the reservation, served as her co-investigator, and, Loew says, sparked the original idea for much of their tribal youth media work.

There are few better examples of the Wisconsin Idea in action, Stanley says, when it comes to sharing the department’s communication expertise and scholarship with a broader audience.

And, in this case, that sharing is with a community that few can reach as effectively as Loew. Loew has the ability to connect in a special way, Stanley notes, because of her deep tribal roots and connections. People know her and see her knowledge and respect for tribal life and culture. That understanding and empathy is not always common among academics.

“A lot of time in academia, we don’t understand that,” Stanley says. “Researchers come in, extract what they want and leave. But people you are working with relate on a scale that is much more real and visceral when they’re dealing with somebody who gets it.”

And Loew gets it.

“She’s got incredible street cred,” Stanley says of Loew’s work on the reservation. “It’s a blast traveling with her up there. Everybody is a family member. Everybody is ‘Hey, Patty!’ and big hugs. I also think that because she doesn’t take herself so seriously, she’s really approachable.”

Indeed, Loew is quick to laugh, and a talker. She will enthuse equally about her work or a Green Bay Packer game (she is a devoted fan). She evokes laughter from her students when, passing by a reservation boat flying a Packer pennant, she says, casually, “Oh, look. The tribal flag!”

Loew is quick to point out an important caveat when it comes to her work with the Bad River community as it relates to the Wisconsin Idea. This is not about just transferring knowledge from the campus to the reservation, she says. In fact, she prefers the phrase “knowledge exchange.”

The tribes, Loew says, are a rich and unrecognized source of information about the natural world. The elders and others on the reservation have much to share, and that traditional knowledge can inform and extend science and natural resource management in the non-Indian world, notes Loew.

In the Ojibwe, Loew sees a people who have valuable lessons for us in how to combine culture with a respect for the natural workings of the planet.

“Over the past 25 years, I’ve seen a real need for scientific information that has cultural relevance,” Loew says. “Native communities may be poor in an economic sense but they are rich in natural resources. And the culture is attached to those resources in a way that can’t be separated.

“So it’s a two-way street,” Loew continues. “We don’t necessarily have the scientific capacity. But what we do have is storytellers and people who know and embrace the culture.”

Loew did not come to these understandings suddenly. They are the result of a slow and gradual awakening on her part to her own Native American heritage and a lifetime spent learning the communication skills that would one day allow her to bring the power of story to bear on sharing the history and culture and struggles of not only the Ojibwe but all of Wisconsin’s tribes.

Loew’s path has led her to a very professorial office in Hiram Smith Hall on the UW–Madison campus, home to the Department of Life Sciences Communication (LSC) and just a stone’s skip from Lake Mendota.
But Loew, as her colleagues will point out, seems to have trouble staying in that comfortable office. Everyone who works with her in Hiram Smith Hall has had the pleasant experience of meeting a wide-eyed Loew in the hallway and being greeted by the phrase “Hey! I have an idea I wanted to try out on you.”

It is more than a charming aspect of her character. It is how she works, bringing to life the cherished Wisconsin ideal of “sifting and winnowing.”

Loew is an idea factory. In recent months, her friends and co-workers have listened and watched as Loew has worried about the many employees who will be out of work when Oscar Mayer’s Madison factory closes. Perhaps, she muses as she talks with her colleagues, there is a way one of her video classes can help provide video resumes.

More often than not, those ideas become reality.

“She’s phenomenal at taking ideas and making them come to fruition,” says Stanley.

Professor and LSC department chair Dominique Brossard says Loew heightens the department’s effectiveness at giving students a more global perspective on the intersections of culture and science in the natural world. Her courses in ethnic studies and Native American issues and the media are very popular, she notes.

And with her extensive background in television and video production, Loew is a key player in achieving another of the department’s goals—providing foundational communication skills to students.
“She’s uniquely positioned to do this kind of thing,” Brossard says.

Loew has traveled a long road to reach this stage in her career. She grew up on Milwaukee’s north side, little aware of her Native American background and the important role it would play as her life unfolded.

“I didn’t know I was Indian until I was 13,” Loew recalls. “I was just a kid growing up in a housing project in Milwaukee.”

Looking back, Loew believes her mother, who was born on a reservation, and her grandfather, who lived with the family, were trying to shield her from the discrimination frequently faced by Native Americans. Her grandfather, Edward DeNomie, was raised in the Tomah Indian Boarding School. Life in such schools was harsh, and children were often punished severely for speaking their native language or clinging to other aspects of their culture.

Even so, Loew heard and relished the stories of her ancestors. And by the late 1960s, she had become well aware not only of her rich cultural heritage but also the ugliness of racial prejudice. She recalls a growing sense of outrage, especially in the 1970s as Native American rights became a prominent news story.

Loew pursued a career in broadcast journalism. She earned a degree from UW–La Crosse and started her broadcasting career working in the city as a TV and radio reporter.

Eventually Loew moved to Madison, where she worked her way up to the anchor’s desk at the ABC affiliate, WKOW–TV. Her awareness of Native American culture and her desire to tell the stories of Wisconsin’s tribes grew. In the 1980s, she earned awards and gained respect throughout the state for her coverage of the fierce legal battle and sometimes ugly boat-landing confrontations as the Ojibwe fought to reestablish off-reservation hunting and fishing rights that had been included in the treaties.

Loew would go on to make dozens of documentaries telling the stories and covering the struggles of Wisconsin’s Native American communities. After moving on to Wisconsin Public Television, she made reporting on the tribes a regular part of her job as host of the show Weekend.

In a 2006 interview in the magazine Diverse: Issues in Higher Education, Loew described the important connection between her rediscovered culture and her professional life.

“As a journalist, a researcher, you have questions,” Loew said. “You realize you are struggling for answers about yourself. So you want to be open, to make connections to people. You find yourself being very relational, and that’s very Native.”

That willingness to be up-front about her debt to her past, and to be outspoken about the indignities that Native Americans have had to endure, have sometimes landed her in interesting, if not difficult, positions.

After she gave a talk about some of the more unpleasant truths of the first Thanksgiving, she earned the ire of none other than radio talk show host Rush Limbaugh. He accused Loew of being part of a “multicultural curriculum which is designed to get as many little kids as possible to question the decency and goodness of their own country.”

Few of Loew’s documentaries received more attention than Way of the Warrior, an exploration of the role of Native American soldiers in the U.S. military that aired on PBS in 2007. During her research, she stumbled across a film about her grandfather’s World War I outfit. Her quiet Ojibwe grandfather, it turned out, had fought in seven of WWI’s major battles as part of the 32nd Red Arrow Division.

Later, in another serendipitous discovery, she would find his diary. She describes how touched she was and how she is still so taken by the idea of Edward DeNomie raising his hand to take the oath and enlist in the U.S. Army—even though he had been denied citizenship in the country for which he was willing to give his life. Native Americans were not granted citizenship in the United States until 1924.

The popular, eye-opening documentary told the stories of many such Native American soldiers. And, later, after earning her master’s and doctoral degrees in journalism and joining the Department of Life Sciences Communication, Loew would continue telling the stories of Wisconsin’s tribes and of her own people at Bad River. She’s written several popular books, including Indian Nations of Wisconsin: Histories of Endurance and Renewal—which has been adapted for children and is now widely used in public schools—and, most recently, Seventh Generation Earth Ethics, a collection of biographies about 12 Native Americans who were key figures in environmental and cultural sustainability.

Sitting in the stern of one of the boats winding through the reservation sloughs, Loew reflects on her storytelling past and connects it with the ancient tradition of the Ojibwe and other native cultures.

“We are oral storytellers,” Loew says. But she is lending a new twist to the revered tradition. By adapting digital media to the old stories, the power of their message is amplified and made more accessible, especially important when it comes to lessons regarding nutrition and health among tribal members.

For example, some of the young tribal videographers have scoured the reservation collecting information from elders about age-old gardening and cooking skills. They hope to use that information at some point, Loew explains, to create “teen cuisine” cooking shows focused on healthy eating.

It makes so much sense to combine the old and the new, Loew says. After all, she adds, by the year 2020, 80 percent of content on the World Wide Web is expected to be video.

“These are new tools to help us be who we are, to help us capture the essence of who we are,” says Loew. “It’s a way to preserve our stories and a really unique approach to documenting life on the reservation at this particular time in history.”

Students from the Global Health Institute class, traveling with Loew on weeklong field trips, have worked side by side with tribal youth to gather information for the health and nutrition project and to create videos.

Cali McAtee, a CALS biology major who went with Loew to Bad River in August, wrote in her journal about not only establishing close relationships with tribal young people, but also of gaining valuable insight into another culture. She recalls in her writings the feeling of traveling through a sea of rice at the edge of Lake Superior.

“I have seen a lot of wild rice in my life, but from far away. I probably assumed it was a field because you can’t really see the water in between,” wrote McAtee. “I liked hearing about the importance of rice to the Ojibwe because I don’t think I necessarily have anything as important or meaningful in my life as rice is to theirs.”

Loew has felt the power of story in her own life and in her own search for connections. Researching one of her books, Loew found herself reading the classic book Kitchi-Gami: Life Among the Lake Superior Ojibway, by Johann Georg Kohl. In the book she came across a story in which Kohl brings to life a meeting he had with a tribal elder.

That elder was none other than Loew’s great-great-grandfather, Loon’s Foot. Kohl wrote how, during his conversation with the old man, Loon’s Foot stepped back into his lodge and came out with a smoky, stained birchbark scroll. Unrolling it and speaking in French, Loon’s Foot showed Kohl the story of his family told on the scroll and the dots and lines that denoted the passing years and decades. The story reached back to the year 1142.

“Here I was just reading Kohl, and then holy smokes!” Loew recalls. “Not bad for an oral culture.”

Loew firmly believes it is possible to capture that same kind of magic today with new approaches to traditional storytelling.

Don Stanley has watched as Loew has found a way to navigate between two worlds—the quickly receding years of the elders and the fast-paced, media-rich present of the tribal young—to create a new way to tell and preserve story and tradition, and then apply their lessons to modern-day problems.

As an example, Stanley describes how, as part of the nutrition project, he has seen Loew work with Native middle school students, teaching them how to videotape an elder speaking about traditional foods and health. While Loew is helping the teens develop communication skills, she knows full well that she is also preserving the knowledge of that tribal elder for future generations.

No less an expert on Ojibwe tradition than tribal elder Joe Rose admires and respects Loew’s ability to bridge old and new worlds. He says that with the passing of the generation that experienced the assimilation policies of the boarding schools, it’s important that the young be able to hear the elders’ voices—to see their faces, lined and carrying the weight of the years, but still alive with the resilience and strength and wisdom of their ancient heritage.

“It is very important, since we do come from an oral culture,” Rose says of Loew’s task. “But you’ve heard the expression that a picture is worth a thousand words? Well, there’s truth in that, too.”
As for Loew, she says that the girl growing up in the Milwaukee projects has found her place.

“I’m doing what I was supposed to do,” Loew says. “I’m incredibly grateful that Don and I have found such a dedicated, caring community—our students, our volunteers, the Bad River kids and their families—with whom to pursue this work. They’re the ones who make it possible.”

The Future, Unzipped

John Ralph PhD’82 talks with the easy, garrulous rhythms of his native New Zealand, and often seems amiably close to the edge of laughter.

So he was inclined toward amusement last year when he discovered that some portion of the Internet had misunderstood his latest research. Ralph—a CALS biochemist with joint appointments in biochemistry and biological systems engineering—had just unveiled a way to tweak the lignin that helps give plants their backbone. A kind of a natural plastic or binder, lignin gets in the way of some industrial processes, and Ralph’s team had cracked a complicated puzzle of genetics and chemistry to address the problem. They call it zip-lignin, because the modified lignin comes apart—roughly—like a zipper.

One writer at an influential publication called it “self-destructing” lignin. Not a bad turn of phrase—but not exactly accurate, either. For a geeky science story the news spread far, and by the time it had spread across the Internet, a random blogger could be found complaining about the dangers of walking through forests full of detonating trees.

Turning the misunderstanding into a teachable moment, Ralph went image surfing, and his standard KeyNote talk now contains a picture of a man puzzling over the shattered remains of a tree. “Oh noooo!” the caption reads. “I’ll be peacefully walking in a national park and these dang GM trees are going to be exploding all around me!”

That’s obviously a crazy scenario. But if the technology works as Ralph predicts, the potential changes to biofuels and paper production could rewrite the economics of these industries, and in the process lead to an entirely new natural chemical sector.

“When we talk to people in the biofuels industry, what we are hearing is that creating value from lignin could be game-changing,” says Timothy Donohue, a CALS professor of bacteriology and director of the UW–Madison-based Great Lakes Bioenergy Research Center, where Ralph has a lab. “It could be catalytic.”

After cellulose, lignin is the most abundant organic compound on the planet. Lignin surrounds and shapes our entire lives. Most of us have no idea—yet we are the constant beneficiaries of its strength and binding power.

When plants are growing, it’s the stiffening of the cell wall that creates their visible architecture. Carbohydrate polymers—primarily cellulose and hemicelluloses—and a small amount of protein make up a sort of scaffolding for the construction of plant cell walls. And lignin is the glue, surrounding and encasing this fibrous matrix with a durable and water-resistant polymer—almost like plastic. Some liken lignin to the resin in fiberglass.

Without lignin, the pine cannot soar into the sky, and the woody herb soon succumbs to rot. Found primarily in land plants, a form of lignin has been identified in seaweed, suggesting deep evolutionary origins as much as a billion years ago.

“Lignin is a funny thing,” says Ralph, who was first introduced to lignin chemistry as a young student during a holiday internship at New Zealand’s Forest Research Institute. “People who get into it for a little bit end up staying there the rest of their lives.”

The fascination is born, in part, from its unique chemistry. Enzymes, proteins that catalyze reactions, orchestrate the assembly of complex cell wall carbohydrates from building blocks like xylose and glucose. The types of enzymes present in cells therefore determine the composition of the wall.

Lignin is more enigmatic, says Ralph. Although its parts (called monomers) are assembled using enzymes, the polymerization of these parts into lignin does not require enzymes but instead relies on just the chemistry of the monomers and their radical coupling reactions. “It’s combinatorial, and so you make a polymer in which no two molecules are the same, perhaps anywhere in the whole plant,” says Ralph.

This flexible construction is at the heart of lignin’s toughness, but it’s also a major obstacle for the production of paper and biofuels. Both industries need the high-value carbohydrates, especially the cellulose fraction. And both have to peel away the lignin to get to the treasure inside. A combination of heat, pressure, and caustic soda is standard procedure for liberating cellulose to make paper; bleach removes the remaining lignin. In the biofuels industry, a heat and acid or alkaline treatment is often used to crack the lignin so that it is easier to produce the required simple sugars from cellulose. Leftover lignin is typically burned.

The economic cost of these treatments alone is significant, and lignin pretreatment is at the heart of many of the more egregious environmental costs of paper. On the biofuels side, lowering treatment costs to liberate carbohydrates from lignin could change the very economics of biofuels. In these large-scale, industrial processes, saving a percentage point or two is often worthwhile, but the Holy Grail is a quantum jump.

“Because it’s made this way”—Ralph jams his hands together, crazy-wise, fingers twisted together into a dramatic representation of lignin polymerization—“there is no chemistry or biology that takes it apart in an exquisite way,” he says. “We actually stepped back and thought: How would we like to design lignin? If we could introduce easily cleavable bonds into the backbone, we could break it like a hot knife through butter. How much can you actually mess with this chemistry before the tree falls down?”

Ralph’s team had their eureka moment more than 15 years ago, and have been trying to bring it to life ever since.

With a background in forage production and ruminant nutrition, John Grabber, an agronomist at the USDA–Agricultural Research Services’ Dairy Forage Research Center in Madison, got pulled into lignin chemistry through the barn door. On his family’s dairy farm he grew up with lignin stuck to his boots, though he never knew it. But during graduate school he became interested in how plants are digested by cows. Cell walls are potentially a great source of digestible carbohydrates—most plants contain anywhere from 30 to 90 percent of their mass in their cell walls—but it is entangled with lignin. “You quickly find out that lignin is the main barrier to feed digestion,” he says.

Grabber began working on a model system to understand plant lignification—for corn in particular—in 1989. After meeting at a conference, Grabber joined Ralph and plant physiologist Ronald Hatfield at the Dairy Forage Research Center back in 1992. There were many projects ongoing, but Grabber remained interested in trying to fully understand the structural characteristics of the lignin: how it’s made and how to modify it. In his model system they could make any kind of lignin they wanted to study, and see how the changes affected utilization.

Ralph and Hatfield advocated for the work, helping to find funding and offering their expertise. “If I had worked for somebody else I probably wouldn’t be doing this work,” says Grabber. “John and Ron gave me freedom and support to do it.”

Around the same time, Fachuang Lu joined Ralph’s lab seeking a Ph.D. His journey into lignin chemistry was not, at first, his idea. A native of mainland China, he’d enjoyed a successful undergraduate career in Beijing studying chemical engineering, then found himself assigned by the college to a master’s program in lignin chemistry. Lignin is an ingredient in the slurry of chemicals used in oil drilling, and that was his specialty. In 1989 Lu left Beijing for a teaching position at Guangxi University, but three years later he decided to continue his education. Though he’d never met Ralph, he was fascinated by the chemistry and applied to study in his lab.

As Ralph, Grabber, Hatfield and Lu continued to tinker with lignin chemistry, momentum began to build in the lab. Though lignin created a snowflake universe of different molecules, there were rules of assembly. A complex chemical pathway enabled lignin construction, with a mechanism that remained constant across different families of plants, but with many potential building blocks.

Ralph and his colleagues were the first to detail what was happening to lignin as the controlling genes of the biosynthetic pathway were turned on and off, a task ably completed by a slew of outstanding collaborators worldwide with expertise in biotechnological methods—but who lacked the diagnostic structural tools to determine what the plant was doing in response.

Ralph’s team quickly learned that lignification was somewhat flexible. “We figured that we could engineer lignin well beyond the previously held bounds,” says Ralph. As various pathways and chemical possibilities danced in their heads, it struck them: What if, during lignification, they could persuade the plant to slip in a few monomers that had easily broken chemical bonds? If they did it right, lignin would retain its structural value to the plant, but be easier to deal with chemically.

“In the course of our conversation we realized that if plants could do this, it could really revolutionize how readily you could make paper,” recalls Grabber. Says Ralph: “It’s almost impossible to tell which one of us actually verbalized it first—it is one of those great outcomes of the group dynamic.”

Lu’s particular genius was synthesizing the various complex chemicals needed, particularly a novel monomer-conjugate called coniferyl ferulate. It was the key to the zip-lignin—the teeth of the zipper. “He’s got to be one of the best in terms of making molecules,” says Grabber.

They were thrilled by such a revelation, but, in retrospect, they soon realized it was sort of an obvious idea—one suggested by the underlying chemistry and biochemistry of a pathway that was becoming increasingly well understood. Yet it was a discovery of huge potential value. They dropped into stealth mode and began to work on it. They finished important research and stuck it in drawers—signature research, the kind that, when finally published, would capture journal covers. And yet they sat on it, quietly chipping away for nearly a decade.

It helped that there was a flurry of controversy in the field—what Chemical & Engineering News called “the lignin war.” “Part of the reason we could sit on it was that, at the time, making these kinds of molecules was so far-fetched,” says Grabber. “Probably if we had talked about it, people would have laughed at us.”

But as the idea for zip-lignin grew in principle, it became stronger. Lu, Hatfield and colleague Jane Marita MS’97 PhD’01 found that balsa trees and a fiber crop known as kenaf produced very small amounts of coniferyl ferulate. But even as the idea seemed more and more feasible, Hatfield and Marita couldn’t isolate the gene needed to manufacture coniferyl ferulate because of its very low expression in these plants.

And they got stuck. “At the beginning we were thinking that this is just a fantastic idea, but we really didn’t have that much confidence,” says Lu. “Maybe John [Ralph] had more confidence than me.” So they just kept at it. “Every step you think, yes, we are closer, closer, closer.”

In 2008 Ralph moved his work from the Dairy Forage Research Center into UW labs, with research projects under the recently formed Great Lakes Bioenergy Research Center (GLBRC). The center, launched with a $125 million grant from the U.S. Department of Energy that has since been renewed, was just one manifestation of the money and intellectual heft infusing biofuels research—and for zip-lignin it was a lucky move.

During the center’s first full meeting, Curtis Wilkerson, a plant biologist at GLBRC partner Michigan State University, was sitting in the audience when Ralph took his turn at the podium.

Wilkerson is a cell wall specialist. Though lignin is a third of the wall’s carbon and is essential to the way plants conduct water, he confesses he’d never given it much thought. In a room full of cell wall specialists, Ralph would “likely be the only person talking about lignin,” he says. “It just split that way a long time ago. People like myself had very little exposure to what John was thinking.”

It was this kind of academic silo that a place like GLBRC was supposed to breach. Ralph talked about putting ester bonds into lignins and his team’s long search for the elusive enzyme. Wilkerson saw a solution. Due to recent technical advances, the price of determining all of the expressed enzymes in a plant had become more refined and much less expensive. He offered to use these recent developments to try to find the missing enzyme to enable zip-lignin.

From the previous work, Wilkerson knew essentially the size and shape of the puzzle piece he was looking for. He began, quite literally with Google, trolling through the scientific literature looking for a plant that made a lot of coniferyl ferulate. The Chinese medicinal “dong quai” or Chinese angelica (Angelica sinensis) soon emerged as a candidate. Its roots contained about 2 percent coniferyl ferulate.

The team used knowledge about the likely type of enzyme they were searching for and successfully identified the gene and its enzyme that could produce coniferyl ferulate. The whole search took less than six months.

Would you believe an essential tool for the genetic engineering of poplars is a hole punch? That’s the word from Shawn Mansfield, a molecular biochemist at the University of British Columbia, who took the zip-gene from the Angelica and made it work in poplar, a popular tree in the biomass and forest products industry.

Working from Wilkerson’s gene, the first job was figuring out how to tag the new protein so that it fluoresced during imaging. While not necessary to the function of the genetically modified plant, it essentially allows the scientists to check their work: see where the protein is, how much is there, and if it is behaving as a protein should.
Mansfield’s lab also had to find a way to turn the gene on at the right time and place. It could make all the coniferyl ferulate one wanted, but if it wasn’t made at the right time and tissue, there would be no zip-lignin.

After perfecting these finer points, the gene is inserted into a special bacterium—and then the hole punch finally comes into play. Disks punched from poplar leaves are mixed with bacteria that have been inoculated with a special chemical that stimulates the bacteria to share their DNA around. Then the leaf disks are put in a special growth medium. As many as 12 shoots might emerge off of a single disk, but the lab would select and nurture only one shoot from each disk.

In the end they had about 15 successful transgenic candidates that they grew in the greenhouse and then shipped off to Wilkerson and Ralph for further study. Final selection was made based on the amount of fluorescent yellow the trees gave off, and from a newly devised analytical method developed by Lu and Ralph that was particularly diagnostic for the incorporation of the zip monomer into the lignin polymer.

The team knew that genetically modified organisms are not popular or easily talked about—never mind the exploding trees. The idea of reworking a fundamental building block of the plant world will breed resistance.

Ralph argues that this is already part of nature’s vocabulary: they’ve found their building blocks within the plant kingdom, including mutants that do similar things. And now that they know what they are looking for, Steven Karlen, a member of Ralph’s group, is continuing to find more evidence that Mother Nature is doing it herself. “We managed to persuade plants to do this,” Ralph says. “Chances are that nature has already attempted it and you could actually get there by breeding.”

It’s no surprise that Mansfield, who created the final transgenic tree, argues that there is a role for this kind of technology. “We as scientists should be wise in advocating for the proper use of it,” he cautions. “I would never force it on anybody. I would never try to sway people to think that it is the end-all or be-all for everything.”
But given the growing human population and rising CO2 levels, something like zip-lignin has a definite use in reducing the carbon footprint by reducing processing energy and chemical loads. “That means there are less environmental pollutants that need to be cleaned up afterwards,” Mansfield says.

“Our ecological footprint can be much reduced using these kinds of transgenic trees,” he argues. “The caveat is that we need to be very smart about where and how we plant them.”

Not many things in the natural world can take apart lignin, but any homeowner with a deck knows that fungi are up to the task. A recent analysis of mushroom genomes suggests that fungi evolved this ability about 300 million years ago. This is about the end of the Carboniferous era, when earth’s coal production began to slow down. Coincidence? Perhaps not. Now that wood could rot, it probably slowed the burial of organic carbon via tree trunks and other lignin-rich plants.

Could the discovery of zip-lignin signal another transition, and hasten our move away from fossil fuels laid down in the Carboniferous?

Tim Donohue likes to think so. He likens biofuels now to the early oil industry, when oil was simply being turned into liquid fuel while the by-products were burned or dumped. It took a few decades for inventors to capitalize on this now valuable stream of raw materials to build the modern chemical industry.

“Lignin is about 25 to 30 percent of carbon in the plant. So if we’re going to catalyze an industry that makes clean energy and chemicals from plant biomass, figuring out what to do with the lignin is going to be key,” Donohue says.

People in the industry used to joke that you could do a lot of things with lignin except make money from it. But that may be changing. “The economics and profitability of the industry will be very different if lignin can be turned into valuable compounds,” says Donohue.

One of the early efforts to make use of lignin was in Rothschild, Wisconsin, at a company now known as Borregaard LignoTech. When processed properly, lignin has many uses, from the manufacture of vanilla flavor to additives for concrete. There is even a small amount of it in the battery of your car that allows it to keep recharging.

Jerry Gargulak is research manager at Borregaard LignoTech, and learned about zip-lignin recently in his capacity as a scientific advisor to the GLBRC. Despite its many uses, Gargulak and his colleagues dream about a time when lignin can replace carbon black in tires and be used to build carbon fibers and structural plastics.

Zip-lignin and the ideas behind it could bring this day closer. “It gives us a technology that might yield a more interesting lignin-derived starting material,” Gargulak says. “It could potentially lead to a lot of innovation downstream in lignin technology.” But he emphasizes, “There are a lot of i’s to be dotted and t’s to be crossed.”

This story is just beginning. Zip-lignin has a patent and has excited industrial interest that could be worth significant dollars. Ralph and his colleagues continue working to further refine the process, increasing the percentage of zippable bonds in poplar and also inserting the gene into more plants, such as corn and Brachypodium, both grasses.
And in the basement of the shiny new Wisconsin Energy Institute building, where the GLBRC is based, two massive new nuclear magnetic resonance (NMR) spectrometers work 24/7, providing a level of detail into lignin that Ralph has never had before.

“We spend a lot of time looking at these Rorschach test–like figures,” Ralph says of the information generated from the NMR. “The detail in them is unbelievable. These things have been revolutionizing what we do.”

The New Old Forest

Jodi Forrester got the call while she was in the forest. The loggers were ready to go. So on a cold winter day in northern Wisconsin, she found herself riding shotgun in a harvester. Forrester, a research scientist in forest and wildlife ecology, watched as the loggers cut down the trees she and her team had carefully selected in the Flambeau River State Forest. Another huge vehicle, a forwarder, clambered behind, pinching the cut trees in its claw and moving them to where they were needed. All the while, the loggers played a little game, dodging between laundry baskets placed around the forest floor to catch leaves and falling debris. In the end, they managed to avoid all but a few.

It was not a typical job for the loggers. Instead of harvesting trees for timber, they were taking part in an experiment—the second phase of a research project on a large scale. Under the supervision of CALS forest and wildlife ecology professor David Mladenoff, Forrester and her colleagues had already been working for years to plan a forest experiment that would stretch over almost 700 acres. The loggers were there to implement that plan. Because all the wood they were cutting was going to be left in the forest as part of the experimental setup, the loggers were not able to remove any of it. It went against their nature.

“Every once in a while, the loggers had to cover their eyes,” says Forrester with a smile. “There are a lot of beautiful, valuable trees in that forest, and I think they weren’t too sure about what they were being asked to do.”

But the loggers had agreed to the job because they knew it was part of an experiment that would push the science of forest management in Wisconsin forward. All the work, including the tough job of watching the wood get left behind, was being done in the name of science—specifically, in the name of bringing the characteristics of old-growth forests back to the state.

Old-growth forests have been a scarce sight in Wisconsin since the early 20th century. Clear-cutting in the late 1800s and early 1900s left few old-growth stands. In the Upper Midwest, most big trees had been cut down by the 1930s. In the place of those stands, younger second-growth forests emerged.

Starting in the 1980s, a push to promote and protect old-growth forests picked up steam. It started in the Pacific Northwest, where obligate species, such as the spotted owl, live only in old-growth forests. As the interest in these forests moved east, people in the Midwest began recognizing the valuable ecosystem services provided by old-growth forests, such as storing carbon, maintaining soils and fostering biodiversity in plants, animals and microbes by offering needed habitats.

In Wisconsin it wasn’t a matter of protecting old-growth forests, it was a question of creating them again, or at least some of the functions they provide. And that was no small task. Creating old-growth forests requires defining them, and even that can be difficult. It’s not just a matter of age—and age doesn’t always mean the same thing. A 40-year-old aspen forest would be old, notes Mladenoff; a 40-year-old sugar maple forest, on the other hand, would be quite young.

“It’s not always the age that matters,” says Mladenoff. “Sometimes what really matters are the characteristics and features of the forest.”

With the features of Upper Midwestern old-growth forests unclear, Mladenoff and scientists at UW–Madison, other UW campuses and the Wisconsin Department of Natural Resources (DNR) in 1992 started Phase 1 of what was dubbed the Old Growth Project.

Phase 1 was a comparative study. The researchers looked at forests of various ages and histories—a total of 46 different areas—to determine what was unique to the older, unmanaged forests. They considered features like plant and tree species and sizes, woody debris on the ground, snags or standing dead trees, soil characteristics and forest wildlife. Different scientists looked at different aspects, the collaboration creating a complete picture of the forests.

After a decade of collecting and comparing enormous amounts of data, Mladenoff and his colleagues found that many of the features of old-growth forests had to do with two structural elements: the size and distribution of gaps in the forest canopy and coarse woody debris—sizable logs—on the forest floor.

Gaps are openings in the forest canopy caused when large trees fall. With sunlight able to reach the forest floor, these areas become places of regeneration and growth, and the diversity of understory plants is often higher in gap areas than in the surrounding forest.

Coarse woody debris, meanwhile, provides shelter for salamanders, insects and other small animals as well as food for fungi, insects and even other trees like hemlock and yellow birch. Logs also sequester carbon on the forest floor and reduce the amount of carbon dioxide returning to the atmosphere.

“We wanted to explore the importance of those two elements in more detail,” explains Mladenoff. “We wanted to know if creating those structural elements in second-growth northern hardwood forests could restore functional old-growth characteristics.”

Phase 2—The Experiment

Mladenoff, Forrester and their colleagues—including Craig Lorimer and Tom Gower, emeritus and former CALS professors of forest and wildlife ecology, respectively—wanted to address that question using an experimental setup. Phase 2 of the Old Growth Project, the Flambeau Experiment, was born. The first step of that phase, however, was not a trivial one. They had to find a piece of land on which to conduct the experiment. They needed a site that was big enough for all the treatments they envisioned and that would otherwise be undisturbed for a long period of time—50 years, in fact.

With help from the DNR, Mladenoff and his colleagues used geographic information systems—GIS—to look at forests at different sites to find one that would fit the bill. After two years of looking, the researchers, including a postdoctoral student dedicated to the project, finally chose the site in the Flambeau River State Forest—a hardwood stand around 100 years old, dominated by sugar maples.

Before the experimental treatments were applied to the newly found forest, pretreatment data were collected. Scientists could then compare the data collected after treatment to this baseline information. Forrester and her colleagues, including several graduate students, used grids that they laid on the forest floor to count and catalog understory plant species such as trout lilies, wild leeks, nodding trillium and jack-in-the-pulpits. They also observed and measured tree species and diversity, leaf litter that fell in the forest, nutrient cycling, activity of soil microbes and more.

Finally, after spending two years looking for a site and two more years collecting pre-treatment data, the Flambeau site was ready for treatment in January 2007. In came the loggers and machinery to create the canopy gaps and coarse woody debris. The researchers also put up fences surrounding some of the plots to exclude deer and remove their influence from those treatment areas.

For five years after Forrester first rode shotgun in the harvester, she, graduate students and other scientists worked year-round to collect data. In the winter, researchers made the four-hour trip from Madison to Flambeau to check equipment, take measurements, replace batteries and mend fences. Once the spring thaw came, their work ramped up.
A typical summer day in the forest lasted about 10 hours. The scientists would ride from their rented cabins to the Flambeau Forest, walk about a half-mile to the research site and start collecting data. These days would last until October or November, when the researchers would start to see the orange vests of hunters.

“We’d head out in the morning and take our lunch and everything we needed for the day,” says Forrester. “We’d walk into the site, do our work, then head back to the cabins and crash.”

Their work included collecting a huge number of plant and soil samples. Without any university buildings at the Flambeau site, Forrester and her colleagues had to transport all of those samples back to Madison in their vans. Once back on campus, the samples and data needed to be analyzed and entered into spreadsheets.

“We have gobs of soil and wood samples, and we employed a lot of undergrads to help us,” says Forrester, laughing. “Some folks would help in the field in the summers and then continue working in the lab in the fall while they took classes.”

Ten years into Phase 2, Forrester, Mladenoff and their collaborators are just now beginning to shape a picture of the effects of their treatments. While a decade seems like a long time for research, they have another 40 years ahead of them. Such is the course of a 50-year experiment. And researchers have a vast array of forest components to consider and measure.

At this point they have some preliminary data and even some surprising results. One of the unexpected outcomes has been in the plots with coarse woody debris. While the researchers were expecting that the effects of woody debris would take years to recognize as the wood decayed, they are already beginning to see changes in the carbon dynamics. The woody debris affected rates of decomposition and what kinds of microbes were present in the soil, for example, within just a few years after being left on the forest floor.

“I thought someone else would be seeing what happens to the wood in the future, that I would just be seeing the effects of the canopy gaps,” explains Mladenoff. “But it didn’t turn out that way.”

The researchers are also seeing more expected results. Saplings and understory vegetation are growing more quickly in areas with canopy gaps and more light, for example. Also, the deer exclusion fences make a difference. In areas without the fences, the deer are eating all of the sprouts growing from the stumps of harvested trees, which can change the composition of the forest, leaving more of the less palatable and lower value trees such as ironwood.

After five years of intense sampling after treatment, the researchers are now spacing out their measurements and sampling to allow the forest time to grow, settle, decay and cycle. With such a long-term experiment, some of the time must be spent waiting.

That time will also be spent securing funding for the project as it goes forward. The DNR provided money both for Phase 1 of the project and to get the experimental Phase 2 going. That initial funding for Phase 2 allowed the researchers to do the preliminary work, after which other funding started flowing in.

“The DNR was really helpful in getting this project started,” says Forrester. “They provided all that base funding for us to get established, and only once we started were we able to get other money.”

The USDA has provided a five-year grant, and Mladenoff and his colleagues have also received funding from the Department of Energy and USDA McIntire-Stennis grants for graduate students. Forrester is now working to secure funds for the years ahead.

The USDA grant afforded Forrester and her colleagues an unexpected benefit—the opportunity to teach a new generation of forest ecologists. The grant was awarded based on their proposal to integrate an educational component into their research, and to fulfill that aspect, Forrester created a summer internship program. Undergraduate students from around the country and the world, most with little experience in forest research, joined the scientists in the Flambeau.

“Initially we taught them the basics of forest ecology measurements and had them help us with our measurements,” explains Forrester. “As summer rolled on, we helped them focus on a topic and develop an independent study project.”

Around 40 students participated in the program over the four years it was available. At the end of each summer, they’d hold a symposium to allow the students to present their work and interact with the scientists. The graduate students gained valuable mentorship experience. It was a beneficial experience for all involved, and one that both Forrester and Mladenoff discuss with pride.

“It was an important part of the project, and it turned out to be a really great component of those summers,” says Forrester.

DNR Collaboration

In addition to providing funding, scientists at the DNR are also long-term collaborators with CALS researchers. They are working on a parallel 50-year project called the Managed Old-Growth Silviculture Study, or MOSS. Silviculture is the practice of managing forests to meet various needs or goals.

Having worked with Mladenoff and his team from Phase 1 of the project and into Phase 2, the DNR wanted to look at many of the same elements of old-growth forests, but with a more operational spin. They wanted to find out how to create the characteristics of old-growth forests while also allowing for economically beneficial harvesting of timber.

“There were three objectives for the MOSS project,” says Karl Martin BS’91, a former wildlife and forestry research chief at the DNR who is now with UW–Extension as state director of the Community, Natural Resource and Economic Development (CNRED) program. “We wanted the study to be applicable to the forest industry, we wanted to do something on a large scale so we could look at impacts on wildlife, and we wanted to show this was economically viable from a commercial standpoint.”

Martin worked closely with Mladenoff and other CALS and UW scientists to collaborate on the parallel MOSS project. One of the three MOSS sites is just north of the CALS site in the Flambeau River State Forest, with the two other sites located in the Northern Highland American Legion State Forest and the Argonne Experimental Forest.

Many of the treatments used on those three tracts of land are the same as those the CALS team is using in their experiment—canopy gaps, coarse woody debris and deer exclosures. The MOSS project also considered snags, or standing dead trees, which are another feature of old-growth forests.

Before establishing the treatments, Martin and his team spent several years surveying and measuring the trees. Because they wanted to harvest timber, they had to carefully consider which trees would be cut down and which would be left behind. Yellow birch trees were rare in the sites, so those were immediately off the table for harvesting. They also wanted to avoid cutting down the largest trees in the stands. To establish snags, the researchers chose crooked or highly branched trees that were of low economic value. While such trees make good habitat for wildlife, they are most likely to be used for low-valued pulpwood or firewood if harvested.

“We took three or four years before treating to really get things in place,” says Martin. “The problem with a 50-year study is that if you rush into it, you’re going to look back and wish you’d done something differently. We really wanted to cover all our bases.”

As with the CALS study, MOSS is in the early stages of gathering data and there are many angles to consider. The economic viability of silviculture that encourages old-growth characteristics is one of the main questions MOSS aims to answer, and Tom Steele MS’83 PhD’95, director of the Kemp Natural Resources Station in Woodruff, has been instrumental in finding that answer. Early data suggest that treatment cost of traditional harvests and the MOSS harvests is similar. In addition, the difference in timber revenue that a landowner would receive is quite minimal—just a few percent.

With years ahead to uncover the economics of such a system, MOSS is well positioned to understand and implement silviculture systems that are both economically and ecologically viable. That, in the end, is what the CALS–DNR collaboration is all about. It’s a partnership that brought about an otherwise unlikely project.

“The idea behind the collaboration is to leverage the resources of both organizations to help the citizens of the state,” explains Martin. “The scale of this study would not have been possible without the partnership of the university and the DNR. You need those resources, both intellectual and financial, to come together in a cohesive project.”

The size and scope of the Flambeau Experiment and MOSS are what make the projects so powerful—and so promising. There are decades of study ahead for researchers, and many of the original scientists will have to pass the project on to new researchers before it’s over. But the goal is clear: To determine if diverse ecosystems of old-growth forests can be developed through management while allowing for sustainable timber harvests. The outcome of the projects will have major impacts on forest management and harvests as well as on property owners, residents and visitors.

“With long-term studies, we work in the present, build on those that came before us, and count on colleagues in the future to continue the work,” says Mladenoff. “This research will be essential for long-term sustainable ecosystems and the services they provide.”

Forestry technician Donald Radcliffe BS’15, who graduated with CALS degrees in forestry and life sciences communication, contributed to reporting this piece.

Bitten

There’s no ignoring it. Some of the students enrolled in this medical entomology class are far more attractive than others. They know it, their classmates know it, and so does Susan Paskewitz, professor and chair of the Department of Entomology.

Paskewitz describes herself as “relatively unattractive,” and she proceeds to prove it using the same test her students have just performed. She fills a small vial with warm water, rubs it between her palms to coat it with volatile compounds from her skin, then places the vial on top of a thin membrane stretched over the top of a plastic container akin to an economy-sized ice cream tub. She invites a visitor to do the same.

Waiting on the other side of that membrane are 20 blood-starved specimens of Aedes aegypti, commonly known as the yellow fever mosquito. Hungry as they are, the insects don’t show a lot of interest in Paskewitz’s vial. They hover near where it touches the membrane, but only two or three land. The visitor’s vial, on the other hand, is a busy spot. At least a dozen have landed and are testing the surface with their needle-like proboscises.

“Wow,” says Paskewitz. “You’re really attractive!”

In another context, those three words could make your day. But not here. Nobody wants this kind of animal magnetism. Nobody wants to be the person who’s cursing and slapping and reaching for the DEET while others are calmly eating their brats and potato salad.

If you’re that person, take heart. Paskewitz can tell you a little bit about why you might have more than your share of interspecies charisma and offer some suggestions on how to scale it back. But first, let’s talk about why this matters.

An average American adult outweighs an average-size mosquito by about 30 million to one. Ounce for ounce, that’s like the USS Nimitz vis-a-vis a good-size duck. But while it’s a safe bet that a 100,000-ton aircraft carrier won’t change course to avoid a six-pound mallard, it’s almost certain that, on a regular basis, you change your behavior to avoid being bitten by a 2.5-milligram mosquito.

Mosquitoes cause us to do things we’d rather not, like dosing ourselves with a repellent that’s sticky and smelly and comes with a sobering warning label (you can apply it to your kids’ skin, but keep the bottle out of their reach), or pulling on long pants, long sleeves, a hat and maybe a head net on a sweltering midsummer day.

Mosquitoes keep us inside when we’d much prefer to go out. In the summer of 2009, Paskewitz and environmental economist Katherine Dickinson, of the Colorado-based National Center for Atmospheric Research, asked a sample of Madison residents how they coped when mosquitoes got fierce.

The second-most-common answer (right after applying repellent) was to stay indoors. About two-thirds of the respondents said they had curtailed outdoor household activities—gardening, yard work, sitting on the deck—in the past month because of mosquitoes, especially in the evening hours, which, for working people, may be the only time available to get a little fresh air. About a third said they had avoided outings, and a similar share said they had avoided outdoor exercise.

Nobody wants to be outside more than John Bates, of Manitowish. An author of seven books about Wisconsin’s north woods and a naturalist by trade, Bates leads interpretive hikes year-round—except in June: “We just kind of throw the month out. The mosquitoes cause too much discomfort for people to listen to interpretation. All we can do is keep walking. People hire me because they want to learn more about the place than they knew before they came. If they can’t stop to listen, what’s the point?”

If we do venture out when mosquitoes are massing, we may not get the experience we were hoping for. Andrew Teichmiller, an outfitter of bikes and paddling gear in Minoqua, recalls mountain biking in 2014, arguably the area’s worst mosquito year ever. “You had to ride the complete trail without stopping, all the way back to the parking lot, and jump in the car, quick, because if you stopped there were 15 or 20 mosquitoes on you immediately.” As for camping: “It’s a different type of experience when you can’t sit by the fire at night and tell stories. You’re forced to run for your tent. It definitely affects the feel of the trip.”

But let’s be clear: A ruined camping trip is far from the worst possible consequence of a mosquito bite.

Mosquitoes transmit diseases that kill nearly a million people every year and sicken hundreds of millions. Tropical and subtropical areas bear the brunt of this, but no place is immune, including Wisconsin. Malaria plagued the immigrants who settled in Wisconsin in the 1800s, and various types of encephalitis are diagnosed on a regular basis.

But today the biggest concern is West Nile virus (WNV). Wisconsin has been relatively lucky since the first case arrived here in 2002, with a total of 230 cases reported through 2014. But all four adjacent states have had bigger outbreaks—notably Illinois, with 2,093 cases total and 884 in its worst year, most of them just across the border in the Chicago area. Wisconsin’s worst year brought 57 cases.

Most cases of WNV bring no symptoms, according to the Centers for Disease Control, but about one in five can involve a fever, headache, body aches, vomiting and a fatigue that can last for weeks or months. Fewer than 1 percent of WNV victims display severe neurologic symptoms, including disorientation, coma, tremors, seizures or paralysis, and of those, about 1 percent die.

Nevertheless, Wisconsin residents are bothered much more by the nuisance of biting mosquitoes than they are worried about West Nile virus. The Madison residents responding to Katherine Dickinson’s 2009 survey said they’d be willing to pay an average of $149 for a hypothetical program to control nuisance mosquitoes, but wouldn’t pay anything for one targeted at mosquitoes carrying WNV when risks were as low as they were at the time (about one case per year in Madison with a population of 250,000).

It’s not surprising to find that attitude in Wisconsin, where mosquito-borne disease is relatively rare, but Dickinson says that people tend to think the same way in places where mosquito bites are often fatal. She observes that in Tanzania, biting mosquitoes were a major factor motivating people to use bed nets. “It was a similar situation to ours,” she says. “Some mosquitoes are more noticeable and more of a nuisance, but those that transmit malaria are kind of sneaky; people don’t feel them biting as much. In areas where mosquitoes were more of a nuisance, people used the bed nets more.”

Biting-wise, there’s an important distinction between nuisance mosquitoes and the ones that transmit WNV. The former come at us aggressively, in such staggering numbers that they’re impossible to ignore. They remind us to protect ourselves. Culex pipiens, the WNV vectors, are more subtle and harder to notice.

Nuisance mosquitoes and the WNV carriers also show up at different times. The most annoying biters—Aedes vexans in particular—are floodwater species that breed after a stretch of wet weather. Culex breed in water that stagnates during a dry spell.

“When it’s been really dry, the water just sits in the stormwater catch basins that are the biggest sources of the WNV vectors,” says Paskewitz. “There’s not enough rain to flush them. Things get more fetid, stinkier. That’s the year when we see a ton of Culex.”

The take-home message: If you only grab the DEET when the biting is so bad that you can’t stand to be without it, you’re not protecting yourself against West Nile virus.
“You need to protect yourself against bites even if you’re not getting a lot of them,” says John Hausbeck, director of environmental health services for Dane County and the City of Madison. “We’ll see summers where it’s really dry and the floodwater mosquitoes are very limited, but we still have plenty of small pools that the Culex can breed in.”

That “biting pressure” is something that Hausbeck needs to stay on top of, and Paskewitz helps with that. She and former grad student Patrick Irwin PhD’10 were able to characterize the types of sites where Culex are most likely to breed and identified alternatives for treating them—for example, introducing fathead minnows to feed on Culex larvae. She and her students analyze the mosquitoes trapped in the area to see how many are Culex and whether they’re carrying WNV. Their data tell Hausbeck whether he needs to issue a public alert.

It’s important to remain vigilant. “When West Nile first came into the country, people doubted it would make it through the first winter,” Paskewitz says. “Well, it did persist, and in a very short period of time it whipped across the whole country. We’ve had a lot of cases in new places. First it was really bad in North and South Dakota. Then Colorado and Arizona. Then Texas, Illinois. It’s really hard to predict. And given the vagaries of climate, we just don’t know whether the next year it might be Wisconsin.”

Maybe WNV hasn’t changed Wisconsin residents’ ideas about why to guard against mosquito bites, but it certainly has spurred a lot of questions about how. There is a seemingly endless list of products and strategies, that, according to somebody, will eliminate mosquitoes or repel them—and since WNV arrived, Paskewitz has been getting questions about pretty much all of them.

“They call me to ask, ‘Would this work or wouldn’t it?’ There is a lot of misinformation out there and not many good sources of information, so I realized I needed to get a better idea of what the science was behind these things,” Paskewitz says.

As she comes up with answers, she posts summaries online. Her website, http://go.wisc.edu/mosquitoes, gets plenty of visits (55,000 last year) and triggers a lot of calls from media from across the nation.

A few of her findings:

• Repellents can be very effective, but comparing them is tricky. There are lots of products with varying active ingredients offered in different concentrations and combinations. Generally speaking, DEET, Picaridin, IR3535, and oil of lemon eucalyptus have good track records. There are also a number of other plant-based compounds—garlic, catnip oil, vanilla and oil of cloves, for example—for which there’s less research and conflicting results. The website sums all this up and gives links to more information.
Yard traps get a thumbs-down. “We tested those and didn’t get any positive outcome,” Paskewitz says. Yard traps lure mosquitoes by releasing C02, light or octenol, a compound contained in our breath and sweat. Sure, they can catch mosquitoes by the hundreds, Paskewitz says. But does this significantly reduce the numbers that bite you? Properly controlled studies say “no.”

• “Sonic” devices—wristbands, smartphone apps, etc.—do better at extracting your money than keeping mosquitoes off your deck. “You can test them yourself,” Paskewitz says. “Sit at the picnic table and count how many mosquitoes land on you, then turn on the device and count again. Or you can trust the research and save your money.”

• Bats are busted. The idea that a colony of bats can consume millions of mosquitoes per night came from a study in which someone put a bat in a room full of mosquitoes and estimated how many it ate. The question is, given the choice, is that what bats eat in the wild? Researchers who examined the stomach contents and fecal pellets of bats have found bigger insects, like butterflies, moths and beetles, but very few mosquitoes. “Bat houses are great for conserving bats,” Paskewitz says, “but not for mosquito control.”

• Avoiding bananas—When she first heard the idea that eating bananas makes you more attractive to mosquitoes, Paskewitz raised her eyebrows. “I thought, okay, we’ll debunk that,” she says. She was teaching medical entomology at the time with 24 students—enough for a robust sample—so she made it a class project. For several weeks, each student ate a banana and then performed an attractiveness assay at prescribed intervals. “We were really intrigued. It did look like we were getting an increase a couple hours after eating the bananas.”

Paskewitz repeated the trial the next two times the course was offered, with a few tweaks to the methodology: Half the students ate bananas, the other half grapes. “The third trial was the best of all—the strongest statistical evidence and the most repeatable,” Paskewitz says. “We did it three times and saw a strong difference between the groups. Grapes didn’t matter, bananas did. At that point I was convinced. I think it’s real,” she says. Does that mean you if you leave bananas out of your picnic fruit salad, you can skip the bug spray? Probably not, Paskewitz says.

Because “less attractive” is not the same as mosquito-proof, Paskewitz gets plenty of mosquito bites, probably more than her share, because she spends a lot of time around mosquitoes—in the woods doing field research, in her garden, and in her lab. When you’re a mosquito researcher, getting bitten comes with the job.

What Makes You Attractive?

It sounds like the topic of an article in Seventeen magazine—and, interestingly, some of the same general categories apply whether you’re talking about your appeal to a mosquito or to a certain someone of your own species.

Your breath. If you breathe, you’re mosquito bait. Every breath adds to a plume of carbon dioxide (CO2 levels in your breath are 100 times that of the atmosphere) emanating from where you stand. “That’s the big signal,” says entomology professor Susan Paskewitz. “Insects are very sensitive to chemical cues. They’ll zigzag to pick up the chemical as it gets stronger and stronger, circling to narrow in on you.”

Your aroma. Once they find you, mosquitoes use chemical cues to decide whether to land and dig in. They have a lot to sort through: You emit roughly 400 different compounds from your skin and 200 in your breath. Many mosquito species won’t land on humans, even if they’re starved for blood. Others will bite us in a pinch but prefer other hosts, Paskewitz says.

Your genes. Perhaps you were born to be bitten. A pilot study at the London School of Hygiene & Tropical Medicine found that identical twin sisters were significantly more alike in their attractiveness to mosquitoes than were non-identical twins. Since identical twins are closely matched genetically, this suggests that some of your Culicidae charisma is inherited. Some volatile compounds on our skin are produced by skin cells (others are produced by bacteria), which would be gene-regulated, the study’s authors note.

Your jeans. What color you wear matters. This is based on a series of studies in which researchers draped different colors of cloth on human volunteers or on robots heated to simulate human body temperatures, then counted mosquito landings. For the most part, darker colors were more attractive. White was least attractive, followed by yellow, blue, red and black.

Your smelly feet. “The malaria mosquito is really attracted to the smell of funky feet,” Paskewitz says. “It’s a classic story in medical entomology. The compound that makes feet smell funky and attractive to mosquitoes is the same one that causes Limburger cheese to smell the way it does.” That compound is produced by bacteria that can accumulate in the moist spots between your toes, and are kin to those used to culture Limburger.

Your drinking habits. A number of researchers speculate that drinking alcohol makes you more attractive to mosquitoes. A team in Japan put this to the test. They asked some volunteers to drink 350 ml of beer while a control subject did not. The percentage of mosquito landings after alcohol consumption increased substantially. Why this happens is unresolved, although some have speculated that people who have been drinking are easier targets because they move more slowly.

Getting Under Your Skin

Maybe you don’t get more mosquito bites than other people. Maybe your body just makes a bigger deal of it. The swelling, redness and itching are signs of your immune system kicking into gear, explains Apple Bodemer, an assistant professor of dermatology at the UW–Madison School of Medicine and Public Health. And some people’s immune systems kick harder than others.

A mosquito bite involves give and take. Before drawing out up to .001 milliliters of your blood, the mosquito injects a bit of its saliva, which contains anticoagulants to prevent clotting. You can spare the blood, but the saliva is a problem. That’s how disease gets transmitted. And the saliva contains foreign proteins, or antigens, that spur your immune system to create antibodies, Bodemer explains. “When antibodies bind to the antigens, it initiates an inflammatory response, which includes the release of histamine, which causes the blood vessels to dilate, which brings the swelling and redness and the inflammatory mediators that are responsible for the itching.”

This doesn’t happen the first time you’re bitten. It’s the second time, when your body has built up the antibodies, that your immune system engages. If you get bitten enough times by the same strain of mosquito, you may become desensitized and have either a very mild reaction or no reaction at all to the bites. “People often have more vigorous immune responses early in the season and then, as the summer goes on, they don’t have as much swelling and redness and itching,” Bodemer says. “But when you go a winter without any exposure, you often become resensitized.”

For the same reason, younger kids tend to have more aggressive reactions. Once they’ve had several years of mosquito exposure, their response tends to die down, Bodemer says.
As for scratching? Doctor’s orders: Don’t! “Scratching really promotes the full inflammatory reaction. It causes more irritation, causing the blood vessels to be more dilated and further dispersing the inflammatory mediators. It initiates a cycle of swelling, redness and itching. If you can avoid scratching, a lot of times the bumps will disappear.”

Antihistamines can ease the itching, she says, or you can try a home remedy: “I paint a little clear nail polish on the mosquito bite. That will stop the itching to some degree and allow the inflammation to clear up more quickly,” Bodemer says. “Some people cover the bite with Scotch tape for two to four hours. The tape stops you from scratching and when you peel it off, it removes some of the mosquito saliva.”

Wisconsin’s Pestilent Past

Wisconsin’s 19th-century settlers knew that mosquitoes were biting them, and they knew that something was making them sick—but they didn’t put the two together.

Their doctors blamed the ailment on “malarial vapors” emitted by decaying vegetation in the swamps, according to Peter T. Harstad, a UW–Madison educated historian who authored several articles on the health of Midwestern settlers. Harstad used reports by military and civilian doctors as well as immigrants’ diaries and letters to chronicle the devastation caused by what was sometimes called “intermittent fever” because the symptoms—chills, aches and a general fatigue—often recurred over a period of months or years.

“I became sick as soon as I came here and have been sick for eighteen months with malarial fever, which is very severe and painful and sometimes fatal,” reads one letter excerpted by Harstad, written in 1941 by a resident of Muskego. “My wife and I are now somewhat better, but far from being well. This year seventy or eighty Norwegians died here … Many became widows and fatherless this year.” About 13 percent of Muskego’s population died that year, Harstad estimates. The town was hard hit because of an abundance of marshes, a relatively warm climate, and the fact that Norwegian immigrants had no resistance to the disease.

Soldiers also suffered. Harstad cites army reports of malaria outbreaks as far north as Ft. Snelling, near present-day St. Paul. Hardest hit was Ft. Crawford, located amid miles of Mississippi River wetlands at Prairie du Chien. In the fall of 1930, there were about 150 cases reported among the 190 soldiers stationed there. To treat the disease, army surgeons were directed to “extract from twelve to twenty ounces of blood, an operation which it is sometimes required to repeat once or twice.” Wisconsin was mostly malaria-free by the end of the 19th century, as farmers drained wetlands and better housing shut out mosquitoes.

Eyes on the Green

Traveling around the windswept golf course called The Straits, with its massive greens of bentgrass and rumpled, horizon-bound fairways of fescue, it’s easy to see why course manager Michael Lee BS’87 would arrange to keep his own yardwork to a minimum.

“My lawn takes me 20 minutes,” says Lee. It’s a cool spring morning, and we’re bouncing his pickup around the stunning environs of The Straits, one of two Kohler Company 18-hole courses that comprise Whistling Straits on the shores of a steely-surfaced Lake Michigan in Haven, Wisconsin.

“I have mostly mulch and woody ornamentals,” Lee says of his home lawn. “Everything I have to do for weed control I can do while I mow my lawn.”

This is in great contrast to the daunting challenge Lee faces in maintaining what has been deemed one of the country’s great championship golf courses.

And now the task has become almost herculean. The Straits, built and owned as part of The American Club by the Kohler Company, is hosting the prestigious PGA Championship this summer. From August 10 to 16, the eyes of the world will be on that course.

Though Lee will be toiling anonymously that week, guiding a staff of hundreds, his hard-earned skills as a golf course manager will be very much on display. Few, however, will truly understand what Lee and his staff do behind the scenes to maintain fairway and tee and rough and allow the television cameras to create what, in effect, is golf course art on our screens—sweeping vistas of perfectly tended dune and grass and emerald greens, with the big lake shining in the background.

But more than artful views are at stake. Lee, personable and easygoing and quick to smile, stands up well to pressure, those who know him say. And pressure there will be.

The PGA Championship, which dates back to 1916, is one of the most heralded events in golf. Each of the last two PGA Championships played at Whistling Straits, in 2004 and in 2010, drew upward of 300,000 people, and millions of households around the world tuned in to television broadcasts. The Wisconsin economy benefited to the tune of more than $76 million for each of the tournaments.

Lee is the first to say he could not shoulder the responsibilities of preparing The Straits for such worldwide scrutiny without plenty of help. And one of the places he counts on most for guidance in dealing with the course’s fussy turf is his alma mater, the College of Agricultural and Life Sciences at the University of Wisconsin–Madison—and, more specifically, the CALS-affiliated O.J. Noer Turfgrass Research and Education Facility, named for Oyvind Juul Noer, a CALS alumnus and one of the earliest internationally known turfgrass agronomists.

The facility, where scientists use tools ranging from high-powered microscopes to lawn mowers, opened in Verona, Wisconsin, in 1992 as a partnership between the Wisconsin Turfgrass Association, the University of Wisconsin Foundation, and the CALS-based Agricultural Research Stations.

Toiling in its maze of test plots, often on their hands and knees, are researchers who study everything from insects and soil to plant disease. For Lee, they are like a staff of doctors who can, at a moment’s notice, diagnose what is ailing a green or a fairway and prescribe a treatment. The Kohler Company (like many other golf course operators) contracts with the facility annually for these services.

Before and during the PGA championships, that role becomes even more crucial. The university specialists help Lee keep disease and insect problems at bay throughout the year. But in the weeks leading up to the championship they become his urgent care clinic, providing immediate help if something suspicious shows up. During the week of the championship they staff on-site, portable laboratories.

“We’re kind of at Mike’s beck and call,” says Bruce Schweiger BS’84, a CALS plant pathology researcher who serves as manager of the Turfgrass Diagnostics Lab housed at O.J. Noer. “If he calls, we’ll be there. We’re CSI Turf! That’s who we are.”

Of course, such high-profile events are just a small—albeit exciting—part of the facility’s wide-ranging mission. And you certainly don’t have to be running a world-class golf course to seek help from the scientists at O.J. Noer.

The turfgrass industry is a $1 billion-a-year business in Wisconsin and keeps about 30,000 people in jobs. Chances are, if you manage a sod farm or a park, maintain an athletic field, try to keep a 9-hole golf course at the edge of town up and running, or just wonder why your lawn looks like a bombing range, you could benefit from expert advice.

Paul Koch BS’05 MS’07 PhD’12, a CALS professor of plant pathology and a UW–Extension turf specialist who once worked as an intern for Lee, says the broad reach of the CALS turfgrass program, throughout the state and the country, is a fine example of the Wisconsin Idea at work.

“Just think of all the mom-and-pop golf courses around the state,” Koch says. “There are all these excellent little 9-hole courses. The owners have to manage their problems within the confines of the budgets they have. They really rely on our experts.”

Lee, preparing his course for the world stage, takes full advantage of the sharing of knowledge upon which the Wisconsin Idea is based. He long ago learned how important the concept is to people in all corners of the state. It was part of his education at UW–Madison, he says. Lee graduated in 1987 with a degree from CALS in soil science, specializing in turf and grounds management. He also worked as a student hourly helping conduct research in the Department of Plant Pathology.

Lee credits that education and several crucial golf course jobs—including five years as assistant superintendent at the Blue Mounds Golf and Country Club in Wauwatosa—with equipping him to handle the rigors of managing a course such as The Straits.

It was mostly his work afield at CALS that best prepared him, Lee says. He remembers long days spent crawling around test plots with a magnifying glass looking for diseases with names like dollar spot or nearly invisible insects such as chinch bugs. He literally learned his craft on the ground, he says.

“I learned the technical side of the business,” Lee says. “The need to know what’s going on at deeper and deeper levels.”

The willingness to work hard and learn has long been one of Lee’s most noticeable traits. At age 14, he went to work at the Blackhawk Country Club golf course in the Madison suburb of Shorewood Hills. His boss was Monroe Miller BS’68, now retired but for many years the respected and colorful superintendent at Blackhawk.

“He was a real special kid,” Miller says. “There were two things about Mike. He was smart and he had a great work ethic. He was probably never, ever, ever once, late for work.”

Miller recalls that off-season was always a time for catching up on chores such as painting. Around Thanksgiving in 1982, he told Lee and another young worker that among the jobs on their list was painting the inside of a pump station.

“They went down there on Thanksgiving Day and went to work,” Miller says. “I had to go down and kick them out so they would go home and spend time with their families.”

As for Lee, he says of Blackhawk and his apprenticeship with Miller: “I learned to work. I learned discipline.”

It was apparent even in those days, Miller says, that Lee had a special talent for everything to do with maintaining a golf course, from a love of the machinery to understanding the special care grass needs to become the meticulously groomed stage necessary for the game.

“Mike is one of those guys you could call a turfgrass clairvoyant,” Miller says.

Whistling Straits is a world unto itself, a haunting landscape that seems to have been dropped from the ancient countryside of the British Isles onto the Lake Michigan shoreline. That was exactly the intent of Kohler Company CEO Herbert Kohler and legendary golf course designer Pete Dye when they created both The Straits and The Irish, the other 18-hole course on the property.

The Straits, especially, evokes the rugged environs of renowned seaside courses such as the Old Course at St. Andrews in Scotland, frequent site of the British Open. These are known in the golfing world as links courses, dramatically different from the grassy, intensely manicured courses most Americans are familiar with. Greens are connected less by fairways than by long reaches of rugged, seemingly unkempt terrain pocked by deep, cylindrical bunkers known as pot bunkers. These are another naturally occurring feature of the old courses, terrifying hazards into which unlucky golfers can disappear for long moments before chopping their wayward ball out again.

The old links courses in Ireland, Scotland and England are characterized by a coastal topography of dune and scrub-covered ridges. They evolved as the setting for a terribly frustrating game called golf because they were good for little else other than grazing the sheep that chomped away while early golfers swung away.

Though some may associate the word “links” with linked golf holes, the word actually comes from Old English and predates the game. It is the name given to that particular harsh and scrubby landscape behind a beach.

This is the world that Dye wanted to create with The Straits. He started with a wasteland along the shore of Lake Michigan, a flat and dismal area that had been the site of a military antiaircraft training range. He ordered up 7,000 truckloads of sand and went to work.
What emerged was a course of bluff and dune along two miles of Lake Michigan shoreline with holes named Gremlin’s Ear and Snake and Cliff Hanger and Widow’s Watch and Pinched Nerve. Each hole has a view of the lake. There are four stone bridges and a stone clubhouse that looks as though it were transported rock by rock from the Scottish countryside. A flock of Scottish blackface sheep roam the grounds.

“We had to hire a shepherd,” Lee says. “Sometimes one of the sheep gets lost and we all have to look for it. You can spend hours out there looking for that one last sheep. It’s like something straight out of the Bible.”

But few characteristics connect The Straits to the old-style links courses more strongly than the wind. Lee, traveling the course, seemed almost always aware of the wind off the big lake.

“Out of the north today,” he says, during our drive. “Look at those waves.”

The wind gave the course its name. Herbert Kohler was walking the property during construction and, apparently teetering in a steady gale that whistled along the course’s heights and raised whitecaps on the lake, the name came to him very naturally.

The attention to detail in the course’s design, construction and maintenance has impressed the world’s best golfers. Lee keeps a file of comments from professional golfers, and he pulled out one from Tom Lehman, three-time winner of the PGA’s Player of the Year, who was interviewed about the course during the 2004 PGA Championship.

“It’s quite a feat of construction,” Lehman said. “I mean, it’s quite a vision they had . . . This golf course is almost otherworldly.”
Lehman also spoke of the course’s ruggedness. Players and spectators alike generally come off The Straits exhausted, Lee notes. During the 2010 championship he spent part of his time giving rides to exhausted spectators worn out by walking the up-and-down course.

Lee enjoys banging around the course in his truck, sharing its charms and its quirks, especially now as preparations for this summer’s championship are well under way. On one jaunt he points out the paths that are designed like narrow country lanes (no carts here; every golfer walks with a caddy). He pauses at the large staging areas for gravel and sand that will serve as platforms for the big corporate suites and viewing stands.

The course is being set up, Lee says, to make it more spectator-friendly, with better walking areas and viewing locations that place golf fans close to the action.

And Lee shares an interesting and somewhat startling detail that, upon reflection, makes perfect sense for a course owned by the Kohlers of bathroom fixture fame. He stops his pickup truck and points to what looks like gravel along the side of the road.
“We used crushed toilets to make that,” Lee says matter-of-factly, but with a faint smile playing on his face.

On this early spring day, the bentgrass on the greens and the fescue in the fairways has yet to begin changing from winter’s browns to the green of spring. But that green will soon enough begin creeping across the course—and Lee will be paying close attention to any disease or other problems that may try to establish a foothold.

For Lee and his staff, preparation for the PGA Championship has been going on for years: the close monitoring and treatment for disease and insects, the careful maintenance of the course throughout the playing season, when Lee’s crews are out morning and night raking, mowing and grooming.

Staff with the PGA have been on the site for two years, working from a large office trailer and keeping track of preparations, figuring out such details as where structures are going to go and where ropes will be placed to guide and control spectators.

The PGA course conditioning guidelines for championship competition give some indication of just how much attention to detail is necessary—consistent green speeds that are calculated with an instrument called a stimpmeter, mowers that are very precisely calculated to mow greens between .150 and .100 of an inch, the required use of bunker sand with grains that are measured so that no more than 25 percent of them are .25 mm or smaller.

“We go out all day with the guys from the PGA,” says Lee. “We’ve learned to pack a lunch.”

So it’s easy to see why Lee’s relationship with the experts at CALS becomes even more important as the championship draws near. Though Lee is adept at dealing with most of the challenges turf has to offer, the researchers at the Turfgrass Diagnostics Lab can often spot problems that remain invisible to most.

Back at the lab, Bruce Schweiger remembers puzzling over disease samples sent in by another client. To the client, the problem looked like dollar spot, but Schweiger knew that was not the issue. CALS entomology professor and UW–Extension specialist Chris Williamson was working nearby, and Schweiger asked him to take a look.

“Oh,” Williamson said. “Ants.”

It turned out that Williamson had done research on the problem some time before and had discovered that, during the mating season, some ant species go to war. They attack each other by spraying a nerve toxin that contains formic acid. That acid burns the turf and leaves lesions that look suspiciously like dollar spots, Schweiger recounts.

Such are the strange problems that could arise to plague Lee and his crew as they tend the course during the championship.

And those worries are on top of the intense maintenance that requires around-the-clock diligence once the event begins. Most crew members stay on-site working hours on end during championship week, Lee says, sleeping in big shelters set up for that purpose, snoozing in reclining chairs and watching the golf action on television screens.

Plant pathologist Paul Koch worked during the 2004 championship as an intern on one of the two- and three-person green crews that are charged with caring for a particular green and making sure during the week that it is cut morning and night and maintained to the PGA’s exacting specifications.

Sometimes, Koch says, that requires a cut of a mere sliver, no more than the depth of three credit cards or so stacked one upon the other.

One damp early morning during the championship, Koch recalls, Lee dispatched crews to squeegee the dew from tees. Koch was met during the chore by one of the professional golfers, who marveled at what Koch was doing.

“He said, ‘I can’t believe you guys are doing this so that we don’t have to walk in dew,’” Koch recalls.

Through the entire championship, Koch says, Lee remained cool and collected.

Of course, going into the week of a championship, Lee has already made sure there is little that can go wrong. A recent tour of the course included a visit to the maintenance building garage, located just outside the door from Lee’s spartan office (aerial shots of the course being the most elaborate decoration).

Lee walked to one of the 60 big mowers lined up and gleaming in neat rows. He tilted one up and suggested running a finger across one of the blades.

It was razor sharp.

Learn more at the following websites:
O.J. Noer Turfgrass Research and Education Facility: http://ojnoer.ars.wisc.edu
Whistling Straits: www.americanclubresort.com/golf/whistling-straits
PGA Championship: www.pga.com/pgachampionship

The Fox, the Coyote­—and We Badgers

Once upon a time during the last few years, a red-haired girl new to the University of Wisconsin–Madison crested Bascom Hill and cast her eyes upon the cozy arrangement of buildings and lawns, the tree-lined city by the fair lake. Her nature and upbringing led her to think: Yes, this is good. I should meet the right boy here. I hope the food is good.

The UW–Madison campus is a well-worn locale for such scouting. Last year 31,676 prospective students scoped out dorms and classrooms. Hundreds of elite athletes measured the environment against their precise needs. Thousands more informal visits were made, all driven by the same question: Can I thrive here?

But our young visitor is in a new class altogether—wild members of the canid clan. As it happens, their food is quite good, and she—technically a vixen, or female fox—did find the right dog. After spending a winter holed up under Van Hise Hall, she gave birth to a litter of eight, and in early March of 2014 began to let the young kits gambol about.

They were a campus sensation—stopping lectures, cars and buses, inspiring a popular Tumblr blog, drawing hundreds of rapt spectators. Their appearance provided a fortuitous teachable moment for David Drake, a professor of forest and wildlife ecology and a UW–Extension wildlife specialist, who was just beginning to delve deeper into studying the foxes and coyotes of Madison.

Coyotes have been intermittent, if secretive, Madisonians for more than a decade. In the last few years reports of coyotes by visitors to Picnic Point have been rising, and people from the Lakeshore Nature Preserve asked Drake if he could investigate. But the rise of the urban fox population is a relatively new canine twist.

“It’s very timely,” says Dan Hirchert, urban wildlife specialist with the Wisconsin Department of Natural Resources. While no comprehensive data have been collected, from where he sits foxes and coyotes are gaining throughout the state. And while the coyotes have been present for a couple of decades, the fortunes of the fox seem to be following the rise in urban chicken rearing.

Because most wildlife research happens in rural areas, we may not know as much as we think about our new neighbors. “Does what we’ve learned about these animals in the wild apply in urbanized settings?” asks Drake. Most major cities employ a forester, but very few cities have a wildlife biologist on staff. Much more common is the pest management paradigm: animal control.

“It doesn’t make any sense to me,” Drake says. “If 85 percent of Americans live in cities, why aren’t we doing more? That’s where people are interacting with wildlife.”

These questions prompted Drake to found the UW Urban Canid Project, a hyperlocal study with far-reaching implications.

“The number of urban canid sightings on campus, primarily red fox and coyote, have been on the rise and have been met with mixed emotions from all different members of society,” notes Drake. “This research aims to understand more about the complex interactions between coyotes, foxes and humans in this urban area—as well as provide information and resources for residents to reduce the potential for conflict with these amazing creatures.”

As morning light seeped into a cold January dawn, David Drake and his grad student Marcus Mueller prepared to lead a small convoy from Russell Labs, winding toward the wild corners of campus to check 18 restraint traps that had been set the evening before.
“Are you feeling lucky today?” Drake asks, climbing into the truck.

“Always,” says Mueller.

“I had a hard time getting to sleep last night,” says Drake. “This is like the anticipation of Christmas morning. Every day you go out to see if you caught something.”

First stop is the old Barley and Malt Laboratory, between the retaining wall of University Avenue and the physical plant. It hardly seemed like habitat, but Mueller traced a clear track laid down by the repeated passage of many small feet. The animals were using the buildings for cover, in transit to someplace else.

Drake is hopeful—he’d already received a call from someone who’d seen a fox at 5:20 a.m. on the football practice field. “They were running through Breese Terrace all last year,” he says. At least one fox was digging in an area under the west side bleachers of Camp Randall for a possible den, notes Drake, but no kits were ever seen there. “It is funny to find these spaces on campus that the animals are using,” says Drake. “I ride my bike by here every day and never really thought about it.”

And in one of the three traps an annoyed raccoon waits impatiently. Donning protective gloves, Drake and Mueller release the coon, who scuttles away, anxious for cover.

Next stop is a small cattail marsh next to Willow Beach, behind the new Dejope Residence Hall. The day before, Drake and Mueller had baited the marsh with parts of a deer carcass. On the short trail we flush an eagle from its perch, perhaps planning its own morning snack of carrion.

This little ecological pocket typifies the habitat opportunities that fox and coyote are exploiting. It’s not big enough to call home, or even to get a regular meal. But link it together with dozens of other nooks and crannies and dumpsters around campus, and the sum total is a complex and productive niche.

Fox and coyote are urban adapters: flexible enough to range across a variety of landscapes, from rural to urban. For animals to survive in a city, they typically need to be this kind of habitat generalist, able to exploit a range of hunting and scavenging environments.

The other part of the equation is habituation—how animals get accustomed to human activities. As a species moves into the city, those who survive realize over time that bad things don’t necessarily happen when they encounter humans. Instead of running at the first sign of people, they sit and watch. This knowledge gets passed down from mother to pup, eventually leading to the Van Hise foxes romping in full view of adoring crowds.

The restraints behind Dejope are set for fox, and this morning there is nothing. Drake looks around and connects the dots in the surrounding environment. West across the ice is University Bay Marsh, where four more restraints await. A few ticks to the north is Picnic Point, and the lake beyond.

The last traps of the day are located in the Biocore Prairie, where the research began when a few trail cams confirmed that a group of coyotes were ranging through the preserve, and probably enjoying the fruits of the Eagle Heights gardens as well.
Drake hopes to learn how urban agriculture is influencing canid behavior. Backyard vegetable gardening is flourishing, and each year more city dwellers add chicken coops to their homesteads.

The chickens are an obvious attraction—chickens have probably been preferred canid targets since even before their domestication. Gardens also attract the small mammals that canids prefer. They will even snack on berries and vegetables.

Last year Drake secured four radio collars—two for each species—and, with the assistance of Lodi trapper Mike Schmelling, researchers were able to collar a pair of coyotes and one fox. Among the first discoveries was that the animals are running the frozen lake. The researchers learned this when one collared coyote disappeared. At first they suspected a malfunction, but a citizen report led them to Maple Bluff, where they reestablished radio contact. The coyote had apparently run all the way across the lake, possibly snacking on ice-fishing gut piles along the way. Another ran north and was killed by a car on County M, near Governor Nelson Park.

This year the research hits full speed, with 30 fox collars and 30 coyote collars available. The ambitious work plan includes collaring an entire fox family, kits and all.

And in the snow-covered landscape of the Biocore Prairie, the first glimpse of the third restraint trap offers a rush of hope. The area around the restraint is beaten up, with dark leaves interrupting the white. An animal was clearly held at some point, but all that’s left is a bit of hair and a kinked and ruined cable.

Back in the truck, Drake teases Mueller. “Marcus, I don’t have a good feeling about your luck.”

“Not yet, anyway.”

“You’re not an unlucky person, are you?”

“I hope not.”

“Because I have fired more than one graduate student for being unlucky . . .”

It’s just as dark and even colder the next morning, yet the party adds an undergraduate wildlife ecology student, Cody Lane, and Laura Wyatt MS’87, a program manager with the Lakeshore Nature Preserve. John Olson, a furbearer biologist for the DNR, is in town, and has come to check out the project before putting in a day of lab work.

Behind the Barley and Malt Laboratory, Olson kneels down to evaluate the tradecraft of the empty restraint—a simple loop of airline cable noose suspended from a dark length of stiff wire. “They don’t even see these as traps. They see them as sticks,” Olson explains.

These unique cable restraint traps were named and developed with DNR assistance as part of a national humane trap research program in the early 2000s. “The important thing with these kinds of sets is non-entanglement,” he says. The radius of the multistrand wire must be clear of any potential snags. The size of the loop is determined by the animal you’re selecting, while a stopper keeps it from getting too tight. It works much like a choker collar.

During testing they trapped just over 200 coyotes, and only two died. One had a bad case of mange and died of exposure. The other was shot by someone who didn’t realize the animal was restrained. “It’s a very safe tool,” Olson says. “Cable restraints never damaged any coyotes in the three years that we studied them.”

The convoy moved on to Willow Beach—and, finally, success. A young male fox waits suspiciously, huddled in the reeds. The wind probes at his deep winter coat while the party retreats and summons Michael Maroney BS’85, a veterinarian with the UW–Madison Research Animal Resources Center.

Together Mueller and Maroney estimate the fox’s weight at 12 pounds, and draw a mix of ketamine and xylazine. Mueller secures the animal with a catch pole while Maroney injects the cocktail into the rear leg muscle, provoking an accusing glare from the fox. The clock starts. Within six minutes Maroney looks at Mueller and announces: “He’s clearly gorked.”

Everybody laughs at the non-technical yet thoroughly accurate terminology, and the work begins. They figure they have about 40 minutes. Laying the animal out on a white towel atop a blue tarp, Mueller secures a cordura muzzle, then pulls out electric clippers and shaves one dark foreleg to make it easier to find a vein. Maroney watches his technique while the undergraduate Lane records data.
The fox breathes steadily, and the three talk quietly, as if he were only asleep. Without the wind ruffling his coat, the fox seems smaller, more vulnerable. After the blood draw, nasal and fecal swabs are taken, and the mouth examined. Finally, they weigh the animal—a sturdy 13.5 pounds—and affix the radio collar.

Removing the muzzle, they carry him away from an opening in the marsh ice—a gorked animal doesn’t always behave rationally—and lay him out again on the tarp, out of the wind. A few minutes later and a dark ear twitches, as if to displace a fly. A few more minutes, and the ear twitches pick up. Suddenly the fox stands up shakily, and surveys the audience of onlookers. He quickly takes cover in the marsh, where he gathers his wits for a few more minutes, then slips from view.

Mueller and Drake are giddy, ebullient. “We are off and running,” says Drake. “That was pretty cool.” Last year it took forever to catch a fox; this year they begin with one. “Great start,” says Mueller, and then recounts the steps to himself in a low voice, as if to help remember: the sedation, the blood draws, the recovery.

Mary Rice first saw the coyote in her backyard sometime in the summer of 2012. It was getting dark, and first she wondered, “Whose dog is that?”, followed quickly by: “Oh, my god, a coyote.”

“We were a little alarmed,” she says.

Rice canvassed the neighbors, warning them there was “a coyote lurking” about. Some didn’t know, others did, and some even thought they’d seen wolves. She was wondering how to deal with it, who to call, when she saw another one, smaller. “Remove one, there will be another,” she realized.

A graduate coordinator in the Department of Food Science, Rice remained somewhat unsettled for a few months, worrying about her cats and unsure about her own safety. Then one day at work she learned about Drake’s UW Urban Canid Project and decided to give them a call.

“Can you try to track it and figure out what it’s doing here?” she asked. “We can hopefully live with it. If we’re not going to be able to remove it, maybe we can learn from it and learn how to live among them.”

Before long, with the cooperation of another neighbor, a restraint trap was set. This was Mueller’s first solo set: he decided where to put it, and configured and camouflaged it. Within a week, in early March they had a 36-pound male coyote who had been cutting behind a brush pile. On her way to work, Rice stopped to see the animal and help the team record its vitals. She couldn’t wait to tell her coworkers why she was late.

Rice’s coyote experience is a perfect example of how the project can work, says Drake, with outreach engaging members of the public and connecting them with scientists in the field. On most trap-checking mornings Drake’s team has company—each day a new handful of visitors. Sometimes they’re wildlife students or other friends of the program, but often they’re just curious early risers who follow the group’s progress on social media.

And with hundreds of followers on Facebook and Twitter, public fascination is strong. Because of our strong cultural connection to dogs, our affinity may even be a little hardwired. From Wile E. Coyote and fox or coyote tricksters in folklore to the Fantastic Mr. Fox, these are animals we all know on some level, however mythic.

Still, fox and coyote don’t get quite the same reception. The fox is easy to anthropomorphize. It’s small, cute and generally non-threatening. Coyotes aren’t typically seen as often, and your first thought can be, like that of Mary Rice: Whoa, that’s a pretty big animal.

“Just because you see a coyote doesn’t mean it’s a bad animal, and doesn’t mean it’s going to create problems for you or that you should be afraid of it,” says Drake. The key is to not create, or exaggerate, a conflict. And that’s almost always about food. It’s important to secure bird feeders and outside pet food, and to take care with pets out of doors. If the coyotes become too bold, make an effort to scare the animals away. “We’re really trying to help people to understand how wonderful it is to have these animals here, but also to be vigilant,” Drake says.

“Are you nocturnal yet?” I ask Mueller as I climb into a white UW van at 9 p.m. in early March. He laughs—it won’t be long now. As soon as early-morning trap checks are done, he’ll be swinging full-time on the second shift. These dogs are nocturnal, and if you want to learn where they are at night, you’ve got to get out there with the radio tracker.

The research plan calls for tracking each animal at least once a week. Some nights it’s boring, and Mueller catches naps between hourly triangulations. But the newly collared fox has been a real challenge. He was tracked one night moving from south of Fish Hatchery Road and Park Street all the way up to John Nolen Drive, where he spent time on frozen Monona Bay and eventually made it to Muir Woods on campus. That’s about four miles as the crow flies—never mind the urban labyrinth he had to navigate between those points. He did all that traveling within a five-hour period.

“It truly was a game of cat and mouse trying to keep up with him that night,” says Mueller. Is he a young transient who hasn’t yet established a home range? Is he trying to find a mate? Or can home ranges for urban foxes really be that big?

Some nights Mueller can track only one animal, but on others they are close to each other. On one recent night the fox and the coyotes were all on campus, just a short distance from each other. “I was flying all over campus,” says Mueller. “It was a crazy night of telemetry.”

It was a perfect scenario for answering a really big question. In wilder terrain foxes and coyotes are mutually exclusive, but Madison is different. “We know from the animals we’ve got on radio that the fox and the coyote are sharing the same space, and sometimes they are sharing the same space at the same time,” says Drake. “They are crossing paths.”

Are the foxes using humans and elements of our built environment to protect themselves from coyotes? Or are there simply enough resources that they don’t have to compete as strictly—more rabbits and squirrels, more compost piles and chicken coops?
The scientists are a long way from answering those questions. First they need to relocate the coyote.

Mueller parks around the corner from Mary Rice’s house in a residential pocket south of the Beltline and raises the antenna, a three-element Yagi that looks like a refugee from the old days of analog TV.

The first reading comes from the west, and from the strength of it Mueller guesses we’re a mile or more away. Crossing back over the Beltline, a little under a mile as the crow flies, and another reading: now the signal’s coming from the east. Another three-
quarters of a mile into a dead-end parking lot, and the signal is now east and south. But back over the Beltline.

In quarter-mile and half-mile increments Mueller is in and out of the van, swinging the antenna around, squawk box to his ear, taking compass readings. After a few more readings he finalizes the coyote’s location in a small wetland not far from one of the many bike paths that probe south from the city. He stayed put until 2 a.m., when Mueller called it a night.

“I can’t wait,” says Mueller, thinking ahead 12 months, when he’s got hundreds of hours of data plotted on a map and can begin to see patterns. “The underlying goal of this project is to be able to coexist with these animals more effectively, to avoid conflicts,” he says. “We don’t want to have to remove coyotes from a population because they are too habituated to people.”

As a summer job during college, Mueller used to take calls at a wildlife rehab center in Milwaukee. “A lot of times people just don’t know much about the ecology and life history of these animals, and that lack of understanding leads to fear,” he says. One call in particular stuck with him, a man worried about a turkey walking around in Milwaukee.

“He said, ‘You’ve got to take it back to nature. It’s not supposed to be here,’” Mueller remembers. But the turkey had already redefined nature—and so have coyotes and foxes and deer and raccoons and . . .

“Cities aren’t going anywhere,” says Mueller. “And the way that these animals are adapting, I think it’s only going to allow for more animals to continue this trend.”

Keep up on all the latest information from the UW Urban Canid Project at their new website, http://uwurbancanidproject.weebly.com/, as well as on Facebook and on Twitter: @UWCanidProject. If you have any questions, or are interested in observing or volunteering, please email: uwurbancanidproject@gmail.com.
To see more campus fox photos by E. Arti Wulandari, visit: http://go.wisc.edu/campusfoxes.

Plant Prowess

It may look jury-rigged, but it’s cutting-edge science.

In a back room in the university’s Seeds Building, researchers scan ears of corn—three at a time—on a flatbed scanner, the kind you’d find at any office supply store. After running the ears through a shelling machine, they image the de-kerneled cobs on a second scanner.

The resulting image files—up to 40 gigabytes’ worth per day—are then run through a custom-made software program that outputs an array of yield-related data for each individual ear. Ultimately, the scientists hope to link this type of information—along with lots of other descriptive data about how the plants grow and what they look like—back to the genes that govern those physical traits. It’s part of a massive national effort to deliver on the promise of the corn genome, which was sequenced back in 2009, and help speed the plant breeding process for this widely grown crop.

“When it comes to crop improvement, the genotype is more or less useless without attaching it to performance,” explains Bill Tracy, professor and chair of the Department of Agronomy. “The big thing is phenotyping—getting an accurate and useful description of the organism—and connecting that information back to specific genes. It’s the biggest thing in our area of plant sciences right now, and we as a college are playing a big role in that.”

No surprise there. Since the college’s founding, plant scientists at CALS have been tackling some of the biggest issues of their day. Established in 1889 to help fulfill the University of Wisconsin’s land grant mission, the college focused on supporting the state’s fledgling farmers, helping them figure out how to grow crops and make a living at it. At the same time, this practical assistance almost always included a more basic research component, as researchers sought to understand the underlying biology, chemistry and physics of agricultural problems.

That approach continues to this day, with CALS plant scientists working to address the ever-evolving agricultural and natural resource challenges facing the state, the nation and the world. Taken together, this group constitutes a research powerhouse, with members based in almost half of the college’s departments, including agronomy, bacteriology, biochemistry, entomology, forest and wildlife ecology, genetics, horticulture, plant pathology and soil science.

“One of our big strengths here is that we span the complete breadth of the plant sciences,” notes Rick Lindroth, associate dean for research at CALS and a professor of entomology. “We have expertise across the full spectrum—from laboratory to field, from molecules to ecosystems.”

This puts the college in the exciting position of tackling some of the most complex and important issues of our time, including those on the applied science front, the basic science front—and at the exciting new interface where the two approaches are starting to intersect, such as the corn phenotyping project.

“The tools of genomics, informatics and computation are creating unprecedented opportunities to investigate and improve plants for humans, livestock and the natural world,” says Lindroth. “With our historic strength in both basic and applied plant sciences, the college is well positioned to help lead the nation at this scientific frontier.”

It’s hard to imagine what Wisconsin’s agricultural economy would look like today without the assistance of CALS’ applied plant scientists.

The college’s early horticulturalists helped the first generation of cranberry growers turn a wild bog berry into an economic crop. Pioneering plant pathologists identified devastating diseases in cabbage and potato, and then developed new disease-resistant varieties. CALS agronomists led the development of the key forage crops—including alfalfa and corn—that feed our state’s dairy cows.

Fast-forward to 2015: Wisconsin is the top producer of cranberries, is third in the nation in potatoes and has become America’s Dairyland. And CALS continues to serve the state’s agricultural industry.

The college’s robust program covers a wide variety of crops and cropping systems, with researchers addressing issues of disease, insect and weed control; water and soil conservation; nutrient management; crop rotation and more. The college is also home to a dozen public plant-breeding programs—for sweet corn, beet, carrot, onion, potato, cranberry, cucumber, melon, bean, pepper, squash, field corn and oats—that have produced scores of valuable new varieties over the years, including a number of “home runs” such as the Snowden potato, a popular potato chip variety, and the HyRed cranberry, a fast-ripening berry designed for Wisconsin’s short growing season.

While CALS plant scientists do this work, they also train the next generation of researchers—lots of them. The college’s Plant Breeding and Plant Genetics Program, with faculty from nine departments, has trained more graduate students than any other such program in the nation. Just this past fall, the Biology Major launched a new plant biology option in response to growing interest among undergraduates.

“If you go to any major seed company, you’ll find people in the very top leadership positions who were students here in our plant-breeding program,” says Irwin Goldman PhD’91, professor and chair of the Department of Horticulture.

Among the college’s longstanding partnerships, CALS’ relationship with the state’s potato growers is particularly strong, with generations of potato growers working alongside generations of CALS scientists. The Wisconsin Potato and Vegetable Growers Association (WPVGA), the commodity group that supports the industry, spends more than $300,000 on CALS-led research each year, and the group helped fund the professorship that brought Jeff Endelman, a national leader in statistical genetics, to campus in 2013 to lead the university’s potato-breeding program.

“Research is the watchword of the Wisconsin potato and vegetable industry,” says Tamas Houlihan, executive director of the WPVGA. “We enjoy a strong partnership with CALS researchers in an ongoing effort to solve problems and improve crops, all with the goal of enhancing the economic vitality of Wisconsin farmers.”

Over the decades, multi-disciplinary teams of CALS experts have coalesced around certain crops, including potato, pooling their expertise.

“Once you get this kind of core group working, it allows you to do really high-impact work,” notes Patty McManus, professor and chair of the Department of Plant Pathology and a UW–Extension fruit crops specialist.

CALS’ prowess in potato, for instance, helped the college land a five-year, $7.6 million grant from the U.S. Department of Agriculture to help reduce levels of acrylamide, a potential carcinogen, in French fries and potato chips. The multistate project involves plant breeders developing new lines of potato that contain lower amounts of reducing sugars (glucose and fructose) and asparagine, which combine to form acrylamide when potatoes are fried. More than a handful of conventionally bred, low-acrylamide potato varieties are expected to be ready for commercial evaluations within a couple of growing seasons.

“It’s a national effort,” says project manager Paul Bethke, associate professor of horticulture and USDA-ARS plant physiologist. “And by its nature, there’s a lot of cross-talk between the scientists and the industry.”

Working with industry and other partners, CALS researchers are responding to other emerging trends, including the growing interest in sustainable agricultural systems.

“Maybe 50 years ago, people focused solely on yield, but that’s not the way people think anymore. Our crop production people cannot just think about crop production, they have to think about agroecology, about sustainability,” notes Tracy. “Every faculty member doing production research in the agronomy department, I believe, has done some kind of organic research at one time or another.”

Embracing this new focus, over the past two years CALS has hired two new assistant professors—Erin Silva, in plant pathology, who has responsibilities in organic agriculture, and Julie Dawson, in horticulture, who specializes in urban and regional food systems.

“We still have strong partnerships with the commodity groups, the cranberries, the potatoes, but we’ve also started serving a new clientele—the people in urban agriculture and organics that weren’t on the scene for us 30 years ago,” says Goldman. “So we have a lot of longtime partners, and then some new ones, too.”

Working alongside their applied colleagues, the college’s basic plant scientists have engaged in parallel efforts to reveal fundamental truths about plant biology—truths that often underpin future advances on the applied side of things.

For example, a team led by Aurélie Rakotondrafara, an assistant professor of plant pathology, recently found a genetic element—a stretch of genetic code—in an RNA-based plant virus that has a very useful property. The element, known as an internal ribosome entry site, or IRES, functions like a “landing pad” for the type of cellular machine that turns genes—once they’ve been encoded in RNA—into proteins. (A Biology 101 refresher: DNA—>RNA—>Protein.)

This viral element, when harnessed as a tool of biotechnology, has the power to transform the way scientists do their work, allowing them to bypass a longstanding roadblock faced by plant researchers.

“Under the traditional mechanism of translation, one RNA codes for one protein,” explains Rakotondrafara. “With this IRES, however, we will be able to express several proteins at once from the same RNA.”

Rakotondrafara’s discovery, which won an Innovation Award from the Wisconsin Alumni Research Foundation (WARF) this past fall and is in the process of being patented, opens new doors for basic researchers, and it could also be a boon for biotech companies that want to produce biopharmaceuticals, including multicomponent drug cocktails, from plants.

Already, Rakotondrafara is working with Madison-based PhylloTech LLC to see if her new IRES can improve the company’s tobacco plant-based biofarming system.

“The idea is to produce the proteins we need from plants,” says Jennifer Gottwald, a technology officer at WARF. “There hasn’t been a good way to do this before, and Rakotondrafara’s discovery could actually get this over the hump and make it work.”

While Rakotondrafara is a basic scientist whose research happened to yield a powerful application, CALS has a growing number of scientists—including those involved in the corn phenotyping project—who are working at the exciting new interface where basic and applied research overlap. This new space, created through the mind-boggling advances in genomics, informatics and computation made in recent years, is home to an emerging scientific field where genetic information and other forms of “big data” will soon be used to guide in-the-field plant-breeding efforts.

Sequencing the genome of an organism, for instance, “is almost trivial in both cost and difficulty now,” notes agronomy’s Bill Tracy. But a genome—or even a set of 1,000 genomes—is only so helpful.

What plant scientists and farmers want is the ability to link the genetic information inside different corn varieties—that is, the activity of specific genes inside various corn plants—to particular plant traits observed in the greenhouse or the field. The work of chronicling these traits, known as phenotyping, is complex because plants behave differently in different environments—for instance, growing taller in some regions and shorter in others.

“That’s one of the things that the de Leon and Kaeppler labs are now moving their focus to—massive phenotyping. They’ve been doing it for a while, but they’re really ramping up now,” says Tracy, referring to agronomy faculty members Natalia de Leon MS’00 PhD’02 and Shawn Kaeppler.

After receiving a large grant from the Great Lakes Bioenergy Research Center in 2007, de Leon and Kaeppler decided to integrate their two research programs. They haven’t looked back. With de Leon’s more applied background in plant breeding and field evaluation, plus quantitative genetics, and with Kaeppler’s more basic corn genetics expertise, the two complement each other well. The duo have had great success securing funding for their various projects from agencies including the National Science Foundation, the U.S. Department of Agriculture and the U.S. Department of Energy.

“A lot of our focus has been on biofuel traits, but we measure other types of economically valuable traits as well, such as yield, drought tolerance, cold tolerance and others,” says Kaeppler. Part of the work involves collaborating with bioinformatics experts to develop advanced imaging technologies to quantify plant traits, projects that can involve assessing hundreds of plants at a time using tools such as lasers, drone-mounted cameras and hyperspectral cameras.

This work requires a lot of space to grow and evaluate plants, including greenhouse space with reliable climate control in which scientists can precisely measure the effects of environmental conditions on plant growth. That space, however, is in short supply on campus.

“A number of our researchers have multimillion-dollar grants that require thousands of plants to be grown, and we don’t always have the capacity for it,” says Goldman.

That’s because the Walnut Street Greenhouses, the main research greenhouses on campus, are already packed to the gills with potato plants, corn plants, cranberries, cucumbers, beans, alfalfa and dozens of other plant types. At any given moment, the facility has around 120 research projects under way, led by 50 or so different faculty members from across campus.

Another bottleneck is that half of the greenhouse space at Walnut Street is old and sorely outdated. The facility’s newer greenhouses, built in 2005, feature automated climate control, with overlapping systems of fans, vents, air conditioners and heaters that help maintain a pre-set temperature. The older houses, constructed of single-pane glass, date back to the early 1960s and present a number of challenges to run and maintain. Some don’t even have air conditioning—the existing electrical system can’t handle it. Temperatures in those houses can spike to more than 100 degrees during the summer.

“Most researchers need to keep their plants under fairly specific and constant conditions,” notes horticultural technician Deena Patterson. “So the new section greenhouse space is in much higher demand, as it provides the reliability that good research requires.”

To help ameliorate the situation, the college is gearing up to demolish the old structures and expand the newer structure, adding five more wings of greenhouse rooms, just slightly north of the current location—out from under the shadow of the cooling tower of the West Campus Co-Generation Facility power plant, which went online in 2005. The project, which will be funded through a combination of state and private money, is one of the university’s top building priorities.

Fortunately, despite the existing limitations, the college’s plant sciences research enterprise continues apace. Kaeppler and de Leon, for example, are involved in an exciting phenotyping project known as Genomes to Fields, which is being championed by corn grower groups around the nation. These same groups helped jump-start an earlier federal effort to sequence the genomes of many important plants, including corn.

“Now they’re pushing for the next step, which is taking that sequence and turning it into products,” says Kaeppler. “They are providing initial funding to try to grow Genomes to Fields into a big, federally funded initiative, similar to the sequencing project.”

It’s a massive undertaking. Over 1,000 different varieties of corn are being grown and evaluated in 22 environments across 13 states and one Canadian province. Scientists from more than a dozen institutions are involved, gathering traditional information about yield, plant height and flowering times, as well as more complex phenotypic information generated through advanced imaging technologies. To this mountain of data, they add each corn plant’s unique genetic sequence.

“You take all of this data and just run millions and billions of associations for all of these different traits and genotypes,” says de Leon, who is a co-principal investigator on the project. “Then you start needing supercomputers.”

Once all of the dots are connected—when scientists understand how each individual gene impacts plant growth under various environmental conditions—the process of plant breeding will enter a new sphere.

“The idea is that instead of having to wait for a corn plant to grow for five months to measure a certain trait out in the field, we can now take DNA from the leaves of little corn seedlings, genotype them and make decisions within a couple of weeks regarding which ones to advance and which to discard,” says de Leon. “The challenge now is how to be able to make those types of predictions across many environments, including some that we have never measured before.”

To get to that point, notes de Leon, a lot more phenotypic information still needs to be collected—including hundreds and perhaps thousands more images of corn ears and cobs taken using flatbed scanners.

“Our enhanced understanding of how all of these traits are genetically controlled under variable environmental conditions allows us to continue to increase the efficiency of plant improvement to help meet the feed, food and fiber needs of the world’s growing population,” she says.

Sidebar:

The Bigger Picture

Crop breeders aren’t the only scientists doing large-scale phenotyping work. Ecologists, too, are increasingly using that approach to identify the genetic factors that impact the lives of plants, as well as shape the effects of plants on their natural surroundings.

“Scientists are starting to look at how particular genes in dominant organisms in an environment—often trees—eventually shape how the ecosystem functions,” says entomology professor Rick Lindroth, who also serves as CALS’ associate dean for research. “Certain key genes are driving many fantastically interesting and important community- and ecosystem-level interactions.”

How can tree genes have such broad impacts? Scientists are discovering that the answer, in many cases, lies in plant chemistry.
“A tree’s chemical composition, which is largely determined by its genes, affects the community of insects that live on it, and also the birds that visit to eat the insects,” explains Lindroth. “Similarly, chemicals in a tree’s leaves affect the quality of the leaf litter on the ground below it, impacting nutrient cycling and nitrogen availability in nearby soils.”

A number of years ago Lindroth’s team embarked on a long-term “genes-to-ecosystems” project (as these kinds of studies are called) involving aspen trees. They scoured the Wisconsin landscape, collecting root samples from 500 different aspens. From each sample, they propagated three or four baby trees, and then in 2010 planted all 1,800 saplings in a so-called “common garden” at the CALS-based Arlington Agricultural Research Station.

“The way a common garden works is, you put many genetic strains of a single species in a similar environment. If phenotypic differences are expressed within the group, then the likelihood is that those differences are due to their genetics, not the environment,” explains Lindroth.

Now that the trees have had some time to grow, Lindroth’s team has started gathering data about each tree—information such as bud break, bud set, tree size, leaf shape, leaf chemistry, numbers and types of bugs on the trees, and more.

Lindroth and his partners will soon have access to the genetic sequence of all 500 aspen genetic types. Graduate student Hilary Bultman and postdoctoral researcher Jennifer Riehl will do the advanced statistical analysis involved—number crunching that will reveal which genes underlie the phenotypic differences they see.

In this and in other projects, Lindroth has called upon the expertise of colleagues across campus, developing strategic collaborations as needed. That’s easy to do at UW–Madison, notes Lindroth, where there are world-class plant scientists working across the full spectrum of the natural resources field—from tree physiology to carbon cycling to climate change.

“That’s the beauty of being at a place like Wisconsin,” Lindroth says.

Want to help? The college welcomes your gift toward modernizing the Walnut Street Greenhouses. To donate, please visit: supportuw.org/giveto/WalnutGreenhouse. We thank you for your contribution.
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