Corn Conundrum

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

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

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

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

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

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

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

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

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

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

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

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

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

In the Field: Alumni Making Their Mark in Veterinary Medicine

Daryl Buss MS’74, PhD’75

Daryl Buss grew up on a small Minnesota farm where he enjoyed daily work with a variety of animals. On the farm, Buss quickly realized the importance of the local veterinarian and regarded him as an early role model. This early fascination with veterinary medicine propelled Buss down a path of academic accomplishments, beginning with a veterinary medicine degree from the University of Minnesota and followed by a lifetime of accomplishments at UW–Madison. Buss received his master’s degree from the Department of Veterinary Science in 1974 and rolled straight into his Ph.D., focusing his research on the cardiopulmonary system. From there, Buss held a variety of academic and research positions at numerous institutions such as the Max Planck Institute for Physiological and Clinical Research in Germany and the University of Florida, Gainesville. In 1994, Buss returned to Madison and was hired as the dean of the UW School of Veterinary Medicine. He served for 18 years and helped solidify the school’s position as one of the top professional schools of veterinary medicine in the country. Today, Buss utilizes his years of expertise as the editor-in-chief of the Journal of Veterinary Medical Education. “After many years in academic administration, this role has offered a new and complementary venue for continued national and international engagement with veterinary medical education,” Buss says.

Kris Ellingsen BS’79

Spending your workday surrounded by fluffy felines may sound like a fantasy for cat lovers, but for Kris Ellingsen it’s just another day at the office. As a veterinarian with a special interest in cat care, Ellingsen enjoys interacting with both the feline patients and their owners while helping make cats better understood and cared for properly. Her journey to feline medicine began at age 16 with her first job, working for a local veterinarian — a job she kept while pursuing her CALS undergraduate degree in bacteriology. After the UW School of Veterinary Medicine (SVM) opened in 1983, Ellingsen realized she could combine her passion for medicine with her love for animals. She applied and was accepted into the Class of 1988. After graduation from the SVM, she headed to the Pacific Northwest, where she spent 11 years in Seattle and the past 18 in Portland, Oregon. In Seattle, Ellingsen found her ideal position at Cats Exclusive Veterinary Center, one of the first feline-only clinics in the U.S. She currently lives in Portland, where she works as a veterinarian for Cat Care Professionals. Aside from her daily veterinary medical practice, Ellingsen has also been involved with the non-profit Feral Cat Coalition of Oregon since 2001. In 2008, she was elected president of the organization, which helps to feed, treat, and spay or neuter more than 6,000 feral and stray cats annually

Kathy Huntington MS’91

If you ask Kathy Huntington how she chose a career in animal pathology, she may argue that it chose her. “Pathology is like a big puzzle to figure out, and I love that challenge,” she says. “That, along with my love of wilderness and wildlife, makes it a pretty amazing combination for me.” In hindsight, it seems like an obvious fit, but her path to pathology wasn’t so simple. Huntington began her career with a degree in zoology before coming to the UW–Madison campus, where she received a D.V.M. followed by a master’s degree in veterinary science and wildlife diseases. She relocated to Alaska upon graduation and began practicing as a small animal veterinarian. After a few short years, Huntington was sure of two things: she loved Alaska, but she was not content as a small animal veterinarian. Luckily, her degree in wildlife diseases was there to rekindle a forgotten passion and jump-start her career in wildlife pathology. Huntington now works as a diagnostic pathologist and owner of Alaska Veterinary Pathology Services. There she acts as a consultant and research pathologist on projects with marine and wildlife agencies such as the Alaska Department of Fish and Game, the U.S. Geologic Survey, and the U.S. Fish and Wildlife Service. In the field, Huntington is able to learn all about the diverse species that inhabit what she calls one of the United States’ most transformative and scenic states.

Travis Kuhlka BS’03

Travis Kuhlka became interested in animal agriculture when he was a freshman in high school. He accepted a job at a local hog farm, where he found his niche caring for sows and piglet litters. When it came time to choose a career, Kuhlka stuck to his experience and pursued a bachelor’s degree in animal sciences from CALS. Here he worked as a large animal reproduction technician for a campus lab and acted as the head student veterinarian at the UW–Madison Veterinary Medical Teaching Hospital. This clinical experience solidified his career path into veterinary medicine. Upon graduation, Kuhlka applied to the UW School of Veterinary Medicine, where he earned his D.V.M. Today, Kuhlka lives in North Dakota and practices as a large animal veterinarian through his private company TK Veterinary Services. Though his technical training is in veterinary medicine, Kuhlka credits CALS for his foundational skills, such as how to safely handle cattle, relate to farmers’ lifestyles, and understand clients’ needs. “I attribute my background in livestock handling to my relationships and experiences with those in the Department of Animal Sciences,” Kuhlka says.

Gayle Leith MS’85

Gayle Leith says she has achieved her childhood dream. “I grew up in southern California riding horses and was fortunate to realize my career goals as an equine veterinarian at a very young age,” she says. Leith earned her master’s degree in veterinary science and D.V.M. at UW–Madison. Today she is an owner and partner of an equine referral practice through Arizona Equine Medical and Surgical Centre. There she acts as a self-named “family practitioner for horses,” making routine and emergency visits to stables. But these stables aren’t always nearby. Once a year, Leith organizes a group of veterinarians and hikes into the Grand Canyon to provide veterinary medical care to the horses of the Havasupai Tribe. “My favorite part of my work is helping horse owners maintain the health of their fourlegged friends,” Leith says. Now a seasoned veterinarian, Leith enjoys passing on her expertise to students and interns. In 2010, Leith took her passion for teaching a step further by completing a master of arts degree in learning with technology, and she has been teaching an undergraduate science class at Ashford University ever since. Keeping horses healthy and happy may be her dream, but Leith also enjoys a rewarding life outside of the office. She loves to travel and enjoy the outdoors with her husband, Preston, and daughter, Jordyn, but horses never stray too far from her mind. Some of her favorite equine activities include trail rides with her family and training her young thoroughbred gelding for the show ring.

David Lunn MS’87

David Lunn was born in Wales and received his bachelor’s degree in veterinary science at the University of Liverpool in 1982. After spending two years practicing as a veterinarian, he ventured to America and earned his master’s degree in veterinary science from UW–Madison. In 1988, he returned to the U.K. and received his Ph.D. from the University of Cambridge in 1991. Just a year later, Lunn became a certified diplomate of the American College of Veterinary Internal Medicine and returned to UW–Madison. Here he served as a professor in the School of Veterinary Medicine for nine years before accepting a job as an associate dean and director of the UW–Madison Veterinary Medical Teaching Hospital. Today, Lunn serves as the dean of the North Carolina State College of Veterinary Medicine. He is a renowned expert in equine immunology and infectious disease, backed by more than 90 academic publications, 16 book chapters, and service on countless boards, committees, and review panels. At NC State, he enjoys a busy but exciting career. As the veterinary medical college’s dean, Lunn is responsible for many, many things, but student education continues to be his top priority. “Our most important role is making better vets,” he says. “We are constantly trying to find ways to improve education at every level and find the best opportunities for these young people.” Even the busiest careers require occasional rest and relaxation. In his downtime, Lunn hikes with his wife, Kathy, raises terrier pups, and skis inexpertly but enthusiastically

Fermentation Education

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Class Act: Kai Rasmussen — ‘Let’s Grow Plants in Space’

Kai Rasmussen BSx’18 spends much of his time studying how plants react to being in outer space. For many of his friends, this calls to mind Mark Watney, the protagonist in the novel-turned-movie The Martian, who devised a way to grow potatoes in a failing space station on the Red Planet’s surface. And Rasmussen agrees. So he wrote a song about it.

Visit Rasmussen’s SoundCloud web page and you’ll find “Young Mark Watney,” an original composition filled with references to the emerging (but still relatively obscure) field of astrobotany. It’s punctuated by a simple chorus that underscores his mission: “Let’s grow plants in space.” For Rasmussen, a junior majoring in biology, this musical venture is just one way he hopes to engage the public in his passion.

Rasmussen’s interest in astrobotany was ignited after taking a class with UW–Madison botany professor Simon Gilroy and learning about his research in the field. Rasmussen soon began working in Gilroy’s lab, where he was offered funding by literal rocket scientists.

“There was just no way I could pass up the opportunity to work on something funded by NASA,” Rasmussen says.

The lab’s research involves mimicking spaceflight using an in-house test structure, but it also integrates the real thing. In 2014 and late 2017, the Gilroy lab sent plants to the International Space Station, and the genetic data beamed back to Earth revealed how enzymes in the plants were affected by the journey.

Scientists have knocked down numerous long-standing barriers to sustainable spaceflight, but many remain. Botany and horticulture systems are critical components of life on Earth, but they evolved over billions of years. Creating similar systems from scratch in space requires some creative solutions.

Cue forward thinkers like Rasmussen.

“We don’t want to send supplies from Earth every time our astronauts need to eat,” he says. “We want them to have self-sustaining systems that provide them with food [and] water.”

But that’s a long-term project. Meanwhile, Rasmussen has created an astrobotany website and T-shirt — all in an effort to bring the science of space plants back down to Earth.

Mongoose Tracker

Imagine if squirrels were fearless and rabid and preyed upon your pets rather than the acorns in your yard. In Puerto Rico, this is quite common. The small Indian mongoose — a sleek, fierce, weasel-like critter — has been troubling the island for decades, yet little is known about this invasive species and how to control it.

Diana Guzmán-Colón PhD’18, a doctoral student in the Department of Forest and Wildlife Ecology and a Puerto Rican native, is no stranger to these animals. Through her work at UW–Madison’s SILVIS Lab, she has chased her childhood curiosity and dedicated the last five years of her life to making sense of these mysterious carnivores.

They may be modest in size, typically measuring about two feet from snout to tail, but small Indian mongooses have a large impact on Puerto Rico. Native to India, they were first introduced to the island in the 1890s by sugar plantation owners to hunt rats. Since then, the mongoose population has exploded while expanding its menu to include native birds, amphibians, and domestic animals like cats, chickens, and small dogs. These attacks frighten and infuriate citizens. Today, the mongoose is so common in Puerto Rico that locals often refer to them as squirrels.

The small Indian mongoose, first introduced to Puerto Rico by sugar plantation owners, has been plaguing the island for decades.

Local and federal agencies have tried to keep the mongoose population in check, but because they are aggressive and often rabid, most strategies have failed. “Mongooses are an extremely resilient invasive species and seem to be unaffected by past control measures,” says Guzmán-Colón.

By tracking the mongoose population, Guzmán-Colón hopes to uncover how the species has spread throughout Puerto Rico, where they thrive, and where they may go next. But how do you keep tabs on an entire community of such elusive little creatures? Guzmán-Colón believes the answer lies in their DNA.

By live-trapping and collecting samples from local mongooses, she will be able to piece together a web of genetic relations similar to a family tree. These relationships can shed light on their population structure and movement patterns throughout the island and indicate where the species is successful. From there, Guzmán-Colón can help identify which mongoose populations should be priorities for management measures.

Since Hurricane Maria ravaged the island in September 2017, Guzmán-Colón has faced a new set of challenges in both her professional and personal life. Thankfully, her family was unharmed, but such an environmental disturbance will certainly affect her research. Still, she remains optimistic.

“The storm was devastating to Puerto Rico, but I try to see this as a rare opportunity for science,” says Guzmán-Colón. “It isn’t every day that researchers are able to observe the reemergence of an entire ecosystem.”

As for the mongooses, Guzmán-Colón sees a possible boom in their population. “Mongooses live in burrows underground, are efficient scavengers, and reproduce quickly. My prediction is that they’ll be unaffected by or benefit from the hurricane.”

All the more reason for further research.

A Precise Hope

Mason Konsitzke is 7. He loves food (especially when he can share it with others) and anything military (both of his grandfathers served). He likes to fly kites and play with his 5-year-old sister, Alexandra. But Mason was born with a disease called neurofibromatosis type 1, or NF1, and each day can present new challenges for him and his family.

NF1 is a genetic disease caused by changes, or mutations, to a single gene in the human DNA library. Roughly one out of 3,000 babies born in the United States has it. That’s more than three times the incidence of cystic fibrosis, a much better-known condition. Yet few people have heard of NF1.

Mutations in the NF1 gene cause defects in the neurofibromin 1 protein, which acts as a tumor suppressor. Children with NF1 can develop painful tumors along their nerve tracts, sometimes in their skin and in their eyes, which can render them blind. They are often diagnosed with autism spectrum disorder, though not all children with NF1 also have autism, and they are sometimes diagnosed with attention deficit hyperactivity disorder. They may have soft bones that bend and break easily. They are at a higher risk for cancer. And there is no cure.

It was not a disease Mason’s parents, Charles and Malia Konsitzke, had ever heard of. As a newborn, he was healthy, but when Mason was 6 months old, the couple began to suspect something was wrong. Mason developed coffee-and cream-colored spots all over his body, which his father later learned are a hallmark of NF1. Mason received a genetic diagnosis of the disorder just before his first birthday.

“We were like deer in the headlights,” Malia says. “We were in shock, wondering, what does this mean for us? What does it mean for Mason?”

At 18 months, Mason began to lose his ability to speak. He was falling over, screaming constantly, and deliberately banging his head. That’s when an MRI revealed a tumor called a plexiform neurofibroma in a mesh of nerves in the left side of his face. It was growing fast.

A Father and Science Facilitator

Charles (who goes by Chuck) is a research administrator and the associate director of UW–Madison’s Biotechnology Center, a sort of one-stop shop for scientists in need of DNA sequencing, genome editing, and other services.

Upon Mason’s diagnosis, he began to delve into published NF1 research. He wanted to know where it was happening, who was doing it, and how he might be able to help. He sought opinions from experts, wondering how the field could be improved. Many identified the same bottleneck: the lack of a good research model.

In biology, research models are animals, cells, plants, microbes, and other living things that allow scientists to study biological processes and re-create diseases in order to better understand them. Good models yield information relevant to humans, but the right model can sometimes be difficult to find.

A breed of pigs called Wisconsin Miniature Swine was created by a team of UW–Madison scientists to help better model and understand human diseases, including NF1. Photo by Jeff Miller

NF1 is especially complex, affects many systems of the body, and touches many areas of scientific inquiry, from cancer research to neurobiology. Chuck began to search for a better model and, in 2013, when Mason was 3, he settled on pigs. Pigs are similar to humans in many ways that other common research animals, such as mice and fruit flies, are not. That includes their size, which means drugs and devices that work on humans can also be tested on pigs. They have a robust immune system, which rodents lack. And they’re intelligent, so scientists can study changes in their cognition.

Knowing all of this, Chuck went on the hunt for researchers who studied swine.

Braving the Risks

Dhanansayan (Dhanu) Shanmuganayagam BS’97 PhD’06, assistant professor of nutrition and animal sciences at CALS, has spent most of his career using swine to study human diseases, particularly heart disease. In fact, he and colleagues in the animal sciences department created the Wisconsin Miniature Swine, a pig that, like people, can develop heart disease under the right conditions.

Dhanansayan “Dhanu” Shanmuganayagam describes his research during a Neurofibromatosis Type 1 (NF1) symposium for patients and families held at the UW–Madison Health Sciences Learning Center in May 2017. Photo by Jeff Miller

Dhanu’s office was a few blocks from Chuck’s, but they’d never met until a few years ago, when they bumped into each other while helping to campaign for the new UW Meat Science Laboratory. They got to know each other, and Chuck asked Dhanu whether he had ever heard of NF1. He hadn’t. Chuck told him about Mason, about the need for a better model, and about the promise that pigs offered to help understand and treat the disease. Then he asked Dhanu if he would join forces to help create that model.

Taking some time to think about it, Dhanu consulted the members of his laboratory who would all be helping to forge this new path. His risks would be their risks. A pig model could fail, leading them all down a blind alley.

Dhanu told Chuck he was in.

The risks remain significant, Dhanu says, “but I’ve come to terms with it, and it’s fine. I’ve been lucky in my career to work on things that have gone to clinic. If it works, it’s going to be impactful.”

There aren’t many places in the world where this kind of work — melding basic science with clinical research and a large animal model like swine — is possible. UW–Madison has large biomedical research centers, the capacity for high-powered basic science, and a 1,500-pig research facility called the Swine Research and Teaching Center (SRTC) in Arlington, a 35-minute drive from campus.

“It’s a brave new frontier, to move into swine,” says David H. Gutmann, a physician and researcher at the Washington University School of Medicine in St. Louis, who is considered one of the foremost NF1 experts in the world. “I’m glad they’re doing this work at UW–Madison because the combination of specialized resources and expertise are found in very few places worldwide.”

Like Scissors for Genes

Seen through a microscope, researcher Kathy Krentz guides a micro-needle to inject DNA into one of several pig embryos at UW–Madison’s Biotechnology Center. Photo by Jeff Miller

Dhanu and Chuck determined that the course they wanted to chart included gene editing using a powerful new tool known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. The genetic technology is reshaping basic biological research. Like a pair of molecular scissors, CRISPR enables scientists to target a stretch of cellular DNA for alteration. They can cut out pieces of DNA or swap out letters in the genome, changing the message it encodes or shutting off genes entirely.

The two set their sights on creating pigs that carry the NF1 mutations they and other researchers are most interested in studying. “But we had to figure out where to start,” Dhanu says. “It’s like learning to fly a space shuttle.”

With Dhanu’s lab manager and lead scientist Jen Meudt at the helm, the team dove in. But the challenges were many. They had to learn about swine reproduction, about CRISPR and gene editing, how to perform the necessary surgeries on pigs, how to time events so no step of the process failed and ruined all the efforts before it. Again and again, they hit roadblocks.

It took more than a year, but finally, they came up with a plan: The researchers would use artificial insemination to impregnate a female pig carefully primed to produce more eggs than she naturally would. Shortly after fertilization, they would remove the embryos, whisk them to the Biotechnology Center, and inject them with a solution containing the gene-editing CRISPR. This would have to be done quickly, while the embryos were still a single cell. This way, when the single cell divided, all the subsequent cells would contain the NF1 mutation. (Inject too late and the pig would develop into a mosaic of cells that contain the mutation and those that do not.) Then it would be off to the surrogate mother, a pig chosen to reproductively match the embryo-donating pig. The researchers would perform surgery to implant the CRISPR embryos into her womb. If all went well, months later she would give birth to piglets, at least some of which would carry the desired NF1 mutations.

A few months passed. On Nov. 7, 2016, Chuck and Dhanu were meeting in Madison with a group from the Neurofibromatosis (NF) Network, which supports NF1 research and clinical care. They were sipping coffee when a text came in from Jen: “The mom carrying NF piglets is delivering right now.”

The piglets — eight in all, and four with the NF1 mutation — were a living embodiment of the team’s hard work. They had proved that they could create pigs genetically engineered to carry the disease. It was an emotional experience for the scientists, involving tears and prayers. They immediately went out to celebrate.

Then they set to work building on that success. One of the four piglets with the mutation is a male. Mason named him Tank. His job is to sire more piglets with the mutation since the changes conferred by CRISPR were designed to be passed on from generation to generation.

The team took the process they’d developed and applied it to other NF1 mutations, including some related to cancer. And they set an even more ambitious goal: precision medicine. In other words, a pig personalized for every child with NF1.

With CRISPR, the researchers believe they can take the genetic fingerprint of an individual child’s NF1 mutation and create a pig with that same mutation. They can then test potential medications and treatments and see if they’ll work. Can tumors, like the one that afflicts Mason, be shrunk?

The Promise of Precision

By the time Mason reached prekindergarten, the tumor in his face had grown into his cranial sinus. His parents were told he could lose his sight and his ability to taste. Surgery wasn’t an option. It was too risky and could leave Mason in even greater pain, permanently. “He’s literally been in pain his whole life,” Malia says.

Then, for reasons doctors couldn’t explain, the tumor stopped progressing. He regained his speech and no longer screamed or struggled to stay upright. His doctors keep a close watch on the tumor with MRI scans. They continue to work to determine the best medication regimen for the other symptoms that come with his particular variant of NF1. His treatment must be continuously modified.

Mason still exhibits some of the behavioral challenges often associated with NF1, which for him began at age 3. At age 5, he was diagnosed with autism. His parents say that, although it’s relatively late to get such a diagnosis, it opened up more therapeutic doors. Most doctors and insurance companies are unfamiliar with the social and behavioral implications of a NF1 diagnosis, but autism is well recognized and the need for early intervention well studied. Mason now sees an occupational therapist and speech-language pathologist in and out of school and a psychiatrist several times each year.

The therapy helps, but managing Mason’s disease has also taken a toll on the family. In 2016, with “everything fraying at the edges,” Malia says, the couple decided she would take time off from work to help refocus and slow down. She prepared to resign from her job working for a school district; instead, they offered her a one-year leave of absence. It provided the family the respite they needed, but it also presented a significant financial strain. “We laugh a lot because you have to,” Chuck says.

Alexandra and Mason Konsitzke play with their parents, Chuck and Malia Konsitzke, at the family’s home in Stoughton, Wis. To help the family face the challenges of living with NF1, Chuck says, “We laugh a lot, because you have to.” Photo by Jeff Miller

Laughter is just one way to cope with a disease with so many different faces. NF1’s unique manifestations make each child and each child’s treatment plan experiments unto themselves. But pigs develop faster than children do, so they offer the possibility of helping to predict how NF1 might affect a particular child, enabling parents, doctors, teachers, and others to prepare. Earlier intervention for a child who develops autism could lead to better outcomes. Doctors could start working to find drugs to treat tumors before they grow too large.

“Precision medicine is more than matching the right drug to the right gene. With NF1, it’s more complicated and involves searching for the factors that make each individual with NF1 unique,” says Washington University’s David Gutmann. “This is an amazing opportunity to find the risk factors that put an affected child at risk for developing a brain tumor, a bone defect, or another serious complication of NF1.”

Dhanu, Chuck, and Jen are not doing this work on their own. The team now includes many talented individuals like Biotechnology Center scientists C. Dustin Rubinstein, Kathy Krentz, and Michael Sussman, along with Jamie Reichert, manager of the Swine Research and Teaching Center, and his team. And there’s now a broader research group, the UW NF1 Translational Research team, which includes Thomas Crenshaw, an animal sciences professor and department chair, and Marc Wolman, a professor of integrative biology.

They have also enlisted the skill and knowledge of Neha Patel, a pediatrician at the UW–Madison School of Medicine and Public Health who treats about 150 children with NF1 in Wisconsin and surrounding regions.

Dhanu hopes to make the NF1 pigs accessible to other researchers around the country, charging only what it costs to produce them. And the team plans to use the pigs to help identify metabolic and cellular pathways common to the variety of NF1 mutations to help target and develop better drugs.

But to accomplish all of this requires funding.

“We’re at a critical moment,” Dhanu says. “We have to turn our successes into funding opportunities.”

The UW NF1 Translational Research team has bootstrapped most of its work so far, relying primarily on funding and donations from the NF Network. Most of that comes from an annual charity golf tournament the Konsitzkes and four other families help organize and run. Called Links for Lauren, the tournament honors Lauren Geier, an 8-year-old girl in Madison with NF1.

Finding funding for rare diseases through federal agencies like the National Institutes of Health can be challenging. However, families can play a surprisingly influential role in the fight against rare diseases.

“They often provide critical resources and financial support at the earliest stages of a highrisk project, when funding from federal agencies is not possible,” David Guttman says. “Our families, they inspire us because they ask us to do things that are really meaningful and take risks by taking the roads not frequently traveled. Through their involvement, they can move the field forward in ways that no one else can.”

‘Where There’s Research, There’s Hope’

Larry Britzman had no idea there were pigs at UW–Madison that might one day help children like his 12-year-old daughter, Mackenzie. He learned that, and much more, in May when he traveled to campus from La Valle, Wisconsin, for a symposium for NF1 patients and their families.

“I didn’t realize each child is specific,” he says. “I didn’t realize UW has swine research and there aren’t too many facilities in the country researching NF1.”

The NF1 team hopes to host the symposium each year, to invite families to learn more about the science of NF1, to give them a chance to meet researchers and clinicians, and to ask questions and meet other families living with the disease.

“We’ve gone very far in two years because it hasn’t been just about building a model, it’s also been about creating a community around it,” Dhanu says.

Larry Britzman and his 11-year old daughter, Mackenzie, who has NF1, talk to health advocate Lindsay Geier during the NF1 symposium. Photo by Jeff Miller

The opportunity to work so closely with and on behalf of the people who may ultimately benefit from his work is not something he’d ever experienced. And he has found it profoundly rewarding.

Not long ago, he invited a family into his lab whose college-aged daughter has NF1. They’d been donors to NF1 causes for years but had never talked to a researcher. “It meant a lot to them, and my first thought was: ‘How can we do more of this?’”

He and his lab members now participate in running events like the Madison Half Marathon, often with the NF Team organization, to raise money for NF1 research and to increase awareness. The runners sport neon yellow performance shirts with bold, black lettering. They also participate in the annual charity golf tournament.

“As scientists, we don’t often see the payoff of what we’re working on,” Dhanu says. “It redefines our research priorities, and it also aids discovery. The best people to note observations are the people who live with it.”

To him, success can be measured by individuals. “Even if our research just raises awareness and someone gets treated because of what we do, that alone is big,” he says.

Chuck believes the disease is underdiagnosed because very few people are genetically tested for it, and most physicians are not familiar with it. So they may diagnose patients with autism or a behavioral disorder and miss the broader picture.

That has frustrated Danielle Wood, a teacher and mother of two who lives in Reedsburg, Wisconsin. Her daughter, Bernadette, is 2 and was diagnosed with NF1 as an infant. Along with springy blonde curls and an arresting smile, Bernadette has a weak abdominal wall, which causes her pain and may require surgery. She wears braces to support her frail ankles.

Danielle, too, has NF1. Her mother had it and so did her grandmother. Though her condition is mild — she simply wears glasses for poor vision caused by a tumor on her optic nerve — deciding whether to have children was hard. Because it is a dominant mutation, Danielle and her husband had at least a 50 percent chance of giving birth to a baby with the disease. Having grown up with NF1, Danielle felt she had a good idea of what to expect. She now sees herself as an advocate for Bernadette.

“While things never move as fast as we want them to, there’s a tremendous amount of exciting progress in this field, and where there’s research, there’s hope,” David Gutmann says. UW–Madison is “in a really great position because (it has) young faculty who are excited and a patient community that is challenging them to improve the lives of people with NF1 through research.”

This is what drives Chuck, Dhanu, and the rest of the UW NF1 Translational Research team, which is working to establish a NF1 Center for Excellence at UW–Madison. Not only is this possible, David says, it is necessary. “There is no established therapy for NF1 and no magic bullet that works for all kids or adults. The challenge for us is to learn more about this disorder so that personalized and effective treatments emerge.”

Moreover, he says, what NF1 teaches researchers will inform their approaches to other conditions, like some types of cancer. And he’s excited to see what the future holds.

“All of us in the NF field get up every morning and are excited to get to work. What we learn from our colleagues and our families each day brings us one step closer to that better future for children and adults with NF,” he says. “I can imagine getting up every morning and running to work to see what’s happening with those pigs.”

For Mason, pigs — including Tank — don’t play much of a role in his daily life today. Instead, he continues regular visits to therapists and other professionals to help him manage his symptoms. He also benefits from the support of his family, from Chuck and Malia to aunts and uncles who have learned all they can about NF1. And the family dog, Donatella, is his packmate, Malia says. But at 7, Mason can still take all of that for granted and focus on what he loves best. Like sharing the tastiest mini pizzas he can make. He would absolutely love it if you tried one.

Gut Dwellers

Fermentation Fest

Fermentation Fest, sponsored by the Wormfarm Institute, is an annual celebration of “live culture” held in Sauk County. These scenes are from the 2017 fest, where Federico Rey gave a presentation on the human gut microbiome. Photos by Katrin Talbot MS’85

The second floor gallery of the Wormfarm Institute in Reedsburg, Wisconsin, is a far cry from the funky glassware and biosafety protocols of a working microbiology lab. One corner contains an improv kitchenette, circa 1987. Sprout — the mascot offspring of the Jolly Green Giant — waves improbably from behind a cubicle wall across the room; the child-size plastic statue is missing a hand. A cool draft of autumn rain and small-town traffic noise flows through an open window.

Assistant professor of bacteriology Federico Rey chats with his Wormfarm hosts as more than three dozen attendees of the annual Fermentation Fest assemble into a casual arc of folding chairs and a couple of vintage couches. These are people who already understand the idea of microbes as friends. Makers of coleslaw and kimchi, kombucha and beer — they are motivated by microbes and have paid to hear Rey’s summary of the state of current human microbiome research.

Across the life sciences, the microbiome is the buzziest of buzzwords, invoking a symphony of hope, hyperbole, and high expectations. Rey shares in the overall enthusiasm, but he is careful about the speculative details. Yes, the microbiome might even match our frothiest expectations. And no, he can’t cure your diabetes or make you leaner, faster, or smarter. He can’t even tell you if your microbiome is healthy. Not today.

Because nobody can.

In front of a large wall hanging of textile orange circles representing the bubbles of fermentation, he begins where he has to begin, very near the beginning. “Microbes are the most abundant form of life on this planet,” he says, his thick Argentinian accent backlit by a docent’s enthusiasm. “They can live in places where we cannot imagine life.”

“Microbes outnumber us by many orders of magnitude. They power almost everything on the earth,” he says. They convert as much carbon dioxide into organic compounds as plants do and emit more methane than the oil and gas industry. “Literally, there is no place on earth where there are no microbes,” he continues.”It is impossible to get rid of them.” And despite our germophobia, they’re mostly good company: “A very small fraction of microbes are pathogens. Most of them are commensal — they don’t do good or bad — or they are beneficial for humans.” These last ones, the microbes that fuel our fantasies of easy cures and everlasting health, truly capture Rey’s interest.

Every surface on our bodies is colonized by some kind of microbe, and microbiologists have identified thousands of species of bacteria that can inhabit the human gut. Each of us, in turn, has a collection of between 100 and 200 different bacteria strains, comingled with other life forms from fungi and protists to viruses and archaea. These enteric ecosystems — different for every single human, even more unique than a fingerprint — each contain 100 times the genetic information of our own cells. They both supplement and interact with our bodily blueprints.

Deciphering who’s who is not even half the problem. How exactly do our bodies gather these microbes? What shapes the resulting ecosystem? How do humans and microbes interact? In 2017 alone, Rey published new research about microbiome effects in diabetes, Alzheimer’s, and the cycling of the nutrient choline (which may positively affect fetal brain development but also can lead to heart disease later). “Every single disease or health condition scientists look at, they find a microbiome connection,” he says.

And yet there is no single definition of a healthy microbiota. And what is healthy for you may not be healthy for me.

Research Revolution

Federico Rey arrived in the United States in 1999 with advanced biological questions on his mind and little idea that microbes could hold the answer. As a research fellow at the Henry Ford Health Sciences Center in Detroit, he focused on hypertension and vascular disease. But when he moved to the University of Iowa for his Ph.D. in 2001, he met Rhodopseudomonas palustris during a lab rotation. These extravagantly versatile bacteria are known for their ability to use four different modes of metabolism to scavenge energy, nitrogen, and carbon from a variety of sources — with or without oxygen. Intrigued by the diversity and adaptability of microbes, Rey says he fell in love with the bacterium.

R. palustris was an obvious stepping-stone towards biofuels. But in 2005, Rey saw a talk by Jeff Gordon, a pioneer in the study of human-microbiome interactions. Gordon began examining the development of the mammalian gut in the 1980s. Eventually he realized that microbes were essential to the process, and he set out to untangle this complex relationship using early sequencing techniques and transgenic and germ-free mice.

Rey joined Gordon’s lab at Washington University in St. Louis as a postdoc in 2006 just as microbiome science was gaining momentum. Tools for reading the genetic code were getting faster, cheaper, and more versatile. Computers used to crunch burgeoning data sets were growing in power as new statistical methods were increasing in sophistication.

One of the earliest hints of the power of microbes was that transplanting the microbiome from one mouse to another could also transfer basic metabolic conditions, such as obesity. It was in Gordon’s lab that Rey first met CALS professor of biochemistry Alan Attie — through the microbes of his mice. In Attie’s efforts to unravel the many mysteries of diabetes, his lab sent Gordon microbiome samples from genetically distinct mice that had been placed on a high-fat or a chow (i.e., grain-based) diet. It was known that both diet and genetics had a significant effect on the metabolic health of these mice. Gordon helped to show that the microbes played a role as well.

Rey took the project with him when he was hired by CALS in 2013, and he’s been collaborating with Attie since. It’s a task of daunting complexity: integrate two genetically complex systems that play a role in metabolic disease. Neither is close to being perfectly understood, yet they interact with each other, coalescing in each individual.

Hundreds of mammalian genes are already understood as part of the metabolic pathways that go awry on the way to diabetes. The human microbiome, meanwhile, produces thousands of chemicals that act within the genetic framework of humans. We’ve long understood how these microbes help us break down the complex compounds in the plant-based foods we eat, providing about 10 percent more energy. More recently, we’ve learned how these microbial bioreactors produce molecules called short-chain fatty acids — acetic acid, propionic acid, butyrate, and other products of fermentation that signal our bodies in health-promoting ways.

Our bodies sense these molecules, helping regulate things like gastrointestinal motility. Less well understood are the thousands of chemicals that train our immune system and help regulate everything from kidney function to brain chemistry.

“This is one of the most important aspects of the microbiome that is revolutionizing biology,” Rey says. But unraveling the interplay between host genetics and metabolism is anything but easy.

Julia Kreznar inspects a germ-free mouse while performing cage maintenance. Sterile germ-free mouse facilities on the UW– Madison campus provide a controlled model in which to study the interactions of microbial communities within mammals and how they impact anatomy, physiology, behavior, and susceptibility to disease. Photo by Michael P. King

In the Rey lab, senior scientist Bob Kerby holds two sealed test tubes (left) containing a pure strain of bacterium from a human fecal sample. The cloudy sample has been incubated for 24 hours; the clear sample has just been prepared. The Petri dish holds the bacterial colony. Photos by Michael P. King

In work published in Cell Reports in 2017, Rey’s student Julia Kreznar used eight different mouse strains and microbial transplants to help unravel this tangled web. The study found measurable differences in the microbiome established in the different strains. These microbes, in turn, influenced the likelihood that the mice would succumb to metabolic disease. The work also demonstrated a novel link between the gut microbiome and insulin secretion.

“We can show that microbiota affected pancreatic islet physiology and function,” Kreznar says. It’s a promising step, but it’s also an indirect interaction. Identifying the mediators of these microbe-host interactions is really challenging.

“It’s the dawn of a new field,” Attie says. “We have 3 or 4 pounds of organisms that are producing so many molecules, and we don’t know the least of them.”

“I’m feeling daunted,” he admits. “We had this idea that we would potentially connect the dots genetically. It is enormously complex, and it’s hard. It’s harder than we even thought it was going to be.”

A Big Genetic Black Box

Back in Reedsburg, Rey knows the probiotic question is coming, so he makes a preemptive strike: “When I talk about microbiota, I’m not talking about probiotics. The probiotics that you can get at Walgreens are basically microbes from dairy, microbes that can live in milk. Microbes that are not adapted to live in our intestines.”

If the microbiome has taught him anything, it’s that generalizations are tricky. “If they work for you, you should continue,” he emphasizes, trying to claim middle ground. Because of course, probiotics are microbes, and there actually is a lot of evidence that some may provide immune benefits.

But you won’t get a better microbiota by eating probiotics, and if you don’t eat your yogurt on Saturday, by Sunday those yogurt microbes are pretty much gone. They just pass through. “The effect is good as long as you keep eating them. And that is the perfect model for a company, right?” he says, with a tone of innocent mischief.

But if you look at probiotics through the lens of the microbiota, you have to acknowledge this essential truth: It’s been a landmark decade, but we still don’t have tools that are sophisticated enough to measure the microbiota in sufficient detail. We still don’t have an adequate biological understanding of what makes a healthy microbiota. And we barely understand the complex dance these microbes do with our body. Add in the fact that probiotics are dietary supplements, and thus not well regulated.

“You have to be careful. You have to do your research,” Rey says. “There are many different strains of probiotics, and there are big differences between different strains.” This is further complicated by the difficulty of even properly identifying bacteria, which can evolve rapidly. “There is a big difference between George Clooney the actor and somebody named George Clooney who lives in Atlanta. They have the same name, but they are completely different people,” he explains. “There are thousands of strains of Lactobacillus rhamnosus. Some may have an effect. Many of them probably don’t.”

In fact, it is our ability to identify these subtle differences in microbes that sparked the current revolution in microbiome science. First came 16S ribosomal RNA. Essential to the construction of proteins, 16S changes very slowly, which allowed scientists to, finally, reliably identify the members in a microbial community.

We talk about DNA as the book of life. At first, just reading a few pages was a chore. Then we developed machines to read more pages, faster. Then we learned how to read the sequels: DNA makes RNA, which makes proteins and enzymes responsible for carrying out cellular processes, including the making and breaking of sugar for energy. The technology responsible for reading these interrelated genetic codes is called next-generation sequencing, and it has powered this first golden age of microbiome research. The challenge now is sifting through that data to find biological meaning. Postdoc Lindsay Traeger PhD’15 is one of Rey’s primary number crunchers. “I’m attracted to very broad questions that we can throw a data hammer at and see what falls out,” she says.

Right now Traeger is focused on the next stage of collaboration with Attie and several other UW–Madison faculty including Joshua Coon (biomolecular chemistry), Karl Broman (biostatistics and medical informatics), and Brian Yandell (statistics). “We know that the gut microbiome is influenced by diet,” Traeger says. “But there is also this genetic component, which is a black box.”

Using genetically distinct mouse strains is advantageous when you’re trying to model a particular disease. But if you’re trying to tease out broader biological principles, using a single strain of mice could lead to bias. That’s why the labs are using a special breed called Diversity Outbred, a strategic genetic mash-up of common lab strains and some wild strains.

In one hand, Traeger has the genetic code of each individual mouse. And in the other, she has the genetic code of the microbiome of each mouse. Using advanced statistics, she’s searching for patterns that suggest some molecular matchmaking.

A germ-free mouse in its sterile quarters on the UW–Madison campus. Photo by Michael P. King

“I’m trying to identify how the host is selecting for or deselecting for the presence and abundance of certain microbial functions. Because the microbes are interacting somehow with the host.” One gene of interest is responsible for creating the important immune protein TNF-alpha, which plays roles in cancer and autoimmune disease. Early returns suggest that the TNF gene is also involved in sensing and responding to bacteria that have flagella.

Of course, the TNF gene is only one of about 23,000 genes, while the genes associated with bacterial flagella are just a few out of potentially hundreds of thousands. With numbers that big, there’s a lot of noise to filter out. And lots of distractions. “It’s a little hard to focus,” she laughs. “I think I could just spiral off. [Rey] keeps me thinking about the biology.” Rey’s endless creative energy helps. “He’ll just bust into the office and say, ‘I have this idea!’”

The immensity of the black box also keeps the work exciting. “We do think we’re going to find some interesting examples of interaction of host and microbiome,” she says.

Two T-Bones a Day

The microbiome is a dynamic force. Change the diets of lab mice, and overnight the communities that live in their gut change dramatically. So why care what microbes are in your gut if you can switch it up that quickly?

Rey points to his classic Argentinian upbringing as an example. “I grew up eating a T-bone for lunch and a T-bone for dinner,” he says. “Twenty-five years. And I miss it very much,” he quips, evoking another laugh from his audience. “But if I became vegetarian long term, I would definitely select for different microbial communities. And I would likely have new microbes colonize me.”

But even while your gut community is adaptable, the microbes in your gut can also have long-term consequences. That T-bone? “There are components in meat that microbes love and that cause problems,” Rey warns. “But you might not have them.” Which could mean several things: You’ve never been exposed to them, or you’ve been exposed but they didn’t take. Or maybe they’re there, but other microbes keep them in check. All of those are open biological questions, which now makes nutrition even more complicated.

In 2011, Stanley Hazen of the Cleveland Clinic published a paper linking microbes to the breakdown of lipid phosphatidylcholine (lecithin) into several choline-related compounds, particularly TMAO (trimethylamine N-oxide), a chemical already found to be a strong predictor of heart disease risk. Specifically, microbes metabolized choline into trimethylamine (TMA), which is then converted in the liver to TMAO.

While diet is a big part of this risk — eggs, milk, liver, red meat, poultry, shellfish, and fish are major dietary sources — the combination of microbial and host biology leading to TMAO accumulation intrigued Kymberleigh Romano PhD’17, who decided to dig deeper for her doctoral work with Rey and was co-mentored by Daniel AmadorNoguez, an assistant professor in bacteriology with expertise in metabolomics. Despite years of lab experience, she’d never worked with lab animals before, but she knew the time had come. “A lot of the phenotypes we study exist only in the context of a host-microbe interaction,” she says. “A test tube is never going to develop heart disease.”

First she needed microbes. Harvard researcher Emily Balskus had identified the genes involved in microbial conversion of choline to TMA, and Romano began looking for them in human-associated microbes and constructing experimental mixes of microbes. As she tinkered she found that, in mice at least, you need a TMA producer present in the intestinal microbiota to see TMA accumulation. And as you add more TMA-producing species, less choline is left for the host.

Even though she’d narrowed down the difference to a single organism in her custom microbiota, it still wasn’t enough. One bacterium contains anywhere from 3,000 to 5,000 genes — that’s a lot of variables. Fortunately, her collaborator from Harvard had identified a genetically tractable choline consumer and knocked out the TMA production gene. “Now the only difference in my communities was a single gene.”

Cardiovascular risk aside, choline is an underappreciated nutrient contributing to the process of epigenetic regulation of gene expression, and those without enough of it are more likely to suffer metabolic disease. In mice and rats, there is even a two-day window during pregnancy where lack of choline can impact fetal brain development. “Biology is never simple,” says Romano. “If it’s simple, you’re missing something.”

Eat Your Vegetables

Talking about poop makes people laugh, and as Rey wraps up in Reedsburg, the crowd has stayed engaged, surviving even his brief foray into 16S sequencing.

His advice for microbial health is folksy and charming. “Spouses share more microbes than people that don’t live together,” Rey tells the crowd. “We have found that spouses who get along together share more microbes than spouses that don’t. There is a lot of exchange going on there.” (In fact, if you’ve had to take antibiotics, he suggests family time will do more to restore your microbes than probiotics.)

And, noting that the most diverse microbiomes are found in places like the Amazon, he says being exposed to dirt is probably a good thing. “Get your hands dirty working in your garden,” he says. “I think that’s a health habit that we have lost over the years.”

Still, stubborn ideas persist among those gathered in the room. About a dozen times people bring up their pet microbiome theories for validation: probiotics, kombucha, fermented food, raw food, red wine vinegar, minimal vegetable washing, fecal transplants.

“The microbiome has come to mean anything you want it to mean,” Rey says disarmingly, for another laugh.

But “I don’t know” is his most honest answer. It’s a conundrum: The microbiome is hot in part because of some stunning findings. Most remarkable is the use of fecal transplants to cure drug-resistant Clostridium difficile infections, with cure rates running above 90 percent in some studies.

That extraordinary outcome certainly got the attention of both the medical community and the fad diet community. And even as it validates the power of the microbiome, that outcome actually runs against the grain of all the variation Rey is trying to figure out. “My lab is very interested in understanding the consequences of our interpersonal differences,” he explains.

“I can sequence your microbes, and I would not be able to tell you what vegetables to eat,” he says. “Maybe in 5 or 10 years personalized nutrition will be a reality, but it is not today. The one recommendation we can give right now is try to think about feeding your microbes. Because we cannot tell you what will be the best for your microbiota.”

In other words, eat your vegetables. Let’s say you eat pizza, with regular flour dough and cheese. Your body can digest every single ingredient of that pizza. By the time it reaches your large intestine, where most of your microbes live, your body has absorbed everything of nutritional value.

“You’re not sharing any of your food with your microbes,” he explains. “That’s one of the things we are doing with our Westernized diets: we are starving our microbes.”

“Maybe broccoli is the best for your microbiota whereas cabbage is the best for my microbiota,” he concludes. “But in general, if you eat a diverse diet that contains plant polysaccharides, eventually you are going to help the good guys

New Resources for Discovery

Dean Kate VandenBosch

The University of Wisconsin–Madison is a mighty force for research by many measures, from its life-changing discoveries to its global reputation for scientific excellence. Yet another measure is the extent to which the university sustains its research enterprise.

In recent years, successive cuts at the state level have reduced UW’s overall budget, making the prioritization of core activities a major challenge. This hinders our ability to attract research funding, and the impact of this trend can be seen in national rankings. Between 1972 and 2014, the National Science Foundation (NSF) consistently ranked UW–Madison among the top five institutions in research expenditures. In 2015, following a steady four-year decline in those numbers, the university slipped to sixth place.

In response, Chancellor Rebecca Blank has called for a significant reinvestment in UW in a variety of ways. This means greater legislative and private support, but it also means the campus needs to find new, stable revenue streams. To boost our research endeavors, campus leadership has developed new seed funding mechanisms. These programs are designed to help our scientists do the arduous preliminary work that is necessary for securing major grants from large government agencies and nonprofits.

Today, we seem to be on the right track. In 2016, UW–Madison’s research expenditures rose, and the university’s NSF ranking held steady. Another encouraging fact: faculty, staff, and students at CALS are making the most of these new opportunities.

For example, the UW2020 Initiative was established in 2015 to fund high-risk, high-impact projects. Selected proposals receive an average award of $300,000 for two years, and CALS projects have been among the winners in all three rounds. In fact, in 2017, one third of the awardees hailed from CALS, with projects in areas ranging from artificial intelligence in dairy farm management to the role of the human gut microbiome in health and disease.

Speaking of the microbiome, UW’s Microbiome Initiative was established in 2017 with goals similar to that of UW2020. But it was also designed to encourage interdisciplinary work in an area where UW has a high concentration of expertise. Twelve of the 13 microbiome proposals selected for funding involve CALS faculty, many of them as principal investigators. These projects, covering topics such as how gut microbes might influence Alzheimer’s disease and the role of the tomato’s microbiome in pathogen resistance, have the potential to make transformative discoveries.

UW2020 and the Microbiome Initiative are both made possible by funding from the Wisconsin Alumni Research Foundation and other sources. But university funds will support yet another program to encourage interdisciplinary work that will make UW–Madison more competitive in garnering extramural research support. Over the next three to five years, around 70 faculty will be hired in 20 different strategic “clusters” — groups of scholars, chosen for their shared research interests and specialties, who can collaborate and pool resources from where they are situated in departments across campus. A campus committee is now reviewing proposals for these clusters, and many touch upon areas of expertise that can be found in abundance at CALS. I look forward to updating you on this initiative in the future.

I know that our exceptional researchers will continue to experience great success with these programs. Their efforts will keep CALS in the vanguard of the agricultural and life sciences while helping UW–Madison retain its traditional place as a premier research university. I am excited for what the future holds.

Winter Awakens Spring Flowering

Rick Amasino
Photo by Frederic Bouche

It’s springtime in Wisconsin again. Home gardeners and farmers are busy tending to their beds and fields, relishing the fresh sprouts of flowers, vegetables, and crops. It begs the question: What happens in the inner workings of plants as they prepare for spring? What’s the science that governs the growing season for different flora?

Rick Amasino, a plant biochemist and professor in the Department of Biochemistry, may have the answers — or at least some of them. He studies plant development and, specifically, how and when plants produce flowers. In 2016, his expertise earned him a place on a National Academies of Sciences, Engineering, and Medicine committee tasked with investigating the impacts of genetically engineered crops.

Many plants have effectively evolved a way to avoid flowering prior to winter. Instead, they use the cold season to help activate flowering when the weather warms. Amasino’s research sheds light on what conditions a plant must experience in order to flower. In particular, he focuses on unraveling the genetic basis of the effects these conditions have on plants as they stimulate or repress flowering. His findings may allow other scientists and plant breeders to develop crops that are more efficient and have higher yields of food or energy.

How do plants respond to spring?

There are a wide range of responses. For example, some plants need to be exposed to winter cold to flower in the spring, whereas others form spring flowers as a result of being exposed to the decreasing hours of sunlight during the fall season. Apple and cherry trees are in this latter category — their flowers are actually formed in the previous fall in buds that become dormant. Then, when it gets warm the following spring, everything that was crammed into those buds in the fall just unfolds. Other plants like lilies, for example, require exposure to cold in order to flower. When they are growing in the fall, flowering is blocked. But over winter, the block is removed and they flower in the spring. The underlying processes for this involve a lot of biochemistry, and that’s what we’ve studied in my lab. Specifically, we study how flowering is blocked in the fall and how exposure to cold results in the removal of this block. The block removal process is known as vernalization; this word is derived from vernal, which means “relating to spring.”

Are there any more examples of plants that need winter to flower?

Some common examples include many of the vegetables we plant in the spring, such as cabbage, carrots, and beets. We don’t usually see these particular vegetables flowering because they will not flower until they experience winter, and we harvest them before they have a chance to flower. Many grasses go through this process as well.

Why should we be interested in this process?

This requirement to go through winter in order to flower is important agriculturally; food plants keep growing without flowering all summer long and, therefore, the part which we consume can get very large. However, if you left a carrot in the ground after the summer, it would flower the next spring, and the underground part of the carrot we eat would become shriveled as it provides the nutrients for flowers to form.

If it gets warmer earlier, is that a problem?

An early warming trend in itself isn’t problematic if it continues into spring, but our climate is likely to be more variable than that. So, if we have unusually high temperatures late in the winter and cherry blossoms in Door County open, but then we get a blast of cold afterward, the flowers will be destroyed and fruit cannot form.

What’s going on on the inside of the plant that determines whether or not it flowers?

In the plants we study that require winter, there is a gene encoding a repressor protein that is expressed in the fall that prevents the plant from flowering. Then, over the winter, control of the repressor gene is altered in a way that the repressor is no longer expressed. Consequently, plants can flower when it gets warm, and they resume growth in the spring in the absence of the repressor protein. We’ve recently published research specifically on the small Mediterranean grass called Brachypodium. Previous work has shown that a gene called VRN1 is responsible for activating flowering in these grasses after the winter. But what’s the repressor gene keeping VRN1 in check in the fall? That was previously unclear. We did genetic screens and found several of the genes that repress the VRN1 gene prior to winter. We just published a scientific paper on one of these, calling it RVR1, for its role in repressing VRN1.

Why are gene discoveries like this important for this area of research?

Scientists that breed cereal grains may find this newly identified gene interesting. However, we think it could also impact biofuels research. I am part of the U.S. Department of Energy’s Great Lakes Bioenergy Research Center (GLBRC) here on campus. Although switchgrass, which can be used to make biofuels, doesn’t go through the vernalization process, there’s a good chance that taking the RVR1 gene from Brachypodium and putting it in switchgrass will delay switchgrass flowering. Delaying switchgrass flowering to various extents may improve yield.

Why is understanding this process important?

In basic research like ours, we often don’t know where exactly it’s going, but it often ends up having practical relevance. Our goal is to understand the biochemical pathways that plants have evolved to flower at certain times of the year. But in crops, in which the timing of flowering is important, this research can be applicable. For example, we share our unpublished work with wheat breeders who can translate some of the knowledge into increased efficiency in a breeding program. Also, our work has revealed basic principles of how genes are regulated, which has implications for many areas. Another example of applicability, although not directly from our research, was useful for sugar beet farmers, who plant in the spring. A spring cold spell will trigger some of the sugar beets to flower, and flowering plants do not produce the part of the beet the farmers harvest. Scientists in Europe modified genes involved in the flowering response to cold and came up with a sugar beet variety that doesn’t flower if it is exposed to cold. Now farmers can plant their beets in the fall rather than the spring to allow them to have a much longer growing season and to grow bigger — and they don’t have to worry about the beets flowering. This has significantly increased the yield per acre of sugar beets.

What’s your next step in this research?

We are going to continue to work with other GLBRC researchers to study Brachypodium and how different varieties of the plant live and persist in winters that have varying temperatures and lengths. How did one variety evolve a system tweaked to require 16 weeks of cold? Why does another one require just two weeks of cold? In other words, what’s the genetic and biochemical difference between the requirement for a short winter versus a long winter? Grasses are really important crops, and this model for studying flowering can tell us a lot about how they work

Catch up with … Anna Snider BS’98 Horticulture

Anna Snider’s recent volunteer work has taken her to Nigeria, Bangladesh, and beyond, but her love of horticulture and farming started in Wisconsin. She grew up in a rural area outside of Fond du Lac, where she served as president of the local FFA chapter and spent most of her time outside — either in the garden or at her uncle’s and grandparents’ farms.

At UW–Madison, Snider immersed herself in her horticulture major. She became president of the university’s Horticulture Society and organized its first tour of Costa Rica with the help of faculty mentor Jim Nienhuis PhD’82. That trip marked the first of many related to the world of international agriculture. As a volunteer with the USAID-funded Winrock International Farmer-to-Farmer program, she travels to developing countries all over the world to provide technical assistance for farmers, farmers’ organizations, and agribusinesses.

How did you become interested in working in agriculture and Farmer-to-Farmer learning?

After my undergraduate degree, I worked for horticulture professor Jiwan Palta, and that was my first job with international experience. I managed projects in Wisconsin, California, Ecuador, and Florida, and it prepared me for international work. During my master’s degree work, I became fascinated with the social issues that affect agriculture and food security in developing countries. I wanted to understand the reality in these countries, including how agribusinesses and consumers in developed countries can have a positive influence on environmental and social conditions. When I started working for Cornell Cooperative Extension, I felt that there was really a lack of experience in sustainable agriculture in many places, and I wanted to help.

What have you done on your trips with the organization?

My earlier projects focused mainly on sustainable production practices and composting. Those projects were in Kyrgyzstan, Lebanon, and Bangladesh. In Nigeria and Senegal, I worked with the leaders of farmers’ organizations on strategic planning, leadership, and engaging women and youth in entrepreneurship. Farmers’ organizations in these countries rely heavily on funding from the government or support from nonprofit organizations, and we work together to figure out how they can become more self-reliant and resilient.

What do you like best about the work?

I love working with farmers to solve problems. I also love that it gives you opportunities to see places, interact with locals, and understand the country in a way that you never could if you were just traveling. For example, in Senegal, I was invited to the hut of the village chief to discuss challenges and concerns with the administrative council of the local banana cooperative. The group was quite frank about the problems of trust or conflict among the members and how they deal with that according to their cultural traditions of arbitration with tribal elders. It was fascinating.

Farmer-to-Farmer is always looking for volunteers. Visit to find opportunities.