Spring 2014

Cover Story

Photos by Wolfgang Hoffmann BS'75 MS'79

1. The Genomics Revolution

When CALS geneticist Fred Blattner sequenced the genome of a harmless strain of E. coli back in the mid-1990s, it was a big deal. The bacterium was among the earliest organisms to be sequenced, and the effort, which landed a high-profile article in Science in 1997, took years to complete and involved the participation of more than 269 people.

Genetics professor Fred Blattner.

How times have changed.

“Now you can just send something like that to a sequencing center and one person can do the work overnight,” says genetics professor Audrey Gasch, who joined UW–Madison in 2003 as part of a strategic hiring initiative to bolster research in genomics, the field of science that looks at the full set of DNA within organisms.
Over the years, UW researchers have also helped sequence the genomes of potatoes, corn (maize), multiple strains of mice, the leaf-cutter ant, the plant pathogen that caused the Irish Potato Famine and 99 strains of cold virus, among others.

Beyond sequencing itself, CALS researchers are using genomic information to:

• study molecular evolution,

• better understand virulence genes in pathogens,

• find genes involved in human health and disease,

• develop an optical map of the bovine genome,

• locate genes associated with infertility in dairy cows, and much more.

Gasch, in one bioenergy-related project, compares the genomes of traditional laboratory yeasts to those of their wild relatives in order to pinpoint the genes that make the wild strains more stress tolerant.

“Down the line, this information will help us make customized yeast strains that are optimized to produce different types of biofuels,” she says.

New dairy barn at CALS’ Arlington Agricultural Research Station.

2. Bigger, Better Dairy

The last 25 years of dairy research, education and outreach at CALS have driven progress and productivity gains in the Wisconsin dairy business. Since 1989, average milk production per cow per year has climbed 57 percent, from 14,000 pounds to nearly 22,000 pounds per cow today. The state’s dairy farmers reversed a 16-year decline in milk production in 2005. In the last nine years they have boosted annual output by 25 percent, producing a record 27.7 billion pounds in 2013.

These gains, the result of a combination of advancements in cow genetics, reproductive management, nutrition and facilities; adoption of professional management techniques; and a well-educated, receptive group of dairy producers, have revitalized dairying in the Dairy State.

CALS scientists developed mechanisms to mine the bovine genome and then put the results in the hands of dairy producers. Researchers refined and produced the tools needed to take advantage of genetic knowledge with novel methods for breeding and selecting cattle. Dairy nutritionists at UW–Madison probed feedstuffs and the rumen to create total mixed rations that enable cows to produce to their full genetic potential.

Biological systems engineers, veterinarians and dairy scientists collaborated to develop new bedding and stall types to keep cows comfortable and productive. A complementary mix of educational resources—statewide UW–Extension programs, CALS Farm and Industry Short Courses, and campus teaching facilities and faculty—helped dairy farmers learn and adapt the new technologies to their needs. That extensive research and outreach network gives dairy producers access to the latest and most sophisticated management practices—a partnership that promises to keep Wisconsin dairy strong.

3. Coping with the Climate

CALS researchers were part of an international team studying how changing levels of carbon dioxide and ozone affect forest ecosystems, using these plots in northern Wisconsin.

CALS scientists had our changing climate on their radar screens 25 years ago, but it wasn’t on their research agendas. Today the issue influences work being done in every corner of the college. CALS scientists are studying climate impacts at the ends of the earth, in the Lake Mendota basin and everywhere in between. They’re looking at the big picture (using satellites) and small (using genomic sequencing). They’re looking under tree bark and inside the guts of dairy cows, and they’re looking at impacts on the human animal—on farmers’ management practices, for example, and the migration patterns of residents of low-lying coastal areas.

To name some examples: soil scientist Jim Bockheim is looking at whether warming will turn permafrost in Antarctica from a carbon sink to a carbon source, while wildlife ecologist Christine Ribic investigates what melting sea ice means for Adelie penguins. Forest ecologist Phil Townsend and entomologist Ken Raffa are studying the climate-fueled spread of tree-killing bark beetles into new habitats in the Rocky Mountains, while entomologist Rick Lindroth studies how rising levels of carbon dioxide affect forest tree susceptibility to a variety of insects. Soil scientist Matt Ruark leads a multistate project to help dairy farmers reduce their carbon footprint and adapt to weather extremes.

And Chris Kucharik, a climate scientist on the agronomy faculty, helps lead a campus-wide effort to model the impact of climate change on water quality, water quantity and crop yields right where he lives—in the Yahara River watershed—over the next 60 years. Kucharik also serves as co-chair of the agricultural working group with the Wisconsin Initiative on Climate Change Impacts (WICCI), a partnership between UW–Madison, the Wisconsin Department of Natural Resources and an array of other public and private institutions.

These are but a few highlights. It is safe to say that researchers in every CALS department are working in some way on mitigating or adapting to the impacts of our changing climate.

4. Cross-Cutting Studies

There’s a growing trend on campus toward interdisciplinary learning, and it’s highly evident at CALS.

Consider the college’s newest majors: agroecology, introduced as a graduate degree program in 2006, and environmental sciences, which debuted for undergraduates in fall 2011. Or such programs as the Undergraduate Certificate in Global Health, which launched in fall 2011 through the department of nutritional sciences and is open to students from all majors, and the Integrated Studies in Science, Engineering and Society (ISSuES) certificate, which has enjoyed steady CALS student participation since its inception in 2009.

Agroecology students visiting Fantome Farm.

Demand for learning that crosses disciplines reflects a “millennial mindset,” observes Sarah Pfatteicher, CALS associate dean for academic affairs. Many students are interested in addressing the big global issues of our times (depleting energy sources, changing climate and threats to food security, to name a few examples). “They’re driven to pursue an education because they’re driven by grand societal challenges rather than necessarily by a specific career path,” she says.

That kind of thinking is nurtured by CALS faculty, many of whom have long-standing affiliations with the Nelson Institute for Environmental Studies or shared appointments and other close working relationships with various departments and units across the college and campus.

“A lot of the faculty we hire, their research cuts across departments or doesn’t fit under neat labels that we’ve had for the 125-year history of the college,” notes Pfatteicher. “And so we continue to see faculty interest in teaching and advising and thinking about curricula in ways that cut across departments and colleges.”

The college formally adopted an interdisciplinary approach to teaching, research and outreach in its new strategic plan. Under the leadership of Dean Kate VandenBosch, with participation and input from all corners of CALS and the statewide CALS community, the plan identifies the following areas as CALS’ “priority themes”: food systems, bioenergy and bioproducts, healthy ecosystems, changing climate, health and wellness, and economic and community development.

Pursuing those themes is nothing if not an interdisciplinary effort, VandenBosch says: “I’m expecting we’ll see more new courses and programs that harness the energy of our students who want to cross disciplines to develop better solutions.”

5. The Skinny on Obesity

Mice, fat and slim.

In 1982, a discovery by Dale Schoeller, now a CALS emeritus professor of nutritional sciences, turned the scientific community’s understanding of obesity on its head.
Previously, it was believed that obese people had a low-energy requirement, meaning they burned off calories more slowly than others. But when Schoeller, who was at the University of Chicago at the time, applied a technique known as the doubly labeled water method to measure human energy expenditure, he proved this pervasive hypothesis false.

“This group actually had the same energy requirement, or even a little bit higher, but had been under-reporting their caloric intake on surveys,” says Schoeller.
This paradigm shift changed obesity researchers’ assumptions, helping to point many research projects in the proper direction.

Biochemistry professor James Ntambi

Over the past two decades, scientists—including a number from CALS—have also made great progress understanding the role that genes play in obesity. Biochemist James Ntambi, for one, cloned and studies the SCD-1 gene, which produces an enzyme critical in how the body stores fat. Mice that lack SCD-1 can eat a high-calorie, fat-laden diet but put on virtually no weight.

Fellow biochemist Alan Attie discovered the gene responsible for diabetes susceptibility in obese mice, and nutritional sciences professor Eric Yen is probing the effects of MGAT, a gene involved in energy metabolism.

While drug companies seek a weight loss pill based on this kind of work, it’s heartening that obesity rates seem to have leveled off—though at 35 percent of the U.S. adult population.

“People are starting to pay attention,” says Schoeller. “They are choosing a healthier lifestyle—walking more and eating better.”

6. Bioenergy Booms

Nearly 10 years ago, when the U.S. Department of Energy (DOE) was considering how best to jump-start efforts to convert biomass into biofuel, it convened scientists from UW–Madison and Michigan State University (MSU) at a workshop to identify critical research gaps.

Bioenergy researcher at work in the lab of bacteriology professor and GLBRC director Tim Donohue. Photo by Lauree Bacque

DOE awarded CALS $125 million over five years to pursue those questions, establishing the Great Lakes Bioenergy Research Center (GLBRC) in 2007 in partnership with MSU and involving a number of other institutions on and off campus. It was the largest federal grant the college had ever received.

GLBRC and other bioenergy researchers have found a new home at the Wisconsin Energy Institute, and their work already has yielded numerous discoveries. Among their achievements:

• Advancing the understanding and use of lignin, a tough compound in plant cell walls that must be broken down to release sugars for processing into biofuel. New enzymes have been discovered to aid in its breakdown, modified plants are in trials, and pretreatment methods have opened the door to using lignin as a valuable co-product.

• Designing pretreatment and conversion processes in tandem. When creating fuels biologically, yeast are often sensitive to the by-products of the fermentation process, including ethanol itself. Working together, yeast experts and engineers have reduced the processing time and improved yeast to better tolerate those conditions.

• Reimagining the dairy farm as a potential biorefinery in which manure is separated and converted into products ranging from biogas and fertilizer to useful chemicals and bio-plastics, animal bedding, mulch and starting material for ethanol fermentation.

• Committing to economic and environmental sustainability—a cornerstone of the GLBRC’s mission—by producing data on such topics as the impact of biofuel crops on biodiversity, bioenergy crop yield and the feasibility of growing biofuel crops on marginal lands.

More discoveries are under way. The center recently was awarded $125 million from DOE to continue for another five years.

7. The Rise of Organic

Harvesting at Tipi Produce, an organic farm in Evansville owned by Steve Pincus BS’90

When the late Josh Posner, a CALS professor of agronomy, began field trials at the Arlington Agricultural Research Station in 1989 growing crops using a diverse rotation, minimal applications of fertilizer and pesticides, and other “low input” methods, he was also launching one of CALS’ first major efforts to support organic farming. The Wisconsin Integrated Cropping Systems Trial Project (WICST), still going strong, is one of the nation’s longest-running systems trials including organic management.

That same year, the Center for Integrated Agricultural Systems (CIAS) was founded to serve as an incubator and outreach center to farmers and citizens for the college’s burgeoning sustainable agriculture research programs.

Wisconsin now has more organic dairy farms than any other state and is home to the Organic Valley farmer cooperative, which is approaching
$1 billion in annual sales and enjoys strong participation among Wisconsin producers.

CALS and UW-Extension efforts in organic farming research have both contributed to and grown with that boom, inspiring interdisciplinary collaborations from agronomy, horticulture, soil sciences, plant pathology, entomology, dairy science and other departments as well as undergraduate courses in organics to help develop future leaders, notes Erin Silva, who joined agronomy in 2006 as the college’s first dedicated organics researcher.

Optimizing organic management practices and plant breeding for organic systems are two areas in which CALS has been particularly strong, Silva says, citing a pasture management project conducted in collaboration with Organic Valley and two organic plant breeding fellowships funded by Seed Matters, an initiative of the nonprofit Clif Bar Family Foundation.

Part of Silva’s job is to foster university–industry partnerships—and she sees more of them happening in the future. “They have definitely increased over the last few years,” says Silva. “As organic producers have been in business for a longer period of time, they’re realizing the need for more research-based recommendations and more advanced management practices.”


In the conservatory of the D.C. Smith Greenhouse.

8. The New CALS Campus

Campus buildings often tell a story about directions in research, education and outreach. If you take a walk along and around Henry Mall, you’ll see facilities opened during the past 25 years that have been key to CALS activities:

• The Genetics–Biotechnology Center Building (1995) on Henry Mall, housing the Biotechnology Center, the Genome Center of Wisconsin, the Center for Nanotechnology and the Laboratory of Genetics, which is comprised of the Department of Genetics (CALS) and the Department of Medical Genetics (School of Medicine and Public Health).

• D.C. Smith Greenhouse (1996) on Babcock Drive, a 10,000-square-foot space used to grow plants primarily for CALS instruction, especially for undergrads. The greenhouse is also used for outreach to learners of all ages as well as public receptions and other events.

• The Microbial Sciences Building (2007) on Linden Drive, home to CALS’ Department of Bacteriology and the Food Research Institute as well as the Department of Medical Microbiology and Immunology (School of Medicine and Public Health).

• The Dairy Cattle Center (2013) on West Linden Drive, a remodeled facility offering a state-of-the-art home to 88 milking cows in a tie-stall barn, established in partnership with the School of Veterinary Medicine and located one block away from the classrooms and laboratories of CALS’ Department of Dairy Science.

• Our newest construction: The Hector F. DeLuca Biochemical Sciences Complex (Henry Mall), which includes the Biochemistry Building, the Biochemical Sciences Building and the Biochemistry Laboratories, each bearing DeLuca’s name. The facilities house members of the Department of Biochemistry in CALS and the Department of Biomolecular Chemistry in the School of Medicine and Public Health. Dedication ceremony on April 24; details at

Nearby and noteworthy:

• The Wisconsin Institutes for Discovery (2010), on North Orchard Street, and the Wisconsin Energy Institute (2013), on University Avenue, serve as home to numerous CALS researchers who have labs and offices there. Many CALS activities for the public take place in both facilities, most notably during Science Expeditions and the Science Festival.

9. Discoveries Hit the Market

The Wisconsin Alumni Research Foundation (WARF), the nation’s first university-based patent and licensing office, was launched with a discovery from CALS. Biochemist Harry Steenbock learned how to fortify food with vitamin D by exposing it to ultraviolet light, an innovation that led to the almost complete eradication of rickets. Steenbock wanted to ensure that proceeds from university-based patents would be invested in further university research—and so WARF was born.

That was last century, but the path from CALS through WARF to the marketplace remains vibrant. We asked the intellectual property staff at WARF to consider significant CALS-based inventions from the past 25 years based on such criteria as benefit to the university, societal impact and staying power. We present a half-dozen standouts*:

1990 Ann Palmenberg (biochemistry)

An RNA translation enhancer to enable the efficient production of proteins outside of cells, offering biotech companies a more effective way to produce commercial-scale amounts of proteins that they can sell for scientific study and other uses.

1996 Mark Cook (animal sciences), Michael Pariza (food science)

Biochemistry professor Hector DeLuca’s pharmaceuticals have been highly lucrative for UW – Madison.
Photo: Wolfgang Hoffmann

Products using conjugated linoleic acid (CLA), a natural fatty acid that has many positive health effects, including preventing body fat accumulation and increasing lean body mass, reducing inflammation and decreasing atherosclerosis. CLA also helps improve feed efficiency and fat quality in animals.

1998 Hector DeLuca (biochemistry)

Zemplar, a prescription drug based on an active form of vitamin D, used to treat renal disease. Zemplar is one of eight pharmaceuticals to have come from the DeLuca lab over a 30-year period (1968–1998) based on the discovery of the vitamin D endocrine system. Altogether they have earned WARF and UW–Madison more than $500 million.

2002 Franco Cerrina (engineering), Michael Sussman (biochemistry), Fred Blattner (genetics)

DNA arrays, chips containing microscopic DNA spots for genetic research. Scientists use DNA chips to measure the gene expression levels of large numbers of genes—thousands of them—all at the same time. This invention simplifies the process of making the chips, making them much more affordable for researchers everywhere.

2004 Eric Johnson (bacteriology)

Highly purified botulinal toxins for the treatment of neurological disorders (including involuntary muscle movements and spasticity) as well as for potential use in removing wrinkles. “Evabotulinum toxin,” as it is called, is now in clinical trials and is being pitched as a longer-lasting, better formulated alternative to Botox.

2005 Brent McCown (horticulture), Eric Zeldin (horticulture), Peter Normington

HyRed cranberry, a high-pigment, high-yield cultivar that matures quickly, thus allowing farmers in cold-weather regions to harvest their cranberries after full development of fruit color.

* Some of these inventions encompass multiple patents; the listed dates represent the year the invention was first licensed or introduced into the market.

10. Growing with GMOs

Twenty-five years ago there weren’t any genetically modified (GM) crops available for farmers to plant. Since then, hundreds of different GM corn hybrids and soybean varieties have been developed, and top performers are grown widely across America’s cornbelt.
How did this explosion happen?

One early advance had a CALS tie-in: CALS-trained plant breeder John Sanford helped jury-rig the first gene gun, a tool to insert foreign genetic material into plants, while working at Cornell.

“It was literally a gun—an air pistol—that he modified to shoot DNA into plant tissues,” says Joe Lauer, a CALS professor of agronomy and UW-Extension corn specialist.
Today the gene gun has largely been replaced by an approach called “bacterial-mediated transformation”—a process whereby natural, DNA-transferring bacteria are used to insert genes into plants—and most GM crop varieties are developed by large agribusiness companies. Yet CALS still does a significant amount of work in this area.

Agronomy professor Heidi Kaeppler, a plant molecular geneticist, runs one of the few public labs that regularly performs GM transformations in crop plants. Much of her work is relatively basic, focusing on understanding how the process works and how to increase its efficiency. On a routine basis, however, her lab also produces GM crops for researchers in the Great Lakes Bioenergy Research Center seeking to develop improved biofuel feedstocks.

Lauer, for his part, has been gathering, assessing and disseminating key performance data about GM corn hybrids for the past 18 years as part of the Wisconsin Corn Hybrid Performance Trials. He recently partnered with researchers in agricultural and applied economics to analyze this huge data set and quantify the value of GM corn for farmers.

Other CALS agronomists are monitoring the rise of herbicide-resistant weeds associated with some types of GM crops, and developing management strategies that farmers can use to minimize their spread.

Last but not least, notes Lauer, “We’re the nation’s largest producer of plant breeders. CALS is instrumental in educating the students who go on to work in the areas of crop breeding, genetics, biotechnology and production.”

11. RNA: More Than a Messenger

The central dogma of biology is often summed up this way: DNA → RNA → Protein

This simple equation describes the flow of genetic information in living organisms: from the genes in our DNA to messenger RNA to proteins—the building blocks of our bodies.

For a long time, messenger RNA, or mRNA, was the only RNA known to science. In recent decades, however, it’s become clear that there are many, many other kinds.

Known by abbreviations such as rRNA, tRNA, snRNA, miRNA, long ncRNA, and siRNA, these other RNAs play similarly critical roles in the body. Some function as the key catalytic components of cellular machines, while others regulate gene expression by binding to particular mRNAs and turning them “off.”

“We now know that there are hundreds of these RNAs that affect gene expression, and we missed them forever. They’re involved in cancer and in other diseases. They’re everywhere,” says biochemistry professor Marv Wickens, who co-founded the RNA MaxiGroup in the late 1990s to bring together the university’s diverse RNA research community.

The RNA MaxiGroup currently includes 32 faculty members who hail from bacteriology, biochemistry, genetics, nutritional sciences and plant pathology, as well as from various medical school units.

They are a powerful force, having made numerous key contributions to the field. To name a few:

• Figuring out the 3-D structures of important protein-RNA complexes that control key events in our cells

• Identifying molecules that degrade specific RNAs or deploy them for new purposes

• Discovering families of proteins that modify and control RNAs and play important roles in stem cells

The list goes on and on—and it’s getting longer every day.

Wisconsin became an artisan cheese mecca over the last two decades. Photo courtesy Wisconsin Milk Marketing Board

12. Wisconsin Cheese Gets Artisanal

It’s hard to believe, but at the time of CALS’ centennial there was no such thing as a Wisconsin Master Cheesemaker. That certification program, launched in 1994, marked the renaissance of a Wisconsin specialty cheese industry that now encompasses 55 Master Cheesemakers and more than 600 kinds of cheese, and accounts for 22 percent of Wisconsin’s cheese production.

And the market is still growing. Production of specialty cheese in Wisconsin in 2012 totaled a record 611.2 million pounds, up 6 percent from 574.9 million pounds in 2011. In terms of quality, Wisconsin specialty cheeses—which include both artisan dairy (handmade products made in small batches) and farmstead dairy (products made on the farm from milk produced by cows on that farm)—regularly win top awards at national and global competitions.

This exciting new sector was cultivated with care, and a number of players contributed to its success. Chief among them was the CALS-based Wisconsin Center for Dairy Research (CDR), which shares its cutting-edge findings and innovations with the cheese industry through both product development assistance and hands-on training. The CDR partnered with the Wisconsin Milk Marketing Board to offer Wisconsin Master Cheesemaker certification, a rigorous three-year program unique to Wisconsin, as a way to both brand the state’s artisan cheese and ensure the highest level of expertise in the people making it.

Other key players in developing the specialty cheese sector include the Wisconsin Department of Agriculture, Trade and Consumer Protection, which ensures food safety and quality, and such industry affiliates as the Wisconsin Cheese Makers Association, the Wisconsin Specialty Cheese Institute, Wisconsin Cheese Originals, the Wisconsin Artisan Cheesemaker Guild and the former Dairy Business Innovation Center.

Cooperation continues to fuel the success of Wisconsin cheese. The CDR surpassed its private fundraising goal of $16 million to begin construction of a state-of-the-art dairy research and education facility on campus, now in the design phase—an achievement made possible only through the support of industry, government, alumni and other committed stakeholders throughout the CALS community.

Join the Celebration

Your place for all things CALS quasquicentennial is There we invite you to share your favorite CALS historical moments, keep apprised of events and learn more about the college’s past. Events featuring anniversary celebrations include:

• Science Expeditions, April 4–6

• CALS Undergraduate Research Symposium, April 22

• Dedication ceremony for the Hector F. DeLuca Biochemical Sciences Complex, April 24

• Commencement reception, May 17

• Department of Soil Science’s 125th, May 23

• Department of Horticulture’s 125th, June 19

• Barn Dance at Susan Crane’s family farm, June 28

• Science Festival, October 16–19

• Honorary Recognition Awards, October 16

More info at

This article was posted in Communities, Main feature, Spring 2014.

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