Even Cows are “Texting”

Douglas J. Reinemann is a professor and chair of the Department of Biological Systems Engineering at UW–Madison and a milking equipment/energy specialist with UW–Extension. His research focuses on machine milking, energy use and energy production in agricultural systems. He is a member of the sustainability group of the UW–Madison-based Great Lakes Bioenergy Research Center, where he examines environmental impacts of biofuels production systems. He also leads UW–Madison’s “green cheese” team, which investigates synergies between dairy and biofuels production systems in Wisconsin. Reinemann has directed activities of the UW Milking Research and Instruction Lab since 1990. His extensive work with machine milking includes serving as the U.S. representative and chair of the International Dairy Federation’s working group on machine milking as well as the U.S. representative on machine milking committees with the International Standards Organization. He also has chaired machine milking committees with the American Society of Agricultural and Biological Engineers and the National Mastitis Council.

What kinds of things are cows texting their owners?
This is a development that’s come about through the implementation of robotic milking systems. A robotic milking system has a computer for a brain, and, of course, computers can communicate with us, so dairy farmers have the option of selecting what sorts of information they’d like to get from the dairy herd and how often and when they’d like to get that information.

For example, earlier this year I was at the National Mastitis Council meeting and some dairy farmers there were frequently checking their cell phones to monitor what was going on back home—how’s the robot doing, are the cows showing up to be milked, is the machine working—and even tracking individual cows’ health status and milk production. How’s this cow doing today?

What kind of information is texted to a cell phone?
There are several levels of alert. There are more important things such as, for example, if the machine breaks down and it’s not working—that’s a very high level of alert. And the computer will call you up on your phone and say, “We have a problem with unit No. 2, it doesn’t seem to be operating. Come out and have a look at it or send someone to have a look at it.”

What other kinds of information are dairy farmers collecting from their herds?
With robotic milking in particular, but also in conventional parlors, we can collect the most basic information—milk yield, for example, so that we know how much the cow is giving at each milking. With that information you can determine that if today’s yield is down by a certain percentage, you might want to have a look at that cow. That’s a text message you might receive: “Cow No. 3765, Elsie, is down to half of what we should expect, and you might want to have a look at her today.”

What are some advantages of this kind of technology on the dairy farm?
It falls into the general category of precision agriculture. This kind of information allows a dairy manager to track individual cow information, as opposed to the more general trend in the industry toward group management in the last decade or so. This is a move back toward more individual cow management, which allows the farm to be more efficient.

You mentioned that this is “too much information’ for some farmers. . .
[Laughs] The game changer with robots is that when a robot is milking the cow, there’s not a person standing there. That really created the need for some kind of automated communication system. The robot has to be able to communicate with a human being in the event that something goes wrong. When you install a robot, one of the big questions is, “Who gets the call?”

Some farmers think that this is just fantastic. They say, “I don’t have to worry about the robot, I can just let it run,
and if something goes wrong, it will give me a call and then I’ll go look at it, but otherwise I don’t have to worry about it.”

On the other hand, you have people who hate it because they say, “I’m always on call and I’m always nervous about
getting the call, and it’s driving me crazy!”

So that’s a really interesting dynamic, I think. And it raises all kinds of questions. Do we trust this technology? Do we want the information? We certainly want to know when something’s going wrong—but on the other hand, sometimes we really don’t.

What other information can be collected on a dairy cow?
Right after milk yield, mastitis detection is near the top of the list. Even in conventional parlors we have ways of detecting whether a cow might be developing a mastitis infection. But in a robotic milking system, that detection technology is more sophisticated.

How about feed management, walking activity. . .
There’s a whole variety of sensors that tell us about different aspects of cow activity. The one we’ve been using the longest would be a simple pedometer to tell us how many steps the cow is taking. I recently got a Fitbit myself, so now I’m counting my steps as well.

Activity monitoring is used for a number of things, primarily reproduction—it’s used for heat detection—but it also can be used for lameness detection. And more sophisticated systems can actually locate the cow in the barn, so we know whether the cow is in the feed bunk or whether she’s lying down. That allows us to look at time budgets, the percentage of time spent resting or eating. An even more sophisticated technology detects the rumination activity of a cow. Rumination monitors can be put in the rumen, like a large pill, and they transmit information wirelessly.

How does such up-close information about the rumen help a dairy farmer?
It’s used to manage nutrition. Cows are ruminants, and rumination is what drives milk production, so a decrease in rumination activity is an indication that there is something wrong either with animal health or potentially something wrong with the dairy ration.

What resources are available to help farmers adopt these new technologies?
I actually ran a series of user groups for managers of milking parlors, which we established through UW–Extension agents. We got milking parlor managers together and talked about what technologies they were using and how they were using it. It was a very effective way to break the chicken-or-egg syndrome. You don’t really know what the technology can do for you until you actually start using it. And you don’t even know how to go about using it unless you know what it can do for you. The user groups are farmers saying, “I tried this and it really helped.”

One of the challenges is, salespeople sometimes make big promises about what their technology can do, and it can’t really do it. So people become hesitant. Once you’ve had a few experiences with some technology that promises you the world and then it doesn’t work, it sours you on technology in general. User groups are a way to get feedback from someone who’s tried it and can confirm that it’s helpful in managing dairy operation.

There are also user groups organized by companies that produce a particular technology, including robotic milking. These companies seem to be doing a good job facilitating
user groups.

Look into your crystal ball. Where can this go from here?
The move toward automation in dairy farming has been steadily progressing over the last 100 years. So this progression is really just a continuation of more automation in the dairy industry. What that means for dairy producers is economic efficiency, better animal welfare and better quality of life for the cow and the farmers.

Going for the Gut

How do we keep food animals healthy when bacteria and other pathogens are so good at outsmarting drugs intended to work against them?

In an innovation that holds great promise, CALS animal sciences professor Mark Cook and scientist Jordan Sand have developed an antibiotic-free method to protect animals raised for food against common infections.

The innovation comes as growing public concern about antibiotic resistance has induced McDonald’s, Tyson Foods and other industry giants to announce major cuts in antibiotic use in meat production. About 80 percent of antibiotics in the United States are used by farmers because they both protect against disease and accelerate weight gain in many farm animals.

The overuse of antibiotics in agriculture and human medicine has created a public health crisis of drug-resistant infections, such as multidrug-resistant Staphylococcus aureus (MRSA) and “flesh-eating bacteria.”

“You really can’t control the bugs forever; they will always evolve a way to defeat your drugs,” says Cook.

Cook and Sand’s current work focuses on a fundamental immune “off-switch” called Interleukin 10 or IL-10, manipulated by bacteria and many other pathogens to defeat the immune system during infection. He and Sand have learned to disable this off-switch inside the intestine, the site of major farm animal infections such as the diarrheal disease coccidiosis.

“People have manipulated the immune system for decades, but we are doing it in the lumen of the gastrointestinal system. Nobody has done that before,” Cook says.
Cook vaccinates laying hens to create antibodies to IL-10. The hens transfer the antibody to their eggs, which are then blended, pasteurized and sprayed on the feed of the animals he wants to protect. The antibody neutralizes the IL-10 off-switch in those animals, allowing their immune systems to better fight disease.

In experiments with more than 300,000 chickens, those that ate the antibody-bearing material were fully protected against coccidiosis and other gastrointestinal diseases that commonly affect poultry.

Smaller tests with larger animals also show promise. In one example, animal sciences professor Dan Schaefer and his graduate research assistant, Mitch Schaefer, halved the rate of bovine respiratory disease in beef steers by feeding them the IL-10 antibody for 14 days.

Cook and Sand, who have been working on the IL-10 system since 2011, are forming Ab E Discovery LLC to commercialize their research. One of the four patents they have filed through the Wisconsin Alumni Research Foundation has just been granted, and WARF has awarded a $100,000 Accelerator Program grant to the inventors to pursue the antibiotic-replacement technology. The Discovery to Product partnership between UW and WARF played a key role in helping Cook and Sand prepare it for commercialization.

Cook has already turned his research and some 40 patented technologies into start-up companies including Aova Technologies, which improves animal growth and feed efficiency, and Isomark LLC, which is developing a technology for early detection of infection in human breath.

PHOTO: Eggs from these hens contained antibodies that were used to test the antibiotic replacement. (Photo courtesy of Mark Staudt, WARF)

The MBA of Dairy

The average age of a Wisconsin farmer is over 56 and rising, and the state has been losing around 500 dairy farms per year. It’s no surprise, then, that experts say it’s critical to prepare young people to step into farm roles in order to keep the state’s $88 billion agricultural economy strong into the future.

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

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

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

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

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

As part of the program, apprentices attend a seminar about pasture-based dairy and livestock through the Wisconsin School for Beginning Dairy and Livestock Farmers (WSBDF), which is co-sponsored by the CALS-based Center for Integrated Agricultural Systems and the Farm and Industry Short Course. The seminar involves a 32-hour commitment, which is generally fulfilled through distance education and includes instruction from CALS professors from dairy, animal and soil sciences.

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

In 2009, GrassWorks, Inc. turned to WSBDF director Dick Cates PhD’83 for guidance and access to a well-respected educational curriculum to help get the DGA up and running—and the WSBDF team has been involved ever since.

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

As part of the most recent round of funding, DGA’s partners at CALS will lead an effort to quantify the program’s broader impacts.
“They have already proven that participants are moving along to their own farms after the apprenticeship, so they have an established track record,” says Alber. “This new study will look at some of the program’s other impacts, including economic, environmental and social.”

Second Life for Phosphorus

Phosphorus, a nutrient required for growing crops, finds its way from farm fields to our food and eventually to our wastewater treatment plants. At the plants, the nutrient causes major problems, building up in pipes or going on to pollute surface waters.

Brushite bounty: Phil Barak displays brushite produced during trials at the Nine Springs Wastewater Treatment Plant of the Madison Metropolitan Sewerage District. Each jar contains brushite harvested from 30 gallons of anaerobic digest. Photo courtesy of Phil Barak

Brushite bounty: Phil Barak displays brushite produced during trials at the Nine Springs Wastewater Treatment Plant of the Madison Metropolitan Sewerage District. Each jar contains brushite harvested from 30 gallons of anaerobic digest.
Photo by Rick Wayne

But soil science professor Phil Barak has an idea about how to retrieve the nutrient from wastewater in a valuable form—and it started from a basic lab experiment. “I was doing some work on crystallizing phosphorus, just out of pure academic interest,” explains Barak. “That led me to crystallize a mineral called struvite. Then I realized it was forming in wastewater treatment plants as a nuisance.”

If he could form crystals in the lab, he reasoned, why couldn’t it be done in the wastewater treatment plants in a controlled way? It could. And, even better, if he collected the phosphorus early on in the treatment process in the form of a mineral called brushite, he could harvest even more of it.

Beyond removing phosphorus from wastewater, brushite can serve as a nutrient source for growers. While Barak will do further testing to prove its utility, brushite is a phosphate mineral that’s actually been found in agricultural fields for years.

“When conventional phosphorus fertilizers are added to soil, brushite forms. I maintain that we’ve been fertilizing with brushite for decades, but nobody’s been paying attention to it,” says Barak.

Being able to remove phosphorus from wastewater and supply it back to growers is a win-win situation, Barak notes. “We’re collecting phosphorus where it’s localized, at really high concentrations, which is the most economical place to collect it,” says Barak. “This works out in just about every dimension you can consider, from the treatment plants to the cost of recycling phosphorus as opposed to mining it new.”

Graduate students in Barak’s lab suggested that he commercialize the technology and start a company. After the Wisconsin Alumni Research Foundation (WARF) passed on the patent, Barak and his students sought help from the UW Law and Entrepreneurship Clinic. They received two federal Small Business Innovative Research grants, and, with some additional funds from the state, including the Wisconsin Economic Development Corporation, their efforts have turned into a spinoff company: Nutrient Recovery & Upcycling, LLC (NRU).

The company’s next step was a big one. This summer, a phosphorus recovery pilot plant is being implemented in a wastewater treatment plant in Illinois. The pilot project will test the research ideas on a larger scale.

Additionally, the NRU team will participate in the Milwaukee Metropolitan Sewerage District’s granting system to determine if a pilot project would be a good fit in Milwaukee. They hope to start collecting and analyzing data from Illinois by September, using that pilot system to lay the groundwork for others in Milwaukee and beyond.

Uganda: The Benefits of Biogas

Generating enthusiasm for a new kind of technology is key to its long-term success. Rebecca Larson, a CALS professor of biological systems engineering, has already accomplished that goal in Uganda, where students at an elementary school in Lweeza excitedly yell “Biogas! Biogas!” after learning about anaerobic digester systems.

Larson, a UW–Extension biowaste specialist and an expert in agricultural manure management, designs, installs and upgrades small-scale anaerobic digester (AD) systems in developing countries. Her projects are funded by the Wisconsin Energy Institute at UW–Madison and several other sources. Community education and outreach at schools and other installation sites are an important part of these efforts.

Children get excited by the “magic” in her work, she says. “It’s converting something with such a negative connotation as manure into something positive,” Larson notes. In an AD system, this magic is performed by bacteria that break down manure and other organic waste in the absence of oxygen.

The resulting biogas, a form of energy composed of methane and carbon dioxide, can be used directly for cooking, lighting, or heating a building, or it can fuel an engine generator to produce electricity.

Larson’s collaborators in Uganda include Sarah Stefanos and Aleia McCord, graduate students at the Nelson Institute for Environmental Studies who joined forces with fellow students at Makarere University in Kampala to start a company called Waste 2 Energy Ltd.
Along with another company, Green Heat Uganda, which has built a total of 42 digesters, Waste 2 Energy has helped install four AD systems since 2011.

“Most of these digesters are locally built underground dome systems at schools and orphanages,” Larson explains. Lweeza’s elementary school is a perfect example.

The AD systems use food waste, human waste from pit latrines and everything in between. The biogas generated by the digester is run through a pipeline to a kitchen stove where the children’s meals are prepared. Compared to traditional charcoal cooking, the AD systems greatly reduce the school’s greenhouse gas emissions.

Larson and her team are now focusing on enhancing the efficiency and environmental benefits of these systems. Their goals are to improve the digester’s management of human waste, reduce its water needs, increase the amount of energy it produces and generate cheap fertilizer to boost food crop yields.

“Our overall goal is to create a closed-loop and low-cost sustainability package that addresses multiple local user needs,” Larson says.

The beauty of the project is that all these needs can be met by simply adding two new components to the existing systems: heating elements and a solid-liquid separator.

To help visualize the impact of the fertilizer, Larson set up demonstration plots that compare crop yields with and without it. Down the road, a generator could be added to the system to provide electricity in a country where only 9 percent of the population currently has access.

As a next step, Larson hopes to replicate the project’s success in Bolivia. She is finalizing local design plans with Horacio Aguirre-Villegas, her postdoctoral fellow in biological systems engineering, and their collaborators at the Universidad Amazonica de Pando in Cobija.

Give: Hands-On Fieldwork

Before last summer, Vera Swanson’s only exposure to plant sciences had been through classes in introductory biology. That changed big-time when Swanson, a junior majoring in environmental sciences and Russian, signed on to intern at the CALS-based Arlington Agricultural Research Station as a crop scout.

Crop scouts are used in agricultural management to diagnose stress factors in a field—such elements as potentially negative soil and climate conditions, the presence of pests, and threatened crop performance—and determine which management practices are appropriate for the goals of a specific plot. As part of her training, Swanson spent copious hours learning to identify weeds by walking through the fields and the Weed Garden, which displays dozens of invasive plants accompanied by their names.

Swanson paired her internship, which was run through the Department of Agronomy, with an independent research project involving biofuel crops being tested at Arlington. For that work Swanson drew on her growing knowledge of weeds to test the effect of three biofuel crop systems—native prairie, switchgrass and continuous corn—on the soil’s weed seed bank, or the viable seeds present in the soil and its surface. The project involved working one-on-one with research scientists in Randy Jackson’s grassland ecology lab. Jackson is running the crop trials through his affiliation with the UW’s Great Lakes Bioenergy Research Center, housed in the Wisconsin Energy Institute.

The intense focus on plants got Swanson thinking a lot more about soil. “It is such a finite resource, yet so much of what we depend on comes from it—our food, clothing and the materials that we build with,” says Swanson.

It also got her more interested in food systems, to the point where she chose to make horticulture a disciplinary focus within her major and a possible new career direction. “I’d love to work for an organization where I would be able to complement my interests in agriculture, development and language within a global context,” she says.

Swanson’s path exemplifies the power of “beyond classroom” experiences to dramatically shape, and in many cases transform, a student’s education and career goals. These experiences—which include internships, research projects, study abroad, honors thesis stipends, field courses and more—are the hallmark of a CALS education.

“They’re a big part of what makes CALS CALS—and they offer our students a major advantage in both their personal and professional development,” says Sarah Pfatteicher, the college’s associate dean for academic affairs. “Our goal is to ensure that each student can participate in at least four of these important opportunities.”

To help support the CALS Student Experience Fund, visit: http://go.wisc.edu/student-experience

Plant Prowess

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


The Bigger Picture

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

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

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

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

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

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

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

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

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

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

You might expect that the most important break- through in feeding dairy cattle in years would rate
a snazzy name. Instead, you get “total tract neutral detergent fiber digestibility”—TTNDFD for short.

“Yes, I know. That’s a terrible name. But unless someone comes up with something better it’s TTNDFD,” says CALS dairy nutrition scientist David Combs.

No matter. For an idea this good, a clever name isn’t needed.

The discovery of TTNDFD, a new forage test, lays to rest a mystery that’s perplexed researchers and dairy farmers since scientific forage analysis began 40 years ago: Why cows would wolf down one finely tuned dairy ration but turn up their noses at another that, on paper, was identical?

“We couldn’t put a finger on it,” Combs says. “You’d get your forage analysis, balance the ration, and everything seemed fine. But one time the cows would eat everything up, the next time you’d get a high rate of refusal.”

That mystery cost money. When cows eat to capacity, they produce milk to capacity, and milk sold off the farm is what pays the bills. “It wasn’t so much good forage, bad forage. Those things we can detect. It was those times when everything seems fine and the cows would not eat as much as expected or not produce as well as before,” Combs says.

Cows are professional eaters and highly discern- ing about what gets served. They’ll eat a lot of differ- ent things but will eat a great deal more of the things they like best. What the Combs team figured out— through research that involved 20 years of reaching into the 30-gallon vats known as cow rumens—was that how much cows gobbled up and turned into milk was influenced by the rate of fiber digestion. Developing a test to account for it ushered in a new feeding system that offers several advantages.

For one, the new forage fiber test lets farmers
see the differences in the feeds they have on hand. For another, it helps them grow and buy the types of feeds most favored by cows. For yet another, plant breeders can use the test to create the type of crops cows want the most. And most important, the test can help milk producers make more money.

“How fiber is digested can easily make five to six pounds per day difference in milk production in a dairy cow,” Combs says.

There could also be some positive ripple effects. As people applied the test to all kinds of forage, they discovered that grass is something of a magic missing ingredient in the daily dairy diet. The right kind of grass is really good for cows, and the test can help farmers select the right grasses to grow.

Reintroducing grass to dairy diets on a large scale could be great for the landscape. Grass soaks up carbon and nutrients, holds soil in place, covers otherwise bare ground during the winter, and can help absorb manure applications.

The test also opens opportunities for entrepre- neurs. When Rock River Labs in Watertown hired John Goeser BS’04 MS’06 PhD’08, who’d earned a doctorate under Combs, it became the first lab in the world to offer this new analysis to the dairy community.

“It’s started a little slow. But it went from no
tests to 5,000 tests in a season,” Combs says. Now Combs uses a large spreadsheet to review the data being generated by thousands of TTNDFD tests performed by Rock River. More labs are looking into offering TTNDFD results as part of a forage analysis package.

Chris Barrett PhD’94

Chris Barrett PhD’94 Agricultural and Applied Economics • In January Chris Barrett began a new position as the David J. Nolan Director of Cornell University’s Charles H. Dyson School of Applied Economics and Management, whose undergraduate and graduate programs rank in the top five nationwide. Barrett takes on that leading role in educating applied economists at a crucial time for the field, he says, citing global challenges posed by the rapid growth in demand for food, feed, fuel and fiber. As a CALS graduate student Barrett found a collaborative network of scholars and practitioners who have been formative in his success as both a teacher and a scholar. Among Barrett’s experiences as a CALS student, he fondly remembers enjoying Babcock ice cream with his children while watching the UW Marching Band practice.

Rogier van den Brink PhD’90

Rogier van den Brink PhD’90 Agricultural and Applied Economics • As a Washington, D.C.-based lead economist with the World Bank in the department of poverty reduction and economic management, Rogier van den Brink works on economic policy and related concerns with a number of countries in Southeast Asia, his region of interest. Recently he helped establish a multimillion-dollar budget in support of relief operations following Typhoon Haiyan in the Philippines. Now a Distinguished Alumni Lecturer with UW-Madison, van den Brink became aware of the “special powers” of agriculture in reducing poverty while a student at CALS, he says, a lesson that his career continues to affirm. When he’s not working, van den Brink pursues music production, an interest he discovered at Amy’s Cafe and Bar in Madison. Sometimes he mixes work and pleasure, most recently when he recorded an album, “Zsa Zsa Exactly,” while in Mongolia. Proceeds from the album will go to Typhoon Haiyan relief efforts.

Diana Fletschner MS’95 PhD’02

Diana Fletschner MS’95 PhD’02 Agricultural and Applied Economics • China, Colombia, Russia, Peru and Uganda are just some of the places in which Diana Fletschner has had the opportunity to work. Fletschner serves as senior director of research, monitoring and evaluation for the Seattle-based NGO Landesa, which works to secure land rights for the world’s poorest populations. Fletschner’s role includes evaluating projects, fostering a network of professionals aimed at strengthening women’s land rights, and supporting national and international advocacy of land issues. For Fletschner, being a CALS student served as a platform for exploring new experiences from around the world as well as the opportunity to build formative relationships with “mentors with a capital M,” as she puts it.

Joseph Glauber PhD’84

Joseph Glauber PhD’84 Agricultural and Applied Economics • Henry C. Taylor, the first chief economist with the USDA, was a Badger—and today another alum, Joseph Glauber, holds that title. Glauber’s duties include preparing the department’s agricultural forecasts and projections as well as advising the Secretary of Agriculture on the economic implications of agricultural legislation. Time spent around the chalkboards discussing and debating economic issues belongs to Glauber’s fondest memories of CALS. He will also forever value the Department of Agricultural and Applied Economics for its diversity and an open climate that facilitated forming lifelong friendships. In his free time Glauber bikes 3,500 to 4,000 miles a year, including commuting to work—a hobby, he explains, that balances his love of food.