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 Clues to Healthy Bones for People with PKU

Individuals with the metabolic disorder phenylketonuria, or PKU, cannot metabolize the amino acid phenylalanine. Without careful dietary management, it can accumulate at high levels in their blood, leading to cognitive impairment, seizures, and other serious health problems.

There is no cure for PKU, and patients must adhere to a lifelong diet of medical foods that contain protein but are low in phenylalanine. Traditionally, these medical foods have been made using synthetic protein substitutes derived from mixtures of amino acids. But these amino acid- based medical foods could be contributing to the skeletal fragility seen in many PKU patients, according to a new study led by nutritional sciences professor Denise Ney and Bridget Stroup PhD’17.

The researchers also discovered that an alternative medical food, developed by Ney from a protein called glycomacropeptide (GMP) — a natural byproduct found in the whey extracted during cheese production — could allow PKU patients to manage their diets without compromising their bone health. This study represents the first human clinical trial comparing how different PKU-specific diets affect the bone health of people living with the disease.

Ney helped develop GMP-based foods for PKU patients just over a decade ago. In subsequent studies, she has shown that mice fed GMP-based diets have larger and stronger bones than mice on amino acid based diets. “It was a vital clue that there could be a link between amino acid medical foods and the skeletal fragility seen in many PKU patients,” says Ney, a researcher at UW–Madison’s Waisman Center.

For the current study, Ney and her research team assigned eight individuals with PKU to a diet of amino acid-based medical foods before switching them to GMP-based foods with a low dietary acid load. The researchers found that PKU patients had higher amounts of calcium and magnesium in their urine while on the amino acid based diet, a sign of bone breakdown, which can impair bone health.

“The amino acid medical foods have high acid loads, which can change the overall acid-base balance within the body,” Stroup says. Bones are able to buffer high acid loads in the body, but over time this leads to a breakdown and release of minerals. On the other hand, Glytactin (the trademarked brand name for the formulation used in the study) GMP medical foods do not have high acid loads.

Although the researchers did not directly measure bone breakdown and density in this study, other studies have found that reducing the acid content of diets leads to lower urine-calcium excretion and increased bone density.

These findings, Ney says, could also help patients with other kinds of metabolic disorders, like maple syrup urine disease. And although the sample size of the study was relatively small, it is typical of investigations into rare diseases; Ney hopes to secure additional funding for further study.

Ney is working on a larger clinical trial to study the metabolism of calcium and other minerals in PKU patients consuming amino acid or GMP medical foods. “We will be looking at bone health and also other physiological aspects, such as the gut microbiota,” she says.

“Legacy Phosphorus” and Our Waters

For decades, phosphorous has accumulated in Wisconsin soils. Though farmers have taken steps to reduce the quantity of the agricultural nutrient applied to and running off their fields, a new study reveals that a “legacy” of abundant soil phosphorus has a large, direct and long-lasting impact on water quality.

The study, published in the journal Ecosystems and focused on southern Wisconsin’s Yahara watershed, may be the first to provide quantifiable evidence that eliminating the overabundance of phosphorus will be critical for improving the quality of the state’s lakes and rivers.

For example, the results indicate that a 50 percent reduction in soil phosphorus in the Yahara watershed’s croplands would improve water quality by reducing the summertime concentration of phosphorus in Lake Mendota, the region’s flagship lake, by 25 percent.

“If we continue to apply phosphorus at a greater rate than we remove it, then phosphorus accumulates over time and that’s what’s been happening over many decades in the Yahara watershed,” says Melissa Motew, the study’s lead author. Motew, working with CALS agronomy professor and co-author Christopher Kucharik, is a doctoral candidate at the UW–Madison Nelson Institute for Environmental Studies.

Phosphorus seeps into soils primarily by way of fertilizer and manure, and what crops and other plants don’t use to grow then leaks into waterways with rain and snowmelt runoff. Scientists have long believed that excess soil phosphorus is a culprit behind the murky waters and smelly algal blooms in some of Wisconsin’s lakes and rivers.

Conventional efforts, like no-till farming and cover crops, have tried to address nutrient runoff by slowing its movement from soils to waterways. However, the study shows that simply preventing runoff and erosion does not address the core problem of abundant soil phosphorus, and this overabundance could override conservation efforts.

“Solutions should be focused on stopping phosphorus from going onto the landscape or mining the excess amount that is already built up,” says Kucharik.

Using newly advanced computer models, the study shows the watershed has about four times more phosphorus in its soil than is recommended by UW–Extension, which writes the state’s nutrient management recommendations based on what crops need and a landscape’s potential for nutrient runoff.

Currently, the only method known to draw down soil phosphorus is harvesting crops, but Kucharik explains that plants take up only a small amount of the surplus each year.

“It is unlikely that any cropping system will quickly draw down the excess,” he says.

It will require working with farmers to practice better nutrient accounting and counter the tendency of some to apply more fertilizer, as an insurance measure, than is needed.

Food production need not be compromised by potential solutions, Kucharik says. There is enough excess phosphorus in our soils “to support plant nutrient needs for a long time.”

The research, funded by the National Science Foundation, is part of UW–Madison’s Water Sustainability and Climate project.

The “Icing” on the DNA

XUEHUA ZHONG, an assistant professor of genetics, studies epigenetics, a growing area of research focused on how chemical tags on DNA can change the expression of genes. She and her team at the Zhong Lab of Epigenetic Regulation, located at the Wisconsin Institute for Discovery, are especially interested in the modification of genes involved in growth and development, and how epigenetics can be affected by the changing environment.

As evidence for a link between environmental factors and epigenetics grows, so does public interest in the topic as people consider the impact of their lifestyles and diets not only on themselves but also on the next generation. Zhong and her team hold talks for the public about their work and conduct a number of hands-on programs about epigenetics for undergraduate and K-12 students, including a summer science camp for local high school students, a field trip for middle-schoolers, a youth apprenticeship program in her lab and a “tabletop exploration station” about how lifestyle choices can affect gene expression. Zhong hopes opportunities such as these will raise interest in and encourage the next generation to study this rapidly growing field.

What is epigenetics?

It’s a very interesting question, I would say. The definition of epigenetics has been really challenging over the years because there are different concepts of epigenetics. Most people accept the definition that epigenetics is modifications on the genetic material, the DNA, that changes expression of the underlying genes. I like to say that epigenetics is like a Christmas decoration. You decorate the DNA in a different way, and then the expression of genes is different.

I would also use another comparison: If you think about a cake, the base of the cake is the DNA, the genes. Then the epigenetics is the frosting, the decoration on the cake. And the nice thing about that is if you don’t like the frosting, you can remove it. You can redecorate it differently, and it looks like a different cake.

Can epigenetics be passed on from one generation to the next?

This is another reason why epigenetics is so debatable—the question of inheritance. The modification on top of DNA has been well accepted, but whether it’s heritable is still being debated. Some modifications are very transient and unstable. But some of the modification, for example, methylation—the process of adding methyl groups to the DNA molecule—is fairly stable and can be inherited by the next generation. That is called transgenerational inheritance.

We talk a lot about how your diet, your exercise and your environment have a huge impact on you, obviously, but can also impact your children and even grandchildren through transgenerational inheritance. There are cases from World War II of women who lived through famine, and even 20 years later when they were leading a healthier life, those women tended to have children with more diseases and stress through- out life.

How is this inheritance being studied?

It’s very challenging to study transgenerational inheritance in humans. We’re talking about 60, 70 or 80 years for each generation. But in plants, it’s been very clear that certain epigenetic patterns can be transgenerationally inherited. For example, the Wisconsin cold can induce modifications of genes that can then be inherited. This is an area we are very interested in—environmentally induced epigenetic modifications and to what extent these modifications are transmitted to the next generation.

What plant do you use to study inherited epigenetics?

Currently we are primarily utilizing a flowering plant called Arabidopsis thaliana, or thale cress. It’s a model system that is widely used. We use it because it has a small genome, and because most of our studies are done at the whole genome scale, it’s cheaper than other model systems. Also, the generations are very short, only eight weeks. You can look at six generations in just a year. We’ve also started to extend our work to rice and maize through other collaborations on campus.

Can you explain what you’ve learned about plant aging in your work?

We have been finding that one epigenetic complex in particular is very important to make sure that a plant senesces, or ages, at the right time. Early senescence can reduce yields, so if we can find a way to delay senescence we can hopefully increase productivity. And that’s exactly what we see. If we get rid of the complex we’ve found, senescence is significantly delayed.

While we often talk about how delaying aging is good, the opposite can be true, too. Here in Wisconsin, we have relatively short windows for growing plants. If we can promote senescence, we can maybe shorten the plants’ growing season to better fit our weather patterns.

Now we are trying to understand the mechanism behind these changes because only when we know the mechanism can we really manipulate the system. Ideally, we will be able to manipulate things both ways by fine-tuning the epigenetics to different levels. It’s not all or nothing—it’s kind of an art.

How can your work help address concerns about climate change?

Heat and drought will make the areas that can grow plants limited and challenging in the future. This is a big motivation for us. We want to know what kind of epigenetic modifications happen in response to heat and drought—how strongly, uniformly, stably and rapidly do these modifications happen? Also, is this inheritable? If we treat a plant with heat and collect its seeds, will the next generation “remember” that past experience? Can that memory help the plant?

Why is it difficult to study the influence of environmental factors on epigenetics?

In the lab, it’s simple because we can control each factor and use one kind of stress. But in the real world, you are going to have multiple factors, and how they crosstalk is very complicated. Heat is associated with drought, and there may be long, dark nights and short days as well. I am interested in finding the epigenetic complexes responding to all of these factors. Ideally I want to combine all this information to establish an environmental epigenetic regulatory network. And if there is one key complex responding to all kinds of factors, that can be our target.

Is there a way to do very targeted epigenetic work?

One area we are getting into is epigenome editing (also named epigenome engineering) using a modified CRISPR–dCas9 system that others are using for genomic editing. This lets us target the genes involved in aging, let’s say, and then change only those few genes we have identified to be important. We can put a modification only in that place or on those genes. It’s more efficient.

Using CRISPR–dCas9, the epigenetic changes hopefully will be stable. That’s a question right now because we haven’t gotten to that step yet, but I hope that’s true. Ideally once we have the modification on there, it should stay and do its job.

How are epigenetic studies being used beyond the lab?

I am most interested in how epigenetics can be applied to horticulture and agriculture, but many people are interested in epigenetics for drug discovery. In human medicine, there is already a drug used clinically called azacitidine, which is used to treat a bone marrow disorder called myelodysplastic syndrome and works by blocking the methylation of DNA. This is still a huge, growing area, and whether lab findings can be used in the field or in practice is a million-dollar question. We need efforts to take the discovery from the lab into the field. Making that connection is important and challenging work in all areas of research.

Xuehua Zhong uses plants to study epigenetics, an exciting new field that is broadening our understanding of how some traits might be passed down from one generation to the next. Photo credit: Sevie Kenyon BS’80 MS’06

Lactation Sensation

WHEN THE CITY GIRL decides to study lactation, she must first learn to milk a cow. Laura Hernandez, an assistant professor of dairy science at CALS, remembers that lesson.

Her tutor that day was Jessica Cederquist, then a fellow grad student and now CALS herd manager. “People who have never milked are used to what you see in the movies,” Cederquist explains. You know the choreography: grab a teat, pull down, milk squirts into the bucket. But that technique simply squeezes milk back into the udder. And just about everybody makes the mistake. “It is a rite of passage to stand back and laugh,” she admits.

“She thought it was very funny,” Hernandez recalls. “I think that was the beginning of a very good friendship.”

The milking got a little crazier once Hernandez ramped up her inquiries into how lactation works. Her first experiments required milking two halves of the same cow, comparing milk production. Because she was pairing the front right with the back left and vice versa, she had to replumb two half milkers, using a surplus of hoses and buckets. She’d also recently had knee surgery.

“You’re already kind of crowded in there and now you’ve got her fancy contraption and all of her buckets and a big old knee brace,” says Cederquist. And it’s a waterbed stall, so every time anybody moves, the floor moves, and the buckets yaw precariously. “She’s darn near laying on the floor under the cow, trying to figure out how she’s going to get this thing to stay on.”

Hernandez is still making things unusual for Cederquist. Lactation is a delicate enough phenomenon that the typical dairy farmer puts animals who are in the late stages of pregnancy on vacation. This is exactly when Hernandez needs to poke and prod, monitor and manipulate.

The hassle seems worth the reward: Her exploration of the role of serotonin in lactation has the potential to significantly improve animal health and boost milk production. There may also be profound lessons about the role of serotonin in human health. While seratonin was once considered the miracle molecule of mental health, Hernandez is helping unravel its role in many more parts of the body.

“There is still an infinite box of things it probably does that we can’t understand,” says Hernandez. Which is all the more interesting because it’s such a simple molecule, just a modified amino acid. It’s as if a Lego block were able to control a nuclear reactor. “I really am just completely fascinated by how a modified amino acid can regulate what feels like the universe at times,” Hernandez says.

On the road between Hernandez’s hometown of El Paso, Texas, and the New Mexico State University campus in Las Cruces, a line of dairy farms stretches across the landscape. Despite her urban upbringing, the cows fascinated her. “As an athlete I was like: how does she do that?” recalls Hernandez, then a scholarship swimmer. “I just thought they were really cool animals, what they could do from a biological standpoint.”

Drawn to biology, Hernandez chose animal science over straight biology because she was more interested in working with mammals than with crabs and nematodes. But her real immersion didn’t begin until her senior year, when she transferred to New Mexico State from Iowa State University. In Ames her swimming schedule had kept her out of the lab, but that changed when she got to Las Cruces.

“I loved working in the lab,” says Hernandez. “That was where I found my home.” When she couldn’t decide between professional schools, she continued at New Mexico State to earn a master’s degree in animal science and toxicology.

In 2005 she started her doctorate at the University of Arizona with Bob Collier, a physiologist in the dairy sciences. He was interested in how genes interacted with the environment, and lactation was the ideal process to study: genetically programmed, but initiated and controlled by changes in the environment of the cow.

The year before Hernandez arrived, the small world of lactation science had been upended by the unexpected discovery that serotonin, long considered simply a neurotransmitter, also had a role in regulating lactation. Collier reached out to Nelson Horseman at the University of Cincinnati, where the discovery had been made. Horseman studied breast development, but his central interest was breast cancer. Collier offered his dairy expertise and suggested that they collaborate on expanding this discovery from the mouse to the cow.

Hernandez undertook the research for her dissertation, supervising many of the active experiments. Deeper she went, her work encompassing an intense collaboration into the complex molecular underpinnings of milk production.

After finishing her Ph.D. she began a postdoc in Horseman’s lab. One day in Cincinnati, Gerard Karsenty, a geneticist visiting from Columbia University, presented his research involving gut serotonin, calcium and bone mass. Afterward Hernandez turned to Horseman and wondered aloud: If gut serotonin had a role in bone mass, could this also help explain its role in lactation?

Nursing typically requires more calcium than diet alone can provide, and the difference comes from the mother’s bone. A nursing mouse will lose up to 20 percent of bone mass in 21 days. Human mothers can lose 6 to 10 percent of their bone mass over six months. Studies in West Africa and Korea suggest that the longer a woman breast-feeds, the lower her bone density.

It’s not surprising that serotonin might have more than one role in the body. Along with dopamine it’s the oldest known hormone, and nature loves to reuse its creations. In fact, serotonin first evolved in plants. Plants have no nervous system, so it couldn’t have been a neurotransmitter. How a simple molecule engages in complex processes is by acting as a molecular key in many different cellular locks. Scientists have now identified 20 different serotonin receptors. The mammary gland alone has five.

So how to uncover serotonin’s role in withdrawing calcium from bone? Scouring some old genetic assays, Hernandez found a likely ally: parathyroid hormone-related protein (or PTHrP). Her initial tests were so strong that she suspected her equipment was off.

But further experiments confirmed that serotonin was causing an increase in PTHrP in the mammary gland during lactation. This, in turn, was a key signal liberating calcium from bone for the mammary glands.

Hernandez’s research portfolio made her an obvious match when a position opened at CALS. As a newly hired professor in 2011, her first question was obvious: Could she leverage our knowledge of PTHrP in the dairy cow?

Lactation is hard, and one of the biggest problems faced by dairy farmers is the “transition cow,” a cow in the three weeks before and after calving. Between the physiologic stress of birth and the metabolic stress of commencing lactation, for the first 20 to 30 days of lactation the cow is expending more energy than she can take in.

Calcium complicates things, as it takes a couple of days to activate the mechanism that borrows from the bone. Sometimes that leads to a calcium deficit—or hypocalcemia, also knownas milk fever. Because calcium is critical for biological functions, assisting with everything from muscle contraction to immune function, a shortage can lead to a variety of potential health problems including ketosis, displaced abomasum and retained placenta. Gut issues can arise because the intestines aren’t contracting. Reduced immune function leaves the cows more susceptible to mastitis.

“That’s a precarious time frame for them,” Hernandez says. “If you have a calcium problem, other issues compound.”

It’s a daily concern for dairy farms. Even on a very good farm, 3 to 5 percent of the animals are going to wind up with milk fever. Scaled up to a 10,000-herd farm, that means one or two affected cows every day.

“Not every farmer is going to automatically relate to Hernandez’s deep molecular work,” says herd manager Jessica Cederquist. But put it in terms of milk fever and the transition cow, and “every dairy farmer on the planet knows what that means,” she says.

With startup money tight and a big idea, Hernandez developed an ambitious research agenda. She found a collaborator in Jimena Laporta, a graduate student fresh from Uruguay. Laporta read the plan and committed the very next day. “We were throwing all of the chips on the table and hoping for a win,” says Hernandez.

The idea was simple: Could you boost PTHrP levels with nutritional supplements? They fed rats two amino acids—5-hydroxytryptophan (abbreviated as 5-HTP) and straight tryptophan. Both are chemical precursors in the synthesis of serotonin.

They began with rats, and feeding was the easy part. The hard part? They also had to milk them. Forty-five rats. Every day. How do you milk a rat?

After knocking it out with sleeping gas, you inject a minute quantity of the hormone oxytocin. A small suction device evacuates the teats; each animal has 10. It was a time-consuming, two-person job. Hernandez and Laporta sacrificed weekends and postponed professional travel. Eventually they got the process down to about an hour and a half.

The 5-HTP worked. Then they confirmed that it works in the cow via IV infusion. Now the lab is working on developing a cow feed that accomplishes the same thing.

Meanwhile, on the molecular level they were focusing on how the serotonin was actually affecting the mammary gland and how it translated into the chemical signals that drive bone resorption. In addition to the PTHrP they identified a gene—already nicknamed sonic hedgehog—as another link in the chain in collaboration with researchers Chad Vezina and Robert Lipinski at the UW–Madison School of Veterinary Medicine.

“It’s a very big picture of a very small molecule,” says Laporta, now teaching at the University of Florida. “Nobody knew that serotonin could do all these things. I think we opened a black box.”

Repeat: lactation is hard. Hernandez became a mother in the first year of her professorship, and nursing was as fulfilling as it was excruciating. She was lactating, she was teaching about lactation, she was manipulating lactation. Under the grueling stress of a new research program she took only nine days of maternity leave.

One day in mid-February her husband came home to find Hernandez crying on the bathroom floor. She couldn’t find time to pump, and her hair was falling out. He suggested it might be time to stop nursing. She’d made it seven months under a colossal workload. They still had some milk stored to facilitate transition to the bottle. “But I want to make it a year,” Hernandez objected. “I’m a lactation biologist! I must!”

“It was so hard,” she reiterates. “It’s made me even more of an advocate for helping women after they give birth. That’s where my biggest interest is: The mother’s ability to deal with lactation and to do so healthily for herself while also taking care of her baby.”

And so Hernandez has forged into human health. As the role of serotonin beyond brain chemistry continues to unfold, obvious questions arise. Selective serotonin reuptake inhibitors, or SSRIs, now dominate the antidepressant market and include such household names as Prozac, Paxil and Zoloft. Among their side effects is a decrease in bone density. Nursing also decreases bone density. With 12 percent of pregnant women taking SSRIs, does the combination of SSRIs and nursing set these women up for severe bone health issues later in life?

Most studies that looked at nursing and SSRIs focused on the infant. “Almost nothing out there looks at the long-term implications for the mother,” reports Sam Weaver, a third-year Ph.D. student in Hernandez’s lab. Weaver began as an undergraduate in the lab, assisting Laporta with her milking. Now Weaver supervises her own mouse dairy as she tries to untangle the precise impact of SSRIs on lactation and the health of the mother.

Weaver harvests more than milk. The mice are dissected with precise determination as blood, mammary glands, kidneys, intestines and bone tissue are examined for health and their reactivity to serotonin. Their femur bones are sent off to a collaborator in Boston for specialized imaging.

“Can we somehow help women breast-feed but also stay on their medication, and help them avoid some of these long-term bone issues?” asks Hernandez. She hopes to begin working with human populations soon.

Now that the lab has characterized the complexity of serotonin in lactation, the team is trying to get a handle on its role as one of the body’s master regulators. Only about 2 percent of serotonin actually resides in the brain; the vast majority circulates throughout the rest of the body. “We’re finding it popping up in all sorts of places,” says Weaver.

A newer project is working on yet another serotonin-lactation connection. Obese women tend to have higher serotonin levels—and they also have a harder time initiating nursing. This suggests yet another crucial role for serotonin as a regulator of energy balance in the body. By unlocking its role, they hope to find a way to make nursing easier for these mothers.

The legacy of Wisconsin is so milk-soaked it can be hard to remember that lactation still holds mystery and marvel. It’s a unique biological process that has given up its secrets slowly, and there is still much to learn. Experiments with a wide variety of mammals have shown that as long as you keep removing milk, the gland will keep making it.

Though she’s unlocked some of the secrets behind this apparent superpower, Hernandez remains entranced: “It just fascinates me that it can continue to do that.”

It’s not a stretch to call lactation one of the more significant developments in the evolution of life on this planet. The expanded ability to feed our young has allowed mammals to adapt to a wide array of variations in our environment. “Keep the baby alive,” says Hernandez. “I think it ties back to that, making us better mothers.” Our human accomplishments are stamped with an indelible mammalian signature.

Hernandez’s peculiar dairy, with its few hundred mice and few dozen patient cows, keeps producing under the labors of a handful of motivated students. “Sometimes it’s overwhelming, and it feels like we’re not getting anywhere and we’re not going to get anywhere,” Hernandez says. “Because with every answer comes another question.”

Even as she continues her fine-scale investigations, Hernandez hopes that young farmers can go back to their dairies and incorporate some wonder into our conversations about animal agriculture.

As Hernandez and dairy farmers know, when it comes to a cow’s well-being, milk is a marker.

“If cows are not being fed properly, or taken care of properly or housed properly, they are not going to make a lot of milk,” Hernandez says. “That’s a basic mammalian response. That should tell you something about the welfare of the animals.”

Class Act: Timothy Guthrie

Biochemistry senior Timothy Guthrie knows that science and success are about small steps. It’s those tiny strides that drive him to excel both in the lab and in the pole-vaulting pit.

Last summer Guthrie, a student athlete, earned a summer Biochemistry Undergraduate Summer Research Scholarship and spent lots of time in the lab of biochemistry professor Judith Kimble. There he worked, and continues to work, on making different mutations in a protein important for stem cell renewal.

“When I finally get something right in the lab that I’ve been working on for a month or two, it’s a really satisfying feeling,” says Guthrie, who plans to apply to medical school this summer.

Guthrie’s work allows the lab to better understand the molecular mechanism behind stem cell renewal in a tiny roundworm species called Caenorhabditis elegans, used as a model because their stem cells are easier to study than those in humans. Stem cell renewal is essential for the organism to keep producing cells it needs to develop and reproduce. By making different mutations to a protein important to this process, researchers can work to determine the role of the protein.

“The ultimate goal of stem cells is for therapeutic use, but we’ve got to work to understand the stem cells first—and the only way to do that is piece by piece,” says Guthrie. “That’s what Professor Kimble’s lab is doing.”

Getting involved in undergraduate research has helped Guthrie gain critical lab experience and also helped build connections between what he learns about in class and the experiments he performs in the lab.

“Along with knowledge of lab techniques and research, I’ve gained a better appreciation for the scientific discoveries we’ve already made,” he says. “All of those big successes and drugs we’ve discovered were made up of small steps like the ones I get to be a part of in the lab.”

Timothy Guthrie, Biochemistry senior, works with data on stem cells research.
Photo by: Robin Davies/UW–Madison MediaLab at Biochemistry

Undergrad helps teach orphans about hydroponic farming

There are capstones, and there are capstones.

For his capstone—a discipline-spanning research project required of all students graduating from CALS—soil science student Jacob Kruse BS’16 spent a summer working with orphans in Lima, Peru, to set up and run a hydroponic growing system.

More than 60 children from the Casa Hogar Juan Pablo II orphanage—a mission of the Diocese of La Crosse, Wisconsin—participated in growing crops that included tomatoes, peppers, bok choy and lettuce. The kids learned all about hydroponics, the art of growing plants in water, sand or gravel instead of soil, adding nutrients as needed.

But the project’s overarching benefits ran deeper. Beyond producing and learning about healthy food, “The goals were to teach children about water and natural resource use and reuse, help build connections between families and friends through common interests and projects and help the children develop responsibility,” says Kruse.

Kruse spent three months helping build the system and offering hands-on instruction on the basics of hydroponics—one class for older children and another for the younger ones. The kids learned about the environmental benefits of hydroponics, how to build home hydroponics out of household items and how to care for the garden.

A manufacturer of specialty chemicals for construction and industry, Sika Peru S.A., funded the project and built the garden structures with recycled materials. Mantisee, a nonprofit organization, provided the system design and plants. Both organizations, Kruse says, are concerned with natural resource use and social development, and they see the hydroponic system as a way to teach water use and nutrient efficiency—an important point in Lima, the world’s second-driest capital city.

Sika has also set up a scholarship and internship program for children at Casa Hogar who complete the hydroponic classes. “Sika’s scholarship and internship program will truly be life-changing for our children, and this collaborative project will have a lasting impact on our orphanage and the children who call it home,” says Jordan Zoroufy, Casa Hogar’s director of development.

Kruse’s faculty advisor, soil science professor Phillip Barak, is both impressed and delighted with the project. “We like our capstone experiences to be very hands-on and to have a service component,” Barak says. “Jake’s self-designed capstone sets a very high bar—food, children and education. Helping build a hydroponic food system from the ground up and turning it over to the children in the orphanage is quite an accomplishment.”

Adventures in Global Health

When it comes to study abroad experiences, an elephant ride in Thailand is pretty hard to beat.

“The entire time we were around the elephants, I was smiling uncontrollably,” says Gilad Segal, a microbiology major. “It was amazing to interact with them and get a sense of their personalities. Riding on the back of an elephant through the jungle and into a watering hole is something I never imagined I would do.”

And it was a great way to learn about the animals and efforts to protect them. Located in the “Golden Triangle”—the fabled convergence of Thailand, Myanmar and Laos—the Anatara Elephant Sanctuary improves the health and well-being of elephants by renting them from their owners and then caring for the elephant, the owner and his family as they continue to work humanely with tourists. In that part of the world, elephants frequently are victims of exploitation in the tourist industry, where their owners, called “mahouts,” earn a living by offering rides and having elephants perform tricks, often while not receiving adequate care.

“This solution allows the mahout to still live comfortably in that the camp provides them with a place to live and a monthly stipend for their elephant,” explains fellow microbiology major Lauren Raasch. “The elephants are cared for and are not overworked for tourist purposes.”

The students also examined the elephants’ microbiota by swabbing various parts of the animals and isolating and identifying microorganisms back in the lab at Mae Fah Luang University in Chiang Rai, Thailand.

The elephant camp was only one of several excursions during the seven-week, five-credit study abroad experience. The combined Microbiology 304/ Languages and Culture of Asia 300 program was the brainchild of bacteriology instructor Jon Roll BS’88 PhD’96, who developed the idea with biology advisor Todd Courtenay and teamed with Anthony Irwin, a doctoral student in the Department of Asian Languages and Cultures, to lead the course’s cultural components.

The program debuted last summer with 14 students and is poised to reach its cap of 20 students in summer 2017. It satisfies a required field study component for the popular Undergraduate Certificate in Global Health, a CALS-administered program in UW–Madison’s Global Health Institute.

Roll got the idea when visiting Mae Fah Luang University to explore research collaborations. “I saw their instructional lab facilities and was very impressed,” he says.

The course kicks off with a week of cultural orientation at another institution, the International Sustainable Development Studies Institute in Chiang Mai. There students learn some basic Thai and become acquainted with various aspects of Thai culture, which include wearing uniforms to class (a white top and dark pants or skirts); not pointing at things (which is considered rude); taking shoes off when entering a home; eating dinner food for breakfast (the Western idea of breakfast food doesn’t exist); and, above all, keeping voices down. “Tone it down like 10 notches,” advises Raasch in a blog she kept on the trip, noting that the Thai communication style tends to be quieter and less confrontational.

In addition to the elephant camp, field trips included meeting with SOLD, a nonprofit that offers job training to young people at risk for sex trafficking, and learning about nutrition and food safety from a monk who is well known for his scholarship in those areas.

As for the basic science component, although Microbiology 304 is a demanding course, students appreciated the program’s hands-on, in-the-field approach to learning.

“The microbiology lab helped me learn a lot not only about microbiology, but also how science applies to everyday life,” says biology major Therese Renaud.

Students came home with a much bigger picture of the world.

“I just want to talk forever about everything I had the opportunity to experience,” says Raasch. “The cumulative experience of adapting to and gaining an appreciation of a new culture was by far the most memorable part.”

Catch up with . . . Jacquelynn Arbuckle BS’91 Genetics

Dr. Jacquelynn Arbuckle’s exposure to the medical field began when her younger brother Adrian was born with cystic fibrosis. Arbuckle, only six at the time, recalls a childhood consumed with Adrian’s care. “We spent many days and weeks at the children’s hospital. I watched the doctors and nurses carefully try to find ways to keep Adrian alive,” Arbuckle says. Each year he was expected to have only a limited time to live.

That experience led Arbuckle to dedicate her life to medicine. After graduating from the UW–Madison School of Medicine and Public Health (SMPH) and completing her surgical residency in Massachusetts, Arbuckle returned to Madison, where she is an associate professor and surgeon at UW.

Arbuckle’s path to success was not easy. A native of Spooner, Wis., and an Ojibwe, Arbuckle grew up on the St. Croix reservation. She experienced firsthand how difficult the transition from a reservation community to a college campus can be. Now, as director of the SMPH-based Native American Center for Health Professions, she encourages young people to enroll at UW–Madison. She hopes that, once trained, they can help strengthen communities that often lack medical infrastructure and other resources—the same resources that ultimately saved her brother’s life.

What are some difficulties you experience when recruiting young Native Americans?

Coming from a close, familiar environment to a large campus can leave a student feeling isolated. Our Native culture is part of everyday life, and it can be challenging to feel free to practice our Native teachings without fear of humiliation. The Native American Center for Health Professions attempts to provide a safe cultural home for students and a place for community by providing mentoring, support and guidance as well as opportunities to explore our Native cultures around the state.

Why is it important for more Native American students to enter the medical field?

We need more Native healers in our state and across our nation. We need to be able to provide improved health care in our home communities, and we need to provide good mentors and role models for our young people. Our reservations have limited funds and limited access to health care. We need providers at all levels of health, including public health researchers, nurses, doctors, physician assistants, physical therapists, social workers and pharmacists. At NACHP, we reach out to interested students around the state and encourage them to consider coming to UW for their education. We are able to provide rotations at tribal clinics for those who are interested in this experience. During the rotations, students are exposed to true patient-centered, coordinated care as well as a wealth of cultural experiences.

How do you maintain your connection to the St. Croix reservation?

Mainly through my family. I go home routinely and spend time there. I have made connections with our tribal health director as well as our education director, and we are working on ways to improve resources and motivate young people together.

Photo courtesy of University Communications

A New Weapon Against Bacterial Disease

Bacteria that are resistant to antibiotics are one of the biggest problems facing public health today. About 800,000 children worldwide die before their fifth birthday from diarrheal diseases that evade treatment. The concentration of those diseases is highest in parts of Africa and Asia.

To address the problem, CALS biochemist Srivatsan (“Vatsan”) Raman hopes to harness the power of phages—viruses that infect bacteria but leave humans unscathed. With help from a grant from the Bill and Melinda Gates Foundation, Raman’s team is designing phages to specifically target bacteria that are causing diseases in infants.

Raman describes antibiotics—how doctors usually fight infections—as hammers that take out many bacteria, both harmful and beneficial. This means they can affect the entire human microbiome, which is the community of microbes on, inside and around the human body.

“We do not yet have the tools to selectively edit the composition of a microbiome,” Raman explains. But that is one of the goals of his lab’s work with phages. Unlike antibiotics, phages are very specific. A phage only infects one type of bacterial host. It is this specificity that presents Raman and his researchers with opportunities—but also some challenges.

Phages, which resemble lunar landers, locate bacterial hosts by attaching to specific receptors on the cell’s surface. Once they have found their host, some phages, called obligate lytic phages, quickly infect the cell and replicate. Once replication is complete, the new phage progeny burst out of the cell, ready to infect and kill the next available host.

Raman’s goal is to be able to control many steps in this process. He is investigating a way to engineer a phage that can be programmed to target specific bacteria. By changing just the “legs” of the lunar lander, the designer phage can target and eliminate any bacteria the researchers wish.

However, while destruction of bacteria is the ultimate goal, the process also creates problems. Many bacteria contain toxins that are released if the bacteria die in large numbers. So Raman’s team is also trying to control the rate at which phages infect and kill cells inside the body. “We can keep the phage on a leash and determine when and where it can infect,” describes Kelly Schwartz, a postdoctoral fellow in Raman’s laboratory.

Raman believes “designer phages” have great promise for human health.

“I was drawn to this research because designer phages can provide a potential solution to the antibiotic resistance problem,” notes Raman. “These bacteria are resistant to anything you throw at them and are killers in developing countries.

“And the next question, if we are successful, is ‘How can we turn these phages into actual medications that can be delivered to these areas?’ That challenge awaits us further down the road,” Raman says.

Vatsan Raman in his lab: The biochemist is engineering viruses that can vanquish harmful bacteria. Photo by Robin Davies/UW–Madison MediaLab at Biochemistry

Growing Veggies with City Kids

Natalie Hogan, a sophomore majoring in dietetics and Spanish, hopes to practice nutrition education in schools, teaching kids about healthy foods. This past summer she honed her skills by gardening and cooking with school-age children in the Young Scientists Club, a program run by the Milwaukee-based Urban Ecology Center. Most of the kids were of Latino and African American backgrounds, and many live in neighborhoods where fresh produce is hard to come by.

In addition to preparing dishes like whole wheat pizza with fresh veggies—a big hit, Hogan says—kids took part in lessons about nutrition, sustainability and climate change, including such concepts as sustainable agriculture and carbon footprints from farm to table.

Hogan and her project partner, sophomore Katherine Piel, developed their curriculum through a Wisconsin Open Education Community Fellowship, an award totaling up to $6,000 offered by the Division of Continuing Studies and the Morgridge Center for Public Service.

Hogan learned as much from the children as they learned from her. The kids at the Urban Ecology Center’s Menomonee Valley branch were excited about gardening— planting, watering, harvesting and even weeding—while kids at Washington Park loved to cook. Hogan and Piel tailored lessons to suit those preferences, recognizing that enthusiasm is a key ingredient in learning.

The experience led Hogan to broaden her career goals. She still wants to teach children, but she’d like to include families and the larger community. “The parents are the ones buying the groceries and cooking the meals,” says Hogan. “In order to make a difference, I must work to make an impact on parents, educators, policy makers—on all those who play a role in the health of our planet and people.”

And she relished the small victories, like getting 8-year-old Victorio to eat a radish. Initially he made a “yuck” face, but out in the garden, after being the first to spot the red tops, he took charge of harvesting, washing, cutting and adding them to a salad.

“When it came time to eat them, he described them as ‘crunchy and spicy, but still pretty good!’” says Hogan. “That was a positive experience because we could see his change in attitude. And he wasn’t the only one!”

Five things everyone should know about . . . Pulses

1. You’ve eaten them without knowing it. If the word “pulse” as a food leaves you flummoxed, fear not. The word pulse comes from the Latin word “puls,” which means thick soup or potage. No doubt you’ve enjoyed dried beans, lentils and peas in a soup or stew. Pulses are the edible dried seeds of certain plants in the legume family. Soybeans, peanuts, fresh peas and fresh beans are legumes but not considered pulse crops. Some lesser-known pulses like adzuki bean and cowpea play critical roles in diets around the world. Many pulses are economically accessible and important contributors to food security.

2. They’re very nutritious. Pulses contain between 20 and 25 percent protein by weight—twice the amount you’ll find in quinoa and wheat—and next to no fat. Around the world, they are a key source of protein for people who don’t eat meat or who don’t have regular access to meat. Pulses need less water than other crops, which adds to their appeal and value in areas where water is scarce.

3. Pulse crops have other environmental benefits as well. As members of the legume family, pulses are capable of taking nitrogen from the air and putting it back in the soil in a form available to plants. This makes legumes a critical part of any crop rotation and contributes significantly to sustainable farming. Pulses are grown worldwide but are particularly well adapted to cool climates such as Canada and northern states in the U.S.

4. We’re learning a lot about pulses from a recently sequenced genome. Adzuki bean was domesticated 12,000 years ago in China and is one of the most important pulses grown in Asia. There it is known as the “weight loss bean” because of its low calorie and fat content and high levels of protein. A recent genome sequencing collaboration among scientists in India and China revealed that genes for fat were expressed in much higher levels in soybean than in adzuki bean, while genes for starch were expressed at greater levels in adzuki bean. Their findings suggest that humans selected for diversified legumes in their diet—some that would provide oil and others that would provide starch.

5. It’s their year! The 68th UN General Assembly declared 2016 the International Year of Pulses, so now is the time to eat and learn. Events taking place all around the world focus on everything from cooking pulses (sample recipes: fava bean puree, carrot and yellow split pea soup) to growing them and incorporating them into school lunches. Learn more at www.fao.org/pulses-2016/en/.