Forever Rising

To begin to understand the outsized potential and sheer weirdness of yeast, it helps to consider the genetics behind one of the world’s most successful and useful microorganisms. It also helps to consider lager.

Lager, or cold-brewed beer, is made possible by the union of two distinct species of yeast. About 500 years ago, these two species, Saccharomyces eubayanus and Saccharomyces cerevisiae, joined in a Bavarian cellar. They gave us a hybrid organism that today underpins an annual global market for lager estimated at one-quarter of a trillion dollars.

“We would not have lager if there hadn’t been a union equivalent to the marriage of humans and chickens,” notes Chris Todd Hittinger PhD’07, a CALS professor of genetics and a co-discoverer of S. eubayanus, the long-sought wild species of yeast that combined with the bread- and wine-making S. cerevisiae to form the beer. “That’s just one product brewed by one interspecies hybrid.”

Yeasts, of course, are central to many things that people depend on, and the widespread domestication in antiquity of S. cerevisiae is considered pivotal to the development of human societies. Bread and wine, in addition to beer, are the obvious fruits of taming the onecelled fungi that give us life’s basics. But various strains and species of yeasts also are partly responsible for cheese, yogurt, sausage, sauerkraut, kimchi, whiskey, cider, sake, soy sauce and a host of other fermented foods and beverages.

Baker’s yeast, according to yeast biologist Michael Culbertson, an emeritus professor and former chair of UW– Madison’s Laboratory of Genetics, ranks as “one of the most important organisms in human history. Leavened bread came from yeast 5,000 years ago.”

Beyond the table, the microbes and their power to ferment have wide-ranging applications, including in agriculture for biocontrol and remediation, as well as for animal feed and fodder. They are also widely used to make industrial biochemicals such as enzymes, flavors and pigments.

What’s more, yeasts are used to degrade chemical pollutants and are employed in various stages of drug discovery and production. Human insulin, for instance, is made with yeast. By inserting the human gene responsible for producing insulin into yeast, the human variant of the hormone is pumped out in quantity, supplanting the less effective bovine form of insulin used previously.

Transforming corn and other feedstocks, such as woody plant matter and agricultural waste, to the biofuel ethanol requires yeast. Hittinger is exploring the application of yeast to that problem through the prism of the Great Lakes Bioenergy Research Center (GLBRC), a Department of Energy-funded partnership between UW–Madison and Michigan State University. Hittinger leads a GLBRC “Yeast BiodesignTeam,” which is probing biofuel applications for interspecies hybrids as well as genome engineering approaches to refine biofuel production using yeasts.

“There are lots and lots of different kinds of yeasts,” explains Hittinger. “Yeasts and fungi have been around since Precambrian time—hundreds of millions of years, for certain. We encounter them every day. They’re all around us and even inside us. They inhabit every continent, including Antarctica. Yeasts fill scores of ecological niches.”

The wild lager beer parent, S. eubayanus, for example, was found after a worldwide search in the sugarrich environment of Patagonian beech trees—or, more specifically, in growths, called “galls,” bulging from them. (How S. eubayanus got to Bavaria hundreds of years ago and made the lager hybrid possible remains a mystery.) It is possible, notes Hittinger, to actually smell the S. eubayanus yeast at work, churning alcohol from the sugars in the galls themselves.

Though the merits of known yeast species for making food, medicines and useful biochemicals are numerous, there are likely many more valuable applications of existing and yet-to-bediscovered yeasts.

For Hittinger and the community of yeast biologists at UW–Madison and beyond, a critical use is in basic scientific discovery. The use of yeast as a research organism was pioneered by Louis Pasteur himself, and much of what we know about biochemical metabolism was first studied in yeasts.

Since the 1970s, the simple baker’s variety of yeast has served as a staple of biology. Because yeasts, like humans and other animals, are eukaryotes— organisms composed of cells with a complex inner architecture, including a nucleus—and because of the ease, speed and precision with which they can be studied and manipulated in the lab, they have contributed significantly to our understanding of the fundamentals of life. And because nature is parsimonious, conserving across organisms and time useful traits encoded as genes, the discoveries made using yeast can often be extended to higher animals, including humans.

“The model yeast, S. cerevisiae, has been instrumental in basic biology,” says Hittinger. “It has told us something aging. In terms of understanding basic processes, it’s a tough model system to beat. It’s a champion model organism for genetics and biochemistry.”

“It is widely unappreciated how thevast terrain of biology has been nourished by yeast,” argues Sean B. Carroll, a CALS professor of genetics and one of the world’s leading evolutionary thinkers. It was in Carroll’s lab a decade ago as a graduate student that Hittinger first turned his attention to yeast, coauthoring a series of high-profile papers that, among other things, used the yeast model to catch nature in the act of natural selection, the proof in the pudding of evolutionary science.

Now the model is about to shift into an even higher gear. The work of Hittinger and others is poised toenhance the yeast model, add many new species to the research mix, and begin to make sense of the evolutionary history of a spectacularly successful and ubiquitous organism. The advent of cheap and fast genomics—the ability to sequence and read the DNA base pairs that make up the genes and genomes of yeasts and all other living organisms—along with the tools of molecular biology and bioinformatics promise a fundamental new understanding and order for yeast biology.

“This is all about weaponry,” explains Carroll, noting that Hittinger, in addition to possessing “great benchtop savvy and skill,” has armed himself remarkably well to exploit yeast genetics through the mutually beneficial prisms of molecular biology, evolutionary biology and bioinformatics (which harnesses computers to help make sense of the bumper harvests of data). “He has a determination and resolve to get the answer to any important question— whatever it takes,” says Carroll.

The big questions on the table for Hittinger and others include ferreting out “the genetic factors that drive species diversification and generate biodiversity,” and weaving that granular understanding into the larger fabric of biology. Because the functional qualities of all the various yeast species differ in order for the microbe to thrive in the many different environments it inhabits, the genetic code that underpins their different physiological and metabolic features varies accordingly.

In short, it takes a diversity of talents to inhabit every major terrestrial and aquatic environment the world has to offer. Species that thrive in South American tree galls and species that eke out a living on human skin require different skill sets in order to cope with vastly different environments and utilize different resources. Each of those skills is determined by the organism’s genetic makeup, and as scientists discover and extract the lode of genomic data found in new species discovered in the wild, new and potentially useful genetic information and metabolic qualities will come to light.

These are big, basic biological questions. But their answers promise far more than simply satisfying scientific curiosity. Yeasts are big business. They are medically and industrially important. The secrets they give up will, without a doubt, amplify our ability to produce food, medicine and industrial biochemicals.

To lay the groundwork, Hittinger and an international collaboration of yeast biologists are setting out, with support from the National Science Foundation (NSF), to map the genetic basis of metabolic diversity by sequencing the genomes of the 1,000 or so known species of yeast in the subphylum that includes Saccharomyces. Three hundred times smaller than the human genome, a typical yeast genome consists of 16 linear chromosomes and, roughly, 6,000 genes and 12 million letters of DNA.

“This is the best possible time to be a yeast biologist,” avers Hittinger. “Our collections have been vastly improved, and we can sequence genomes a hundred at a time. The important thing to know is that yeast is not just one organism or one species. There are thousands of yeasts, and they each have their own evolutionary history.”

Acquiring new species from the wild and sequencing their genomes will enable Hittinger and his colleagues to construct an accurate yeast family tree.

“If we don’t understand what’s out there and how they evolved, we’re notgoing to understand how to make use of them,” Hittinger notes. “Now, we can rip ’em open, get a peek at their genomes and see what the differences are and how they’ve changed over time.”

Thus stalking new strains and species of yeast in the wild is an essential part of the program, according to Hittinger, who routinely dispatches students, including undergraduates, to seek out new yeasts in nature. Half of all the known species of yeast have been described scientifically only within the past 15 years, meaning scientists have only a limited understanding of the world’s yeast diversity.

“Until recently, most strain collections have been paltry and biased towards domesticated strains,” says Hittinger. “If we can expand our understanding of the wild relatives, we can use them as an evolutionary model.Yeasts have a much less welldeveloped history in ecology and natural history.”

A recent yeast hunting excursion in Wisconsin by one of Hittinger’s students yielded three strains of the same S. eubayanus lager yeast parent found in tree galls in South America. Discovered near Sheboygan, the yeast has been cultured in Hittinger’s lab and samples have been provided to CALS food science professor James Steele, whose group is setting up a new comprehensive program in fermentation science and, with the help of a gift from Miller-Coors, a new pilot brewery lab in Babcock Hall. (Steele is also looking to support other fermented beverages in Wisconsin—namely, wine and cider— in both production and education. See sidebar on page 20.)

“We grew up a few hundred billion cells, gave them to Jim Steele to brew beer, and we’re eagerly awaiting the results,” says Hittinger, who explains that another focus of his lab is making interspecies hybrids, such as the lager hybrid. “Now that we’ve identified the wild species, we can make crosses in the lab to make hybrids that produce flavors people are interested in.”

In the food science realm, says Steele, yeast research is focused on the functional characteristics—fermentation qualities, sugar utilization, flavors—of a particular strain of yeast. “How does microbial physiology link to flavor in fermented beverages?” he asks.

Saccharomyces strains are the workhorse and best-known yeasts, including many of the most medically and biotechnologically important. With the $2 million award from NSF,
Hittinger and his colleagues will use the genomes to develop a robust taxonomy of important yeasts and look for the genetic footprints that give rise to yeast biodiversity, an  evolutionary history of their metabolic, ecological and pathogenic qualities. Such an understanding will elevate yeast to a new plane as a model and will undoubtedly serve as the basis of valuable new technologies.

Hittinger cautions, however, that sequencing yeast genomes is only a start: “We can very easily read gene sequences, but we don’t yet know how to interpret them fully. We will need to read those bases and make functional predictions” to extend both the knowledge of yeast biology and their potential use in industry.

“But if it weren’t for that natural diversity, we wouldn’t be able to enjoy Belgian beers,” says Hittinger, referencing the gifts conferred by different yeasts and their varied genetic underpinnings, resulting in the different flavors of ales, lagers and Belgians.

One of the central metabolic qualities of the familiar yeasts, of course, is their ability to ferment. Put simply, fermentation is a process by which cells partially oxidize or burn sugar. Among yeasts, the propensity to ferment in the presence of oxygen has evolved only in Saccharomyces species and a few others.

“To make a living using this process, you have to be a glucose hog,” says Hittinger. “But you don’t burn it all the way. You leave some energy on the table. Ethanol burns because it is unoxidized fuel.”

Different kinds of cells can perform fermentation if they become oxygenstarved Human cells, for example, ferment when starved of oxygen, causing painful muscle cramps. Given enough sugar, cancer cells can ferment, and do so to survive in oxygen-poor environments.

Indeed, Hittinger’s research on the cellular resemblance between Saccharomyces yeasts and cancer cells (for which he recently was named a Pew Biomedical Scholar) focuses on identifying which steps in yeast evolution were key to making the transition from respiratory to fermentative metabolic activity, as well as the sequence of those evolutionary events.

“Armed with that information, we should be able to shed some light on how cancer cells make that same transition over an individual’s lifetime,” says Hittinger.

Genes, Hittinger knows, hold the secrets to the functional qualities of yeast. Those microbial secrets, in turn, promise us food, fuel, pharmaceuticals— and, of course, beer. Like bread and wine, the gift of lager is no small thing. Who knows what other gifts, large and small, may lurk in the genes of these microorganisms?


Headed into the wild? If so, you could help Chris Todd Hittinger’s team identify new yeast species and strains. To learn more, visit http://go.wisc.edu/wildyeast

To watch an interview with Chris Todd Hittinger, visit http://go.wisc.edu/hittingerinterview


Brewing Beer-6005

Food science professor James Steele (left) and students are creating a red lager to be brewed by the Wisconsin Brewing Company. Steele and colleagues are launching a fermented foods and beverages program to take research and teaching to the next level.

“Farm to Glass” and More: Fermenting a Growth Industry

We all know Wisconsin as the land of beer and cheese. But in the not too distant future, Wisconsin may also become famous for other fermented products, notably wine and cider, thanks to growing public taste for those products and a blossoming wine- and cider-making culture in the Badger State.

Wisconsin now has about 110 wineries—up from 13 in 2000—and has been adding around a dozen new ones each year in recent years. Many of these operations could use some help, which is on the way in the form of a newly appointed CALS-based outreach specialist whose job is to support the state’s wine and hard apple cider industry.

Leaders of the Wisconsin Grape Growers Association, the Wisconsin Vintners Association and the Wisconsin Winery Association worked with CALS faculty in food science and horticulture to apply for a Specialty Crop Block Grant to support the position through the Wisconsin Department of Agriculture, Trade and Consumer Protection, with the associations providing matching funds. The specialist is scheduled to start working in early 2015.

The position is part of a larger effort to boost fermentation in Wisconsin. CALS food science professor James Steele and his colleagues are laying the groundwork for a comprehensive fermented foods and beverages program through the Department of Food Science—a program that will take to the next level much of the research and teaching the department has been building on for decades.

Already the program is bearing fruit—or, one might more literally say, “bearing beer.” Over the spring 2015 semester, students participating in Steele’s Fermented Foods & Beverages Laboratory will create and develop a new red lager recipe to be brewed by the Wisconsin Brewing Company and sold at the Memorial Union.

A central goal of the program, Steele explains, is to help improve the quality of fermented food and beverage products. As such, the functional roles played by yeast to influence such characteristics as flavor, color and other attributes will be very much in the spotlight.

“Yeast is a key player, beyond the shadow of a doubt,” says Steele. “It is extremely important, but from a food science perspective, it hasn’t gotten a lot of attention.”

With the help of yeast researchers such as Chris Todd Hittinger and his genetics colleague Audrey Gasch, Steele hopes to create an environment where the food science nuances of fermentation are teased out to the benefit of both growers and the producers of fermented foods and beverages.

The basic fermentation characteristics of various yeast strains are of interest, according to Steele: “For example, how does microbial physiology link to flavor in fermented beverages? These collaborations give us opportunities to look for new strains or develop new strains that could allow for the production of beverages with different flavors. And what we learn in one industry, we can apply to another.”

From Trash to Treasure

CDR food technologist Dean Sommers showing a beaker of acid whey. The high-tech filters used to separate the various components are inside the metal pipes.

CDR food technologist Dean Sommers showing a beaker of acid whey. The high-tech filters used to separate the various components are inside the metal pipes.

With exploding consumer demand for Greek yogurt, production is up. That’s great for food companies’ bottom lines, but it also leaves them dealing with a lot more acid whey, a problematic by-product of the Greek yogurt-making process.

Acid whey, if not properly disposed of, can cause environmental problems. Currently, companies typically pay to landspread it on farmers’ fields or dump it down the drain. Where the option is available, some plants are starting to send it to anaerobic digesters, where it’s fermented to produce methane.

But scientists at the CALS-based Wisconsin Center for Dairy Research (CDR) are developing a better option, one that will transform this trash into treasure.

“The whole goal is to take this problematic mixture of stuff—acid whey—and isolate all of the various components and find commercial uses for them,” says Dean Sommer, a CDR food technologist.

That’s no easy task.

Food companies have been fractionating the components of sweet whey—the by-product of cheese production—for more than a decade now, extracting high-value whey protein powders that are featured in muscle-building products and other high-protein foods and beverages.

Compared to sweet whey, however, acid whey from Greek yogurt is hard to work with. Similar to sweet whey, it’s mostly water—95 percent—but it contains a lot less protein, which is considered the valuable part. Some of the other “solids” in acid whey, which include lactose, lactic acid, calcium, phosphorus and galactose, make it more difficult to process. For instance, thanks to galactose and lactic acid, it turns into a sticky mess when it’s dried down.

Instead of drying it, CDR scientists are developing technologies that utilize high-tech filters, or membranes, to separate out the various components.

“We’re taking the membranes that are available to us and stringing them together and developing a process that allows us to get some value-added ingredients out at the other end,” says dairy processing technologist Karen Smith, who is working on the project.

At this point, the CDR has set its sights on lactose, an ingredient that food companies will pay good money for in food-grade form.

“It’s the lowest-hanging fruit, the most valuable thing in there in terms of volume and potential worth,” says Sommer.

The technology is quite far along. While Sommer can’t divulge names, a number of companies are already implementing lactose-isolating technology in their commercial plants.

Isolating the other components will come later, part of the long-term vision for this technology. When it’s perfected, explains Sommer, acid whey will be stripped of its ingredients until there’s nothing left. “It will just be water,” he says.

Turning them on

CALS biochemistry professor Hazel Holden is excited about science. So when she witnessed science becoming “boring” in her daughter’s classroom—a feeling several classmates shared—she decided to take matters into her own hands.

Some five years ago she created Project CRYSTAL—Colleagues Researching with Young Scientists, Teaching and Learning—a program designed to challenge middle schoolers who show an aptitude for science. The program is funded by the National Science Foundation.

Each school year, Holden takes four eighthgrade students under her wing for weekly hands-on sessions. “We’re trying to de-stigmatize science by exposing kids to material they otherwise would never have been exposed to,” she says.

And it’s impressive stuff. The students start by extracting DNA from yeast cells they have grown themselves. They then use the extracted DNA to practice the art of polymerase chain reaction (PCR for short), the process by which a piece of DNA is replicated to produce thousands to millions of copies of a targeted DNA sequence.

Switching between 10-minute lecture and lab segments keeps the kids motivated, and with clever anecdotes sprinkled throughout the lecture material, the young students are never bored.

This class format is used to progress to more advanced skills such as protein purification—the isolation of proteins from, in this case, E. coli cells— and X-ray crystallography, a tool used by the students to identify the molecular structure of a crystalline protein. The year ends with a group poster presentation— a rite of passage that most students don’t experience until much later.

“I was able to work in a real lab and gain lab experience. I do not think many 12-year-olds are able to have an experience like that,” says Project CRYSTAL alumna Manpreet Kaur, now a high school senior. “Before the program I did not have any knowledge of X-ray crystallography, and now I am able to explain the process in science classes.”

The program inspired Kaur to take several AP Science classes and affirmed her plans to become a doctor.

Holden has published her curriculum as an 80-page book, and Project CRYSTAL was introduced at Indiana University–Purdue University Indianapolis during the current school year.

The program has benefited graduate students almost as much as the youngsters, giving them experience teaching complex science at the most basic level.

“This class puts our own graduate work in perspective. You get more excited about your own research by watching them get excited about the small things, like pipetting,” reflects biochemistry doctoral student Ari Salinger.

Looking ahead, Holden hopes that what she has created will inspire other universities to implement similar programs.

“The students want to learn more—and they are ready for it,” Holden says.

New “Bug Guy” on Campus

Are bed bugs getting you down? Is a hard-to-identify pest ravaging your vegetable garden? You can get in touch with PJ Liesch MS’10, manager of the UW–Madison Insect Diagnostic Lab, where he succeeds the retired Phil Pellitteri BS’75 MS’77. Liesch (sounds like “leash”), who earned his master’s degree in the lab of entomology professor and UW–Extension specialist Chris Williamson, has been working as a research scientist on campus for the past few years and served as interim manager of the Insect Diagnostic Lab before being named to the position permanently.

He greatly enjoys interacting with the public. When he receives an inquiry, he not only does his best to answer the question, he also tries to provide more information about the insect and to share additional photos and links to help people learn more. Liesch started a blog, “What’s Crawling in the Lab,” to share what people in Wisconsin are finding in their homes, backyards, forests and fields—you can see it at http://go.wisc.edu/ insect blog. He also started a Twitter account people can use to reach him, @UW_InsectLab. And you can always reach him by phone at (608) 262-6510.

Unpuzzling Diabetes

The body makes it seem so simple.

You take a bite of supper, and the black-box machinery of metabolism hums into life, transforming food into fuel and building materials. It’s the most primal biology: Every living thing must find energy, and must regulate its consumption.

But for an alarming and ever-increasing number of people, the machinery breaks down. The diagnosis? Diabetes.

Alan Attie, a CALS professor of biochemistry, has been peering into the black box for two decades now, trying to identify the pathways in our bodies by which the disease is formed. “You can’t find a better excuse to study metabolic processes than diabetes,” he says. “It’s very, very rich.”

Type 2 diabetes, caused by an inability to produce enough insulin to keep the body’s blood glucose at normal levels, is a global health crisis that has accelerated at a frightening speed over the last 20 years—roughly the same time Attie has been studying it.

It’s an enormously complex disease driven by both genetics and the environment. A DNA glitch here, an external variable there, and the body slides irretrievably out of balance. But only sometimes. Most people who develop type 2 diabetes are obese, yet most people who are obese don’t actually wind up diabetic.

Tracking this riddle has led Attie and his lab to several major discoveries, chief among them identifying two genes associated with diabetes: Sorcs1 and Tomosyn-2. Through years of elaborate experimentation, Attie and his team teased them from the genetic haystack and then relentlessly deciphered their role in metabolic malfunction.

Science has uncovered more than 140 genes that play a role in diabetes, yet genetic screening still has little value for patients. As with any part of a large and complicated puzzle, it’s hard to see precisely how Sorcs1 and Tomosyn-2 fit in until we have more pieces. The biology of diabetes is so complex that we can’t be certain what the discoveries may ultimately mean. But both genes have shed light on critical stages in metabolism and offer intriguing targets for potential drugs.

Attie need not look far to replenish his motivation. His own mother suffers from diabetes, and she used to quiz him weekly about when he would cure her. “The painful answer is that translation of basic research into cures takes a long time,” Attie once told the American Diabetes Association. “The most important clues that can lead to cures do not necessarily come from targeted research or research initially thought to be relevant to the disease.”

Alan Attie grew up an expatriate in Venezuela, where his father, Solomon, originally from Brooklyn, New York, ran a textile factory (Attie’s mother had family in South America). Poverty and then World War II had kept Solomon from traditional schooling, but he managed to put himself through high school at night, and he nurtured a deep passion for literature, poetry, history and politics. At home he ran the family dinner table like a college seminar. “Our evening meal was like a 20-year course,” recalls Attie. “It was the most stimulating part of our day growing up. I was reading Shakespeare with my father and my siblings when I was 10 years old.”

Still, Attie wasn’t quite prepared for the academic rigor of UW–Madison when he arrived in 1972. He’d never had to work particularly hard in high school and was shocked by how much time and effort college required. His grades were poor and his introduction to chemistry lackluster.

But the BioCore curriculum—an intercollege program focusing on doing science, not memorizing facts—turned Attie’s natural inquisitiveness and enthusiasm toward science. During a cell biology course where his lab reports had to be written like journal articles, Attie decided he really wanted to be a biologist. Following graduate school at the University of California, San Diego, he found himself back at UW– Madison as a young assistant professor. Ten years had passed since his freshman matriculation.

Attie’s first research focus was cholesterol metabolism, but his curiosity led him elsewhere. Until 2001 he held a joint appointment with the School of Veterinary Medicine, where he taught an introductory class in biochemistry. While preparing for the class he read broadly in metabolism and found himself continually drawn toward the quandary of diabetes.

Increasingly he found himself suffering from “discovery envy,” he says. “And then I finally decided one day I do want it to be me.” Midcareer course changes are never easy, but Attie plotted a careful transition that gained momentum with hard work and good fortune.

In 1992 Dennis McGarry, a prominent diabetes scholar, published a provocative thought experiment in Science. It had been observed for centuries that diabetics had sweet urine, and one of the earliest researchers in the disease, Oskar Minkowski, had surmised that diabetes was therefore a dysfunction of sugar metabolism. McGarry speculated that if Minkowski had had no sense of taste and had relied instead on the smell of a diabetic’s urine, he would have smelled ketone bodies, a hallmark of lipid metabolism. Might he have concluded instead that diabetes was a defect in lipid metabolism?

Soon afterward, McGarry and Attie wound up at the same research symposium in Edmonton and shared breakfast every morning. “I’m really interested in diabetes,” said Attie. “Is there room for someone like me who has been working on lipid metabolism for 20 years?” McGarry encouraged Attie, a pep talk that gave him confidence that maybe he wasn’t committing career suicide.

Gradually Attie’s new focus gathered steam. When another UW diabetes researcher left for Washington state, Attie was able to bring on researcher Mary Rabaglia from that lab. She was highly skilled in the lab manipulation of pancreatic islets, the home of the beta cells that produce insulin. Her arrival jump-started Attie’s efforts. “It was an unbelievable stroke of luck because she brought all that expertise,” says Attie.

Attie also felt he needed a new analytical toolbox, and he saw real potential in using mouse genetics to study diabetes. With one small problem: He didn’t know any genetics. So he went to the Jackson Laboratory in Bar Harbor, Maine—a global center of mouse research—and took a mouse genetics course (which he now teaches there).

The learning soon paid off. Gene chip technology was just becoming available, and industry pioneer Affymetrix was looking to commercialize the expensive technology. The company was interested in funding labs to demonstrate that the power was worth the price. Attie proposed looking at how genes were turned on and off in the fat-storing cells of diabetic mice, and Affymetrix approved the project.

Exploring gene expression—which genes get turned on and off—was an important first clue in figuring out which genes might contribute to diabetes. With thousands of proteins and a still unknown quantity of genes in play, diabetes is vexingly elaborate. Gene chip technology brought previously unimaginable power to the equation. “The reason for doing genetics is we can’t imagine the complexity of these processes,” Attie explains. “We really do need the serendipity of genetics to find our way.”

Attie sent Sam Nadler, a new M.D./ Ph.D. candidate, off to Maryland and California for training. It was an ambitious project, and the old analytical tools broke under the mountain of new data. Enlisting the help of Brian Yandell, a CALS professor of horticulture with a joint appointment in statistics, they were able to interpret their data.

In late 2000 the team published the first paper on genome expression changes in diabetes using gene chip technology. It was premature to get too excited—they were, in effect, translating a book of unknown length, and had only finished the first of many chapters.

But it was an important demonstration of the power of their new tools. And Attie and his lab were now a known quantity in the world of diabetes research, and part of the conversation.

Attie’s team could now assess any DNA they got their hands on, but there was still too much static hiding the working genes. Only by basing his experiments on other, more tangible clues could Attie find anything useful.

He decided to tackle the obesity link. “Most people who have diabetes are obese, but most people who are obese don’t have diabetes,” he notes. To get at the problem, Attie’s team took two strains of lab mice: a standard control strain known as “black 6” (B6) and a diabetic strain (BTBR) that, when the mice became obese, were diabetic. The team intercrossed the two strains for two generations, testing the second generation of mice for diabetes. Offspring were strategically bred to enable the lab to pinpoint the genes responsible for diabetes susceptibility.

The collaboration that had begun with Brian Yandell now expanded to include Christina Kendziorski, a professor of biostatistics with the School of Medicine and Public Health. Teasing conclusions from large data sets was an exciting new field, and the team saw real potential for developing new techniques— and they had the statistics grad students to do it. Some even took up residence in Attie’s lab to be closer to the puzzles cascading from each successive experiment. It was like game after game of Clue, only with a half million possible rooms, a half million possible murder weapons, and a half million possible suspects. And as many homicides as you wanted to look for. Some computations took days.

Ultimately they were looking for genes, but what they found at first were just general target zones, located on chromosomes 16 and 19. That was a big first step, but chromosomes are constructed of many millions of base pairs—the building blocks of DNA . Considered relatively small, chromosome 19 still runs to about 61 million base pairs. The first round of sifting reduced the search zone to a neighborhood with only 7 million base pairs, an almost 90 percent narrowing of the field.

Pinpointing the gene required a constant shuffling of the genetic deck, counting on the random nature of sexual reproduction to winnow away the chaff, revealing the kernel of the gene. It’s a process that can take years, measured in mouse generations. Finally, in 2006, they were able to pinpoint the precise location of Sorcs1. It was a triumph, but it also set the stage for heartbreak.

Meanwhile, other projects kept rolling. Sushant Bhatnagar, a postdoctoral scholar in biochemistry, was working on the other target zone—chromosome 16. In 2011 he zeroed in on Tomosyn. “It was crazy,” he says of the work needed to sift through so many mouse generations.

But in the end they discovered that Tomosyn-2 played a critical role in diabetes. Tomosyn was also more willing to give up its secrets. Most of the myriad proteins in a beta cell are positive regulators, which means they facilitate flipping the insulin switch to “on.” Tomosyn is an off switch—one of very few known to exist.

Though mouse and human diabetes are different, the lab confirmed that the human version of Tomosyn plays a similar role. Now the challenge is using the clue to develop a targeted therapy. “Loss of insulin secretion leads directly to diabetes,” Bhatnagar explains. “If you can fix insulin secretion you can fix the majority of diabetes.”

Finding Sorcs1 had been difficult enough, but unlocking how it worked would prove devilishly complex. Two students tried and failed, and eventually left research altogether, demoralized by the dead ends. Attie felt terrible. “I always feel responsible for everything that goes on in the lab,” he says.

Then, in 2012, Attie welcomed a new postdoctoral scholar. The only problem was that Sorcs1 was a beta cell problem, and Melkam Kebede did not come to Madison to work on beta cells.

A child prodigy from Ethiopia by way of Australia, Kebede was through college by age 18 and had her Ph.D. at 23. After spending most of her career on beta cells, she was looking for something  different in her second postdoctoral position. Able to go almost anywhere, she chose Madison, and Attie.

“Of all the places I interviewed, Alan was the most passionate about teaching,” Kebede says. And she liked the way he encouraged people. She’d always been told that she was exceeding expectations, and nobody challenged her during interviews. Except for Attie. “I wanted someone to push me more, so I can do more than what I’ve been doing,” she says.

Pushing people, of course, is a delicate process, and easily fumbled. Attie instead seems to pull with a magnanimous curiosity. And with Kebede he was patient but persistent. Attie would keep asking: Why were the Sorcs mice diabetic? “You still have the parents of these mice waiting in the hallway at the hospital,” he would say. “They are buying so many coffees. You’ve got to come up with a reason why they are diabetic.”

Finally, Kebede couldn’t resist the puzzle—the opportunity to find the link between obesity and diabetes. While the lab hadn’t cracked Sorcs, they had narrowed the focus. And Angie Oler, an invaluable technician with 20 years of experience, would help her get the end game rolling.

In an obese person, cells do not respond completely to normal insulin levels—this is called insulin resistance. To compensate, the body typically produces more insulin. Type 2 diabetes develops when the insulin resistance outpaces the body’s attempt to make more. Sorcs seemed to play a role, but how?

“There are so many things in the body that contribute to controlling glucose levels in the blood,” Kebede explains. A beta cell has to sense an increase in glucose and secrete insulin, which then triggers other reactions that lead, ultimately, to glucose being removed from the blood and absorbed by the cells that need it. Sorcs1 could work anywhere in this great game of cellular call and response.

Despite all of the genetic and biochemical tools at Kebede’s disposal, it was ultimately a simple observation in a microscope that yielded the key. Insulin is manufactured in advance and stored by beta cells in the pancreas, then released as needed. Typically only 1 to 4 percent of the insulin is released at any one time, and a healthy beta cell would simply reload and release more insulin as needed. Examining hundreds upon thousands of cells, Kebede realized that the diabetic beta cells were partly emptied of insulin—but not enough to reveal an insulin secretory dysfunction.

The problem was that a standard lab testing for insulin production was a one-shot deal. The Sorcs1-deficient cells could handle that first test, but not a second test. Finally she understood: The diabetes was caused not by a lack of insulin, but by a failure to reload in a timely way.

The team had the answer—but after their first submission to the prestigious Journal of Clinical Investigations, they were asked to do 22 more experiments.

Kebede had been thinking along the same lines and had already begun the additional work. “We wanted to make sure we got the story right,” she says.

It took an extra eight months, but in August 2014 the paper was finally released. It was an exciting and novel find. In type 2 diabetes, it often seems as if the insulin-producing pancreatic beta cells are wearing down. The Sorcs1 discovery suggests a possible explanation for that, and also provides an important change in how to work with beta cells.

Around the same time, a related discovery came from, of all things, a single-celled organism called Tetrahymena thermophila being studied at the University of Chicago. Attie and Kebede went down to brainstorm with Aaron Turkewitz, a professor of molecular genetics and cell biology. It was an inside-baseball connection, the kind that might take pages to explain and doesn’t show up in grants or co-authored papers. But it personifies the role of a researcher like Attie in an endeavor as complex as decoding diabetes.

“His interests at the most basic scientific level have immense medical implications, and in that way, he connects to a large swath of investigators,” explains Peter Arvan, M.D., Ph.D., director of the University of Michigan Comprehensive Diabetes Center. “There are few like him, but he is a model investigator for the 21st century. As the science gets more complex, the field needs investigators like Alan to connect us.”

Once upon a time, Alan Attie had a bumper sticker that said, “Don’t believe everything you think.”

And Attie thinks about so many things. He makes very good wine and is an accomplished amateur photographer. As much as he loves research, he’s passionate about teaching. Conversations glide from the unification of Germany and money in politics, to Ebola and science funding, to income inequality and student debt.

Attie’s not the happiest of scientists right now. As the United States has reduced its lead in science funding, he’s become acutely aware that the kind of midcareer leap he made into diabetes would be impossible in today’s funding environment. He’s got fewer mice in inventory than at any time in recent memory—and to him that means discovery is languishing.

“We can’t pursue all of our good ideas. We can’t pursue all of our bad ideas, either. But we don’t know which ideas are good or bad until we try. The thing is, we’re not trying as much,” he concludes, frustrated. He worries that we’re losing our edge.

For example, he has a lead on a protein that appears to be involved in both Alzheimer’s and diabetes—perhaps the two greatest challenges to health care financing. “I won’t write the grant because it has zero chance of receiving funding,” Attie says. I

In an age where science seems so often a political pawn, it’s refreshing to hear it talked about as a human ideal.

In Attie’s vision, scientific thinking isn’t just running the numbers and picking the ones you like. It’s about “being self-critical, being introspective about how you think and what algorithm you’re using to arrive at a conclusion about anything in the world,” says Attie. “If that were a widespread value, I think our society would be different, better. We would have less hatred, less racism. We would be more nuanced in the way we judge other people.”

Meanwhile, there are mice to study and students to train. Attie’s been involved in the Collaborative Cross, a massive multi-institutional effort to refine mouse genetics to better allow the study of human disease. Using new mice strains, his team is beginning a major fishing expedition, a multiyear project focusing on insulin secretion and beta cell biology in general—utilizing brand new genetic techniques that already are being hailed as game-changing.

Attie knows there will likely be moments of eureka as well as dead-end heartbreak. The team that he loves so much will grow and change as members adapt to the shifting landscape of discovery. He’ll miss the old students and technicians as they move on, but he’ll gain new students and collaborators as he keeps asking the questions that come so naturally to him.

“Being in science is very humbling because I’ve been wrong about a lot of things over time,” says Attie. “That’s part of learning to be a scientist—and yet I think it’s also part of learning to become a better human being.”

Catch up with … Kartik Chandran

Kartik Chandran

Kartik Chandran

Kartik Chandran (PhD’01 Biochemistry) has spent years studying an organism that most of us hope never to experience: the Ebola virus. Last year the infectious agent not only spread within West Africa but also for the first time reached the United States. The ensuing panic prompted a number of national broadcast news media outlets to turn to Chandran for answers.

Ebola is a major focus of Chandran’s research as a professor of microbiology and immunology at the Albert Einstein College of Medicine in New York. His contributions include helping to identify both the chemical pathway Ebola uses to invade host cells and a specific mechanism inside of cells that acts as an Ebola receptor.

• What fascinates you about viruses?

So many things! They are just these incredible nanomachines, and are often so beautiful to look at. This is what got me into virology in the first place. My Ph.D. adviser at UW–Madison, Max Nibert, showed me some gorgeous image reconstructions of reovirus particles and I was hooked.

Viruses form such a crucial part of life on earth. Indeed, life as we know it wouldn’t exist without viruses. I’m fascinated by the perpetual war, ancient yet modern, that viruses and hosts wage against each other, and by how much that has shaped biology on this planet.

• In light of the recent Ebola outbreaks, do you have any words of comfort or hope? 

It has been horrifying to watch the Ebola epidemic take hold in West Africa. I am hopeful that the resources needed to control it are finally being brought to bear, with the U.S. leading the way. But it’s happening so slowly! We need to multiply our efforts by an order of magnitude and do it quickly— it still feels like the world is in denial about what is happening. I am optimistic also that we will be able to throw vaccines and therapeutics into the fight in the next few months.

But in the meantime, we need to find ways to short-circuit the delays involved in creating infrastructure like treatment centers and the challenge that staffing such centers entails. We have to do more to reduce the spread of the virus at the local level. This seems desperate, but I think we need to help people care for their own family members “in place” by providing the resources and information they need—personal protective gear, chlorine, food. And we have to do this in communities on a regular schedule, not just once by handing out a kit.

• What else would you like to tell the public about Ebola? 

We need a different approach to develop vaccines and therapeutics against emerging agents like Ebola that are not considered major public health threats (or were not, until a few months ago). This and other episodes illustrate the failure of our planet-spanning civilization to act with foresight and plan for the future. The model of letting the marketplace dictate which therapeutics get developed is clearly inadequate to this purpose, since it rewards only short-term thinking. Unfortunately, the government-driven model is not really optimal either—it takes too long to act and disburses funding too anemically.

I don’t pretend to know what the right models are, but I hope we will actively work on coming up with them in the coming months and years. Because this is definitely going to happen again—if not with Ebola, then with some other infectious agent.

Science for Citizens

Entomology professors Walter Goodman and David Hogg

Entomology professors Walter Goodman and David Hogg

CALS is acclaimed as one of the best schools in the nation for training top-notch researchers and practitioners. Less known is the fact that CALS offers challenging, creative courses to undergraduates from outside of the natural sciences as well—in keeping with the college’s mission to cultivate science literacy as a vital component of good citizenship. For many students, these classes may be their only exposure to college-level science.

Two classes exemplifying that mission are Entomology 201—“Insects and Human Culture” —and Plant Pathology 123, “Plants, Parasites and People.” Both are highly popular classes that use insects and plants as ways to connect students with essential information about the natural world.

“It offers a window to science as it relates to their everyday lives,” says plant pathology professor Mehdi Kabbage.

“This is really biology with insects on top of it,” says entomology professor Walter Goodman, who’s been teaching Ent 201 for more than 20 years. “We use insects as a vehicle for describing biology and looking at the practical aspects of biology, like agricultural entomology as well as medical entomology.”

Both classes engage students in a range of hands-on activities. In Entmology 201, students take home the tiny eggs of a tobacco hornworm, or Manduca sexta, and over a period of two months raise it to maturation, keeping a daily logbook in which they describe its metamorphosis from fat turquoise caterpillar to large brown moth. In Plant Pathology 123, each student is given a “mystery microbe” in a petri dish—a Pseudomonas aureofaciens bacterium, for example, or a Fusarium oxysporum fungus—and devise various experiments to determine which microbe they have.

The students are having fun—but they’re also sharpening their observational skills and learning about the scientific process as well as how to make and critique a scientific argument. Their engagement with science often has deep and far-reaching consequences.

Education major Tess Bashaw signed up for Entomology 201 simply to fulfill her science requirement— and instead, “It opened up so many roads to me,” she says. In addition to gaining new skills and information—“learning how to catch and pin insects, how to collect leeches in floods, how camouflage really works”—the course made her grow as a writer, she says.

The lessons stuck. And as a teacher of lowincome children, she’s been sharing those lessons in her classroom for the past decade. “I love teaching writing, and science is a favorite of mine,” Bashaw says.

Given the important mission and high student demand for this signature style of science education, CALS would like to expand offerings to more departments and more students.

To learn more about supporting those efforts, please contact Sarah Pfatteicher, CALS’ associate dean for academic affairs, at sarah.pfatteicher@wisc.edu, tel. (608) 262-3003. To make a gift, please visit supportuw.org/giveto/calssignature.

Mariah Leeseberg

Mariah Leeseberg

Mariah Leeseberg

Mariah Leeseberg BS’05 Wildlife Ecology
Madagascar ’06–’08

Mariah Leeseberg was first introduced to the Peace Corps at a CALS Career Day event and was intrigued by the opportunity to explore a foreign country’s environment, animals and culture. She was sent to the exotic island of Madagascar, where she had the not-so-exotic task of overseeing the construction of 10 pit latrines and three wells. She also helped organize a youth camp that promoted discussion of HIV/AIDS, environmental
concerns and career goals. Her work thereafter has included surveying fish, plants and animals in Alaska and elsewhere. Today she works for the Alaska Department of Fish and Game, where she is involved in efforts to survey sport fishing boats.

Bridging the Gap

International support: Food science major Hannah Fenton (bottom left) carrying BRIDGE partner Kanokwan Duangkunarat, of Thailand; and Jenny Falt, from Sweden (bottom right), carrying her fellow landscape architecture student Sherry Yang.

International support: Food science major Hannah Fenton (bottom left) carrying BRIDGE partner Kanokwan Duangkunarat, of Thailand; and Jenny Falt, from Sweden (bottom right), carrying her fellow landscape architecture student Sherry Yang.

Food science major Hannah Fenton gratefully recalls the kindness shown to her during the three years she and her family spent in Thailand. “I know what it’s like to live in a foreign place and to feel lonely and in need of a friend,” she says.

That’s why Fenton joined BRIDGE—short for “Building Relationships in Diverse Global Environments”—a campus program that matches U.S.-born Badgers with students from around the world. “I wanted to give international students the love, support and guidance that I had when I was in Thailand,” says Fenton.

Last fall Fenton was paired with Bangkok native Kanokwan “Kim” Duangkunarat, who credits BRIDGE with helping her make the most of her five months in Madison. “Before I came here, I thought that the international students would be treated differently,” Duangkunarat says. “However, I was wrong.”

The feeling of “fitting in” she describes is at the heart of BRIDGE’s mission. Offered through International Student Services (ISS), BRIDGE seeks to ease the transition of foreign students to campus while giving U.S. students the opportunity to connect as cultural ambassadors. Each semester an interview process matches international and domestic students according to their interests and gathers these pairs into teams of 14 to 20 students.

To cultivate participants’ leadership and cross-cultural communication skills, each BRIDGE team is assigned to design and host a special event for the others. Past activities have included tours of research labs, visits to a traditional Wisconsin farm, a trip to a corn maze, and even a tailgate party at Miller Park.

After a focus group of CALS undergraduates revealed that many students appreciated the diverse origins of their peers in the classroom but were unsure how to connect socially, CALS administrators reached out to ISS to sponsor a college-specific BRIDGE team.

Now in its fourth semester, the CALS team has attracted students from all corners of the globe, including Germany, Brazil, Malaysia, Singapore and China. Participants have included majors in biochemistry, animal sciences, microbiology, and community and environmental sociology, though the program welcomes international students from non-CALS majors as well. Inspired by CALS’ success, two other colleges on campus are sponsoring college-specific teams this year.

“Now I have many good friends from different countries,” says Duangkunarat. “I have learned that UW–Madison is a really great place to study and live.”

Meanwhile, Fenton has enjoyed seeing her campus through the eyes of students for whom their time here is study abroad. “My favorite question to ask them is, ‘How do you like Madison?’” she says. “I enjoy showing them my favorite things and hearing about their new adventures as well.”