Exploring bugs and bioenergy: Gina Lewin’s path to the Currie Lab

For many college students, summer provides a chance to test-drive future career paths. When Gina Lewin took advantage of such an opportunity, her test drive hit the jackpot.

In the summer of 2009, Lewin participated in a National Science Foundation-funded program called Research Experience for Undergraduates (REU), which invites college juniors and seniors to join research projects around the country.

At the Great Lakes Bioenergy Research Center (GLBRC) at the University of Wisconsin–Madison, Lewin worked in the lab of chemical and biological engineering professor Brian Pfleger. She was tasked with coaxing a bacterium to produce diesel fuel compounds.

As summer progressed, Lewin’s interest in bioenergy and microbiology grew, but she also found herself falling in love with the big research campus of UW–Madison and the city that surrounds it.

“The REU was my first time doing microbiology research,” Lewin says. “I had been thinking about going to graduate school since the end of my freshman year, but being here definitely cemented that interest.”

ants_large horizontal

Ants from the Currie Lab. Photo: Wolfgang Hoffman

She applied for graduate school and joined UW–Madison’s microbiology doctoral training program in the fall of 2010.

Lewin, the daughter of two lawyers, grew up in a semi-rural part of central New Jersey. One of her favorite childhood memories is attending summer nature camps at a nearby environmental education center where she learned to identify the bugs she caught in the woods and streams.

After graduating from high school in 2006, Lewin moved across the country to Pomona College, some thirty miles east of Los Angeles, where she was drawn to science and majored in molecular biology.

But it was not until her REU at UW–Madison that Lewin discovered a connection between her childhood interest in bugs and bioenergy research.

In the lab of GLBRC researcher Cameron Currie, Lewin now studies how insects use microbes to break down cellulose, the sugars found in the cell walls of woody plants, in order to procure nutrient-enriched food. Understanding the insects’ process for breaking down cellulose could ultimately inform GLBRC’s own efforts to convert biomass to ethanol and other biofuels.

Lewin’s particular focus is on the insects’ powerful ability to partner with a community of microbes.

“Scientists have long studied how a single microbe in a flask degrades cellulose,” Lewin says. “But in the environment, organisms don’t exist in isolation; they have evolved to be part of a community. Our goal is to apply the power of these symbiotic relationships to biofuel production.”

Leaf-cutter ants found in tropical rainforests are a particularly impressive example of these mutually beneficial relationships.

Living as a highly organized society in colonies that can grow large enough to be visible from space, the vast majority of leaf-cutter ants work to support their queen. In return, the queen maintains the colony by laying up to 20,000 eggs a day for up to twenty years in the lab.

What is perhaps most remarkable, however, is that the leaf-cutter ants are miniature farmers who have perfected their agricultural activities — deconstructing biomass and cultivating a fungus — over the course of ten million years. Humans, in contrast, have spent a mere 12,000 years developing and fine-tuning their agricultural expertise.

Leaf-cutter ants collect and degrade large amounts of fresh leaves that the fungus converts to food.

“The fungus makes a fuzzy pearl-like structure that contains the nutrients the ants need,” Lewin says. “The larvae and the queen only eat these fungal structures, while the adult workers also feed on leaf sap and fruits.” Some species of leaf-cutter ants even grow a bacterium on their body that protects the fungus from pathogens.

Each colony’s fungus farm consists of a garden, where the plant material is first deposited and partially degraded, and a dump, a dedicated waste management site that may be located under- or aboveground, depending on the ant species.

“Seventy percent of the leaves’ cellulose is carried to the dump for final degradation. It turns out that the dump’s microbial community is much more efficient at degrading cellulose than any individual strain we have studied thus far,” Lewin summarizes her dissertation findings.

Gina Lewin_Cameron Currie

Gina Lewin and thesis advisor Cameron Currie present their research to then-Secretary of Energy Steven Chu. Photo: Matthew Wisniewski

Currie, Lewin’s advisor, is as pleased with these results as with Lewin’s success in obtaining external funding for her work.

“I teased Gina that the offer letter for the National Science Foundation’s predoctoral fellowship [dated around April 1, 2012] was probably an April Fool’s joke,” Currie recalls. “These fellowships are incredibly competitive. I’ve never even heard of anyone getting one in their second year.”

Graduate school clearly suits Lewin well, whether she peers through the microscope, gathers fungal samples in Costa Rica, or applies for a research fellowship.

“In college, I had to choose between ecology and molecular biology,” Lewin remembers. “When I decided to major in molecular biology, I was a little sad to leave behind the outdoor activities we did in the ecology classes. But graduate school has allowed me to bring those two interests back together.”

Last but not least, Lewin has also contributed significantly to GLBRC’s education and outreach efforts.

In the summer of 2011, Lewin worked with high school science teacher Craig Kohn from Waterford, Wis., who participated in GLBRC’s Research Experience for Teachers (RET) program. Together they designed a classroom activity that adapted Lewin’s lab assay for demonstrating the breakdown of cellulose for a high school level.

“We figured out that Craig could make a cheap growth medium for microbes by mixing Miracle Gro fertilizer from a garden center with tap water,” Lewin explains.

To see if an environmental sample, such as a scoop of cow manure, contains microbes capable of growing on a piece of cellulosic filter paper, Kohn’s high school students put the sample, the paper, and the fertilizer in a test tube. The students then quantified cellulose degradation by counting the days until a complete tear was observed in the paper.

The following two summers, Lewin and John Greenler, director of GLBRC’s education and outreach program, presented the activity to teachers attending the Bioenergy Institute for Educators. And in the fall of 2014, the activity was expanded for UW–Madison freshmen and used in a First-Year Interest Group (FIG) course in bioenergy.

“In today’s world, just being a great researcher and doing teaching assistant duty for one semester is no longer enough to become a successful faculty member. Gina is a poster child for the importance of translating her research into engaging classroom material,” Greenler says.

“In the six years since her REU, Gina has grown into a real spokesperson for GLBRC,” Greenler adds.

The GLBRC is one of three Department of Energy Bioenergy Research Centers created to make transformational breakthroughs and build the foundation of new cellulosic biofuels technology. For more information on the GLBRC, visit www.glbrc.org.

This story was originally published on the Great Lakes Bioenergy Research Center website.

Day in the life of a microbiology grad student

Meet Gina Lewin, a graduate student in the Microbiology Doctoral Training Program. She conducts research in Cameron Currie’s bacteriology lab where she studies microbial communities and leafcutter ant systems. By studying these ants, scientists like Lewin can learn how to break down plants like corn stalks to convert them into biofuels.

Daniel Amador-Noguez engineers better bacteria for biofuels

In high school,” Daniel Amador-Noguez recalls, “I took a science class where one of the lectures was all about the future – where the research was taking us, what were some potential future discoveries – and I thought, ‘oh, all this sounds really cool, so how come it hasn’t happened yet?’”

Seventeen years later, it’s not at all difficult to square that eager young man with the energetic scientist Amador-Noguez has become. An assistant professor of bacteriology at the University of Wisconsin–Madison and researcher at the Great Lakes Bioenergy Research Center (GLBRC), Amador-Noguez emanates anticipation, for next week’s result, the future of his research, and the future of biofuels.

Stevenson-Amador-Noguez

David Stevenson (left), research specialist, and Daniel Amador-Noguez examine a plate of microbes in the Microbial Sciences Building. Photos by Matthew Wisniewski.

“It’s difficult to come up with a biological process that isn’t affected by bacteria,” he says. “They are virtually everywhere, not just in the environment but also inside our bodies. And if we can improve our understanding of microbes we can do a lot of enormously important things, including improving biofuels.”

Amador-Noguez’s lab focuses on understanding metabolism in biofuel-producing bacteria with the goal of engineering microbes that can more efficiently convert plant biomass to energy. It’s exciting research, but it’s also the kind of data-driven work that Amador-Noguez hungered for from a very early age.

Growing up in Pachuca, a small city in central Mexico, in the 1980s Amador-Noguez struggled to find information on biology, the subject that interested him most. Science education in Mexico at that time was not strong, the Internet was not yet in widespread use, and bookstores were scarce, so Amador-Noguez found himself reading and re-reading the same encyclopedia periodical his mother had arranged to be sent to the house.

“I must have read that encyclopedia three or four times by the time I was nine or ten,” he says. “My favorite volume had a section on genetic mutations with all this classic imagery of flies, where you have all these different flies with three eyes or four wings. It’s a bit creepy but for a kid that’s really interesting!”

After high school, Amador-Noguez headed to the Monterrey Institute of Technology in northern Mexico, where he had his first real exposure to science, including laboratory research. Since he hadn’t been able to find a good biology program in Mexico, he majored in chemistry.

After graduating from Monterrey in 2001, Amador-Noguez pursued a doctorate in molecular genetics at Baylor College of Medicine in Houston, Texas. While studying the molecular mechanisms of aging in the long-lived Ames Dwarf mice and Little mice, Amador-Noguez discovered that liver metabolism played a key role in the mice’s longevity. His research has focused on metabolism ever since.

He left Baylor with doctorate in hand in 2007 and headed to Joshua Rabinowitz’s lab at Princeton University to do a postdoctoral fellowship in cellular metabolism. He began using mass spectrometry, an analytical chemistry technique, to study the metabolism of bacteria related to biofuel production, and there his interest in biofuels was born.

After five years at Princeton, Amador-Noguez joined UW–Madison and GLBRC in the fall of 2013. To study bacteria in his lab, he now uses metabolomics, a relatively new, systems-level approach to understanding the behavior of metabolites and the regulation of metabolism in microorganisms.

Amador-Noguez uses analytical tools such as mass spectrometry and liquid chromatography, which enable him to identify and measure most of the metabolites inside bacteria, as well as determine the bacteria’s metabolic flux, or which of the bacteria’s metabolic pathways are the most active (or inactive) as the cell converts nutrients into the energy and building blocks it needs to grow.

Amador-Noguez-Lab

The Amador-Noguez Lab

Metabolic flux, the extent to which carbon is passing through one metabolic pathway versus another, is of particular importance to biofuel production. Often, the way to engineer bacteria that are more efficient at converting biomass into biofuels is to maximize flux through pathways known to be involved in biofuel production.

The linked nature of metabolic pathways also makes inhibition of any one pathway a significant issue in studying bacteria; if one pathway is not working, a cell will simply shut down the rest of its metabolism.

In one recent GLBRC project, Amador-Noguez and his team sought to understand how a particular toxin inhibits the conversion of plant sugars into biofuels. The toxin in question is produced from lignin – the woody backbone of plants – during the process of breaking down plant biomass into its sugar components such as glucose.

Amador-Noguez discovered that, in general, these “lignotoxins” are powerful inhibitors of the enzymes the cell needs to synthesize nucleotides, which are essential to the cell’s DNA.

Now that Amador-Noguez knows which enzymes are affected, he and other researchers can find a way to direct those particular enzymes to be more resistant to lignotoxins. Or he can break the regulatory connections between nucleotide biosynthesis pathways and fermentation pathways so that the bacteria would simply remain unaware that a particular biosynthetic pathway was not functioning properly, and would thus continue to produce biofuels.

Looking to the future, Amador-Noguez is excited about the possibility of developing new metabolomics tools that could help reveal how metabolism is regulated within entire bacterial communities, and not just in isolated bacterial species. He says that much remains unknown about how bacteria play nice with one another but that gaining an understanding of the community’s rules could yield powerful results.

“If we could understand how different bacteria interact with each other metabolically in these complex bacterial communities we could do a lot of things,” he explains. “We could understand what shapes the bacterial communities living inside of our bodies, which would have important ramifications for human health, and we could engineer each bacteria in those communities to specialize in doing one thing, which could make the process of biofuel production much more efficient.”

“Biofuels,” he adds, “are an important solution for many of our energy issues. We’re always going to need fuel and we’re always going to need chemicals. And the biological production of biofuels and high-value chemicals from plant biomass is one of the most promising strategies for the sustainable generation of these essential commodities.”

Like many scientists working today on energy-related research, Amador-Noguez remains motivated by the impact his day-to-day research could have on the national and global energy picture, as well as by his long-burning desire to make important advances happen.

“The fact that what we’re doing can contribute to solving big problems in society, that is very motivational,” he says.

This story was originally published on the Great Lakes Bioenergy Research Center website.

Mining bacterial blueprints yields novel process for creation of fuel and chemical compounds

Tim_Donohue

Tim Donohue, UW-Madison bacteriology professor and director of the Great Lakes Bioenergy Research Center, supervised the lab that identified the makeup of 19Fu-FA — a compound with promising potential applications. Photo: Great Lakes Bioenergy Research Center

A team of researchers at the University of Wisconsin-Madison has identified the genes and enzymes that create a promising compound — the 19 carbon furan-containing fatty acid (19Fu-FA). The compound has a variety of potential uses as a biological alternative for compounds currently derived from fossil fuels.

Researchers from the Great Lakes Bioenergy Research Center (GLBRC), which is headquartered at UW-Madison and funded by the U.S. Department of Energy, discovered the cellular genomes that direct 19Fu-FA’s synthesis and published the new findings Aug. 4 in the journal Proceedings of the National Academy of Sciences.

“We’ve identified previously uncharacterized genes in a bacterium that are also present in the genomes of many other bacteria,” says Tim Donohue, GLBRC director and UW-Madison bacteriology professor. “So, we are now in the exciting position to mine these other bacterial genomes to produce large quantities of fatty acids for further testing and eventual use in many industries, including the chemical and fuel industries.”

The novel 19Fu-FAs were initially discovered as “unknown” products that accumulated in mutant strains of Rhodobacter sphaeroides, an organism being studied by the GLBRC because of its ability to overproduce hydrophobic, or water-insoluble, compounds. These types of compounds have value to the chemical and fuel industries as biological replacements for plasticizers, solvents, lubricants or fuel additives that are currently derived from fossil fuels. The team also provides additional evidence that these fatty acids are able to scavenge toxic reactive oxygen species, showing that they could be potent antioxidants in both the chemical industry and cells.

Cellular genomes are the genetic blueprints that define a cell’s features or characteristics with DNA. Since the first genome sequences became available, researchers have known that many cells encode proteins with unknown functions according to the instructions specified by the cell’s DNA. But without known or obvious activity, the products derived from these blueprints remained a mystery.

As time has gone on, however, researchers have realized that significant pieces of these genetic blueprints are directing the production of enzymes — proteins that allow cells to build or take apart molecules in order to survive. These enzymes, it turned out, create new and useful compounds for society.

“I see this work as a prime example of the power of genomics,” Donohue says. “It is not often that one identifies genes for a new or previously unknown compound in cells. It is an added benefit that each of these compounds has several potential uses as chemicals, fuels or even cellular antioxidants.”

A cross-disciplinary, collaborative effort between GLBRC chemists, biochemists and bacteriologists in departments at UW-Madison and Michigan State University yielded the chemical identity of the fatty acid compounds and identified the specific genes that direct their synthesis in bacteria.

“I don’t think this discovery would have been possible,” says Rachelle Lemke, the paper’s lead author and a research specialist in Donohue’s lab, “without the analytical and intellectual expertise of the members from this center.”

Two CALS teams among winners of Wisconsin Energy and Sustainability Challenge

Two CALS-based teams took silver in the 2014 Wisconsin Energy and Sustainability Challenge.

Second place in The Dvorak Energy Innovation Prize contest – and $1,500 – went to Team Drsti.

Vitamin A deficiency is a health concern throughout the developing world that affects more than 200 million children every year. Team Drsti, made of members Chris Johnson and Mary Pitassi, both masters students in Bacteriology, have described their product as “a sustainable solution to vitamin A deficiency.” Project Drsti will develop a probiotic bacterium engineered to make a precursor of vitamin A. The strain will be inexpensive to produce, store and transport, and can be easily added to yogurt or other fermented dairy products.

Second Place in The Global Stewards Sustainability Prize – and $1,500 – went to a team called Sustainable Fertilizer Recovery from Wastewater.

The Sustainable Fertilizer Recovery from Wastewater team is made of Tyler Anderson, a soil science graduate research assistant, Rania Bashar, PhD in biological systems engineering, Cody Calkins, soil science undergraduate, Grant Herrman, biological systems engineering undergraduate, and Logan Voellinger, biological systems engineering. Their concept is to develop and incorporate an electrodialysis cell at existing wastewater treatment facilities to capture and concentrate nitrogen, which can be used in fertilizers.

Richard Gourse elected to American Academy of Arts and Sciences

University of Wisconsin-Madison bacteriologist Richard L. Gourse is among leaders from academia, business, public affairs and the arts and humanities elected to membership in the American Academy of Arts and Sciences, it was announced today.

Richard L. Gourse

Richard L. Gourse

The Ira L. Baldwin Professor of Bacteriology, Gourse joins an eminent class of inductees that includes Nobel laureates, winners of the Wolf and Pulitzer Prizes as well as Grammy, Emmy, Oscar and Tony award winners.

Gourse joined the UW-Madison faculty in 1988 and is currently chair of the bacteriology department.

Working primarily with the model organism Escherichia coli, Gourse is well known for his studies of how genes are expressed in cells, primarily transcription initiation and the control of ribosome synthesis. Previous honors include election as a fellow for the American Academy of Microbiology and the American Association for the Advancement of Science, both in 2003. In 2007, he received the National Institutes of Health Merit Award.

The American Academy of Arts and Sciences was established in 1780 and each year elects “thinkers and doers” as fellows, among them George Washington, Benjamin Franklin, Daniel Webster, Ralph Waldo Emerson, Margaret Meade and Martin Luther King. Its current membership includes 250 Nobel laureates and more than 60 Pulitzer Prize winners.

Wisconsin team to search for new antibiotics from untapped microbes

Facing an imminent global public health crisis, a University of Wisconsin-Madison research team has been awarded up to $16 million from the National Institutes of Health to find new sources of antibiotics to combat the rising number of deadly antibiotic-resistant infections.

“The number of antibiotic-resistant strains has increased while the discovery of new antibiotics has slowed to a crawl. In fact, there are no new antibiotics,” said Dr. David Andes, professor of medicine and division chief of infectious diseases at the UW School of Medicine and Public Health.

In the 1980s, pharmaceutical companies were seeking Food and Drug Administration (FDA) approval of 10 to 20 antibiotics a year. Andes said there has been more than an 80 percent decrease in development of antibiotics since that time.

“The inability to mine novel natural resources for antimicrobials is a major bottleneck for attacking the drug-resistance crisis,” he said.

“Our team has developed a completely new paradigm for anti-infective drug discovery,” said Andes. “We have developed novel ways of finding new antibiotics and testing them rapidly. It’s a fresh approach catalyzed by complementary input from basic and physician scientists, microbiologists, chemists and pharmacologists who are thinking about the same problem.”

New sources for symbiotic organisms

Andes is a co-principal investigator for a National Institutes of Health (NIH) Center of Excellence for Translational Research (CETR). The other is Cameron Currie from the department of bacteriology in the UW College of Agricultural and Life Sciences. Other members of the team are Michael Hoffman, Dr. Bruce Klein, Dr. Rod Welch and Harvard researcher Jon Clardy. The project grant runs for five years.

Traditionally, soil has been mined for antimicrobials that are used to develop antibiotics. But the UW-Madison team has been studying other natural products from animals, insects, plants and marine life. Andes said the study of soil has become a dead end because the same microbes are turning up over and over again.

Andes said the scientists are looking in new places for symbiotic organisms, those that have an interdependent relationship, that are highly likely to have a biological effect.

The scientists are traveling around the globe to harvest insects, plants and marine life. Once specimens are collected, Currie sequences the genome of each product and then decides if it is promising enough to merit further testing.

Tim Bugni, an assistant professor of pharmaceutical sciences, then uses a rapid and accurate method to determine if the microbes are making something never found before. A third part of the research attempts to coax an organism to make compounds by mimicking its environment.

“We’ve also seen that the compounds that microbes are making are evolutionarily selected to be safe because they protect the animal from the environment, from infection threats,” said Andes.

The team is looking at two groups of relevant microbes: fungi associated with infections in immunocompromised patients like cancer and transplant patients, and bacteria responsible for the majority of U.S. hospital infections. The U.S. Centers for Disease Control and Prevention says more than two million drug-resistant infections a year are reported.

“There are patients in almost every hospital with infections that have absolutely no treatment options,” said Andes.

 Building on previous research

The research builds on the work of the UW Antimicrobial Drug Discovery and Development Center, established in 2007. The Wisconsin Partnership Program and various NIH Challenge grants funded the research.

“We’ve been finding large numbers of new compounds at a rate greater than what the pharmaceutical industry ever did,” said Andes.

The goal of the Center of Excellence for Translational Research is to find one drug lead in each of the next five years.

The project is funded by NIH grant number U19AI109673.

This article was originally published on the UW-Madison School of Medicine and Public Health News & Events webpage.

Saving the honeybee

This video features CALS entomology professor Christelle Guedot and bacteriology professor Cameron Currie discussing the issue of Colony Collapse Disorder and scientific efforts at CALS to understand this devastating disease of honeybees. It aired twice in early 2014 during the Wisconsin edition of the Big Ten Network show “Live Big.”