Biomarker-Vol-8

BIOMARKERmagazine

P I O N E E R I N G A DVA N C E S I N T H E L I F E S C I E N C E S

I N S T I T U T E F O R G E N O M I C B I O L O G Y

Vol. 8 University of Illinois at Urbana-Champaign

Biomarker magazine promotes the

interdisciplinary & collaborative

research taking place at the

Institute for Genomic Biology (IGB)

at the University of Illinois.

1UNIVERSITY OF ILLINOIS

Biomarker is published by the Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignGene Robinson, DirectorJennifer Quirk, Associate DirectorSusan Jongeneel, Managing EditorNicholas Vasi, Director of Communications1206 West Gregory Drive Urbana, IL 61801WWW.IGB.ILLINOIS.EDU

D E S I G N : Kathryn CoulterW R I T E R S : Deb Aronson, Susan Jongeneel, Claudia Lutz, Claire Sturgeon, Diana YatesP H OTO G R A P H Y: Haley Ahlers, Kathryn Coulter, Glenn Fried, Don Hamerman, Jason Lindsey, Marc Morrison, Tom Murphy, L. Brian Stauffer, Claire Sturgeon, Nick Vasi

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Institute for Genomic Biolog y Biomarker2 INSTITUTE FOR GENOMIC BIOLOGY B I OM A R K E R

The very spice of life

T he diversity of life on our planet is a seemingly endless source of inspiration for innovators of all kinds. In remote environments and inside our own bodies, we see organisms in myriad forms, and the incredible adaptations that allow them to survive. The past year at the Institute for Genomic Biology has revitalized our appreciation for hidden examples of diversity. The world around us is more varied than anyone once suspected, and great value lies in understanding this variation. In this issue of Biomarker, we are sharing some of the exciting advances we have made.

Sometimes, promising new directions emerge not from new tools or new discoveries, but from a new intellectual approach. Ecologist and IGB Fellow Scott Woolbright has emphasized the great research potential of climate relicts: tiny, isolated biological communities composed of species that were once much more widespread in the area they inhabit. These remnants of past climates and ecological conditions allow the systematic study of intricate ecosystem responses to climate change, on a manageable scale. Nature has provided an ideal set of experiments for examining how the genome mediates these responses, a question that motivates work done by Woolbright and his colleagues in the Genomic Ecology of Global Change research theme.

A collaboration among members of the Gene Networks of Neural and Developmental Plasticity and the Biocomplexity research themes uncovered a different example of biological variation hiding in plain sight. The study, spearheaded by citizen scientist Paul Tenczar, has disproved the once-prevalent assumption that all worker honey bees are equally industrious. With assistance from an automated flight-tracking system that rivals the efficiency of the Illinois Tollway’s I-PASS technology, Tenczar and colleagues found that a small but constantly changing group of bees within a colony do the majority of work to bring in resources, a discovery that adds new depth to our understanding of how complex societies function.

Assistant Professor of Bioengineering Princess Imoukhuede, an affiliate of

Gene E. Robinson Director, Institute for Genomic Biology

D I R E C TO R ’ S M E S S A G E

the Regenerative Biology and Tissue Engineering research theme, has also leveraged cutting-edge technologies to reveal important distinctions within groups that previously appeared homogenous—but at the level of individual cells, not organisms. Cancerous tumors contain multiple subpopulations of cells, which vary in their susceptibility to different treatments. Imoukhuede’s laboratory has developed new ways of quantifying and analyzing the genomic profiles that identify these subpopulations; these techniques could eventually enable the design of more personalized and effective treatments for individual

cancer patients.

The other stories we have chosen to highlight our progress this year emphasize the power of re-examining the familiar with better tools and fresh ideas. We invite you to learn how members of the IGB have refined an ecological model inspired by Lewis Carroll’s Through the Looking Glass; used DNA sequencing

to clear up centuries-old cases of mistaken elephant identity; and begun to explore the hypothesis that some viruses may help, rather than harm, their hosts.

In some ways, the strengths of the IGB resemble the biological systems that we study. Our research goals and strategies are not static; as new technologies and new challenges emerge, we continue to grow and adapt. Our members come together to tackle difficult problems and tantalizing questions, but it is also our diverse backgrounds and diverse expertise that fuel our resilience and ingenuity.

“The diversity of life on our planet is a

seemingly endless source of inspiration for innovators of all kinds.”


The cells that make up tumors have different populations of receptors that promote blood vessel growth. Imoukhuede says these receptors can serve as biomarkers, helping doctors predict drug responsiveness by providing a quantitative way to profile cells.

“If there is a traffic jam and you block a freeway, you’ll find that cars will go through some of the side streets. We can try to block some of those side streets, but cars will still try to find a way through,” Imoukhuede

said, describing the way anti-angiogenic drugs block receptors that encourage tumor growth. “This is the problem with cancer research, where you block one marker, receptor, or molecule, the tumor still finds another way.”

For personalized cancer treatments to become a reality, Imoukhuede says scientists must understand the tumor microenvironment, find a way to count the number of receptors, then apply that data to computational models that predict cancer drug efficacy and suggest the best treatment options for each patient.

“The most exciting take-home message is that we are able to find certain cells within the tumor microenvironment that we haven’t profiled previously,” Imoukhuede said. “We determined that a certain subset of these cells had very high levels of expression of one of these angiogenic receptors that could actually negate some of the effects of a common anti-angiogenic drug.”

The anti-angiogenic cancer drug, Avastin, has already been developed and is approved for many types of cancer, including brain, lung, and colorectal cancer; however, the Food and Drug Administration revoked approval for metastatic breast cancer due to evidence that the survival benefits did not outweigh the side effects for many patients.

Imoukhuede’s research may someday make these drugs available to a subset of metastatic breast cancer patients who experience significant survival benefits.

The American Cancer Society, Illinois Division Basic Research Grant, National Institutes of Health, United Negro College Fund, Merck, and the Federation of American Societies for Experimental Biology supported Imoukhuede’s work.

P E R S O N A L I Z I N G C A N C E R T R E AT M E N T S B ioengineer Princess Imoukhuede’s research on the formation of blood vessels is akin to controlling war zone supply routes. Her lab is working to increase the number of routes funneling supplies to main operating bases, like the brain and heart, while cutting off supply routes to enemy camps, like tumors and cancers.

She is currently developing models that will provide researchers and clinicians with a “Google Earth perspective” on the widespread impacts of blocking certain routes while developing others.

Most types of tumors, including cancer, require a supply of blood to grow larger than a few millimeters. Scientists have made great progress in combating cancer by finding effective ways to stop the formation of new blood vessels, a process called angiogenesis.

Her lab may be able to personalize angiogenesis inhibition cancer treatments through their understanding of the tumor microenvironment. They want to understand why the same type of tumor behaves differently in people, like two mulberry trees reacting differently to the same herbicide.

“My lab is trying to understand whether there is a subset of patients for whom anti-angiogenic treatments are especially useful, and if so, find out how we identify those patients,” said Imoukhuede, a member of the Regenerative Biology & Tissue Engineering theme. “That’s where we get into the area of personalized medicine, being able to tailor anti-angiogenic treatments specifically to a patient.”

The Imoukhuede Systems Biology Laboratory includes ( lef t

to r ight) Al i Ansar i , Jared Weddel l , Wendy Woods, Spencer

Mamer, and PI Pr incess Imoukhuede.


C L A S S I C L E W I S C A R R O L L C H A R A C T E R I N S P I R E S N E W E C O L O G I C A L M O D E L

“ W ell, in our country,” said Alice, still panting a little, “you’d generally get to somewhere else — if you run very fast for a long time, as we’ve been doing.”

“A slow sort of country!” said the Queen. “Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!” -Lewis Carroll, Through the Looking Glass

Inspired by the Red Queen in Lewis Carroll’s Through the Looking Glass, collaborators from the University of Illinois and National University of Singapore improved a 35-year-old ecology model to better understand how species evolve over decades to millions of years, as reported in Ecology Letters.

The new model, called a mean field model for competition, incorporates the “Red Queen Effect,” an evolutionary hypothesis introduced by Lee Van Valen in the 1970s that suggests organisms must constantly increase their fitness in order to compete with other ever-evolving organisms in an ever-changing environment.

The mean field model assumes that new species have competitive advantages that allow them to multiply, but over time new species with even better competitive advantages will evolve and outcompete current species, like a conveyor belt constantly moving backwards.

The model gets its name from field theory, which describes how fields, or a value in space and time, interact with matter. A field is like a mark on a map indicating wind speeds at various locations to measure the wind’s velocity. In this ecological context, the “fields” approximate distributions of species abundances.

Ecologists can use models to predict what happens next and diagnose sick ecosystems, said Assistant Professor of Plant Biology James O’Dwyer, who co-authored the study.

C R E AT I N G A M O D E L E C O L O G Y M O D E L

The mean field model has improved a fundamental ecology model, called neutral biodiversity theory, which was introduced by Stephen Hubbell in the 1970s. Neutral theory does not account for competition between different species, thus considering all species to be selectively equal.

“The neutral model relies on random chance,” said O’Dwyer, who is a member of the Biocomplexity theme. “It’s like a series of coin flips and a species has to hit heads every time to become very abundant. That doesn’t happen very often.”

Neutral theory can predict static distributions and abundances of species reasonably well, but it breaks down when applied to changes in communities and species over time. For

instance, the neutral model estimates that certain species of rainforest trees are older than Earth.

“At one end of the spectrum, we have this neutral model with very few parameters and very simple mechanisms and dynamics, but at the other end, we have models where we try to parameterize every detail,” O’Dwyer said. “What’s been hardest is to take one or two steps down this spectrum from the neutral model without being sucked down to this very complicated end of the spectrum.”

By creating a more realistic model that incorporates species differences, O’Dwyer and co-author Ryan Chisholm, an assistant professor at National University of Singapore, have taken an important step down that spectrum.

“Our model is not the ecological equivalent of Einstein’s General Theory of Relativity, which was a conceptual leap for physics,” O’Dwyer said. “It is an incremental step at this point. But we will need those conceptual leaps that incorporate the best parts of different models to really understand complex ecological systems better.”

The Templeton World Charity Foundation supported O’Dwyer’s work.

I N S P I R E D B Y T H E R E D Q U E E N I N L E W I S C A R R O L L’ S T H R O U G H T H E L O O K I N G G L A S S , R E S E A R C H E R S I M P R OV E O N 3 5 - Y E A R - O L D E C O L O G Y M O D E L


B ioengineers who seek to improve drug delivery systems encounter a principle that evokes the fabled race between the tortoise and the hare: many of the chemicals produced naturally by the body to promote growth or healing are released in a slow and steady manner. Although intuition suggests that more medicine means a faster cure, drug delivery devices meant to reproduce biological signaling are actually less effective if they release (and run out of) drug too quickly. Finding better ways to reproduce this type of biological signaling is important to a variety of innovative treatments, including tissue regeneration, but creating materials that mimic this controlled release has proved technically challenging.

Assistant Professor of Chemical and Biomolecular Engineering and Institute for Genomic Biology member Hyunjoon Kong (below) and colleagues have developed an ingenious solution; an easily synthesized substance that, when implanted in tissue or placed in a water-based solution, folds itself into a shape that controls and directs the release of hormones or other embedded drugs.

Hydrogels, water-absorbing solid materials that resemble a sturdier version of Jell-O, have been used previously for controlled biomolecule delivery. Hydrogels can be chemically modified to bond directly to the drug or chemical of interest, and gradually release the drug as the chemical bonds degrade. This approach has several difficulties: the chemical modifications

used can negatively affect both the drug and the hydrogel, the process of modifying the gel is usually expensive, and it is difficult to synthesize the gel in shapes that allow the released drug to infiltrate nearby tissue.

To address these difficulties, Kong, Materials Science and Engineering graduate student Kwanghyun Baek, and their fellow researchers created a hydrogel with two layers comprising the same type of material, but made to differ in how each layer changes in shape when exposed to water. These differences are what drive their hydrogel’s ability to fold itself into a multi-layered tube.

The way this folding occurs may seem familiar to anyone who has ever curled decorative ribbon with a pair of scissors. As the ribbon is pulled over a sharp edge, the outside surface of the ribbon is stretched more than the inside surface. Because the outside surface is now just a little bit longer than the inside surface, the ribbon must compensate by curling, with the now-shorter inner surface always taking the inside track.

The two layers of the hydrogel designed by Kong and others behave in a similar way: when placed in solution, the outer layer becomes longer relative to the inner layer. The formerly flat gel rolls up into a tube, one that coils more tightly

or more loosely according to what structural properties are selected for each layer of the gel.

One advantage of this tubular shape is that it can be used to physically limit the release of biomolecules of interest. If a drug is loaded into the inner layer of the two-layer hydrogel, the drug-laden surface area that is exposed in the folded shape is very limited; no chemical modifications are necessary to slow and prolong the diffusion of the drug from the gel. The drug will also be forced to diffuse mainly from the two ends of the tube, directing the release toward a particular area or tissue.

Baek, Kong and colleagues examined the efficacy of their hydrogel in promoting blood vessel growth when this inner layer was loaded

with growth factor. Tissue implanted with the self-folding gel showed more vessel growth than tissue implanted

with gel strips, rings or discs containing the same initial quantity of growth factor. Because it is relatively easy to produce and control the structural properties of similar self-folding hydrogels and load them with any of a variety of biomolecules, this innovation has a broad range of potential therapeutic applications.

Kong was the principal investigator and Baek the first author on a recent communication in Advanced Materials that reported these and related findings. Other authors of the study were postdoctoral researcher Jae Hyun Jeong, graduate student Artem Shkumatov, and Electrical and Computer Engineering Professor and Institute for Genomic Biology affiliate Rashid Bashir.

S L OW A N D S T E A DY: A D R U G D E L I V E RY I M P L A N T T H AT F O L D S – A N D PA C E S – I T S E L F

Hydrogels, water-absorbing solid materials that resemble a sturdier version of Jell-O.

Hydrogels i l lustrated in 10.18.13 issue

of Advanced Mater ia ls .


Paul Tenczar, r ight , volunteers to fur ther the bee research

conducted by Gene Robinson, the director of the Inst i tute for

Genomic Biology.

I nspired by I-PASS, the automated tollway system, one Illinois lab is now studying a different type of traffic: the flights of foraging honey bees. Scientists attached radio-frequency identification (RFID) tags to hundreds of individual honey bees and tracked them for several weeks. The effort yielded two discoveries: Some foraging bees are much busier than others; and if those busy bees disappear, others step up to take their place.

Tagging the bees revealed that on any given day, about 20 percent of the foraging bees in a hive brought home more than half of the nectar and pollen gathered to feed the hive.

“We found that some bees are working very, very hard – as we would have expected,” said Institute for Genomic Biology director Gene Robinson, who led the research. “But then we found some other bees that were not working as hard as the others.”

Citizen scientist Paul Tenczar developed the technique for attaching RFID tags to bees and tracking their flight activity with monitors. He and neuroscience Program graduate student Claudia Lutz measured the foraging activities of bees in several locations, including some in hives in a controlled foraging environment. Vikyath Rao, a graduate student in the laboratory of Swanlund Professor of Physics and Biocomplexity theme leader Nigel Goldenfeld, analyzed the data using a computer model Rao and Goldenfeld developed.

Previous studies, primarily in ants, have found that some social insects work much harder than others in the same colony, Robinson said.

“The assumption has always been that these ‘elite’ individuals are in some

way intrinsically better, that they were born that way,” he said.

While it is well known that genetic differences underlie differences in many types of behavior, the new findings show that “sometimes it is important to give individuals a chance in a different situation to truly find out how different they are from each other,” Robinson said.

When the most active bees in a colony were removed, some of the previously low-activity bees increased the frequency of their flights almost five-fold. The change occurred within 24 hours, Tenczar said. This demonstrates that other individuals within the hive also have the capacity to become elites when necessary, Robinson said.

“It is still possible that there truly are elite bees that have some differential abilities to work harder than others, but it’s a larger group than first estimated,” Robinson said. “Or it could be that all bees are capable of working at this level and there’s some kind of colony-level regulation that has some of them working really, really hard, making many trips while others make fewer trips.”

Perhaps the less-busy bees function as a kind of reserve force that can kick into high gear if something happens to the super-foragers, Robinson said.

“Our observation is that the colony bounces back to a situation where some bees are very active and some are less active,” he said. “Why is that? We don’t know. Do all bees have that capability? We still don’t know.”

The National Science Foundation and the Christopher Family Foundation supported this research. The findings are reported in the journal Animal Behaviour, and featured in a New York Times ScienceTake video.

C I T I Z E N S C I E N T I S T PA U L T E N C Z A R D E V E L O P E D T H E T E C H N I Q U E F O R AT TA C H I N G R F I D TA G S TO B E E S A N D T R A C K I N G T H E I R F L I G H T A C T I V I T Y W I T H M O N I TO R S

R A D I O F R E Q U E N C Y I D TA G S O N H O N E Y B E E S R E V E A L H I V E DY N A M I C S


T hanks to their ability to withstand heat, high salinity, low oxygen, utter darkness, and pressures that would kill most organisms, the hardy Halomonas bacteria can live in deep sandstone formations that are also useful for hydrocarbon extraction and carbon sequestration.

An Energy Biosciences Institute-funded study led by IGB member Bruce Fouke, professor of geology and microbiology and director of the Roy J. Carver Biotechnology Center, provides the first unobstructed view of the microbes living more than a mile below the surface of sandstone formations.

“We are using new DNA technologies to understand the distribution of life in extreme natural environments,” Fouke said. “Astonishingly little is known of this vast subsurface reservoir of biodiversity, despite our civilization’s regular access to and exploitation of subterranean environments.”

To address this knowledge gap, Fouke and his colleagues collected microbial samples from a sandstone reservoir 1.8 kilometers (1.1 miles) below the surface.

Using a probe developed by the oilfield services company Schlumberger that reduces or eliminates contamination from mud and

“This means that these indigenous microbes would have the adaptive edge if hydrocarbon migration eventually does occur,” Fouke said. A better understanding

of the microbial life of the subterranean world will “enhance our ability to explore for and recover oil and gas, and to make more environmentally sound choices for subsurface gas storage.”

The research appears in the journal Environmental Microbiology. The team included scientists from The Institute for Systems Biology in Seattle; Mayo Clinic; the Asia Pacific Center for Theoretical Physics in South Korea; Shell Oil Co.; Argonne National Laboratory; four U. of I. departments: chemical and biomolecular engineering, civil and environmental engineering, natural resources and environmental sciences, and animal sciences; and the Illinois State Geological Survey at the Prairie Research Institute at Illinois.

The Energy Biosciences Institute is a research collaboration involving the U. of I., the University of California at Berkeley, the Lawrence Berkeley National Laboratory, and BP, the energy company that funds the work.

O I L - A N D M E TA L -M U N C H I N G M I C R O B E S D O M I N AT E D E E P S A N D S TO N E F O R M AT I O N S

R E S E A R C H L E D B Y B R U C E F O U K E , A B OV E , A L L OW S F O R N E W I N S I G H T I N TO S U B T E R R A N E A N M I C R O B E S

microbes at intermediate depths, they sampled sandstone deposits of the Illinois Basin, a vast, subterranean bowl and rich source of coal and oil underlying much of Illinois and parts of Indiana, Kentucky, and Tennessee.

A genomic analysis of the microbes the team recovered revealed “a low-diversity microbial community dominated by Halomonas sulfidaeris-like bacteria that have evolved several strategies to cope with and survive the high-pressure, high-temperature, and nutrient-deprived deep subsurface environment,” Fouke said.

An analysis of the microbes’ metabolism found that these bacteria are able to use iron and nitrogen from their surroundings and recycle scarce nutrients to meet their metabolic needs. (Another member of the same group, Halomonas titanicae, is so named because it is consuming the iron superstructure of the Titanic.)

Perhaps most importantly, the team found that the microbes living in the deep sandstone deposits of the Illinois Basin can metabolize aromatic compounds, a common component of petroleum.


N estled in a field of germinating soybeans is an out-of-place research plot where slender green spikes protrude from murky, umber-colored water. This rice paddy, the first at the University of Illinois, may help researchers improve the productivity of rice, a staple for nearly half of the world’s population.

Yu Tanaka, a visiting professor from Kyoto University, is leading a study that will test rice performance at Illinois and Kyoto University in Japan. The two plots, which were planted on the same date, should reveal clues about what factors help the plants more efficiently convert the sun’s energy into food, known as photosynthetic performance.

This experiment is part of the Realizing Increased Photosynthetic Efficiency (RIPE) project, a five-year effort funded by a $25 million grant from the Bill & Melinda Gates Foundation to substantially improve the productivity of worldwide staple food crops.

“Rice is the number one source of calories for humans, worldwide, and increasingly we are not producing enough,” said RIPE Director Stephen Long, Endowed Professor of Plant Biology and Crop Sciences. “This paddy is one of the first steps of a multinational attempt to achieve new innovations in improving rice production. Rice improvement is a major interest of the Bill & Melinda Gates Foundation, which is funding a major effort to improve crop photosynthesis at the university.”

The experimental paddy, located on the South Farms at Illinois, is being used to provide a

northerly limit in trials of some new rice genetic materials that are also being tested in warmer climates, including the plot at Kyoto University.

While rice is not a crop associated with Central Illinois, it is grown not so far away in Southeast Missouri. It is also grown extensively in places such as Northern Italy and Northern Japan, where summer climates are similar to that of Illinois, Long said.

The Illinois rice plot contains several varieties of rice, including wild varieties and mutant lines, which have different photosynthetic characteristics that may increase yields under various conditions.

“When we consider actual production, or the crops’ physiological responses and performance, it is really important that we grow the rice in the fields,” Tanaka said. “Without this feasibility experiment, we wouldn’t have a chance to grow the rice in a natural environment in Illinois, which would limit the RIPE project.”

Tanaka and his graduate student Yu Iwahashi conducted preliminary research in growth

chambers that revealed that some of these mutants have a lower transpiration rate, which improves the crops’ drought tolerance.

“When rice is grown in a paddy field, there is definitely no shortage of water,” Tanaka said. “But in many parts of the world, rice is grown on upland fields. For those regions, drought tolerance would be critical. We are expecting to see these lines better conserve water throughout this summer.”

Tanaka is visiting Illinois to take part in progressive photosynthetic research with Long, where he has access to state-of-the-art laboratories, space to research transgenic ecology, and equipment that can more accurately detect photosynthetic performance.

“I was impressed by Steve Long’s progress to achieve increased crop production through photosynthesis,” Tanaka said. “If we can combine the strong points of my work with transpiration physiology and Steve’s work with biochemical pathways—we can achieve better progress through this photosynthetic study.”

The RIPE project is built upon a foundation of collaboration, bringing together world leaders in photosynthetic research from Australian National University, Rothamsted Research, University of Essex, Chinese Academy of Sciences-Max Planck Institute, Louisiana State University, University of California, Berkeley, and United States Department of Agriculture Agricultural Research Service.

A F L O O D E D PA R C E L O F A R A B L E L A N D

Kyoto University visiting professor and study lead Yu Tanaka plants rice varieties in a paddy on the South Farms at Illinois.

“Rice is the number one source of calories for humans, worldwide,

and increasingly we are not producing enough,” said RIPE

Director Stephen Long.


D utch pharmacist Albertus Seba was a wealthy man with an insatiable interest in natural history. He would ask sailors and ship surgeons to bring him exotic plants and animals from their travels that he could use to make drugs or add to his cabinet of natural curiosities.

One day, the Dutch West India Company brought an elephant fetus in a glass jar of spirit back from Africa and invited Seba to see their pickled pachyderm. Seba drew a life-size illustration of the specimen, which was included in his “very rich thesaurus of the principal and rarest natural objects,” published in 1734.

N A M I N G , A N D R E N A M I N G , E L E P H A N T S

As the father of modern taxonomy, Carl Linnaeus had the first opportunity to name more than 10,000 plants and animals - including elephants. In his definitive work Edition 10 of the Systema Naturae, Linnaeus named the elephant Elephas maximus and cited several examples of the newly named species, including Seba’s elephant fetus.

“I am pleased that the little elephant has arrived,” Linnaeus wrote to a friend after Swedish King Adolf Fredrik and Queen Lovisa Ulrika purchased the specimen from Seba’s collection. “If he costs a lot, he was worth it. Certainly he is as rare as a diamond.”

Later African elephants were separated into the genus Loxodonta with two designated African species, the African bush elephant (L. africana) and African forest elephant (L. cyclotis), while Asian elephants remained E. maximus.

Under the International Code of Zoological

Nomenclature, when a species is given a scientific name, a “type” specimen is preserved, usually in a museum or research collection so that other researchers can refer to it for physical details about the species.

Because Asian elephants retained the original name, E. maximus, Linnaeus’s descriptions of the fetus became a syntype for Asian elephants, regardless of historical evidence and physical characteristics that suggested it was actually an African elephant.

Unlike Asian elephants that have domed heads, relatively small ears, and a single “finger” at the end of their trunks, Seba’s fetus had a convex-shaped head, relatively large ears, and two “fingers” at the end of its trunk—characteristics of an African elephant.

S O LV I N G A C A S E O F M I S TA K E N I D E N T I T Y

In a study in the Zoological Journal of the Linnean Society, researchers reported that a peptide sequence and three single nucleotides differ in Asian and African elephants. In the study, they found the fetus had the African elephant peptide sequence and nucleotides, confirming that the 300-year-old type specimen for Asian elephants was actually an African elephant.

Alfred Roca, an animal scientist, and Yasuko Ishida, a research specialist in his lab, compared the mitochondrial DNA (mDNA) of the fetus to the mDNA of African elephants from different regions of Africa. Using a database with DNA from more than 650 African elephants, Ishida found the fetus was from West Central Africa, the

very place where historical records suggest the fetus was collected.

Once researchers established that the fetus was an African elephant, they set out to find an Asian elephant lectotype, which serves as a single type specimen for a species that was originally described by several syntypes.

After scrutinizing references by Linnaeus in Systema Naturae, researchers discovered a detailed description of an elephant skeleton observed in Florence, Italy, by the famous 17th century naturalist John Ray in 1664.

“One of the things Ray mentions is that the sternum of the elephant was missing,” Roca said. “We did a little bit of sleuthing and contacted the National History Museum of the University of Florence. Sure enough, they have a specimen there that has a wooden replica of a sternum. We were able to use the museum records and track this elephant all the way back to the 1600s when Ray first saw it.”

Due to the specimen’s size, bone structure, and teeth wear, researchers determined that the skeleton was a 25 to 30-year-old female Asian Elephant. DNA analysis confirmed that the skeleton belongs to E. maximus.

In accordance with the International Code of Zoological Nomenclature, researchers designated the elephant skeleton in Florence, catalogue number MZUF-734, as the lectotype for E. maximus to “preserve the traditional understanding and application of this name to the Asian elephant.” This change went into effect January of 2014.

“It is remarkable to think that combining observations made more than 200 years ago by Linnaeus, Seba and John Ray, with state-of-the-art analysis in ancient proteomics and DNA, has enabled us to give the Asian elephant its correct type specimen,” said first author Enrico Cappellini, an assistant professor at the Centre for GeoGenetics at the Natural History Museum of Denmark at the University of Copenhagen.

T WO E L E P H A N T S , O N E A N D T H E S A M E

Through an exhaustive investigation of historical literature, researchers discovered undeniable links between this new lectotype and the famous 17th century circus elephant, Hansken, suggesting they are one and the same.

Both were born in 1630 in Ceylon. Both were female Asian elephants with absent or very small tusks. Both traveled in Germanic lands. Both had

R E S E A R C H E R S U N M A S K C E N T U R I E S - O L D E L E P H A N T I M P O S T E R


lectotype for Asian elephants 320 years after Linnaeus named the species.

The United States Fish and Wildlife Service supported Roca and Ishida’s research by funding earlier studies that contributed to these discoveries.

their weight measured at 6,600 pounds while in the presence of royalty.

An account from 1651 said Hansken was 21 years old, meaning that four years later she would have been 25—the same estimated age of the Florence elephant at its death in 1655.

Most convincingly, both are said to have been

able to draw a sword with their trunks. “How many elephants were in Europe at the time, and how many were said to be able to draw a sword?” Roca said. “That’s what convinced me.”

The world may never know if Hansken’s skeleton remains in Florence, but thanks to modern technology, researchers were able to resolve the identity of Seba’s fetus and establish a credible

I llinois researchers have disproved decades of rumors and hearsay surrounding the ancient Battle of Raphia, the only known battle between Asian and African elephants.

“What everyone thinks about war elephants is wrong,” said Alfred Roca, a professor of animal sciences, who led the research published in the Journal of Heredity.

Over the years, there has been a lot of speculation about a Greek Historian’s account of the battle between Ptolemy IV, the King of Egypt, and Antiochus III the Great, the King of the Seleucid kingdom, in which the African elephants (obtained by ancient Egyptians from what is today the country of Eritrea) were said to be smaller than the Asian elephants.

“Until well into the 19th century, the ancient accounts were taken as fact by all modern natural historians and scientists, and that is why Asian elephants were given the name Elephas maximus,” said Neal Benjamin, an Illinois veterinary student who studies elephant taxonomy and ancient literature with Roca.

“After the scramble for Africa by European nations, more specimens became available and it became clearer that African elephants were mostly larger than Asian elephants.”

“At this point, speculation began about why the African elephants in the Polybius account might have been smaller,” Benjamin continued. “One scientist, Paules Deraniyagala, even suggested that they might even have been an extinct smaller subspecies.”

In 1948, Sir William Gowers reasoned that Ptolemy must have fought with forest elephants that fled from larger Asian elephants, as the Greek Historian described. Since then, the idea has been cited and re-cited in many papers.

Until now, the main question remained: Did Ptolemy employ African savanna elephants (Loxodonta africana) or African forest elephants (Loxodonta cyclotis) in the Battle of Raphia?

“Using three different markers, we established that the Eritrean elephants are actually savanna elephants,” said Adam Brandt, a doctoral candidate in Roca’s laboratory and first author

of the paper. “Their DNA was very similar to neighboring populations of East African savanna elephants but with very low genetic diversity, which was expected for such a small, isolated population.”

The markers also revealed that these Eritrean elephants have no genetic ties to forest or Asian elephants, as other authorities have suggested. Roca and Brandt hope their findings will aid conservation efforts.

“We have confirmed that this population is isolated and may be inbred,” Brandt said. “This population will require habitat restoration and preservation to minimize the possibility of human conflict. That’s really the issue—not having a place to go.”

This research was supported by the United States Fish and Wildlife Service. The late Jeheskel Shoshani, an evolutionary biologist and world-renowned elephant specialist, was instrumental in this research.

WA R E L E P H A N T M Y T H S D E B U N K E D B Y D N A

First author Adam Brandt, lef t , shown

with Professor of Animal Sciences and

IGB member Al f red Roca .


W hile hiking through the Ozarks’ characteristic oak and hickory forests as a teenager, ecologist Scott Woolbright, below, discovered something decidedly uncharacteristic for the region: prickly pear cacti growing on an exposed, rocky ledge.

In a recent paper published in Trends in Ecology and Evolution, Woolbright describes how populations and communities like these, known as climate relicts, can help scientists understand how ecological communities are affected by climate change.

Rocky, well-drained slopes in the Ozarks often create habitat “islands” within the surrounding forest known as glade ecosystems, said Woolbright, who is a postdoctoral fellow in the Genomic Ecology of Global Change research theme.

In the Ozarks, glades often help to preserve isolated communities of cacti and other desert and prairie species that dominated the area during the Hypsithermal, a period of warming that occurred four to eight thousand years ago.

Ecologists have recently begun to discuss climate relicts as potential “natural laboratories” for studying the evolution of single plant species. Woolbright and co-authors suggest expanding such studies to include interactions between plants and other organisms that can drive community and ecosystem patterns.

It can be very difficult to replicate the long-term effects of climate change over very large

geographic areas in the laboratory or field. But isolated climate relicts that are distributed across landscapes create “natural experiments” that help to overcome these problems of scale.

Using the genomic technologies he’s learned at the IGB, Woolbright hopes to develop a research program that investigates climate-driven changes in species interactions at the gene level. While such a program would contribute to basic community and ecosystem research, it also has significant implications for ecological conservation and restoration.

“We’re learning that you often can’t just go out and preserve a single species,” Woolbright said. “Interactions with other species can play very important roles in species survival. If we don’t take those interactions into account, we can miss things that are really important.”

Many climate relicts are threatened by small population size, ongoing environmental change in already stressful environments, invasions from species in adjacent non-relict communities, and human encroachment. Woolbright said it will take the cooperation of many stakeholders to conserve relicts for their historical, ecological and aesthetic value.

The Institute for Genomic Biology fellows program supported Woolbright, who was inspired to pursue a career in climate change ecology by his encounter with Ozark glades.

C L I M AT E R E L I C T S M AY H E L P R E S E A R C H E R S U N D E R S TA N D C L I M AT E C H A N G E

A satel l i te image of a glade at Round Bluff Natural Preserve in

Shawnee Hi l ls , Johnson County, I l l inois, one of several g lade

ecosystems that occur throughout Southern I l l inois.

E c o l o g i s t s h a v e r e c e n t l y b e g u n t o d i s c u s s c l i m a t e r e l i c t s a s p o t e n t i a l “ n a t u r a l l a b o r a t o r i e s ”

“We’re learning that you often can’t just go out and preserve a single species.”


A new analysis reported in Environmental Science and Technology suggests the planet can produce much more land-plant biomass–the total material in leaves, stems, roots, fruits, grains and other parts–than previously thought.

According to plant biology professor Evan DeLucia, director of the Institute for Sustainability, Energy, and Environment and an Energy Biosciences Institute affiliate, “Most previous research assumes that the maximum productivity you could get out of a landscape is what the natural ecosystem would have produced. But it turns out that in nature, very few plants have evolved to maximize their growth rates.”

Estimates derived from satellite images of vegetation and modeling suggest that about 54 gigatons of carbon is converted into terrestrial plant biomass each year. This value has remained stable for several decades, leading scientists to assume that it represents an upper limit on global biomass production.

But this assumption does not take into account human efforts to boost plant productivity through genetic manipulation, plant breeding, and land management, which have already yielded some extremely productive plants. For example, a hybrid grass Miscanthus x giganteus can produce 10 to 16 tons of above-ground biomass per acre without fertilizer or irrigation, more than double the productivity of native prairie vegetation or corn.

Some non-native species also outperform native species, DeLucia said. He notes that many of these plants would not be desirable additions to native or managed ecosystems, but they represent the untapped potential productivity of plants in general.

To obtain a global estimate of the limit of net primary production (NPP), the team used a model of light-use efficiency and the theoretical maximum efficiency with which plant canopies convert solar radiation to biomass. This newly calculated limit was roughly two orders of magnitude higher than the productivity of most

current managed or natural ecosystems.

“We’re not saying that this is even approachable, but the theory tells us that what

is possible on the planet is much, much higher than current estimates,” DeLucia said.

Taking into account global water limitations reduced this theoretical limit by more than 20 percent everywhere except in the tropics, DeLucia said. “But even that water-limited NPP

E A RT H C A N S U S TA I N M O R E T E R R E S T R I A L P L A N T G R OW T H

I N N AT U R E , V E RY F E W P L A N T S H AV E E V O LV E D TO M A X I M I Z E T H E I R G R OW T H R AT E S

is many times higher than we see in our current agricultural systems.”

DeLucia cautions that scientists and agronomists have a long way to go to boost plant productivity, and the new analysis does not suggest that shortages of food or other plant-based resources will cease to be a problem.

“I don’t want to be the guy that says science is going to save the planet and we shouldn’t worry about the environmental consequences of agriculture (or) runaway population growth,” he said. “All I’m saying is that we’re underestimating the productive capacity of plants in managed ecosystems.”

The Energy Biosciences Institute is a public-private collaboration involving the U. of I., the University of California at Berkeley, the Lawrence Berkeley National Laboratory, and BP, the energy company that funds the work.

“We’re underestimating the productive capacity of plants in managed ecosystems.”


the costs and benefits of chronic infections. Mark Young, a professor of virology at Montana State University, will study these interactions in a natural hot spring using a device developed by Sascha Hilgenfeldt, a professor in the Department of Mechanical Science and Engineering at Illinois.

Evolutionary ecologist Joshua Weitz from Georgia Tech University will use Whitaker and Young’s findings to develop a theoretical and computational eco-evolutionary model of how viruses and microbes interact.

“We are figuring out the parameters that will go into the model, then using the model to project what’s happening in nature, and finally going into

nature to see if it works,” Whitaker said. “We will also learn things about natural populations that we didn’t know and that we can test in the lab then apply in our models. It will be an iterative process.”

To study the natural populations systematically, a method is needed to separate the host cells from the viruses. Hilgenfeldt has developed a device that currently separates particles by size that are between two to ten micrometers in diameter. In comparison, a human hair is about 75 micrometers wide. Archaeal cells, however, are just one micrometer wide and viruses are about 10 times smaller.

Hilgenfeldt says he will have to use some “fluid-dynamical tricks” on his device to make it

W H AT WO N ’ T K I L L Y O U , M I G H T M A K E Y O U S T R O N G E R

Left to r ight : Researchers El izabeth

Rowland, Samantha Dewerff , and María

Baut ista wi th Associate Professor of

Microbiology Rachel Whitaker.

V iruses are responsible for much more than sore throats and stuffy noses. Researchers now believe that some viruses may protect hosts from competitors and help them survive. Despite the fact that viruses are practically everywhere and affect every living thing, scientists know very little about their positive impact on their hosts.

The National Science Foundation awarded a five-year, $2-million grant to microbiologist Rachel Whitaker and an interdisciplinary, multi-institutional team to explore the idea of viruses and their hosts coevolving together in the lab in the model system of hot springs at Yellowstone National Park.

“I hope to find that viruses are not just

N E W R E S E A R C H S E E K S TO F I N D O U T I F V I R U S E S C A N B E F R I E N D S A S W E L L A S F O E S

pathogens—that they are influencing dynamics in a bigger way,” said Whitaker, who is a member of the Biocomplexity theme. “Sometimes they are good for their hosts, acting as symbionts or mutualists. I think it would be really neat if there were little infectious particles that could help the organisms they infect to survive and

compete against their foes.”

Preliminary data has already shown that if an organism survives infection, it can use the virus to kill its competitors in the environment.

“It was once thought that viruses infect a microbe and kill it, or they don’t infect at all,” Whitaker

said. “We have realized, given genomics and metagenomics, that it is a much more complex dynamic. Now we are asking, if hosts can use their viral infection as a weapon against their competitors, how does that affect these populations and their ecosystems? It’s a new way of looking at things.”

Through laboratory experiments, Whitaker’s team will study host-viral interactions, including

p. 22

“If hosts can use their viral infection as a weapon against their competitors, how does that affect these populations and their ecosystems?”


A ntibiotic resistance is depleting our arsenal against deadly diseases and infections, such as tuberculosis and Staph infections, but recent research shows promise to speed up the drug discovery process.

In a study reported in ACS Chemical Biology, University of Illinois researchers developed a new technique to quickly uncover novel, medically relevant products produced by bacteria. Past techniques involved screening more than 10,000 samples to find a novel product, said principal investigator Doug Mitchell, Assistant Professor of Chemistry.

By using this new technique, Mitchell’s lab discovered a novel product after screening just a few dozen soil bacteria.

Soil bacteria, which naturally produce antibiotics to fend off competitors, are the most significant source of antibiotic and anticancer drugs. Indeed, over the past 30 years, natural products

or simple derivatives thereof account for 50 and 75 percent of all FDA-approved anticancer and antibiotic drugs, respectively.

“Many companies have stopped working on natural product discovery because it is difficult and not as profitable as other therapeutic areas,” said microbiology graduate student Courtney Cox, who pioneered the new technique. “As academics, this is exciting because we are better positioned to advance human health by finding

new natural products where most companies are reluctant to pursue this line of research.”

A N E W A N T I B I OT I C D I S C OV E RY T E C H N I Q U E

The most historically popular method for natural product discovery, called bioassay-guided isolation, often rediscovers the same

highly abundant (or highly active) compounds over and over again, similar to fishing in a lake and always catching the most plentiful species while sparse species never take the bait.

But this new technique helps researchers find lakes with fewer fish, permitting the effortless identification of species that have already been

caught, and ultimately, catch the desired new fish species.

Using genomics, researchers are able to screen soil bacteria that are likely to produce novel antibiotic products. During the screening process, a chemical tag is added to the compounds of interest. The addition of the tags adds mass to the product so researchers can easily detect the reactive products using mass spectrometry.

A major advantage of this strategy is that the natural product does not have to be present at a therapeutic concentration, a prerequisite for bioassay-guided isolation. Rather, it only has to be detectable by mass spectrometry, which is renowned for its sensitivity.

“Using genome mining to find new compounds is not a new concept. Semi-synthetically derivatizing (tagging) natural products is also not a new idea,” Mitchell said. “But we bring these two ideas together to create a powerful discovery platform.”

Mitchell estimates that other researchers should be able to use this straightforward method to discover low abundance novel products that would be impossible to locate via bioassay-guided approaches.

They are working to patent the technique.

I N N OVAT I V E T E C H N I Q U E M AY T R A N S F O R M T H E H U N T F O R N E W A N T I B I OT I C S A N D C A N C E R T H E R A P I E S

Pictured lef t to r ight : Courtney Cox, James Doroghazi , Joel

Melby, pr incipal invest igator Doug Mitchel l , Jonathan Tietz,

and Karol Sokolowski .

p. 22

“We are better positioned to advance human health by finding new natural products.”


“C4 is sort of a fuel-injected photosynthesis that maize and sorghum

and millet have,” Leakey explained. “Our previous work here at Illinois has shown that their photosynthesis rates are not stimulated by being at elevated CO2. They already have high CO2 inside their leaves.”

More research is needed to determine how crops grown in developing regions of the world will respond to higher atmospheric CO2.

“It’s important that we start to do these experiments in tropical climates with tropical soils, because that’s just a terrible gap in our knowledge, given that that’s where food security is already the biggest issue,” Leakey said.

The study, which is reported in Nature, included researchers from Harvard University (which led the effort); Ben-Gurion University of the Negev in Beer Sheva, Israel; the U. of I.; the University of California, Davis; the U.S. Department of Agriculture’s Agricultural Research Service; the National Institute for Agro-Environmental Sciences in Ibaraki, Japan; the University of Melbourne, Australia; the University of Arizona; the University of Pennsylvania; and The Nature Conservancy, Santa Fe, New Mexico.

R esearchers have some bad news about the food of the future: As carbon dioxide levels rise this century, some grains and legumes will become significantly less nutritious than they are today.

Atmospheric CO2 concentrations are approaching 400 parts per million and are expected to rise to 550 ppm by 2050. The researchers looked at multiple varieties of wheat, rice, field peas, soybeans, maize, and sorghum grown in fields with atmospheric carbon dioxide levels like those expected in the middle of this century.

The teams simulated high CO2 levels in open-air fields using a system called Free Air Concentration Enrichment (FACE), which pumps out, monitors, and adjusts ground-level atmospheric CO2. All other growing conditions (sunlight, soil, water, temperature) were the same for plants grown at high CO2 and those used as controls.

The experiments revealed that the nutritional quality of a number of the world’s most important

crop plants dropped in response to elevated CO2.

“When we take all of the FACE experiments we’ve got around the world, we see that an awful lot of our key crops have lower concentrations of zinc and iron in them (at high CO2),” said plant biology and IGB professor Andrew Leakey (below left), an author on the study. “Zinc and iron deficiency is a big global health problem already for at least two billion people.”

Zinc and iron went down significantly in wheat, rice, field peas, and soybeans. Wheat and rice also saw notable declines in protein content at higher CO2.

“Across a diverse set of environments in a number of countries, we see this decrease in quality,” Leakey said.

Nutrients in sorghum and maize remained relatively stable at higher CO2 levels because these crops use a type of photosynthesis called C4 that already concentrates carbon dioxide in their leaves.

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N U T R I T I O N A L Q UA L I T Y O F WO R L D ’ S M O S T I M P O RTA N T C R O P P L A N T S D R O P P E D I N R E S P O N S E TO E L E VAT E D C O 2


A multi-institutional team reports that it can increase sugarcane’s geographic range, boost its photosynthetic rate by 30 percent, and turn it into an oil-producing crop for biodiesel production.

If the researchers achieve their goal, growers will be able to meet 69 percent of the U.S. mandate for renewable fuels by growing the modified sugarcane on abandoned land in the southeastern United States.

These are only the first steps in a bigger initiative that will turn sugarcane and sorghum, two of the most productive crop plants known, into even more productive, oil-generating plants.

“Biodiesel is attractive because with soybean, once you’ve pressed the oil out it’s fairly easy to convert it to diesel,” said Stephen Long (above far right), IGB faculty member and Gutgsell Endowed Professor of Plant Biology and Crop Sciences, who leads the initiative. “You could do it in your kitchen.”

But soybean is not productive enough to meet the nation’s need for renewable diesel fuels.

“Sugarcane and sorghum are exceptionally productive plants, and if you could make them accumulate oil in their stems instead of sugar, this would give you much more oil per acre,” Long said.

Working first with the laboratory-friendly plant Arabidopsis and later with sugarcane, the team introduced genes that boost natural oil production in the plant. They increased oil production in sugarcane plants to about four percent. They hope to increase the oil content of sugarcane stems from its current two percent to about 20 percent.

A second research direction was to use genetic engineering to increase photosynthetic efficiency in sugarcane and sorghum by 30 percent.

To boost cold tolerance, researchers are crossing sugarcane with Miscanthus, a related perennial grass that can grow as far north as Canada. The new hybrid is more cold-tolerant than sugarcane, but further crosses are needed to restore the other attributes of sugarcane while preserving its cold-tolerance.

Long said that the team hopes to integrate all of these new attributes into sugarcane.

“Our goal is to make sugarcane produce more oil, be more productive with more photosynthesis, and be more cold-tolerant,” he said.

The research team includes scientists from Brookhaven National Laboratory, the University of Florida, and the University of Nebraska. The team presented its findings in February 2014 at the U.S. Department of Energy’s ARPA-E Energy Innovation Summit in Washington, D.C.

T E A M C O N V E RT S S U G A R C A N E TO A C O L D - TO L E R A N T O I L - P R O D U C I N G C R O P


O S H E R L I F E L O N G L E A R N I N G I N S T I T U T E P R O G R A M H E L P S S E N I O R C I T I Z E N S E X P L O R E N E W C A L L I N G S

A lbert Himoe stands in front of a cluttered lab bench and holds a plastic tube up to the light, looking for the small mass of DNA clinging to the side of the tube. Himoe has spent the last four days preparing this seemingly insignificant speck of genetic material.

This DNA contains a special gene that will play an integral role in genetic research on Fragile X Syndrome (FXS), the most common cause of inherited cognitive impairment, with 20 to 30 percent being diagnosed with autism.

Stephanie Ceman, a professor of cell and developmental biology and an affiliate with the Institute for Genomic Biology, has been studying this condition since 1997. Himoe joined Ceman’s lab in 2011 as a citizen scientist through the Osher Lifelong Learning Institute (OLLI), a member-driven learning community for people over the age of 50.

OLLI citizen scientists are matched with scientists at Illinois based on their knowledge, skills, and interests. They volunteer in a lab for several hours every week, oftentimes being delegated their own task to manage for the lab.

“What we appreciate about this program is that it allows our members to explore new areas and make important contributions even after their own careers may be behind them,” said Christine Catanzarite, OLLI director. “That’s a valuable lesson about the importance of lifelong learning.”

The Citizen Scientist Program was conceived by Art Kramer, Director of the Beckman Institute at the University of Illinois, Gene Robinson, Director of the IGB, and Kathleen Holden, former Director of OLLI, in 2009. Today the program has about 15 citizen scientists who are involved in a variety of disciplines and subject areas, from entomology to neurology. Past participants include retired school teachers, bankers, gardeners, scientists, and others.

“What’s funny is that, despite their different backgrounds, they all just wanted to contribute to the scientific community,” said Geena Skariah, who managed the fledgling program for two years and is currently a neuroscience doctoral student in Ceman’s lab. “In a sense, they were

all self-selected because they all wanted to do something scientific and be part of the scientific community. Their personalities may range from very talkative to very friendly to absolutely quiet people, but they all find their own niche in each lab.”

For Himoe, the Citizen Scientist Program was the perfect way for him to put his background in science to work.

“When I was 13 or 14, my sister got my father talking about the periodic table, which I’d never heard of before,” Himoe said. “It was fascinating, a whole new world to me.”

From that moment on, Himoe was enamored with the discipline. He took all the science courses available in his high school: chemistry, physics, and biology. Himoe went on to earn a bachelor’s degree in chemistry from Reed College in 1959 followed by a doctorate in organic chemistry from the University of Chicago in 1964.

At the age of 75, Himoe has seen first hand how

research has evolved over the years. When he began his career computers came with punch cards and calculators only did the most elementary of operations. Before automatic pipettes, he used neoprene bulbs to suck up liquids.

Today Himoe manages the lab for Ceman and her graduate students, Skariah and Phillip Kenny, a doctoral student in molecular biology. With his cluttered lab bench and paper-covered desk, Himoe has found an academic home in their lab.

“He loves talking about new stuff he’s discovered,” Skariah said. “He knows he can come back and discuss it with us and feel like he’s had a good conversation. I think the scientific environment is what he benefits most from.”

In the lab, Himoe clones DNA, makes buffers, fills solutions, maintains the water baths, sterilizes the lab’s supplies, disposes of the bio-waste and biodegradable materials, and much more. “When Albert does these tasks, and we know they are done right, that’s gold,” Ceman said. “That unburdens me, and that unburdens the graduate students, and he does it without complaining.”

Himoe also isolates DNA that contains that special gene called FMR1. For most people, this gene provides the body with instructions to make a protein called FMRP, which is vital for a healthy, functional brain. People with FXS have an abnormal and repressed FMR1 gene so their bodies can’t make the vital FMRP protein.

Eventually, Himoe spots the DNA isolate clinging

C O L L A B O R AT I V E L E A R N I N G : T H E O L L I C I T I Z E N S C I E N T I S T P R O G R A M

“We are so grateful for our OLLI volunteers. They truly make the wheels turn in our lab so that we’re able to get this work done.”


Cel l and Developmental

Biology Professor

Stephanie Ceman, lef t , wi th

grad student Phi l l ip Kenny,

OLLI c i t izen scient ist Albert

Himoe, and grad student

Geena Skar iah. Himoe has

worked with the Ceman lab

s ince 2011.

to the side of the test tube. He carefully removes the excess ethanol with an automatic pipette, an overlooked mainstay of 21st century science.

The four-day process has yielded about a milligram of DNA, which would weigh about as much as a paperclip. It’s enough to keep the lab’s FXS experiments going for nearly three weeks.

The small white mass is dissolved with a buffer and poured into an eppendorf tube, which is nestled in a box of other tubes, marked with other dates. Inside each tube lies thousands of copies of that special gene, with each gene containing the same secret instructions to understanding cognition, and perhaps one day, curing FXS. ––––––––––––––––––––––––––––––––––

S allie Miller is not one to sit still. After her retirement from various positions in the healthcare industry, Miller took the opportunity to invest her time, efforts, and expertise in volunteering.

During tax season, Miller volunteers as an AARP tax aide. Other days, she is helping with the State Health Insurance Program (SHIP) to assist people when they have Medicare questions. She’s also on the YWCA board, Presence Life Connections Board, and the American Association of University Women (AAUW) Illinois Board. She participates in a tutoring program called Project READ through Parkland College, and is a Court Appointed Special Advocate (CASA) volunteer, a program that provides an adult advocate for children in the court system who have been removed from the home due to abuse or neglect.

And then, for one afternoon a week, Miller is also a citizen scientist. She volunteers at the Beckman Institute for Susan Schantz, who heads the Children’s Environmental Health and Disease Prevention Research Center, which studies whether chemicals in plastics and personal care products alter child development, cognition, or other behaviors.

In the lab, she assists with calling and recruiting participants and inputting data—a vital task for the center, as they’re working to test more than 600 mothers and babies. As all scientists know, there’s a lot that goes on behind the scenes to make science happen, and Miller makes sure this work gets done.

“I like that I can help them in the process of answering some important questions about the role of chemicals in childhood development,” she said. “I like learning about what kind of research is being done, and interacting with the lab members and the other citizen scientists in the lab.”

For Miller, an outgoing 68-year-old, it’s also an opportunity to socialize and meet new people.Miller started working in this program after hearing about it from another citizen scientist in Schantz’s lab, Linda McEnerney, another OLLI member who is a former pediatrician and works directly with the mothers and babies. There are six citizen scientists in the Schantz lab, and each are trained in their specific areas by lab members.

“We are so grateful for our OLLI volunteers. They truly make the wheels turn in our lab so that we’re able to get this work done,” said Schantz. “We have some working with the database and participant scheduling, and some working directly with the participants. We love them—we couldn’t

do our work without them.”

Before she began the OLLI program, Miller wanted first to see if she fit in with any of the labs that needed help. “It seemed like a very unusual and interesting program, and I like volunteering, so I offered my services and they matched me with this program,” Miller said. “My theory is always that you need to stay current—you need to know what’s going on in the world, be aware of your environment, and keep your skills as current as you can. If there’s opportunity for training or education, take advantage of it. So I did.”

“I know I could be slowing down,” Miller added. “But I like doing this. I was interested to see what they were doing, what they wanted me to do, whether I would enjoy doing it or not. It keeps me active and it keeps my mind sharp. Why wouldn’t I take advantage of that?” ––––––––––––––––––––––––––––––––––– OLLI (the Osher Lifelong Learning Institute at the University of Illinois) is a member-centered community of adult learners that is supported by the Bernard Osher Foundation, the Illinois Office of the Provost, and the generous donations of OLLI members and community partners. Any lab or faculty member at the Beckman Institute or IGB can request to have an OLLI member work in their lab, and all OLLI members are encouraged to participate.


H U M A N M I C R O B E S B E T T E R T H A N T H O S E O F C OW S O R T E R M I T E S AT B R E A K I N G D OW N B I O M A S S C E L L WA L L S

Isaac Cann, professor of animal

sciences and microbiology and

deputy director of the Energy

Biosciences Inst i tute.

A fter scouring cow rumens and termite guts for microbes that can be used to break down biomass cell walls in the production of next-generation biofuels, IGB researchers have reported in Proceedings of the National Academy of Sciences that some of the best candidates may live in the human lower intestine.

One barrier to producing ethanol from biomass is that the sugars necessary for fermentation are trapped inside the cell walls, which resist degradation. Isaac Cann, professor of animal sciences and microbiology and deputy director of the Energy Biosciences Institute, animal sciences professor Roderick Mackie, and M.D./Ph.D. student Dylan Dodd have been looking for microbes that can break down xylan, a common hemicellulose (fiber) in human diets as well as in the cell walls of the biomass used to produce biofuel, and release the sugars necessary for fermentation.

Initially, they looked at cow rumen.

“We found that Prevotella bryantii, a bacterium

that is known to efficiently break down hemicellulose, gears up production of one gene more than others when it is digesting plant matter,” Cann said.

When searching a database for similar genes in other organisms, the researchers found two human gut microbes, Bacteroides intestinalis and Bacteroides ovatus, that belong to the same bacterial phylum as Prevotella from the cow.

“We expressed the human gut bacterial enzymes and found that for some related enzymes, the human ones actually were more active (in breaking down hemicellulose) than the enzymes from the cow,” Cann said.

When the researchers examined the structure of the human enzymes, they saw something unusual: many single polypeptide (protein) chains contained two enzymes, one of which was embedded in the other. Further analysis revealed that the embedded component was a

carbohydrate-binding module (CBM) that latches onto carbohydrates such as hemicellulose, shredding it so that other enzymes can work on it to break it down into its unit sugars.

Working with U. of I. biochemistry professor Satish Nair, the researchers also noticed that the CBM “put a kink” in the fiber when it bound to it, bringing it closer to the other enzyme in the protein and allowing it to break the bonds between the sugars.

“In addition to finding microbes in the cow rumen and termite gut, it looks like we can actually make some contributions ourselves,” Cann said. “And our bugs seem to have some enzymes that are even better than those in the cow rumen.”

The Energy Biosciences Institute is a public-private collaboration involving the U. of I., the University of California at Berkeley, the Lawrence Berkeley National Laboratory, and BP, the energy company that funds the work.

S E A R C H F O R B E T T E R B I O F U E L M I C R O B E S L E A D S TO T H E H U M A N G U T

“Our bugs seem to have some enzymes that are

even better than those in the cow rumen.”


I GB faculty member May Berenbaum has been awarded the National Medal of Science, the nation’s highest honor for achievement and leadership in advancing science and technology.

The National Medal of Science was created in 1959 and is awarded annually to individuals who have made outstanding contributions to science and engineering.

“Professor Berenbaum’s work has fundamentally changed what we know, how we study, and how the public understands the role of insects in nearly every aspect of human life and development,” said U. of I Chancellor Phyllis M. Wise. “This is transformative scholarship on a global scale and has implications for every person on the planet.”

Berenbaum, a Swanlund Chair and the head of

the department of entomology, has been a U. of I. faculty member since 1980. Her research, which studies the chemical mechanisms underlying interactions between insects and their host plants, including the detoxification of natural and synthetic chemicals, has produced hundreds of peer-reviewed scientific publications and 35 book chapters.

“Through her inspired work on insects, Professor Berenbaum has had an unparalleled impact on the environmental sciences, with a rare combination of path-breaking scientific discovery and influential public engagement,” said IGB Director Gene Robinson, a long-time colleague of Berenbaum.

A member of the National Academy of Sciences, Berenbaum has chaired two National Research Council committees, the Committee on the

Future of Pesticides in U.S. Agriculture and the Committee on the Status of Pollinators in North America.

An academic who is devoted to teaching and fostering scientific literacy through formal and informal education, Berenbaum also has authored numerous magazine articles and six books about insects for the general public. She also created the Insect Fear Film Festival, now in its 32nd year on campus. The festival entertains hundreds of viewers each year with feature-length films and shorts, commentary on the films, an insect petting zoo, and an insect art contest.

Berenbaum graduated summa cum laude with a bachelor’s degree in biology from Yale University in 1975. She earned a Ph.D. in ecology and evolutionary biology from Cornell University in 1980.

M ay Berenbaum was recently appointed to the Directorate for Biological Sciences Advisory Committee (BIO AC) at the National Science Foundation (NSF).

During the three-year appointment, Berenbaum will advise the directorate on how BIO can best serve the scientific community through its mission, goals, and programs as well as its institutional administration and policies. She will also help prioritize support for areas of biological research and promote educational opportunities in the biological sciences.

“Since NSF is the principal funder of basic life science research, the advisory committee has the potential to have a significant impact on the future direction of basic life science research across the country,” Berenbaum said. “In the past, NSF has really encouraged and facilitated curiosity-driven research that could be considered high risk, but high risks, in my opinion, often lead to big rewards.”

As a member of the committee, Berenbaum hopes to emphasize the importance of “basic, curiosity-driven, investigator-instigated, bottom-up” research in the face of economic and political pressures that could draw resources elsewhere.

“It is of utmost importance for U.S. scientific competitiveness that politics remain out of the process by which decisions are made that relate to funding basic research,” she said. “I am more than willing to do whatever I can to preserve the integrity of the process of funding basic research.”

Berenbaum said she is also “paying it forward” to the NSF, which has supported her research since her career began in 1980.

M AY B E R E N BA U M AWA R D E D N AT I O N A L M E DA L O F S C I E N C E

H E L P I N G N S F S E R V E T H E S C I E N T I F I C C O M M U N I T Y


Through a SEED project funded by the Institute for Genomic Biology, Whitaker is also using a similar approach to examine how bacterial adaptive immunity and virus infection affects population dynamics of human pathogens.

“Every organism on Earth gets infected by viruses. Understanding these dynamics will have a great impact on our understanding of the microbial world.”

W H AT WO N ’ T K I L L Y O U , C O N T I N U E D

I N N OVAT I V E T E C H N I Q U EC O N T I N U E D

Sascha Hi lgenfeldt , a professor in the

Department of Mechanical Science and

Engineer ing, developed a device that

separates part ic les by s ize (r ight) .

D I S C OV E RY O F A N E W A N T I B I OT I C

After screening only a handful of soil bacteria, Mitchell’s group discovered a novel product, cyclothiazomycin C (CC), an antibiotic that is effective against gram-positive bacteria like Bacillus anthracis (anthrax) and Staphylococcus aureus (Staph/MRSA).

“It isn’t as good at killing these bacteria as some clinically approved antibiotics are, but that’s not the point in this early stage of the drug discovery process,” said organic chemistry graduate student Jonathan Tietz, who confirmed the antibiotic’s structure. “You want to discover something that is unique because then you can modify the structure to improve its medicinal properties. If the compound works by a different mechanism, then that creates a new avenue to address drug resistance.”

CC, which belongs to a class of natural products known as thiopeptides, looks like a “Do Not” sign. Another thiopeptide antibiotic, thiostrepton, which was discovered in the 1950’s, has been approved for topical use in veterinary medicine.

“There is a serious effort right now in some

pharmaceutical companies to enhance the therapeutic properties of other thiopeptides,” Mitchell said. “There are multiple clinical trials going on right now with other members of the thiopeptide class.”

C O L L A B O R AT I O N

Mitchell said the Institute for Genomic Biology made this study possible by creating a collaborative research environment.

“The IGB facilitated this research by bringing together the right units on campus, like-minded researchers who share resources, and by promoting the free dissemination of ideas amongst our group,” Mitchell said. “I didn’t come to this university with this exact idea; it was born out of being in the type of environment that the IGB fosters.”

The Mitchell lab collaboration also included undergraduate researcher Karol Sokolowski, chemical biology graduate student Joel Melby, and IGB postdoctoral fellow James R. Doroghazi.

This study was supported by an NIH Director’s New Innovator Award Program, the David and Lucile Packard Fellowship for Science and Engineering, the Robert C. and Carolyn J. Springborn Endowment, the American Society for Biochemistry and Molecular Biology Undergraduate Research Award, National Center for Research Resources, National Institutes of Health, and the IGB.

work for such small particles: the larger archaeal cells are captured in a tiny vortex caused by an oscillating bubble, while the smaller viruses are able to pass unhindered through the channel. (See video of this process at http://bit.ly/1sQEcY4.)

“It’s a tunable size filter because the strength of the transport flow and the bubble vibration strength decide what particle size gets through and what particle size is retained,” Hilgenfeldt said. “We are excited to apply this principle to the samples from hot springs to figure out how the population dynamics can change.”

Through this grant, Whitaker also plans to study microbial adaptive immunity, where a host is able to recognize infectious particles (such as

viruses) and degrade them if they are infected again.

“This work is pretty important because there is not a very good understanding of how adaptive immunity affects the evolution of pathogens,” Whitaker said. “We are hoping to apply some of the things we learn by looking at this simple adaptive immunity system and its diversity in order to understand the evolutionary impacts of diversified adaptive immunity in general.”

The ant ib iot ic cyclothiazomycin

C (CC), effect ive against

gram-posi t ive bacter ia,

resembles a “Do Not” s ign.


The IGB partnered with the Department of Anthropology and the Native American and Indigenous Studies Program at the University of Texas at Austin to host the Summer Internship for Native Americans in Genomics (SING) Workshop for 2014. The workshop was held June 1-7, 2014 on the University of Texas campus in Austin.

This was the third year that the SING Workshop has been offered. The workshop aims to facilitate discussions of how genomics research is conducted and to create a support network for Native American students in the sciences. Attendees also learn

fundamental concepts and methods in genomics and bioinformatics, including both theoretical aspects and practical laboratory- and computer-based training.

The workshop is open to tribal college students, community college students, university undergraduate students and graduate students, and individuals from Native American communities. The 2015 workshop will be held at the University of Illinois at Urbana-Champaign; full details and the online application can be found at http://conferences.igb.illinois.edu/sing/.

Each fall, hundreds of children, parents, and friends of the IGB attend Genome Day, an open-house event for community members of all ages to learn about genomes, genes, DNA, and evolution. The event is held each year on a Saturday in early November at the Orpheum Children’s Science Museum in Champaign.

Genome Day features hands-on, child-friendly activities related to genomics. In past years, attendees have learned how organisms relate to each other on the Tree of Life, constructed their own models of DNA and cells, and extracted strawberry and banana DNA to make necklaces. For the last two years, volunteers from SACNAS (Society for Advancement of Chicanos and Native Americans in Science) have provided language assistance for Spanish-speaking attendees.

As part of the outreach mission of the IGB, events such as Genome Day strive to present the key concepts of genomics research. Next year’s Genome Day is already on the calendar for November 14, 2015.

O U T R E A C H | R E A C H O U T

G E N O M E DAY

P O L L E N P OW E R ! S U M M E R C A M P

S U M M E R I N T E R N S H I P F O R N AT I V E A M E R I C A N S I N G E N O M I C S ( S I N G )

G E N O M I C S F O R ™ T E A C H E R S

Twenty-six girls from around East Central Illinois came to participate in Pollen Power!, a week-long science day camp hosted July 7-11 by the IGB. Campers investigated the up-close structure and function of pollen, and discovered connections between the biology of pollen and larger scientific ideas.

The camp was designed to give girls a kaleidoscopic picture of what it means to be a plant biologist: activities included using the IGB Core Facilities’ high-powered microscopes, designing and printing 3D pollen grains at the Champaign-Urbana Community Fab Lab, planning and recording a climate newscast with green screen technology, and hearing guest talks from IGB researchers on the crucial role that women play in STEM fields.

This was the second year that Pollen Power! has been offered; it is funded in part by the National Science Foundation. Planning is already underway for next year’s camp, which will take place July 13-17, 2015. Registration for next year’s camp will open in spring 2015.

Science teachers need access to curricula that reflect current scientific understanding and training to expand their own knowledge; this is especially important for topics such as genomic biology, in which the boundaries of knowledge are advancing rapidly. Project NEURON, a University of Illinois at Urbana-Champaign curriculum development group, partnered with the IGB in July 2014 to offer a new course, Genomics for™ Teachers, addressing teacher professional development needs.

Attendees of the Genomics for™ Teachers workshop engaged in and critiqued hands-on curriculum activities related to genomics, explored and discussed the recently published Next Generation Science Standards, heard presentations from University of Illinois faculty on the societal impacts of genomic biology, and received guidance and peer feedback on independent curriculum development projects.

Project NEURON, which is funded by an NIH Science Education Partnership Award, combines the expertise of scientists and education researchers to produce cutting-edge biology curriculum materials and to provide continuing education opportunities for teachers.


W h e r e W i l l S c i e n c e Ta ke U s I n 2 0 Ye a r s ?

IGB Director Gene Robinson was among the first contributors to a new blog from The Science Coalition, an association dedicated to telling the stories of what federally funded university research makes possible and to calling attention to the importance of sustained support for scientific research. The blog, SCIENCE 2034, features predictions on the future of science and innovation.

“It’s absolutely essential that policymakers and the public make the connection between the dollars allocated for research today and the world we, and our children and grandchildren, will live in 20 years from now,” said Science Coalition President Jon Pyatt. “While we don’t know what the next ‘Big Thing’ will be, chances are it will be an innovation born from basic scientific research.”

The blog was unveiled as Congress returned to Washington.

Robinson predicted that in the year 2034, we will have solved a fundamental mystery of the brain: how past experience affects future behavior. This discovery could contribute to reducing rates of mental illness, helping people live healthier, more productive lives.

B r e a k i n g B a r r i e r s t o R e p r o g r a m m i n g C e l l s The discovery that cells of the human body (somatic cells) can be reprogrammed to generate pluripotent stem cells has enormous implications for regenerative medicine and could lead to revolutionary treatments for chronic diseases, including cancer.

Pluripotency refers to the ability of some stem cells to develop into any cell type. Induced pluripotent stem cells (iPSCs) generated in the laboratory from somatic cells seem to be equivalent to true stem cells while being easier to grow in large quantities and having greater differentiation potential.

The problem is that multiple cellular mechanisms inhibit reprogramming of gene expression in

somatic cells throughout the process of iPSC generation. Until recently, these barriers to reprogramming were poorly understood.

Researchers have now catalogued these barriers.

“Cells generally become committed to increasingly differentiated fates during the course of their normal development, but experimental paradigms for cellular reprogramming have shown that differentiation is reversible,” explained Founder Professor of Physics and of Bioengineering and IGB faculty member Jun Song, one of the project’s lead scientists.

I n s e c t A g g r e s s i o n L i n ke d t o B r a i n M e t a b o l i s mIGB scientists studying fruit flies and honey bees have found a causal link between brain metabolism and aggression.

Previous research from IGB director Gene Robinson’s laboratory found that some metabolic genes in honey bees were suppressed when the bees faced down an intruder–a counterintuitive finding because aggression seems to require more energy, not less. These genes play a key role in oxidative phosphorylation, the most efficient type of energy generation in cells.

In the new study, postdoctoral researcher Clare Rittschof found that aggression increased with dose level when drugs were used to suppress key steps in oxidative phosphorylation in bee brains. However, the drugs had no effect on chronically stressed bees, which were not able to increase their aggression in response to an intruder. In separate experiments, postdoctoral researcher Hongmei Li-Byarlay and undergraduate Jonathan Massey found that reduced oxidative phosphorylation in fruit flies also increased aggression.

The findings offer insight into the immediate and

longer-term changes that occur in response to threats. Animals facing a threat respond within seconds. Changes in brain metabolism take longer and cannot account for this immediate response but make individuals more vigilant to subsequent threats.

“This makes good sense in ecological terms because threats often come in bunches,” Robinson said.

The fact that the researchers observed these effects in two species that diverged 300 million years ago indicates that this mechanism is very robust and well-conserved.

The research, supported by the National Science Foundation, is reported in Proceedings of the National Academy of Sciences.

C e l l M e ch a n i c s M ay A f f e c t C a n c e r S p r e a d a n d R e c u r r e n c eA study by IGB researchers found that cancer cells that break away from tumors may prefer to settle into a soft bed.

Some cancer cells can cause a cancer to spread to other organs or evade treatment, resurfacing after a patient seems to be in remission. The Illinois team and colleagues in China found that these so-called tumor-repopulating cells (TRCs) may lurk quietly in stiffer cellular environments but thrive in softer spaces.

“What causes relapse is not clear,” said IGB affiliate and study leader Ning Wang, Leonard C. and Mary Lou Hoeft Professor in engineering and professor of mechanical science. “Why are there a few cells left that can come back stronger?”

Using a method they developed for selecting TRCs from a culture, Wang’s group isolated TRCs from melanoma, an aggressive skin cancer. To see how the mechanical environment

I G B R E S E A R C H B R I E F S


around the cells affected their ability to multiply and cause new tumors, the researchers grew the cells on gels of different stiffnesses. The TRCs placed in soft gels grew and multiplied; those placed on stiffer gels became dormant. When the dormant TRCs were transferred to a soft gel, they began to multiply.

Wang speculates that initial dormancy followed by reawakening when the mechanical environment is more inviting may explain why soft tissues, such as the brain or lungs, are most vulnerable to metastasis (cancer spread).

Wang hopes that understanding how TRCs work and proliferate can lead to treatments that prevent metastasis.

The National Institutes of Health supported this work, which is published in Nature Communications.

To S e c u r e To m o r r o w ’s Fo o d S u p p l y, E n g a g e To d ay ’s S t u d e n t sStudents who hope to improve societal well-being, combat illness, and protect the environment should consider a career in plant biology research, said Stephen Long, Gutgsell Endowed Professor of Plant Biology and Crop Sciences and IGB faculty member.

Long was inspired by his participation in the Gatsby Plant Science Summer School for undergraduates held near York, England. The week-long intensive course addresses a growing need to promote student interest in plant sciences by highlighting its exciting aspects and social value.

Long said that, while the FAO projects that we will need 70 percent more primary foodstuffs by 2050, this will never be achieved at current growth rates. This is why education about plants is so important.

Long would like to see the U. of I. offer educational opportunities similar to the Gatsby program to biology majors and high school teachers, who could then share enthusiasm for plant sciences with their students. IGB field research projects such as RIPE (Realizing Increased Photosynthetic Efficiency) and SoyFACE would provide participants with meaningful hands-on experience of cutting-edge research.

W h o We r e t h e F i r s t A m e r i c a n s ? A study analyzing genetic information extracted from the tooth of an adolescent girl who fell into a sinkhole in the Yucatan 12,000 to 13,000 years ago could shed light on the origins of the first inhabitants of the Americas.

Most scientists have believed that the original immigrants crossed over a land bridge that connected northeast Asia to present-day Alaska. The oldest remains have baffled researchers, however, because the skulls, like the one of the girl in the sinkhole, are very different from those of Native Americans.

Anthropology professor and IGB faculty member Ripan Malhi’s lab conducted genetic analyses for the new study. Researchers in his lab, in collaboration with researchers at Washington State University and the University of Texas, independently extracted and analyzed mitochondrial DNA from the girl’s tooth. They concluded that the girl belonged to a genetic lineage that is shared only by Native Americans.

“We were able to identify her genetic lineage with high certainty,” Malhi said. “This shows that living Native Americans and these ancient remains of the girl we analyzed came from the same source population during the initial peopling of the Americas.”

The research, reported in Science, was an international effort involving scientists, divers, and technicians from more than a dozen institutions. James Chatters of Applied Paleoscience in Bothell, Washington, led the research. Chatters is known for his work on Kennewick Man, another ancient individual found in 1996 whose origins were debated because his skull differed from those of Native Americans.

I G B R e s e a rch e r Fe a t u r e d i n N a t i o n a l T V S e r i e sKaren Sears, an assistant professor at IGB and the School of Integrative Biology, was featured in the second episode of Your Inner Fish, a three-part PBS series based on a book by the show’s host Neil Shubin that traces 350 million years of human evolution.

In her segment, Sears compared the development of opossum ears with the evolution of mammals’ middle ear bones from reptile jawbones. “They almost go through 300 million years of evolution in terms of their ears,” she said.

Sears said that, even though the three-minute segment took nearly two days to film, the effort was worth it.

“Scientific outreach and these types of programs are incredibly valued today. The manifestations of being featured have the potential to be pretty large, not only for myself but for the field,” she said

“I want to get kids excited about pursuing STEM-related careers and help their parents to understand the importance of funding scientific research, because ultimately it will be up to them to vote in favor of funding science.”

Left to r ight : Jun Song, Ning Wang, Ripan Malhi , Karen Sears


B r y a n W h i t e N i g e l G o l d e n f e l d MAYO CLINIC/NATIONAL INSTITUTES OF HEALTH Microbial Metabolic Toxicity Drives Colon Cancer

M a t t h e w W h e e l e r J o A n n C a m e r o n UNIVERSITY OF MICHIGAN/NATIONAL INSTITUTES OF HEALTH A Bioresorbable Splint for Treating Tracheomalacia

M a t t h e w W h e e l e r J o A n n C a m e r o n NORTHWESTERN UNIVERSITY/NATIONAL INSTITUTES OF HEALTH Nanotechnology Strategies for the Growth of Bones and Teeth

H u i m i n Z h a o J a m e s A l l i s o n C h r i s t o p h e r R a o DEFENSE ADVANCED RESEARCH PROJECTS AGENCY (DARPA) Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB)

I G B G R A N T S I G B

AWA R D SR a s h i d B a s h i r, Professor, Department Head, Bioengineering (REGENERATIVE BIOLOGY & TISSUE ENGINEERING) was selected as Chair of the Nanotechnology Study Section (NANO) in the Center for Scientific Review of the National Institutes for Health.

M ay B e r e n b a u m , Professor, Department Head, Entomology (GENOMIC ECOLOGY OF GLOBAL CHANGE) received the National Medal of Science from the National Science Foundation.

S t e p h e n B o p p a r t , Abel Bliss Professor of Engineering (REGENERATIVE BIOLOGY & TISSUE ENGINEERING) received an Early Concept Grants for Exploratory Research (EAGER) from the National Science Foundation.

I s a a c C a n n , Professor, Microbiology and Animal Sciences (ENERGY BIOSCIENCES INSTITUTE, BIOCOMPLEXITY) was awarded the Paul A. Funk Recognition Award by the College of ACES.

B r i a n T. C u n n i n g h a m , Professor, Electrical and Computer Engineering (MINING MICROBIAL GENOMES) received a Technical Achievement Award from the Institute of Electrical and Electronics Engineers’ Engineering in Medicine and Biology Society. He was also elected as a 2013 Charter Fellow of the National Academy of Inventors.

S h a r o n D o n o v a n , Professor, Noel Endowed Chair in Nutrition and Health (REGENERATIVE BIOLOGY & TISSUE ENGINEERING) received the Spitze Land-Grant Professorial Career Excellence Award from the College of ACES.

B r u c e Fo u ke , Professor, Departments of Geology and Microbiology (BIOCOMPLEXITY) was chosen to serve as the 2014-15 American Association of Petroleum Geologists (AAPG) Roy Huffington Distinguished Lecturer in the Asia/Pacific Region.

M a r t h a L . G i l l e t t e , Professor of Cell and Developmental Biology (GENE NETWORKS IN NEURAL & DEVELOPMENTAL PLASTICITY) received an Early Concept Grants for Exploratory Research (EAGER) from the National Science Foundation.


S t e p h e n M o o s e , Professor, Crop Science (ENERGY BIOSCIENCES INSTITUTE, BIOSYSTEMS DESIGN, GENOMIC ECOLOGY OF GLOBAL CHANGE) received a Faculty Award for Excellence from the College of ACES.

S u a M y o n g , Assistant Professor, Bioengineering (CELLULAR DECISION MAKING IN CANCER) received the Rose Award for Teaching Excellence.

C h r i s t o p h e r R a o , Associate Professor, Chemical & Biomolecular Engineering (BIOSYSTEMS DESIGN, ENERGY BIOSCIENCES INSTITUTE) received the Excellence in Research Award from the College of Engineering.

S a n d r a R o d r i g u e z - Z a s , Professor of Animal Sciences (GENE NETWORKS IN NEURAL & DEVELOPMENTAL PLASTICITY) was named a University Scholar.

J u n S o n g , Professor, Bioengineering and Physics (CELLULAR DECISION MAKING IN CANCER) was named as the department of Bioengineering’s first Founder Professor.

J o n a t h a n S w e e d l e r, Eiszner Family Chair in Chemistry (MINING MICROBIAL GENOMES) received the 2014 Malcolm E. Pruitt Award.

W i l f r e d v a n d e r D o n k , Heckert Endowed Chair in Chemistry (MINING MICROBIAL GENOMES) was elected to the American Academy of Arts and Sciences. He also received the Royal Society of Chemistry’s Bioorganic Chemistry Award for 2014.

A m y Wa g o n e r J o h n s o n , Assistant Professor, Mechanical and Industrial Engineering (REGENERATIVE BIOLOGY & TISSUE ENGINEERING) was awarded a Chair of Excellence by the NanoSciences Foundation.

B r e n d a n H a r l ey, Assistant Professor, Chemical & Biomolecular Engineering (REGENERATIVE BIOLOGY & TISSUE ENGINEERING) received the Everitt Award for Teaching Excellence from the College of Engineering.

Pa u l H e r g e n r o t h e r, Professor of Chemistry (CELLULAR DECISION MAKING IN CANCER) was named a University Scholar.

D e b o r a h L e ck b a n d , Reid T. Milner Professor of Chemical and Biomolecular engineering (REGENERATIVE BIOLOGY & TISSUE ENGINEERING) was elected a 2014 fellow of the Biomedical Engineering Society.

S t e p h e n L o n g , Gutgsell Endowed Professor of Crop Sciences and Plant Biology (GENOMIC ECOLOGY OF GLOBAL CHANGE, BIOSYSTEMS DESIGN) was invited to serve as a Sectional Committee Chair for the Royal Society.

R u by M e n d e n h a l l , Associate Professor, African American Studies of Sociology (GENE NETWORKS IN NEURAL & DEVELOPMENTAL PLASTICITY) was named a Richard and Margaret Romano Professorial Scholar.

J e f f r ey S . M o o r e , Murchison-Mallory Professor of Chemistry (BIOSYSTEMS DESIGN) was named a Howard Hughes Medical Institute (HHMI) Professor.


T ravelers passing through O’Hare International Airport can now enjoy beautiful imagery from the pioneering research taking place at the Institute for Genomic Biology at the University of Illinois.

Located in Terminal 3 near the Concourse G Rotunda, 24 works from the “Art of Science: Images from the Institute for Genomic Biology” exhibit showcase a variety of subjects, from kidney stones to bee brains to plant cell walls .

“The goal of the Chicago Department of Aviation Arts and Exhibits Program is to enhance travelers’ airport experience by presenting engaging and enlightening art and exhibits throughout Chicago’s airports. The Institute for Genomic

Biology’s Art of Science exhibitions at O’Hare and Midway International Airports reflect University of Illinois research that addresses significant issues facing the world’s environment,” said Rosemarie S. Andolino, Commissioner, Chicago Department of Aviation.

The Art of Science exhibition is also on display at the Chicago Midway International Airport, located in Concourse A.

“These images represent much more than art,” said Glenn Fried, Director of the IGB’s Core Facilities, a biological microscopy and image analysis suite that provides faculty and students with state-of-the-art imaging tools and expertise. “They represent scientific breakthroughs and discoveries that will impact how we

treat human diseases, produce abundant food, and fuel a technologically-driven society.”

The artwork reflects the IGB’s collaborative,

interdisciplinary approach to addressing some of the grand challenges that exist today in health, energy, agriculture and the environment. The collection’s managing artist, Kathryn Faith Coulter, works with researchers to choose and also enhance some images for display, and also serves as the Institute’s multimedia design specialist. “To have science be accessible to everyone through images and described in a way that helps us to understand it is refreshing,” said Coulter.

In addition to O’Hare and Midway, images are on display in the communal areas of the Champaign Willard Airport.

I G B A RT O F S C I E N C E I M A G E S F E AT U R E D AT O ’ H A R E A I R P O RT

T H E T R AV E L I N G A RT E X H I B I T I O N F E AT U R I N G R E S E A R C H I M A G E S F R O M T H E I N S T I T U T E F O R G E N O M I C B I O L O G Y M A K E S I T S WAY TO C H I C A G O ’ S O ’ H A R E A I R P O RT.

Research images featured in the

IGB’s Art of Science exhibi t can

now be seen at O’Hare airport .

“These images represent much

more than art. They represent scientific

breakthroughs.”

G I V E TO I G BThe vision of scientific research is limited by innovation. New technologies let us see the physical world more clearly, in greater detail, in finer scales of space and time. Genomic research, around which the IGB is focused, is particularly tied to advancing technologies.

To continue our record of high-quality research, we need to maintain our position at the forefront of the field. We move past traditional divisions between disciplines of study by constructing a network of collaborations.

Gifts to the IGB help us to foster the collaborative environment that we believe is vital for progress in genomic research. Philanthropy helps us create opportunities for building strong working relationships and allows us to provide grants for daring, boundary-breaking research projects that more traditional funding agencies might be hesitant to support. With your help, we will continue to forge a path toward our vision of a better world.

For more in format ion, v is i t :

w w w. i g b . i l l i n o i s . e d u /G I V I N G

S TAY C O N N E C T E D W I T H T H E I G BStay connected to news, events, and program information at the Institute for Genomic Biology. By joining our mailing list, you’ll receive our e-newsletter and Biomarker with details about seminars, workshops, and symposia at the IGB.

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Thank you for YOUR support

C a r l R . Wo e s e R e s e a rch F u n d Donations may be made to the Carl R. Woese Research Fund to support research on evolution, systems biology and ecosystem dynamics at the Institute for Genomic Biology. Dr. Woese approved this fund in his name to help the next generation of scientists and to recognize his discoveries and work that spanned nearly half a century at the University of Illinois at Urbana-Champaign.

L e w i n L e c t u r e t o H o n o r I G B Fo u n d i n g D i r e c t o r The IGB is proud to honor Harris Lewin with its first named endowment. “The Harris A. Lewin Pioneer in Genomic Biology Distinguished Lecture” will recognize the lecture of a world-renowned scientist in the Pioneers in Genomic Biology lecture series. Through his foresight and determination, Dr. Lewin spearheaded the effort at the University of Illinois to create an interdisciplinary campus institute to advance life science research and stimulate economic growth.

S H A P I N G T H E F U T U R E O F S C I E N C E & S O C I E T Y

T h e Wa l k o f L i f eThe double helix – the classically beautiful twisting ladder that forms the shape of DNA – is beautifully depicted within the Walk of Life. Located to the west of the IGB building, adjacent to the historic Morrow Plots, Walk of Life pavers are the perfect way to commemorate anniversaries or special events, or to honor a loved one’s special achievements.

OR CONTACT:

M e l i s s a M c K i l l i p I G B D ev e l o p m e n t & O u t r e a ch D i r e c t o r 2 1 7 - 3 3 3 - 4 6 1 9 m m ck i l l i @ i l l i n o i s . e d u

BIOMARKERmagazine

I N S T I T U T E F O R G E N O M I C B I O L O G Y

U N I V E R S I T Y O F I L L I N O I S AT U R BA N A - C H A M PA I G N1 2 0 6 W E S T G R E G O RY D R I V E U R BA N A , I L L I N O I S 6 1 8 0 1 W W W. I G B . I L L I N O I S . E D U

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