IU Bloomington researcher working to reveal genetic clues behind long-term survival in ovarian cancer

Although not as common as some forms of cancer in the U.S., ovarian cancer ranks among the top causes of cancer death in women. It’s notoriously difficult to detect early, and most women who receive an advanced stage diagnosis do not survive more than five years.

Kenneth P. Nephew

Kenneth P. Nephew

But a small percentage of patients live far longer. To find out why, IU Bloomington researcher Kenneth P. Nephew is a part of the Ovarian Cancer Consortium for Long-Term Survival, which recently received “Phase II” funding from the Department of Defense Ovarian Cancer Research Program.

As a co-investigator in the consortium, Nephew is working to help more women join the ranks of these long-term survivors. He will investigate and describe the epigenome of tumors from ovarian cancer survivors who have survived 10 or more years following a diagnosis of advanced stage ovarian cancer.

“We’re working to reveal the secrets of these tumors to find out what makes these women genetically unique,” said Nephew, a professor of cellular and integrative physiology and obstetrics and gynecology in the Medical Sciences Program at the IU School of Medicine-Bloomington. “We want to identify these genetic differences, and build upon this knowledge to work toward improving the long-term survival and quality of life for all women impacted by this disease.”

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IU sophomore on ‘front end’ of sustainability research on bird migration, climate

“If there’s ever a fire, we’re supposed to grab that book first.”

That’s how one researcher describes the only copy of a binder containing nearly 50 years of painstakingly collected data on the migratory patterns of dark-eyed juncos in southern Indiana.

The person currently contributing new information to this priceless document is Lia Bobay, a sophomore environmental science major in the School of Public and Environmental Affairs who is collecting and analyzing data on the birds as a 2020 Sustainability Scholar.

Undergraduates in IU’s 2020 Sustainability Scholars Program participate in two semesters of sustainability research with access to world-class faculty on the IU Bloomington campus. Bobay’s research mentors are Ellen Ketterson, IU Distinguished Professor in the IU Bloomington College of Arts and Sciences’ Department of Biology, and Adam Fudickar, a postdoctoral researcher in Ketterson’s lab.

A renowned expert on birds, Ketterson started her research on dark-eyed juncos in the early 1960s in collaboration with the late Val Nolan Jr., IU professor of law and biology, and Ketterson’s husband. The junco data log sits on a shelf outside her office in Jordan Hall on the IU Bloomington campus.

Lia Bobay and Adam Fudickar

Lia Bobay and Adam Fudickar hold birds captured at the IU Research and Teaching Preserve. Birds are released after tagging. Photo by Eric Rudd

The logs contain hundreds of pages of measurements — times, temperatures, climate conditions, bird weight and sex — with each line representing a single junco captured and released in the field. Collecting data on a single bird can take hours.

Since the fall, Bobay has been working with Fudickar to determine whether climate change has altered the male-to-female ratio of dark-eyed juncos in southern Indiana. The birds, which breed in the boreal forests of northern Canada and Alaska, migrate to Indiana during the cold-weather months of November to April. Historically, males outnumber females in Indiana and females outnumber males in southern states.

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White House highlights IU’s role in initiative to preserve water quality on Indiana farmlands

A summit on water quality hosted by the Obama administration on March 22 highlighted a program to improve water quality in the nation’s heartland led in part by Indiana University.

Todd V. Royer

Todd V. Royer

The project is the Indiana Watershed Initiative, which uses watershed-scale conservation methods to reduce nutrient runoff from regional farms. Todd V. Royer, an associate professor in the IU School of Public and Environmental Affairs, is a member of the project led by University of Notre Dame’s Environmental Change Initiative.

“It is an honor for our work to be recognized by the White House during this period of increased concern about water quality in the United States,” said Royer, who also chairs the Illinois Environmental Protection Agency’s Nutrient Science Advisory Committee. “We’re confident that our research will provide information that can be used throughout the Midwest to improve water quality while maintaining productive farmland.”

An expert on the ecological and biogeochemical processes that affect water quality in streams and rivers, Royer’s work has a strong focus on Indiana farms. In his laboratory at IU, he and his students conduct work to identify and reduce the sources of pollution to water, such as nitrogen and phosphorus in agricultural regions, and road salt and pharmaceutical compounds in urban settings.

The Indiana Watershed Initiative, a part of Notre Dame’s Environmental Change Initiative supported by the U.S. Department of Agriculture’s Regional Conservation Partnership Program, combines two practical conservation methods that prevent nutrient and sediment loss from cropland. These are the planting of winter cover crops and the restoration of floodplains.

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IU to host Society for Ecological Restoration annual chapter meeting

Over 200 individuals from 13 U.S. states and Colombia are expected to arrive at Indiana University April 1 to 3 for the annual meeting of the Midwest-Great Lakes Chapter of the Society for Ecological Restoration.

The event, “Overcoming Challenges to Ecological Restoration in the 21st Century,” will be held in the Indiana University Memorial Union on the IU Bloomington campus.

A keynote presentation by Douglas Ladd, director of conservation for the Nature Conservancy in Missouri, will take place as part of the event from 1:45 to 2:45 p.m. on April 2 in the IMU. The title of his talk is “Does Ecological Restoration Need a Rethink?”

Midwest-Great Lakes Chapter of the Society for Ecological Restoration logo

The Midwest-Great Lakes Chapter of the Society for Ecological Restoration promotes the science and practice of ecological restoration across seven states, including Indiana.

Registration is open to the public. Registration is $170 ($95 for students) for all three days or $100 ($50 for students) for one day. On-site registration is available at the IMU East Lounge from 9:30 a.m. to 6:30 p.m. April 1 and from 7 to 11 a.m. April 2.

“This event is an opportunity to share information on the science and practice of the ecological restoration of forests, grasslands, urban areas, wetlands, streams and rivers,” said Mary Damm, a graduate student in the IU Bloomington College of Arts and Sciences’ Department of Biology and a member of the organizing committee for the meeting. “Restoring land includes not only planting native trees and herbs, but also re-establishing ecosystem processes such as ground water storage for wetlands and controlled burns to oak forests, savannas and prairies.”

The Midwest-Great Lakes Society for Ecological Restoration Chapter, which serves a seven-state region of Ohio, Indiana, Michigan, Illinois, Wisconsin, Minnesota and Iowa, is one of the society’s largest regional chapters in the world. The chapter promotes the science and practice of ecological restoration to assist with the recovery and management of degraded ecosystems throughout the Midwest and Great Lakes region of the U.S.

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Craft brewing is a passion and a business for IU biochemist and cancer researcher Matt Bochman

When Matt Bochman arrived at Indiana University Bloomington three years ago as an assistant professor of molecular and cellular biochemistry — fresh off a postdoctoral fellowship at Princeton University — one of the first things he did was pay a visit to some of the craft breweries throughout the region.

But this tour of the local watering holes was as much business as pleasure.

“I wanted to get my name out there as the local ‘yeast guy,'” he said.

IU assistant professor Matthew Bochman, center, with graduate student Cody Rogers, left, and Caleb Staton, director of sour operations at Upland Brewing Co. The trio hold glasses of the brew recovered based upon research in Bochman’s lab and conducted in collaboration with the local brewery.

Although his primary work involves conducting basic research with applications to cancer, Bochman also has a passion for the science of craft brewing, including the microscopic organisms that are key to the brewing process.

Shortly after making the rounds of local breweries, Bochman struck up a fruitful partnership with Flat 12 Bierwerks, a craft brewery in downtown Indianapolis just a mile east of Monument Circle. The owners reached out because they wanted to create “an all-Indiana beer.”

“They peppered me with all sorts of questions — about quality control, setting up a lab, experimenting with yeast — but what they really wanted to do was create a whole new brew,” Bochman said. “They had Indiana water, they had Indiana hops, they had barley that was grown and malted in the state, but they needed the yeast.”

Fortunately, brewer’s yeast grows on trees — literally. Tree bark is one of the best sources for the tiny microbes. So are flowers, fruits, berries and many other natural resources across the state. Soon Bochman had helped Flat 12 identify a strain of yeast for their project.

He has also consulted with breweries and craft distilleries such as Cardinal Spirits and Upland Brewing Co. in Bloomington; Sun King Brewery and Central State Brewing in Indianapolis; and the Maui Brewing Co., based in Hawaii.

But collaboration with Flat 12 also sparked an idea for a business. In 2015, Bochman successfully applied for a $13,000 translational research pilot grant from the Johnson Center for Innovation and Translational Research, an IU Bloomington-based organization in Simon Hall that works with faculty throughout the campus to identify current and new research programs that hold commercial potential and to protect intellectual property.

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Nobel Laureate and IU professor’s seminal paper highlighted in journal Genetics

Anyone perusing the 100th anniversary issue of the journal Genetics will be treated to a spotlight on a seminal paper from 1943 by a former Indiana University faculty member and Nobel Prize winner.

Salvador Luria in 1948

Salvador Luria at work at IU Bloomington in 1948. Photo courtesy IU Archives.

Salvador E. Luria, a member of the IU faculty from 1942 to 1950, conducted an experiment in Bloomington that went on to inform a revolutionary article titled, “Mutations of bacteria from virus sensitivity to virus resistance,” which contributed to his winning the 1969 Nobel Prize in Physiology or Medicine.

Born in Italy, Luria fled to the United States from France during the Nazi invasion in the spring of 1940. He soon became an instructor, then assistant professor, then associate professor of bacteriology at IU, where he developed an experiment — in collaboration with Vanderbuilt University’s Max Delbruck — that shed important new light on the ways in which certain bacterial cultures rapidly develop resistance to viral infection.

Luria and colleagues’ experiment explained previously mysterious inconsistent mutation rates in bacteria. They found that bacterial mutations arising quickly after viral infection resulted in descendants with mutations present in many cells, whereas descendants whose mutations occurred in later generations had mutations present in only a few cells. The experiment became known as the “fluctuation test.”

The idea for the experiment struck at a strange moment – watching a colleague win $3 in dimes from a slot machine during a Saturday night faculty dance. The moment inspired Luria to examine the role of random spontaneous mutation in bacterial response to infection, with bacteria mutating shortly after viral infection effectively “winning the jackpot.”

The experiment is also regarded as an important early demonstration that statistical analysis can shed light on biological processes inaccessible through direction observation.

In addition to his Nobel Prize, Luria has a connection to another famous Nobel Laureate who taught at IU. His first graduate student at IU Bloomington was James D. Watson, who just three years after earning his doctorate under Luria’s direction co-discovered the structure of DNA with Francis Crick.

Luria received an IU honorary doctor of science degree in 1970.

Meet Lekeah Durden, NSF Research Fellow and IU Ph.D. student in biology

Lekeah Durden, a Ph.D. student in the IU Bloomington College of Arts and Sciences’ Department of Biology, was recently featured by the National Science Foundation during Black History Month as an NSF Research Fellow.

Photo of Lekeah Durden, a PhD student in Biology who is participating in the National Science Foundation social media campaign for Black History Month.

Lekeah Durden, an IU Ph.D. student in biology

“My involvement in eco-evolutionary research allows me to be the positive change I want to see in the world because seeing other underrepresented groups in graduate studies helps create a diverse student body and future faculty that is more inclusive and representative of our community,” she said on the site.

Durden was also named a James P. Holland Fellow in the IU Bloomington Department of Biology in 2014-15. Her work in the lab of Keith Clay, IU Distinguished Professor of Biology, investigates host-microbe interactions in a fungus found in plants.

What first interested you in pursuing a career in biology?

I was always an inquisitive young kid; I loved being outside and observing the world around me. I think a fascination for the natural world got my attention and never let go.

Why did you choose IU to pursue your Ph.D. degree?

I chose to pursue my Ph.D. at IU because the Evolution, Ecology and Behavior Graduate Program was highly rated and had several professors studying host-microbial interactions and performing research that I found interesting. The Department of Biology has so many great scientific minds that I get to interact with on a daily basis, I find it really easy to get engaged with the research going on here.

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IU paleobotanist plays role in discovery of ‘Jurassic butterflies’

What looks like a butterfly, acts like a butterfly, but isn’t a butterfly?

A study out today in the Proceedings of the Royal Society: B that features IU paleobotanist David Dilcher as a co-author identifies a Jurassic-age insect whose behavior and appearance closely mimic a butterfly — but whose emergence on Earth predates the butterfly by about 40 million years.

Dilcher — who made international headlines last year for his role in discovering the mythical “first flower” — said these proverbial “first butterflies” survived in a similar manner as their modern sister insects by visiting plants with “flower-like” reproductive organs producing nectar and pollen.

NHB13-0012_04.tif

An artist’s rendering of Oregramma illecebrosa consuming pollen drops from bennettitales, an extinct order of plant from the Triassic period. Image by Vichai Malikul, scientific illustrator, Smithsonian Institution

The butterfly-like insects, which went on to evolve into a different form of insect from the modern butterfly, is an extinct “lacewing” of the genus kalligrammatid called Oregramma illecebrosa. Another genus of this insect — of the order Neuroptera — survives into our modern era, and are commonly known as fishflies, owlflies or snakeflies.

The discovery of this insect was made possible by the examination of well-preserved fossils recently recovered from ancient lake deposits in northeastern China and eastern Kazakhstan. The study was led by Conrad Labandeira, a curator at the Smithsonian Institution’s National Museum of Natural History, and Dong Ren of Capital Normal University in Beijing, China, where the fossils are housed. Dilcher is an emeritus professor in the IU Bloomington College of Arts and Sciences’ Department of Geological Sciences.

“Poor preservation of lacewing fossils had always stymied attempts to conduct a detailed morphological and ecological examination of the kalligrammatid,” Dilcher said. “Upon examining these new fossils, however, we’ve unraveled a surprisingly wide array of physical and ecological similarities between the fossil species and modern butterflies, which shared a common ancestor 320 million years ago.”

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Confocal microscope acquisition opens new possibilities at IU Light Microscopy Imaging Center

Down the stairs near the first floor entrance of Myers Hall on the IU Bloomington campus, IU scientists are peering beyond what’s visible to the naked eye to reveal the complex hidden mechanisms that drive biology, chemistry and other processes in the natural world.

The IU Light Microscopy Imaging Center is home to nearly a dozen extremely powerful instruments capable of, among other things, tracing the delicate contours of the brain, mapping a chemical’s path though cellular channels or capturing the smallest details of an iridescent insect’s wing.

EZattara_LeicaSP8_Copepod

A 3-D image of a cladoceran, or water flea, created using the new instrument. Image courtesy Eduardo Zattara

Recently, the center acquired the latest in its collection of ultra-advanced imaging technology: a Leica TCS SP8 spectral confocal microscope system.

A confocal microscope uses a combination of intense laser illumination and ultra-sensitive light detectors to capture the interior details of microscopically small objects layer by layer, after which the images are automatically reconstructed to create a 3-D picture.

The high-powered instrument, which was acquired with support from the IU Bloomington College of Arts and Sciences and Office of the Vice President for Research, is the first upgrade of this particular technology at the Light Microscopy Imaging Center since 2007 – a significant leap in power and capability, including the ability to capture near-real-time images.

“Up until recently, the majority of imaging technology has only been able to provide scientists with structural information; the real cutting-edge is real-time imaging,” said Jeff Zaleski, a professor in the College’s Department of Chemistry and associate vice provost for sciences at IU Bloomington. “Today, our researchers need the ability to see changes in structural events in real time and watch processes as they happen — to view not just biological structures but also the actual physical processes that occur during those events. This new instrument moves us significantly further in that direction.”

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Science the Second Time Around: Plenitude Today

Editor’s note: In this ongoing series, “Science the Second Time Around,” IU author and mythologist Gregory Schrempp is sharing his experience going “back to school” in science with support from a New Frontiers Experimentation grant from the IU Office of the Vice President for Research.

The astronomy course I recently finished auditing changed direction at mid-term. The first half had emphasized our solar system and the great paradigms brought to it: Ptolemaic, Copernican, Universal Gravitation, Electromagnetism, Relativity.

But the second half surveyed the known contents of the universe. I started to tell a friend about the new direction. “A zoo?” he asked. Yes, the second half was an organized display of “cosmic species.”

I was initially concerned that the “zoo” would be less interesting than the great paradigms, but the feeling did not last. Popular science writers constantly claim that if you are into wonder, there is more of it to be found in reality than in fantasy. I got a taste of what they mean. The array of cosmic things leaves me in sheer, speechless amazement.

Enceladus

Enceladus

My personal favorite had always been Saturn, with its intricate, perfect rings. But now I have others — including a scrappy little moon of Saturn called Enceladus, which shoots out the most impressive plumes of water vapor. The moon and its plumes looked so much like a little satellite with a retro-pack that I couldn’t help but wonder if those eruptions could ever alter the little guy’s orbit.

We love lists. Many of the artistic genres studied by folklorists and ethnomusicologist suggest that enumeration is a basic source of artistic and intellectual pleasure. There are long mythic-cosmogonic genealogies that go on interminably naming the things found on earth, in the sea, and in the sky.

Musicians use the term “list-song” to describe a popular format: “A, you’re adorable; B, you’re so beautiful…” Religious litanies follow the same principle: “Saint Benedict, pray for us; Saint Luke, pray for us…”

A parade is a list that marches past you. A clear night sky gives us a cosmic parade, one that telescopes and space-probes now allow us to check out up-close.

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