The fate of the blue catfish and more than 60 other species of large-river specialist fishes depends on conservation of suitable habitat and connectivity between the Mississippi River and its tributaries, a UW-Madison study shows. (Brenda Pracheil, Center for Limnology)

Large-river specialist fishes — from giant species like paddlefish and blue catfish, to tiny crystal darters and silver chub — are in danger, but researchers say there is greater hope to save them if major tributaries identified in a University of Wisconsin-Madison study become a focus of conservation efforts.

The study says 60 out of 68 U.S. species, or 88 percent of fish species found exclusively in large-river ecosystems like the Mississippi, Missouri and Ohio rivers, are of state, federal or international conservation concern. The report is in the April issue of the journal Frontiers in Ecology and the Environment.

Brenda Pracheil with a longnose gar caught in the Missouri River.

On the other hand, says lead author Brenda Pracheil, a postdoctoral researcher in UW-Madison’s Center for Limnology, the study offers some good news, too.

Traditionally, the conservation emphasis has been on restoring original habitat. This task proves impossible for ecosystems like the main trunk of the Mississippi River — the nation’s shipping, power production, and flood control backbone. While the locks, dams and levees that make the Mississippi a mighty economic force have destroyed fish habitat by blocking off migration pathways and changing annual flood cycles species need to spawn, removing them is not a realistic conservation option.

But, says Pracheil, we’re underestimating the importance of tributaries. Her study found that, for large-river specialist fish, it’s not all or nothing. Some rivers are just big enough to be a haven.

For any river in the Mississippi Basin with a flow rate of less than 166 cubic meters of water per second, virtually no large-river specialist fishes are present. But in any river that even slightly exceeds that rate, 80 percent or more of the large-river species call it home.

That means Mississippi tributaries about the size of the Wisconsin River and larger are providing crucial habitat for large-river fishes. When coupled with current efforts in the large rivers themselves, these rivers may present important opportunities for saving species.

“Talk to any large-river fish biologist, and they will tell you how important tributaries are to big river fish,” says Pracheil. “But, until now, we’ve not really understood which rivers are most important. Our study tackles that and shows which tributaries in the Mississippi River Basin show the most promise for conservation of large-river fishes.”

Current policies governing large river restoration projects are funded largely through the U.S. Army Corps of Engineers, which requires that funds be spent on mainstems — or the big rivers themselves. Pracheil’s study suggests spending some of that money on tributary restoration projects might do more conservation good for fish, while also letting agencies get more bang for their habitat restoration buck.

“Tributaries may be one of our last chances to preserve large-river fish habitat,” Pracheil says. “Even though the dam building era is all but over in this country, it’s just starting on rivers like the Mekong and Amazon —places that are hot spots for freshwater fish diversity. While tributaries cannot offer a one-to-one replacement of main river habitats, our work suggests that [they] provide important refuges for large-river fishes and that both main rivers and their tributaries should be considered in conservation plans.”

Story by Adam Hinterhuer, Center for Limnology

These assays were used to assess the effects of new agents to disrupt communication among pathogenic staph bacteria. Research shows promise for a new approach to thwarting staph infections, which are increasingly resistant to conventional antibiotics. (Photo courtesy of Blackwell Lab)

In an age when microbial pathogens are growing increasingly resistant to the conventional antibiotics used to tamp down infection, a team of Wisconsin scientists has synthesized a potent new class of compounds capable of curbing the bacteria that cause staph infections.

Writing online in the Journal of the American Chemical Society, a group led by University of Wisconsin-Madison chemistry professor Helen Blackwell describes agents that effectively interfere with the “quorum sensing” behavior of Staphylococcus aureus, a bacterium at the root of a host of human infections ranging from acne to life-threatening conditions such as pneumonia, toxic shock syndrome and sepsis.

“It’s a whole new world for us,” says Blackwell, whose group identified peptide-based signaling molecules that effectively outcompete the native molecules the bacterium uses to communicate and activate the genes that cause disease.

Bacteria use quorum sensing to assess their population density and coordinate certain behaviors. They do so through the use of pheromone-like chemicals, which bind to receptors either in the bacterial cell or on its surface and tell it if there are enough companion bacteria around to switch on genes that perform certain functions. In the case of Staphylococcus aureus, quorum sensing activates toxin production, manifesting disease in the host.

Interfering with bacterial quorum sensing to stymie disease is considered a promising new antibiotic strategy, says Blackwell. Staph, she adds, is an excellent target as the bacterium is not only a prevalent pathogen, but some strains, notably methicillin-resistant Staphylococcus aureus or MRSA, have developed resistance to commonly used antibiotics such as penicillin and its derivatives.

The new compounds synthesized by Blackwell and her colleagues are peptides that work at very low concentrations by blocking the chemical receptors the bacterium uses to regulate quorum sensing. The new agents devised by Blackwell and her group work on the four subtypes of staph, all of which use different quorum sensing signals and are found in different infection types.

“We had not worked much in this area because the (signaling molecules) are somewhat challenging to synthesize,” explains Blackwell. “We now have developed methods to make these molecules and analogs much more efficiently, which helped fuel this new study.”

For now, the compounds devised by the Wisconsin team will have their greatest impact in the lab as research probes to further study the role of quorum sensing in Staphylococcus aureus. In addition, the gritty details of how these synthetic agents work in the cell need to be determined in order to optimize their potential use in both the lab and clinic. Such studies are ongoing.

“The impact of these new peptides could be significant because staph is an important and increasingly scary pathogen. There is plenty of scope,” notes Blackwell.

The new research was conducted with support from the Office of Naval Research, the Burroughs Welcome Fund and the Kimberly-Clark Corp.

Story by Terry Devitt, University Communications

Tehshik Yoon (right), associate professor of chemistry, holds a discussion with graduate research assistant Travis Blum (left) and research associate Dani Schultz (center), both members of Yoon’s research group, in Yoon’s lab in the Chemistry Building. (Bryce Richter, University Communications)

Flipped classrooms. MOOCs. Clickers for real-time class surveys. New technologies are constantly changing the educational landscape.

Tehshik Yoon, associate professor of chemistry at the University of Wisconsin-Madison, is one of the professors at the forefront when it comes to thinking about and testing out new technologies while teaching. His students and colleagues say his efforts have not gone unnoticed.

Because the current crop of dedicated online learning platforms can be a bit clunky, Yoon says he tries to bring into the classroom the tools students are already using in their personal lives: Facebook, Twitter, blogs, and other social platforms.

In 2006, as social media and social platforms were coming into their own, each student in his Advanced Organic Chemistry 346 class wrote 12 blog posts demonstrating his or her conceptual understanding of the experiments conducted during labs. He envisioned this approach helping future scientists better communicate their work to non-scientists.

Between classes and his group’s catalysis research, Yoon took a moment to reflect on how he has incorporated social media into his classes. An edited transcript of the conversation follows.

Q: What were your initial goals in having your students blog?
TY: It was both to build a community in the class and to evaluate the students’ comprehension. Over the course of the semester, they wrote 12 blog posts, which were graded for participation. I used the posts as was a way to identify the students who had problems with writing so I could intervene before their lab reports were due. I didn’t really use the posts as an evaluation tool in terms of their understanding of science, per se.

Q: So each student wrote a blog post prior to submitting a lab report?
TY: Yes, the idea was that they would write a post after each experiment, and they would write about the experiment. I liked this approach for a lot of reasons. It reinforced what they had just done so they didn’t forget about it until they wrote the lab report. They had to write about it in terms that their grandmas would understand, so they had to understand exactly what they did at a really deep level, which is important for that kind of a class. And then, when they were all reading one another’s posts, it was also a metacognitive exercise to see if someone else noticed something about the experiment that they didn’t  The idea was to try to build a loose community and get the students more engaged with their work, rather than giving them the assignment only to have them run through the recipe and forget about it later.

Q: You’ve also experimented with online office hours. How did you come up with that idea?
TY: That idea grew out of using instant messaging (IM), and it was largely desperation more than anything else. During office hours, I ended up getting lots of drop-in students who would show up and not know what to say. They would say “I’m not doing very well. Can you tell me how to do better?” So I was inspired by the fact that about six or seven years ago, everyone was on IM. Instead of doing regular office hours, I held online office hours. I was online almost every evening because that’s when I do most of my writing. So I was already at the computer, and if someone had a question, they could IM me and ask the question really quickly. The idea was that students were going to have the best and most interesting questions when they were actually studying and engaged with the material — and that was in the evenings and on the weekends. And that’s also when I happen to be at the computer myself.

Q: How did the students respond to that approach?
TY: It worked really well. I used it for about two years, and then IM died. So when I was looking for something else to use, I realized that everyone uses Facebook. I transitioned the idea over to Facebook and created a Facebook page for my class. That’s actually been the most successful experiment so far. You can use the platform to show actual diagrams — you’re not limited to text as we were with IM. The really cool thing is that every once in a while, someone will ask a question and then other students will answer. That’s amazing. It helps me because it reduces my workload. It also makes it so that instead of getting 20 questions about something I didn’t explain very clearly, someone will post it there and a bunch of people will pile on to the same comment. Then I can go in and clarify, rather than dealing with 20 individual emails that say exactly the same thing.

Q: What’s the benefit to the student?
TY: I really love that when they help one another, it has the same metacognitive effect, and they’re all engaged in one another’s educations. The really good students are helping out the weaker students, and the platform helps them create study groups. The goal of creating a learning community in the classroom is really benefited by the fact that Facebook is really good at creating communities.

Story by Libby Dowdall, Department of Chemistry

The massive IceCube telescope is comprised of more than 5,000 digital optical modules suspended in a cubic kilometer of ice at the South Pole. (Photo courtesy IceCube Collaboration/National Science Foundation)

A massive telescope in the Antarctic ice reports the detection of 28 extremely high-energy neutrinos that might have their origin in cosmic sources. Two of these reached energies greater than 1 petaelectronvolt (PeV), an energy level thousands of times higher than the highest energy neutrino yet produced in a manmade accelerator.

The IceCube Neutrino Observatory, run by an international collaboration and headquartered at the Wisconsin IceCube Particle Astrophysics Center (WIPAC) at the University of Wisconsin-Madison, identified the neutrinos, which were described May 15 in a talk at the IceCube Particle Astrophysics Symposium at UW-Madison.

Halzen

“We’re looking for the first time at high energy neutrinos that are not coming from the atmosphere,” says Francis Halzen, principal investigator of IceCube and the Hilldale and Gregory Breit Distinguished Professor of Physics at UW-Madison. “This is what we were looking for,” he adds. “I would never have imagined that the science would be more exciting than building this instrument.”

Because they rarely interact with matter and are unimpeded by gravity, neutrinos can carry information about the workings of the highest-energy and most distant phenomena in the universe. Though billions of neutrinos pass through the Earth every second, the vast majority originate either in the sun or in the Earth’s atmosphere. Far rarer are high-energy neutrinos that may hail from the most powerful cosmic events — such as gamma ray bursts, black holes, or star formation — where they would be created in association with high-energy cosmic rays that can reach energies up to thousands of PeVs.

In his talk, postdoctoral fellow Nathan Whitehorn described 28 high-energy neutrino events captured by the detector between May 2010 and May 2012. These events, including two that exceeded the unprecedented energy level of 1 PeV, were one of the main goals for building a detector such as IceCube.

“Their properties are strongly inconsistent with what you would expect of atmospheric sources and are almost exactly what you would expect from an astrophysical source,” Whitehorn says.

It is premature to speculate where these neutrinos originated, he adds, but the IceCube collaboration is continuing to refine and expand the analysis.

IceCube is comprised of more than 5,000 digital optical modules suspended in a cubic kilometer of ice at the South Pole. The National Science Foundation-supported observatory detects neutrinos through the tiny flashes of blue light produced when a neutrino interacts with a water molecule in the ice.

The first hints of high-energy neutrinos came with the unexpected discovery in April 2012 of two detector events above 1 PeV. An analysis of those events was reported last month in a paper submitted to the journal Physical Review Letters. An intensified search, led by Whitehorn and fellow WIPAC scientists Claudio Kopper and Naoko Kurahashi Neilson, turned up 26 additional events exceeding 30 teraelectronvolts (TeV; one-thousandth of a PeV), which will be described in a forthcoming publication.

The IceCube Neutrino Observatory was built under a National Science Foundation (NSF) Major Research Equipment and Facilities Construction grant, with assistance from partner funding agencies around the world, and is supported by the NSF’s Division of Polar Programs and Physics Division. The NSF Office of Polar Programs continues to support the project with a Maintenance and Operations grant. UW-Madison is the lead institution, and the international collaboration includes 250 physicists and engineers from the U.S., Germany, Sweden, Belgium, Switzerland, Japan, Canada, New Zealand, Australia and the U.K.

Story by Jill Sakai, University Communications

Sarah Morton – L&S

Professors, instructors and advisers enlighten, challenge and inspire us. They can shape our opinions, push our work to new heights and spark an interest to learn more about a topic or discipline.

In the 2011-12 academic year, the College of Letters & Science asked graduating seniors to nominate faculty or staff members who impacted their lives. Hundreds of students wrote in with inspiring, moving and even funny stories of people who enhanced their UW-Madison experiences.

We are proud to present the following 10 faculty and staff members for our inaugural photo series: Best in Class. These 10 faculty and staff members were repeatedly praised, but only represent a handful of the faculty and staff who make a difference for UW-Madison students.

To see the 10 standouts and to nominate your choice, visit our Tumblr page.

King

Suzanne King, a doctoral candidate in the Department of Communication Sciences and Disorders at the University of Wisconsin-Madison, recently won the 2013 Plural Publishing Research Scholarship.

The award is given by the Council of Academic Programs in Communication Sciences and Disorders.

King’s research focuses on the pathogenesis of vocal fold scar and the immunological response of stem cell-biomaterial based therapies for vocal fold tissue regeneration.

Shakhashiri

Bassam Shakhashiri, a chemistry professor and William T. Evjue Distinguished Chair for the Wisconsin Idea at the University of Wisconsin-Madison, has received the 2013 Carl Sagan Award for Public Understanding of Science.

Named for the astronomer whose enthusiasm and broad scientific knowledge helped inspire a generation to look at science as a fascinating discipline that makes a different in the real world, the Sagan Award was made by the Council of Scientific Society Presidents. The leaders of 60 societies with more than 1.4 million members comprise the council.

Shakhashiri is the immediate past president of the American Chemical Society, the world’s largest scientific society. Long known for his standing-room-only Christmas chemistry demonstrations, his recent efforts include the American Chemical Society Climate Science Toolkit, which encourages scientists to communicate the objective scientific facts about climate change.

“In a democracy,” Shakhashiri said, “people should act wisely and avoid being bamboozled into making foolish decisions where matters of science and technology are concerned. Today the biggest challenge to science and society is to help sustain Earth and its people in the face of population growth, finite resources, malnutrition, spreading disease, deadly violence, war, climate change, and the denial of basic human rights, especially the right to benefit from scientific and technological progress.”

“Dr. Shakhashiri has long been a staunch advocate on the importance of science and scientific literacy for all people and all ages, and has a very distinguished career in promoting science and science education internationally,” said Patricia Simmons, chair-elect of the Council of Scientific Society Presidents. “He continues to serve as a dynamic advocate for policies that serve our society through advances in science and technology.”

Story by David Tenenbaum, University Communications

A student studies amid blooming tulips in the Department of Botany’s Botanical Garden. (Sarah Morton – L&S)

Historic Chamberlin Hall stands to the left; Lathrop Hall to the right. Across the street, construction crews continue working on a new development towering toward the sky. Buses and bicycles seem to ferry across University Avenue by the minute.

Quiet, but not forgotten, is the University of Wisconsin-Madison Botanical Garden, a small yet well-traveled green space on campus since 1961.

A favorite project of the late UW-Madison President Conrad A. Elvehjem, the Botanical Garden is home to a gazebo, benches, a dry riverbed, and a small waterfall among more than 500 species of plants. On warm days, classes and groups gather for discussion. This month, you can find sprouting tulips and crocus.

“The gardens boast tremendous aesthetic value,” says Mo Fayyaz, director of the UW-Madison Botanical Garden and Greenhouses.

The garden also boasts a one-of-a-kind design. Its layout is based on the Angiosperm Phylogeny Group (APGII) system of plant classification, meaning the garden is organized into 11 sections in a system that describes the evolutionary relationship between plants. Botanists today use the garden to study plants’ genetic relationships to one another and the garden is the first in the world to be organized based on this system.

“We need to keep green areas green with the goal of education in mind,” says Fayyaz.

But for most of the campus community and visitors, the Botanical Garden is a place to eat lunch, sketch, or read a book.

Fayyaz says one of his favorite parts of the job is giving garden tours to school groups. He estimates thousands of students have visited either the Botany Garden or the UW-Madison Botany Greenhouses on one of his tours over the past 30 years.

Other groups of prospective Badgers visit the garden, which is a stop for tours as part of the Visitor and Information Programs that bring 42,000 people to campus annually.

If you venture into this green space, Fayyaz points out two natural treasures that may go unnoticed. The first is the Newton Apple tree, a direct descendant of the original tree said to have grown the apple that instigated Sir Isaac Newton’s theory of gravitation. The tree was presented in 2001 to then Chancellor John Wiley as a gift from Congressman Jim Sensenbrenner.

“When the tree was planted in the garden, it was a 2-foot skinny plant,” says Fayyaz. “Today it’s monstrous.”

The second treasure is the shidare sakur, or snow fountains weeping cherry tree. This tree was planted in 2011 by a Japanese Tsunami Relief student group to serve as a memorial to honor the victims of the disaster. Blossoming with the start of the new school year in Japan (April), these trees symbolize new start and strength.

Story by Aimee Katz

Thanks to the generous support of alumni and friends, the department was able to recognize students for their outstanding achievements in chemistry teaching and learning, research, and outreach.

This year’s award winners were:

2013 Summer Undergraduate Research Awards
Ackerman Scholarship / Don Brouse Scholarship: Andrew Bartling
Ackerman Scholarship / Edwin & Kathryn Larsen Scholarship: David Schuman
Eugene & Patricia Kreger Herscher Scholarship: Kyle Desrochers, Samantha Fix
Walter & Young-Ja Toy Scholarship: Yicong Ge
Undergraduate Student Support in Chemistry Scholarship: Seth Berger, Scott Burlingham, Joshua Shutter

Departmental Undergraduate Awards for 2013-14
Ackerman Scholarship: Carl Buttke, Abner Jacobson
Margaret McLean Bender Scholarship: Kaitlyn Mayer
Andrew Dorsey Memorial Scholarship: Prashanth Prabakaran
Henry & Eleanor Firminhac Scholarship: Kimberly Dinh, Si Wang
Richard Fischer Scholarship: Anders Knight
Eugene & Patricia Kreger Herscher Scholarship: Haley Albright, Hannah Grossberg
Wayland Noland Undergraduate Research Fellowship: Tong Wang
Lindsay Theresa Plank Memorial Scholarship: Paul Vang
Mabel Duthey Reiner Scholarship: Yurun Zhang
Robert Franklin Taylor Scholarship: Brian Cornille
Undergraduate Student Support in Chemistry Scholarship: Joshua Shutter, Matthew Sternke, Ethan Zager
Martha Gunhild Week Scholarship: Dongyu Zhang
George & Arleen Ziarnik Scholarship: Nicholas Sánchez

Other Undergraduate Awards
Berbee-Walsh Awards: Excellence in Analytical Chemistry: Ailin Mao; Excellence in Organic Chemistry: Ho On Alston Conrad Chiu, Sohil Shah; Excellence in Physical Chemistry: Brian Cornille
Francis Craig Krauskopf Memorial Awards: Hatem Alhothali, Erin Drees, Michael Josephson, Alexander Retzlaff, Benjamin Van Domelen, Yui Chun Wan
John & Elizabeth Moore Awards for Excellence: Helene Altmann, Lixue Cheng, Nathan Delvaux, Morgan Heller

Departmental Graduate Awards
Roger Carlson Award: Chris Rose
Harry & Helen Cohen Research Award: Elliot Farney, John Lukesh, David Mortenson
Eastman Summer Research Award: Joshua Fishman
Goering Organic Chemistry Award: Brent Amberger, Adam Weinstein, Alison Wendlandt
Hirschfelder Prize Graduate Award: Kuang Yu
Hirschmann/Rich Graduate Award in Bioorganic Chemistry: J.P. Gerdt, Joe Grim, Mario Martinez Farias
Michael McCoy Memorial Award: Joe Yeager
K.V. Reddy Award in Physical Chemistry: Somenath Bakshi
Charles & Martha Casey Excellence in Research Awards: Analytical Chemistry: Gloria Sheynkman; Inorganic Chemistry: Kasia Kornecki; Materials Chemistry: Fei Meng; Organic Chemistry: Paul White; Physical Chemistry: Jennifer Laaser
Outstanding Chemistry TA Awards: Brent Amberger, Jeremiah Erickson, Judy Hines, Brandon Kilduff, Sriteja Mantha, Kaz Skubi, Daniel Tabor

Other Graduate Awards
GSFLC Mentor Awards: Fei Meng, Nicole Woodards, Joe Yeager

Story by Libby Dowdall, Department of Chemistry

A Digital Optical Module in the IceCube array descends into the South Pole ice in December, 2010. (Photo by Robert Schwarz)

Deep in the Antarctic ice, more than 5,000 detector modules sit in frozen darkness, waiting for the blue bursts of radiation released by particle interactions. Optimized to detect signs of neutrinos — tiny, nearly massless particles that can travel from the edges of the universe — these basketball-sized detectors comprise the IceCube Neutrino Observatory, one of the biggest astrophysics projects in the world.

For some of the scientists who work on this massive telescope, the experience can be almost as quiet. A handful of intrepid souls, referred to as “winterovers,” brave the -100 F temps of the Antarctic winter to maintain the facility between on-site work seasons.

On Wednesday, May 8, Freija Descamps, an IceCube researcher who stayed at the South Pole Station during the austral winter of 2009-10, will present a special edition of Wednesday Nite @ the Lab at the Wisconsin Institutes for Discovery. The event begins at 6 p.m. with free hands-on activities for all ages to explore physics, computer programming, and ice drilling and to learn about how and why IceCube was built. At 7 p.m., Descamps will share photos and videos from her experiences as a winterover responsible for maintaining the detector, troubleshooting, and helping provide data to the research collaboration.

“One experience that I often still think about from my time at the South Pole was a time I remember walking out of the IceCube Lab. It was the dead middle of winter, no moon, super dark. This one time, however, it was like the sky was raining down on me in this bright green curtain of an aurora [australis]. It was fast moving, ever changing, and really very bright,” says Descamps.

For more than 10 years, the University of Wisconsin-Madison has played a key role in designing, building, and developing IceCube, sending hundreds of Wisconsin people and products to the South Pole as part of the National Science Foundation-funded project. The Wisconsin IceCube Particle Astrophysics Center (WIPAC) will host the international IceCube Collaboration in May and provide opportunities for the public to learn about science at the South Pole, from Descamps’ firsthand account and an interactive multimedia exhibit.

During the week of May 6-10, the Wisconsin Institutes for Discovery will host an interactive light and sound installation based on cosmic ray data from IceCube. The installation, called Quasar 2.0: Star Incubator, was created by Toronto-based artists Jean Michel Crettaz and Mark-David Hosale. The structure, which includes fiber optics, reflective surfaces, and info screens, combines data from IceCube and real-time data gathered by sensors embedded around the exhibit.

The Wednesday evening event is part of a statewide program funded by WIPAC and the Ira and Ineva Reilly Baldwin Wisconsin Idea Endowment.

It took more than a decade and the efforts of an international collaboration of scientists, engineers, and technicians to design, test, and build IceCube, which is now exploring the highest energy phenomena in the universe. The worldwide effort is supported by the National Science Foundation and rooted squarely in Wisconsin, with key partners at the University of Wisconsin-Madison and staff and suppliers from around the state.

Story by Jill Sakai, University Communications