Wisconsin Institutes for Discovery

WARF Essential Topics September 23 by chrisnajdowski
09/16/2014, 11:22 am
Filed under: Discovery Events, Town Center | Tags:

Commercializing campus-produced software: A two-part miniseries

Creating and customizing software code is increasingly common on campus and reaches across many disciplines. When does such work rise to the level of invention and what opportunities might there be for broader impact and commercialization?

WARF explores these topics in a two-part series with experts from campus and beyond. The series is free and open to faculty, students, staff and the public. Visit warf.org/EssentialTopics to register.

Part I: Intellectual property protection for software will take place at 3:30 p.m. on Tuesday, September 23.


Robert Stoll
Former U.S. Patent and Trademark Office commissioner
Partner and co-chair of the intellectual property practice group, Drinker Biddle & Reath LLP

Michael Remington
Washington, D.C., counsel to WARF
Partner, Drinker Biddle & Reath LLP

Part II: Challenges and opportunities in commercializing software will take place on Thursday, November 13.

Wisconsin Science Festival Events October 16-19 by chrisnajdowski
09/09/2014, 10:21 am
Filed under: All Posts, Discovery Events, Town Center | Tags:


We’ve added lots of events to the online guide for the Wisconsin Science Festival. Visit our website at WiSciFest.org to see if there’s an event near you.

DIY Science September 12 by chrisnajdowski
09/03/2014, 7:02 am
Filed under: All Posts, Discovery Events, Town Center | Tags:


Have you ever wondered exactly how plants turn sunlight into chemical energy? Or why you need all those essential minerals in your body? Learn how a UW–Madison researcher uses light and quantum mechanics to unveil how photosynthesis works, and if we could ultimately harvest a plant’s potential to utilize energy from the sun. Perform experiments with high-end equipment that interacts light with matter and see how scientists peer into the atomic world.

Register for DIY Science on September 12

Kevin Eliceiri to bring multi-scale imaging focus to Morgridge Institute by ckopietz
08/28/2014, 11:13 am
Filed under: All Posts, Discovery science, Research
Kevin Eliceiri. Photo by UW-Madison, University Communications © Board of Regents of the University of Wisconsin System

Kevin Eliceiri. Photo by UW-Madison, University Communications
© Board of Regents of the University of Wisconsin System

Scientific imaging has long been a research strength at the University of Wisconsin-Madison, home of major advances in cellular-scale optical imaging, human-scale medical imaging and many spaces in between.

The “everything in between” is of keen interest to Kevin Eliceiri, director of the Graduate School’s Laboratory for Optical and Computational Instrumentation (LOCI) and new associate director of medical engineering at the Morgridge Institute for Research. Eliceiri sees great potential in bringing all of the different scales and modalities of imaging together to improve visual understanding of biology and disease — and address the things we can’t yet see.

“We want to focus on multi-scale imaging in a new way that gets scientists outside of their own worlds of imaging scales and bridge across scale,” says Eliceiri. “Those communities are not as tightly linked as they could be. There is great opportunity, for example, to go from sub-cellular, to cellular, to tissues, to systems-level understanding with multi-scale imaging. There is really no better place than the Morgridge Institute to make this happen.”

Eliceiri joined the Morgridge Institute this month and will serve an important role in the leadership transition period when Rock Mackie, director of Medical Engineering, retires at the ends of 2014. But Eliceiri is no stranger to the program, having active research partnerships and collaborations for several years in both the medical engineering and virology focus areas at Morgridge.

Eliceiri will be initiating a new research team in multi-scale imaging this fall, starting with hiring two new imaging principal investigators. The goal will be to “foment a community” with support from the new hires and build capacity with the best available talent, regardless of imaging modality.

“The enthusiasm on campus is incredible for this resource,” he says. “I’m a firm believer that our primary interests at Morgridge should be on great scientists, because the equipment is ultimately an easier challenge than the expertise to build it and leverage it for new discovery. We want to take our current campus expertise to a new level.”

The idea will be to bring together different modalities and imaging size scales and look for ways they can register, link and operate together. That includes image size, temporal stages, and animal vs. human scales.

“We want to address the gap between animal and human models, as well as the resolution gap,” he says. “With the Fabrication Lab, unique computational resources such as the Morgridge computational technology group, and campus partners such as LOCI, we have the capacity to build next generation instrumentation.”

One of the current strengths of the medical engineering program is the integration of student talent from the undergraduate to the postdoctoral level. Close to two-dozen students have independent research projects with Morgridge under the mentorship of Mackie, Eliceiri and other scientists. Current students have worked on projects such as creating better detection models for breast cancer, new radiotherapy techniques, and microfluidic approaches to testing new drugs.

Eliceiri sees that relationship with engineering students continuing and expanding with the departments of biomedical engineering, (BME), electrical and computer engineering (ECE) and medical physics. BME has a strong curriculum program in biomedical design, with most projects stemming from real community-based needs in healthcare. BME students have worked with medical engineering on many of these projects.

The Advanced Fabrication Laboratory will continue to be an important resource for faculty and student prototyping and innovation. It has unique resources in areas such as 3D printing and in microfluidics with the recently opened foundry in collaboration with BME Professor David Beebe. These instrumentation capabilities will serve as an important piece of the multi-scale imaging effort and enhance instrumentation efforts of the UW-Madison bioengineering community.

Core partners in this effort will be the departments of biomedical engineering and medical physics. Major technology partners will include the departments of electrical and computer engineering, industrial and systems engineering, physics, chemistry, computer science and biostatistics and medical informatics. The biology partners will include the Virology Institute, the Comprehensive Cancer Center, biochemistry, cellular and molecular biology and others.

“Almost all scientific departments rely on imaging to some level and they all need different types and scales,” he says. “At Morgridge, we will keep our primary focus on imaging for disease. We want to be a primary collaborative research center for expertise and instrumentation development.”

“Our goal will be to think broadly about how we can conduct great science at the multi-scale level across a wide array of disease models, disseminate it to the public and keep moving forward.”

— Brian Mattmiller

Anthony Gitter: Taking the statistical road less traveled by ckopietz
08/27/2014, 10:06 am
Filed under: All Posts, Discovery science, Research

AGitter2Much of biostatistics involves finding and mapping the predictable pathways that can tell us something about what makes a disease tick. But Anthony Gitter finds equal importance in the statistical back roads that other scientists might ignore.

Gitter, a new UW-Madison assistant professor of biostatistics and medical informatics and Morgridge Institute for Research investigator, studies the interconnected relationships in biological functions. Gitter says his work often looks at how multiple genes or pathways — each of which could be unimportant alone — might be very important to a disease process when working together.

“Everything I do is framed in networks and pathways, and I want to understand whether there is something important in the less frequent ‘other’ and start to look for interesting signals,” Gitter says.

Gitter’s statistical principles are being put to work in the Morgridge virology focus area led by Paul Ahlquist. It’s a particularly rich area for this type of networked analysis, since viruses use a complex symphony of actions to invade cells, hijack their functions and continue to infect.

One of Gitter’s objectives in virology is describing what’s happening inside a cell that is stressed in some way by a virus. “The cell will stimulate a lot of immune response conditions and try to defend itself, but it’s not clear what steps are taken,” he says. “Why are some cells more successful than others in waging a defense?”

Gitter also is concerned with gathering dynamic data — not a single snapshot, but how the cellular response might change over minutes or hours of exposure. “Biology isn’t static, there’s a constant ebb and flow of production.”

During his PhD work at Carnegie Mellon University, Gitter developed a network model that helps explain what’s taking place during the early cellular response to viral infection, including what proteins are in play, what messages are passed and what genes are turned on and off. This work will continue at Morgridge, which has a large bank of data on genetic function of viruses.

Gitter came from a nontraditional postdoctoral experience that included an assignment with Microsoft Research in addition to the Massachusetts Institute of Technology. That academic-private relationship worked well and was a deciding factor in choosing UW-Madison, with the private Morgridge connection. The commitment to basic research questions seems especially strong here, he says.

“When working with a private R&D lab — and I suspect this will hold true for the Morgridge Institute — you have an organizational structure and a funding model that enables you to do research based on the value of the science, as opposed to dealing with the nagging question in the back of my head, ‘will somebody ever fund this?’”

“You want to grow a vibrant program that attracts funding because you’re doing good research,” Gitter adds. “But you don’t want to be overwhelmed and have the financial issues push out the scientific exploration.”

Gitter’s biological work began with the model organism yeast, which is well-researched and its cellular pathways have been highly defined. As more and more human network and disease data came online, Gitter ventured into virology and cancer research. In his cancer work, Gitter has focused on how the same type of cancer can look very different when manifested in individual patients.

With the potential for personalized medicine and the plummeting cost of whole genome sequencing, it will be important to address the heterogeneous nature of cancer, along with the common bank of knowledge on the disease.

Being part of a computational team addressing human health issues, Gitter is motivated by “moving the needle in two different ways.” One outcome is creating an ingenious method on the computational side to assemble and analyze data in ways previously impossible. On the biological side, he can work to make better predictions of what groupings of genes might play an important role in the path of disease.

“The answer for me is the same as it is for the wet lab scientists working on disease: We want to find the next potential targets and learn something new about the system,” he says. “It’s too bold to say that when we find something interesting, we just need to get a chemist to develop the drug, and that’s the end of the day. But we’re contributing to the knowledge of what’s really happening with those diseases that will inform new therapies.”

– Brian Mattmiller

Afterschool Expeditions resumes September 29 by chrisnajdowski
08/26/2014, 7:46 am
Filed under: All Posts, Discovery Events, Town Center | Tags:

Aug. 20, 2013. (Photo © Andy Manis)

The Discovery summer science program has ended for the year, but Afterschool Expeditions will resume September 29. Visit afterschoolexpeditions.org for more information.

Desirée Benefield: Using microscopy to battle ‘microbial overlords’ by ckopietz
08/25/2014, 11:04 am
Filed under: All Posts, Discovery science, Research | Tags: ,

Desiree BenefieldBy Courtni Kopietz

From artist to microbiologist, Desirée Benefield has always been a very visual person. Before she was in graduate school studying the structure of bacterial toxins, Benefield was a glass blower.

“I was pleasantly surprised to see that there was a lot of overlap with the processes in the studio, with art or craft, and in a laboratory,” Benefield says. “I felt very much at home having these strange tools or instruments, complicated processes and evaluation of the work. It just came very naturally.”

While her tools may have changed, Benefield’s visual nature still plays out in her scientific research. As part of the virology lab at the Morgridge Institute for Research, Benefield is using electron microscopy to examine the specific interface of pathogens once they’re in a host cell.

Electron microscopy is very fulfilling as an imaging technique in terms of the information you can get out of it, Benefield says. “The rapid output of visual information is so exciting, so rewarding.”

The lab, led by Howard Hughes Medical Institute (HHMI) Investigator Paul Ahlquist, studies several different classes of virus. Benefield will initially focus on positive-strand RNA viruses, the source of many serious infections.

“Desiree is a dynamic researcher and outstanding collaborator who will bring our critical molecular imaging studies to important new levels,” Ahlquist says.

The research opportunity allows Benefield to work with two of her loves: pathogens and microscopes. She first gained an interest in pathogens during undergraduate courses in microbiology and immunology at the University of Tennessee at Chattanooga.

“It was like this epic battle between us and our microbial overlords on a day-to-day basis,” Benefield says. “I was fascinated by it. I knew this was where I wanted my emphasis to be.”

During her graduate studies at Vanderbilt University, Benefield started doing crystallography of different proteins and bacterial toxins. When she was introduced to a collaborator that encouraged her to try electron microscopy, she never looked back.

A sample of Desiree Benefield's glass art. She was a glass blower for years before entering scientific research.

A sample of Desiree Benefield’s glass art. She was a glass blower for years before entering scientific research.

Electron microscopy can be a powerful technique for addressing questions of protein and virus structures, and what’s happening when different pathogens are interacting with host cells, including human cells. Electron tomography, an extension of the traditional technique, captures very detailed 3D structures.

“Electron microscopy complements genetics, biochemistry and other approaches,” says Ahlquist. “It provides nanoscale images that strikingly reveal the architecture and subcellular context of the molecular machines that carry out biological processes.”

While the results are rewarding, Benefield says the technique definitely requires patience.

“It’s not impossible by any means, and it’s a thrilling challenge,” Benefield says, “but it’s tricky. Just because you know how to do something doesn’t mean that your sample is going to cooperate or your microscope is going to cooperate.”

Nonetheless, the technique’s influence is starting to grow and Benefield, along with her fellow researchers, is looking forward to making it an even stronger force in the sciences.

“I’m very excited to see Morgridge and the University of Wisconsin ready to embrace this technique and push it further in terms of developing more biology-oriented electron microscopy work,” she says.


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