IPiB News

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    Three professors at the University of Wisconsin–Madison — including one Intregrated Program in Biochemistry (IPiB) faculty member — are among the 2019 class of Simons Fellows in Mathematics.

    Gheorghe Craciun of IPiB, along with Autumn Kent and Andreas Seeger, are among the 48 distinguished scientists named to fellowships.

    Each year, the Simons Foundation selects as many as 50 fellows conducting research in math and the physical sciences, providing funding for an academic leave from a term to a full year. The support, according to the foundation, is meant to help recipients “focus solely on research for the long periods often necessary for significant advances.”

    Craciun, a professor of mathematics and biomolecular chemistry, studies mathematical and computational methods for understanding properties of the biochemical networks in cells, like those that regulate gene expression, send signals and manage metabolism. The Department of Biomolecular Chemistry and the Department of Biochemistry are the two departments that make up IPiB. 

    Kent, an associate professor of mathematics, likes to work at the intersection of fields — studying families of geometric objects through hyperbolic geometry, topology and group theory.

    Seeger, a professor of mathematics, works in harmonic analysis. His research interests include problems on wave propagation, singular and oscillatory integrals, Fourier and spectral multipliers, and function spaces.

    Founded in 1994 by Jim and Marilyn Simons, the Simons Foundation supports basic scientific research undertaken in the pursuit of understanding the phenomena of our world.

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    Students in the Integrated Program in Biochemistry (IPiB) all love science — but also don’t forget how they came to love it. A group of IPiB students spent a Saturday in February helping judge the Wisconsin Regional Science Olympiad as part of an outreach event planned by the IPiB Student Faculty Liaison Committee (SFLC).

    SFLC serves graduate students in the program and is a conduit for the students to provide input on the graduate program. However, they also recognize the importance of reaching outside the university. The three current outreach chairs — Joshua Mitchell (Mosher Lab), Katherine Senn (Dvinge Lab), and Josie Werner (Wildonger Lab) — plan and organize outreach events for IPiB graduate students and postdocs to participate in. They describe the situation as a win-win.

    “I think it’s great to have a designated group to find and plan these events so students and postdocs can get involved easily and gain scientific outreach experience,” Werner says. “However, it’s also a huge benefit for the kids we are reaching and sharing science with. We look for events of all kinds, from elementary to high school kids.”

    The Science Olympiad is the Olympics for science, where middle school and high school students get hands-on experience in science with everything from rocket building and bridge construction to forestry and molecular modeling, which is what the IPiB students judged. The competitors pre-built a protein model to bring to the competition, build another protein model on site, and take a written exam.

    “It was awesome to see models that accurately showed a protein come together in just 40 minutes, and the test showed that the competitors actually understood the protein’s structure and function,” Senn says. “I could tell that the students had dedicated a lot of time and energy to preparing for the modeling event, which was only one of several events that they competed in throughout the day.”

    The outreach chairs say that anyone should reach out to them to learn more about outreach opportunities like Science Olympiad, or even to coach a team for the event next year.

    “Once you get into graduate school it can be easy to forget about outreach when you’re focused on projects in the lab but it’s important to think about what got you interested in science in the first place,” says Mitchell, who participated in Science Olympiad in Michigan while in high school. “It was likely an event like this!”

    Read more about SFLC at the link below. 

    URL: https://ipib.wisc.edu/c_students_sflc.php

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    Assistant professor of biochemistry Ophelia Venturelli was recently named to a list of 34 young researchers featured in the journal Biochemistry’s “Future of Biochemistry: The International Issue” special issue.

    “I am excited to be included in this list of outstanding new investigators,” says Venturelli, who is also an affiliate of the Department of Bacteriology and Department of Chemical and Biological Engineering. “The research areas are quite diverse and illustrate the breadth of cutting-edge research in Biochemistry.”

    For the special issue, her and her team wrote a perspective piece on the importance of understanding and engineering the interactions of microbial communities. Microbiomes — the collections of microbes that reside in almost all environments — are extremely complex and Venturelli’s lab works to make sense of their many microbial interactions through, for example, mathematical modeling.

    To read more about Venturelli's research see the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-venturelli-makes-future-biochemistry-list-2019-02-18

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    On a beautiful September Sunday, hundreds of bicyclists pedaled the roads of eastern Dane County on The Ride to raise money for cancer research.

    This weekend, their fundraising came home to support cancer research at the University of Wisconsin-Madison as scholarships totaling $365,488 were awarded at Friday’s Badger hockey game. Two Integrated Program in Biochemistry (IPiB) faculty members were among the scientists working in cancer research that received funding.

    “We’re grateful to all the riders, donors and volunteers who have enabled us to provide funding for some really innovative cancer research,” says Deric Wheeler, PhD, director of The Ride and associate professor of human oncology at the UW School of Medicine and Public Health. “Thanks to our sponsors, all the money raised through The Ride goes to UW cancer researchers and programs to jump-start research projects that could one day lead to better treatments and even save lives.”

    The two faculty members include John Denuprofessor of biomolecular chemistry, whose research centers on targeting DNA as a strategy to kill cancer cells and Joshua Coon, professor of chemistry, whose research focuses on developing cutting-edge chemical instrumentation to measure proteins in human cells and tissues to create better targeted therapies.

    For more on The Ride and a full list of winners the see the link below from the UW–Madison School of Medicine and Public Health. 

    URL: https://www.med.wisc.edu/news-and-events/2019/february/the-ride-raises-365000-for-carbone/

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    Huda Zoghbi of the Baylor College of Medicine will give the 2019 UW–Madison Department of Biochemistry Steenbock Lectures in early March. All members of the campus community are invited to attend these lectures and learn from this pioneer in understanding the molecular basis of human neurological disorders.

    Zoghbi is best known for discovering the molecular basis of two neurological disorders — Rett syndrome and spinocerebellar ataxia (SCA). She was awarded the Breakthrough Prize in Life Sciences in 2016 for these seminal contributions. More broadly, her investigations explore how key regulators impact neuronal development, neuronal physiology, the brain, and human disease. 

    Her first lecture is titled “Genetic and physiological approaches to tackle neurodevelopmental disorders” and will be at 3:30 p.m. on Monday, March 4. Her second is titled “Insights from rare disorders shed light on common neurodegenerative diseases” and will be at 3:30 p.m. on Tuesday, March 5. Both seminars will be in the Ebling Symposium Center, Microbial Sciences Building (1550 Linden Drive). Monday’s talk will be followed by a reception in the Hector F. DeLuca Biochemical Sciences Building atrium.

    Read more about the lectures at the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-zoghbi-give-2019-biochemistry-steenbock-lectures-2019-02-13

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    After filming a movie, scenes are cut and rearranged to tell the director’s story. A similar editorial process occurs in our cells in a process called RNA splicing. Before the DNA code is translated into a protein, it must first be converted into RNA, its single-stranded mirror image. The resulting strand of RNA is spliced to generate an edited strand that is used to code for new proteins.

    RNA splicing allows cells that contain the same genetic information to code for different proteins and to complete different functions.

    “You can imagine, depending on what scenes you use or add into a movie, you get a slightly different meaning out of it. Splicing is a way for one gene in our cell to have these slightly different meanings,” Heidi Dvinge, assistant professor in the Department of Biomolecular Chemistry and IPiB faculty member, said. Dvinge joined the UW Carbone Cancer Center in 2017 and studies the mechanisms and consequences of RNA splicing and how errors in splicing can give rise to cancers.

    Splicing is a normal function in healthy cells. However, sometimes splicing can go wrong, and portions of the RNA are rearranged or removed in a way that will negatively affect protein structure and function. Researchers have only recently found that these rogue edits can be involved with cancer and other diseases. 

    “In some cases, if you take out a scene, suddenly the whole movie doesn’t make sense. Imagine Titanic where the ship never hits the iceberg. Then for the rest of the movie, all these people running around jumping into the water and it doesn’t make any sense whatsoever,” Dvinge said. “That’s what happens when things go wrong with splicing. In the last 5-6 years, people have really started to realize how changes in splicing can act as a disease driver.”

    To read more about Heidi's research, go to the link to a story by the Carbone Cancer Center below. 

    URL: https://www.uwhealth.org/news/the-directors-cut-heidi-dvinge-looks-at-rna-splicing-with-a-film-critics-eye/52532

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    For Danielle Lohman, her passion for science policy began when she heard a Ph.D. chemist speak at a career conference about the American Association for the Advancement of Science (AAAS) fellowship at the State Department in Washington, D.C.

    Lohman, recently a postdoctoral fellow in Dave Pagliarini’s Department of Biochemistry lab at the Morgridge Institute for Research, was in her second year of graduate school as part of the Integrated Program in Biochemistry (IPiB) at the University of Wisconsin–Madison at the time. 

    “I just thought her life was really cool,” Lohman says. “When I saw her speak, it was the first time that I realized scientists could do things that weren’t strictly laboratory science.’”

    AAAS is a multidisciplinary scientific society and research publisher based in the nation’s capital whose mission includes advancing science and promoting scientific research. AAAS fellowships give talented scientists the opportunity to work in a broad range of fields, from engineering to neuroscience to astronomy.

    At Morgridge, Lohman has been working in the Pagliarini Lab, part of the Metabolism theme, investigating the role of mitochondrial dysfunction in human diseases.

    But even with her success in the lab, Lohman knew science policy was a path she wanted to pursue. This year, her dream became a reality.

    After a period of intensive interviewing with six different federal agencies in Washington, D.C., Lohman was one of 271 candidates selected for a prestigious AAAS Science & Technology Policy Fellowship. Lohman will be working in the Office of Biological Policy in the Bureau of International Security and Nonproliferation — an area of the State Department that deals with issues like biological weapons and biosecurity.

    For more about Danielle and her fellowship, click the link before to the Morgridge website. 

    URL: https://morgridge.org/story/metabolism-scientist-wins-prestigious-aaas-fellowship/

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    In high school, Judith Simcox pored over scientific literature to try to understand the link between her sister’s Down Syndrome and type 1 diabetes. It was the first time she asked a question that didn’t have an answer yet — and it led her down the path of answering unknown questions as a metabolism researcher and advocate for diversity in science.

    Simcox, whose work specifically focuses on how organs communicate through lipid signaling to respond to the energy demands of cold exposure, has joined the University of Wisconsin–Madison Department of Biochemistry and Integrated Program in Biochemistry (IPiB) as its newest assistant professor. IPiB is the joint graduate program of the Department of Biochemistry and Department of Biomolecular Chemistry. 

    “Madison is an incredible environment that cultivates creativity and innovation while having a firm appreciation for the historical discoveries in research,” she says. “Any field I ventured into, even during my undergraduate, seemed to have leaders from the department. It is surreal that I will be starting my lab in the same building as researchers who have left me star struck as a young student.”

    She joins Biochemistry from a postdoctoral fellowship at the University of Utah, where she also earned her Ph.D. in 2014. She spent her undergraduate years at Carroll College. At UW–Madison she will research metabolism and the impact of cold exposure on lipids in the body.

    Read more about Simcox at the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-simcox-joins-biochemistry-newest-faculty-member-2019-02-01

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    A major goal of the Great Lakes Bioenergy Research Center is to harness the power of microbes to create biofuels. But often, it’s an expensive challenge for scientists to identify the most useful individual variants among thousands of similar microbe strains. A new study led by Vatsan Raman, an assistant professor of biochemistry at the University of Wisconsin–Madison, unveils a biosensor that may light the way to the best microbial candidates for biofuel production.

    In search of the best biofuel-producing microbes, scientists may need to make millions of variants via genetic modifications. But only a handful of these variants are likely to produce large amounts of biofuel. To identify the most promising strains, scientists currently have to crack open the cells and test for the desired molecules one microbe at a time, an expensive and extremely labor-intensive process. 

    In a paper published January 12, 2019, in ACS Synthetic Biology, Raman’s team describes a new biosensor capable of reporting a microbe’s biofuel production capacity to scientists from within the cell. It’s a faster, cheaper, and less disruptive means of identifying the most promising biofuel-producing microbes. The paper is co-authored by Yang Liu, a graduate student in Raman’s lab, and Robert Landick, UW–Madison professor of biochemistry and bacteriology. Liu is part of the Integrated Program in Biochemistry (IPiB).

    To read more about this research, see the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-new-biosensor-highlights-best-biofuel-producing-microbes-2019-01-18

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    The National Magnetic Resonance Facility at Madison (NMRFAM) housed in the UW–Madison Department of Biochemistry is home to state-of-the-art technology for biomolecular nuclear magnetic resonance (NMR) spectroscopy and related techniques. The facility’s equipment requires helium, and with worldwide supplies dwindling, has recently installed a helium recovery system to increase sustainability and cut costs.    

    NMR enables researchers to probe the structures and dynamics of biological macromolecules and to identify structure-function relationships. The facility offers instrumentation, software, and expertise. NMR excels at uncovering molecular interactions, for example, between drugs and drug targets or between macromolecules themselves. NMR can also be used to probe the composition of small molecules in biological fluids, such as plasma, cerebral spinal fluid, urine, and cell/organ extracts. This type of structural work is important in many areas of research, such as the search for new antibiotics.

    All nine of the NMR magnets at NMRFAM are “superconducting.” As long as they remain cooled at liquid helium temperature (4º Kelvin or about ‒450º Fahrenheit), they behave like permanent magnets. The liquid helium used to cool each system boils off slowly and has to be replenished. The problem is that helium is a scarce nonrenewable resource extracted from the ground, which escapes from the Earth’s atmosphere when released.

    Read more about the helium recovery system at the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-nmrfam-reduces-helium-use

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    If you’ve ever grown carrots in your garden and puzzled over never once seeing them flower, don’t blame a missing green thumb.

    Carrots, beets and many other plants won’t flower until they’ve gone through winter. The extended cold gives them the signal to flower quickly once spring arrives, providing the plants an edge in the race to produce seeds.

    But cold isn’t always required. In the 1930s, two English scientists discovered that some crops in the grass family, like rye or wheat, can use short days instead of cold to tell them when winter has come.

    “But nothing was known about how it works,” says Rick Amasino, a professor of biochemistry and genetics at the University of Wisconsin–Madison.

    Now, more than 80 years later, Daniel Woods and others in Amasino’s group have finally discovered how grasses count the short days of winter to prepare for flowering. In most plants, a protein called florigen induces flowering during the lengthening days of spring and summer. Grasses have multiple copies of the florigen gene, thanks to an ancient duplication in their genomes. One of those copies has been repurposed to be expressed during the short days of winter, giving some grasses a new way to prepare for spring.

    The work is published Jan. 8 in the journal eLife. The new research provides valuable insight into how winter-adapted grasses gain the ability to flower in spring, which could be helpful for improving crops, like winter wheat, that rely on this process.

    To read more about this research, see the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-ancient-gene-duplication-gave-grasses-multiple-ways-wait-out-winter-2019-01-08

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    New research on transcriptional pausing, which helps control gene expression in cells, will aid in the understanding of the enzyme RNA polymerase — a key player in the process and an important drug target.

    The lab of IPiB faculty member Robert Landick has provided this new insight on the mechanism underlying the control of gene expression in all living organisms in a study published today (Jan. 8) in eLife.

    The findings could ultimately improve the understanding of how certain antibacterial drugs work against the enzyme RNA polymerase (RNAP) in treating conditions such as Clostridium difficile infections and tuberculosis.

    To read more of this research, see the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-scientists-provide-new-insight-how-gene-expression-controlled-2019-01-08