IPiB News

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    To better describe its purpose and mission, the Student Faculty Liaison Committee (SFLC), has changed its name to the Graduate Leadership & Development Committee (GLDC).

    As the group has evolved over the years, its goals have grown beyond just serving as a student voice on faculty committees to include career and professional development events, scientific outreach to the community, departmental social events, recruiting the next class of Integrated Program in Biochemistry (IPiB) students, and more. Each year, the group also organizes the annual IPiB Retreat.

    “Our new name reflects not only what our committee does, but also the training and experience that those on the committee can gain,” says current GLDC Chair Josie Werner of the Wildonger Lab. “The name allows us to better tell our story. Along with giving students a voice in the department, we also get to enrich the experience of graduate students with leadership and professional development events.”

    The group’s mission reads: “The Graduate Leadership & Development Committee contributes to the professional development of IPiB graduate students in a holistic manner by creating opportunities to foster research, scholarship, career development, and community engagement skills. We provide organized mechanisms for graduate student professional development and service to the IPiB and greater Wisconsin communities. Additionally, we promote an inclusive and tightly-knit community of students and faculty through recruitment of future graduate students, the annual IPiB Retreat, and departmental social events.”

    All IPiB students are encouraged to join GLDC and attend its monthly meetings on the first Wednesday of the month at 11 a.m. A series of sub-committees with individual chairs and members help carry out its activities each year.

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    Peter Favreau joined the Department of Biochemistry in July as the new manager of the Biochemistry Optical Core (BOC). The research core is housed in Biochemistry but serves as a resource for all campus researchers — including all Integrated Program in Biochemistry (IPiB) students and faculty — using or interested in using microscopy in their research.

    Favreau joins the BOC from the Morgridge Institute for Research, where he was a postdoctoral scholar in the lab of biomedical engineering professor Melissa Skala. The project he worked on investigated cancer drug screening. In the Skala Lab he utilized multiple microscopy techniques to help physicians find the right drugs for cancer patients.

    “I’ve always been fascinated by the machinery of protein interactions, cells, and tissues, which all take place underneath the world we see with just our eyes,” he says. “I look forward to helping scientists from across campus answer their questions in this area using microscopy. Researchers should always feel free to email me or just stop into my office to discuss a project.”

    For more info on the BOC and its new manager, see the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-biochemistry-optical-core-new-manager-2019-08-08

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    When Robert Kirchdoerfer was offered a faculty position in the University of Wisconsin–Madison Department of Biochemistry, it was a bit of a homecoming. The 2006 undergraduate alumnus and Oregon, Wisc. native will be arriving back on campus in mid-August — this time as an assistant professor in Biochemistry and the Institute for Molecular Virology.

    Following his Bachelor of Science with majors in biochemistry and genetics, Kirchdoerfer earned his Ph.D. in biophysics at Scripps Research Institute in Southern California and continued there as a postdoctoral scholar before coming back to UW–Madison. During graduate school he became fascinated by viruses while working on the flu virus and it’s an interest that guides his research today. As a member of the Department of Biochemistry, he will be a trainer in the Integrated Program in Biochemistry (IPiB). 

    “Viruses are so fascinating to study because they defy expectations,” he explains. “For every rule and trend in biology, there is a virus out there that somehow breaks it. This means that viruses have a lot to teach us about what biological systems are capable of.”

    His position in the Institute for Molecular Virology is part of its recent Metastructures of Viral Infection cluster hire initiative, supported by the Office of the Provost. The cluster is creating three new positions in total to leverage and improve UW–Madison’s current strengths in RNA virology, DNA virus epigenetics, and atomic-level imaging, and expand the institute’s research portfolio into the evolving field of metastructural virology. UW–Madison’s Cluster Hiring Initiative was launched in 1998 as an innovative partnership between the university, state and the Wisconsin Alumni Research Foundation (WARF).

    To read more about Kirchdoerfer, see the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-kirchdoerfer-joins-biochemistry-and-institute-molecular-virology-2019-07-25

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    Dan Blasiole’s career is a synthesis of his two intellectual passions: the sciences and the humanities. After honing his science knowledge with a Ph.D. in biochemistry from the lab of professor Alan Attie, he found the perfect combination of these two interests as a patent agent.

    Originally from Pennsylvania, he attended Franklin and Marshall College intending to get a degree in a science field. Instead, he left with a degree in philosophy and headed to the University of California, San Diego for a master’s degree in the philosophy of science. After spending several years researching molecular epidemiology in a Department of Defense lab in California he moved to Madison for his Ph.D. in biochemistry with Attie, which he finished in 2008, and discovered the patent field. Today he works at DeWitt LLP, a law firm in Madison, Wis.

    “I enjoyed doing science in the lab, but I loved learning and studying the theoretical aspects of science even more,” Blasiole explains. “I felt either too narrowly focused (in the lab) or too distanced from the scientific forefront (in the philosophy of science), neither of which was the right fit for me. I had a skill set in critical analysis and argumentative writing that I had developed studying philosophy, and I wanted to leverage this along with my passion for science in my future career.”

    Through networking with professionals at the Wisconsin Alumni Research Foundation (WARF), he learned of the patent field and got interested. As a patent agent he specializes broadly in biotechnology. Patent agents are the negotiating liaisons between inventors and the United States Patent and Trademark Office (USPTO). Blasiole often works with WARF in his role.

    UW–Madison researchers who want to patent an invention, some even from the Department of Biochemistry, first approach WARF. WARF then connects with patent attorneys and agents like Blasiole, who talk with WARF and the inventor to learn about the invention and understand the science behind it. Blasiole then drafts all the materials for a patent application, sends it to the USPTO, and negotiates back and forth with the USPTO to get it approved as a patent.

    Read more about Blasiole and his career at the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-blasiole-biochemistry-alumni-profile-patent-agent-20190718

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    Scientists at the University of Wisconsin–Madison have identified blood-based fingerprints – human protein markers – associated with the pre-cancerous forms of colon cancer that are most likely to develop into disease. They say their findings are a promising start to what could ultimately lead to a new blood test for the cancer.

    The lab of biochemistry professor Michael R. Sussman, in collaboration with researchers at the McArdle Laboratory for Cancer Research and UW–Madison School of Medicine and Public Health, used a technique called mass spectroscopy to isolate biomarkers in mouse and rat models of the disease and then test patient blood for the same markers. The researchers presented their newest advancements in the spring of 2019 in a study published in the Proceedings of the National Academy of Sciences.

    “The most commonly used technologies such as colonoscopy are highly invasive or utilize stool samples for testing, which may not be appealing to patients,” Sussman says. “Because colon cancer is highly curable if detected early enough, setting up tests for the earliest signs of colon cancer to provide as many early diagnostic options as possible is critical. That is the logic behind what we were trying to do.”

    Since nearly all cases of colon cancer are curable if caught early enough, this should make screening tests straightforward. However, this is not the case because colon cancer screening suffers from a paradoxical combination of low compliance rates and what is called ‘over-screening’ with colonoscopies.

    While the gold standard for colon cancer screening is a colonoscopy, patients must complete a day-long prep to empty their bowels before undergoing an invasive procedure – factors that contribute to low screening compliance. On the other hand, research from UW–Madison shows many of the polyps found and biopsied during a colonoscopy are regressing or static and not at risk of being harmful. A blood test that can detect if a polyp is growing or cancerous would give a better indication that a colonoscopy is needed.

    “It would not be meant to replace a colonoscopy in any way,” says Melanie Ivancic, the study’s lead author who started in the Sussman Lab as a graduate student and was then a postdoc. “But the blood test could serve as a pre-screen to detect polyps that have the greatest propensity to turn into cancer.”

    Read more about this work at the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-screen-using-blood-based-fingerprints-colon-cancer-shows-promise-2019-07-11

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    With a new method to synthesize a popular pain-relieving medication from plants rather than fossil fuels, researchers at the Great Lakes Bioenergy Research Center have found a way to relieve two headaches at once.

    A team led by John Ralph, a professor of biochemistry and Integrated Program in Biochemistry (IPiB) faculty member at the University of Wisconsin–Madison, has been awarded a patent for a method to synthesize acetaminophen — the active ingredient in Tylenol — from a natural compound derived from plant material. The approach offers a renewable alternative to the current manufacturing process, which uses chemicals derived from coal tar. It also creates a useful product from an abundant but difficult-to-manage component of plant cell walls called lignin.

    “Lignin is an extremely complex, messy polymer. No two molecules in a plant are exactly the same,” Ralph says. “It’s very effective for providing structure and defense for the plant, but it’s challenging for us to break down into useable materials.”

    The lignin in bioenergy crops, such as poplar, can create a headache for bioenergy researchers due to its recalcitrant tendencies, Ralph says. Once plant sugars are used to produce biofuels, the lignin that remains is typically burned for energy.

    The patent application, filed by the Wisconsin Alumni Research Foundation, describes a way to convert a molecule found on lignin into acetaminophen. It was awarded in May to Ralph, Steven Karlen of UW–Madison, and Justin Mobley, a former GLBRC postdoctoral fellow who is now at the University of Kentucky.

    Read more about this research at the link below. 

    URL: https://news.wisc.edu/relieving-two-headaches-with-one-process/

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    A report today (June 27) in PLOS Pathogens shows how inhaled fungal spores exit the lung and trigger a fatal infection in mice.

    The study solves a mystery of mycology: Why are spores of a certain fungal strain deadly while the yeast form of that same fungus is harmless?

    Study leader Christina Hull, professor of biomolecular chemistry and medical microbiology and immunology at the University of Wisconsin–Madison, focuses on Cryptococcus, the most deadly inhaled fungus. The short answer, she says, is that lung macrophages abandon their posts as bodyguards and begin smuggling spores into the bloodstream. Hull is a faculty member in the Integrated Program in Biochemistry (IPiB).

    Normally, macrophages chew up pathogens and spit out their inert fragments. But in Cryptococcusinfections, the immune cells serve as Trojan horses, concealing a deadly cargo.

    The study revealed that macrophages in mouse lungs were packed with live Cryptococcusspores. “These immune cells are acting as a vehicle to invade the rest of the body,” says first author and IPiB alumna Naomi Walsh, “with the spores hidden inside, protected from other types of immune attack.”

    Read more of this press release at the link below. 

    URL: https://news.wisc.edu/a-trojan-horse-immune-cells-ferry-deadly-fungus-from-mouse-lung-into-the-blood/

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    With a Grand Challenges Explorations grant from the Bill & Melinda Gates Foundation, University of Wisconsin–Madison scientists Ophelia Venturelli and Brian Pfleger are working to further research on how to use human-associated intestinal microbes to combat malnutrition in developing countries.

    Grand Challenges Explorations (GCE) supports innovative thinkers worldwide to explore ideas that can break the mold in how scientists solve persistent global health and development challenges. IPiB faculty member Venturelli and Pfleger’s project is one of approximately 50 Grand Challenges Explorations Round 22 grants announced by the Bill & Melinda Gates Foundation. Since the program’s launch in 2007, UW–Madison has been represented among nine of these projects, four of those being specifically from the Department of Biochemistry.

    To receive funding, they and other Grand Challenges Explorations winners demonstrated in a two-page online application a bold idea in one of seven critical global heath and development topic areas. The title of their project is “Modeling of Microbial Community Dynamics to Enhance Ecological Stability and Growth.”

    Read more about this work at the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-venturelli-receives-gates-grand-challenges-grant-exploratory-work-microbiome-and

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    The Integrated Program in Biochemistry (IPiB) is pleased to continue its commitment to teaching and mentorship by announcing the 2019 graduate student awards that celebrate these important aspects of the program. The awards were given out at the IPiB Summer Reception on Friday, June 7.

    Evan Glasgow, from the lab of Professor Brian Fox, and Nathan Thomas, from the lab of Professor Katherine Henzler-Wildman, received the 2019 Denton Award for Graduate Student Excellence in Teaching and Mentoring. Andrew Voter, from the lab of Professor James Keck, received the 2019 Sigrid Leirmo Memorial Award in Biochemistry.

    The Denton Award honors IPiB students who consistently provide quality guidance and scientific training in mentoring undergraduate students in their research efforts and show evidence of quality, commitment, and innovation in teaching.

    “I seek teaching and mentoring opportunities because working with young, interested scientists, and seeing them struggle and earn their growth, is its own reward,” Glasgow says. “But receiving recognition for the many hundreds of hours I’ve spent being their mentor is a tremendous honor. Knowing that the IPiB community recognizes and supports my efforts to teach and train these students is a huge encouragement to keep forging these growth and mentoring relationships.”

    The award is made possible by the generosity of Arnold E. and Catherine M. Denton. IPiB is the joint graduate program of the Department of Biochemistry and Department of Biomolecular Chemistry.

    “This award is truly an honor, and it is humbling to be nominated for it, let alone selected to receive it,” Thomas says. “As a grad student, having the opportunity to teach and mentor other grad students and undergraduates is a great privilege and a daunting responsibility. Receiving this award is greatly encouraging, and it demonstrates the high value this department places on training future scientists.”

    The Leirmo Award recognizes graduate or postdoctoral students who exemplify the spirit of Sigrid Leirmo. Leirmo received her Ph.D. from the Department of Biochemistry in 1989. She was widely acknowledged among her fellow students and colleagues as a promising researcher and enthusiastic friend and mentor.

    “I am honored and humbled to have been selected for the Sigrid Leirmo award,” says Voter, who recently finished his Ph.D. and is now headed back to medical school to complete his M.D./Ph.D. program. “My thesis work was made possible through the generous help and guidance I’ve received from the Keck Lab and the IPiB community, and I hope I’ll be able to pay it forward.”

    IPiB’s Student Faculty Liaison Committee (SFLC) also announced its newest round of officers at the reception.

    • Chair: Josephine Werner
    • Vice Chair: Dana Dahhan
    • Treasurer/Fundraiser: Jennifer Peotter
    • Career: Peyton Spreacker, Nathan Murray
    • Recruiting: Elizabeth Larson, Alex Duckworth
    • Social: Aryel Clark, Matt Blackburn
    • Outreach: Josh Mitchell, Katherine Senn, and Lily Miller
    • Student Lunch Symposium: Will Kasberg
    • Student Invited Speaker: Tina Lynch
    • Curriculum Chair: Adam Lewis
    • NSOC: Harriet Saunders
    • Retreat: Rachel Cueny and Christine Hustmeyer
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    Biochemistry professor and Morgridge Institute for Research investigator David Pagliarini received a 2019 H.I. Romnes Faculty Fellowship. Eleven total University of Wisconsin–Madison faculty received the fellowship, which recognizes faculty up to six years past their first promotion to a tenured position.

    The award is named in recognition of the late Wisconsin Alumni Research Foundation (WARF) trustee president H.I. Romnes, and comes with $60,000 that may be spent over five years. Support for the award is provided by the UW–Madison Office of the Vice Chancellor for Research and Graduate Education(VCRGE) with funding from WARF. Among just the current biochemistry faculty, 14 others have also held this honor.

    “The Romnes is a special recognition because it sends the message that the university values what we are doing and is willing to further invest in our success,” says Pagliarini, who is in his 10th year on campus. “This fellowship is also yet another reminder of how generous and empowering WARF is to our campus. We are quite fortunate to have them as partners in our research efforts.”

    Pagliarini, director of the Morgridge Institute for Research’s Metabolism Theme, studies mitochondria — ubiquitous organelles essential for cellular metabolism. His lab integrates classic biochemistry with large-scale methodologies to systematically define the functions of uncharacterized mitochondrial proteins and to establish the detailed mechanisms that drive disease-related mitochondrial pathways. This combination of approaches, he adds, has worked well for his lab and will help them continue to venture into the dark corners of this organelle.

    Read more about Pagliarini's award at the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-pagliarini-awarded-romnes-faculty-fellowship-2019-05-30

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    Researchers at the University of Wisconsin School of Medicine and Public Health have developed a novel strategy to address the role of vital proteins during early embryonic development.

     In all animals, early development is controlled by products put into the egg by the mother, and it is not until hours or days later that the zygote takes control of its own development. During this time, the genome of the zygote remains silent as it is reprogrammed to allow for the development of an entirely new organism.

    Specialized proteins, termed pioneer transcription factors, drive this reprogramming both in the early embryo and in laboratory cultures during the generation of induced pluripotent stem cells (iPSC). While this pioneer factor-mediated reprogramming is essential for development, much remains unknown about how these proteins function, according to Melissa Harrison, associate professor of biomolecular chemistry.

    Using fruit flies to model this conserved process, Harrison’s team uncovered fundamental features of the protein, Zinc finger early Drosophila activator protein, or Zelda, which is a pioneer transcription factor necessary for preparing the early embryo for development.

    “We set out to test whether this essential protein was continuously required to reprogram the genome or whether it was only required during the initial phases and that the process was then carried out by additional, downstream factors,” Harrison said.

    The research was recently published in the journal Molecular Cell.

    A major challenge, however, was the rapid nature of this early development.

    To overcome this challenge, the researchers developed a strategy that uses blue light to rapidly and reversibly inactivate Zelda – a literal light switch to turn “off” or turn “on” Zelda function. Using this novel technique, they showed that Zelda was required throughout the process of genomic reprogramming.

    Read more about this work at the link below. 

    URL: https://www.med.wisc.edu/news-and-events/2019/may/zelda-zygotic-gene-activation-/

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    A University of Wisconsin-Madison researcher has established a new approach to understanding how protein and RNA molecules in a cell cooperate to direct the proper expression of genes.

    The approach improves upon a well-established method called genetic suppression, developed more than a century ago. A genetic suppressor is a second mutation that corrects the defect of a primary mutation, according to David Brow, professor of biomolecular chemistry.

    The research was recently published in the journal Genetics.

    By using a customized targeting sequencing technique, Brow found that he could identify suppressor mutations much more easily and in much larger numbers than before.

    By mapping the mutations on existing molecular structures, he obtained new insights into an essential step of gene expression called pre-messenger RNA splicing.

    “This approach should be broadly useful for understanding the dynamics of many different complex biological assemblies or pathways,” Brow said.

    The new research targeted a specific cold-sensitive mutation, U4-cs1, that blocks activation of the spliceosome, essentially an incredibly small machine within the nucleus of a cell. It is made of RNA and protein and removes meaningless information from cellular RNAs.

    The approach identified five new genes in which mutations can overcome the block created by U4-cs1.

    Read more on this story by Andrew Hellpap at the School of Medicine and Public Health at the link below.

    URL: https://www.med.wisc.edu/news-and-events/2019/may/david-brow-molecular-signaling-living-cells/

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    Biochemistry professor Judith Kimble has been honored with a Wisconsin Alumni Research Foundation (WARF) Named Professorship, as one of 10 distinguished campus researchers receiving them this year.

    Support for the award is provided by the University of Wisconsin–Madison Office of the Vice Chancellor for Research and Graduate Education (VCRGE) with funding from WARF. The awards, which come with $100,000, honor faculty who have made major contributions to the advancement of knowledge, primarily through their research endeavors, but also as a result of their teaching and service activities. Among just the current biochemistry faculty, nine others also currently hold this honor.

    “These awards are made to very distinguished researchers across campus, so it’s a real honor to be included among them,” Kimble says. “It will be immensely helpful for my lab and students. As both a department and campus citizen, it’s a privilege to be part of such a significant group here in Biochemistry but also across this outstanding university.” 

    Kimble’s history of scientific excellence on campus is long. In 1981 she discovered the first stem cell niche, and since has unraveled the genes, pathways and networks that regulate stem cell self-renewal and differentiation. Her research, based on analyses of microscopic nematodes, has revealed molecular mechanisms operating in all animals with implications for human disease.

    Read more about Kimble's award and research at the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-kimble-earns-2019-warf-named-professorship

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    The Department of Biochemistry is pleased to announce its 2019 undergraduate and graduate student departmental awards and fellowships. These awards and fellowships celebrate talented students in the department and are made possible by generous gifts to the department to fund graduate and undergraduate research.

    “It’s always a pleasure to honor so many brilliant young people in this ceremony every year,” said department chair Brian Fox at the awards reception on Friday, April 26. “These awards highlight the hard work of these students, mentorship of their faculty advisors, and generosity of our supporters.”

    The 2019 Department of Biochemistry Graduate Fellowship awardees include Dana Dahhan, Zack Kemmerer, Kyle Nishikawa, and Dylan Plaskon.

    Graduate student fellowships cover a student’s tuition and stipend for an academic year. They provide students flexibility in their research endeavors by not being tied to a specific grant. By freeing up funds, they also, for example, allow faculty to purchase new equipment for labs. Students who receive these fellowships are part of the Integrated Program in Biochemistry (IPiB), the joint graduate program of the Department of Biochemistry and the Department of Biomolecular Chemistry.

    This year’s department graduate fellowships are sponsored by the Denis R. A. and Martha Washburn Wharton Fund, Dr. James Chieh-Hsia Mao Wisconsin Distinguished Graduate Fellowship Fund, Arthur B. Michael Fund, and Robert and Katherine Burris Biochemistry Fund.

    “This award is both a form of recognition of the contributions my research is making to the field of plant biochemistry and an encouraging sign to continue on,” says Dana Dahhan, an IPiB student in the lab of Professor Sebastian Bednarek. “Because of this award, I will be able to attend the annual American Society of Plant Biologists meeting. There I will be able to interact with a host of plant researchers in fields which are new to me.”

    The department also congratulates Nathan Thomas on his Louis and Elsa Thomsen Wisconsin Distinguished Graduate Fellowship from the College of Agricultural and Life Sciences.

    To read more about the awards and undergraduate awardees, see the link below. 

    URL: https://biochem.wisc.edu/news/2019/news-biochemistry-announces-2019-student-awards

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    Three University of Wisconsin–Madison Integrated Program in Biochemistry (IPiB) students recently earned 2019 National Science Foundation (NSF) Graduate Research Fellowships, with two additional students receiving honorable mentions.

    Aryel Clarke and Jennifer Peotter, both of the lab of Professor Jon Audhya, and Katherine Senn from the lab of Assistant Professor Heidi Dvinge received fellowships. William Kasberg and Iryna Pustova, both members of the Audhya Lab, made the list of honorable mentions.

    “I am simply overjoyed that the National Science Foundation has chosen to recognize Jen, Aryel, Iryna, and William for their talent, commitment, and innovation,” Audhya says. “Both I and IPiB are fortunate to have recruited such amazing students.”

    The Graduate Research Fellowship Program recognizes and supports outstanding, early-career graduate students who are pursuing research-based master's and doctoral degrees in science, technology, engineering, and mathematics (STEM) fields. Awardees are selected based on their potential for significant research achievements that can benefit society. A total of 40 students at UW–Madison received fellowships this year. 

    “Being awarded the fellowship has been a really validating experience for me as a first-generation woman scientist,” Clarke says.

    Fellows receive three years of financial support from NSF, consisting of a $34,000 annual stipend and a $12,000 education allowance. Each year, IPiB students are consistently well represented among the recipients of these NSF fellowships. 

    “I am very honored to have received an NSF Graduate Research Fellowship,” Peotter says. “It was very rewarding to see my research experiences come together, and I am excited to continue working in the Audhya Lab and expand my outreach involvement.”

    Many of the awardees, such as Senn, excel not only at research but also have a passion for scientific outreach.

    “For her graduate work, Kathy has taken on a challenging project about the biochemical and functional genomic differences between transcription factor isoforms,” says Dvinge, Senn’s advisor. “In addition to being an excellent scientist, she is also a dedicated member of the IPiB outreach team through the program’s Student Faculty Liaison Committee (SFLC). Kathy's commitment to STEM really embodies the two main criteria for the NSF GRFP, namely intellectual merit and broader impacts.”

    Of about 12,000 applicants nationally, 2,050 received awards. A total of 29 UW–Madison students were given honorable mentions in this year's competition. Eleven UW–Madison alumni who are now at another institution also received awards.

    “The number of UW–Madison students who have received this fellowship is a testament to the strong research enterprise here, and the spirit of curiosity that motivates our students to succeed," says Graduate School Dean William J. Karpus. “With the mentorship they will receive from world-class faculty, and with this support from the National Science Foundation, these students are well-positioned for impactful scholarship at this early stage of their careers.”

    To see a list of all UW–Madison students who received NSF fellowships, see the link below.

    URL: https://news.wisc.edu/msf-awards-40-fellowships-to-uw-madison-students/

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    Numerous researchers in the University of Wisconsin–Madison Department of Biochemistry perform in vivo biochemical studies. Meaning “within the living,” these studies focus on understanding a particular molecular process in the context of an entire organism rather than isolating it in an artificial tissue, culture cell, or test tube, called in vitro.

    The two methods of scientific experimentation are powerful and each has its advantages and disadvantages, but with the advent of gene editing technologies such as CRISPR, the in vivo studies are cracking open exciting new ways to understand what’s going on at the genetic and molecular levels in organisms. These researchers use model organisms, such as the fruit fly Drosophila melanogaster — like in the lab of Assistant Professor Jill Wildonger — and Caenorhabditis elegans, a microscopic worm — like in the lab of Professor Judith Kimble.

    These organisms allow scientists to study fundamental processes in vivo and make inferences about how those processes work in larger organisms like humans. Other faculty members who are performing in vivo studies include professors Wes Pike and Alan Attie, who use mice as a model in their research. They study areas like vitamin regulation and diabetes, respectively. In vivo can also be interpreted to mean work in an entire bacterial or fungal cell, as is the case with Associate Professor Aaron Hoskins’ work in yeast.

    In the Q&A at the link below, biochemistry faculty Kimble and Wildonger share what this type of study entails both broadly in the department and in their research. Click the link below to read more. 

    URL: https://biochem.wisc.edu/highlights/2019/highlights-vivo-studies-department-biochemistry

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    Hans Clevers of Utrecht University will deliver the 2019 UW–Madison Department of Biochemistry International Steenbock Lectures on May 20 and 21.

    Clevers is a world leader in the field of adult stem cell biology. The signatures of his award-winning research have been defining the role of Wnt signaling in stem cell control and cancer, and launching the use of “organoids” to analyze stem cells in their 3D context within a tissue. Clever won one of the inaugural Breakthrough Prizes in the Life Sciences in 2013, and has also received many other honors over the course of his career.

    His first lecture, “Wnt, gut stem cells and cancer,” will be at 3:30 p.m. on Monday, May 20. His second lecture, “Human stem cell-based organoids for disease modelling,” will be at 3:30 p.m. on Tuesday, May 21. Both lectures 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-clevers-gives-biochemistry-international-steenbock-lectures

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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