Shouting “Sam” in the lab of University of Wisconsin–Madison biochemistry professor Alessandro Senes won’t get you far. Three talented young scientists will turn their heads: Samantha Anderson, Samson Condon, and Samuel Craven.
All three graduate students in the Integrated Program in Biochemistry (IPiB) ended up in the same lab, which studies membrane proteins. IPiB is the joint graduate program of the Department of Biochemistry and Department of Biomolecular Chemistry. Although from slightly different backgrounds, they are linked by their research interests and, of course, their names.
“The lucky thing is we all have different full first names, which is kind of surprising,” says Anderson, a fifth year in the lab. “People call us the three Sams mostly. I’ve heard the Senes Sams, but not often. It also doesn’t help that my initials are SMA. When I started, Samuel and Samson were already in the lab and I wrote my initials on my first freezer box. ‘That’s not gonna work’ they laughed.”
What sparked their interest in science is varied. Anderson has a fun story about falling in love with science at a plant exhibit at Disney World. Condon found biochemistry research after floating law school and a patent law career, while Craven says his proficiency in math and chemistry from a young age steered his choice of study.
The coincidence has come with a fair share of hilarious stories from the lab. For new lab members, there’s a learning curve to knowing that asking for “Sam” will only result in confusion. Luckily, they just go by their full first names or their last names.
“Some are better at it than others,” says Craven, who is in his sixth year. “Samson and Samantha are actually in the same bay in the lab and sometimes I’ll go over there and even I’ll just say ‘Sam.’ There will be a pause until I realize I have to say the other part of the name.”
While their names may bring funny moments into the lab, the science in the Senes Lab is no joke. The lab studies proteins embedded in cell membranes, which are notoriously difficult to study. To get around this, they study them with conventional laboratory experiments and also use computation to help make predictions about them.
Read more about the Sams and their research at the link below.
Biochemistry assistant professor and Integrated Program in Biochemistry (IPiB) faculty member Srivatsan “Vatsan” Raman has received a Director's New Innovator Award from the National Institutes of Health (NIH). The $2.2 million-grants fund high-risk, high-reward research performed by early stage investigators. Compared to traditional NIH grants, the New Innovator Award supports “unusually creative early stage investigators” whose research can have a broad impact on biomedical sciences.
Raman’s project is focused on understanding protein allostery. Allostery is a property by which when something happens to one part of a protein, a signal is somehow communicated to another part of the protein, where another action takes place. This “long-distance” communication is called allostery.
“Allosteric proteins are nature’s switches,” explains Raman, who is also affiliated with the Department of Bacteriology and the Great Lakes Bioenergy Research Center. “The classical view, one that every biochemistry textbook follows, is that only some proteins exhibit allosteric properties. However, this view is dated. There is increasing recognition that allostery is a fundamental property of all proteins, just as folding is, and that allosteric behavior is more pronounced in some proteins than others. Allosteric proteins regulate many essential cellular processes required for life. They switch states from on to off or off to on and that’s how they turn on and off a very large number of genes. However, sometimes they acquire a mutation that causes the switch to be permanently on or off when it shouldn’t be. This dysfunction is responsible for many diseases, including cancer, because activities inside a cell are no longer regulated.”
Because of their central role in regulation, these proteins are popular drug targets. Raman says almost half of all current drug targets are allosteric proteins. Yet, little is understood about how allostery itself works.
Read more about this award and Raman's work at the link below.
Coon’s research group focuses on expanding the field of proteomics by developing new technologies and methods to address fundamental questions in biology. His lab is particularly focused on mass spectrometry-based technologies — used to precisely weigh molecules — that probe the proteome, which is the collection of all proteins that can be expressed in an organism.
These technologies allow his group to study a broad range of biological systems ranging from symbiosis to human diseases like diabetes, cancer, and Alzheimer’s.
“I am delighted and humbled to have received the 2018 HUPO Discovery Award,” Coon says. “This award is really a testament to the fantastic team of researchers I have had the good fortune to work with over the past decade here at UW–Madison.”
Coon is a co-recipient of the award with Ulrike Kusebauch of the Institute for Systems Biology. The award was sponsored by the Journal of Proteomics.
A molecular basis underlying the neurodegenerative condition hereditary spastic paraplegia (HSP) has been identified in a study by numerous Integrated Program in Biochemistry (IPiB) faculty members, students, and collaborators. The research, published in Cell Reports, shows how a mutation in the TFG gene – one of several linked to HSP – impairs neurons from forming the structures needed to transmit signals properly.
Hereditary spastic paraplegia includes several inherited disorders that make walking difficult to impossible.
To make an arm or a leg move, neurons – up to one meter in length – are required to send the brain’s signal to the limb through cell extensions called axons. Individuals with early-onset HSP begin to lose signaling to their legs during infancy and are often never able to walk. Advances in genome sequencing have linked more than 70 genes to HSP development, but their individual contributions to the disease state have never been clear.
“The main approach people have used in the past is to overexpress a mutant protein in a generic immortalized cell line, and then see the impact on cellular physiology. We took a different strategy by first engineering the mutation into human stem cells and then differentiating those cells into human neurons,” said Anjon Audhya professor of biomolecular chemistry and senior author on the study. “The major implication of this work is that we found a result you could never identify using a standard cell line.”
Audhya and his team first used CRISPR-mediated gene editing in induced pluripotent stem cells (iPSCs) to introduce a TFG mutation found in hereditary spastic paraplegia patients. Then, they differentiated the stem cells to develop into cortical neurons, the same type of neurons affected in these patients.
Read more of this story on the School of Medicine and Public Health website at the link below.
Recent IPiB graduate Keren Turton has received a 2018 Wisconsin Initiative for Science Literacy (WISL) Award for Communicating Ph.D. Research to the Public for including a chapter in her thesis to describe her research to non-science audiences.
The chapter, called “How do cells of the immune system change shape and travel to sites where needed? Leveraging proteomics data to investigate eosinophil morphology” appeared in her thesis titled “Case studies of cryptic proteins contributing to shape change in eosinophils.”
Eosinophils are a type of white blood cell that helps the body fight disease. They are part of the first line of general defense against infections, before things like T cells and antibodies join the fray. Eosinophils are also involved in conditions like asthma when they react to allergens. For her Ph.D. research, Turton, from the lab of Professor Deane Mosher, studied three proteins involved in how eosinophils change their shape to release toxic granule proteins to fight off invaders. Little was known about these proteins and her investigation began to piece together their importance in this essential process. The Mosher Lab is also affiliated with the UW–Madison Department of Medicine and is able to study cells from the blood of human donors.
“I feel that it is in keeping with the Wisconsin Idea to make research findings intelligible and meaningful to anyone who might be interested,” Turton says. “It was educational to work with the WISL editors to write this chapter.”
In 2010, WISL Director Bassam Shakhashiri started a program to encourage Ph.D. students in the chemical sciences to include a thesis chapter geared at a general audience and pledged a cash award from the organization for each successfully completed chapter. The goal of the chapters is to explain the candidate's scholarly research and its significance to a wider audience that includes family members, friends, civic groups, newspaper reporters, state legislators, and members of the U.S. Congress.
Numerous other students in IPiB or in faculty labs have received the award in the past. Thiago Santos of the Weibel Lab, Ananya Ray-Soni of the Landick Lab, and Emily Wilkerson of the Coon Lab received the award in 2017. Ambalika Sagarika Khadria from the Senes Lab received the award in 2015, as did Jason Russell of the Coon Lab in 2012.
Jason Cantor could describe himself as an engineer, biologist and biochemist, but don’t try to put his expertise into one box.
Cantor, a scientist exploring the environmental influences on cancer cell metabolism, is launching a new lab in the Metabolism Theme at the Morgridge Institute for Research and joining the University of Wisconsin-Madison departments of biochemistry and biomedical engineering this August 2018. By joining Biochemistry, he will be a faculty member in the Integrated Program in Biochemistry.
“I have this half engineering, half fundamental biology background, and it’s a bit difficult to fit cookie-cutter style into one traditional department or one theme,” Cantor says. “Morgridge and UW-Madison embrace my hybrid training and accept that I’m trying to mix and match and merge these disciplines together in my work.”
Cantor earned his bachelor’s degree in chemical engineering at Cornell University, and it was about halfway through his undergraduate career that he realized the engineering mindset could also be applied to biological questions. He went on to do doctoral work at the University of Texas at Austin where he came up with new strategies to engineer enzymes for cancer treatment.
Read more about Cantor and his research at the link below.
The University of Wisconsin–Madison campus is saying goodbye to a beloved natural landmark. An elm tree that has stood for more than 100 years fell victim to Dutch elm disease and is in the process of being removed from the Hector F. DeLuca (HFD) Biochemical Sciences Complex by UW–Madison grounds staff.
The tree – often known informally as Elmer – has a rich past with the Department of Biochemistry and surrounding departments in the College of Agricultural and Life Sciences (CALS), such as the Department of Horticulture. The HFD Biochemcial Sciences Complex also houses the Department of Biomolecular Chemistry, the other department, along with Biochemistry, that hosts IPiB. Thousands of students who have taken biochemistry courses or frequented that area of campus have gazed up at the old elm or enjoyed breaks in the shade it provided.
Many staff members and scientists on the upper floors of labs or offices overlooking Elmer have spent decades watching the seasons through the tree – leaves falling in autumn, snow coating its sturdy branches, leaves returning in spring. They’ve watched birds come and go, including famed campus hawks, and some students say finches, perched among Elmer’s limbs, watched them work in lab.
Read more about Elmer at the link below.
The Integrated Program in Biochemistry (IPiB) Student Faculty Liaison Committee (SFLC) is happy to announce that registration for the 2018 IPiB Retreat is now open.
The event will be held from 8:30 a.m. to 7 p.m. on Friday, Sept. 7 at the Discovery Building. Registration will close at 11:59 p.m. on Wednesday, Aug. 29.
If you would like to attend, please use this link to register
To complete the form, please log into Google using your UW–Madison NetID. This is to avoid duplicate registrations and help us keep track of everyone registered for the event. If you have any difficulty accessing the form, please email firstname.lastname@example.org.
The retreat is open to all members of the IPiB community — the Department of Biochemistry and Department of Biomolecular Chemistry. The day will feature twelve formal 20-minute talks from students, faculty, and a guest representative from Thermo Fisher, as well as two one-hour poster sessions. Research talks will span 15 minutes with 5 minutes for questions and discussion.
This year we are pleased to announce that we will be joined by alumni from IPiB, who will be serving as poster judges during the poster sessions. Keep an eye out for them at the retreat. They can be a great resource for learning what it's like to secure a job after a Ph.D.
A plated lunch will be provided to those who register accordingly. The day will conclude with a reception where beverages and hors d'oeuvres will be served. Please note that light refreshments will be provided that morning, but this is not intended to replace breakfast; we recommend breakfasting before arriving.
If you have any changes to your registration form or to your poster title/authors (if you choose to present a poster), please let us know by Friday, Aug. 31 at 4 p.m. Beyond this time, we will not be able to make changes to the program or lunch preferences. Please let us know if you have any questions or concerns.
Drs. Elizabeth Wright, Jason Cantor, Feyza Engin, Christina Hull, and Samuel Butcher
John Cowgill, on behalf of Dr. Baron Chanda
Sarah Hansen, on behalf of Dr. Aaron Hoskins
Nathan Thomas, on behalf of Dr. Katherine Henzler-Wildman
Siddhant Jain, on behalf of Dr. Peter Lewis
Anji Trujillo, on behalf of Dr. Joshua Coon
Samantha Anderson, on behalf of Dr. Alessandro Senes
Ms. Blanca Carbajal-Gonzalez, on behalf of Thermo Fisher
Sometimes cancer development is not just about a cell having mutations in its DNA, but about when and how those mutations change the cell’s behavior.
IPiB faculty member Peter Lewis, who is at the Wisconsin Institute for Discovery, is a member of the UW Carbone Cancer Center and studies how these behavioral changes can lead to cells becoming cancer – and how clinicians and researchers can take advantage of these changes to more effectively target cancers.
In one aspect of his research, Lewis focuses on how genes are turned on and off during embryonic development, and how misregulation in those genes can lead to some childhood cancers.
“In most adult cancers, tumors likely arise from the accumulation of mutations to tumor-suppressing and promoting genes over many years, and in the right context those mutations can lead to cancers,” Lewis said. “But of course children don’t have decades to accumulate mutations, so how do children get tumors early?”
To read more about Lewis's research on cancer, see the link below.
Metabolism is referred to as the “chemistry of life” and any dysfunction in its various pathways can greatly affect human health. A new scientific meeting hosted by the Morgridge Institute for Research will focus on the underlying mechanisms of metabolic diseases and innovations in the tools used to study them.
The Frontiers in Metabolism – Mechanisms of Metabolic Diseases meeting will take place Sept. 17-19, 2018, at the Discovery Building in Madison, Wis. Biochemistry professor Dave Pagliarini, who is the director of the Metabolism Theme at the Morgridge Institute, is the meeting organizer.
Pagliarini says the meeting will bring together a diverse group of leaders who investigate the basic mechanistic underpinnings of metabolic disorders and pioneer new approaches for probing and quantifying metabolic processes. The broad swath of topics will span cancer metabolism to lipid dysregulation to mitochondrial signaling.
“We have a vibrant, growing metabolism community in Madison, and the Morgridge Institute and UW–Madison are emerging leaders in this field,” Pagliarini says. “It’s a place that greatly values this area of research and is heavily investing in its future.”
Researchers from around the world — 25 international leaders in total — will be presenting in sessions regarding:
Several faculty members in the Integrated Program in Biochemistry (IPiB) will be presenting their work as part of the meeting. IPiB is the joint graduate program as the Department of Biochemistry and the Department of Biomolecular Chemistry.
UW–Madison biochemistry professor Alan Attie, an expert on the genetics of metabolic diseases like diabetes, will be presenting his work in a talk titled “Genetics and Genomics of Type 2 Diabetes.” Biochemistry Emeritus Professor Dave Nelson will be presenting a special session on the university’s history of studying metabolism.
Advances in technology are bringing new insights into metabolic processes and revealing that there are more gaps in knowledge than previously thought, Pagliarini says.
“There’s also been an important realization that metabolism isn’t merely a readout of what's otherwise happening in the body, but instead is a fundamental driver of diverse biological processes,” Pagliarini says. “Metabolites are increasingly appreciated as robust signaling molecules, demanding that we arrive at a deeper appreciation of how and when they are produced, and where the go.”
To register and learn more: https://morgridge.org/research/metabolism/frontiers-in-metabolism/
This meeting is conducted by the Morgridge Institute for Research in partnership with UW–Madison and the Lausanne Integrative Metabolism and Nutrition Alliance (LIMNA).
The University of Wisconsin–Madison Integrated Program in Biochemistry (IPiB) — the joint graduate program of the departments of Biochemistry and Biomolecular Chemistry — has removed the GRE as a requirement for admission.
“After much discussion, the Integrated Program in Biochemistry is no longer going to require the GRE as a component of our admissions requirements,” says biochemistry professor Ivan Rayment, the chair of the IPiB Steering Committee. “We are joining the growing number of programs that recognize that the GRE does not correlate with the success of a graduate student. Indeed, it places some students at a disadvantage.”
All other admissions requirements remain the same. The change is effective immediately for students applying to join the program in the fall of 2019. For more information see the program’s About Us page.
Heart disease is the number one killer in the United States, and high triglyceride levels in the blood are cited as just one of several risk factors. Millions of lipid panels, blood tests that look at cholesterol levels as well as triglycerides, are performed in clinics each year.
Two new Morgridge Institute for Research studies suggest the current tests, which measure the abundance of lipid classes, are insufficient. Rather, lipids identified and studied at the individual species level—instead of grouped in classes—may be better signatures of metabolic health.
Lipids, or fats, are incredibly important to human health, yet one of the hardest biomolecules to study. Harnessing advances in mass spectrometry technology, Morgridge scientists measured almost 150 lipid species in the blood and liver of mice and identified some that can act as signatures of healthy or unhealthy metabolic states.
For patients getting a lipid panel—something the American Heart Association suggests for everyone over the age of 20—results will include a reference to triglyceride levels. These tests look at triglycerides in bulk, as a group, and measure how much is in the blood.
But Molly McDevitt, a graduate student in biochemistry professor Dave Pagliarini’s lab at Morgridge and co-first author on the papers, says looking at individual species of triglycerides provides a much more accurate picture. McDevitt is a student in the Integrated Program in Biochemistry (IPiB), the joint graduate program of the Department of Biochemistry and Department of Biomolecular Chemistry.
Read more about this research at the link below.
Biochemistry professor Mike Sussman, longtime director of the UW-Madison Biotechnology Center, has announced that he is stepping down from that position to serve as director of the Genome Center of Wisconsin, located within the Biotechnology Center.
"With DNA analysis now permeating all aspects of research, our economy and our lives, aggressive attention to changes in the technology and its applications on campus is needed to ensure that we stay at the forefront of genomic sciences," Sussman says. "Moving forward, together with the excellent faculty already present in the center and the new ones that we hope to recruit in the future, I would like to help us attain a national and international leadership position that a powerhouse research institution like UW-Madison deserves."
Sussman was recently awarded UW2020 funding to acquire an Illumina NovaSeq DNA sequencer on behalf of the Biotechnology Center. The sequencer is expected to help boost UW-Madison's DNA sequencing capabilities.
Read more about Mike and his new position at the link below.
On a rainy day last fall, chemist Scott Wildman left his office on the UW–Madison campus and drove to a retirement community on the city’s west side to bring 40 years of scientific work out of the dark.
His trip brought him to the home of Laurens “Andy” Anderson, emeritus professor of biochemistry. There, packed away in a closet, Wildman found a cache of dark green boxes holding nearly 800 meticulously organized vials of purified chemicals, each one stoppered with real cork and labeled with intricate handwriting. Many of the vials boasted a tiny drawing of a structural chemical formula for identifying the white or sometimes colored powders inside. Wildman wrapped the glass treasures in protective plastic and chaperoned them to their new home — and new purpose — at the UW Carbone Cancer Center’s Drug Development Core (DCC).
The so-called “green box collection” contains the physical legacy of Anderson’s career with the Department of Biochemistry. While cleaning his house one day, it occurred to him that the molecules could be useful for carbohydrate chemistry researchers, so he approached the department about donating the collection. In the end, it was decided they would have the biggest impact at the DDC, where they can serve as a resource for the next generation of scientists looking to discover new drugs for treating diseases.
In the complicated process of drug discovery, scientists screen large collections of molecules — called libraries — in search of a range of properties that indicate they could be used as antibiotic, antifungal, or anticancer agents, or even neurological drugs. A molecule with one or more of these properties is called a “hit” and can be further investigated as a possible drug. A hit gives researchers an important starting point for deeper research in drug design. But when compared to the types of molecules synthesized for drug discovery today, the old-school way in which Anderson’s molecules were made gives them some unique properties, so they are taking on new significance in their present home.
“Learning about him and what he did while he was here 20 years before I was born has been very interesting, especially because I am now one of the keepers of the fruits of that labor,” says Wildman, who is an associate scientist at the DDC. “As scientists, we have a finite period of time in which to make an impact. But in this case, we just gave his impact a whole new lease on life. In a way, he can start over, even without being in the lab.”
Read the rest of this feature story at the link below.
The human gut is teeming with microbes, each interacting with one another in a mind-boggling network of positive and negative exchanges. Some produce substances that serve as food for other microbes, while others produce toxins – antibiotics – that kill their neighbors.
Scientists have been challenged trying to understand how this collection of gut microbes – known as the microbiome – is formed, how it changes over time and how it is affected by disturbances like antibiotics used to treat illnesses. A new study from Ophelia Venturelli, a biochemistry professor at the University of Wisconsin–Madison, and her collaborators at the University of California, Berkeley, may help alleviate some of that difficulty.
Published on June 21 in Molecular Systems Biology, the study provides a platform for predicting how microbial gut communities work and represents a first step toward understanding how to manipulate the properties of the gut ecosystem. This could allow scientists to, for example, design a probiotic that persists in the gut or tailor a diet to positively influence human health.
“We know very little about the ecological interactions of the gut microbiome,” Venturelli says. “Many studies have focused on cataloging all of the microbes present, which is very useful, but we wanted to try to understand the rules governing their assembly into communities, how stability is achieved, and how they respond to perturbations as well.”
Read more about this research at the press release below.
The Integrated Program in Biochemistry (IPiB) is excited to announce its 2018 awards that celebrate teaching and mentoring. The awards were given out at the IPiB Summer Reception on Friday, June 8.
Kasia Dubiel, a graduate student in the Keck Lab, and Sarah Hansen, a graduate student in the Hoskins Lab, are recipients of the 2018 Denton Award for Graduate Student Excellence in Teaching and Mentoring. Kate Henderson, a postdoctoral scholar in the Record Lab, received the 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.
“Earning the Denton Award serves as encouragement to continue to gather skills so that I can help inspire the next generation of scientists,” Dubiel says. “I have had the opportunity to work with students in a wide range of environments and from these experiences I have learned that each student has a different view point and unique needs. I hope to pursue a career in teaching at a primarily undergraduate university. I believe this award will help show that I am passionate about teaching and mentoring.”
“I am very happy to receive this award because I have a passion for working with undergraduate students in the classroom and lab,” Hansen says. “I’ve been a graduate teaching assistant for seven semesters here at UW–Madison and have mentored four undergraduate students in the Hoskins Lab. My career goal is to teach and lead a research lab at a primarily undergraduate institution. This award will help me be competitive in this job search as well as in my future search for a tenure-track position.”
The Leirmo Award recognizes graduate or postdoctoral students who exemplify the spirit of Sigrid Leirmo. Sigrid 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.
“It’s an honor just to be nominated for the Leirmo Award, let alone be chosen,” Henderson says. “I absolutely love the research we do in Professor Tom Record’s lab and truly enjoy teaching and helping others. Tom and my lab mates are simply fantastic, and I’m thankful for the opportunity work with all of them.”
IPiB’s Student Faculty Liaison Committee (SFLC) also announced its newest round of officers at the reception.
University of Wisconsin–Madison biochemistry assistant professor Philip Romero and neuroscience assistant professor Ari Rosenberg are the recipients of 2018 Shaw Scientist Awards from the Greater Milwaukee Foundation. The awards come with $200,000 in seed funding to support innovative research approaches and the career development of young investigators.
Romero’s work uses new technologies to understand how proteins work and how to design new ones. Using computational methods, he is able to analyze large amounts of data that help him investigate the relationships between protein sequence, structure and function. This allows him to pull out sequences that lead to useful properties and design new proteins with desired functions.
His research has many implications because the proteins can be engineered to have specific functions, such as in bioenergy, chemical production and human health. Projects are investigating how to help convert biomass to fuel and develop cancer therapeutics. Along with these applications, the group also focuses on developing new protein engineering methods.
“The Shaw Award will enable us to pursue new high-risk projects that wouldn’t be supported by the standard funding agencies,” Romero says. “We’re excited to think longer term about where our field is headed, and how we can make a large impact on engineering biological systems.”
Romero joined the department in July 2016. He earned his Ph.D. at the California Institute of Technology. At UW–Madison, he is also affiliated with the Department of Chemical and Biological Engineering.
Romero joins a decades-long line of Department of Biochemistry faculty members in receiving the award. In 2017, assistant professor Ophelia Venturelli received a Shaw Award and the year before that, so did assistant professor Vatsan Raman, with many more before them.
Read more about Romero and his work at the link below.
The complexity of life makes it difficult to study. In biochemistry, there are often just too many processes and reactions taking place in a cell for humans to wrap their heads around. What helps biochemists make sense of it all?
Cue computational biology and biochemistry. Computation has been used in biology and biochemistry since the dawn of computers and is used today by many researchers in the University of Wisconsin–Madison Department of Biochemistry.
“The main reason people use computers in biochemistry is because biological systems are composed of thousands of interacting components and predicting the behaviors of these complex systems becomes way too difficult to grasp within your brain,” says assistant professor Philip Romero, who uses computation in his lab in the Department of Biochemistry. “Computers are much better at handling large amounts of information.”
Computational biochemistry can be defined as the use of computational methods and simulations to predict and understand various biological processes. Scientists are able to use computers to make sense of large amounts of data and use that data to make predictions.
Read the rest of this story on the link below.
Particular fungi have always been hard to treat, but, increasingly, some that were once easy to manage are becoming ever more difficult to tackle.
So, the race is on to design antifungal drugs that can circumnavigate this medical conundrum. One new and surprising contender is nylon.
Over recent years, researchers from the University of Wisconsin-Madison have been investigating nylon polymers' ability to fight fungi.
The authors of the new study, which was led by Nancy Keller, wanted to locate a compound that would interact with the fungus in the same way that peptides in the immune system do.
Peptides are short chains of amino acids, so the team looked at other short chain molecules, and they settled on nylon.
Integrated Program in Biochemistry (IPiB) faculty members Anjon Audhya, Baron Chanda, and Michael Sussman are the principal investigators on recently awarded UW2020 Round 4 projects. Numerous other IPiB faculty members are serving as co-principal investigators or collaborators on theirs and UW2020 other projects.
The awards represent the fourth round of UW2020 funded projects since the initiative was launched by the Office of the Vice Chancellor for Research and Graduate Education. The goal of UW2020 is to stimulate and support cutting edge, highly innovative, and groundbreaking research at the University of Wisconsin–Madison and the acquisition of shared instruments or equipment that will open new avenues for innovative and significant research. UW2020 is underwritten by the Wisconsin Alumni Research Foundation (WARF) with combined funding from other sources.
IPiB is the joint graduate program of the Department of Biochemistry and the Department of Biomolecular Chemistry. A summary of the faculty from both departments on the fourth round of UW2020 projects is below.
Biochemistry professor Robert Landick has been elected to the American Academy of Arts and Sciences, one of three faculty from the University of Wisconsin–Madison that make up the 2018 class of members.
Founded in 1780, the American Academy honors leaders in science, the arts, business and American life. Other members elected this year include former president Barack Obama, Supreme Court Justice Sonia Sotomayor and actor Tom Hanks. Alexander Hamilton, Charles Darwin and Martin Luther King Jr. are among those previously recognized by the Academy.
“It's both humbling and an exceptional honor to be included among such an illustrious group of people,” Landick says. “The real accomplishment, though, belongs to the students and researchers who have worked with me over the years to figure out mechanisms of gene expression. Without their spectacular accomplishments, there would be little for the American Academy of Arts and Sciences to recognize.”
Read more about Landick's award and research at the link below.
The award is supported by an educational development fund created to honor CALS Dean Glenn S. Pound upon his retirement in 1979. It is given to honor an outstanding, early-career CALS research scientist and to promote continued excellence in research.
“It is a great honor to be recognized with this award for young investigators,” Hoskins says. “A lot of credit for this goes to the wonderful students and scientists who have worked in my laboratory as well as my mentors and collaborators here at UW–Madison.”
Read the rest of this story at the link below.
The RNA transcripts of virtually all human genes must be processed by one cellular machine: the spliceosome. The mind-boggling array of proteins and RNAs that make up the spliceosome allow it to control how genes are expressed. Many researchers are interested in the dynamic interplay between these components of the spliceosome and how they evolved, likely from a parasitic RNA that invaded eukaryotic cells at around the same time eukaryotic and bacterial cells became distinct from one another approximately two billion years ago.
The spliceosome is also a reason that complex organisms like animals and humans can exist. Through splicing, the cell is able to get several different transcripts out of just one gene, meaning a more diverse array of proteins can be made from a relatively small amount of DNA. This creates evolutionary diversity much more rapidly than other mechanisms, allowing complex organisms to evolve more quickly.
Researchers chip away at the spliceosome and its dynamic components by several approaches. One approach, facilitated by recent advances in cryo-electron microscopy (cryo-EM), involves determining three-dimensional structures of fully assembled spliceosomes. Another approach involves studying smaller sub-complexes, which allows more detailed views of protein-RNA interactions and also provides tractable in vitro systems for testing specific hypotheses about function.
The laboratories of biochemistry professor Sam Butcher and biomolecular chemistry professor David Brow at the University of Wisconsin–Madison recently took the latter approach to hone in on a protein called Prp24 and a seven-protein ring called the Lsm2-8, both of which recruit a critical RNA called U6 into spliceosomes. In their newest study published in Nature Communications on May 1, 2018 they reported for the first time the structure of these eight proteins interacting with the U6 RNA.
Read the rest of this story at the link bleow.
People who eat a high-fat, high-sugar “Western” diet typically exhibit physiological changes associated with type 2 diabetes. However, not everyone responds the same way to the Western diet; genetics plays a strong role in determining one’s susceptibility to develop diabetes.
In type 2 diabetes, islet cells in the pancreas can’t produce enough insulin and other hormones that control blood glucose (sugar). If left uncontrolled, this leads to dangerously high levels of glucose in the blood that may result in tissue and organ damage and early death.
So, finding genes that promote insulin secretion could be a valuable source of treatment strategies for type 2 diabetes. And that’s just what researchers in the lab of biochemistry professor Alan Attie at the University of Wisconsin–Madison and collaborators at The Jackson Laboratory discovered when comparing the genetic variations associated with type 2 diabetes in humans with those of a special, genetically diverse mouse population fed on a diet high in fat and sugar.
The work, published in the journal Genetics, is the first to show how a Western-style diet alters the regulation of genes in the pancreatic islets of mice. It also demonstrates that the Diversity Outbred (DO) mouse population can stand in for humanity in laboratory studies of genetic risk variants found in human genome-wide association mapping.
This press release was written by Joyce Dall'Acqua Peterson of The Jackson Laboratory and was originally published on their news site.
To read more about this work, see the link below.
Three Integrated Program in Biochemistry (IPiB) students are recipients of 2018 National Science Foundation Graduate Research Fellowship awards.
The NSF Graduate Research Fellowship Program recruits high-potential scientists and engineers and supports their graduate research training in STEM fields. Fellows receive three years of financial support through a $34,000 annual stipend and $12,000 education allowance. More than 12,000 students from across the United States applied, with 2,000 receiving awards.
To see a list of all UW–Madison students who received NSF fellowships, see the link below.
The University of Wisconsin–Madison Department of Biochemistry will welcome Elizabeth Wright in July as a faculty member and director of the department’s newly established cryo-electron microscopy (cryo-EM) facility.
Wright is an expert in cryo-EM, a technique able to obtain atomic or near-atomic level resolution images of biological molecules by imaging with electrons. It is a burgeoning technology that can help UW–Madison researchers make significant new contributions to many areas of structural biology, including enzymology, virology, cell biology, and medicine.
“I am very excited to be joining the department to develop this technology at UW–Madison,” says Wright, who will also be an affiliate of the Morgridge Institute for Research. “In the fields of fundamental biochemistry and structural biology, the department is one of the strongest in the country. I was drawn to UW–Madison by the vision the department has for this facility. We are not just thinking about the present but about the next decade and beyond by establishing an advanced cryo-EM resource and building a community to push forward scientific understanding across many biological research areas by using cryo-EM.”
To read more about Wright and her work, see the link below.
Think of neurons like cities, which need to be able to transport goods and services throughout themselves. In cities this is done on highways by cargo trucks. In neurons it’s done on microtubules by motor proteins. To direct traffic, cities have signals like lights and road signs, while in neurons these signals are thought to come in the form of post-translational modifications.
These modifications on the microtubules are hypothesized to ensure that cargo in these neurons gets to the right place at the right time. The lab of assistant professor Jill Wildonger at the University of Wisconsin–Madison Department of Biochemistry studies these modifications and their impact on the transport of cargo. New research from the Wildonger Lab led by postdoctoral scholar Brian Jenkins investigated a particular post-translational modification, using a new approach to find that researchers’ assumptions about the modification might not have been as correct as once thought. Their research was recently on the cover of the Journal of Cell Science.
Read about this work at the link below.
University of Wisconsin–Madison graduate programs in biochemistry are once again ranked among the nation’s best in the 2019 edition of U.S. News & World Report’s “Best Graduate Schools.” The university ranks 8th in the nation in the biochemistry specialty category under chemistry.
The UW–Madison Integrated Program in Biochemistry (IPiB) is the joint graduate program of the Department of Biochemistry in the College of Agricultural and Life Sciences and the Department of Biomolecular Chemistry in the School of Medicine and Public Health. The program is home to around 100 graduate students and 52 world-class faculty pursuing cutting-edge research in all areas of biochemistry.
“It is great to see this recognition of our program,” says biochemistry professor Ivan Rayment, director of graduate studies and the chair of IPiB’s steering committee. “It is testament to the quality of our students and faculty and their commitment to research and training. You will find our graduates all over the world in a host of professional activities. Ultimately they are the best measure of our success.”
IPiB faculty make contributions to biology and chemistry, researching a diverse array of biological processes including plant flowering; protein structure; membrane trafficking and transport; vitamin and hormone action; signal transduction mechanisms; RNA processing; DNA replication, recombination and transcription; cell division and differentiation; viral replication and transcription; and animal development.
“The fact that so many of the graduate programs at UW–Madison are ranked is a testament to our senior leadership, who foster an environment of academic excellence; our outstanding faculty and staff, who lead cutting-edge research programs; and our creative students, who bring curiosity and vibrancy to address the most important questions that society faces today,” says William Karpus, dean of UW–Madison’s Graduate School.
This story was adapted from a press release by Käri Knutson of University Communications that was originally published on the UW–Madison news site.
Biochemistry professor Richard Amasino has been awarded a Wisconsin Alumni Research Foundation (WARF) Named Professorship. 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.
“It's an honor to be recognized with this award,” Amasino says. “Because it’s a university-wide award it is even more humbling to receive it given all of the great faculty at this outstanding university.”
Amasino has a long history of extraordinary research, teaching, and service to the university, state of Wisconsin, and the worldwide scientific community. His research as a plant biochemist has combined biochemistry, molecular biology, and genetic approaches to investigate the molecular basis of how plants sense the seasonal cues of changing day-length and temperature and use these cues to flower at the appropriate time of year. He also participates in the research program of the Department of Energy-funded Great Lakes Bioenergy Research Center (GLBRC), studying how to increase yield of grasses used for biomass production, and for the first 10 years of the GLBRC served on the management team that oversaw the research portfolio.
Read more about Amasino's work at the link below.
Proteins are an impressive bunch. Starting with amino acids as their basic building blocks, these complex molecules fold into intricate 3D structures and control just about every biological process that keeps us alive.
Phil Romero wants to understand how proteins accomplish that job so that he can eventually apply their power to important problems in medicine, agriculture, chemistry and bioenergy.
“Describing how proteins perform a vast array of biological functions is tremendously challenging for two reasons,” says Romero, an assistant professor of biochemistry at the University of Wisconsin-Madison. “One, they are highly dynamic molecules that constantly change their shape; and two, their properties emerge from the collective behavior of many interacting components.”
So instead of relying on a bottom-up approach that uses the laws of physics to predict biological behavior, Romero, who has an affiliate appointment with the Department of Chemical and Biological Engineering, is betting on the top-down approach: learning how protein sequence translates into function by analyzing massive data sets.
“Our ability to generate, store and analyze biological data has exploded during the last decade,” Romero says. “That’s why data-driven approaches are playing an increasingly important role in biological discovery and engineering.”
To read more about Romero's work, see the link below.
The Department of Biochemistry and Department of Biomolecular Chemistry invite you to the 39th annual Steenbock Symposium on May 29-June 2, 2018. Registration is now open, and early discounted registration ends April 15.
This year’s symposium, entitled “Iron-Sulfur Proteins—Biogenesis, Regulation and Function,” will bring together scientists from across UW–Madison, the country, and the globe to discuss this unique class of proteins.
Patricia Kiley, professor and chair of Biomolecular Chemistry, and John Markley, biochemistry professor and director of the National Magnetic Resonance Facility at Madison (NMRFAM), are serving as this year’s organizers.
“This is really the only meeting on this class of proteins out there,” Kiley says. “We have held a meeting on iron-sulfur proteins in different locations in the United States and Europe for several years now — this year under the banner of Steenbock Symposium at UW–Madison — and it’s a unique and exciting event for those who work in this field. This is actually the second time that UW–Madison has hosted the meeting and reflects our rich history of investigations of Fe-S proteins beginning with Helmut Beinert, who pioneered spectroscopic methods that enabled their study.”
Twenty speakers are slotted for the event, and an additional 20 will be promoted from submitted abstracts. For more information on the symposium and to register, go to this link: https://biochem.wisc.edu/symposia/steenbock/39th.
The Steenbock Symposium is supported by the Steenbock Endowment to honor Professor Harry Steenbock’s work as a distinguished Biochemistry faculty member, whose contributions spanned many areas of nutrition and biochemistry.
Integrated Program in Biochemistry (IPiB) graduate student Mark Klein and IPiB faculty member Peter Lewis took to the ice during the Wisconsin Badgers vs. Penn State Nittany Lions hockey game on Saturday, Jan. 27 to receive awards to help fund their cancer research.
Klein is in the lab of biomolecular chemistry professor John Denu and Lewis is an assistant professor of biomolecular chemistry. Both labs are part of the Wisconsin Institute for Discovery and affiliated with the University of Wisconsin Carbone Cancer Center.
The awards were sponsored by The Ride, a fundraising event hosted by the Carbone Cancer Center. In its second year, it drew more than 1,250 bike riders to the roads of eastern Dane County in September of 2017 to raise money for cancer research. One hundred percent of the $352,000 raised went back to cancer research at the university in the form of 14 research awards. Awardees were invited onto the ice to be recognized.
“It was really exciting to win this award and get acknowledged at the hockey game,” says Klein, who has already signed up to participate in the next Ride in September 2018. “We spend a lot of time hunkered down in our labs but getting this award helps us step back and see that our work is novel and meaningful. It was great to have our work on cancer be recognized this way in front of an entire hockey stadium.”
Klein studies a particular protein that has been implicated in many forms of cancer. Research shows that in ovarian cancer cells, the protein is deficient but when it’s overexpressed in the cells, the protein can prevent cancer. His next step is seeing if he can find a synthetic molecule that can be used to mimic this overexpression and hence possibly help with preventing cancer. However, he says this work also provides an important understanding of the basic mechanisms and functions behind this protein and any synthetic compounds he studies.
“Mark’s research is focused on understanding how a tumor suppressor enzyme called SIRT6 can be activated by endogenous molecules and on developing a synthetic compound that could function similarly,” Denu says. “Mark has a unique skill of fostering collaborations with other researchers on this campus, including Professor Weiping Tang who is synthesizing potential compounds.”
Lewis studies how protein molecules that “spool” the DNA in cells can regulate cellular function and influence how cancer cells grow and respond to treatment. These protein molecules called histones keep the DNA wrapped up in an inaccessible ‘off’ state and releases it when certain genes are needed by the cell. Research shows that specific mutations to the histones are drivers of certain types of pediatric cancers in humans.
The Lewis Lab is trying to figure out how and why this happens. They’ve found that specific “oncohistone” mutations drive some pediatric cancers by transforming histone proteins into potent inhibitors of gene regulatory processes. Their work explores fundamental questions in biology but also clinically relevant ones.
“It was a great surprise and honor to be selected as a Ride Scholar,” says Lewis, who will also participate in the 2018 Ride. “You see the huge amount of work that goes into organizing events like this and the effort all the bikers put in. It’s so great to know their hard work is going directly to cancer research. It’s very humbling to have received an award.”
A new chair at the Morgridge Institute for Research takes aim at osteoarthritis, a debilitating and painful disease that affects more than 27 million Americans. Currently, osteoarthritis is largely treated with palliative care to help patients alleviate their symptoms.
“I think because arthritis is life-altering, not life-threatening, it doesn’t attract the research dollars required to find a solution,” says Peggy Pyle. “It’s time to change that!”
And Peggy knows. Since she was diagnosed with osteoarthritis, she’s been shocked at the lack of research into prevention and irradication of the disease. Treatment options are limited to medications like NSAIDs or joint replacement with no way to stop osteoarthritis’s progression.
Peggy’s commitment to battling the disease has only increased since her husband Tom was diagnosed with arthritis and underwent a hip replacement.
Now with support from the Thomas and Margaret Pyle Chair, which honors Tom’s longtime service on the Wisconsin Alumni Research Foundation Board of Trustees, there’s a new commitment to tackling osteoarthritis at the University of Wisconsin-Madison.
Joshua Coon, a professor of chemistry and biomolecular chemistry and Morgridge Institute affiliate, is the inaugural recipient of the chair. The Coon Lab specializes in creating and applying high-powered must-have technologies that help scientists answer biomedical questions with applications for human health.
“We hope to accelerate technology and accelerate all areas of biological research,” he says. “I really consider our team ‘technologists.’ We are building and developing new tools to measure biomolecules.”
Coon is a renowned innovator of mass spectrometry technology with more than 100 research collaborations across UW-Madison and the world, including the Morgridge Metabolism Initiative directed by Dave Pagliarini, the Great Lakes Bioenergy Research Center and ongoing research supported by the National Institutes of Health to identify molecular markers of Alzheimer’s disease.
For more of this story, see the link below.
Science is a visual enterprise. Scientific imagery created with microscopes, telescopes, cameras and scanners makes even parts of the world that our eyes can’t perceive visible, understandable and often beautiful.
To recognize the visual and exploratory value of scientific imagery, the 8th annual Cool Science Image Contest is soliciting the best images from members of the University of Wisconsin–Madison community.
Sponsored by Promega Corp. with additional support from the UW–Madison Arts Institute and DoIT Digital Publishing and Printing Services, the Cool Science Image Contest offers an opportunity to show off compelling science images made by students, staff or faculty.
To read more about the contest rules and how to submit an entry see the link below.
“It’s exciting to be invited to be part of this group, but what’s more exciting is that the rest of the researchers in this group are phenomenal,” Raman says. “I know some of them personally and they really cover the entire spectrum of research and represent the next big things in biochemistry. I’m happy to be a part of an amazing group of people that I respect.”
For the special issue, he wrote a perspective piece on understanding and designing allosteric proteins, a major part of his research lab. These proteins are mysterious in how they function but play major roles in cellular function, such as signaling, gene regulation, and transport.
Read more about Raman and his research at the link below.
The phrase seeing is believing doesn’t just apply to supernatural phenomenon; biochemists often say the same thing when imaging proteins or other molecules for the first time.
Imaging is a powerful tool in many biochemists’ repertoire. The Department of Biochemistry at the University of Wisconsin–Madison is home to a large collection of equipment and facilities, including the Biochemistry Optical Core (BOC) and upcoming UW–Madison cryo-electron microscopy (cryo-EM) facility, that allows scientists to pursue their many imaging endeavors. The department’s goal is simple: to provide faculty, researchers, and students from the department and all across campus with access to these resources and the training to operate them, even if they’ve never used them before.
Elle Kielar-Grevstad, the director of the BOC and supervisor to the department’s core facility staff, serves to promote and facilitate the department’s mission by helping researchers with their light and fluorescent microscopy needs.
“Imaging is really capturing a state of being,” she says. “That can mean a lot of things depending on what resolution you require. Whether you are looking at a whole animal, a tissue, a single cell, or a single protein, you’re still capturing a state of being, or in many cases multiple states of being. Your research question will determine the resolution requirements and that in turn dictates what type of equipment you need. The great thing about all the core facilities at Biochemistry is that we can likely help you meet your imaging or experimental needs, and if we can’t, it is our job to connect you with others on campus that can.”
Learn more about Biochemistry' imaging capabilities and how students can access these resources at the link below.
Coenzyme Q (CoQ) is a vital cog in the body’s energy-producing machinery, a kind of chemical gateway in the conversion of food into cellular fuel. But six decades removed from its discovery, scientists still can’t describe exactly how and when it is made.
Dave Pagliarini, associate professor of biochemistry and Intergrated Program in Biochemistry faculty member, says the list of unknowns is daunting. How does it migrate around in the cell? How does it get used up and replenished? What genes and proteins are responsible for CoQ dysfunction? Why does its presence decline as people age?
Pagliarini, also director of metabolism at the Morgridge Institute for Research, and his group are dedicated to chipping away at many of these knowledge gaps in CoQ production and in understanding the role of CoQ deficiency in human disease. CoQ deficiencies are implicated in scores of diseases, including liver and lung failures, muscle weakness, deafness and many brain disorders such as Parkinson’s and cerebellar ataxia. The coenzyme is almost exclusively produced within the body and is often very difficult to replenish through nutritional supplements.
Against this backdrop, the Pagliarini lab is developing new tools to shed light on CoQ function, primarily by finding and defining proteins that have a direct link to the chemical. In the past month, Pagliarini’s team has published three collaborative papers that gather multiple layers of information on cells where proteins have been manipulated.
“A fundamental challenge in biology lies in connecting the many ‘orphan’ proteins in our cells with specific biological processes, such as CoQ biosynthesis,” says Pagliarini. “Once we have a handle on their functions, a second challenge is to devise ways to manipulate the activity of these proteins, pharmacologically or otherwise, to control key biological processes and, ultimately, improve health.”
Research published in the journals Cell Systems (Dec. 13), Molecular Cell (Dec. 7) and Cell Chemical Biology (Nov. 29) all reveal new clues to coenzyme Q production and function.
Read about the findings from these three papers at the link below.