News Archive


MicroRNA misregulation in muscular dystrophy

Assistant Professor of Biochemistry, Auinash Kalsotra, and colleagues have discovered the process by which myotonic dystrophy affects activity of the small bits of genetic material called microRNAs in the heart. Cardiovascular dysfunctions are the second leading cause of death in people with this particular type of muscular dystrophy. Their findings were published in the journal Cell Reports on January 9, 2014.

According to Dr. Kalsotra, myotonic dystrophy is a multi-systemic disease that affects about 1 in 8000 people. It occurs because of a change in a gene that is important for muscles. (Specifically, it is a trinucleotide repeat expansion in the dystrophia myotonica-protein kinase gene.) While most myotonic dystrophy research has focused on problems related to types of messenger RNAs produced from our genes by altered RNA splicing, this study demonstrates additional problems with expression of a class of regulatory RNAs known as microRNAs.

Dr. Kalsotra has appointments in both the College of Medicine and the School of Molecular and Cellular Biology at the University of Illinois at Urbana-Champaign.

Read the paper in Cell Reports     
Posted January 24, 2014
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Kalsotra Awarded Nationally Competitive March of Dimes Research Grant

Assistant professor of biochemistry and medical biochemistry, Auinash Kalsotra, has been awarded the Basil O’Conner Starter Scholar Research Award from the March of Dimes. Created in 1973 and named for the first March of Dimes chairman and president, this program provides funding to young investigators to start their own research projects on topics related to the March of Dimes mission. The grant provides $150,000 over a two-year period for research on alternative splicing’s role in Myotonic Dystrophy, a multi-systemic disease that affects about 1 in 8000 people.

Alternative splicing is a key mechanism that produces precise assortment of proteins for each cell type. It is a highly regulated process, which when gone awry results in diseases like myotonic dystrophy type 1 (DM1). DM1 arises due to an unusual mutation where a small DNA segment of the mutated gene is repeated hundreds of times. When the mutated gene is copied into RNA, it gets trapped inside the nucleus and becomes toxic by disrupting function of muscleblind like (Mbnl) family of splicing regulatory factors. Mbnl proteins normally participate in regulation of developmental splicing transitions. Their inactivation in DM1 results in expression of embryonic splicing patterns, which is detrimental to the function of adult tissues.

While the role of Mbnl1 in DM1 skeletal and cardiac muscle pathology is clear, the effects of its loss of activity in the gastro-intestinal and other tissues are poorly understood. Dr. Kalsotra's project aims to characterize Mbnl1 function in the liver by identifying its RNA targets and determining the consequences of its loss on liver physiology and function. These studies will advance our understanding of Mbnl1 function in liver development and provide new insights into DM1 pathophysiology.

The mission of the March of Dimes is to promote healthy pregnancies and to support research that can lead to the prevention of birth defects. Dr. Kalsotra’s research will lead to our understanding of molecular mechanisms that may be responsible for the developmental defects observed in this debilitating disease. Dr. Kalsotra holds appointments in both the College of Medicine and the School of Molecular and Cellular Biology at the University of Illinois at Urbana-Champaign.

Posted February 19, 2014
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Microbial Diversity – A Tribute to the Life and Work of Abigail Salyers

During her 40-year career as a professor of microbiology, Abigail A. Salyers, PhD, revolutionized how we think about the bacteria that live in the human intestinal tract, made major contributions on carbohydrate metabolism and the transfer of antibiotic resistance carried on mobile elements in humans and animals and provided advice and insights on bioterrorism, transgenic plant safety, antibiotic resistance in medicine and agriculture, and more.

The Department of Microbiology is hosting a special symposium in celebration of the life and work of Abigail A. Salyers.

For more information about the exciting lineup of speakers and scientific program, as well as meeting registration, accommodations, and donation opportunities, please visit the symposium website.

The registration deadline is Friday, October 17, 2014.

Salyers Memorial Symposium Website     
Posted June 24, 2014
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Side-chain rotamers make a difference

This influx of cations is the first step in a series of events that culminate in, for example, muscle contraction or neurotransmitter release, and its rate is tightly regulated. Indeed, naturally occurring mutations that slow down or speed up this flow of ions lead to disease.

Previous mutagenesis work from the Grosman lab on the ring of glutamates in the charge-selectivity filter region of the muscle nicotinic receptor led them to propose that the rate at which ions permeate depends not only on the number of these glutamates, but also, on the conformation of their side chains. Because these inferences were made on the basis of electrophysiological observations, however, they decided to test the plausibility of these ideas using molecular simulations, thus taking advantage of the atomic detail and high temporal resolution that only these computational methods can provide. Remarkably, the simulations gave ample credence to all aspects of their proposal and allowed them to gain insight into the effect of specific glutamate rotamers on single-channel conductance.

Read the full article here.     
Posted July 29, 2014
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Dr. Claudio Grosman named Romano Professorial Scholar

Dr. Claudio Grosman has been named a Richard and Margaret Romano Professorial Scholar. The three-year appointment recognizes outstanding research achievement and campus leadership through the College of Liberal Arts and Sciences. Richard and Margaret Romano have generously served and supported the University of Illinois for more than 30 years. In addition to providing annual financial support to the College of Liberal Arts and Sciences, in 2003 the Romanos created the Romano Professorial Scholar Program. This program provides significant support for the research of some of the College's most outstanding faculty members across many disciplines. Dr. Grosman is a Professor of Molecular and Integrative Physiology.

Posted August 06, 2014
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How Heat-Loving Organisms Are Helping Advance Medicine

Read about it at livescience     
Posted August 20, 2014
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A radical reaction utilizes two of the most popular cofactors for tRNA modification

Approximately a quarter of cytoplasmic tRNAs in eukaryotic organisms contain a modified uridine at the wobble position, which plays a crucial role in maintaining the efficiency and fidelity of protein translation. The lack of this modification severely affects translation of several important proteins whose genes use biased codons that require modified tRNAs. Genetic studies indicated that the eukaryotic Elongator complex, which consists of six subunits of Elongator protein (Elp1-Elp6), performs the central step of the modification, but the mechanism was unknown. In humans, defects in the Elongator complex have been linked to several neurological diseases such as familial dysautonomia (FD), rolandic epilepsy (RE), and amyotrophic lateral sclerosis (ALS).

To provide insight into the mechanism of the modification reaction carried out by the Elongator complex, Huang and coworkers first performed bioinformatic analyses and found that only Elp3 (not Elp1-2 and Elp4-6) is present in archaea, which lacks the genes responsible for a distinct tRNA modification found in bacteria. This knowledge, along with the fact that Elp3 possesses a radical SAM and a HAT domain, led the researchers to hypothesize that tRNA wobble uridine modification in archaea is similar to the one found in eukaryota, and only Elp3 is required for catalysis. This hypothesis was subsequently confirmed by their in vitro reconstitution experiment using a recombinant archaeal Elp3 protein.

Huang commented that, among several interesting mechanistic details of the Elp3-catalyzed reaction revealed by additional chromatographic and spectrometric experiments, generating a radical on the methyl group of acetyl-CoA is particularly significant. Acetyl-CoA can be regarded as “the carbon currency” of living organisms, as the overwhelming majority of carbon metabolism goes through it. To their knowledge, this is the first example of a radical reaction occurring on the methyl group of acetyl-CoA, providing potentially new tools for biosynthesis/modification of natural products and macromolecules in living organisms that require formation of a carbon-carbon bond.

Read the full article here.     
Posted August 25, 2014
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Biochemistry notes the passing of noted former faculty member, J. Woodland "Woody" Hastings

Read a tribute to Dr. Hasting’s life and work, published in the New York Times.     
Posted August 22, 2014
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NSF awards BRAIN EAGER grant to team led by Martha Gillette

Gillette’s project plans to bring together neuroscientists, engineers, and chemists from across campus, to develop and use newly created, complementary technologies that will non-invasively control, measure, and analyze brain network dynamics and change in real time. Their hope is to examine how neurons in the brain are activated in response to experiences, in order to see how they cause behavioral changes and subsequent activities of the neurons, also known as brain plasticity.

Gillette will work with three other faculty at the Beckman Institute: Jonathan Sweedler, professor of Chemistry, Molecular and Integrative Physiology, Neuroscience, and member in NeuroTech; Gabriel Popescu, professor of Electrical and Computer Engineering and member Bioimaging Science and Technology; and John Rogers, professor of Materials Science and Engineering and member in the 3D Micro- and Nanosystems Group.

“The challenge of understanding the dynamic brain—how it remembers, enables us to move or be moved, to awake and sleep each day of our lives—lies before us. The exceptional tools we will develop under the BRAIN initiative are possible because of the science and engineering innovation and the collegial spirit at Illinois. They hold tremendous promise for identifying the signatures of neural activity that generate complex behaviors, insights not previously possible,” said Gillette. “These are truly exciting times.”

Gillette’s project has an educational element: training students to merge disciplines such as neuroscience, imaging technology, engineering of new materials for electrodes, and high-resolution analysis of neuron-to-neuron signals.

The project will contribute to NSF’s growing portfolio of investments in support of President Obama’s BRAIN Initiative, a multi-agency research effort that seeks to accelerate the development of new neurotechnologies that promise to help researchers answer fundamental questions about how the brain works.

The EAGER grant is for $300,000 over a two-year period.

Read the NSF announcement here.     
Posted August 26, 2014
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Scientists discover a new role for estrogen in the pathology of breast cancer

Scientists have discovered a previously unknown mechanism by which estrogen prepares cells to divide, grow and, in the case of estrogen-positive breast cancers, resist cancer drugs. The researchers say the work reveals new targets for breast cancer therapy and will help doctors predict which patients need the most aggressive treatment.

The University of Illinois team reports its findings in the journal Oncogene.

Estrogen pre-activates the unfolded-protein response (UPR), a pathway that normally protects cells from stress, the researchers report. The UPR spurs the production of molecular chaperones that prepare cells to divide and grow. Without chaperone proteins to do the work of folding and packaging other proteins, cells – including cancer cells – cannot divide. For this reason, chaperones are a popular target for new cancer therapies.

Activation of the UPR is known as a normal response to stress – when a cell lacks adequate oxygen or nutrients, for example, or is exposed to cancer-killing drugs. UPR activation prepares the cell for major changes associated with cell growth, division and survival under stress.

It wasn’t known before this study, however, that estrogen initiates this pathway before such stresses appear, said University of Illinois biochemistry professor David Shapiro, who led the new analysis with lead author, M.D.-Ph.D.-student Neal Andruska.

“This is a new role for estrogen in the pathology of cancer,” Shapiro said. “Others have shown that stress activates this pathway, helping to protect some tumors. What is new is our finding that estrogen can pre-activate this pathway to protect tumors.”

When estrogen binds to its receptor it sparks a cascade of molecular events in the cell. A key event occurs when a channel opens in the membrane of a compartment that stockpiles calcium, and calcium floods into the cell.

“That’s a signal to activate the UPR pathway, the stress pathway,” Shapiro said. “It’s also a signal that many researchers think has something to do with cell proliferation. The calcium itself may be a proliferation signal.”

The stress-response pathway induces the production of chaperone proteins.

“I like to think of this pathway as an assembly line,” Shapiro said. “In order for cells to divide, you’re going to have to produce a lot more proteins. The chaperones help you to package, fold up and ship all these proteins.”

The UPR also is a mediator of cell death. If a normal cell is exposed to too much stress, the stress response spurs apoptosis, a kind of cellular suicide. In cancer, however, mild activation of the UPR by estrogen blunts this cell-death pathway, allowing cancer cells to survive and even resist drugs, the researchers found.

The team also looked at the expression of UPR-related genes in publicly available data from samples of breast tumors obtained from women who had been diagnosed up to 15 years prior.

“Andruska, who spearheaded the research and carried out the computer analysis of the breast cancer data, found that UPR activation is a very powerful prognostic marker of the course of a woman’s disease,” Shapiro said.

The analysis revealed that among women with estrogen-receptor-positive breast cancer who underwent tamoxifen therapy, breast cancer was 3.7 times more likely to recur in those overexpressing the UPR. Ten years after a breast cancer diagnosis, only 15 percent of those with the highest level of UPR-gene expression were disease-free, compared with 80 percent of women with minimal UPR expression.

“Our marker helps identify breast cancers that are likely to be highly aggressive and therefore require intensive therapy,” Shapiro said.

U. of I. graduate student Xiaobin Zheng, postdoctoral researcher Xujuan Yang and food science and human nutrition professor William Helferich contributed to the research.

The National Institute of Diabetes and Digestive and Kidney Diseases at the National Institutes of Health funded the research.

Written by: Diana Yates, News Bureau Life Sciences Editor

Read the full article here.     
Posted October 02, 2014
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Scientists engineer human T cell receptors against cancer antigens

T cell receptors are found on the surface of T cells, where they bind to antigens such as those on cancer cells. After activation by the binding of the receptor, the T cell destroys the cancer cell. One of the problems associated with cancer is that a patient’s own T cells may not have the proper T cell receptors that can bind to such antigens. Over the past 15 years, the Kranz group has developed various strategies to attempt to engineer receptors that can serve these purposes, by taking a single receptor from a known T cell clone and improving its affinity for an antigen. In the present study, published in the journal Nature Communications , the scientists showed that it was possible to take a T cell receptor against one antigen (Figure) and using entirely in vitro, directed evolution techniques, to convert this receptor to a completely different specificity. The strategy could thus allow the development of specific receptors, at will, against a large array of known cancer antigens.

The approach involved computational analyses to guide the design of “libraries” that contain millions of mutated T cell receptors. The mutants are each displayed on the surface of a yeast cell, and then high-speed instruments called fluorescence activated cell sorters could be used to select only those yeast cells displaying a T cell receptor that binds to the antigen of interest. In the present study, the antigen of interest was derived from human melanoma (Target B in Figure), and the original T cell receptor had been derived from a T cell clone that recognized a viral antigen (Target A in Figure). Various mutational approaches, and molecular dynamics simulations by the Tajkhorshid group, provided insight into how the specific mutations found in the selected T cell receptors allowed binding only to the melanoma antigen.

A major implication of the study is that the design approach could be extended to other target antigens providing a platform to rapidly discover T cell receptors against many antigens. Current methods have required that each engineered T cell receptor be generated from human T cell clone, which can take years to produce. Engineered T cell receptors have already reached clinical trials in various therapeutic formats. The present approach provides an additional discovery strategy for their use in the treatment and detection of cancer, viral diseases, and autoimmune diseases, depending on the target antigen chosen for the specific T cell receptor.

Read the full article here.     
Posted November 07, 2014
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Professor Jongsook Kim Kemper and collaborators discover FXR and CREB as key physiological regulators of autophagy, published in the journal Nature.

Lysosomal degradation of cytoplasmic components by autophagy is essential for cellular survival and energy homeostasis under nutrient-deprived conditions. Acute regulation of autophagy by nutrient-sensing kinases, such as mTOR and AMPK, is well defined, but longer-term transcriptional regulation is not.

In this study, Sunmi Seok and Ting Fu (co-first authors) in the Jongsook Kim Kemper lab in the Department of Molecular and Integrative Physiology and collaborators, including Jian Ma’s group in the Department of Bioengineering, have identified the feeding-activated nuclear receptor FXR and the fasting-activated transcriptional factor CREB as key physiological regulators of autophagy.

There are several important aspects to this study. First, it was believed that autophagy occurs only under extremely stressful nutrient-deprived conditions but we show that it actually occurs physiologically during feeding/fasting. Second, autophagy does have important metabolic functions, for example lipophagy is dynamically regulated by the FXR/CREB axis. Third, this is the first report that FXR and CREB are transcriptional regulators of the autophagy gene network. Fourth, defective autophagy has been implicated in many diseases but excess autophagy is also harmful because it promotes cell death and also may provide a favorable microenvironment for tumor growth.

The team's discovery that the FXR/CREB axis tightly regulates the autophagy gene network reveals potential new targets for developing new drugs to treat human diseases associated with autophagy dysfunction, including metabolic disorders, neurodegenerative disease, and cancer. This study was supported by grants from National Institutes of Health to Professor Kemper.

Read the full article here.
Read a Perspective review here.     
Posted November 13, 2014
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Professor Tajkhorshid Awarded Supercomputing Capacity at DOE National Laboratory

The U.S. Department of Energy Office of Science selected Professor Emad Tajkhorshid’s project for a 2015 Innovative and Novel Computational Impact on Theory and Experiment (INCITE) award. The award provides 96 million hours of massive supercomputing at a Leadership Computing Facility that focuses only on the most ambitious research projects with the potential for major breakthroughs.

Tajkhorshid’s lab has been exploring the precise way in which nutrient molecules enter cells and waste molecules leave cells. Proteins known as membrane transporters undergo structural changes to allow a unidirectional transfer of molecules, functioning as active pumps, but just how the pumps work is unknown.

“The Holy Grail of structural biology of membrane transporters is to describe this whole transition. Right now we only have the initial and final structures,” said Professor Tajkhorshid.

Understanding the transition could allow drug developers to design more targeted drugs for major pathophysiological conditions such as psychological disorders, cancer, and multi-drug resistance.

Tajkhorshid’s project, which has been developed and tested in his lab, will study the transition between structural intermediates of a number of transporters using a novel combination of several replica-based techniques coupling a massive array of all-atom molecular dynamics simulations, which are only possible with this type of supercomputing capacity.

The goal of the project is to develop an atomistic view of membrane transporter transitions and to understand the ways in which the membrane transporters use energy to function as one-way pumps.

The Department of Energy accords supercomputing hours to a small number of projects every year through the INCITE program, which aims to accelerate scientific discoveries and technological innovations to projects that address “grand challenges” in science and engineering. Tajkhorshid’s INCITE award is a two-year grant with the possibility of renewal, and uniquely, the award includes a staff liaison for scientific support.

Dr. Tajkhorshid is a professor of biochemistry, pharmacology, and biophysics and computational biology and an affiliate of the Beckman Institute. “This award is order of magnitude larger than anything else we have had in the past. I am very pleased (actually honored) that our project was selected,” he said.

To learn more about the fundamental questions involved in this research, watch Dancing Proteins: Cell Membrane Transporter Motion May Revolutionize Drug Therapies. Video courtesy of The Beckman Institute.

Read the press release from the US Department of Energy.     
Posted November 19, 2014
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Jongsook Kim Kemper’s lab discovers that elevated acetylation of FXR in obesity promotes hepatic inflammation, published in the EMBO Journal

Posttranslational acetylation of transcriptional regulators is often persistently elevated in nutrient-excessive obesity conditions. In this study, we investigated the functional consequences of such elevated acetylation of the key metabolic regulator and bile acid nuclear receptor FXR.

Proteomic studies identified Lys-217 as the FXR acetylation site in diet-induced obese mice. In vivo studies utilizing acetylation-mimic and acetylation-defective Lys-217 mutants and gene expression profiling revealed that FXR acetylation increased proinflammatory gene expression, inflammatory responses, and liver fat levels, and impaired insulin sensitivity. Mechanistically, agonist-activated FXR is SUMO2-modified at lysine 277 by the PIASy SUMO E3 ligase. SUMOylation of FXR inhibits inflammatory gene expression in response to inflammatory signaling. Selective transrepression of inflammatory genes results from increased interaction of SUMO-FXR with NF-kB. In obese mice, FXR acetylation at lysine 217 inhibits its SUMOylation and diminishes SUMO2-dependent FXR anti-inflammatory action.

There are several important aspects to this study. First, although posttranslational modifications (PTMs) of proteins have been extensively studied, there is little evidence establishing the physiological/pathological relevance of PTMs and the mechanisms underlying PTM-mediated selective gene regulation. The present study, for the first time, demonstrates the relevance in vivo of a functional antagonism between acetylation and SUMOylation of FXR in diet-induced obese mice. Second, agonist-activated SUMOylated FXR selectively trans-represses NF-κB target inflammatory genes without transcriptionally regulating conventional FXR/RXRα target genes and further, the results indicate that the underlying mechanism is the selective interaction of SUMO2-FXR with NF-κB and not with RXRα. Third, since FXR is expressed in many non-hepatic tissues, including intestine, kidney, endothelial cells, and macrophages, the dysregulated acetyl/SUMO switch identified for liver FXR in obesity may also play a role in the pathogenesis of inflammatory diseases in other tissues, such as inflammatory bowel disease and atherosclerosis, as well as, liver steatohepatitis. Targeting the dysregulated acetyl/SUMO switch of FXR may provide novel therapeutic options and diagnostic markers for obesity-related inflammatory and metabolic disorders.

This study was supported by grants from National Institutes of Health to Professor Kemper and a post-doctoral fellowship from America Heart Association to Dong-Hyun Kim.

Read the full article here.     
Posted December 09, 2014
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Professor Phillip Newmark elected Fellow of the American Association for the Advancement of Science (AAAS).

Newmark was cited for his work in developmental biology, with particular emphasis on regeneration and germ cell development in flatworms, which carry profound implications for the field of regenerative medicine by their ability to regenerate from just a small sample of tissue. Newmark studies how their stem cells contribute to regeneration and tissue maintenance.

He earned his PhD from the University of Colorado at Boulder in 1994 and joined the U of I faculty in 2001. Newmark is also an investigator of the Howard Hughes Medical Institute, and the recipient of a CAREER Award from National Science Foundation, and a Damon Runyon Scholar Award from the Damon Runyon Cancer Research Foundation. He has been named a University Scholar.

The AAAS, the world’s largest general scientific society, was founded in 1848. Fellows have been elected to the organization since 1874. The organization’s stated goal is to “advance science, engineering, and innovation throughout the world for the benefit of all people.”

Posted December 18, 2014
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