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UR Center for RNA Biology Members and Alumni Attend RNA 2023 in Singapore
Friday, June 9, 2023
Pictured above, from left to right: Jessica Perciaccante (Genetics Grad Student, Anderson Lab); Douglas Anderson, PhD (Assistant Professor, Medicine, Aab CVRI); Yi-Tao Yu, PhD (Professor of Biochemistry & Biophysics); Xin Li, PhD (former UR Biochemistry & Biophysics Faculty, currently Professor at Zhejiang University); Sean Lindley (Biology Grad Student, Anderson Lab); Eric Phizicky, PhD (Professor of Biochemistry & Biophysics); Lynne Maquat, PhD (Professor of Biochemistry & Biophysics; Director of the UR CRB ); Eric J. Wagner, PhD (Professor of Biochemistry & Biophysics; Associate Director of the UR CRB); Weifeng Gu, PhD (UR Alumn – PhD 2005, currently Assistant Professor, UCR); Tatsuaki Kurosaki, PhD (Research Assistant Professor, Maquat Lab); Sara Ali (Biophysics Grad Student, Mathews Lab), Yi Pan (Biochemistry Grad Student, Yu Lab)
A large number of UR Center for RNA Biology members and alumni attended the 28th Annual RNA Society Meeting (‘RNA 2023’) held at the Suntec Convention Centre from May 30th-June 4th, 2023. In addition to those pictured, Douglas Turner, PhD, Professor Emeritus of the Department of Biochemistry and Member Emeritus of the Center for RNA Biology, attended and received the 2023 The RNA Society/Cold Spring Harbor Laboratory Press Distinguished Research Mentor Award, which recognizes outstanding mentorship by RNA Society members and highlights the importance of fostering the academic and professional development of trainees in RNA research.
Read More: UR Center for RNA Biology Members and Alumni Attend RNA 2023 in SingaporeA Search Engine for mRNA: Algorithm Identifies Optimal Sequences to Improve COVID Vaccines
Friday, May 19, 2023
Messenger RNA vaccines proved their worth in the COVID pandemic, and new software stands to make the already transformative technology even more powerful.
Scientists developed an algorithm to identify the most stable, efficient mRNA sequences for vaccines. Tests show that the algorithm-derived mRNAs resist deterioration longer, produce more COVID spike protein, and dramatically increase antibody levels in mice compared to currently used mRNA vaccines. The results were reported in the journal Nature.
Study authors believe their tool will be valuable to companies that make mRNA vaccines and to research teams developing mRNA-based therapies for genetic disorders, cancer and a plethora of other diseases that can be treated by using mRNA to express a needed protein.
Searching for the Strongest mRNA
The COVID shots given throughout the pandemic have many advantages—scalable production, safety, efficacy—but suffer from some big drawbacks, including the need for ultra-cold storage and the resultant distribution challenges, and waning immunity. These limitations are due to the fact that mRNAs are inherently unstable and prone to degradation (they are constantly being “eaten” by enzymes present in cells).
The “secret sauce” for creating stronger mRNA sequences requires the right balance of two factors: structure and genetic code. Past research shows that mRNAs with a tight, rigid structure, as opposed to a floppy, unconfined structure, degrade more slowly (structure consolidates mRNAs and provides protection from hungry enzymes). Consequently, they stay in cells for a longer period and have more time to make the desired protein.
The mRNA used in COVID vaccines directs our bodies to make the COVID spike protein. The number of mRNA sequences that encode the spike protein is enormous—larger than the number of atoms in the universe. But, some of these genetic instructions are more efficient than others: one set may allow cells to churn out protein more quickly, while a different set might have redundancies that lead to sluggish protein production.
So, how do you find the right combination of structure and code? RNA expert David Mathews, MD, PhD and computer scientist Liang Huang, PhD, collaborated to create an algorithm that assesses both factors. Like a Google search for mRNA sequences, their algorithm spits out the top result for a specific protein amongst the almost infinite number of possibilities.
“Our tool is designed to identify the best sequence out of a huge space that you could never explore experimentally,” said Mathews, co-corresponding author of the Nature study and the Lynne E. Maquat professor of Biochemistry and Biophysics at the University of Rochester Medical Center. “Prior approaches did a poor job of searching this space. We hope this breakthrough will help companies to develop or improve their mRNA therapies.”
Read More: A Search Engine for mRNA: Algorithm Identifies Optimal Sequences to Improve COVID VaccinesDavid Mathews Publishes Study in Nature on Algorithm to Optimize mRNA Vaccines
Thursday, May 4, 2023
The professor of Biochemistry and Biophysics partnered with an Oregon State University computer scientist to develop the algorithm to help research teams find the most stable, efficient mRNA sequences for vaccines and other therapies, such as monoclonal antibodies and anti-cancer drugs. Tested in COVID-19 mRNA vaccines, the algorithm substantially increased protein expression and antibody levels compared to currently used mRNA sequences.
Read More: David Mathews Publishes Study in Nature on Algorithm to Optimize mRNA VaccinesStudy: Yi-Tao Yu, Paul Boutz Harness Power, Precision of RNA to Make Mutations Invisible
Monday, March 6, 2023
Scientists have discovered a new way to suppress mutations that lead to a wide range of genetic disorders. A study in the journal Molecular Cell describes a strategy that co-opts a normal RNA modification process within cells to transform disease genes into normal genes that produce healthy proteins. The findings are significant because they may ultimately help researchers alter the course of devastating disorders such as cystic fibrosis, muscular dystrophy and many forms of cancer.
Negating Nonsense
Around 15 percent of mutations that lead to genetic diseases are called nonsense mutations. Aptly named, nonsense mutations occur when an mRNA molecule contains an early “stop” signal. When the mRNA takes genetic instructions from DNA to create a protein, this early stop sign orders the cell to stop reading the instructions partway through the process. This results in the creation of an incomplete protein that can lead to disease.
Led by Yi-Tao Yu, PhD, a team of researchers from the University of Rochester Center for RNA Biology designed an artificial guide RNA – a piece of RNA that can modify other types of RNA – to target mRNA molecules that contain early stop signals (also called premature termination codons). Guide RNAs are a natural mechanism that cells use all the time; Yu’s team altered this already existing process.
Like DNA, RNA is made up of molecular building blocks that are represented by the letters A (adenine), G (guanine), U (uracil), and C (cytosine). Premature termination codons always have the building block U in the first position (for example, UAG, UAA or UGA). The team’s artificial guide RNA was designed to modify the U in the first position, changing the molecular makeup of the targeted mRNA so that the stop signal is no longer – or less well – recognized by the cell.
Read More: Study: Yi-Tao Yu, Paul Boutz Harness Power, Precision of RNA to Make Mutations InvisibleRNA Biologist Lynne Maquat Awarded 2023 Gruber Genetics Prize
Thursday, February 23, 2023
Lynne E. Maquat, PhD, the founding director of the Center for RNA Biology at the University of Rochester, has been awarded the 2023 Gruber Genetics Prize for her discovery of nonsense-mediated mRNA decay or NMD in humans. The Gruber International Prize Program, administered by Yale University, honors scientists from around the world whose groundbreaking work leads to fundamental shifts in knowledge and benefits mankind.
Maquat has spent her career deciphering the many roles that RNA plays in sickness and in health, and is best known for elucidating the complexities of NMD in mammalian cells and human disease. One of the major surveillance systems in the body, NMD protects against mistakes in gene expression by targeting and eliminating deleterious mRNAs that could lead to the production of incomplete and potentially toxic proteins. Maquat’s lab also revealed that NMD helps our cells adjust to changes in development and in their environment, and more rapidly respond to certain stimuli.
“Lynne’s scientific prowess and steadfast commitment to her research is exemplary and has helped catapult the field of RNA biology to the forefront of medicine over the past decade,” said Mark B. Taubman, MD, CEO of the University of Rochester Medical Center and dean of the School of Medicine and Dentistry. “This is an exciting time, as Lynne and other scientists are putting her mechanistic findings related to NMD to use to design treatments. She is incredibly deserving of this honor.”
Read More: RNA Biologist Lynne Maquat Awarded 2023 Gruber Genetics PrizeA serendipitous discovery and the choreographed dance of fragile X research
Tuesday, October 18, 2022
The choreography of development is a delicate dance. Beginning in utero, chromosomes, DNA, genes and RNA twirl, tap, and sashay their way in a precise pattern. A misstep or a missing step that changes the routine causes body and brain functions to go awry – as is the case with many intellectual and developmental disabilities (IDD). Fragile X syndrome is the most common known single-gene cause of inherited IDDs, including autism. Scientists know the misstep in this syndrome is in the gene FMR1. FMR1 is responsible for making the protein FMRP, which is necessary for typical brain development.
Lynne Maquat, Ph.D., founding director of the Center for RNA Biology at the University of Rochester, and professor of Biochemistry & Biophysics, Oncology, and Pediatrics, did not set out to study fragile X. It was through another line of research – her seminal discovery of and decades’ worth of work on nonsense-mediated mRNA decay (NMD) – that fragile X syndrome entered her radar. NMD is a cellular quality-control mechanism that plays a role in both healthy and disease states, and her lab discovered that it is overactive in people with fragile X.
“It was complete serendipity,” Maquat said. “No one ever thought to look at NMD and fragile X. So now we’re trying to figure out what happens at the molecular level when FMRP is absent; we want to understand the network of altered gene expression by identifying mis-regulated messenger RNAs (mRNAs).”
One of the most prominent surveillance systems in the body that protects against mistakes in gene expression that lead to disease, NMD is a complex pathway that is at the heart of many of the collaborations between Maquat and other University of Rochester scientists. Together, with funding from the National Institutes of Health (NIH) and the FRAXA Research Foundation, they aim to gain a deeper understanding of the sophisticated mechanisms related to NMD that will contribute to developing new drug therapies for genetic disorders such as fragile X syndrome, cystic fibrosis, and hundreds of others.
INTO THE BRAIN
Associate professor of Biomedical Genetics Christoph Pröschel, Ph.D., has spent much of his career interested in neurogenetic diseases that primarily affect the white matter of the brain, which carries signals throughout the organ. His lab started working with induced pluripotent stem cells (iPSCs) to understand different neural cell types, providing a solid foundation for their IDD research. “My lab and the Maquat lab have a mutual interest in the molecular mechanism of fragile X,” said Proschel. “It is key to finding any kind of hope for a future therapy.”
The Pröschel lab makes and differentiates neural stem cells that mimic fragile X syndrome, allowing his team to test hypotheses and understand how different therapies impact cell biology and function. He and Tatsuaki Kurosaki, Ph.D., research assistant professor in the Maquat lab, used these neural stem cells to understand the relationship between FMRP and NMD. They discovered that NMD controls the amounts of messenger RNAs deriving from a wide range of genes throughout the brain, including genes that govern motor control and cognitive processes related to attention, learning, and language. They also found that when FMRP is absent from cells, as it is in people with fragile X syndrome, NMD shifts into overdrive.
This work was part of a 2021 study published in Nature Cell Biology led by Maquat that revealed that tamping down NMD with small molecule inhibitors restored a large proportion of neurological functions in these cells.
Most recently, Pröschel co-authored research published in Molecular Cell led by Maquat and co-authored by Hana Cho, Ph.D., and Elizabeth Abshire, Ph.D., of her lab. The study highlighted a complex molecular dance between NMD and the enzyme AKT, which plays a key role in cell growth and survival. Both AKT and NMD are overactive in fragile X. Using neural stem cells that lack the FMRP protein, they tested a drug called Afuresertib, which inhibits AKT. They discovered that blocking AKT in the fragile X cells decreased its activity and decreased NMD. These cells then acted more like typical, non-disease cells.
There is still a lot the team doesn’t know about how AKT and NMD interact, because they both influence and regulate multiple activities in cells, but this work provides good direction that could inform the development of future treatments for fragile X syndrome.
“This has been one of the real fun chapters of my career – working with this group,” said Pröschel. “Everyone brings such a different perspective to the project.”
FROM SURGERY TO THE LAB
As a neurotologist (subspecialist of Otolaryngology), Hitomi Sakano, M.D., Ph.D., spends time in the clinic with patients with hearing issues or hearing loss. In the lab, she aims to understand how the brain adapts to sound information.
Her work with fragile X syndrome began as a resident at the University of Washington when she took interest in FMRP, which is highly expressed in the auditory brainstem nuclei of a typical brain and is the same protein missing in fragile X patients. When Sakano came to the Medical Center in 2018, she brought the fragile X mouse model to study this and joined the Center for RNA Biology.
“I also use the [knockout] mouse model to study hyperacusis – extreme sensitivity to sound,” said Sakano. “We know that fragile X patients have sensory and auditory sensitivity, so this model is a great tool to study both.” Hyperacusis is also very common in the general population (some report up to 15 percent) so understanding the mechanism could potentially impact our broader community.
Sakano hypothesizes that FMRP regulates genes that enable neuroplasticity to maintain
From left: Hitomi Sakano, M.D., Ph.D., and Lynne Maquat, Ph.D.
normal processing of auditory information. If true, there may be therapeutic targets for symptoms like auditory hypersensitivity in fragile X. Funding from the Schmitt Program in Integrative Neuroscience (SPIN) through the Del Monte Institute for Neuroscience Pilot Program and a NIH Research Career Development Award for clinician-scientists are supporting her research, which involves investigating the gene expression abnormalities in the auditory brainstem of the fragile X mouse model that might explain the auditory hypersensitivity in these mice. To date, she has found some interesting RNAs that encode synaptic proteins. These findings open up the possibility of targeting these genes for the treatment of hyperacusis.
She co-authored a study with the Maquat and Pröschel labs in Genome Biology. The research used the mouse model whose FMR1 gene is knocked-out. These findings build upon Maquat’s previous research that showed NMD hyperactivation in neuronally induced stem cells from fragile X patients. This hyperactivity negatively impacts many neuronal mRNAs important to brain development. The Genome Biology paper showed NMD goes into overdrive in the brain during early development in a mouse with fragile X. These researchers are now testing various therapeutics to inhibit NMD.
“Being able to collaborate to gain meaningful results to move this science forward is the value of being at an academic medical center like Rochester,” said Sakano. “These steps are what will ultimately lead to treatments and therapies that I use in the clinic someday to help my patients.”
ON THE HORIZON
Forthcoming research aims to broaden the scope of the fragile X work at the Medical Center. One of the world’s largest clinics for fragile X is in Israel, where an estimated 80 percent of women are screened for the inherited disease. Michael Telias, Ph.D., assistant professor of Ophthalmology, Neuroscience, and Center for Visual Science, began studying fragile X as a graduate student in Israel. He uses human embryonic stem cells that carry the mutation for fragile X to look inside neurons at the molecular and cellular levels to shed light on the human-specific mechanisms affected by this syndrome.
“Human neurons have shown us that these cells have a problem receiving information and communicating information to the next cell,” said Telias. “We cannot do this work in humans, so using human cells enables us to know what to target in the cell. That is the only way we will be able to develop treatments that work.”
In the Frederick J. and Marion A. Schindler Cognitive Neurophysiology Laboratory, research assistant professor Tufikameni Brima, Ph.D., is aiming to use electroencephalography (EEG) and event-related potentials (ERP) to better understand how the brains of patients with fragile X respond to various stimuli. This work has the potential to build upon the ongoing molecular research being conducted by Telias and others.
“Ultimately, what we are figuring out is what happens when FMRP is absent. We don’t know the whole story,” Maquat said. “However, FMRP is an RNA-binding protein, and in work soon to be published in Molecular Cell, Kurosaki and I have now defined those messenger RNAs that are normally bound by FMRP and how the absence of FMRP binding results in those mRNAs making too much protein. These results have allowed us to identify which genes are affected and how. Our work will pave the way for better therapeutics for those living with fragile X.”
Read More: A serendipitous discovery and the choreographed dance of fragile X researchDouble Duty: Early Research Reveals how a Single Drug Delivers Twice the Impact in Fragile X
Monday, June 27, 2022
Like many neurological diseases, there’s a lot we don’t understand about fragile X syndrome. But, after studying the disorder for several years, Lynne Maquat’s lab knew two important things: the enzyme AKT, which plays a key role in cell growth and survival, and the quality control pathway known as NMD (nonsense-mediated mRNA decay), are both in overdrive in fragile X.
In a new study in the journal Molecular Cell, the team reveals how these two major players interact, highlighting a complex molecular dance that could inform the development of future treatments for fragile X syndrome.
Two paths to pursue
AKT is a hub for cell signaling, helping cells communicate about important processes like cell growth, proliferation and protein production. When cells are stressed – for example, in cancer, diabetes, heart disease and neurological disorders, including fragile X – AKT can send too many (or too few) signals or messages as part of a cell survival mechanism.
NMD is like a molecular guide that helps our cells make smart decisions that (in most cases) improve cellular function and contribute to good health. For example, NMD supports gene expression by flagging and destroying mRNAs (messenger RNAs) that are carrying faulty genetic instructions that could lead to disease. It also helps our cells adjust to changes in development and in their environment, and more rapidly respond to certain stimuli.
Read More: Double Duty: Early Research Reveals how a Single Drug Delivers Twice the Impact in Fragile XIn the Pocket: RNA Binding Discovery Supports ‘RNA World’ Theory of Early Life on Earth
Friday, January 14, 2022
RNA biologists at the University of Rochester Medical Center (URMC) have discovered that RNA, the chemical cousin of DNA, can bind two metabolites (small molecules) at the same time in a single binding pocket, causing those molecules to interact. This discovery, published in Nature Communications this week, could lead to new antibacterial drugs while helping to fill a gap in the controversial “RNA world” theory, which suggests that RNA molecules enabled life to evolve on Earth 3.5 billion years ago.
Read More: In the Pocket: RNA Binding Discovery Supports ‘RNA World’ Theory of Early Life on EarthLynne Maquat spoke with WXXI: 'A wave of the future': local biologist explores what's next for mRNA technology
Wednesday, September 8, 2021
The recent approval of Pfizer and BioNTech’s COVID-19 vaccine by the U.S. Food and Drug Administration, has scientists enthusiastic about the future of the messenger RNA, or mRNA, technology used to produce the vaccine. For RNA biologists, in particular, the pandemic has become a catalyst for modern medicine. “It's a big step forward for mRNA-based therapeutics,” said UR Medicine’s director for centers for RNA biology, Dr. Lynne Maquat. “We've had a worldwide need. And the need has been met.”
Maquat defines mRNA as the messenger molecule between our DNA, and the proteins that our cells need to perform their duties. She says the COVID-19 vaccine produces a piece of the spike protein that surrounds the coronavirus and raises an immune response to it.
“Our immune system will attack the virus, because the spike protein is on the outside of the virus,” said Maquat.
She says the success of the Pfizer and Moderna vaccines is causing scientists to look at other illnesses that could benefit from the mRNA technology like dengue.
“There's lots of infectious diseases, especially in Third World countries that need to be addressed,” Maquat said.
UR Medicine infectious disease specialist Dr. Edward Walsh says existing vaccines can also benefit from messenger RNA.
“If an mRNA vaccine for the influenza vaccine could reach the kind of efficacy data, especially over a six-month period, we really only need to get protection for about six months through the flu season each year,” Walsh said.
He said the flu vaccine is roughly 60% effective, but mRNA technology could increase that...
“If we could get that very high degree of efficacy, it could really do a lot of public health good,” said Walsh.
Maquat said she and her team are already looking at how some cancers could be treated with messenger RNA technology
“Let's say you have a pancreatic cancer,” said Maquat, “you could have your tumor removed, and you can have it characterized for new proteins.”
The new discovered proteins in the tumor would allow scientists to develop an mRNA treatment to combat that protein.
“It's a type of personalized medicine,” said Maquat. "This is a wave of the future"
Read More: Lynne Maquat spoke with WXXI: 'A wave of the future': local biologist explores what's next for mRNA technologyThat's the Rochester Effect: Featuring Dr. Lynne Maquat. PhD
Friday, July 2, 2021
UR Graduate Women in Science (GWIS) 2021 Mentoring-Up Resolution Challenge CONTEST RESULTS
Monday, May 24, 2021
Congratulations, Mentoring-Up Resolution Challenge Winners!
Full-time UR grad students (gender-inclusive) in biomedical, biological, or chemical sciences took charge of their futures by setting and, through mentoring-up, achieving professional and personal goals for Spring 2021. Participants submitted their goals in a January write-up and progress reports on their professional goals in May. The anonymous faculty evaluation committee selected finalists to present on May 20th. All four presenters were selected to win $1500 ea. in technology-related (hardware, software, and/or peripherals) prizes. Of note, submissions for this contest were received from graduate students of 12 different programs!
Read More: UR Graduate Women in Science (GWIS) 2021 Mentoring-Up Resolution Challenge CONTEST RESULTSGraduate Women in Science Receives 2021 Best of Rochester Award
Tuesday, May 4, 2021
Graduate Women in Science has been selected for the 2021 Best of Rochester Award in the University category by the Rochester Award Program.
Each year, the Rochester Award Program identifies companies that we believe have achieved exceptional marketing success in their local community and business category. These are local companies that enhance the positive image of small business through service to their customers and our community. These exceptional companies help make the Rochester area a great place to live, work and play.
Various sources of information were gathered and analyzed to choose the winners in each category. The 2021 Rochester Award Program focuses on quality, not quantity. Winners are determined based on the information gathered both internally by the Rochester Award Program and data provided by third parties.
About Rochester Award Program
The Rochester Award Program is an annual awards program honoring the achievements and accomplishments of local businesses throughout the Rochester area. Recognition is given to those companies that have shown the ability to use their best practices and implemented programs to generate competitive advantages and long-term value.
The Rochester Award Program was established to recognize the best of local businesses in our community. Our organization works exclusively with local business owners, trade groups, professional associations and other business advertising and marketing groups. Our mission is to recognize the small business community's contributions to the U.S. economy.
Lynne Maquat Wins Warren Alpert Foundation Prize
Monday, May 3, 2021
Lynne Maquat, Ph.D., the founding director of the Center for RNA Biology at the University of Rochester, has been awarded the Warren Alpert Foundation Prize for her pivotal discoveries in the field of RNA biology. She shares the prize with fellow RNA biologist Joan Steitz, Ph.D., Sterling Professor of Molecular Biophysics and Biochemistry at Yale School of Medicine.
The award is given by the Warren Alpert Foundation in recognition of work that has improved the understanding, prevention, treatment or cure of human disease. The prize is administered by Harvard Medical School, and since its inception in 1987, 12 honorees have gone on to receive Nobel prizes.
George Q. Daley, dean of Harvard Medical School, said of Maquat and Steitz: "The discoveries made by the two award winners are stunning in their elegance and scope." Earlier this year, the pair won the 2021 Wolf Prize in Medicine for their work. They shared the Wolf Prize with a third RNA biologist, Adrian Krainer, Ph.D., of Cold Spring Harbor Laboratory.
RNA Makes its Mark
Maquat has studied RNA since she started her own laboratory in 1982. But until the development and approval of multiple mRNA COVID-19 vaccines in 2020, RNA wasn't on the public radar. Decades of research by Maquat and Steitz on how RNAs work and how they are involved in human disease helped set the stage for the rapid development of these vaccines, which are key to bringing the COVID pandemic under control.
Many are familiar with DNA, which contains the genetic instructions that make us who we are. But RNA is equally important in the process of gene expression:
- DNA lives in the nucleus of a cell and makes many types of RNA, including mRNA (messenger RNA).
- mRNA takes genetic instructions from DNA, travels out of the nucleus and delivers them to factories in our cells called ribosomes.
- Ribosomes use the instructions to create proteins.
- Proteins carry out myriad functions throughout the body, including ferrying nutrients around, helping with chemical reactions and protecting us from disease.
Many disorders result from problems with our DNA, but over the past several decades Maquat, Steitz and other scientists revealed that mRNA plays a role in a multitude of diseases, too. Cystic fibrosis, fragile X syndrome, Duchene muscular dystrophy and a long list of other inherited and acquired diseases result from defective mRNAs.
"Scientists used to think that gene regulation was all about DNA, and that RNA didn't influence gene expression, the production of proteins or the development of disease," said Maquat, the J. Lowell Orbison Endowed Chair and Professor of Biochemistry and Biophysics, Oncology and Pediatrics at the University of Rochester School of Medicine and Dentistry. "We now know that a very complicated network exists in our cells to regulate how, when and where our mRNAs are produced. This knowledge has opened the door to using RNA as both a treatment target and a tool to develop new therapies."
Read More: Lynne Maquat Wins Warren Alpert Foundation PrizeOyaGen announces a license agreement to develop SARS CoV-2 inhibitor
Tuesday, April 20, 2021
Dr. Harold Smith
OyaGen, a start-up biotech company founded by Harold Smith, Ph.D., Professor of Biochemistry and Biophysics, announced on Monday a licensing agreement with Tonix Pharmaceuticals to develop a drug that was found to be an effective agent against the virus that causes COVID-19. The drug, TNX-3500, was found to block SARS-CoV-2 with an efficacy significantly greater than the current front-line anti-viral used in the clinic, remdesivir. Harold Smith, PhD, Chief Executive Officer and founder of OyaGen, remarked that "We're delighted to partner with Tonix as a clinical stage company on the development of TNX-3500 as we believe Tonix to be ideally capable to bring this drug lead to the clinic in rapid fashion and position it for worldwide commercialization." Tonix Pharmaceuticals Holding Corp. (Nasdaq: TNXP), a clinical-stage biopharmaceutical company, is located in Chatham, NJ. For more information please contact Dr. Smith at Harold.smith@rochester.edu
Hilf Article in Analytical Biochemistry Read Over 2000 Times
Friday, March 26, 2021
Paul Boutz lands first NIH R01 at Rochester
Tuesday, March 2, 2021
Paul Boutz, PhD
Congratulations to Paul Boutz, who received official word that his first NIH R01 application as a faculty member in the Department of Biochemistry and Biophysics at the URMC was funded. Dr. Boutz's project is entitled "Genomics-based approaches to understanding mechanistic alterations of spliceosome function in disease states" and earned a 12th percentile ranking, meaning the grant application was rated as better than 88% of all other grant applications. The goal of this project is to model genetic perturbations found in cancer and developmental disorders in order to understand how they alter spliceosome function. Conventional and novel RNA sequencing methods will be used to generate genome-wide maps of splicing and RNA-protein interactions that will enable the training of deep-learning neural networks, with the goal of deciphering the codes that confer gene-specific sensitivity to disease-causing mutations.
Congratulations Paul!
Wedekind lab research featured on the cover of JBC “The Year in JBC: 2020" issue
Friday, February 12, 2021
Congratulations to Shashank Chavali, Dr. Sachitanand Mali, Dr. Jermaine Jenkins, Dr. Rudi Fasan, and Dr. Joseph Wedekind for being featured on the cover of JBC "The Year in JBC: 2020" issue. Their recent research article, published in the Journal of Biological Chemistry (JBC) December 4, 2020 issue, titled "Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors" has been selected as the representative 'RNA' article for 2020 retrospective collection called "The Year in JBC: 2020."
The cover art below, shows a collage of fluorescence complementation experiments between the [4Fe-4S]-transferring NFU1 and potential partners (performed by Roland et al.), crystal structure overlays of HIV-1 TAR RNA with lab-evolved TAR-binding proteins (reported by Chavali et al.), nonmelanized yeast cells (explored by Chrissian et al.) and a cryo-EM structure of STEAP1, now thought to function as a ferric reductase in heterotrimer form (reported by Oosterheert and Gros). Artwork created by EJ Marklin.
Read More: Wedekind lab research featured on the cover of JBC "The Year in JBC: 2020" issue
Lynne Maquat Awarded 2021 Wolf Prize in Medicine
Tuesday, February 9, 2021
Lynne E. Maquat, Ph.D., the founding director of the Center for RNA Biology at the University of Rochester, was honored with the 2021 Wolf Prize in Medicine. The acclaimed international award is given to outstanding scientists from around the world for achievements that benefit mankind.
Maquat was selected for "fundamental discoveries in RNA biology that have the potential to better human lives." She has spent her career deciphering the many roles that RNA plays in sickness and in health, and is well known for her discovery of nonsense-mediated mRNA decay or NMD. One of the major surveillance systems in the body, NMD protects against mistakes in gene expression that lead to disease. Maquat's lab also revealed that NMD helps our cells adjust to changes in development and in their environment, and more rapidly respond to certain stimuli.
Maquat shares the award with Joan Steitz, Ph.D., Sterling Professor of Molecular Biophysics and Biochemistry at Yale School of Medicine and Adrian Krainer, Ph.D., St. Giles Foundation Professor and Cancer Center Deputy Director of Research at Cold Spring Harbor Laboratory. Steitz and Krainer were also honored for discoveries in RNA biology.
The Wolf Foundation, which celebrates exceptional achievements in the sciences and the arts, is based in Israel, where Maquat's quest to unravel the intricacies of NMD began. In 1980 she traveled to Jerusalem to retrieve bone marrow samples from four children suffering from thalassemia major, the most severe form of the inherited blood disorder thalassemia. Maquat wanted to learn why the children's marrow contained no beta-globin protein, which is necessary for the oxygen-carrying function of red blood cells. Her 1981 breakthrough manuscript, "Unstable beta-globin mRNA in mRNA-deficient beta0 thalassemia," published in Cell, was the first to reveal the role of NMD in human cells and how it can lead to disease.
"Lynne's work on nonsense-mediated mRNA decay is the bedrock of an ever-growing body of research on how mRNAs are monitored and regulated," said Mark B. Taubman, M.D., dean of the University of Rochester School of Medicine and Dentistry. "Her dedication to her science and to the field of RNA biology has opened the door to the development of RNA-based therapeutics for a wide range of disorders that you can't reach with conventional drugs. We're thrilled that her contributions are being recognized with this prestigious award."
RNA secured its place in the public eye in 2020 with the development and approval of multiple mRNA COVID-19 vaccines. Years of research by Maquat, Steitz and Krainer helped set the stage for the rapid development of these vaccines.
The J. Lowell Orbison Endowed Chair and Professor in the Department of Biochemistry and Biophysics at the University of Rochester School of Medicine and Dentistry, Maquat is the recipient of several other significant honors, including:
Winners of the Wolf Prize are selected annually by an international jury committee of the Wolf Foundation; prizes are awarded regardless of religion, gender, race, geographical region, or political view. The official announcement of this year's prize by the President of the State of Israel, Reuven Rivlin, was made on February 9, 2021.
Read More: Lynne Maquat Awarded 2021 Wolf Prize in MedicineUR Center for RNA Biology RNA Presentation Contest Results
Tuesday, February 2, 2021
Thank you to those who participated in and/or viewed the UR Center for RNA Biology's RNA Presentations on Jan 6th, 13th, and 27th, sponsored by the RNA Society and Lexogen. The judging committee was impressed with the quality of the presentations given on all three dates, making final decisions difficult.
All nine of the graduate student, postdoc, and technician presenters, chosen based on their quality of their abstract, will be receiving a one-year membership to the RNA Society. Of these, four who were chosen based on the quality of their presentation will be awarded $375 each to be used toward the attendance of an RNA-centric meeting, in person or virtually.
The four to be awarded a one-year membership in the RNA Society and $375, in alphabetical order, are:
Kamel Awayda (presented Jan 6th )
Technician, Mitch O'Connell Lab
"Characterization of THUMP Domain-Containing Protein 1, and Putative Modulator of RNA Modification"
Chen Bao (presented Jan 13th)
Biochemistry Grad Student, Dmitri Ermolenko Lab
"mRNA Stem-Loops Can Induce Translational Pause through Two Pathways"
Xavier Rambout, PhD (presented Jan 27th)
Postdoc, Lynne Maquat Lab
"Transcriptional Coactivator PGC-1α Contains a Novel CBP80-Binding Motif that Orchestrates Efficient Target-Gene Expression"
Arica VanderWal (presented Jan 13th)
Biochemistry Grad Student, Mitch O'Connell Lab
"The Role of Csx28 in CRISPR-Cas13b Anti-Bacteriophage Defense"
The remaining to be awarded a one-year membership in the RNA Society, in alphabetical order, are:
Lily Cisco (presented Jan 6th )
Pharm-Phys Grad Student, John Lueck Lab
"Testing Therapeutic Intervention for Myotonic Dystrophy Type 1 in a Novel Mouse Model"
Xueyang He (presented Jan 6th )
Biophysics Grad Student, Paul Boutz Lab
"A Novel Method to Capture and Sequence Intron Lariats"
Shon Koren (presented Jan 6th )
Technician, Gail Johnson Lab
"Tau-Ribosome-tRNA Associations Underlie Common Features of Dys sincening Protein Synthesis in Dementia"
Sean Lindley (presented Jan 13th )
Biology Grad Student, Doug Anderson Lab
"StitchR: Ribozyme-Mediated RNA Trans-Splicing and Expression in Mammalian Cells"
Debanjana Maji (presented Jan 27th )
Biophysics Grad Student, Clara Kielkopf Lab
"Representative Cancer-Relevant U2AF2 Mutations Alter RNA Interactions and Splicing"
Beneath the Surface of Fragile X Syndrome: Study Sheds Light on What’s Happening in Nerve Cells
Monday, January 25, 2021
A new study shows that many abnormalities in fragile X syndrome cells are related to glitches with one of the body's major quality control systems. Published in Nature Cell Biology, the research provides fresh insight into the molecular mechanisms of the disorder and a pathway to search for potential treatments.
Fragile X syndrome occurs when individuals don't make the fragile X protein known as FMRP, which is needed for normal brain development. Currently, little is known about how the loss of this crucial protein leads to the intellectual disability and severe learning problems characteristic of the disease.
Rochester researchers found that many irregularities in cells that lack FMRP are due to misregulated nonsense-mediated mRNA decay, or NMD. Discovered by RNA biologist Lynne E. Maquat, Ph.D., NMD is like a molecular guide that helps our cells make smart decisions that (in most cases) improve cellular function and contribute to good health. For example, NMD helps our cells adjust to changes in development and in their environment, and more rapidly respond to certain stimuli.
Through a series of cellular analyses, Maquat's team discovered that NMD influences a wide range of genes throughout the brain, including genes that govern motor control and cognitive processes related to attention, learning and language. They also found that when FMRP is absent from cells, as it is in people with fragile X syndrome, nonsense-mediated mRNA decay shifts into overdrive.
Read More: Beneath the Surface of Fragile X Syndrome: Study Sheds Light on What’s Happening in Nerve CellsNew Research Funding Initiative to Support Young Investigators
Friday, January 15, 2021
Thanks to a partnership between pediatric researchers and the GCH Advancement division, a new funding initiative will seek to provide $25,000 -- matched with grant funds -- to support individual young investigators who are undertaking pediatric research.
These young investigators would be tenure-track assistant professors or post-doctoral fellows who already have a PhD degree and are on the path to obtain a tenure track position. This type of "seed" funding will be critical for fostering the careers of young researchers at URMC and could potentially pay dividends for institutional growth in the long-term, according Tom Mariani, PhD, professor of Neonatology and director of research for the Department of Pediatrics.
"In addition to funding discovery and innovation which could potentially save millions of lives, the career development of one investigator can be leveraged many times over to merit additional external funding, creation of new labs, and stimulate economic growth in the Rochester community."
Alan Wood, owner of the Realty company RE/Max Plus and supporter of GCH, and Lynne Maquat, PhD, endowed chair and professor in the Departments of Biochemistry and Biophysics, Oncology, and Pediatrics, developing this funding idea after Wood and his children visited Maquat's Fragile X Syndrome lab this Fall. Fragile X Syndrome is the most common single-gene cause of autism and intellectual disability, and Wood's family got a thorough education on the scope of Maquat's work, which is examining disease-causing mutations in children, and what those mutations do to gene expression via RNA production.
"My children loved getting first-hand experience touring the lab and seeing real-world visualizations of the work Maquat and her team are doing. Wearing lab coats and gloves, they isolated genetic material from bananas, which turn out to have more genetic material than us humans," said Wood.
Wood will be leading the effort to develop the program and secure funding. Donors who sponsor a young investigator will be able to establish a relationship to learn more about their research as it evolves.
"We have several talented young researchers in the Department of Pediatrics," said Maquat, "providing early support for their career is a long-term goal. The results won't be immediate, but over time, this support will build the foundation for discovery that will improve kids' lives."
Read More: New Research Funding Initiative to Support Young InvestigatorsAlan Grossfield Featured in Biophysical Society Profile
Monday, January 11, 2021
Biochemistry and Biophysics Professor Alan Grossfield was recently featured in a two-page profile piece in the January 2021 Biophysical Society Bulletin. The article details how Dr. Grossfield developed an interest in science and progress from an undergraduate biology major to ultimately making a career in computational studies of biological systems. The entire article can be found here: https://biophysics.cld.bz/Biophysical-Society-Bulletin-January-2021/4/#zoom=z
The Department of Biochemistry and Biophysics hosts its 1st Annual Holiday Decorating Door Contest
Tuesday, December 22, 2020
The Department of Biochemistry and Biophysics recently held its 1st Annual Holiday Decorating Door contest. With only two labs participating in this year's contest, both labs were declared as winners. Congratulations to the Boutz Lab and the O'Connell lab!
O'Connell lab door
Boutz lab door
Department of Biochemistry and Biophysics Annual Toy Drive
Friday, December 18, 2020
The Department of Biochemistry and Biophysics held its annual toy drive this season to collect toys and items for the Golisano Children's Hospital. Dr. Alan Grossfield delivered a cart full of goodies to the Golisano Children's hospital on Tuesday, December 15th. The gifts are given to the children in the hospital during the holiday season. Any remaining gifts are used to support the needs of the children and playrooms throughout the year.
COVID-19 vaccine: What’s RNA research got to do with it?
Monday, December 14, 2020
The US Food and Drug Administration recently approved emergency use authorization for a COVID-19 vaccine developed by Pfizer and the German pharmaceutical company BioNTech.
The vaccine made history not only because it reported a 95 percent efficacy rate at preventing COVID-19 in clinical trials, but because it is the first vaccine ever approved by the FDA for human use that is based on RNA technology.
"The development of RNA vaccines is a great boon to the future of treating infectious diseases," says Lynne Maquat, the J. Lowell Orbison Distinguished Service Alumni Professor in biochemistry and biophysics, oncology, and pediatrics at Rochester and the director of Rochester's Center for RNA Biology.
COVID-19, short for "coronavirus disease 2019," is caused by the novel coronavirus SARS-CoV-2. Like many other viruses, SARS-CoV-2 is an RNA virus. This means that, unlike in humans and other mammals, the genetic material for SARS-CoV-2 is encoded in ribonucleic acid (RNA). The viral RNA is sneaky: its features cause the protein synthesis machinery in humans to mistake it for RNA produced by our own DNA.
For that reason, several of the leading COVID-19 vaccines and treatments are based on RNA technology.
A contingent of researchers at the University of Rochester study the RNA of viruses to better understand how RNAs work and how they are involved in diseases. This RNA research provides an important foundation for developing vaccines and other drugs and therapeutics to disrupt the virus and stop infections.
"Understanding RNA structure and function helps us understand how to throw a therapeutic wrench into what the COVID-19 RNA does—make new virus that can infect more of our cells and also the cells of other human beings," Maquat says.
In the past few decades, as scientists came to realize that genetic material is largely regulated by the RNA it encodes, that most of our DNA produces RNA, and that RNA is not only a target but also a tool for disease therapies, "the RNA research world has exploded," Maquat says. "The University of Rochester understood this."
In 2007, Maquat founded The Center for RNA Biology as a means of conducting interdisciplinary research in the function, structure, and processing of RNAs. The Center involves researchers from both the River Campus and the Medical Center, combining expertise in biology, chemistry, engineering, neurology, and pharmacology.
Read More: COVID-19 vaccine: What’s RNA research got to do with it?Daniel Steiner Wins The Sayeeda Zain Fall 2020 Travel Award
Friday, December 4, 2020
Congratulations to Dan Steiner for winning a Sayeeda Zain Fall travel award. Dan is planning to attend the SPIE Photonics West meeting, to be held at the Moscone Center, San Francisco, California, March 6-11, 2021, He states "I am excited to represent our department and present my work in San Francisco (virtually or otherwise) . Networking and reaching out to labs and PIs at this conference will help me learn more about the entrepreneurial side of science and how to develop my career after I defend." The Sayeeda Zain Travel Award honors the distinguished career and charitable life of Dr. Sayeeda Zain. The award is given in recognition of research excellence to support expenses associated with attendance at a scientific conference or corporate internship to gain practical experience. Dan Steiner is a Biophysics graduate student studying in Dr. Ben Miller's lab
Special Department of Microbiology and Immunology Seminar – Dr. Malika Grayson – November 9th at NOON
Friday, October 23, 2020
How do you make an impact when you are the only person in the room that looks like you? We hear the terms diversity and inclusion but forget that the term representation should be a reflection of diversity and inclusion combined. This isn't always the case. Dr. Grayson discusses her views on what it means to increase diversity and representation as an Individual Contributor. Learn more about her journey as the 2nd Black Woman to graduate with a PhD in Mechanical Engineering from her graduate institution. Hear about her current work as both an engineer, a STEM Advocate, and her most recent success as author of 'HOODED: A Black Girl's Guide to the PhD' where she highlights her time and lessons learned during her PhD Program.
Nazish Jeffery, Biochemistry Ph.D. Candidate Pens Guest Column in the Democrat & Chronicle on Scientists’ Need to Communicate Clearly to the Public
Monday, October 19, 2020
Nazish Jeffery
Graduate student Nazish Jeffery published an editorial-style column entitled "Scientists Must Communicate More Clearly" which appeared on the Opinion page of the Sunday, October 4th edition of the Democrat and Chronicle. Ms. Jeffery argues that scientist have a civic duty to clearly inform and educate the public and public officials with regard to the results of biomedical research. She states "As scientists, our civic duty becomes twofold. Not only must we better our understanding of the world through research, we also need to use our training and expertise to help inform who govern so they can craft policies that are scientifically sound." Ms. Jeffery will be taking a brief hiatus from her laboratory research in Michael Bulger's lab to remotely participate in an internship with the American Institute of Biological Sciences in Washington DC, where she will focus on science and public policy.
Read More: Nazish Jeffery, Biochemistry Ph.D. Candidate Pens Guest Column in the Democrat & Chronicle on Scientists’ Need to Communicate Clearly to the PublicCool Technology Allows for Better Views of Cancerous Blood Cells in Quest for New Treatment
Tuesday, September 15, 2020
Clara Kielkopf, Ph.D., left, and Laura Calvi, M.D., stand by the University's new cryo-microscope
With the recent acquisition of Nobel Prize-winning technology and two new grants, Wilmot Cancer Institute researchers are streamlining their investigations into a malignant blood disease known as MDS, working toward discovering targeted therapies.
Laura Calvi, M.D., and Clara Kielkopf, Ph.D., are leading collaborative teams that will be using a device at the University of Rochester Medical Center — a cryo-electron microscope — that has ushered in a new era in biochemistry. The microscope allows scientists to see 3D snapshots and more details of living molecules than ever before, down to near-atomic resolution, to understand disease and uncover new ways to design drugs. The developers of the technology were awarded the Nobel Prize in Chemistry 2017.
Calvi and Kielkopf each received Edward P. Evans Foundation awards totaling $1.2 million for this project. Evans grants go to scientists seeking a cure for myelodysplastic syndromes (MDS), which originates in the bone marrow and disrupts healthy blood cell formation. MDS often leads to leukemia.
The Kielkopf lab will use the cryo-electron microscope to obtain 3D views of recurrent MDS mutations as guides for targeting molecular therapies. The modern microscope is the first of its kind in the Rochester region, Kielkopf said, and will be accessible to all UR researchers through the Electron Microscopy Shared Resource Laboratory. She is a professor of Biochemistry and Biophysics in the Center for RNA Biology.
Read More: Cool Technology Allows for Better Views of Cancerous Blood Cells in Quest for New TreatmentDavid Mathews, MD, PhD installed as first Lynne Maquat Distinguished Professor in RNA Biology
Tuesday, September 15, 2020
We are thrilled to announce that Professor David Mathews, MD, PhD, was honored at this year's School of Medicine Opening Convocation by being installed as the first Lynne Maquat Distinguished Professor in RNA Biology in the School of Medicine and Dentistry. The professorship was awarded by Dr. Mark Taubman, Dean of the School of Medicine and CEO of the University of Rochester Medical Center. The Convocation was held virtually this year and can be viewed at the link below.
Congratulations to Professor Mathews!
Read More: David Mathews, MD, PhD installed as first Lynne Maquat Distinguished Professor in RNA BiologyGDSC Predoc Adrián Moisés Molina Vargas Passes his Qualifying Exam!
Thursday, September 3, 2020
Adrian Vargas, a pre-doctoral student in the laboratory of Dr. Mitch O'Connell successfully defended his Qualifying Exam proposal entitled "Understanding guide-RNA design rules for efficient and specific Cas13 RNA-binding in human cells". Working on the recently described Type VI CRISPR-Cas system Adrian is investigating unique properties of the effector nuclease Cas13. His work has designed new approaches that will shed light on the mechanisms that govern optimal Cas13 RNA-binding, and potentially enhance its usability in human cells. Pursuing such goals not only will help complete our understanding of the gRNA requirements for on-target efficiency but more importantly, it will assist in uncovering what gRNA features contribute to off-target effects that could hinder the use of Cas13 as a specific RNA-targeting tool. The results will develop a more holistic biophysical model of Cas13 binding and cleavage activity. Congratulations Adrian on a job well done! You can read Adrian's thesis abstract below.
Title: Understanding guide-RNA design rules for efficient and specific Cas13 RNA-binding in human cells.
Abstract: Prokaryotic adaptive immune systems utilize Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and CRISPR Associated (Cas) proteins to target and cleave foreign genetic elements in an RNA-guided manner. The recently described Type VI CRISPR-Cas system contains a single effector ribonuclease, Cas13, that binds and processes a guide-RNA (gRNA), forming an RNA-guided RNA-targeting protein complex. Cas13 has been successfully engineered for potent RNA-knockdown in eukaryotic cells with minimal off-target effects, and other exciting applications described to date include utilizing a nuclease-dead Cas13 (dCas13) as a programmable RNA-binding protein for RNA imaging, RNA-splicing, RNA-detection or RNA-editing applications, among others.
However, the principles of guide-RNA selection for efficient and specific Cas13:gRNA RNA binding remain elusive. Previous work indicates that gRNA choice is important because not all gRNAs yield a robust RNA-targeting, and it is likely that there are different gRNA requirements for RNA-binding compared to RNA-cleavage applications. Furthermore, no predictive models exist for guide-RNA binding efficiency and specificity for Cas13 because no systematic screens have been carried out. Given that no transcriptome-wide measurements of Cas13-binding specificity have been attempted so far, it is unknown what the Cas13 off-target landscape is for human cells. Addressing this knowledge gap and quantitatively understanding the differences between binding and cleavage specificities is integral to the development of specific Cas13 RNA-binding applications.
In this project, I propose a series of approaches that will shed light on the mechanisms that govern optimal Cas13 RNA-binding, and potentially enhance its usability in human cells. Pursuing such goals not only will help complete our understanding of the gRNA requirements for on-target efficiency but more importantly, it will assist us in uncovering what gRNA features contribute to off-target effects that could hinder the use of Cas13 as a specific RNA-targeting tool, particularly for RNA-binding applications. In addition, these findings will be complemented by kinetic studies to dissect the biochemical components underlying Cas13 binding specificity to develop a more holistic biophysical model of Cas13 binding and cleavage activity. Consequently, we will generate a predictive model for Cas13 guide-RNA targeting specificity which will be complied into a comprehensive gRNA design tool tailored to different RNA-targeting applications for any RNA of choice. Finally, using the knowledge we generate and existing structural information, we will attempt to rationally engineer Cas13 and gRNA structure to enhance binding (and cleavage) specificities. Taken together, this work will bolster efforts to develop a range of RNA-targeting tools that can be readily used as research tools to address knowledge gaps in RNA biology, and as potential therapeutics.
RNA Essay Contest Results and Congratulations
Wednesday, August 26, 2020
The UR Center for RNA Biology offered an exercise during the time when COVID-19 became a sufficient threat to largely shut-down our research enterprise. We're pleased to announce the winners of the UR's Center for RNA Biology Essay Contest on "The role of RNA research in community health". These awards are sponsored by a grant from the RNA Society & Lexogen to the UR Center for RNA Biology, and funds from UR RNA Structure & Function Cluster.
Our Gold prize (~$1,000 value) award goes to Sydney Simpson, an Immunology, Microbiology & Virology graduate student in Steve Dewhurst's lab in the Department of Microbiology & Immunology, for her essay: "Nucleoside Analog Inhibitors: Timeless & Timely Beacons of Hope".
The Silver Prize (~$250 value) award goes to Omar Hedaya, a Biochemistry & Molecular Biology graduate student in Peng Yao's lab in the Department of Medicine/Department of Biochemistry & Biophysics, for his essay: "Know the Fundamentals when Seeking the Future".
Omar Hedaya
Sydney Simpson
Both awardees have become members of the RNA Society and will use their winnings toward technology needs for the upcoming semester.
The RNA Society now features our contest results, including the winning essays, in its latest RNA Salon update: https://www.rnasociety.org/featured-salons, see bullet #3.
We would like to acknowledge Honorable Mentions for the following applicants:
- Sai Shashank Chavali -- Graduate student; Biophysics, Structural & Computational Biology; Wedekind Lab
- Lily Cisco -- Graduate student; Cellular and Molecular Pharmacology & Physiology; Lueck Lab
- Gabrielle Kosoy -- Graduate student; Biophysics, Structural & Computational Biology; Miller Lab
- Ashwin Kumar -- Graduate student; Biophysics, Structural & Computational Biology; Topham Lab
- Li Xie -- Graduate student; Genetics, Development & Stem Cells; Pröschel Lab
We thank all who participated -- and our judges, too!
Kielkopf Lab Awarded EvansMDS Research Grant
Thursday, July 16, 2020
Prof. Clara Kielkopf has been awarded an EvansMDS research grant to use the new, state-of-the-art cryo-electron microscope at the U of R Medical Center EM facility. The Kielkopf group will use this revolutionary technique to study 3D structures of mutant U2AF1-splicing complexes in human malignancies. The title of the EvansMDS grant is: "Cryo-Electron Microscopy Structures of Mutant U2AF1-Containing Ribonucleoproteins Associated with Myelodysplastic Syndromes". This grant was made possible by our new Talos cryo-EM.
New article discusses biological implications of the intrinsic compactness of mRNAs
Monday, July 6, 2020
The Mathews and Ermolenko labs have recently showed that RNAs universally fold into secondary structures with short end-to-end distances. In this new article, possible roles of the inherent mRNA compactness in translation and mRNA decay are reviewed.
Cancer Investigators Pivot, Take on Coronavirus Research
Friday, June 12, 2020
While other cancer researchers had to temporarily close their labs in March due to the COVID-19 pandemic, Isaac Harris, Ph.D., and Josh Munger, Ph.D., shifted their focus to the contagion that has reshaped the world.
Using their specialized knowledge of viruses and genomics technology at the Wilmot Cancer Institute, the duo is searching for new and existing, U.S Food and Drug Administration-approved medications that could block the coronavirus.
They've tested 624 drugs on thousands of human lung cells infected with a strain of the coronavirus to see if the drugs have any impact. So far, they've discovered 15 potential compounds that appear to have anti-viral activity. Their criteria for a "hit" is for the drug to block 50 percent of virus-induced cell death. The team is validating the 15 drugs and trying to understand the mechanisms behind their potential anti-viral activity, Harris said.
This type of research is known as high-throughput drug screening -- a process that plays a big role in drug discovery in modern medicine. But instead of finding a new drug, here, investigators are looking to repurpose existing, available drugs for treatment of the coronavirus. This involves using automated, robotic equipment to match drug candidates with cellular events that occur during disease transformation. This form of drug-screening is often less expensive and faster than developing treatments from scratch.
Read More: Cancer Investigators Pivot, Take on Coronavirus ResearchErmolenko lab uncovers a new mechanism causing ribosome pausing
Wednesday, June 10, 2020
Chen Bao
In a new paper just published in the journal eLife, the Ermolenko lab in collaboration with the Grigorieff lab at HHMI uncovers the underlying mechanism by which secondary structure in mRNA causes ribosome pausing. Specifically they show that mRNA stem-loops can cause translation pausing by inhibiting binding of tRNAs to the A site of the ribosome. The lead author on the work is Chen Bao, a Biochemistry graduate student. The work was funded by NIH.
Biophysics Students Win Hooker Fellowships
Tuesday, June 9, 2020
Congratulations to Chapin Cavender and Michael Bryan for winning University of Rochester's Hooker Fellowships, recognizing their achievements in their thesis research. Chapin and Michael are Biophysics students working in the labs of David Mathews and Ben Miller, respectively.
Michael Bryan
Chapin Cavender
This week’s URMC Research Heroes featured the Maquat lab’s Tatsuaki Kurosaki, PhD, and Shuhei Mitsutomi, MS
Wednesday, June 3, 2020
This week's URMC Research Heroes featured the Maquat lab's Tatsuaki Kurosaki, PhD, and Shuhei Mitsutomi, MS, who were recognized today for their work on SARS-CoV-2.
https://www.instagram.com/p/CA-QN7oAl07/
Both Tatsuaki and Shuhei have worked as members of the Maquat Lab (Center for RNA Biology and the Department of Biochemistry & Biophysics) during the sequestration on SARS-CoV-2, collaborating with a lab at Harvard to determine the mechanism by which the virus inhibits human-cell nonsense-mediated mRNA decay (NMD) so as to express and replicate its RNA efficiency.
From Tatsuaki: "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 19 (COVID-19) pandemic, is a novel enveloped RNA virus carrying a large (~30 kb) positive-sense single-stranded RNA genome. Although human cells innately have an RNA surveillance pathway called nonsense-mediated mRNA decay (NMD) that generally protects cells from infection by many different types of viruses, little is known about how SARS-CoV-2 inhibits NMD to proliferate in human cells. We hope that our research helps to elucidate the molecular mechanisms of SARS-CoV-2 proliferation in human cells, eventually contributing toward the development of therapeutic strategies to combat COVID-19."
University of Rochester RNA Essay Contest: “The role of RNA research in community health”
Wednesday, May 20, 2020
Sponsored by the RNA Society & Lexogen, UR RNA Structure & Function Cluster, and UR Center for RNA Biology
Who is eligible: Any University of Rochester graduate student or post-doc with an interest in RNA biology
Entry rules: Essays should be no more than two pages, single-spaced (excluding references, which should be present), 11-point Arial font, with half-inch margins all around.
Prizes: Two prizes will be given out. Gold (valued at ~$1000), and Silver (valued at ~$250). Additionally, winning essays along with photos of the winning authors will be posted on the Center for RNA Biology webpage and featured on the RNA Society's RNA Salon page, offering international exposure.
Details
The UR's Center for RNA Biology is running an essay contest, sponsored by the RNA Society & Lexogen, and UR's RNA Structure & Function Cluster, on "The role of RNA research in community health". This contest, which is open to all UR graduate students and post-docs, aims to promote creative yet data-driven thinking about the importance of RNA in the "big picture".
Considering that reliable technology is required for research in an increasingly virtual world, prizes will consist of a PC or Mac laptop for Gold winners (~$1000), and software licenses or peripherals (e.g., second monitor or laptop dock) for Silver winners (~$250), subject to the needs of each recipient.
Submissions must be emailed to Liz by Monday, July 13th, 2020.
Winners will be announced in the beginning of August.
Links
The RNA Society: https://www.rnasociety.org/
RNA Structure & Function Cluster: http://www.rochester.edu/ucis/rnastructure.html
Center for RNA Biology: https://www.urmc.rochester.edu/rna-biology.aspx
Chris Goodwin, Sierra Fox Celebrate 2020 Commencement at Home Along with 4,000 Students
Monday, May 18, 2020
PALMYRA, NEW JERSEY: New biochemistry doctoral graduates Chris Goodwin and Sierra Fox celebrate at home.
Chris Goodwin and his wife, Sierra Fox, received their doctoral degrees in biochemistry from the School of Medicine. They met at the University years ago and both received master's degrees in 2016. They celebrate Friday at their home in Palmyra, New Jersey. "Going from grad school into quarantine has been very weird," Goodwin says.
They celebrated by baking cinnamon buns and eating them while they watched the online commencement videos and the School of Medicine and Dentistry biochemistry and biophysics department virtual award ceremony. "We had a 'Sierra and Chris' banner left over from our post-thesis defense party months ago and hung that up behind us for a more festive atmosphere," Goodwin says.
Read More: Chris Goodwin, Sierra Fox Celebrate 2020 Commencement at Home Along with 4,000 StudentsBiochemistry & Biophysics Hold First Virtual Awards Ceremony
Saturday, May 16, 2020
On Friday May 15th, the department held it's first virtual awards ceremony. Please see the video below:
Congratulations to all of our graduates:
Ph.D. Program in Biochemistry
Meemanage (Dudarshika) De Zoysa
Sierra Fox
Christopher Goodwin
Wan-Jung (Christine) Lai
Jiyu Wang
Hong Zhu
Ph.D. Program in Biophysics
Debapratim (Dave) Dutta
Letty Leslie Salas-Estrada
Congratulations to our 2020 award winners:
Walter S. Bloor Award
For excellence of the Ph.D. thesis and in the research leading to the dissertation in the Program in Biochemistry
Christopher Goodwin, Jiyu Wang
Marvel-Dare F. Nutting Award In recognition of an outstanding graduate receiving a Ph.D. in Biochemistry
Hong Zhu
George V. Metzger Award For excellence of the Ph.D. thesis and in the research leading to the dissertation in the Program in Biophysics
Leslie Salas-Estrada
Fred Sherman Award Program in Biochemistry award to a student who exemplifies the imagination, the excellence in the pursuit of scientific knowledge, and the commitment to the scientific community that were characteristic of Dr. Fred Sherman
Lisa Houston, Nazish Jeffery
William F. Neuman Award Program in Biophysics award for academic, scientific and personal qualities exemplifying the imagination, enthusiasm and excellence in the pursuit of scientific knowledge which were characteristic of the life of Dr. Neuman
Dan Steiner
William F. & Margaret W. Neuman Travel Award
Lauren Benoodt, Ashlin Poruthoor, Yoshita Srivastava
Elena Gilde Grossfield Biophysics Trainee Presentation Award
Talk -- Matt Brewer
Poster -- Gabrielle Kosoy
Dr. Hong Zhu Receives Marvel Dare Fellows Nutting Award
Friday, May 15, 2020
Dr. Mark Dumont, Advisor. Awarded by the Department of Biochemistry.
Marvel-Dare Fellows Nutting was the first woman to receive the Ph.D. in Biochemistry at the University of Rochester, June 1938. Her thesis, The Anti-Gonado Trophic Hormones in the Normal Blood Serum reflected the interests of Dr. Arthur Elden, Professor of Obstetrics and Gynecology and Dr. Willard Allen, Professor of Anatomy. Prior to beginning the Ph.D., she had worked with Professor Bloor, the first Chairman of Biochemistry and Dr. William McCann, Chair of the Department of Medicine. After time extending her thesis work, she took a position in Washington, DC as a Medical School faculty member, teaching biochemistry to students in the V-12 Program (an accelerated M.D. program designed to provide doctors for World War II)
In 1947, she began a career in the Department of Agriculture in California as an Associate Biochemist, with a focus on vitamins in vegetables, including frozen foods being developed at that time. A specific interest was Vitamin C in tomatoes and in this work she developed photometric and other technology for analysis. She headed a research group in food appraisal and statistics. An avid athlete she remained active in sports until her death in 2005.
She donated her hood from the 1938 graduation ceremony as her means of honoring women graduates in the Department of Biochemistry. In addition she has contributed funds to support the Nutting Student Travel Award as well as for the award associated with the Nutting Hood.
In 2004, at age 94 when the Nutting Hood Award was established, Dr. Nutting wrote:
"Words are inadequate to express my deep and sincere feeling of awe and humbleness in this matter. I can only ask you to extend my great thanks to everyone involved in this unexpected honor with its further extension into other years. I am convinced my thanks are in no way equal to these happenings. They are from the bottom of my heart".
Hong Zhu's thesis project focused on the identification of variant forms of the HIV envelope protein for use in HIV vaccine development. Dr. Zhu initially helped to establish a technology for displaying and detecting the envelope protein on the surface of yeast cells as a system allowing the protein to be subjected to in vitro evolution. Since poor binding of envelope protein to antibody precursors appears to be a major barrier to the elicitation of neutralizing responses to potential HIV vaccines, Dr. Zhu used large-scale random mutagenesis and extensive screening by flow cytometry to identify variant forms of the envelope that exhibit enhanced binding to precursor forms of broadly neutralizing anti-HIV antibodies. The variant forms of the envelope that she identified are likely to be trapped in conformational states that allow enhanced access for antibody binding. While performing this work, Dr. Zhu also completed coursework allowing her to receive a Master of Science Degree in Technical Entrepreneurship and Management jointly from the Simon Business School and the Hajim School of Engineering and Applied Sciences. While conducting her Ph.D. research, she also served as a consultant for Estée Lauder Inc.
Graduate Student Viktoriya Anokhina Elected Co-Chair of Gordon Research Seminar
Monday, May 11, 2020
Congratulations to Viktoriya Anokhina who was elected as a co-chair of the Gordon Research Seminar Nucleosides, Nucleotides and Oligonucleotides, to be held in 2021. The Gordon Research Seminar is a 2-day meeting that precedes a Gordon Research Conference. These seminars are organized by early-career scientists for trainees of all levels and junior scientists. Some of Viktoriya's responsibilities as a co-chair will include Keynote speaker selection and invitation, career panel participants invitations, fundraising, selection of speakers from submitted abstracts, and other organizational activities. To attend the 2019 meeting, Viktoriya was supported by the Sayeeda Zain and Graduate Women in Sciences travel awards.
Center for RNA Biology Contributes to Fighting Coronavirus
Tuesday, April 28, 2020
Viruses like the coronavirus that causes COVID-19 are able to unleash their fury because of a devious weapon: ribonucleic acid, also known as RNA.
A contingent of researchers at the University of Rochester study the RNA of viruses to better understand how RNAs work and how they are involved in diseases. As COVID-19 continues to spread around the globe, RNA research provides an important foundation for developing antiviral drugs, vaccines, and other therapeutics to disrupt the virus and stop infections.
"Understanding RNA structure and function helps us understand how to throw a therapeutic wrench into what the COVID-19 RNA does—make new virus that can infect more of our cells and also the cells of other human beings," says Lynne Maquat, professor of biochemistry and biophysics at the University of Rochester Medical Center and the director of Rochester's Center for RNA Biology.
In the past few decades, as scientists came to realize that genetic material is largely regulated by the RNA it encodes, that most of our DNA produces RNA, and that RNA is not only a target but also a tool for disease therapies, "the RNA research world has exploded," Maquat says. "The University of Rochester understood this."
In 2007, Maquat founded the Center for RNA Biology as a means of conducting interdisciplinary research in the function, structure, and processing of RNAs. The center involves researchers from both the River Campus and the Medical Center, combining expertise in biology, chemistry, engineering, neurology, and pharmacology.
While much of the research across the University has been put on pause, labs that are involved in coronavirus research remain active.
"Our strength as a university is our diversity of research expertise, combined with our highly collaborative nature," says Dragony Fu, an assistant professor of biology on the River Campus and a member of the Center for RNA Biology. "We are surrounded by outstanding researchers who enhance our understanding of RNA biology, and a medical center that provides a translational aspect where the knowledge gained from RNA biology can be applied for therapeutics."
Read More: Center for RNA Biology Contributes to Fighting CoronavirusROC biotech company says lab tests of former cancer drug confirm it stops COVID-19
Wednesday, March 11, 2020
A vaccine for COVID-19 is likely years away. Yet a drug tested in a lab three weeks ago has been found to stop the virus from spreading from cell to cell.
The stunning announcement comes from a Rochester biotech company called OyaGen, Inc. The company is seeking to fast-track the formula to treat people who become infected.
"A treatment right now is the priority," said Dr. Harold Smith of OyaGen. He added the drug already has FDA approval for another use.
The tests were conducted at the federal government's integrated research facility in Fort Detrick, Md. A drug called Oya 1 had already been proven in lab tests there to be effective against Ebola.
"If it worked for Ebola, is it absolutely unique to Ebola, or would it work on other viruses?" asked Dr. Smith - though he said an actual drug for human consumption was never pursued.
The coronavirus was still new and contained to Wuhan, China when a sample of the live virus was shipped to the government lab for testing with Oya 1. Test samples viewed under a microscope show a clear "before" and "after" that indicates properties that allowed the virus to grow and spread were neutralized.
"The drug was so effective that, even though we got through our dose-testing, we had literally sterilized the culture of the virus, so we knew this was a powerful thing," said Dr. Smith.
Under a different name, Oya-1 was first developed in the 1960s as a treatment for cancer. It was later shelved as ineffective, but not before it received approval from the Food and Drug Administration. Safe dosage levels were determined for men, women and children.
"Clinical trials have already been done on this compound and, if safety is a main issue, we feel safety has been addressed years ago," said Dr. Smith.
He said preliminary research indicates a single dose of the medicine stops the progression of COVID-19 for eight days and continues to work at half-strength for another four days.
The question is whether the drug will react to the virus the same way in the body as it has in the lab. When an approved drug is proposed for a new use, the FDA usually requires new clinical trials.
13WHAM News reached out to the FDA, but we have not yet received a response.
OyaGen says the live virus tests were conducted and validated by a third party - the U-S government, and argue that is also a reason the drug should be fast-tracked.
"You've got this compound that's absolutely lethal to the virus, and we know it has a margin of safety in people," said Dr. Smith. "What are we waiting for?"
Read More: ROC biotech company says lab tests of former cancer drug confirm it stops COVID-19Golisano Children's Hospital Thanks the Department for it's Toy Drive Donations
Tuesday, February 11, 2020
Professor Harold Smith Organizes Preclinical Drug Discovery Conference
Thursday, November 14, 2019
Harold Smith, Ph.D., Professor of Biochemistry and Biophysics, will serve as Chair and organizer for the 5th Annual International Preclinical Drug Discovery Conference to be held November 21-23, 2019 in Boston. Dr. Smith will also speak at the conference, and several other University of Rochester students, postdocs and faculty will also participate. The link to the meeting can be found her: https://unitedscientificgroup.com/conferences/drug-discovery/pdfs/DrugDiscovery-2019_Program.pdf
Lynne Maquat Honored by International Union of Biochemistry and Molecular Biology
Tuesday, October 29, 2019
Lynne Maquat, Ph.D., the J. Lowell Orbison Endowed Chair and Professor in the Department of Biochemistry and Biophysics, was honored with the International Union of Biochemistry and Molecular Biology (IUBMB) Jubilee Lectureship in September. The IUBMB unites biochemists and molecular biologists in 75 countries and is devoted to promoting research and education in biochemistry and molecular biology, giving particular attention to areas where the subject is still in its early development.
The IUBMB Jubilee Lectureship was established to commemorate the 50th anniversary of the First International Congress of Biochemistry that was held in Cambridge, England in 1949, at which the initial steps were taken that led to the formation of IUBMB. Maquat gave the keynote lecture at the IUBMB Molecular Biosystems Conference in Puerto Varas, Chile on September 30 and was presented with a medal in recognition of the event.
The founding director of the University of Rochester's Center for RNA Biology, Maquat has spent her career deciphering the many roles that RNA plays in sickness and in health. She's an international leader in the field and is credited with several major discoveries that are informing a new generation of therapies for a wide range of genetic disorders.
Her lecture, titled "Nonsense-mediated mRNA Decay in Human Health and Disease," described her discovery of nonsense-mediated mRNA decay or NMD and how this important surveillance system protects against mistakes in gene expression that lead to disease. She also discussed ongoing work on how misregulation of NMD in Fragile X Syndrome, the most common single gene cause of intellectual disability and autism, results in neuronal defects that typify this disorder.
BMB Faculty Peng Yao co-organizes 2019 Rustbelt RNA Meeting
Monday, October 28, 2019
Peng Yao, Ph.D., an Assistant Professor in the Department of Medicine, CVRI and a member of the Biochemistry and Molecular Biology Graduate Program co-organized the 2019 Rustbelt RNA Meeting with Drs. Hua Lou and Jo Ann Wise of Case Western Reserve University. The conference, with approximately 400 attendees was held on October 25th & 26th, at Case Western University and featured 25 speakers, including a workshop on "Using CRISPR-Cas13 to target and detect RNA" by Dr. Mitch O'Connell and talk or poster presentations by laboratory members from the labs of Drs. Charles Thornton, Dragony Fu, and Peng Yao. BMB Students Omar Hedaya and Feng Jiang helped design and construct the meeting booklet and organize the meeting. The meeting was supported by the University of Rochester Center for RNA Biology and the Department of Biochemistry and Biophysics, among 19 other departments, 10 industrial vendors, and 5 journals/societies.
UR trainees who presented a talk or poster at the 2019 RBR Meeting
Jenna M. Lentini (graduate student from Dragony Fu lab) gave a talk and won an outstanding presentation award for graduate students.
Kejia Zhang (graduate student from Dragony Fu lab) gave a poster presentation.
Matthew Tanner (graduate student from Charles Thornton lab) gave a poster presentation.
Kadiam C Venkata Subbaiah (postdoctoral fellow from Peng Yao lab) gave a talk.
Jiangbin Wu (postdoctoral fellow from Peng Yao lab) gave a poster presentation.
Chris Goodwin Successfully Defends His Thesis
Thursday, August 1, 2019
On July 29, Chris Goodwin successfully defended his thesis, "The intersection of Human Cytomegalovirus infection and innate immune signaling", thereby obtaining his Ph.D. Chris found that the cellular IKK kinases limit the ability of Human Cytomegalovirus to initiate infection. Further, he found that the Human Cytomegalovirus UL26 protein prevents IKKB from inducing the expression of anti-viral interferon stimulated genes. Chris' work sheds new light on the measures and counter-measures taken by viruses and host cells to try to control the outcome of infection. Chris was mentored by Joshua Munger, and was awarded the Fred Sherman Biochemistry Award, the URBest Sharing Science Video Communication Award, and the Biochemistry Student Seminar Award. Good luck as you embark on your independent career Chris!
T32 Trainee Brandon Berry Writes on Criticism and Confidence in Graduate Studies
Wednesday, July 24, 2019
Professor Russell Hilf Receives Recognition for 50 Years of Service to the University
Tuesday, July 23, 2019
Professor Russ Hilf celebrated 50 years of service at the University of Rochester Medical Center on June 19th, 2019, by presenting an overview of his life, career and scientific accomplishments. He was also presented with a plaque commemorating his 50 years of service to the University from the Department of Biochemistry and Biophysics. Dr. Hilf's first appointment, as an Associate Professor, began July 1, 1969.
Dr. Hilf receives the commemorative plaque from Jeff Hayes, Chair of the Department of Biochemistry and Biophysics.
Lynne Maquat Interviewed at the RNA Symposium at Cold Spring Harbor Laboratory
Monday, June 17, 2019
Harold Smith Featured on Roc NORML Radio
Wednesday, May 22, 2019
So what exactly happens inside your body when you consume Cannabis? Dr. Smith outlines the powerful role of the Endocannabinoid System in modulating human health, and discusses the future of Cannabis research and testing.
Read More: Harold Smith Featured on Roc NORML RadioCongratulations Dalia Ghoneim for winning a Born Seekers Fellowship
Wednesday, May 8, 2019
The Born Seekers fellowship is a speech contest that is open to women in STEM. The work they do pushes boundaries and meaningfully impacts society on a local, national, and often global level. The women selected as our 2019 Born Seekers build skills in communication and leadership, serving as role models for the next generation of scientists, engineers, doctors, and STEM professionals.
Dalia Ghoneim is a PhD candidate in Genetics at the University of Rochester in Rochester, NY. She develops and contributes to software that helps us understand the structure and functions of genetic molecules, and has worked to analyze mutations in DNA from patients with severe neurological diseases like epilepsy and autism. This work was instrumental to identifying new genes that cause these diseases. Dalia takes as many opportunities as she can to share science with others by participating in outreach and advocating for inclusion in science. Outside of science, Dalia is a single mother to four wonderful children, a competitive runner, and enjoys figure drawing and learning and experiencing new things.
31st Annual Genetics Day Symposium
Monday, April 22, 2019
The Departments of Biomedical Genetics and Biology, with the support of the University Committee for Interdisciplinary Studies, host the 31st annual Genetics Day Symposium on Thursday, April 25, from 9:30 a.m. to 4 p.m. in the Class of '62 Auditorium and Flaum Atrium. This year's Fred Sherman Lecturer will be Phillip Zamore, a Howard Hughes Medical Institute investigator and professor of biomedical sciences at the University of Massachusetts Medical School, giving a talk titled "piRNAs and the Struggle to Reproduce."
Read More: 31st Annual Genetics Day SymposiumByron Rubin, Ph.D., Adjunct Professor in the Department of Biochemistry and Biophysics, pens article in ASBMB TODAY
Monday, February 18, 2019
Dr. Rubin describes his own battle with prostate cancer, and how as a scientist how he took control of his own treatment. He also describes the impact of personalized medicine on his medical decisions and how he deals with living with cancer. Read the article.
Former Biochemistry Student Jerry Madukwe, Ph.D. travels to West Africa to Speak With Students
Wednesday, January 30, 2019
Jerry Madukwe, Ph.D., who received his Ph.D. in Biochemistry (2018), and is currently a postdoctoral fellow at Yale University, recently completed a 2-week science-outreach trip to West Africa. Jerry was invited by the West Africa Center for Cell Biology of Infectious Pathogens at the University of Ghana, and the Department of Life sciences at the University of Ilorin in central Nigeria to talk about the work he did as a PhD student and about graduate school in the United States. Jerry, who hails from Nigeria, and got his BS from Lee University in Tennessee, also used the opportunity to visit his former elementary school where he talked to fifth grade pupils about science (see photos), and to demonstrate DNA extraction from bananas. The kids were very excited by his visit, and Jerry found the experience very fulfilling.
Chavali, Couch, DeZoysa and Hao Win Sayeeda Zain Travel Award
Tuesday, December 18, 2018
The department is pleased to announce the winners of the Sayeeda Zain Fall Travel awards: Shashank Chavali, Tyler Couch, Meemanage Dudarshika DeZoysa and Fanfan Hao.
The Sayeeda Zain Travel Award honors the distinguished career and charitable life of Dr. Sayeeda Zain. The award is given in recognition of research excellence to support travel and related expenses associated with attendance at a scientific conference or corporate internship to gain practical experience. The next round of Sayeeda Zain Travel Awards will be offered in Spring 2019.
Thank you to all those who applied and congratulations to Shashank, Tyler, Dudarshika and Fanfan!
Professor Harold Smith, Ph.D. appears on Evan Dawson Radio Program
Thursday, November 29, 2018
Harold C. Smith was a guest along with Bob Duffy (CEO of the Greater Rochester Chamber of Commerce), Jason Klimek (attorney with Boylan Code), Zachary Sarkis (co-founder of Flower City Solutions) and Jacob Fox (founder of Closed Loop Systems) on WXXI Connections with Evan Dawson on 11/21/2018 to address the opportunities and questions surround the emerging hemp industry in Up State NY. (listen to Hemp101http://www.wxxinews.org/programs/connections?page=1&ajax=1)
Dr. Smith spoke regarding the future of labeling and dosing of THC-free and THC-containing products relative to what we understanding from scientific and clinical research. Having founded CannaMetrix, LLC, a New York based company, Dr. Smith seeks to establish through patent pending, cell-based assays, to raise the standards for product development and quality control so as to better information patient choices of products containing full spectrum plant cannabinoids or synthetic cannabinoids and advance medicinal use of cannabis.
Wedekind Co-Organizes Nucleic Acids Session at American Crystallographic Association Annual Meeting in Toronto
Friday, November 9, 2018
Highlights of Session 1.1.2 on Nucleic Acid were reported in ACA RefleXions Fall 2018 and provided many new insights into the form and function of nucleic acids and was co-organized by Dr. Joseph Wedekind and Dr. Rui Zhao. Dr. Wen Zhang of Harvard University presented mechanistic studies of non-enzymatic RNA polymerization using custom phosphoramidites with imidazole leaving groups that were caught in the act of catalysis by crystallographic snapshots. This work has implications for catalysis in a pre-biotic RNA world. Sun Cheol Park from Kangwon National University, Korea described DNA recognition by the PadR repressor. Binding of phenolic acid blocks DNA binding to relieve PadR repression, activating downstream detoxification genes. Dr. Yun-Xing Wang from NIH/NCI described use of an X-ray free electron laser to capture conformational changes of the adenine riboswitch during effector binding, providing insights into RNA-mediated translational regulation.
Prof. Clara Kielkopf from the University of Rochester described progress to decode the basis of 3´-splice site recognition of pre-mRNA by U2AF proteins, including polypyrimidine tract recognition and binding to degenerate splice-sites. The work has implications for correction of splicing defects found in human diseases. Dr. Eric Montemayor from the University of Wisconsin described later steps of pre-mRNA splicing, including a model for U6 snRNA remodeling by contacts to the Lsm2-8 ring protein and the Prp24 chaperone. Dr. Soumya Remesh from the Lawrence Berkeley National Lab used small angle scattering and soft X-ray tomography to reveal how small molecules interact with the abundant HU protein to alter DNA supercoiling. The work has implications for controlling bacterial gene expression. The session was anchored by Dr. Ailong Ke of Cornell University who presented structural snapshots that contribute a novel mechanistic framework to describe how bacterial type II-A CRISPR systems create new molecular memories of short, foreign 'spacer' DNAs that invade bacterial cells.
Dumont Receives 2018 Outstanding Graduate Student Teacher Award
Tuesday, November 6, 2018
Biochemistry professor Mark Dumont, Ph.D. is the recipient of the 2018 Outstanding Graduate Student Teacher Award. Established in 2013, this award is given to an outstanding graduate student teacher for record of excellence in classroom instruction. Mark was nominated by graduate students Brandon Davis, Ashwin Kumar and Matthew Raymonda.
This award was presented at the School of Medicine and Dentistry Convocation Ceremony, September 6, 2018.
The department would like to extend congratulations to Mark on this well- deserved honor.
Kielkopf Lab Wins Annual Halloween Door Contest
Thursday, November 1, 2018
The department would like to thank all that participated in the BCBP Halloween Door Contest this year!
This year the winner is…
The Kielkopf Lab!!
Tied for second place are the Ermolenko Lab and the Grossfield Lab! Congratulations to everyone – the doors looked awesome!
Maquat Inducted into National Academy of Medicine
Sunday, October 21, 2018
Lynne Maquat, PhD, was inducted into the National Academy of Medicine (NAM) on Saturday October 13th in Washington, DC. Here, she is receiving her diploma and congratulations from Victor Dzau, MD, President of NAM after being introduced by J. Michael McGinnis, MD, the Executive Officer of NAM.
Clara L. Kielkopf, Ph.D. Receives Drug Development Grant From UR Ventures For Research To Cure Myelodysplastic Syndromes
Thursday, October 18, 2018
Myelodysplastic Syndromes (MDS) are a group of diverse bone marrow disorders, in which the bone marrow does not produce enough healthy blood cells. MDS is often referred to as a “bone marrow failure disorder.”
Congratulations, Clara and her lab!
Department of Biochemistry and Biophysics Loans Famous Statue to University of Rochester’s Laboratory of Laser Energetics
Wednesday, October 17, 2018
The Department of Biochemistry and Biophysics has loaned a statue of J. Robert Oppenheimer and Albert Einstein to the Laboratory of Laser Energetics. The sculpture was commissioned by the Department of Radiation Biology and Biophysics (William Neuman and Aser Rothstein co-chairs) in October of 1968 and was crafted by Achille Forgione, a notable Rochester artist. The work was in place by the fall of 1970, originally at the entrance to the OO wing, then moved to the Blair Library (no longer in existence). The statue has been in the back of the Neuman Room for many years. It is now displayed prominently in the LLE lobby. An engraved plate will be placed next to the statue, reading: "Albert Einstein, J. Robert Oppenheimer, Statue commissioned by Dr. William "Bill" Newman, On loan from the University of Rochester's Department of Biochemistry and Biophysics"
For more information on Dr. Neuman and his work please visit our department featured alumni page.
Wedekind Lab Co-Crystal Structure of HIV RNA in complex with a Lab-Evolved Protein on the Cover of Nucleic Acids Research
Tuesday, July 31, 2018
Co-crystal structure of HIV trans-activation response (TAR) RNA (rainbow ribbon) in complex with lab-evolved protein, TBP6.7 (blue Cα ribbon). A short peptide (pink) binds TAR outside the context of TBP6.7. (art by Joseph Wedekind). The underlying electron micrograph shows HIV virions (CDC image #13472 by Maureen Metcalfe and Tom Hodge).
Nucleic Acids Research Breakthrough article describes structure of HIV TAR complex with engineered binding protein and structure-based synthesis of antagonist
Investigators at multiple research institutes, led by Dr. Joseph Wedekind (University of Rochester) have described the high resolution crystal structure of a laboratory-evolved protein bound to its tightly associated HIV TAR RNA target, and subsequent synthesis and characterization of a stapled peptide mimic of the predominant RNA binding epitope in that protein. The study provided a detailed framework for peptide-mediated TAR recognition that might be generally applicable to target other disease-relevant RNAs.
HIV/AIDS is a global health threat that requires new insights into viral targets, especially those that resist mutation and promote novel aspects of the viral life cycle. In these respects, the HIV-1 trans-activation response (TAR) RNA is of ongoing interest. Previously, investigators (including some from this author group) developed methods to produce a unique lab-evolved protein ('TBP6.7') that recognizes TAR with extraordinarily high affinity compared to known TAR binders [Crawford et al. McNaughton (2016) ACS Chem. Biol. 8, 2206]. However, the molecular determinants of TAR recognition remained obscure, thus limiting the investigators' ability to further exploit that discovery. The crystal structure of this complex allowed investigators to determine that only a subset of the 'evolved' protein sequences are actually involved in RNA binding, with the preponderance of interactions localized to a short β-hairpin. This observation led them to synthesize a short, stapled peptide that mimics the β-hairpin and attenuates TAR-dependent transcription in HeLa nuclear lysate.
The study reported here [Belashov et al. Wedekind (2018) Nucleic Acids Res. 46, 6401-6415] is highly multi-disciplinary, spanning crystallography, site-directed mutagenesis, calorimetry, cell-surface display, ELISA, transcription assays, molecular dynamics simulations, and constrained peptide synthesis. In the end, the conversion of the parental RNA binding protein from single- to double-stranded RNA recognition implies that the protein has sufficient plasticity to recognize numerous RNA folds.
Reviewers and editors familiar with the work have stated that the study is "a strong contribution to a difficult field" that "will have substantial impact in the field of RNA recognition, ranging from applied (specifically targeting therapeutically relevant RNAs) to basic (understanding how RRMs bind to specific RNAs in the cell)"
The Wedekind laboratory at the University of Rochester investigates the mechanisms of action of non-protein-coding (nc)RNAs, and is interested especially in the three-dimensional architectures of these RNAs and how they bind to specific small molecules or peptides, leading to conformations that alter biological function. The research was supported by the University of Rochester Center for AIDS Research, and the National Institutes of Health.
Biochemistry & Biophysics Students Going Places
Tuesday, June 12, 2018
By Dr. Joseph Wedekind
The Department of Biochemistry & Biophysics is pleased to announce the winners of the Sayeeda Zain Fall Travel awards: Debapratim Dutta, Sierra Fox and Hong Zhu.
The Sayeeda Zain Travel Award honors the distinguished career and charitable life of Dr. Sayeeda Zain. The award is given in recognition of research excellence to support travel and related expenses associated with attendance at a scientific conference or corporate internship to gain practical experience.
Debapratim (Dave) Dutta is presenting a poster and was invited to give a talk at the Annual RNA Society Meeting (Berkeley, CA). Sierra Fox presented a poster and was a Keystone Symposia Future of Science Fund Scholarship recipient at the Keystone Symposia in Chromatin Architecture and Chromatin Organization, and Gene Control in Development and Disease Symposia (Whistler, BC, Canada). Hong Zhu presented a poster at the III International Conference on Vaccines Research and Development (Washington, DC).
Debapratim (Dave) Dutta
Sierra Fox
Hong Zhu
Congratulations to the 2018 Biochemistry Graduates!
Tuesday, May 22, 2018
Pictured are Anne Cheng, Venice Magunga, and Anmol Almast following the Arts, Sciences & Engineering commencement ceremony Sunday. Photo reproduced from 5-21-18 issue of @Rochester
The Department of Biochemistry and Biophysics congratulates the 20 young men and women who received their B.S. in Biochemistry this weekend. We look forward to their continued success in their future training and careers! In addition to the University-wide celebration, these graduates received their diplomas at a ceremony in The Class of ’62 Auditorium, attended by their families, friends, and faculty from the many departments involved in their training. The ceremony was officiated by Beth Grayhack, Ph.D., Director of the Undergraduate Program (Biochemistry and Biophysics), and was enriched by addresses from Sina Ghaemmaghami, Ph.D. (Biology) and Mark Dumont (Biochemistry and Biophysics).
Biochemistry and Biophysics Holds Annual Department Awards Ceremony
Sunday, May 20, 2018
On Friday May, 18th the department held it's annual awards ceremony in the Neuman Room. At the event this year the following awards were awarded to our current B&B graduate students:
- Bloor Award - Christina Brule and Lu Han
- Metzger Award - Karl J. P. Smith
- Sherman Award – Bronwyn Lucas
- Neuman Award – Chapin Cavender
- Grossfield Award – Sreyoshi Sur (talk), Lauren Benoodt (poster)
- Student Seminar Award – Fall: Bronwyn Lucas (BMB), Leslie Salas-Estrada (BSCB)
Spring: Viktoriya Anokhina (BMB), Daniel Steiner (BSCB)
- Hooker Award – Dudarshika DeZoysa (BMB), Christina Lai (BMB)
- Goodman Fellowship (3rd place for the Messersmith Award) – Leslie Salas-Estrada
- Faculty Award – Mark Dumont (BMB), Alan Grossfield (BSCB)
- Zain Award – Christine Lai, Lingfeng Luo, Louis Smith
Congratulations to all the winners and our 2018 graduates!
A Hidden Promise in the Language Cells Use to Communicate
Tuesday, May 8, 2018
Scientists have begun to implicate extracellular vesicles and exosomes in everything from cancer to viral infections to basic neural functioning. To Lynne Maquat, the J. Lowell Orbison Distinguished Service Alumni Professor in the Department of Biochemistry and Biophysics, the process shows how parts of the genome we used to think of as junk actually have important functions. “You could say that the host domesticated a viral sequence for its own purposes,” Maquat says. “That’s the beauty of our complexity—[these elements] allow tinkering or fine-tuning of genes.”
Read More: A Hidden Promise in the Language Cells Use to CommunicateMaquat Wins the 2018 FASEB Excellence in Science Award
Sunday, April 22, 2018
Looking to RNA for Answers
Friday, March 23, 2018
Cancer is a group of diseases in which the body's cells divide uncontrollably and invade nearby tissues. Scientists at Wilmot Cancer Institute and the University of Rochester's Center for RNA Biology are working to understand more about how and why this happens.
One piece of the puzzle they're studying is ribonucleic acid, or RNA, which is found in all cells. RNA is made in the nucleus of a cell from our DNA, which holds the instruction manual for life. RNA puts those instructions into action.
RNA comes in many forms. One form, called messenger RNA (mRNA), carries those instructions out of the nucleus to the ribosomes, where proteins are made. These proteins are essential for functions ranging from digestion to protecting us from disease. If the mRNA has a bad copy of instructions, then either a faulty protein or no protein is created, leading to diseases like cancer.
Understanding the quality-control system
Lynne E. Maquat, Ph.D., director of the Center for RNA Biology, studies a quality control process that blocks cells from making faulty proteins. Called nonsense-mediated mRNA decay (NMD), this process comes into play when mRNA has a set of instructions with a mistake that will lead to short or incomplete proteins. NMD acts like a set of factory inspectors that find and destroy this mRNA before the faulty proteins can be made.
Sometimes, though, NMD doesn't catch the mistakes and harmful proteins are made. This process plays a part in one-third of all inherited diseases, such as cystic fibrosis and muscular dystrophy, and one-third of all acquired diseases, including a number of cancers.
One reason is that tumors can influence how these inspectors work. Maquat and her team are looking for ways to stop tumors from interfering with NMD with the goal of finding new ways to treat cancer.
Slowing cancer's growth
A team from Maquat's lab has also identified a protein called Tudor-SN that is important as cells prepare to divide. This protein controls many microRNAs, molecules that are very small RNAs that control the expression of tens of thousands of genes.
The scientists found that when Tudor-SN is removed from human cells, levels of hundreds of microRNAs go up, putting the brakes on genes that encourage cell growth. This slows down the process of cell division known as the cell cycle, which goes awry in cancer.
Maquat and Reyad A. Elbarbary, Ph.D., a former post-doctoral fellow in Maquat's lab, have filed a patent application for methods that target Tudor-SN for the treatment and prevention of cancer. They continue to study how Tudor-SN works in concert with other molecules and proteins so that scientists can identify the most appropriate drugs to target it.
Other avenues
Scientists at the Center for RNA Biology are also looking at RNA's other roles in cancer to find new treatment strategies. For example, Mitchell O'Connell, Ph.D., is studying how microRNAs can interfere with the way genes are expressed and lead to cancer. He and his team are using the gene-editing technology known as CRISPR, which he has adapted to edit RNA, to learn more about the proteins involved in this process.
Yi-Tao Yu, Ph.D., and his team are studying various ways to modify mRNA so that it can override mistakes in genetic instructions. Sometimes there's a premature stop signal that orders a cell to stop reading the genetic instructions in mRNA partway through the process, resulting in an incomplete protein. The Yu lab is working to alter mRNA in ways that turn "stop" signals into "go" signals, creating full length proteins and preventing diseases like cancer.
The study of RNA biology is allowing scientists and physicians to explore entirely new treatment strategies for cancer and a wide range of other genetic and acquired disorders.
Learn more about the work being done at the Center for RNA Biology.
By Lydia Fernandez
Read More: Looking to RNA for Answers
Maquat Wins 17th Annual Wiley Prize in Biomedical Sciences
Tuesday, February 20, 2018
The Wiley Foundation today announced the 17th annual Wiley Prize in Biomedical Sciences will be awarded to Lynne E. Maquat for elucidating the mechanism of nonsense-mediated messenger RNA decay, a fundamental process whereby cells remove defective transcripts that can encode toxic proteins.
Dr. Maquat is a Professor at the Department of Biochemistry & Biophysics in the School of Medicine and Dentistry, the Founding Director of the Center for RNA Biology: From Genome to Therapeutics, the Founding Chair of the University of Rochester Graduate Women in Science, and the J. Lowell Orbison Endowed Chair at the University of Rochester in Rochester, New York.
"The 2018 Wiley Prize honors Dr. Maquat, whose work illuminated how our cells prevent production of toxic proteins by removing defective messenger RNAs," said Dr. Titia de Lange, chairperson of the awards jury for the Wiley Prize at the Rockefeller University in New York City.
"The Wiley Foundation honors research that champions novel approaches and challenges accepted thinking in the biomedical sciences. The work of the 2018 Wiley Prize recipient Lynne Maquat truly upholds this mission," said Deborah Wiley, Chair of the Wiley Foundation. "We are pleased to highlight the impact that her research on messenger RNA decay pathways has had in advancing our knowledge of the cellular cause of many human diseases."
Dutta, Fox, and Zhu Win Sayeeda Zain Travel Award
Tuesday, January 2, 2018
The department is pleased to announce the winners of the Sayeeda Zain Fall Travel awards: Debapratim Dutta, Sierra
Fox and Hong Zhu.
The Sayeeda Zain Travel Award honors the distinguished career and charitable life of Dr. Sayeeda Zain. The award is
given in recognition of research excellence to support travel and related expenses associated with attendance at a
scientific conference or corporate internship to gain practical experience. The next round of Sayeeda Zain Travel
Awards will be offered in Spring 2018.
Thank you to all those who applied and congratulations to Dave, Sierra and Hong!
Lynne Maquat Wins Vanderbilt Prize in Biomedical Science
Tuesday, November 28, 2017
Lynne E. Maquat, Ph.D., the J. Lowell Orbison Endowed Chair and Professor in the Department of Biochemistry and Biophysics at the University of Rochester School of Medicine and Dentistry is the recipient of the 2017 Vanderbilt Prize in Biomedical Science. Established by Vanderbilt University School of Medicine in 2006, the competitive prize honors women scientists with a "stellar record" of research accomplishments who have made significant contributions to mentoring other women in science.
Maquat is internationally known for a huge body of research that describes what goes wrong in our cells during disease. The founding director of the University of Rochester's Center for RNA Biology, she has spent her career deciphering the many roles that RNA plays in sickness and in health.
She's dedicated a great deal of time to helping women advance in scientific careers and in 2003 established the University of Rochester Graduate Women in Science program. Through monthly round-table discussions with high-profile speakers who are using advanced degrees in traditional and non-traditional ways, the program seeks to broaden awareness of what women can do with a Ph.D. Program members can apply for travel awards to attend conferences, seminars or other external events that will help them advance their careers.
Maquat, also a professor in the Wilmot Cancer Institute, is the recipient of other prestigious honors, including the Canada Gairdner International Award; the International RNA Society's Lifetime Achievement Awards in Service and in Science; the Federation of American Societies for Experimental Biology (FASEB) Excellence in Science Award; the Rochester ATHENA Award®; and election to the National Academy of Medicine, the National Academy of Sciences and the American Academy of Arts and Sciences.
Maquat is the 12th recipient of the Vanderbilt Prize in Biomedical Science and will receive the prize on November 29, 2018, when she is scheduled to give a Flexner Discovery Lecture. She will also meet with Vanderbilt faculty and mentor Vanderbilt Prize Scholars, women who are pursuing graduate studies in the biomedical sciences in the School of Medicine.
"We are thrilled that Dr. Maquat is being recognized for her pioneering work in RNA biology, which has catalyzed innovative areas of research and provided insight to the role of RNA regulation in human disease," said Jennifer Pietenpol, Ph.D., Vanderbilt University Medical Center Executive Vice President for Research and director of the Vanderbilt-Ingram Cancer Center. "She is a world-renowned scientist and an exceptional mentor, a role model for us all."
Read More: Lynne Maquat Wins Vanderbilt Prize in Biomedical ScienceLynne Maquat Delivers Harvey Society Lecture at Rockefeller University
Tuesday, November 7, 2017
Lynne E. Maquat, Ph.D., the J. Lowell Orbison Endowed Chair and Professor in the Department of Biochemistry and Biophysics and Director of the Center for RNA Biology gave a Harvey Society Lecture on October 19 at The Rockefeller University in New York City. The lecture series is one of the most prestigious in the country and the lecturers, who are selected by the Harvey Society's leadership council, are leading biomedical researchers from around the world.
Maquat discussed her career path and the discovery of nonsense-mediated mRNA decay (NMD), which she first described for humans in 1981. NMD is a cellular quality control mechanism that derails the production of unwanted proteins in the body that can disrupt normal processes and initiate disease. Maquat is known around the world for her work on NMD, which is critically important in both normal and disease states. UR President Joel Seligman and URMC CEO and SMD Dean Mark Taubman attended the lecture.
Founded in 1905, the Harvey Society sponsors seven lectures annually that are open to the public and are attended by hundreds of scientists from New York City and the surrounding areas. The Harvey Lectures are one of the great traditions in New York science and they are a place where scientists from different institutions meet regularly.
URMC Scientist Lynne Maquat Elected to National Academy of Medicine
Monday, October 16, 2017
Lynne E. Maquat, Ph.D., an internationally recognized researcher who studies what happens in our cells during disease, has been elected to the National Academy of Medicine. The honor is akin to an actor receiving an Emmy for an outstanding performance; current members of the Academy elected Maquat for her exceptional research in the field of RNA biology. The accolade places her amongst an elite group of scientists and physicians who have made significant contributions to health and medicine.
In studying RNA, a close cousin to DNA, Maquat has discovered intricate cellular processes that influence normal genes, as well as genes involved in a wide range of diseases. Her findings are leading to the development of new treatment approaches for everything from cancer and heart disease, to intellectual and developmental disabilities and other neurologic disorders.
“Lynne is at the forefront of a movement to transform our increasing understanding of RNA biology into promising therapies for virtually all disease processes,” said Mark B. Taubman, M.D., CEO of the University of Rochester Medical Center and Dean of the University of Rochester School of Medicine and Dentistry. “She is an incredible asset to the University and will undoubtedly bring a wealth of valuable experience and knowledge to the National Academy of Medicine.”
Formerly called the Institute of Medicine, the National Academy of Medicine is an independent organization of professionals from diverse fields that advises the nation and the international community on issues in health, medicine and related policy. For example, in 2016 the Academy released a report calling for more and better research into ovarian cancer, one of the deadliest cancers, and recently issued a report detailing how physicians can help combat America’s opioid crisis.
The J. Lowell Orbison Endowed Chair and Professor of Biochemistry & Biophysics and of Oncology at the University of Rochester School of Medicine and Dentistry, Maquat is also an elected member of the National Academy of Sciences and the American Academy of Sciences. She was the first individual from upstate New York to receive the prestigious Canada International Gairdner Award, the country’s top award for excellence in biomedical research, which she won in 2015.
The National Institutes of Health has continuously funded Maquat’s research for the past 34 years and she’s published more than 150 papers and reviews. She is the founding director of the University of Rochester Center for RNA Biology and founding chair of the Graduate Women in Science program. She’s committed countless hours to mentoring the next generation of researchers and advocating for young women in the sciences.
When she is formally inducted into the National Academy of Medicine in October 2018, Maquat will join four other active Rochester faculty members: Seymour I. Schwartz in the Department of Surgery: Elizabeth R. McAnarney in Pediatrics; Paul S. Frame in Family Medicine; and Robert C. Griggs in Neurology.
Read More: URMC Scientist Lynne Maquat Elected to National Academy of MedicineBiochemistry & Biophysics students Mukta Palshikar, Erica VanderWal, and Brandon Davis receive awards at UR School of Medicine Opening Convocation
Friday, September 22, 2017
Congratulations to first year students who received awards at the SMD Opening Convocation on September 12, 2017.
Mutka Palshikar, a first year student in the Biophysics, Structural and Computational Biology program won the Graduate Alumni Fellowship, which recognizes an incoming student with promise for exceptional accomplishment in graduate study.
Arica VanderWal, a first year student in the Biochemistry and Molecular Biology program was awarded the Elmer Stotz Fellowship in Biochemistry, which recognizes the meritorious academic and research accomplishments of an incoming graduate student in the BMB program.
Brandon Davis, an incoming student in the Biochemistry and Molecular Biology program, was a recipient of a Robert L. and Mary L. Sproull University Fellowship, which recognizes the exceptional academic record and research talent of selected students in the first year class University-wide.
Congratulations again to Mutka, Arica, and Brandon!
Mutka Palshikar
Arica VanderWal
Brandon Davis
The CARE Network
Friday, September 8, 2017
The CARE Network, a program that helps support students in distress, is now available for SMD graduate students. Students, faculty and staff are encouraged to submit a referral to the CARE Network if they believe that a student is in or headed towards distress, are aware of an act of discrimination on campus, or have a general concern for a student. The CARE Network provides recommendations to campus and community resources, outlets for safe spaces, and coaches on communication skills to work through difficult discussions and situations. You can submit a referral and/or learn more about the CARE Network at www.rochester.edu/CARE.
Read More: The CARE NetworkDumont Selected as the 2017 Recipient of the Graduate Student Society Advocacy Award
Monday, August 28, 2017
Biochemistry professor Mark Dumont, Ph.D. has been selected as the 2017 recipient of the Graduate Student Society Advocacy Award. This award, established in 1994 by the Graduate Student Society (GSS), is bestowed annually to recognize a faculty member in the School of Medicine and Dentistry who has made significant contributions in promoting excellence in graduate education through participation, facilitation, and promotion of GSS goals and events. The faculty member may be nominated by any SMD student, and is chosen by a GSS Executive Board vote.
The award will be presented at the School of Medicine and Dentistry Convocation Ceremony on Tuesday, September 12th at 4:00pm in the Class of 1962 Auditorium.
The department would like to extend congratulations to Mark on this recognition, as it is a well-deserved honor.
Maquat Honored with FASEB Award, Featured on People Behind the Science Podcast
Friday, August 25, 2017
Dr. Lynne Maquat, J. Lowell
Orbison Endowed Chair and Professor of Biochemistry and Biophysics in the School of Medicine and Dentistry, Director
of the Center for RNA Biology, and Chair of Graduate Women in Science at the University of Rochester was recently
featured on the podcast, People Behind the Science.
Lynne discusses her mentors and career milestones, and offers advice to junior scientists. Maquat recently received
the Federation of American Societies for Experimental Biology's Excellence in Science Award, which recognizes women
who have made outstanding contributions to science through research discoveries and by training the next generation
of scientists.
The entire interview can be listened to for free on
iTunes.
Read More: Maquat Honored with FASEB Award, Featured on People Behind the Science PodcastRuss Hilf listed among life-long ASBMB Members
Thursday, August 17, 2017
Dr. Russell Hilf
Russel Hilf, Ph.D., Professor Emeritus in Biochemistry and Biophysics, was listed among American Society of Biochemistry and Molecular Biology members with at least 50 years of membership.
The ASBMB is a nonprofit scientific and educational organization with over 12,000 members, founded in 1906. The Society's mission is to advance the science of biochemistry and molecular biology and to promote the understanding of the molecular nature of life processes. Congratulations Russ!
Biochemistry Graduate Students Sierra Fox and Chris Goodwin Explain CRISPR Gene Editing on YouTube
Wednesday, August 16, 2017
From left: Sierra Fox and Christopher Goodwin
UR Science ROCs: What's CRISPR?
It’s no secret: URMC is home to extraordinary scientific innovations and research.
Our UR Broadening Experiences in Scientific Training (URBEST) program and our Public Relations and Communications office teamed up to offer our students and trainees the chance to highlight our research through original visuals and videos. Four videos earned prizes for their unique science storytelling and will be featured on our intranet site and the UR Medicine Facebook page throughout the month in an ongoing series called "UR Science ROCs."
What is CRISPR?
Fourth-year graduate students Chris Goodwin and Sierra Fox, and third-year graduate student Nick Nobiletti, talk about CRISPR and how it’s helping scientists edit DNA.
Goodwin is a student in the lab of Joshua Munger, Ph.D.(Department of Biochemistry and Biophysics); Fox is a student in the lab of Michael Bulger, Ph.D.(Departments of Biochemistry and Biophysics and Pediatrics); and Nobiletti is a student in the lab of Angela Glading, Ph.D. (Department of Pharmacology and Physiology).
Payea and Mishra are Inaugural Recipients of the Sayeeda Zain Travel Award
Friday, July 14, 2017
The department of Biochemistry and Biophysics recently presented to the inaugural Sayeeda Zain Travel Award to Mathew Payea and Laxmi Narayan Mishra.
Matthew Payea is a 6th year graduate student in the Biochemistry Ph.D. program studying tRNA biology in laboratory of Eric Phizicky. Matthew received his Bachelors in Science from Eastern Illinois University, majoring in Biochemistry. Matthew used the funding provided by the Sayeeda Zain Travel Award to attend the 22nd annual meeting of the RNA Society in Prague, Czech Republic this past June. There, he gave a talk on his research defining an RNA decay pathway in yeast that destroys mutant tRNAs.
Laxmi Narayan Mishra is a postdoctoral associate working in Dr. Jeffrey J Hayes' Lab in the Department of Biochemistry and Biophysics, University of Rochester Medical Center. He has a Masters degree from University of North Bengal, Darjeeling, India and a Ph.D. in Biochemistry from Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India. His research is focused on how epigenetic modifications alter chromosome structure to facilitate gene expression. His Dr. Mishra will use the Sayeeda Zain Travel Award to attend and present his research findings at the international EMBO conference on "The Nucleosomes: From Atoms to Genomes" at Heidelberg, Germany, in August 2017.
The Sayeeda Zain Travel Award is given semi-annually to one or more graduate students and postdoctoral fellows in the Department of Biochemistry and Biophysics at the University of Rochester School of Medicine and Dentistry. The award honors the life and achievements of Professor Sayeed Zain, Ph.D., a longtime faculty member in the Department of Biochemistry and Biophysics. Learn more about the award and Dr. Zain.
Matthew Payea (left) with Dr. Jeffrey Hayes
Laxmi Narayan Mishra (left) with Dr. Jeffrey Hayes
Budding UR Scientists and Science Communicators
Thursday, July 13, 2017
Emily Boynton and Molly Miles from URMC's Department of Public Relations and Communications met with a small group of URBEST trainees to discuss how the Medical Center and other academic institutions are sharing science in the social world we live in. They provided some examples of different types of visuals and videos that get great engagement on Facebook, Twitter and other social media sites. The goal? URBEST and The Public Relations and Communications team wanted to find and offer prizes for three original visuals or videos from students and trainees that highlight UR innovation and research. Money, video packs and fame!
First prize was awarded to a team of scientists: Chris Goodwin and Sierra Fox from Biochemistry and Molecular Biology and their camera man Nicholas Nobiletti from Pharmacology and Physiology for What Is CRISPR? They split $750 of prize money.
Read More: Budding UR Scientists and Science CommunicatorsJeffrey Hayes Helps Increase Our Understanding of DNA's Path Into Cells
Thursday, June 29, 2017
Scientists are a step closer to understanding how DNA, the molecules that carry all of our genetic information, is squeezed into every cell in the body. How DNA is "packaged" in cells influences the activity of our genes and our risk for disease. Elucidating this process will help researchers in all areas of health care, from cancer and heart disease, to muscular dystrophy and osteoarthritis.
DNA is a long, floppy molecule, and there's more than three feet of it in every cell. Our DNA is housed in structures called chromosomes, which condense the DNA to fit into the cell's tight quarters.
Scientists from the department of Biochemistry and Biophysics at the University of Rochester School of Medicine and Dentistry worked with colleagues in France and Japan to describe the first step of DNA packing in a cell. They provided the first-ever detailed picture of the most basic building block of chromosomes, known as the nucleosome, and found that a protein known as H1 (for linker histone H1) helps DNA become more compact and rigid within the nucleosome. In contrast, when H1 isn't present, the DNA is loose and flexible.
The tight structure that H1 creates helps shield our DNA from various factors that can activate or "turn on" certain genes. Without H1, DNA is more accessible to factors that could trigger disease-causing genes.
Published in the journal Molecular Cell, this finding will inform research on all processes that involve chromosomes, such as gene expression and DNA repair, which are critical to the understanding of diseases such as cancer, according to Jeffrey J. Hayes, Ph.D., senior study author and the Shohei Koide Professor and chair of the department of Biochemistry and Biophysics.
The teams in France and Japan used specialized microscopes and X-rays to capture pictures of DNA molecules interacting with H1 and other key proteins. Because of the size of the DNA and protein molecules, the pictures generated by these techniques were fuzzy and difficult to analyze.
Lead study author Amber Cutter, a graduate student in Hayes' lab, put all of the components -- DNA, H1, and other proteins -- together in tiny test tubes and conducted various biochemical experiments. Her tests, coupled with the X-ray images, confirmed H1's role.
Cutter (pictured at right), who is entering her fifth year in Hayes' lab, admits that the science is complex and that a lot more research needs to be done before this work can inform clinical treatment. But, the importance of understanding the most basic biological processes should not be underestimated. "In order to determine what happens when things go wrong in diseases like cancer, we need to know what happens when things go right."
Hayes and Cutters' work was supported by the National Institutes of Health.
# # #
The University of Rochester Medical Center is home to approximately 3,000 individuals who conduct research on everything from cancer and heart disease to Parkinson's, pandemic influenza and autism. Spread across many centers, institutes and labs, our scientists have developed therapies that have improved human health locally, in the region and across the globe. To learn more, visit www.urmc.rochester.edu/research.
Read More: Jeffrey Hayes Helps Increase Our Understanding of DNA's Path Into CellsStudy: A New Way to Slow Cancer Cell Growth
Friday, May 26, 2017
Cells grow and divide during the cell cycle
Cancer is an extremely complex disease, but its definition is quite simple: the abnormal and uncontrollable growth of cells. Researchers from the University of Rochester’s Center for RNA Biology have identified a new way to potentially slow the fast-growing cells that characterize all types of cancer. The findings, reported today in the journal Science and funded by the National Institutes of Health, were made in kidney and cervical cancer cells in the laboratory and are a long way from being applied in people. But, they could be the basis of a treatment option in the future, the authors said.
Cancer: The Cell Cycle Gone Wrong
All cells go through the “cell cycle,” a series of events that culminate in orderly cell growth and division. In cancer, the cell cycle is out of whack; cells divide without stopping and invade surrounding tissues.
Lynne Maquat, Ph.D.
Researchers identified a protein called Tudor-SN that is important in the “preparatory” phase of the cell cycle – the period when the cell gets ready to divide. When scientists eliminated this protein from cells, using the gene editing technology CRISPR-Cas9, cells took longer to gear up for division. The loss of Tudor-SN slowed the cell cycle.
“We know that Tudor-SN is more abundant in cancer cells than healthy cells, and our study suggests that targeting this protein could inhibit fast-growing cancer cells,” said Reyad A. Elbarbary, Ph.D., lead study author and research assistant professor in the Center for RNA Biology and the department of Biochemistry and Biophysics at the University of Rochester School of Medicine and Dentistry.
Elbarbary, who works in the laboratory of senior study author Lynne E. Maquat, Ph.D., a world-renowned expert in RNA biology, adds that there are existing compounds that block Tudor-SN that could be good candidates for a possible therapy.
Putting the Brakes on Cell Growth
Maquat’s team discovered that Tudor-SN influences the cell cycle by controlling microRNAs, molecules that fine tune the expression of thousands of human genes.
When Tudor-SN is removed from human cells, the levels of dozens of microRNAs go up. Boosting the presence of microRNAs puts the brakes on genes that encourage cell growth. With these genes in the “off” position, the cell moves more slowly from the preparatory phase to the cell division phase.
“Because cancer cells have a faulty cell cycle, pursuing factors involved in the cell cycle is a promising avenue for cancer treatment,” noted Maquat, director of the Center for RNA Biology and the J. Lowell Orbison Endowed Chair and professor of Biochemistry and Biophysics.
Maquat, who also holds an appointment in the Wilmot Cancer Institute, and Elbarbary have filed a patent application for methods targeting Tudor-SN for the treatment and prevention of cancer. Research next steps include understanding how Tudor-SN works in concert with other molecules and proteins so that scientists can identify the most appropriate drugs to target it.
Keita Miyoshi, Ph.D., staff scientist in Maquat’s lab, served as lead study author with Elbarbary. Jason R. Myers and John M. Ashton, Ph.D. from the UR Genomics Research Center played an instrumental role in the study analysis.
Read More: Study: A New Way to Slow Cancer Cell GrowthUsing rooster testes to learn how the body fights viruses
Thursday, April 27, 2017
Researchers from the University of Rochester Center for RNA Biology: From Genome to Therapeutics examined the role of piRNA in safeguarding the integrity of the genetic information in germ cells. It's known that piRNA -- a type of ribonucleic acid (RNA) that's found most readily in the testes and ovaries -- shields germ cells by silencing the genetic sequences of viral intruders. It's also known that defects or mutations in piRNA lead to infertility in humans and other animals. What's not known is how piRNAs are generated in the first place.
A team led by Xin Li, Ph.D., assistant professor in the departments of Biochemistry and Biophysics and Urology at the University of Rochester School of Medicine and Dentistry, analyzed rooster testes to find out.
Read More: Using rooster testes to learn how the body fights virusesBMB, BSCB Students Win 2017 Edward Peck Curtis Award for Excellence in Teaching by a Graduate Student
Saturday, April 1, 2017
BMB and BSCB graduate students, Lauren Benoodt, Tyler Couch, and Lisa Houston have been selected as joint winners of the 2017 Edward Peck Curtis Award for Excellence in Teaching by a Graduate Student. The students will be presented with a certificate, as well as checks of $700 for each. The three of them were TA’s for IND 408 (Advanced Biochemistry) in the Fall of 2016.
The Edward Peck Curtis Award for Excellence in Teaching by a Graduate Student was established to recognize graduate students who advance the teaching mission of the University by providing highly skilled and innovative undergraduate instruction.
The strongest nominations show innovation in teaching and a positive impact on the learning of undergraduates.
Congratulations Lauren, Tyler, and Lisa!
Maquat Receives Lifetime Achievement Award in Science from International RNA Society
Tuesday, February 7, 2017
Lynne E. Maquat, Ph.D. has spent her career unraveling what happens in our cells during disease, making seminal contributions to our understanding of RNA's role in sickness and in health. She's also committed countless hours to mentoring the next generation of researchers and advocating for young women in the sciences. For these exceptional efforts, she's receiving the 2017 Lifetime Achievement Award in Science from the international RNA Society.
The J. Lowell Orbison Endowed Chair and Professor in the Department of Biochemistry and Biophysics at the University of Rochester School of Medicine and Dentistry, Maquat began her professional career studying inherited anemias. She discovered a quality control process that blocks the creation of toxic proteins that cause disease. Known as nonsense-mediated mRNA decay or NMD, this process plays a part in one third of all inherited diseases, such as cystic fibrosis and muscular dystrophy, and one third of all acquired diseases, including a number of cancers.
"This award recognizes Lynne's pioneering contributions to understanding the mechanisms of RNA, as well as her outstanding leadership, support and commitment to our field, including her role as a model for new generations of scientists," said Juan Valcarcel Juarez, current president of the RNA Society, who works at the Centre for Genomic Regulation in Barcelona, Spain.
James McSwiggen, CEO of the RNA Society, added, "I can't imagine a more appropriate choice of awardee."
Read More: Maquat Receives Lifetime Achievement Award in Science from International RNA SocietyNew Biophysical Research Service Available
Friday, December 2, 2016
The University has purchased a J-1100 circular dichroism (CD) spectrometer from JASCO Inc. The shared-use instrument will be housed and maintained as part of the Structural Biology and Biophysics facility. Manager Jermaine Jenkins will maintain the instrument, as well as manage user time, train users, and assist with data collection and analysis as needed. Email Jermaine Jenkins, Ph.D. to plan your experiments.
Read More: New Biophysical Research Service AvailableKarl Smith Featured as Part of MAG Hidden Passions Series
Tuesday, November 8, 2016
Biophysics PhD candidate, Karl Smith, is giving a talk at the Memorial Art Gallery, this Thursday at 7pm as part of their Hidden Passions speaking series.
At URMC, Smith studies glass filters 10,000 times thinner than a human hair as part of the Nanomembranes Research Group. It’s because of his rigorous academic schedule that he began the 10-cent project.
The Pittsburgh native has written more than 900 stories, each roughly 500 words, on half sheets of paper. Strangers give him a prompt, and he pecks away. He’s crafted stories about lost loves, lost dogs, sea lions, flying princesses, and frogs who jump over the moon. Stories about babies, treehouses, aardvarks, and dancing polar bears. Stories about murder.
Read more about Karl and his passion.
American Health Council Names Dr. Harold Smith, Ph.D. to Education Board
Monday, September 19, 2016
Dr. Harold Smith, Professor at The University of Rochester, has been selected to join the Education Board at the American Health Council. Dr. Smith will be sharing his knowledge and expertise in the field of molecular biology, molecular virology, RNA biology, and drug discovery.
Dr. Harold Smith became involved in research after beginning his career as a professor in the Department of Biochemistry at The University of Rochester. As a biophysics professor, he utilized his knowledge and expertise in the areas of research and innovation of RNA, protein molecular biology, cell regulation, and drug discovery. Furthermore, Dr. Smith develops curriculum, teaches and mentors students from high school to postgraduate.
Dr. Harold Smith is also the Founder, President, and CEO of OyaGen, Inc. The objective of OyaGen, Inc. is to induce transient and beneficial changes in the protein expression and function in human tissues by involving the editing enzymes in targeting biomedically relevant pathways.
Dr. Harold Smith is a member of The American Heart Association, The Council on Atherosclerosis, The RNA Society, The American Society for Biochemistry and Molecular Biology and a fellow in the The Royal Society of Biology. In addition, Dr. Smith serves on the Scientific Advisor Board of Cannabis Sciences, Inc., IgxBio, Inc. and Trovita Health Sciences as well as the Editorial Board of the International Journal of Virology and AIDS, Frontiers in Microbiology, The Journal of Biological Chemistry, and The Journal of BioDiscovery.
Read More: American Health Council Names Dr. Harold Smith, Ph.D. to Education BoardMiller Receives Patent for Technology that Can Help Detect Flu
Thursday, September 15, 2016
Benjamin L. Miller, Ph.D., professor of Dermatology, recently received yet another patent for a new technology that can detect miniscule amounts of specific molecules in blood or other liquids. The patent focuses on using this technology to make detecting immune responses to the flu quicker and easier.
The AIR™ Platform, marketed by Adarza Biosystems, can detect immune responses to flu vaccines as well as the virus itself. With a small blood sample from a patient, doctors can confirm a flu infection, see if the patient mounts an appropriate immune response to a vaccine, or see if immune responses cross react with several different strains of flu. AIR™ can also be used for viral surveillance.
While Miller’s AIR™ system is not the first to make these things possible, it is a great improvement on previous technologies. Its silicon chip, which is only about the size of the end of a pencil eraser, allows scientists to detect hundreds of different target molecules in a single drop of fluid, and its “label-free” design requires fewer steps and reagents, thus reducing cost and opportunities for error.
“Label-free” systems suppress background noise to detect tiny signals, whereas conventional “labeled” systems use a more cumbersome design to amplify a tiny signal, often creating a lot of background noise in the process.
“It’s like walking through a city during the day and looking up at the buildings,” Miller said. “You have no idea what's going on in the offices because there's so much ambient light, but if you come back at night, it's easy to see.”
Miller suppresses background noise using a near-perfect anti-reflective coating on his silicon chips. For every 100 million photons of light that hit the surface of the chip, only one photon is reflected back. That coating also contains capture molecules meant to bind or “capture” specific target molecules, like antibodies produced in response to the flu virus. The more antibodies that bind to the chip, the more the anti-reflective coating is perturbed, and the more light is reflected and captured by a camera.
This simple and unconventional design and the ability to use capture molecules both big and small makes AIR™ extremely versatile. From cancer and infectious diseases, to agriculture and food safety, AIR™ is poised to expedite research and clinical testing across a wide range of applications.
Biochemistry & Biophysics Faculty Member and Photojournalist Barry Goldstein Covers Republican National Convention for The American Scholar
Wednesday, August 31, 2016
Barry Goldstein is a photographer specializing in portraiture and documentary themes. Originally trained as a physician and biophysicist, he is Associate Professor of Medical Humanities at the University of Rochester Medical Center, Visiting Professor of Humanities at Williams College, and Adjunct Professor of Humanism in Medicine at the NYU Medical School. He was the first Artist-in-Residence at the New York University Medical School on September 11, 2001, an experience that led to his collection Being There: Medical Student Morgue Volunteers Following 9/11. His most recent book, Gray Land: Soldiers on War, is a collection of portraits of, and interviews with soldiers in Iraq and at home. He lectures and exhibits widely, and is a recipient of a Massachusetts Cultural Council Artists Grant in Photography.
Most recently, Barry provided coverage of the Republication National Convention for the American Scholar. His RNC work can be seen at The American Scholar and on his website.
Blanton Tolbert Wins Morton L. Mandel Award For Outstanding Chemistry Faculty
Tuesday, August 9, 2016
Blanton Tolbert
Former Biophysics student, Blanton Tolbert (PhD 2006), mentored by Doug Turner & Ravi Basavappa, has been awarded the Morton L. Mandel endows award for outstanding chemistry faculty members at Case Western Reserve University.
Associate Professor Blanton S. Tolbert, whose work focuses closely on elucidating molecular details of the human immunodeficiency virus, more commonly known as HIV. A member of the Case Western Reserve faculty since 2012, Tolbert paired the honor with extraordinary achievements during the past academic year:
- A featured cover story in the Journal of Molecular Biology that described new three-dimensional structures of molecules in the life cycle of HIV
- A second article about HIV’s molecular structures, published in the Journal of Biological Chemistry that became the journal’s most-viewed RNA (Ribonucleic acid) paper in December 2015
- Multiple online mentions of the work, including the Nov. 16 Science Highlights of the Advanced Photon Source at the U.S. Department of Energy’s Argonne National Library
- Service as director of the chemistry department’s Research Experience for Undergraduates (REU) grant from the National Science Foundation. In that role, Tolbert led efforts that identified and recruited a diverse group of students to work on federally sponsored projects. As part of the 10-week experience learning cutting-edge science, the students also participated in teambuilding and professional development activities. The work proved so successful that one undergraduate was cited as co-author on a publication from his summer project.
Congratulations Blanton!
Read More: Blanton Tolbert Wins Morton L. Mandel Award For Outstanding Chemistry FacultyMeet Karl Smith, the Typewriting Tale Teller
Friday, July 8, 2016
Karl Smith
The "Friends of Joe's Big Idea" is a vibrant community of talented people we think you should meet. With our feature, FOJBI Friday, we're introducing some of these cool communicators of science in their own words. This week: Karl Smith.
Background
I'm a fifth-year biophysics doctoral candidate at the University of Rochester, where I study porous ultrathin silicon membranes. At the moment I'm taking a brief break from my research to be an American Academy for the Advancement of Science Mass Media Fellow at the Manhattan office of Scientific American.
Importance of science communication
I love science communication because it's both hard and important. People need to be told what scientists have discovered and what it means for their lives, but to do that well requires balancing the storytelling needs of journalism against objectivity and sober contextualization. Also, I personally find scientists to be generally fascinating people to write about and hear from.
Current projects
Along with my co-producer Madeline Sofia, I created The Bench Warmer's Podcast, which tells stories of misadventures and victories in science using interviews with current and former graduate students. I think the stories that don't often get told about science — the scoops, the failures, the dead ends, rewrites and rejections — are just as important to tell as the wild success stories. Not only that, but I think we short-sell our successes by not highlighting how rare they are. So, in the podcast, Maddie and I ask questions like "What's the most expensive thing you ever broke in lab?" and "Have you ever embarrassed yourself by dislocating your knee while singing karaoke onstage in front of hundreds of your scientific peers and possible future employers?"
I also write "10-cent stories" for children at the Rochester Museum and Science Center and at a few other places around Rochester. The children give me a prompt and in five minutes I use my typewriter to type them a tale. I've been doing this for about three years now, and I've written well over 800 stories. Sometimes the stories have a STEM bend to them, but sometimes they're just stories. I love this project for a lot of reasons, but most of all because it lets me make the world a stranger, more whimsical place.
Future plans
I've only been at my fellowship for a few weeks, so I'm still deciding if I want to be a science journalist or if my plans lie elsewhere. This is a time of great flux for me, so I don't know yet where I'm heading. But I'm enjoying figuring it out.
Read More: Meet Karl Smith, the Typewriting Tale TellerClara Kielkopf Receives EvansMDS Discovery Research Grant
Saturday, June 11, 2016
Biochemistry & Biophysics Associate Professor, Clara Kielkopf's project, entitled, Structural mechanisms and targeting of MOS-relevant pre-mRNA splicing factors has been selected by EvansMDS for funding for 2016. This year EvansMDS requested 12 full DRG proposals and were able to fund 6 of them. Their hope is that these findings will translate into improvements in therapy that can be delivered to MDS patients.
The Kielkopf lab investigates splicing defects in hematologic malignancies; roles of human pre-mRNA splicing factors in HIV-1 infectivity; development of engineered splicing factors for correction of splicing defects and splice sites and their associated proteins as therapeutic targets.
Mallory Scott Selected for Summer Internship at Bayer Pharmaceuticals
Friday, June 10, 2016
Mallory Scott, Biophysics, Structural and Computational Biology PhD student, in the laboratory of Dr. Paul Kammermeier, has been selected for a summer internship at Bayer Pharmaceuticals in Whippany, NJ in Global Regulatory Affairs. Mallory will gain valuable work experience in the healthcare industry while working with regulatory professionals on various projects to learn about the role of regulatory affairs in drug development and product registration as well as the regulatory landscape. Mallory will be working in the Chemistry, Manufacturing and Controls (CMC) division. Her project is focused on quality by design in continuous manufacturing.
Harold Smith Publishes Commentary on RNA and DNA Editing
Sunday, June 5, 2016
Epigenetics is a popular, yet still mysterious concept in health and medicine. It’s the study of a variety of biological processes that alter the expression of our genes. Sometimes this involves modifying the structure of our chromosomes to mask or unmask genes, and other times the actual genetic code is changed in certain cells. Harold C. Smith, Ph.D., a longtime professor of Biochemistry and Biophysics at the University of Rochester School of Medicine and Dentistry has studied epigenetics in a research focus known as RNA and DNA editing since it was introduced two decades ago. He was invited to write a commentary on the progress and future of this research, published today in Trends in Biochemical Sciences, and answers a few questions about the subject.
Read More: Harold Smith Publishes Commentary on RNA and DNA EditingCongratulations Karl Smith, AAAS Mass Media Fellowship Recipient
Monday, May 23, 2016
Karl Smith, 5th year graduate student in the Biophysics Structural and Computational Biology PhD program, laboratory of Dr. Jim McGrath, has received an AAAS (American Association for the Advancement of Science) Mass Media Fellowship. Karl, sponsored by the American Physical Society, will be spending 10 weeks this summer working at Scientific American in their Manhattan offices as part of his fellowship.
Since its inception, the AAAS Fellowship Program has supported more than 625 student scientists, engineers and medical professionals who, in some cases, produced the only original science-news reporting at their assigned media outlets over the summer. The current 15 fellows, selected from a pool of 130 outstanding applicants, are likely to generate between 200 and 300 original science stories for print articles, blogs, podcasts, radio segments, and multimedia features.
Past participants in the Mass Media Fellows program include Mark Dumont, Professor, Department of Biochemistry and Biophysics, who received the AAAS Mass Media Fellowship in 1975, the second year that it was in existence. Over that summer, he wrote 26 news articles for the San Diego Union.
Other recipients include Erica Goode and Kenneth Chang of the New York Times; Richard Harris, David Kestenbaum, and Joe Palca of NPR; renowned biologist Eric Lander, co-chair of U.S. President Barack Obama's Council of Advisors on Science and Technology; physician and "Law & Order: Special Victims Unit" Executive Producer Neal Baer; Victoria Bruce, author of No Apparent Danger: The True Story of Volcanic Disaster at Galeras and Nevado Del Ruiz; and many others. - from AAAS's website.
Karl Smith places third in University’s Falling Walls Competition
Wednesday, May 18, 2016
Karl Smith, a PhD student in Biophysics and a member of the lab of James McGrath, Professor of Biomedical Engineering, won third place in the University of Rochester's Falling Walls Competition for describing his use of physics to make water behind a filter form a mixer vortex, reducing the difficulty of normal stirring when fluids stick to surfaces. A total of 19 presenters competed.
The competition is associated with the Falling Walls foundation, a non-profit organization that fosters discussions on research and innovation and promotes the latest scientific findings to society. The Rochester winner's idea will compete with others from around the world at the Falling Walls Lab Finale in November in Berlin. This event selects the participants for the annual Falling Walls Conference the following day: an international forum for science and innovation to commemorate the fall of the Berlin Wall. Speakers at the conference have included Angela Merkel, Chancellor of Germany; Nobel Prize winner Sir Paul Nurse; and young inventors from around the world. BBC London said it was where the "brightest minds on the planet" meet.
Last year's Falling Walls Lab Rochester winner, Ryan Trombetta, a BME PhD student in Dr. Awad's lab, finished 12th (out off a 100 finalists worldwide) in the Berlin competition for his description of using 3D printed bone grafts to treat osteomyelitis. See his presentation here.
From left to right, Solomon Abiola, Sara Nowacki and Karl Smith, the top three finishers at the Falling Walls Competition.
The Future of Photonics
Tuesday, February 23, 2016
As hundreds of millions of dollar pour into Rochester to establish the nation's first Photonics Hub, Mark Gruba has a closer look at the technology in a News 8 special report, "The Future of Photonics."
Photonics is the science and technology of generating, controlling and detecting photons, which are particles of light. A display at the Rochester Museum & Science Center houses examples of its many applications. In one, a transmitter converts an audio signal from electrical pulses into light pulses. The laser beam sends that information to the receiver, which converts the light pulses back to electrical pulses and sends them to the speaker for your listening enjoyment.
"We work on optical bio sensors," said Dr. Ben Miller, a researcher at the University of Rochester Medical Center. He's creating a sensor that can detect the presence of hundreds of viruses from a single blood sample, in real time. "We're working to make devices so that you can immediately get that information in the doctor's office," said Dr. Miller.
Read More: The Future of PhotonicsStrong Star Certificate of Appreciation Awarded to Dr. Jermaine “JJ" Jenkins
Tuesday, January 26, 2016
On January 22, 2016, Dr. Jermaine Jenkins, who runs the Structural Biology and Biophysics Facility, was nominated for going 'above and beyond' in his work for a client of the facility. The client commented in their nomination:
The clinical trials group had a very tight timeline to meet for one of our clients. Testing had to be completed by the 25th of January so the client could present the data to the FDA. JJ was aware of the required quick turnaround time and he met the challenge. He worked the weekend so that our client's needs would be met. It is so impressive to work with such a dedicated scientist who takes his job so seriously. With JJ's help, URMC Labs Clinical Trials group made a very good impression on a client.
As Facility Manager of the Structural Biology and Biophysics Facility, Dr. Jenkins offers support services to determine macromolecular x-ray crystal structures, and to investigate protein-protein, protein-nucleic acid or protein-small molecule interactions. Professor Clara Kielkopf – a long time user and co-founder of the Facility commented, JJ quickly, calmly and reliably responds to user needs
. Co-director of the Facility Professor Joseph Wedekind added, Dr. Jenkins is an outstanding and dedicated scientist. We are fortunate to have such a great colleague
. Please join us in expressing your gratitude to JJ for his service and dedication.
The Scientist as Storyteller
Friday, January 15, 2016
Graduate students Clarence Ling (left), Jon Baker,
and Karl Smith rehearse a script for The Bootleggers
at the WRUR studios in Todd Union. (Photo: Adam Fenster)
For Karl Smith, the storytelling bug began with a Montgomery Ward No. 22 typewriter purchased for $5 at a moving sale.
Typewriter perched on his lap, the doctoral student in biophysics has become a fixture at the Rochester Public Market, Corn Hill Arts Festival, and other Rochester-area arts-oriented venues. For 10 cents, he crafts a half-sheet-long tale about grandchildren, lost loves, pets, or the absurd. The clacking of keys on paper draws a curious crowd.
I derive a lot of meaning and joy from making things that other people draw joy from,
says Smith.
As a graduate student at Rochester, Smith has been finding lots of ways to share his love of storytelling. In addition to his peripatetic typewriting, he’s the leader of Rocket Radio Theater, a troupe of radio performers whose core membership includes fellow like-minded medical science graduate students Clarence Ling, Jon Baker, Carolyn Klocke, Bronwyn Lucas, and Matt Payea.
The project began in 2013 with a recording at Smith’s kitchen table. The group, which now records in the studios of campus radio station WRUR, hosts several serial drama podcasts and stand-alone stories created by Smith. Its feature series, The Bootleggers, takes place during prohibition-era Rochester, playing up aspects of local history and landscapes.
In his research as a biophysicist, Smith explores nanoporous silicon membranes in the lab of James McGrath, professor of biomedical engineering. Smith describes the membranes as coffee filters made of glass that are 10,000 times thinner than a human hair.
But he hopes to continue to combine storytelling and science after graduation, perhaps as a science journalist or a podcaster.
I want to live in a world,
he says, where people are standing on street corners writing stories.
Read More: The Scientist as StorytellerB&B Professor Harold Smith and Oyagen's Drug Development Highlighted on Local TV for World Aids Day
Friday, December 4, 2015
OyaGen, a small medical research firm off Jefferson Road in Henrietta, has used federal grants for its HIV drug discovery programs with the goal of finding a cure. Dr. Harold Smith, Professor of Biochemistry & Biophysics at the University of Rochester, and the company's founder, president and CEO got his start as a molecular biologist studying heart disease.
"It became clear to me that the things we were doing to study heart disease and find out why things were happening translated directly into the HIV research arena," Smith said.
By 2010, things kicked into high gear. Advanced robotics were added allowing scientists to work with advanced chemistries. They've now identified a weak point in the HIV virus that's never been exploited before. Vif is a viral defense HIV releases into cells it infects. It destroys the body's natural defense against infections. OyaGen discovered a way to defeat HIV by disabling Vif.
"If we can proceed along track, we will be looking at entering clinical trials within a completely different way of approaching the virus and the disease within three years," Smith said.
B&B Department Mourns the Loss of Rose Burgholzer
Wednesday, June 24, 2015
It is with much sadness that we inform everyone of the passing of Rose Burgholzer, after a long and courageous battle with cancer. Rose worked at the University for 40 years, almost half of that as an administrator in our department. She was a dear friend and colleague and will be greatly missed. Many former students remember Rose fondly and have communicated with her during her illness, and she graciously received a steady stream of visiting faculty and staff in her home these past few years.
A Funeral Mass was held Wednesday, June 17, at St. Kateri at St. Margaret Mary Church in Rochester, with entombment at Holy Sepulchre Cemetery. Memorials may be directed to a charity of your choice. View her obituary and a slideshow from Rose's family.
Blocking Cellular Quality Control Mechanism Gives Cancer Chemotherapy a Boost
Friday, March 27, 2015
A University of Rochester team found a way to make chemotherapy more effective, by stopping a cellular quality-control mechanism, according to a study published today in Nature Communications.
The mechanism is known as NMD (nonsense-mediated mRNA decay), and scientists found that exposing breast cancer cells to a molecule that inhibits NMD prior to treatment with doxorubicin, a drug used to treat leukemia, breast, bone, lung and other cancers, hastens cell death.
The research team, led by Lynne E. Maquat, Ph.D., director of the Center for RNA Biology at the University of Rochester, acknowledges that the work is in the early stages and a long way from being applied in humans. But, they believe their data provide insights that could lead to new treatment strategies for cancer patients in the future.
Read More: Blocking Cellular Quality Control Mechanism Gives Cancer Chemotherapy a BoostLynne Maquat Receives 2015 Gairdner International Award
Thursday, March 26, 2015
Lynne E. Maquat, Ph.D. received the 2015 Gairdner International Award for the discovery and mechanistic studies of nonsense-mediated mRNA decay, a cellular quality control mechanism that derails the production of unwanted proteins in the body that can disrupt normal processes and initiate disease. She is one of five scientists honored with the award, which is given every year to recognize the achievement of medical researchers whose work contributes significantly to improving the quality of human life.
The J. Lowell Orbison Endowed Chair and Professor of Biochemistry and Biophysics at the University of Rochester Medical Center, Maquat is known around the world for her work on nonsense-mediated mRNA decay, which is critically important in both normal and disease states. She is considered the uncontested pioneer on the subject and in 2011 was elected to the National Academy of Sciences for her exceptional research, which has been published in more than 130 peer-reviewed scientific articles.
Maquat is the first scientist from upstate New York to receive the Gairdner International Award, which is recognized for its rigorous peer-led selection process. A panel of active Canadian scientists reviews all nominations and passes their recommendations to a board of two dozen senior scientists from across Canada, the United States, Europe, Australia and Japan. After in-depth study and review, board members cast votes for the nominees whose achievements rise above all others in their field. According to the Gairdner Foundation, of the 313 winners to date, 82 have gone on to receive a Nobel Prize in Physiology or Medicine, a testament to the quality of the awardees.
The award was also highlighted in the Opinion pages of Saturday’s Democrat and Chronicle in the Thumbs up, thumbs down
section: Thumbs up: For Dr. Lynne Maquat, who is one of five biomedical researchers from around the world to win this year's Gairdner International Award. The University of Rochester Medical Center scientist has joined a prestigious group. Since 1959, more than a quarter of the Gairdner International winners have gone on to win a Nobel Prize, too.
Read More: Lynne Maquat Receives 2015 Gairdner International AwardB&B Graduate Students 'Bootleg' Their Way to the Top
Friday, March 20, 2015
The Biochemistry and Biophysics department is pleased to announce that a number of the department's graduate students have undertaken a very creative project. Specifically, six of our graduate students have been writing, producing, and voice acting in a serial podcast about bootleggers smuggling rum across Lake Ontario in 1921.
You can access the first three episodes on iTunes, or you can find them on their Pocket Radio Theater Facebook page. While contingent on their individual research workloads, their plan is to release more episodes on a monthly basis for a total of around 20.
Check out the creative endeavors of your departmental colleagues!
Department Announces Fred Sherman Student Award
Friday, March 6, 2015
The Department of Biochemistry & Biophysics are very pleased to announce a new student award within the Biochemistry and Molecular Biology program, to be given at our annual Awards Ceremony in May.
The Fred Sherman Award will honor the memory of our former colleague, and will annually recognize a student in the BMB program who exemplifies the imagination, the excellence in the pursuit of scientific knowledge, and the commitment to the scientific community that were characteristic of Fred Sherman.
This award will compliment the William F. Neuman Award, given annually to a BSCB student to recognize academic, scientific and personal qualities which exemplify the imagination, enthusiasm and excellence in the pursuit of scientific knowledge which were characteristic of the life of Dr. William F. Neuman.
MSTP Announces 40th Anniversary Celebration!
Sunday, February 1, 2015
Edward M. Eddy
Rubin
The Medical Scientist Training Program (MSTP) is excited to announce a celebration of the 40th anniversary of the MSTP NIH training grant on Friday, October 9, 2015.
The keynote speaker will be an MSTP alumni from the Class of 1980: Edward Rubin, MD, PhD, Director, DOE Joint Genome Institute.
Edward M. Eddy
Rubin is an internationally-known geneticist and medical researcher at the Lawrence Berkeley National Laboratory in Berkeley, California, where he became head of the Genomic Sciences Division in 1998. In 2002 he assumed the directorship of the DOE Joint Genome Institute (JGI) to lead the JGI's involvement in the Human Genome Project (HGP).
For more information and schedule of events for the day, please visit the MSTP 40th Anniversary page.
Colleagues Pay Tribute to Phil Fay
Monday, October 6, 2014
Drs. Sriram Krishnaswamy of the Children's Hospital of Philadelphia & University of Pennsylvania, and Peter Lollar of Emory University recently wrote a fitting tribute to our friend and colleague, Dr. Philip Fay, who passed away June 25, 2014 after a long battle with cancer. The two are researchers working in the same field as did Dr. Fay and published the tribute in Thrombosis and Haemostasis, a leading journal in the field. You can read the tribute here.
Gerald Fink Provides Fitting Tribute to Fred Sherman at 2014 Yeast Genetics Meeting
Friday, September 12, 2014
On July 29th - August 3rd at the Yeast Genetics Meeting in Seattle, Washington, Gerald Fink provided a fitting tribute for Fred Sherman. Gerald Fink, Ph.D. is an American biologist, who was Director of the Whitehead Institute at MIT from 1990-2001. He graduated from Amherst College in 1962 and received a Ph.D. from Yale University in 1965, having elucidated the histidine pathway in the yeast, Saccharomyces cerevisiae.
The above video is a tribute to Gerry's friend and colleague, Fred Sherman, Ph.D. who he and many others have called 'The Founder of Yeast Molecular Biology'. Sherman was the American scientist who pioneered the use of the budding yeast Saccharomyces cerevisiae as a model for studying the genetics and molecular biology of eukaryotic cells.
Dr. Sherman passed away on September 16, 2013 after a long and distinguished career at the University of Rochester, in the department of Biochemistry and Biophysics, for which he was the former Chair (1982-1999). Among Fred's many awards, publications and accolades, none was more deserving than his induction into the National Academy of Sciences.
Read More: Gerald Fink Provides Fitting Tribute to Fred Sherman at 2014 Yeast Genetics MeetingDepartment of Biochemistry and Biophysics Celebrates 15-Year Service Awards
Thursday, July 31, 2014
Sara Connelly (left) and Shelley Burns
We are pleased to celebrate Shelley Burns’ and Sara Connelly’s milestone anniversaries of working for the University of Rochester for 15 years in July 2014!
Shelley is an Administrator who wears many hats in the Department of Biochemistry and Biophysics. She is an expert Grants Administrator for the department and has an uncanny knowledge of NIH forms and regulations, and she keeps the faculty on time and compliant with all grant applications. She also coordinates recruitment and hiring of postdoctoral fellows, manages renovations, and is an authority on immigration and human resources rules and regulations.
Sara is a Technical Associate in the lab of Mark Dumont, Ph.D.. She is a highly accomplished scientist with knowledge and experience in areas ranging from yeast genetics to G protein coupled receptors to HIV envelope protein. She also performs vital roles in managing the Dumont lab (often referred to as the Connelly lab), providing instruction and guidance to students, and making the 3-7500 hallway a fun place to work. We are deeply appreciative of Shelley’s and Sara’s many years of service to our department!
Department of Biochemistry and Biophysics Mourns the Loss of Dr. Philip Fay
Thursday, June 26, 2014
Dr. Philip Fay, Ph.D.
We are very saddened to relay the passing of our colleague and friend Phil Fay, Ph.D, Professor of Biochemistry and Biophysics. Phil passed away Wednesday June 25th after a long and courageous battle with cancer. His incredible strength of character through a most difficult time remains an inspiration to us all.
Calling hours will be 3-6 pm Sunday June 29 at Anthony Funeral Chapel, Brighton, 2305 Monroe Ave. Rochester, NY, US, 14618. His Funeral Mass will be 11 am Monday June 30 at St. Louis Church, 64 S Main St, Pittsford. Burial will follow at White Haven Cemetery, 210 Marsh Road Pittsford, with a reception to follow at the Country Club of Rochester. His Obituary can be found here.
Among numerous awards and significant accomplishments in an esteemed career, Phil and research assistant professor, Hironao Wakabayashi, M.D., Ph.D. were recently nominated for the 2014 RIPLA Distinguished Inventor of the Year Award given by the Rochester Intellectual Property Law Association (RIPLA). They were nominated for their work in the field of Factor VIII technology for treatment of hemophilia A patients.
On July 8th, 2014 the flags at the University of Rochester will be lowered in honor of Dr. Fay.
Professor Mahin Maines Issued Two Patents
Friday, June 6, 2014
HeLa cancer cells dramatically increased in size
and morphology when human BVR is introduced.
Biochemistry and Biophysics Professor Mahin Maines has been issued two patents for identification and
development of a novel cell proliferation and differentiation factor (US patent 6, 969,610), and for Identification
of Biliverdin Reductase as a Leucine Zipper-Like DNA Binding/Transcription Factor. (US, Canada, Europe and Australia
2002360742).
Striking increase in BVR in a human
kidney tumor compared to normal kidney tissue.
The Maines laboratory has identified Biliverdin Reductase (BVR) in human cells as a
novel regulator of cell proliferation and differentiation. Her research shows that HeLa cancer cells dramatically
increase in size and morphology when human BVR levels are elevated within the cells by artificial means. Her lab
also discovered a striking increase in BVR levels in a human kidney tumor compared to normal tissue (see images,
above and below). They found that BVR regulates and/or modulates activity of protein kinases downstream of the
insulin/IGF-1 signaling cascade, including MAPK/ERK1/2 signaling, and that BVR is essential for activation of the
ERK1/2 kinases that control cell proliferation and growth. The work has implications for the treatment of cancer and
has resulted in a patent issued in US, Canada, Europe and Australia for Identification of Biliverdin Reductase as
a Leucine Zipper-Like DNA Binding/Transcription Factor
. (US patent 6, 969,610).
Maines is a leading expert in BVR research and has uncovered many applications for this enzyme, including diabetes
and a US patent was recently issued for this discovery. She also discovered two enzymes, HO-1 and HO-2 that are part
of the same metabolic pathway as BVR. Her research in this area has opened up possible new therapeutic approaches to
cardiovascular disease, diabetes and other disorders.
Fay, Wakabayashi & Maines Featured in Democrat & Chronicle as Nominees for Inventor of the Year
Saturday, May 24, 2014
Among the other nominees for Inventor of the Year were B & &'s very own Drs. Philip Fay and Wakabayashi and Mahin Maines. Fay and Wakabayashi were nominated for the development of Factor VII proteins and Maines was nominated for discovering an unprecedented approach to mimic insulin action and increase glucose uptake for the treatment of diabetes.
Donald S. Rimai was named Distinguished Inventor of the Year at the ceremonies held at the Rochester Museum & Science Center. Rimai received 111 patents during his 34-year career at Eastman Kodak Co. The entire Democrat and Chronicle article is available here.
Pilot Awards Support Three Projects
Thursday, May 22, 2014
The Center for Integrative Bioinformatics and Experimental Mathematics in the Department of Biostatistics and Computational Biology has awarded two projects pilot awards: Identification of Interferon Stimulated Genes Regulating Viral Latency
from Jian Zhu, assistant professor of microbiology and immunology, and Modeling Immune Response in 3-D Bioreactor Cultures of Human Secondary Immune Organ Cells
from David Wu, professor of chemical engineering. One pilot project awarded last year, Quantitative Proteomic Analysis of Influenza-infected Mice
from Sina Ghaemmaghami, assistant professor of biology, received a second-year renewal with supplementary funding.
Ghaemmaghami, a secondary faculty member in Biochemistry & amp; Biophysics, as well as the Center for RNA Biology general interest in understanding the mechanisms of protein expression, folding and degradation. We investigate how cells maintain a homeostatic balance between these processes, and how this homeostasis is effected by disease and aging. The projects in the lab draw on a number of disciplines including cell biology, biochemistry, systems biology and computational biology.
B & B Dept Graduate Student Wins Best Poster Award
Tuesday, May 20, 2014
Biochemistry and Biophysics graduate student Chinmay Surve has won the Best Poster Award at the recently concluded American Society of Pharmacology and Experimental Therapeutics society's, Upstate NY Pharmacological Society meeting in Buffalo, NY. Chinmay works in the laboratory of Dr. Alan Smrcka where he is looking at signaling molecules downstream of G protein coupled receptors (GPCRs) in neutrophils which play a role in neutrophil chemotaxis and how dynamism between these molecules regulate neutrophil chemotaxis.
Dept Faculty Members Fay and Wakabayashi Nominated for the Distinguished Inventor of the Year
Wednesday, April 16, 2014
Dr. Philip Fay, Ph.D.
Hironao Wakabayashi, M.D., Ph.D.
Biochemistry & Biophysics professor, Philip Fay, Ph.D. and research
assistant professor, Hironao Wakabayashi, M.D., Ph.D. have been
nominated for the 2014 RIPLA Distinguished Inventor of the Year Award given by the Rochester Intellectual Property Law Association (RIPLA). They were nominated
for their work in the field of Factor VIII technology for treatment of hemophilia A patients.
Ongoing studies in the Fay lab include physical and biochemical analyses of factor VIII structure, inter-subunit
interactions, and intermolecular interactions with other components of the clotting cascade. Dr. Fay's research
program is aimed at gaining fundamental insights into the structure, activity and regulation of a protein central to
hemostasis. This information will have specific implications for understanding hemophilia A and developing superior
therapeutics for its treatment.
Drs. Fay and Wakabayashi's nomination and significant accomplishments will be recognized before the community at the
Award Ceremony on Wednesday, May 14, 2014 from 6 to 9 pm at the Rochester Museum & Science Center (RMSC). The
department would like to extend our congratulations to both!
Department Alumnus Selected as part of a "Next Gen" Crystallographer Group for 2014 International Year of Crystallography
Thursday, March 27, 2014
Andrew T. Torelli (Ph.D. Biophysics 2008) was invited to attend the Opening Ceremony for the 2014 International Year of Crystallography (IYCr) held at UNESCO headquarters in Paris and served on a discussion panel as a representative of next-gen crystallographers. Many distinguished speakers, UN officials, international scientists, students and several hundred guests attended this historic event. The Secretary General of the United Nations, Ban Ki-moon, addressed the assembly by video, followed by Irina Bokova, Director-General of UNESCO, and the heads of multiple international scientific organizations. Keynote speakers included Jenny Glusker, who delivered a rich historical perspective of crystallography, and Brian Kobilka, who recounted his 2012 Nobel Prize work with Robert Lefkowitz involving G protein-coupled receptors. Other fascinating talks included efforts to expand X-ray crystallography in emerging nations, cutting edge technologies, the first extraterrestrial diffraction measurements used to interpret the mineralogy of Mars, and applications of crystallography and symmetry in the study of art. The Discussion Panel included eight selected, early-career crystallographers from around the world, and communicated critical issues facing the next generation of crystallographers to policy makers and sovereign delegations.
Announcing Faculty Promotions and Awards
Tuesday, March 25, 2014
The Department of Biochemistry and Biophysics is proud to announce the following well-deserved promotions, recently approved by the Board of Trustees and signed by President Seligman:
- Alan Grossfield, promoted to Associate Professor of Biochemistry and Biophysics
- Josh Munger, promoted to Associate Professor of Biochemistry and Biophysics
- Joe Wedekind, promoted to Professor of Biochemistry and Biophysics
- Yi-Tao Yu, promoted to Professor of Biochemistry and Biophysics
We were also very pleased to learn of the following awards in recognition of two very deserving Faculty:
- Eric Phizicky, to receive the 2014 William H. Riker University Award for Graduate Teaching
- Doug Turner (B&B secondary appointment) will receive the 2014 Doctoral Commencement Award for Lifetime Achievement in Graduate Education.
Both of these awards will be presented at the 2014 Doctoral Commencement on Saturday morning, May 17, 2014, at the Eastman Theater.
Please join us in congratulating these faculty! We are grateful for all of their hard work and service they offer our department, and for the contributions they make to the University. We look forward to hosting a party to celebrate their achievements sometime in the coming months.
Biochemistry & Biophysics Alum Patrick Brandt, To Give Seminar on Strategies for Choosing a Postdoc
Tuesday, March 18, 2014
Patrick Brandt, who received his Ph.D. in Biochemistry working with Dr. Robert Bambara in the Department of Biochemistry & Biophysics, will present a seminar entitled Thinking Strategically About Your Postdoc Training
on Friday March 21, 2014 in the Hellen Wood Hall Auditorium, 1W304. A reception will follow the talk, 4 pm - 5 pm. Patrick is also giving an additional talk on Friday, March 21:
Using Microsoft Word to Format Your Dissertation
in the Neuman Room (1-6823) from 9–10:30 AM.
Patrick is the Director of Science, Training and Diversity at the University of North Carolina School of Medicine and Dentistry. All graduate students are encouraged to attend! For more information about Patrick, visit the UNC Science, Training and Diversity page.
Read More: Biochemistry & Biophysics Alum Patrick Brandt, To Give Seminar on Strategies for Choosing a PostdocBiologist Sina Ghaemmaghami Honored with a National Science Foundation Early Career Award
Friday, January 10, 2014
Sina
Ghaemmaghami, an assistant professor of biology and member of the Biology & Molecular Biology
and Biophysics, Structural &
Computational Biology graduate programs at the University of Rochester, has been recognized by the National Science Foundation (NSF) as a scientist who
exemplifies the role
of teacher-scholar. The NSF has named Ghaemmaghami a winner of its Faculty Early Career
Development Award (CAREER).
The award includes a five-year grant totaling $950,000 to fund Ghaemmaghami's research into protein folding. Sina
is already recognized as one of the brightest in his field,
said John Jaenike, chair of
the University's Department of Biology. His work on protein folding and proteomic turnover is of central
importance to understanding basic cell physiology.
As an early-career scientist, this award will go a long way in helping me establish a viable long-term research
program at the University,
said Ghaemmaghami. I especially appreciate the special focus this award places
on the integration of education, which will lead to research opportunities for more undergraduates.
Read More: Biologist Sina Ghaemmaghami Honored with a National Science Foundation Early Career AwardIn Memoriam: Fred Sherman - The First Yeast Molecular Biologist
Tuesday, January 7, 2014
The journal Genetics has published an article in memory of Dr. Fred Sherman, who died September 16, 2013 at the age of 81 years after a long illness. A renowned molecular biologist, Fred obtained his Ph.D. with Robert Mortimer at the University of California, Berkeley, followed by postdoctoral training with Boris Ephrussi in France and Herschel Roman in Seattle. He spent his entire career as a Professor at the University of Rochester School of Medicine. Fred received many awards, including election to the National Academy of Sciences.
Using Yeast to Unravel Premature Aging Disorder
Saturday, June 15, 2013
Like a fence that encloses a backyard, all of the body's cells are surrounded by membranes. Each membrane has its own complement of membrane proteins, which perform critical functions like letting things in and out of the cell, and keeping the inside of the cell informed of what's happening on the outside. Mark Dumont, Ph.D., professor of Biochemistry and Biophysics and Pediatrics, says that more than half of the drugs on the market today target membrane proteins.
Despite their importance, the structures and mechanisms that determine how these proteins work are not very well understood. In a recent study in Science, Dumont and collaborators at the University of Virginia and the Hauptman-Woodward Institute in Buffalo describe the structure of a particular membrane protein called Ste24p that is involved in cutting up other proteins in yeast. If there's a defect in this protein, yeast can't mate.
The obvious next question is, how is yeast's inability to reproduce relevant to people? It turns out, the human equivalent of the protein Ste24p, when mutated, causes progeria -- a premature aging disorder in which children develop hair loss, joint ailments, and heart disease, which they typically die of in their mid-teens. Dumont says that better understanding how this protein works -- in yeast and in people -- will help scientists to design a drug or other treatment for this devastating disorder and learn more about the human aging process.
Nadia Fedoriw, a technician in Dumont's lab, grows yeast used for protein production
Dumont is a senior investigator of the Membrane Protein Structural Biology Consortium, one of nine NIH-funded centers across the country that are trying to solve the structures of membrane proteins. He worked with Kathleen Clark and Nadia Fedoriw from Pediatrics and Sara Connelly from Biochemistry and Biophysics on the study.
Read More: Using Yeast to Unravel Premature Aging DisorderDepartment Faculty Awarded 2013 Provost's Multidisciplinary Award
Friday, June 14, 2013
The Provost's Multidisciplinary Award provides pilot funding for especially exciting scholarly research with a high probability of future support from external sources of funding. The Award is designed to foster collaboration between departments and across schools at the University of Rochester. Five diverse research projects at the University were selected as recipients of the sixth annual Provost's Multidisciplinary Awards. The initiative provides $250,000 each year to support faculty research that crosses disciplines.
Read More: Department Faculty Awarded 2013 Provost's Multidisciplinary AwardNew RNA Structure - the Wedekind Lab has it Covered!
Wednesday, May 22, 2013
Crystal structure of the preQ1-II riboswitch.
Department of Biochemistry and Biophysics Associate Professor Joseph Wedekind and members of his research group (Joseph Liberman, Mohammad Salim and Jolanta Krucinska) published a paper in the June 2013 issue of Nature Chemical Biology. The work describes the structure of an RNA molecule called the preQ1 class II riboswitch (featured on the journal's cover) that functions as a gene regulatory element for bacteria within the Firmicutes phylum, including human pathogens such as Streptococcus pneumoniae. The RNA structure is bound to the small molecule preQ1, which is the last soluble metabolite in the biosynthetic pathway that produces queuosine, a hypermodified base at the wobble position of certain tRNAs that promotes accurate genetic decoding. Because preQ1 is unique to the bacterial metabolome, the class II preQ1 riboswitch has potential as an antibacterial drug target.
The research was performed primarily at the University of Rochester and made extensive use of the Structural Biology and Biophysics Facility. The work also required the Stanford Synchrotron Radiation Lightsource (Menlo Park, CA), as well as Cornell High Energy Synchrotron Source (Ithaca, NY) where crystals were subjected to X-ray diffraction analyses. The work in Wedekind' lab was funded by the National Institutes of Health/ National Institute for General Medical Sciences (NIH/NIGMS).
The preQ1-II riboswitch structure reveals the chemical details of preQ1 binding in a pocket formed at the junction of three RNA helices. Complementary work from Wedekind's lab showed that preQ1 promotes a more compact shape that leads to blocking of a signal that is necessary for protein synthesis, which leads to lower levels of preQ1 in the cell. Of special note was the lab's observation that the mechanism of action used by the preQ1-II RNA riboswitch is entirely different than that used by the class I preQ1 riboswitch, whose structure and mode of preQ1 binding were reported previously by Wedekind's lab. Overall the results expand the known repertoire of metabolite-binding modes used by regulatory RNAs.
Department of Biochemistry & Biophysics Holds Annual Awards Ceremony
Friday, May 17, 2013
The Department of Biochemistry & Biophysics held its annual Awards Ceremony on Friday, May 17, 2013.
Congratulations to our 2013 Graduates:
Ph.D. Program in Biochemistry
- Jennifer DeAngelis
- Kimberly Dean
- Rozzy Finn
- Jason Gloor
- Chenguang Gong
- Athena Kantartzis
- Geoffrey Lippa
- Jessica McArdle
- Adam Miller
- Sharon Pepenella
- Karyn Schmidt
- Wen Shen
- Cody Spencer
- Guowei Wu
Ph.D. Program in Biophysics
- Prahnesh Akshayalingam Venkataraman
- Paul Black
- Zhenjiang Xu
Our department was particularly honored this year to receive the University of Rochester's prestigious Wallace O. Fenn Award named after the first Chairman of the Department of Physiology. This award is given annually to a graduating student from any program within the Medical Center judged to have completed especially meritorious Ph.D. thesis research.
This year, the award was given to two recipients for their thesis originality, creative thinking and excellence in research and both recipients were students from the Department of Biochemistry & Biophysics! Congratulations to Paul Black and Chenguang Gong!
For a complete list of all awards, please see the Awards Ceremony Program. Photos of the event can be viewed on the B&B event photos page.
URMC Biochemistry Professor Named University of Rochester 2013 Presidential Diversity Award Recipient
Thursday, January 10, 2013
University of Rochester President Joel Seligman, with 2013 Diversity Award winners Suzanne Piotrowski (THSP), Kevin Graham (THSP), Alyssa Cannarozzo (THSP), Lynne Maquat of the Medical Center, Kim Muratore (THSP), and Vice Provost for Faculty Development & Diversity Vivian Lewis.
Lynne Maquat, Ph.D., J. Lowell Orbison Endowed Chair & Professor, Biochemistry & Biophysics; Director, University of Rochester Center for RNA Biology: From Genome to Therapeutics; Chair, University of Rochester Graduate Women in Science, has been selected to receive one of two 2013 Presidential Diversity Awards for exemplary contributions to the University's diversity and inclusion efforts. Dr. Maquat is being honored for combining her groundbreaking research agenda with a lifelong commitment to helping women succeed in science. Her remarkable accomplishments include the networking and mentoring programs she initiated as president of the RNA Society; her creation in 2003 of the University of Rochester Graduate Women in Science (GWIS) program; and her award and renewal of an NIH training grant that supports graduate students, including underrepresented minorities, in the cellular, biochemical and molecular sciences.
The Presidential Diversity Awards were created in 2009 by President Joel Seligman to recognize faculty, staff, students, units, departments or teams that demonstrate a commitment to diversity and inclusion through recruitment and retention efforts, teaching, research, multi-cultural programming, cultural competency, community outreach activities, or other initiatives.
Read More: URMC Biochemistry Professor Named University of Rochester 2013 Presidential Diversity Award RecipientLongtime Biochemistry & Biophysics Member, Sayeeda Zain, Ph.D., Dies
Wednesday, November 28, 2012
Sayeeda Zain, Ph.D.
Longtime Biochemistry & Biophysics member, Sayeeda Zain, Ph.D. passed away last week after a long and courageous battle with cancer. Services were held last Sunday for Sayeeda.
Sayeeda did her Ph.D. work with Sherman Weissman in the Dept of Human Genetics, Molecular Biophysics and Biochemistry at Yale University where she carried out some of the very earliest nucleic acid sequencing experiments, determining the sequence of parts of the SV40 virus. She then went to Richard Roberts' group at The Cold Spring Harbor Laboratories, where she applied her knowledge of sequencing to both adenovirus transcripts and genomic DNA -- and co-discovered, with Louise Chow, the phenomenon of mRNA splicing. Roberts later received the Nobel Prize for this work, with Philip Sharp (Nobel Prize in Physiology or Medicine, 1993.
In 1978 Sayeeda took a faculty position in the Microbiology Department at the University of Rochester and later was hired into to the Biochemistry Department by Fred Sherman. Sayeeda's research program focused on eukaryotic gene expression with specific emphasis on proteins involved in Alzheimer's disease and molecular mechanisms of metastasis. She remained an active member of the department, teaching in Molecules-to-Cells, until last year.
Alan E. Senior, Emeritus Professor, Publishes Reflections Article
Tuesday, September 4, 2012
Alan E. Senior, Emeritus Professor in the department of Biochemistry & Biophysics, recently published a Reflections article in The Journal of Biological Chemistry. The article details his life and work defining the F1F0-ATPase (also known as ATP synthase), which is a fundamental component of oxidative phosphorylation, and P-glycoprotein, an important enzyme that confers multidrug resistance to anti-cancer drugs and other therapeutics.
Biophysics, Structural & Computational Biology Program to Hold Annual Retreat
Friday, August 17, 2012
The BSCB program will hold it's annual retreat at the Memorial Art Gallery on Monday, October 8. Our Ph.D. candidates will be presenting short talks throughout the day and posters during an afternoon session. A major highlight of the retreat is a Career Discussion Panel comprising five diverse scientists:
- Prof. Hong Li (Florida State U.)
- Prof. Doros Petasis (Alleghany College)
- Prof. Barry Goldstein (U. Rochester/professional photographer)
- Dr. Matthew Benning (Bruker-AXS, Inc.)
- Dr. Chris Strohsahl (CellTraffix, Inc.)
Lunch and refreshments will be served, courtesy of the BSCB Program's Neuman Educational Endowment, as well as corporate sponsorship from Genscript, Inc., Bruker-AXS, Inc., and GE Healthcare, Inc.
Drs. Clara Kielkopf and Joseph Wedekind are the faculty organizers and student organizers are Anant Agrawal and Karl Smith. Program and additional information will be available in September.
Professor Mahin Maines Recognized for Lifetime Contribution to Heme Oxygenase Community
Tuesday, June 5, 2012
Congratulations to Professor Mahin Maines, Ph.D., who received recognition for her lifetime contribution to the Heme Oxygenase Community. Dr. Maines was presented with a certificate acknowledging her contribution, by her peers at the 7th International Congress on Heme Oxygenases and Related Enzymes, 28th May - 1st June, held at the University of Edinburgh
Longtime Faculty Member, Expert in Effects of Radiation on DNA, Dies
Monday, May 14, 2012
William A. Bernhard, Ph.D., a faculty member of the University of Rochester Medical Center for more than 40 years and
an internationally known expert on the effects of ionizing radiation on the chemical structure of DNA, died May 9 at his home in Mendon, N.Y., after a brief illness.
Bill was a biophysicist of the highest order, working at the forefront of understanding how radiation damages our
genetic material. His unique command of both the biological and physical aspects of radiation damage earned him
the respect and recognition of colleagues worldwide,
said Jeffrey J. Hayes, Ph.D., chair of the
Department of Biochemistry and Biophysics. The longevity of his research
program, funded by the National Cancer Institute for 37 consecutive years, and the successful careers of his
many trainees are testaments to the consistent high quality of his work, the high regard his peers, and his
commitment to training future scientists. Bill also was a wonderful person and colleague.
Read More: Longtime Faculty Member, Expert in Effects of Radiation on DNA, Dies10th Annual Fred Sherman Lecture Highlights Genetics Day 2012
Wednesday, April 4, 2012
Today, the department of Biomedical Genetics 24th Annual Genetics Day
was highlighted by the 10th Annual Fred Sherman Lecture. Dr. Fred Sherman, Professor Emeritus of Biochemistry & Biophysics has been honored for his contributions to Genetics
and Yeast Genetics for the past nine years with a lecture named after him. The NIH has funded Fred for a remarkable 45 years, during which time he
has published over 280 papers, with more on the way.
In 1970, Fred initiated the famous yeast course at Cold Spring
Harbor, which has trained scores of today’s leading investigators. He served as an instructor in this course
for 17 years. Fred’s many landmark contributions to several fields of molecular biology were recognized by his
election to the National Academy of Sciences in 1985.
Genetics
Day is an annual event, including a poster session and plenary lectures, that brings together the University
genetics community defined in its broadest sense. This year, Dr. Gary Ruvkun, Professor of Genetics at Harvard Medical
School, gave the Sherman Lecture entitled, The tiny RNA pathways of C.
elegans.
Former Biophysics Chair and Senior Dean of Graduate Studies Dies
Tuesday, March 13, 2012
Paul L. LaCelle, M.D., a University of Rochester Medical Center faculty member for more than 40 years, a former department chair and former senior dean, died March 9. He was 82.
Dr. LaCelle, a 1959 graduate of the University's School of Medicine and Dentistry, joined the faculty in 1964 as an instructor of what was then the Department of Radiation Biology and Biophysics. He was named a professor in 1974 and chaired what is now the Department of Biochemistry and Biophysics from 1977 to 1996.
Read More: Former Biophysics Chair and Senior Dean of Graduate Studies DiesBiophysics, Structural and Computational Biology Graduate Program Holds Annual Retreat
Tuesday, October 11, 2011
The Biophysics, Structural and Computational Biology Retreat took place on Monday, October 10, 2011 at the Memorial Art Gallery in Rochester, NY. There was a great turnout for the event with presentations by postdoctoral fellow's and students from the Dumont, Mathews, Miller, Miao, Kielkopf and Wedekind labs.
In addition to those talks, Dr. Tom Gunter who recently retired from the Biophysics program gave a retrospective talk of the history of the Biophysics program. There was also a Career Panel Discussion featuring Dr. Lea Michel (alumnus, Dr. Kara Bren's lab) from the Rochester Institute of Technology, Dr. Thomas Gaborski who is the President and CEO of SiMPore Inc. as well as Dr. Jack Daiss, Consultant and Chief Scientific Officer at Codevax. The retreat also featured over 20 poster presentations.
Biochemistry and Biophysics Graduate Students Receive Fellowship Awards
Thursday, October 6, 2011
At this year's opening convocation on October 5, two graduate students from the department of Biochemistry & Biophysics received Graduate Fellowship's. Dejun Lin, a Ph.D. student in the Biophysics, Structural and Computational Biology graduate program, was awarded the Leon L. Miller Graduate Fellowship. This fellowship, established by the Miller family, honors Dr. Leon Miller, Professor Emeritus of Biochemistry & Biophysics, for his contributions to science and the School of Medicine and Dentistry. It is awarded annually to a student with interest in developing a biophysics-related research career.
Sarah Amie, a Ph.D. student in the Biochemistry and Molecular Biology graduate program, was awarded the Elmer H. Stotz Graduate Fellowship. This fellowship, established by the Stotz family to honor Dr. Elmer Stotz, Professor Emeritus and former Chair of the Department of Biochemistry, is awarded to a Ph.D. student in biochemistry.
Department of Biochemistry and Biophysics Holds Annual Awards Ceremony
Friday, May 13, 2011
Robert Bambara and Biochemistry & Biophysics Graduates.
The department of Biochemistry & Biophysics held its annual awards ceremony to celebrate those students that received their doctoral degree this year. Awards were also given out to various students and faculty members for their respective research and teaching contributions. The following awards were given:
- Walter Bloor Award for Excellent Ph.D. Thesis
- Keith Connolly and Christopher Hine
- George Metzger Award for Excellence in Biophysics Ph.D. Thesis
- Jessica Snyder
- Marvel-Dare Nutting Award Recognizing an Outstanding Biochemistry Ph.D.
- Tamara Caterino
- William Neuman Award in Biophysics
- Paul Black
- William Neuman Travel Awards
- Paul Black, He Fang, Nicholas Leioatts, and Wenhua Wang
- Excellent Student Seminar Presentations
- Wen Shen, Karyn Schmidt, Krystle McLaughlin, and Nicholas Leioatts
- Faculty Teaching Awards
- David Mathews, Ph.D. and Lynne Maquat, Ph.D.
- Staff Recognition Award
- Melissa Vera