New article shows that RNAs universally fold into secondary structures with short end-to-end distances
Monday, July 6, 2020
Mathews and Ermolenko 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. The article can be downloaded using this link https://rochester.app.box.com/s/13d9cbgp38uu040u9ap8gktxrfhbc92u
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 Research
Ermolenko lab uncovers a new mechanism causing ribosome pausing
Wednesday, June 10, 2020
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.
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.
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.
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.
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 Students
Biochemistry & 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
Wan-Jung (Christine) Lai
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
George V. Metzger Award For excellence of the Ph.D. thesis and in the research leading to the dissertation in the Program in Biophysics
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
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.Read More: Graduate Student Viktoriya Anokhina Elected Co-Chair of Gordon Research Seminar
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 Coronavirus
ROC 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-19
Golisano Children's Hospital Thanks the Department for it's Toy Drive Donations
Tuesday, February 11, 2020
Professor Yi-Tao Yu is is quoted in Nature article, and a wins major grant award from the Cystic Fibrosis Foundation
Wednesday, February 5, 2020
Professor You was quoted in a Nature review article published February 4th, 2020, entitled Step Aside CRISPR, RNA Editing Is Taking Off. Dr. Yu stated that a large number of genetic diseases are the result of mutations leading to stop codons, resulting in a shortened protein that doesn’t function normally in the body. He noted that the list of such diseases is very long and includes cystic fibrosis, the eye disease Hurler’s syndrome, and numerous cancers. On February 6th, Dr. Yu was notified that he had won a major grand award from the Cystic Fibrosis Foundation entitled "CFTR nonsense suppression by targeted pseudouridylation.” Congratulations to Dr. Yu!Read More: Professor Yi-Tao Yu is is quoted in Nature article, and a wins major grant award from the Cystic Fibrosis Foundation