November 12, 2010
Researchers have developed a technique that identifies genes associated with specific biologically active proteins much more quickly than previously possible.
The approach is potentially useful not just for analyzing gene functions in yeast—the organism on which it's first been demonstrated—but in other organisms as well, including humans. The technique was devised by associate professor Eric M. Phizicky, Ph.D. and research associate professor Elizabeth J. Grayhack, Ph.D. of the department of Biochemistry & Biophysics at the University of Rochester School of Medicine.
September 7, 2010
Leon Miller, M.D., Ph.D.
Leon L. Miller, M.D., Ph.D., a scientist and physician who was part of the fabric of the University of Rochester Medical Center for all but the first dozen years of its 84-year history, died Friday, Sept. 3, at Highland Hospital in Rochester.
Dr. Miller, who arrived at the Medical Center in 1938 – just 14 years after University President Rush Rhees laid the cornerstone of the medical center complex and 12 years after the first baby was born at Strong Memorial Hospital – was 97 years old.
Dr. Miller was as vigorous and lucid a person as you can imagine,said Robert Bambara,Ph.D., chair of the Department of Biochemistry and Biophyics.
He came to every faculty meeting and all the seminars, sitting in the front row, listening intently to presentations and asking very astute questions. He was a deep part of the fabric of our department. He was a real advocate for supporting younger faculty members and gave inspiring talks about how established faculty members should support younger faculty,added Bambara.
September 3, 2010
Fred Sherman Articles Honored as JBC Classics
To celebrate 100 years of Biochemistry and Molecular Biology, the Journal of Biological Chemistry chose to reprint two of Dr. Fred Sherman's articles as well as write a biographical sketch honoring Fred's over four decades of research with cytochrome c. The two reprints, The Mutational Alteration of the Primary Structure of Yeast Iso-1-cytochrome c (1968) and Identification of Missense Mutants by Amino Acid Replacements in Iso-1-cytochrome c from Yeast (1974) speak to Fred's early research in isolation and identification of cytochrome c mutants which continues today. Dr. Sherman is currently Professor Emeritus in the department of Biochemistry & Biophysics at the University of Rochester Medical Center. Please read the entire JBC Centennial tribute to Dr. Sherman.
June 28, 2010
Lynne Maquat, Ph.D., J. Lowell Orbison Chair and Professor of Biochemistry and Biophysics at the University of Rochester Medical Center, was honored with the RNA Society's Lifetime Achievement Award in Service on Saturday, June 26 at the society's 15th annual meeting in Seattle, Washington. Maquat has been a member of the society since its formation in 1993, and has played an extremely active role, holding every elective office from director, to secretary/treasurer, to president.
June 4, 2010
Rex protein in action
Scientists have obtained the first images of a common molecular signal, vitamin B3, which plays a role in making some bacteria potent and some men impotent.
For the first time, researchers have captured three-dimensional images of a protein in the act of responding to oxygen levels by sensing vitamin B3. Vitamin B3, also known as niacin, is essential to convert the food we eat into energy. Vitamin B3 also regulates a variety of processes, including erectile dysfunction, aging and sleep patterns in people. The findings, published in the journal Molecular Cell, could guide future development of antibiotics, and in the long term, new treatments for erectile dysfunction.
Vitamin B3 has been the focus of intense interest since its role as a signaling molecule was discovered, yet no one knew how proteins, the molecular machines of the cell, could sense the slight differences between the oxidized and reduced forms,said Clara Kielkopf, Ph.D., associate professor in the Department of Biochemistry and Biophysics at the University of Rochester Medical Center and lead study author.
March 1, 2010
Lynne Maquat Featured in ASCB Newsletter
Lynne E. Maquat, Ph.D., the Dean's Endowed Chair of the Department of Biochemistry and Biophysics at the University of Rochester Medical Center, has been featured in the March 2010 American Society for Cell Biology (ASCB) Newsletter for her contributions to mRNA research. Maquat demonstrated that in mRNA, the nonsense tidied up after itself through a process called nonsense-mediated mRNA decay (NMD).
The problem goes
way back,explains Joan Steitz of Yale.
But I consider Lynne the pioneer—and it took her a number of years—in figuring out this mysterious process called nonsense-mediated mRNA decay.Nearly everyone working with mRNA realized that somehow cells can tell when a premature stop codon has been inserted into an open reading frame. Yet no one had an explanation of what happened to these nonsense proteins. According to Steitz, the big leap came when Maquat figured out that introns must leave a mark on newly synthesized mRNA. Working with Melissa Moore in the late 1990s and early 2000s, Maquat identified that mark—the exon junction complex (EJC).
The full ACSB March 2010 Newsletter can be viewed here, with Dr. Maquat's profile beginning on page 15.
January 14, 2010
Joshua Munger, Ph.D., an assistant professor of Biochemistry and Biophysics, has received a prestigious Damon Runyon Cancer Research Foundation Innovation Award, which recognizes promising early-career scientists who have outstanding research but lack sufficient preliminary data to get traditional funding.
Munger's research focuses on cancer cell metabolism. A virologist and biochemist by training, he is studying the metabolic activities that are altered when cells transform from normal to malignant. Whereas previous studies have focused narrowly on individual metabolic activities, Munger is taking a more global approach by examining the rates of numerous individual metabolic processes simultaneously.
December 7, 2009
Early roots of the virus that causes AIDS might be found in a tiger that lived thousands or millions of years ago, new research suggests.
It appears the virus took on a bit of a tiger's genetic material, scientists say, and a remnant of that cat remains in the virus to this day. That tiger, in fact, may have bitten a monkey, setting off an evolution of the virus that ultimately led to its infection of humans. The finding shouldn't lead to any immediate breakthroughs in AIDS treatment, experts say. But it does provide more insight into how the virus works.
Unless you really understand how these viruses work, the exact step-by-step chemical process, then you can't really rationally design a new clever kind of therapy that may be effective against the virus,explained study co-author Robert Bambara, Ph.D., Chairman of the University of Rochester's Department of Biochemistry and Biophysics.
December 6, 2009
An ancestor of the AIDS virus hijacked an entire gene, perhaps from some prehistoric cat it had infected, a gene that makes it much better able to infect humans, according to a study published online today in Nature Structural and Molecular Biology. The discovery represents the first instance in which researchers have found an entire animal gene within the genome of the human immunodeficiency virus despite 30 years of intense analyses.
HIV molecular biology is the most studied in history, which makes it remarkable that the presence of an entire copy of this gene, called tRNALys3, could go undiscovered within the HIV genome for decades,said Robert Bambara, Ph.D., Chair of the Department of Biochemistry and Biophysics at the University of Rochester Medical Center, and the study's lead author.
We not only found the gene, but also a plausible explanation for why it is still there after millions of generations: its presence makes HIV dramatically better at reproducing inside of our cells. This suggests new ways to shut down with drugs the ability of the virus to mass produce copies of itself.
September 29, 2008
Flu Virus with Envelope
Viruses dramatically increase cellular metabolism, and existing anti-obesity drugs may represent a new way to block these metabolic changes and inhibit viral infection, according to a study published today in the journal Nature Biotechnology.
Using new fluxomic techniques, our study reveals that viral infection takes control of cellular metabolism and drives, among other things, marked increases in fatty acid synthesis,said Joshua Munger, Ph.D., assistant professor of Biochemistry and Biophysics at the University of Rochester Medical Center, and a study author.
We also found that if you target these increases in fatty acid metabolism using existing anti-obesity and anti-metabolism drugs, you inhibit viral replication.
April 17, 2008
In recent years, researchers at the University of Rochester Medical Center have revealed the existence of a natural surveillance system called nonsense-mediated mRNA decay (NMD) that determines which mRNAs are fit to serve as protein templates and sees to the destruction of those with flaws. Researchers hope to tweak the process such that it catches more genetic errors in some cases, or leaves more templates for helpful proteins in place in others, based on the disease at hand. To do so will require a highly detailed knowledge of the NMD pathway.
The current results uncover a critical and previously unappreciated step during the natural process that finds flaws in mRNAs,said Lynne E. Maquat, Ph.D., J. Lowell Orbison Endowed Chair and professor of Biochemistry & Biophysics at University of Rochester Medical Center, director of the University of Rochester Center for RNA Biology and lead author of the Cell piece.
This work has important implications for our understanding of how one of the human cell's most important activities, protein synthesis, undergoes quality control.
March 1, 2008
Once a month, women graduate students, postdocs, and early-career faculty come together to listen to straightforward advice from accomplished scholars about important steps and critical practices to build a successful academic career. The monthly format provides regular opportunities for women in science to communicate with one another and establish relationships with peers.
The driving force behind the program is its coordinator, Lynne Maquat, Ph.D., J. Lowell Orbison Endowed Chair and Professor of Biochemistry and Biophysics. Maquat offers this important advice to future faculty members:
Do things despite your fears; build a strong curriculum vita—because it is always about merit; know yourself and what your strengths are; and be pragmatic about your career—know what you want to accomplish in the next six months, twelve months, and five years and then stick to your plan.
January 8, 2008
The ability of Streptococcus mutans (S. mutans) to survive in acid is one reason that the species is the main driver of tooth decay worldwide. Past research has shown that this ability has several components including a bacterial enzyme called fatty acid biosynthase M (FabM), which when shut down, makes S. mutans almost precisely 10,000 times more vulnerable to acid damage.
Our first goal is to force the major bacterium behind tooth decay to destroy itself with its own acid as soon as it eats sugar,said Robert G. Quivey, Ph.D., professor of Microbiology & Immunology at the University of Rochester Medical Center and principal investigator for the grant.
After that, this line of work could help lead to new anti-bacterial combination therapies for many infections that have become resistant to antibiotics.
Quivey's partners in the grant application were Elizabeth Grayhack, Ph.D., research associate professor of Biochemistry & Biophysics, Robert Marquis, Ph.D., professor of Microbiology & Immunology, and Eric Phizicky, Ph.D., professor of Biochemistry & Biophysics.
January 2, 2008
Investigators at the University of Rochester Medical Center have uncovered a promising drug therapy that offers a ray of hope for children with Batten disease - a rare neurodegenerative disease that strikes seemingly healthy kids, progressively robs them of their abilities to see, reason and move, and ultimately kills them in their young twenties.
The study, highlighted in the January edition of Experimental Neurology, explains how investigators improved the motor skills of feeble mice that model the disease, helping them to better their scores on successive coordination tests.
No treatment currently exists for these kids – nothing to halt the disease, or even to slow it down,said one of the study's authors, David Pearce, Ph.D., a nationally renowned Batten disease expert and Biochemistry professor at the University of Rochester. His team has published more than 50 studies on the disease's basic mechanisms.
June 19, 2007
David S. Guzick, M.D., Ph.D., Dean of the University of Rochester's School of Medicine and Dentistry, wrote in his recent Dean's Newsletter that,
A truly great scientific career is measured not only by the direct impact of the scientist's original work, but by the impact on the field of his or her progeny--students mentored by the scientist who go on to make substantial contributions themselves.
It is, therefore, truly wonderful to share with you our excitement for Bob Bambara, Ph.D., Professor and Chair of the Department of Biochemistry and Biophysics, who was honored at the University's May 19 Commencement Exercises with the William H. Riker University Award for Excellence in Graduate Teaching,continued Guzick.
This is the first Riker award to go to a faculty member at the medical school. The Riker Award is also for mentoring students who go on to have successful careers. That being said, Bob's students are professors at the University of California, Indiana, Kentucky, Leiden, North Carolina, and Virginia. Two are Professors at the University of Rochester, and two are Deans! Others head large biochemistry programs in biotech, and one is vice president of a major company.
March 6, 2007
Eric Phizicky, Ph.D., professor of Biochemistry & Biophysics, will give a talk titled
tRNA: how and why it's all dressed upas part of a lecture series highlighting biomedical research at the University of Rochester.
Phizicky will speak about the tremendous, recent explosion in the understanding of transfer ribonucleic acid (tRNA), the middleman in the process of converting genetic code into proteins that make up the body's structures, carry its messages and execute its functions. He will speak at 4 p.m. Friday, March 9, in the Case Methods Room (Room 1-9576) at the Medical Center.
December 1, 2006
The American Association for the Advancement of Science (AAAS), the world's largest federation of scientists, has elected four scientists from the University of Rochester as fellows. John Jaenike, Michael K. Tanenhaus, Lynne E. Maquat, and Henry A. Kautz were honored for the advances they've brought to their respective fields. The new fellows will be presented with a certificate at the Fellows Forum during the 2006 AAAS Annual Meeting in San Francisco on Feb. 17, 2007.
Maquat, the Dean's Endowed Chair of the Department of Biochemistry and Biophysics, was nominated
for discovery and characterization of nonsense-mediated mRNA decay.Most recently her work has focused on how human cells protect themselves from constant and potentially destructive changes in gene expression through an RNA-mediated mechanism.
November 9, 2006
A drug that corrects the effects of a genetic mutation has produced encouraging results in tests on patients. The drug, PTC124, is designed to fool a patient's cells into producing a functional protein, even though that protein's gene is mutated.
Lynne Maquat, an RNA researcher at the University of Rochester, says more research is needed. But she adds that there is a real need for drugs of this sort. An antibiotic called gentamycin also causes cells to ignore mutations, but it can cause deafness and kidney failure.
July 25, 2006
Dr. Fred Sherman Receives Genetic Society of America Lifetime Achievement Award
Dr. Fred Sherman was honored at this year's Yeast Genetics and Molecular Biology Meeting sponsored by GSA with the lifetime achievement award. Dr. Sherman has tirelessly led international efforts to firmly establish yeast as the premier genetic eukaryotic model system. He is currently Professor Emeritus, but has served as department Chair of Biochemistry and Biophysics (1982-1999) and Chairman of the Genetics Division of the National Academy of Sciences (2000-2003), of which he is one of only two members at the University of Rochester Medical Center. The meeting was held in Princeton, N.J., July 25-30. There were 820 attendees presenting 81 oral presentations and over 500 posters.
June 1, 2006
Lynne E. Maquat, Ph.D., the Dean's Endowed Chair of the Department of Biochemistry and Biophysics at the University of Rochester Medical Center, has been elected president of the RNA Society. The Society was formed in 1993 to encourage the sharing of experimental results and emerging concepts in ribonucleic acid research.
April 28, 2006
Two researchers, one from the University of Rochester Medical Center and another from the University of Rochester River Campus, were named as new members of the 226th class of the American Academy of Arts & Sciences. Lynne E. Maquat, Professor of Biochemistry and Biophysics, received the honor along with Richard Aslin, Professor of Brain and Cognitive Sciences.
Maquat was honored for decades of work that has advanced the understanding of how human cells protect themselves from constant and potentially destructive changes in gene expression. According to a recent article published in Nature Structural & Molecular Biology, the research is important because the protection itself can contribute to disease, and the ability to side-step it may lead to new treatments for hundreds of genetic disorders.
October 25, 2005
With their latest discovery, researchers have significantly advanced the understanding of how human cells protect themselves from constant and potentially destructive changes in gene expression. According to an article published in this month's Nature Structural & Molecular Biology, the research is important because the protection itself can contribute to disease, and the ability to side-step it may lead to new treatments for hundreds of genetic disorders.
Our study is important because we have determined for the first time that the mRNA-binding protein CBP80 tells the NMD system which mRNAs to review for nonsense codons,according to Lynne E. Maquat, Ph.D., professor of Biochemistry and Biophysics at the Medical Center, and senior author of the Nature article.
September 7, 2005
As part of a $4.88 million grant from the National Science Foundation (NSF), molecular biologists from the University of Rochester Medical Center will join a team seeking to create the first complete wiring diagram of a living cell. By wiring diagram, researchers mean a detailed model, not only of the cell's genes and their function, but also of the interplay between them. When complete, the diagram has the potential to reveal cellular approaches to treating many diseases, including cancer.
With most genes redundant and related to other genes and proteins in predictable ways, we can begin to identify the function of unknown cellular players based on their neighbors and associates,said Eric Phizicky, Ph.D., professor of Biochemistry & Biophysics at the medical center.
That puts us within reach of a completed diagram and the ability to re-wire cells in the treatment of disease.
February 4, 2005
As any dedicated video game player knows, the first requirement for using a weapon or tool is finding it. And it is no different for cell biologists and clinicians who want to take control of gene expression in cells to create therapies to treat disease. While cells have a variety of ways to control gene expression, the trick for players in this game is to recognize them amidst the incredibly complex background of cellular machinery.
Now, in a paper in the January 28th issue of Cell, Lynne E. Maquat, Ph.D., professor of Biochemistry and Biophysics at the University of Rochester Medical Center, and her team, have identified a novel pathway for RNA degradation, a form of regulation that has garnered significant attention in recent years, and one that has the potential to produce a new set of tools for physicians to use to fight disease.
November 18, 2004
A pair of scientists whose discoveries have changed genomic research was honored today by the James P. Wilmot Cancer Center at the University of Rochester Medical Center. Eric Phizicky, Ph.D., and Elizabeth Grayhack, Ph.D., received the 2004 Davey Memorial Award for outstanding contributions to cancer research.
Phizicky and Grahack, a husband-and-wife research team, are considered pioneers in the field of functional proteomics. They were the first to develop a method to identify genes by the activity of their products on a genome-wide scale, by using all of the 6,144 genes of yeast as a model system. Their work has broad implications for biological sciences including cancer research.
October 20, 2003
William Simon, Ph.D., professor in the department of Biochemistry & Biophysics at the University of Rochester Medical Center was featured on National Public Radio's (NPR) Talk of the Nation. Host Lynn Neary reads emails from listeners and then talks with Dr. Simon about his 1971 article in Science and the probability of the World Series going seven games.
May 12, 2003
Eric Phizicky, Ph.D., professor in the department of Biochemistry & Biophysics at the University of Rochester was interviewed and profiled at GenomeWeb. Dr. Phizicky discussed his research at the University Rochester, the library of 6,144 yeast strains, and the fact that his lab has identified genes, in the last four years, associated with more than 38 activities, including just about every biochemical reaction.
May 1, 2003
The Double Entendre: Gerald Fink's Tribute to Fred Sherman
Dr. Gerald Fink of Whitehead Institute at MIT recently honored his friend and collegue, Dr. Fred Sherman, with a tribute in the book, The Early Days of Yeast Genetics. Fink and Sherman taught the Cold Spring Harbor Yeast Course for 17 years together. In the chapter,The Double Entendre, Dr. Fink describes his collegue as being
deadly seriousabout the Yeast course and that he was
constantly inventing inexpensive gadgets for the course to substitute for the costly ones.
zanysense of humor and love for the course and Cold Spring Harbor itself, Gerry would never had to ask if Fred was enthusiastic about teaching the course another summer:
I could tell from the Cheshire grin that squeaked out as he partnered one of the students into the laboratory that he was up for another year.
October 16, 2002
A scientist who studies cellular mistakes was recently honored by the James P. Wilmot Cancer Center at the University of Rochester Medical Center. Lynne E. Maquat, Ph.D., professor of Biochemistry and Biophysics, received the 2002 Davey Memorial Award for outstanding contributions to cancer research.
Maquat was honored for her research into nonsense – flawed molecular coding that results in abnormally shortened proteins and could cause harm. The flaw is oftentimes a mistake in the genetic material, DNA, or its product, RNA, which encodes instructions for making proteins. Mistakes happen routinely and are also at the root of a large percentage of diseases, including cancer.
March 9, 2001
The completion of the first draft of the human genome sequence gives us the potential to understand the precise protein content of every cell in a human being. It is also suddenly within our sights to decipher the function of every protein in the cell, and a number of methods have emerged to meet this challenge.
The Phizicky lab has focused on a genomic approach to biochemical analysis. To this end, a genomic library of yeast strains was prepared, in which each strain expresses a different yeast protein attached to an affinity purification tag. With the purified genomic array of proteins, one can rapidly link any biochemical activity to its cognate gene. This array has been used to identify several different catalytic and binding activities, and can be used to find targets of drugs. A similar array could be developed to analyze the proteins of the human genome.
May 1, 2000
Dr. Fred Sherman Named Chairman of Genetics Section of National Academy of Sciences
Dr. Fred Sherman, Professor of Biochemistry & Biophysics has been named Chairman of of the Genetics Section of the National Academy of Sciences. Dr. Sherman has been investigating various broad aspects of gene expression in yeast, as means to determine processes operating in eukaryotic cells by using iso-1-cytochrome c as a model system for over four decades, and was elected to NAS in 1985.
May 1, 1985
Dr. Fred Sherman Elected to the National Academy of Sciences
Dr. Fred Sherman was elected to join an elite group of exceptional scientists that make up the National Academy of Sciences. A pioneer in yeast genetics (viewed by many as
The Father of Yeast Genetics), his election was based on his research in various areas of yeast biology, including gene expression, protein processing and degradation, mRNA degradation, as well as studies with the pathogenic yeast Candida albicans, as well as hundreds of journal articles, and several books (and chapters) detailing his work. Sherman is currently the Chair of Department of Biochemistry at the University of Rochester.
September 1, 1982
Dr. Fred Sherman Named Chair of the Department of Biochemistry
Dr. Fred Sherman, Professor of Biochemistry has been named Chair of the deparment. Dr. Sherman has led international efforts to firmly establish yeast as the premier genetic eukaryotic model system. He has been investigating various broad aspects of gene expression in yeast, as means to determine processes operating in eukaryotic cells by using iso-1-cytochrome c as a model system.
May 10, 1975
William Simon Featured on 13WHAM News to Talk About Ultrasound Cardiography
William Simon, Ph.D., professor in the department of Biochemistry & Biophysics at the University of Rochester Medical Center was featured on 13WHAM News to talk about his 1973 article published in Radiology. The article published with Raymond Gramiak, M.D. and Robert C. Waag, Ph.D. entitled, Ciné Ultrasound Cardiography, discusses the development of a ciné ultrasonic cardiographic technique which produces cross-sectional motion picture studies of the heart using conventional ultrasonic techniques. The area under consideration is examined using a single slow sector scan which incorporates a minimum of 20 cardiac cycles and simultaneously records an electrocardiogram. This panoramic scan views the anatomic structures sequentially, and also includes the motion of the components.