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Wilmot Scientists Exploit Cell Metabolism to Attack Cancer

Wednesday, October 12, 2016

Cancer cells have their own unique ways of reproducing, involving a shrewd metabolic reprograming that has been observed in virtually all types of cancer but not in normal cells. Now, University of Rochester Medical Center scientists have pinpointed one key source of the problem, which could lead to new treatment opportunities.

In an article published by Cell Reports, the scientific team shows for the first time how cancer-causing mutations control and alter the way cancer cells biosynthesize and replicate.

The discovery is the result of a close collaboration between the laboratories of Joshua Munger, Ph.D., associate professor of Biochemistry and Biophysics, and Hucky Land, Ph.D., the Robert and Dorothy Markin Professor and Chair of Biomedical Genetics and director of research at the URMC’s Wilmot Cancer Institute.

“Every tissue or cell type in the body has different metabolic needs but as cells become cancerous their metabolism shifts in ways that are very different from normal cells,” Munger said. “Being able to identify those differences is critical for developing treatment targets.”

Read More: Wilmot Scientists Exploit Cell Metabolism to Attack Cancer

NIH Director Visits URMC, Says it’s an Exciting Time to be a Researcher

Monday, October 10, 2016

NIH director round tableCollins’ first stop was lunch with 15 graduate students and postdocs who came prepared with a wide range of questions. The discussion covered the importance of communicating science to the public and policymakers, increasing diversity in biomedical research and new mechanisms to support young scientists at the start of their careers. Postdoctoral fellow Sarah Latchney and Ph.D. graduate student Solomon Abiola attended the lunch with Collins and describe the experience here.

Members of the Center for RNA Biology highlighted their most promising work for Collins and Center director Lynne E. Maquat, Ph.D., gave Collins a tour of her lab, where he met more trainees and junior researchers (admittedly, Collins’ favorite part of visits like these).

Dr. Collins SpeakingIn his keynote address at the end of the day, Collins delivered an uplifting message to a packed house in the Class of ’62 auditorium: it is an extremely exciting time to be in biomedical research, and after many lean years we are turning a corner, with the NIH budget finally increasing in real terms. He detailed several of the NIH’s new programs, like the Human Microbiome Project, Big Data to Knowledge (BD2K), the Precision Medicine Initiative and the Cancer Moonshot.

He applauded URMC on the renewal of the CTSI funding and cited the translational research conducted by Arthur J. Moss, M.D., which has led to new treatments for patients with Long QT syndrome (LQTS), and John J. Treanor, M.D., which is helping scientists in pursuit of a universal flu vaccine. Collins outlined several new funding initiatives, including the NIH Director’s Early Independence Award, which is helping assistant professor Elaine L. Hill, Ph.D., study the impact of fracking on infant and child health.

Collins affirmed that the U.S. is the strongest biomedical research country in the world thanks to institutions like URMC. You can view his keynote, “Exceptional Opportunities in Biomedical Research,” here.

Read More: NIH Director Visits URMC, Says it’s an Exciting Time to be a Researcher

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 Board

Miller 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.

Maquat Featured at Cornell-Ithaca Creativity Workshop

Saturday, July 30, 2016

RocHackHealth Group

J. Lowell Orbison Chair of Biochemistry and Biophysics, and of Oncology, Lynne Maquat, PhD, was a featured speaker at The Creativity Spark: a creativity workshop for scientists, a workshop put on by Cornell University, July 25.

The creativity workshop featured award winning scientists and scholars, including two Nobel Laureates, as they discussed the Creativity Spark and its role in science exploration.

Read More: Maquat Featured at Cornell-Ithaca Creativity Workshop

Meet Karl Smith, the Typewriting Tale Teller

Friday, July 8, 2016

Photo of Karl Smith

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.


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, like this one, but sometimes they're just stories, like this one. 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 Teller

URMC Team Revises Understanding of Genetic Code

Friday, July 1, 2016

Grayhack lab photo

Beth Grayhack, Ph.D., with lab
members and grad students
Christina Brule and Jiyu Wang

Scientists for years have known that the genetic code found in all living things contains many layers of complexity. But new research from the University of Rochester cracks the code more deeply, clarifying for example why some genes are inefficiently translated into proteins.

In a study published in the journal Cell, the researchers, co-led by Beth Grayhack, Ph.D., of the UR School of Medicine and Dentistry, discovered the existence and identity of 17 pairs of inefficient codons (DNA nucleotides or bases) within the genetic code.

Scientists have generally considered each piece of the genetic code (or codon) as a single “word” in a language. But the new data suggests some codon combinations act as compound words or phrases whose order and pairing has a significant impact on the translation of genes into proteins.

“Consider the words ‘pancake’ versus ‘cake pan,’ “ said Grayhack, an associate professor of Biochemistry and Biophysics, Pediatrics, and Cancer, in the Center for RNA Biology, at the UR Medical Center.

Read More: URMC Team Revises Understanding of Genetic Code

Review: Giving Gene Editing Technology CRISPR-Cas9 a Boost

Thursday, June 23, 2016

A new gene editing technology called CRISPR-Cas9 has taken the scientific world by storm. It allows researchers to quickly and easily make changes to the DNA of humans, animals and plants. The hope is that CRISPR-Cas9 may be used in the future to eliminate or correct faulty genes that cause disease.DNA

In a recent issue of the journal Cell, Lynne E. Maquat, Ph.D. and Maximilian W. Popp, Ph.D. of the University of Rochester Center for RNA Biology describe how scientists can make this technology more efficient. Understanding the principles of nonsense-mediated mRNA decay (NMD), a cellular mechanism that Maquat discovered early in her career, will help anyone employing the technology achieve a better result – namely, a more complete knock out or deletion of a desired gene.

Read More: Review: Giving Gene Editing Technology CRISPR-Cas9 a Boost

Clara 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.

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 Editing

Harold Smith Inducted into Royal Society of Biology

Friday, April 8, 2016

Dr. Harold Smith, Professor of Biochemistry & Biophysics has been inducted into the Royal Society of Biology.

A long time member of the department, Dr. Smith's primary interest is understanding the composition, regulation and structure of macromolecular complexes involved in regulating gene expression at the level of messenger RNA expression and processing. The lab's focus is on a platform of enzymes that change the genetic code at the DNA or RNA level by deaminating cytidine to form uridine. Current data suggest that this family of cytidine deaminase function with other proteins (auxiliary proteins) as holoenzymes complexes which we refer to as editosomes (for RNA) or mutasomes (for DNA). RNA editing or DNA mutational activity by these enzymes affect the protein coding capacity of mRNAs and thereby can diversify the proteins that are expressed by cells (the proteome). Please visit the Smith Lab for more information. Dr. Smith has a 30 year track record of teaching and mentoring graduate students, medical students and undergraduates at the University of Rochester and has lead curriculum design and reform for these programs.

The Royal Society of Biology (RSB), previously called the Society of Biology, is a learned society in the United Kingdom created to advance the interests of biology in academia, industry, education, and research. Formed in 2009 by the merger of the Biosciences Federation and the Institute of Biology, the society has around 16,000 individual members, and over 100 member organizations. In addition to engaging the public on matters related to the life sciences, the society seeks to develop the profession and to guide the development of related policies.

Professor Harold Smith to Organize Meeting on Drug Discovery

Thursday, March 31, 2016

The Clinical Science and Drug Discovery Conference had its inaugural meeting in 2015 in Baltimore, MD where Dr. Smith was asked to serve as a Keynote Speaker (and judge for poster sessions). The organizers of that meeting nominated him to organize this years meeting in Dundee, Scotland along with Drs. Ian Catchpole from GlaxoSmithKline in the UK and Nikolai Zhelev, professor at Abertay University, the hosting institution. The meeting will be held July 27-29. Dr. Smith will also deliver a keynote lecture at this meeting and chair a special topics session that he is bringing together on 'Host Cell Factors as Therapeutic Targets'. For more information, please visit the Drug Discovery Summit site, see also the CSDD Brochure.

Q&A: Biologist earns raves for work with yeast

Wednesday, March 23, 2016

David Goldfarb, professor of biology and biochemistry, researches yeast as a model organism for understanding the aging process in humans. Goldfarb joined the Rochester faculty in 1988, five years after earning his PhD in biochemistry at the University of California, Davis, and completing postdoctoral work at Stanford University.

Goldfarb holds four patents and has been recognized with more than a dozen honors, including the Johnson & Johnson “Focused Giving Program” Award, the National Society of Collegiate Scholars Distinguished Member Award, and the March of Dimes Health Leadership Award in Education.

Read More: Q&A: Biologist earns raves for work with yeast

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 Photonics

Strong 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. Your comments can be included at the iCare site.

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 Storyteller