Though much of the human genome has been sequenced and assembled, scientists have hit road blocks trying to map unassembled regions of DNA that consist mostly of repetitive sequences. One of these regions, found in every cell, is the centromere.

Researchers from the University of Rochester, along with their colleagues at the University of Connecticut, have now discovered the centromeres of the model genetic organism Drosophila melanogaster (fruit fly), sequencing the most repetitive parts of its genome and unlocking one of the “last frontiers of genome assembly,” says Amanda Larracuente, an assistant professor of biology at Rochester and co-lead author on the study. The research, published in the journal PloS Biology, sheds light on a fundamental aspect of biology, and shows that selfish genetic elements may play a larger role in centromere function than researchers previously thought.

Chromosomes are found in the nucleus of cells and carry tightly wrapped strands of DNA. One of the most essential structures of a chromosome is a specialized region of DNA called the centromere, which is vital for cell division. During cell division, proteins attach to the centromere and coordinate the process of packaging DNA and pulling the chromosome apart to opposite sides of the dividing cell. If centromeres don’t function properly, cells may divide with too few or too many chromosomes, which can result in aneuploidy disorders like Down syndrome.

Centromeres in most plants and animals—including humans—are often found near the center of the chromosome, embedded in blocks of repetitive DNA known as satellite DNA. Larracuente; Ching-Ho Chang, a PhD student in Larracuente’s lab and co-lead author of the paper: and their colleagues used new sequencing technology and genome assembly methods to sequence the repetitive regions of the fruit fly genome, including its centromeres. This is the first time researchers have sequenced all the centromeres in any multicellular organism.

The researchers found that centromeres sit directly over islands of transposable elements — typically thought of as selfish genetic elements that can jump around and spread in genomes and in populations despite often being harmful to their host.  This could mean that genomes are repurposing selfish genetic elements to build essential regions of chromosomes.

Read more here.

Medical Center CEO Mark Taubman has released a video describing a new initiative to streamline and strengthen clinical research at URMC. The Embark initiative will reduce the administrative burden on clinical research teams, allowing them to spend more time caring for study participants and patients.

Ultimately, Embark will enable researchers to conduct more clinical trials at URMC and discover new treatments and cures. Watch the video. (You must be on the URMC network to access this video.)

All URMC community members who are involved in clinical research are also encouraged to attend the upcoming Discover Embark event — featuring a panel discussion and Q&A — to learn more about this initiative, from 2-3 p.m. Wednesday, June 5, in the Class of ’62 Auditorium.

Email Embark with any questions or concerns.

The Medical Center, Burke Neurological Institute, and the Wadsworth Center of the New York State Department of Health (NYSDOH) have been awarded a $5 million grant from the Empire State Development Corporation to speed the development of ground-breaking neurological treatments for those disabled from stroke.

The project is a part of the NeuroCuresNY (NCNY) initiative, a new non-profit formed by the three institutions to accelerate the discovery of novel treatments for chronic neurological impairment and disability. The new state funding will support a two-year pilot study that will be launched in January 2020. This study design will be unique because it will test the efficacy of state-of-the-art robotic-assisted rehabilitation technology combined with drugs to improve the functional recovery of stroke patients.

Neurological conditions such as stroke, traumatic brain injury, and spinal cord injury permanently disable more than one million people each year in the U.S., and stroke is the nation’s leading cause of disability. Clinical trials for neurological disabilities and impairments are usually passed over because of unclear results, high costs, and challenges in recruiting participants. NCNY will seek to lower the barriers to participation in clinical trials by assisting with travel funding for patients, while providing a supportive and guiding environment for patients and their families.

The new study will be conducted at the University’s Neurorestoration Institute, led by Bradford C. Berk, and the Burke Neurological Institute, led by Rajiv R. Ratan. The National Center for Adaptive Neurotechnologies at the Wadsworth Center of the NYSDOH, led by Jonathan Wolpaw, will configure the technology that collects and analyzes the research data.

Read more here.

Originally called Provost’s Multidisciplinary Awards, the University Research Awards provide “seed” grants for promising, high-risk projects.

The fund has been increased from $500,000 annually to $1 million. Half of the funding comes from the President’s Fund, with the rest being matched by the various schools whose faculty members are recipients.

Applications are sought from faculty across the University, and funding is awarded to recipients who demonstrate their projects favor new research with a high probability of being leveraged by future external funding. A review committee of faculty from across the University provides peer review of the applications.

This year’s recipients are:

Kathryn E. Knowles and Ellen M. Matson, assistant professors of chemistry, for Polyoxovanadate Clusters as Single-Source Precursors for Colloidal Vanadium Oxide.
Vanadium oxide (VOx) compounds comprise a diverse class of materials with potential applications in batteries, supercapacitors, thermoelectric devices, smart windows, and solar energy conversion systems. In colloidal nanocrystal form, their size, shape and valency can be precisely controlled. Polyoxovanadate clusters are ideal precursor candidates because their chemical composition, oxidation states, and reactivity can be tuned easily and precisely.

Jude Mitchell, assistant professor, and Michele Rucci, professor, both of the Department of Brain and Cognitive Sciences, for Neural Mechanisms of Foveal Vision.
This study will apply advanced eye-tracking methods to better understand the  dominant role of the fovea — a small depression in the retina of the eye where visual acuity is highest — in visual processing at the neural level.

William Renninger and Jaime Cardenas, assistant professors of optics, for Chirped-Pulse Microresonators.
The goal of this study is to demonstrate the first chirped pulses in normal dispersion microresonators, enabling ultrashort pulses over a dramatically extended range of parameters with the potential for ‘holy-grail’ 100% conversion efficiency from an extremely low-cost platform.

Lewis Rothberg, professor of chemistry, and Alexander Shestopalov, associate professor of chemical engineering, for Surface Chemistry for Reflective Interferometric Sensing.
This study will improve a reflective interferometric method for detection of important biomolecules and develop a portable prototype for field detection of useful biomarkers with potential applications in plant pathology and in child malnutrition in Third World countries.

Yuhao Zhu, assistant professor of computer science, and Nick Vamivakas, associate professor of quantum optics and quantum physics, for Flexible and Efficient Deep Learning in Optics.
This study will investigate a completely different paradigm of deep learning by moving deep neural network (DNN) computations from the digital domain to the optical domain. This leverages the fact that optical systems naturally perform the mathematical operation of convolution – the single most costly computational step in DNNs.

James D. Fry and Sina Ghaemmaghami, associate professors of biology, for What Maintains Genetic Variation Affecting Health and Reproduction? A test of a Novel Hypothesis.
The hypothesis is that mutations that cause a small reduction in protein stability, thus slightly increasing the burden of misfolded protein in cells, sometimes have a compensating advantage by improving the functioning of the majority of the protein that remains properly folded.

James McGrath, professor of biomedical engineering; Andrew Berger and Wayne Knox, professors of optics; Lisa DeLouise, associate professor of dermatology; Jonathan Flax, research assistant professor of urology, and Mahlon Johnson, professor of pathology and laboratory medicine, for Confocal Raman Microscopy for the Identification of Microplastics in Cells and Tissue.
Microplastic (MP) pollutants are now routinely found in sea and fresh water, food and beverages. The team will develop a confocal Raman Microscope capable of examining the ability of MPs to pass through human tissue barriers and accumulate in organs.

Regine Choe, associate professor of biomedical engineering; Imad Khan, assistant professor of neurology, neurosurgery, and medicine; Ross Maddox, assistant professor of biomedical engineering; and Sunil Prasad, professor of surgery and chief of cardiac surgery, for Non-invasive Cerebral Blood Flow and Evoked Potential Monitoring in Adults Undergoing Extracorporeal Membrane Oxygenation.
This study will combine diffuse correlation spectroscopy with sensory-evoked potentials into one device that can monitor the brain in patients with heart or lung failure who receive extracorporeal membrane oxygenation (ECMO), which carries a significant risk of brain injury.

Sally Quataert, research associate professor, and Mark Sangster, research professor, both of microbiology and immunology, for Advancing Translational Research to Drive Universal Influenzae Vaccine Development: Novel Methods for Assessing Clinical Antibody Responses.
One of the leading candidates for a universal influenza vaccine is the conserved stem/stalk region of the HA protein that mediates fusion of the virus with endosomal membrane, an important step in infection. This study’s multiple goals include developing clinical assay methods to detect and quantitate anti-stalk antibodies in sera and to assess antibody affinity/avidity and functional anti-fusion activity.

Farran Briggs, associate professor of neuroscience, for Vision in a Natural Context: More than Meets the Eye?
Neurons in early visual processing centers convey unique information about small bits of the visual scene, like pixel-detectors in a camera. But does a neuron respond the same way when, for example, a red pixel is on a ball moving quickly toward the face as when the red pixel is on a ball sitting in the grass? This study will apply a novel approach to study whether early visual cortical neurons are “purely” visual, or does context alter a neuron’s response?

James Palis, professor of pediatrics, for Embryonic Origin of Natural Killer Cells.
This study will look at the potential of erythro-myeloid progenitors to give rise to Natural Killer cells, which could pave the way to the improved production of NK cell-based therapies for patients with leukemia and other malignant disorders.

Denise C. Hocking, professor of pharmacology and physiology, and Michelle Dziejman, associate professor of microbiology and immunology, for Bacterial Pathogens, Fibronectin Mimicry and Intestinal Permeability.
This study will determine whether fibronectin (FN), a principal component of the extracellular matrix (ECM) of the intestinal wall, contributes to barrier function and explore whether pathogenic bacteria impair intestinal permeability by disrupting ECM FN dynamics.

M. Kerry O’Banion, professor of neuroscience, and Michael Rusty Elliott, associate professor of microbiology & immunology, for Targeting AXL in Alzheimer’s Disease.
This study will explore the hypothesis that activation of Axl, a receptor tyrosine kinase, drives microglial phagocytosis of amyloid and reduces the inflammatory environment around Alzheimer’s disease plaques. This could aid in targeting Axl to ameliorate Alzheimer’s Disease pathology.

Scott Liebman, associate professor of medicine (nephrology); Susan Friedman, associate professor of medicine (geriatrics), and Rebeca Monk, professor of medicine (nephrology), for Safety and Efficacy of Whole Food Plant Based Diet (WFPBD) in the Management of Hypertension in Chronic Kidney Disease.
This study will evaluate whether educating hypertensive chronic kidney disease patients about the benefits of a whole food plant based diet focusing on lower potassium foods will, in the short term, lead to adopting the diet and improved blood pressure without precipitating high potassium levels.

Laurie Steiner and Kate Ackerman, associate professors of pediatrics; Muthu Venkitasubramaniam, associate professor of computer science; and Alex Paciorkowski, assistant professor of neurology, for Novel Approaches to Genetic Diagnoses and Secure Genomic Data Analyses in Critically Ill Infants.
This study’s goals are twofold. 1. Determine whether integration of epigenetic and transcriptomic data improves the diagnostic ability of Whole Genome Sequencing in critically ill infants. 2. Use secure cryptography to develop novel mechanisms for investigators to share biologically relevant sequencing and phenotype data while protecting patient privacy.

Elizabeth (Betsy) West Marvin, ’81E (MA), ’89E (PhD), a highly accomplished researcher and music theorist, who has been named the inaugural recipient of the Minehan Family Professorship at the Eastman School of Music.  The endowed professorship, part of a $5 million commitment to Eastman, was created by Cathy E. Minehan ’68, a UR graduate, former clarinet student in the Community Education Division (CED) of Eastman, and current University Trustee. Marvin, a professor of music theory at the Eastman School, holds a secondary appointment in the Department of Brain and Cognitive Sciences. Her research focuses on music cognition, including the study of cognitive differences among musicians, non-musicians, and absolute-pitch listeners; pedagogical implications of music-cognitive research; comparisons between language and music processing; and, more recently, music and medicine. In 2016, she served as musician consultant during awake brain surgery for a professional musician—in a research collaboration with Bradford Z. Mahon and Webster H. Pilcher of the Medical Center—which was covered by NPR and other national news outlets. Read more here.

The deadline for submitting a CRoFT Pilot Proposal is 5 p.m. May 31, 2019 for projects beginning September 1, 2019.

These pilot projects are for research to inform FDA regulation of tobacco products.  Pilot projects are available through the Center for Research on Flavored Tobacco (CRoFT) at the University of Rochester and Roswell Park Comprehensive Cancer Center.  CRoFT is one of the national Tobacco Centers of Regulatory Science funded through NIH and the FDA.  More detail on the RFA can be found here.

Contact Scott Steele or Deborah Ossip, CRoFT Career Enhancement Core Co-Directors, with questions.

John McAnany, chemistry, “Novel Approaches to RNA – Targeted Compound Discovery.” Noon May 30, 2019. 473 Hutchison Hall. Advisor: Benjamin Miller.

Chang Dong Rho, physics, “Searching for TeV Gamma-ray Emission from Compact Binaries with the HAWC Observatory.” 3 p.m. May 30, 2019. Bausch & Lomb 106. Advisor: Segev BenZvi.

May 28: Forbes Visiting Scholar Lecture: “Genetic Diagnosis of Blood Diseases in the Fetus and Newborn.” Patrick Gallagher,  professor of pediatrics (neonatology), of genetics and of pathology at Yale Medicine and the director of the Yale Center for Blood Disorders, will be visiting as the next Gilbert B. Forbes Scholar. His lecture will be from noon to 1 p.m. in the Ryan Case Method Room (1-9576).

May 31: 5 p.m. deadline to submit applications, sponsored the Medical Center and Roswell Park for pilot funding for research relevant to the regulation of tobacco products. Read the full RFA. Contact Scott Steele or Deborah Ossip with questions.

June 1: Un-meeting to foster new collaborations and ideas and explore innovative approaches to the use of artificial intelligence and machine learning at all stages of the translational science spectrum. Hosted by the University’s Clinical and Translational Science Institute (UR CTSI). 8 a.m. to 3 p.m. Saunders Research Building. Register by Monday, May 13.

June 5: Discover Embark panel discussion and Q&A on a new initiative to streamline and strengthen clinical research at the University of Rochester Medical Center. All URMC community members involved in clinical research are encouraged to attend.  2-3 p.m. Class of ’62 Auditorium. Email Embark with any questions or concerns.