Congratulations Dalia Ghoneim!
Tuesday, July 23, 2019
On July 19, Dalia Ghoneim earned her Ph.D. for successfully defending her thesis, “New functions for RNA elucidated by evolutionary conservation.” She demonstrated that adjacent pairs of codons known to inhibit protein expression and to slow translation in yeast are conserved, rather than avoided. Genes with these conserved codon pairs exhibit altered translation properties. Thus, conservation is evidence that these codon pairs serve a function in yeast, although that function is yet to be determined. Additionally, in collaboration with Xin Li’s lab, Dalia scanned mouse sperm transcriptome data using a machine learning method to identify sets of long-non-coding RNAs with conserved structures. Dalia was mentored by David H. Mathews and Beth Grayhack. During her studies, Dalia was awarded the prestigious Perricone MD Born Seekers fellowship. We wish Dalia all the best for her post-doctoral career!
Thursday, July 11, 2019
After successfully defending his thesis, MJ has completed the PhD portion of his MD/PhD studies. MJ’s studies investigated the genetic basis of bone-matrix quality, an underappreciated property of bone that contributes significantly to bone strength and is of great clinical importance for understanding of bone pathology such as osteoporosis. MJ used both a classical population genetics approach as well as a systems genetics approach, and found that bone matrix characteristics such as morphology and matrix composition are indeed inheritable properties. In addition, using an estrogen-deficient model of post-menopausal bone loss, he was able to identify gene networks that may play an important role in osteoporosis. His results suggest that bone matrix quality is influenced by genetics and participates in maintaining tissue-level mechanical properties. Furthermore, identifying putative regulatory genes is clinically significant as they are presumptive targets for developing novel therapeutics. During his thesis work, MJ was the recipient of a CTSI Pilot Trainee Grant and scored a fundable F31 predoctoral fellowship from NIAMS. With his GDSC doctorate in hand MJ will return to medical school to obtain his M.D. Best of luck in your future ventures, MJ!!
Scott Friedland Defends Thesis
Thursday, July 11, 2019
This week M.D./Ph.D. student Scott Friedland defended his doctoral thesis. Arriving at the GDSC in 2014, Scott pursued his Ph.D. under the mentorship of Dr. Aram Hezel. As a student Scott was granted travel awards to a national physician scientist conference and selective course at Cold Spring Harbor Labs. His thesis, titled Arid1a, a subunit of the SWI/SNF chromatin remodeling complex, is a barrier to KrasG12D-driven tumorigenesis, studied the role of SWI/SNF, a chromatin remodeling complex, in pancreatic function and disease, which has implications for the fields of cancer and developmental biology. These findings may, in time, impact the treatment of diseases such as pancreatitis and pancreatic cancer. Scott will be reinitiating his medical education alongside the class of 2021 here at the University of Rochester School of Medicine, and is interested in pursuing a career as an oncologist and cancer researcher. Congratulations Dr. Scott Carl Friedland!
Studies Led by Douglas Portman Examine Nervous System Changes During Puberty
Tuesday, July 9, 2019
Very little is known about how the onset of puberty is controlled in humans, but the discovery of a new gene in the roundworm C. elegans could be the "missing link" that determines when it’s time to make this juvenile-to-adult transition. Two genes, LIN28and MKRN3, are known to be associated with precocious puberty in humans, where juveniles as young as six may start developing adult features. These genes are found in all animals, including C. elegans, in which they also control the juvenile-to-adult transition. Until the new discovery, it was unclear how these two genes are connected.
The more obvious signs of the transition of juvenile-to-adult tend to be external—body morphology, matured genitalia—but nervous system changes are also happening at the same time. In humans, the maturation of the brain during adolescence is associated with increased vulnerability to a variety of neuropsychiatric disorders, so a better understanding of these processes is important for understanding mental health as well as basic neurobiology.
Two new studies in the labs of Douglas Portman, Ph.D. at the University of Rochester Medical Center and David Fitch at New York University, published in Developmental Cell and eLife, identified a new developmental timing mechanism involving a long non-coding RNA in the microscopic roundworm C. elegans. Their research revealed a surprising new molecular mechanism that controls the timing of sex-specific changes in body shape, the maturation of neural circuits, and behavior.
C. elegans has long been used by researchers to understand fundamental mechanisms in biology. Many of the discoveries made using these worms apply throughout the animal kingdom and this research has led to a broader understanding of human biology. In fact, three Nobel Prizes in medicine and chemistry have been awarded for discoveries involving C. elegans.
The researchers identified a new gene that, when disrupted, delays the transition from the juvenile to the adult stage. Surprisingly, this gene, called lep-5, does not act as a protein, as most genes do. Instead, it functions as a long non-coding RNA (lncRNA), a recently discovered class of genes whose functions remain largely mysterious. The team observed that this lncRNA is important for promoting the juvenile-to-adult transition by directly interacting with LIN-28 and LEP-2, a C. elegans gene similar to MKRN3. Because the human versions of LEP-2 and LIN-28 are both involved in the timing of puberty, the new research suggests that a yet-to-be-discovered lncRNA might be essential to this process in humans as well.Read More: Studies Led by Douglas Portman Examine Nervous System Changes During Puberty
A Graphic Design Revolution For Scientific Conference Posters
Tuesday, June 18, 2019
“Other templates didn't necessarily ask you to think about what you were putting on them because they allowed it all,” says Derek Crowe, a PhD student in biomedical genetics in Hucky Land's lab with a former career in visual communication and design, “In order to use Mike's layout though, my hand is forced.”
With the new template, scientists need to think about their core message, but some people have a difficult time figuring out how to do that, or how to use visuals to present their message. Without proper science communication training, even a better poster template doesn’t work.
Crowe has taken matters into his own hands. Not only does he teach a course on visual communication for scientists at the University of Rochester, but he also shared his poster design tips online. In a nod to Morrison’s “better poster”, Crowe’s is a “butter poster”. He provides step by step instructions on how to organize the poster, and how to think about the content in a visual way.
“Like the graphic novel did for literature, visual languages have the power to add more dimensions to scientific storytelling,” says Crowe, “I’m excited to see what happens as the greater science community begins to take advantage of well-established visual storytelling tools.”Read More: A Graphic Design Revolution For Scientific Conference Posters
GDSC Student, Tom O’Connor Earns First Place in 2019 Sharing Your Science in A Social World Contest.
Monday, June 3, 2019
Finishing his first year of GDSC studies on a high-note, Tom O’Connor (member of the Chakkalakal & Dirksen Labs) together with his teammate Griffin Schroeder, have won first place in the 2019 ‘Sharing Your Science in A Social World’ contest. Sponsored by URBEST, this contest encourages students to communicate their research to a broad audience using videography. For their entry, imbedded above, Tom and Griffin emphasized the work being done in the Noble Lab, where Tom worked during his first rotation. The video, URBEST 2019: Translational Science, highlights how the Noble Lab sets itself apart by re-purposing FDA approved drugs for different clinical applications, expediting the bench-to-clinic transition.
Congratulations Tom and Griffin!
Next-Gen Women in Science: Dalia Ghoneim
Thursday, May 2, 2019
GDSC student Dalia Ghoneim from the Matthews lab was awarded the prestigious Perricone MD Born Seekers fellowship. The $20,000 award recognizes the inspiring achievements of young women in science, and is the culmination of the Scientista Foundation’s video competition, in which young women tell their personal journey in STEM. Dalia was able to tell her remarkable story in the award-winning video clip with the help of two talented fellow GDSC-students: cameraman, sound expert and producer Adam Cornwell, and speech-editor Matt Ingalls. As a single mother of four, Dalia is now approaching the successful completion of her PhD in Genetics. She was invited to give her speech and accept her award at the Scientista Symposium 2019 in Boston, MA. The Scientista Foundation’s vision is to support the next generation of female scientists – and we can’t wait to see what Dalia will do next! Congratulations!!
Jayme Olson earns (CTSI) Trainee Award
Tuesday, April 30, 2019
Jayme a GDSC-graduate student in the Palis Lab was recently awarded a Clinical and Translational Science Institute (CTSI) Trainee Award. This one-year fellowship will fund cutting edge work on the in vitro generation of human red blood cells. Cultured human red blood cells (RBCs) have the potential to serve as a supplemental source of blood for transfusion therapy, and as a tool for clinical and research diagnostic. However, a major barrier in generating sufficient numbers of cultured RBCs cells is the limited ex vivo self-renewal capacity of adult-derived erythroblasts. Work in the Palis Lab has identified Bmi-1, a member of the polycomb repressive complex 1 (PRC1), as a critical regulator of erythroid self-renewal. Bmi-1 also plays a role in normal erythroid precursor maturation. Jayme will test the hypothesis that Bmi-1 regulates erythroid self-renewal and terminal maturation using different PRC1 members. Ultimately, these proposed studies will pave the way for the generation of sufficient numbers of cultured RBCs for blood typing and transfusion therapy, as well as the establishment of in vitro models for the study of erythroid intrinsic diseases.
31st Genetics Day at the University of Rochester
Monday, April 29, 2019
The University of Rochester hosted its 31st Annual Genetics Day Symposium with a poster session displaying genetics research from more than fifty post-doctoral fellows, graduate and undergraduate students. The meeting started with a strong lineup of faculty presentations, highlighting ongoing Genetics Research and as well as new faculty recruits. Speakers included Dr. Amanda Larracuente, Dr. Doug Anderson, Dr. Peng Yao, Dr. Xin Zhiguo Li and Dr. Paul Boutz. Keynote speaker Dr. Phillip Zamore, from the University of Massachusetts, delivered the 17th Annual Fred Sherman Lecture. This year’s poster prizes were awarded to:
- Leigh Wexler: A male-specific neuroendocrine feedback loop couples food signals for feeding behavior in C. Elegans
- Matthew Tanner: Identifying sequence determinants of altered RNA splicing in myotonic dystrophy.
- Dr. Jacquelyn Lillis: Single-cell transcriptome analysis of embryonic erythro-myeloid progenitor cells reveals lineage heterogeneity.
- Jayme L. Olsen: Bmi-1 regulates human erythroblast ex vivo self-renewal.
- Anissa Elahi: Transglutaminase 2 as a therapeutic target to facilitate recovery after spinal cord injury.
- Zhengfen (Jeff) Liu: DNA damage-specific regulation of cell cycle checkpoint by γ-h2ax.
We congratulate each poster winner and look forward to the 32nd Genetics Day next year!
A link to additional Genetics Day 2019 photos can be found here.
Researchers Strike Key to Longevity
Sunday, April 28, 2019
Researchers at the University of Rochester have uncovered more evidence that the key to longevity resides instead in a gene, a Rael-Science post says.
Explorers for centuries have however, dreamt of a Fountain of Youth, with healing waters that rejuvenate the old and extend life indefinitely.
In a new paper published in the journal Cell, the researchers—including Vera Gorbunova and Andrei Seluanov, professors of biology; Dirk Bohmann, professor of biomedical genetics; and their team of students and postdoctoral researchers—found that the gene sirtuin 6 (SIRT6) is responsible for more efficient DNA repair in species with longer lifespans.
The research illuminates new targets for anti-aging interventions and could help prevent age-related diseases.
As humans and other mammals grow older, their DNA is increasingly prone to breaks, which can lead to gene rearrangements and mutations—hallmarks of cancer and aging. For that reason, researchers have long hypothesized that DNA repair plays an important role in determining an organism’s lifespan.
While behaviors like smoking can exacerbate double-strand breaks (DSBs) in DNA, the breaks themselves are unavoidable. “They are always going to be there, even if you’re super healthy,” says Bohmann. “One of the main causes of DSBs is oxidative damage and, since we need oxygen to breathe, the breaks are inevitable.”
Organisms like mice have a smaller chance of accumulating double-strand breaks in their comparatively short lives, versus organisms with longer lifespans, Bohmann says. “But, if you want to live for 50 years or so, there’s more of a need to put a system into place to fix these breaks.”Read More: Researchers Strike Key to Longevity
'Longevity Gene' That Helps Repair DNA And Extend Life Span Could One Day Prevent Age-Related Diseases In Humans
Tuesday, April 23, 2019
Scientists studying longevity believe a gene could explain why some animals live longer.
In 18 species of rodents with varying life spans, researchers looked at sirtuin 6 (SIRT6), a gene that plays a role in bodily processes such as aging, cellular stress resistance and DNA repair.
Over time, DNA inevitably suffers what are known as double-strand breaks (DSBs) that can cause genes to mutate, triggering aging and diseases like cancer.
Dirk Bohmann, a professor of biomedical genetics at the University of Rochester Medical Center, explained in a statement, “[DSBs] are always going to be there, even if you’re super healthy. One of the main causes of DSBs is oxidative damage and, since we need oxygen to breathe, the breaks are inevitable.”
While animals with relatively short life spans don’t have so many DSBs, Bohmann explained, “if you want to live for 50 years or so, there’s more of a need to put a system into place to fix these breaks. The SIRT6 protein seems to be the dominant determinant of lifespan. We show that at the cell level, the DNA repair works better, and at the organism level, there is an extended lifespan.”
To answer whether SIRT6 works harder in species that live longer, the team studied 18 rodents, from mice expected to live around three years to beavers and mole rats with life expectancies of up to 32 years. Animals with stronger SIRT6 proteins were found to live longer.
This was also apparent when they compared the molecular differences in the SIRT6 proteins of mice and beavers. And by dosing human cells and fruit flies with the SIRT6 from a mouse and a beaver, as expected, the scientists found the beaver protein was more potent than the mouse protein.Read More: 'Longevity Gene' That Helps Repair DNA And Extend Life Span Could One Day Prevent Age-Related Diseases In Humans
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 Symposium
Jared Mereness successfully defends thesis
Thursday, March 14, 2019
Last week, Jared Mereness successfully defended his PhD Thesis. Since arriving at the University of Rochester in 2012, Jared has worked with his advisor, Tom Mariani, and studied Lung and Pulmonary diseases. During his studies Jared was awarded an institutional T32 Training Grant in Pulmonary Research, and a Howard Hughes Medical Institute Med-Into-Grad Fellowship in Translational Cardiovascular Research at the University of Rochester. Jared's research and thesis has focused on describing the role of the extracellular matrix component, collagen 6, in lung structure, and its effects on the function of pulmonary epithelial cells. His findings broaden our understanding of potential roles this unique extracellular matrix protein may have in chronic lung disease and the development and maintenance of lung structure. Soon Jared will begin a Postdoc position in Danielle Benoit’s laboratory in Biomedical Engineering at the University of Rochester. Congratulations Jared!
For further Reading, please see: PLOS ONE: Type VI collagen promotes lung epithelial cell spreading and wound-closure by Mereness et al.
Falsey, Mariani Secure $3.8 M NIH Grant to Reduce Antibiotic Overuse
Thursday, February 21, 2019
Ann R. Falsey, M.D., professor of Infectious Diseases, and Thomas J. Mariani, Ph.D., professor of Pediatrics, received a 5-year, $3.8 million grant from the National Institutes of Health to search for a better way to distinguish bacterial and viral respiratory infections. The goal of the study is to define predictive genes – using gene expression profiling of blood – that can be developed into a simple point of care diagnostic that can be used by clinicians to discriminate bacterial and non-bacterial illness. Such a test would allow physicians to optimally manage patients with acute respiratory infections, which are a leading cause of antibiotic overuse and are linked to the rise of antibiotic resistant organisms.
The grant is the result of research done as part of the NIH-funded Respiratory Pathogens Research Center. Falsey and Mariani are the co-principal investigators, and Edward Walsh, M.D., Angela Branche, M.D. and Derick Peterson, Ph.D. are co-investigators.
Matt Ingalls wins Prestigious Poster Prize at Gordon Conference
Friday, February 15, 2019
Matt Ingalls With Poster
Matt Ingalls with other award winners
GDSC student Matt Ingalls won an award for his poster presentation at the 2019 Gordon Research Conference for Salivary Glands and Exocrine Biology in Galveston, Texas (February 2nd – 8th). The GRC brought together leading researchers in the field of salivary gland biology from around the world. Matt’s poster, titled “Lineage Tracing Following Radiation Treatment Unveils Intrinsic Regeneration Potential in Adult Salivary Glands”, highlights differences in radiation response between the submandibular and parotid salivary glands. Utilizing lineage tracing models his work demonstrates the intrinsic regeneration potential of the adult salivary gland. The NIH-supported research was conducted in the laboratory of Dr. Catherine Ovitt and was co-authored by E. Maruyama and P. Weng. -- Congratulations Matt!
GDSC student Adrian Molina-Vargas co-founds ADSE chapter to tackle underrepresentation in STEM
Friday, February 1, 2019
February 1, 2019
In the front row from the left, Keon Garrett, Ellen Matson, Raven Osborn, and Antonio Tinoco Valencia; and in the back row from the left, Marian Ackun-Farmmer, Heta Gandhi, Adrian Molina Vargas, Shukree Abdul-Rashed, and Liz Daniele are among the founding members of the new Rochester chapter of the Alliance for Diversity in Science and Engineering. (University of Rochester photo / J. Adam Fenster)
Raven Osborn thought long and hard about continuing a PhD at the University of Rochester. Other minority students she knew at the Medical Center had also felt the isolation, the constant “being on edge” and “code-switching”—shifting the way they express themselves—that comes with being an underrepresented minority in a STEM field.
“Can I do this for another five and half years?” she wondered.
Antonio Tinoco, a DREAMer who was born in Mexico and raised in Los Angeles, is a fourth year PhD student in the department of chemistry on the River Campus. He can remember only one or two occasions when a visiting faculty member of underrepresented minority background was invited to give a seminar in his department.
“My goal is to go into academia to be a professor, do research, and teach. But there are so few examples to follow,” he says. “I don’t even know of anyone who, as a DACA recipient or DREAMer, is a professor in chemistry. So, I could easily tell myself nobody has done it; it’s impossible; maybe I should look for something else.”
Instead, Tinoco, Osborn, and five other graduate students have banded together to form the University of Rochester chapter of the Alliance for Diversity in Science and Engineering (ADSE). The mission of the national ADSE, which was founded in 2014, is to increase the participation of underrepresented groups in academia, industry, and government through graduate student organizations that reach out to students and scientists of all ages and backgrounds.
Other ADSE chapters are at the University of California campuses at Berkeley and Davis, the University of Central Florida, the University of Colorado, Columbia University, Drexel University, Georgia Institute of Technology, University Maryland, New York University, Northeastern University, and Texas A&M.
Tinoco, the president and founding member of the new chapter, says its immediate goals are twofold:
- Establish a diversity lecture series to bring underrepresented faculty from other universities to Rochester. “It would be an opportunity for underrepresented minority students here to say ‘Wow, there’s someone out there like me who is making it, so maybe there’s hope for me.’” Underrepresented minority postdoctoral fellows would also be invited, especially ones who might be interested in eventually teaching here, Tinoco says.
- Provide a space where underrepresented graduate students in STEM fields from across the University can meet, network, and hold workshops and panels to openly discuss the issues they face. “If we can openly discuss these things, we won’t feel as isolated,” Tinoco says.
The chapter has been certified by the University and will receive funding through the University’s David T. Kearns Center for Leadership and Diversity. ADSE’s goals fall well within the Kearns Center’s mission to expand the educational pipeline through the doctoral degree for low-income, first-generation college, and underrepresented minority students, says Liz Daniele, the center’s assistant director for graduate diversity.
Inviting underrepresented faculty from other campuses to give a science-based talk, but also give a diversity-themed talk about their academic journey “is a great model,” she says. “And that’s why Kearns is happy to support several semesters of lectures.”
“I think this is exactly the type of thing that the University needs right now,” says Ellen Matson, assistant professor of chemistry, who will be the chapter’s faculty advisor. She, too, is excited about the proposed diversity lecture series—as a way to inspire and motivate students to finish their programs and pursue STEM careers, and also “showcase our research programs and facilities to diverse early-career scientists and post-doctoral research fellows interested in pursuing independent academic research careers.”
“Overall, I think that the University of Rochester community, particularly at the graduate level, will really benefit from having a chapter of the Alliance for Diversity in Engineering and Science on campus,” Matson says.
Osborn, who is serving as the chapter’s treasurer, does not regret her decision to stay at Rochester to pursue a PhD in translational biomedical science. “I’ve been very lucky to work with faculty members like Tim Dye, Steve Dewhurst, and Juilee Thakar,” she says.
Osborn received a medical center community outreach award as a leader in the Rochester Young Scientists Club’s program, which encourages pupils at inner-city elementary schools to start thinking like scientists. She is excited to be serving on the search committee for a new vice president for equity and inclusion at the University.
She is hopeful that ADSE will bring together underrepresented graduate students, now separated by Elmwood Avenue “divide” between the River Campus and the Medical Center and the separate “silos” of their STEM disciplines.
And she agrees with Matson that the University will benefit from having a chapter of ADSE.
“This is an amazing institution, and we have so many resources here. If we can make this a place where people who have different backgrounds feel comfortable, where their different perspectives are welcomed, it can only better the institution as a whole.”Read More: GDSC student Adrian Molina-Vargas co-founds ADSE chapter to tackle underrepresentation in STEM