News

May 25
Benjamin Martin, PhD, Associate Professor in the Department of Biochemistry and Cell Biology, has received the Pershing Square Sohn Prize for Young Investigators in Cancer Research for his work with circulating tumor cells The award, granted to promising early career New York City-area cancer research scientists, includes a three-year $600,000 grant, effective July 1. Professor Martin and colleague David Q. Matus, PhD, are using state-of-the-art microscopy and genetic analysis of circulating tumor cells to achieve an unprecedented level of understanding about how these cells exit blood vessels and invade news sites on the body. To help accelerate breakthroughs in cancer research, the Pershing Square Research Alliance has invested $25 million in next generation medical research talent. For more about Professor Martin’s cancer research see this recent published paper Science, and his bio and video explanation on his research. For more about the award and recipients, see this press release.
Apr 09

By combining data on pathology images of 13 types of cancer and correlating that with clinical and genomic data, a Stony Brook University-led team of researchers are able to identify tumor-infiltrating lymphocytes (TILs), called TIL maps, which will enable cancer specialists to generate tumor-immune information from routinely gathered pathology slides.

Published in Cell Reports, the paper details how TIL maps are related to the molecular characterization of tumors and patient survival. The method may provide a foundation on how to better diagnose and create a treatment plan for cancers that are responsive to immune-based anti-cancer therapy, such as melanoma, lung, bladder, and certain types of colon cancer.

The gold standard for cancer diagnosis remains the pathology report from a biopsied tumor tissue. Diagnosis plays a leading role in how a patient will be treated. In certain situations and with forms of cancer treated with immune-based therapies, pathologists are also tasked with making observations on the immunologic features of the tumor tissue to determine which patients are most likely to benefit from these therapies. TILs are unleashed by immunotherapies to destroy cancer cells.

“This paper demonstrates that we can now use deep learning  methods such as artificial intelligence to extract and classify  patterns of immune cells in ubiquitously obtained pathology studies, and to relate immune cell patterns to the many other types of cancer patient molecular and clinical data,” says Joel Saltz, MD, PhD, the Cherith Chair of Biomedical Informatics at Stony Brook University and lead author of the paper, titled “Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.”

The research includes researchers from Stony Brook University, the University of Texas MD Anderson Cancer Center, Emory University, and the Institute for Systems Biology. The work stems from the efforts of The Cancer Genome Atlas (TCGA) project.

In the study, the researchers applied machine learning to digitized pathology images to characterize patterns of immune infiltration present in 4,759 TCGA patients and within 13 cancer types processing more than 5,000 digital images from the cancer types to create a “computational stain” for each. With these, they created TIL maps as a potential new guide to diagnosis and treatment planning.

TCGA is a decade long comprehensive effort spearheaded by the National Cancer Institute (NCI) and the National Human Genome Research Institute in collaboration with the cancer research community worldwide. The TIL map study is part of a cohort of 27 manuscripts published in Cell Press communicating results by the TCGA PanCancer Atlas Initiative,  which has compared and contrasted molecular features of all TCGA tumor samples from more than 10,000 cases comprising 33 different forms of cancer.

“Developing machine learning tools such as this proof of principle project to map lymphocytic infiltration patterns is important for research reproducibility in immune-oncology and will also allow these approaches to begin to be deployed as decision support for pathologists as we evaluate and report our cases for routine decision-making,” says Alexander Lazar, MD, PhD, Professor of Pathology & Genomic Medicine at MD Anderson and a co-author.

The investigators were able to develop the method and proof of concept with the assistance of data collection and calculations by way of high-performance computing systems available through Stony Brook’s Institute for Advanced Computational Science and Division of Information Technology.

Dr. Saltz and colleagues nationwide continue to investigate the use of digital archiving of pathology and the use of machine learning and artificial intelligence to enhance diagnosis and treatment of cancer.

The research was supported in part by the National Cancer Institute, the American Cancer Society, the Cancer Research Institute and the National Science Foundation

Apr 23

A new technology employing endocannabinoids for pain relief, developed by Stony Brook University researchers affiliated with the Institute of Chemical Biology and Drug Discovery (ICB & DD), has been licensed to Artelo Biosciences, Inc. Endocannabinoids are natural marijuana-like substances in the body and have potential as the basis for new medicines. Artelo has an exclusive license with the Research Foundation for the State University of New York to the intellectual property portfolio of FABP inhibitors for the modulation of the endocannabinoid system for the treatment of pain, inflammation and cancer.

Fatty Acid Binding Proteins have been identified as intracellular transporters for the endocannabinoid anadamide (AEA), a neurotransmitter produced in the brain that binds to THC receptors. Animal studies have demonstrated that elevated levels of endocannabinoids can result in beneficial pharmacological effects on stress, pain and inflammation and also ameliorate the effects of drug withdrawal. By inhibiting FABP transporters, the level of AEA is raised. Potential drugs acting in this manner would create elevated levels of AEA. The mechanism of action of such drugs would be similar to that of current antidepressants, which inhibit the transport of serotonin.

During the first year of the agreement, Artelo will collaborate with the Stony Brook research team to identify a lead FABP compound for drug development and formulation. The company will then conduct drug efficacy tests in nonclinical animal models of the compound.

The multidisciplinary research team is led by Dale Deutsch, PhD, Professor in the Department of Biochemistry and Cell Biology, and a member of the ICB & DD.  The research has been supported by a $3.8 million grant from the National Institute on Drug Abuse, an arm of the National Institutes of Health.

“The unique aspect of this research is that our focus is to investigate ways to active natural ‘marijuana’ in our bodies, the endocannabinoids,” said Deutsch. “This system has advantages over the properties of actual marijuana since endocannabinoids are not connected with dependence, potentially leading to addiction, but does act effectively against pain.”

Their research started in 2009 with the identification of the FABPs as the transporters of the endocannabinoids. When these compounds bind to the FABP they resulted in higher levels of AEA specifically. By using computational biology for virtual screening and actual assays, the researchers discovered lead compounds that bind to the FABPs and were analgesics for various types of pain.

The AEA research led to three Stony Brook University patent-covering new chemical compounds (called Stony Brook FABP Inhibitors or SB-FIs), which Artelo will investigate during its drug development plan.

“This licensing agreement gives us access to a promising intellectual property portfolio that is squarely aligned with our strategic direction as a scientific team with a proven track record of success,” said Gregory Gorgas, Chief Executive Officer of Artelo. “Working together to evaluate and identify novel FABP inhibitors based upon existing scientific data for clinical development will be complimentary to our drug pipeline and create a new opportunity for Artelo.”

In order to design the novel FABP inhibitors, members of the FABP Stony Brook research group required expertise in many disciplines, such as biochemistry, chemistry, computational biology, computer science, X-ray crystallography and medicine. The team includes Deutsch; Distinguished Professor Iwao Ojima, also the Director of the ICB & DD; Martin Kaczocha of the Department of Anesthesiology; Robert Rizzo  of the Department of Applied Mathematics and Statistics, and Huilin Li, formerly of the Department of Biochemistry and Cell Biology.

Apr 23

The Microscopy Society of America (MSA) has selected Yimei Zhu — a Stony Brook University adjunct professor and a senior physicist at the U.S. Department of Energy’s Brookhaven National Laboratory (BNL) — to receive the 2018 Distinguished Scientist Award for physical sciences. This award annually recognizes two senior scientists, one in the physical sciences and the other in biological sciences, for their long-standing record of achievement in the field of microscopy and microanalysis.

“I am extremely humbled by this recognition, the highest honor of the society, and to be selected among the most distinguished scientists in the field worldwide,” said Zhu, who is leader of the Electron Microscopy and Nanostructure Group at BNL. “Four Nobel Laureates received the same award before winning the Nobel Prize: Ernst Ruska in 1985, Joachim Frank in 2003, Richard Henderson in 2005, and Jacques Dubochet in 2009. I strongly feel that my award is the result of not only my hard work, persistence, and curiosity about the inner world of matter but also my collaborations with colleagues and support from Brookhaven Lab and DOE over the past 30 years.”

“Yimei Zhu has made significant contributions to advancing ultrafast electron diffraction instruments and developing fast direct-electron-detectors,” said Molly McCartney, awards committee physical sciences co-chair. “Yimei’s contributions to instrumentation and methods are extensive. His most highly recognized achievement is the successful imaging, at atomic resolution, of the atomic structure of bulk catalysts by detecting the secondary electron emission.”

Zhu led the development of an ultrafast electron diffraction system that was commissioned at Brookhaven Lab in 2012 through the Laboratory-Directed Research and Development program, which promotes exploratory, mission-supported research. With an unprecedented temporal resolution 10 orders of magnitude faster than high-speed video cameras, this system is the first of its kind in the world.

“High-speed video cameras capture consecutive images at a rate less than 1000 frames per second, which is equivalent to taking a picture once every millisecond,” explained Zhu. “Our ultrafast system operates at a rate of 100 femtoseconds, or 100 quadrillionths of a second. Using a pump-probe method in which we excite a sample with laser light (the pump) and probe it with electrons while varying the time delay between the pump and probe, we can see the otherwise unobservable motion of atoms and electrons in materials.”

This capability has opened up the possibility for scientists to understand the dynamic behavior of materials—such as the intriguing transition between insulating and   superconducting phases—and to discover “hidden” states of matter beyond the solid, liquid, gas, and plasma states that are observable in everyday life.

“The bottleneck in science and technology today is the lack of materials with the desired properties for applications such as energy storage and quantum computing,” said Zhu. “Overcoming these limitations requires an understanding of the complex interactions between atoms and electrons and the exotic states of matter that are far from equilibrium. Ultrafast methods such as the pump-probe approach can provide us with the dynamic information we need to control the chemical and physical properties of materials so that we can make, for example, smaller batteries with longer cycleability and computer chips with a higher memory capacity.”

Mar 15

Mechanical Engineering Assistant Professor Ya Wang has received the prestigious Faculty Early Career Development Program (CAREER) Award from the National Science Foundation (NSF) for her project, Understanding Dynamics of Ultra-small Magnetic Nanoparticles in the Brain for Neuron Regeneration Therapies​. The award exclusively supports the research of junior faculty with federal grant funding.

The research objective of Professor Wang’s CAREER project is to analyze biological phenomena to predict the neuron regeneration mechanisms. The established microvascular dynamic model, capable of quantifying the neuron regeneration process, is essential for moving closer to clinical success in treating fast-spreading neurodegenerative diseases. Professor Wang proposes that the $500K CAREER grant will potentially lead to a new era of precision medicine and tissue engineering over the next five years.

“Professor Wang is the ninth recipient of the NSF CAREER award in the history of our department,” said Jeff Ge, chair and professor of mechanical engineering. “Her work on modeling the dynamic behavior of magnetic nanoparticles within the brain microenvironment would lay the foundation for quantifying the neuron regeneration process. This opens up the exciting new possibility for the development of a new microchip for brain research.”

Professor Wang intends for this project to lead to groundbreaking discoveries while also creating awareness of nanotechnology and biomedicine. “I strive for this project to increase the participation in STEM programs from minority groups, including women and first-generation college students on Long Island. It will also expose students, high school teachers, clinicians, and the public to STEM-related research, with the intent to support, teach, and inspire,” she said.

As director of the Nanomaterial Energy Harvesting and Sensing (NES) lab, Professor Wang’s research focuses on studying dynamic features of smart materials, structures, and intelligent systems. Her work has been sponsored by NSF, DOE ARPA-E, DOD ONR, DOT UTRC, and local industrials. She was awarded the 2015 Special Congressional Recognition and the 2015 DOE Wave Energy Prize. She is also an advisor to four semi-finalists of Intel/Regeneron Science Talent Search and to several semi-finalists of the Siemens competition. She has authored one book chapter, 28 journal papers, and 30 conference proceeding papers, as well as filed a U.S. utility patent and five provisional patents.

Professor Wang also works extensively with the Stony Brook Simons Summer Research program, the URECA program, and the WISE program to mentor high school and undergraduate students, in particular women, and students from other underrepresented minority groups. As a woman in engineering, Professor Wang’s personal experiences in the U.S. have given her a deep understanding and appreciation of difficulties faced by these students, and she strives to help them succeed in the engineering field.

Mar 29

Professor Robert Patro of the Department of Computer Science has received a 2018 National Science Foundation (NSF) CAREER award for his research proposal, A Comprehensive and Lightweight Framework for Transcriptome Analysis.

In layman’s terms, this project focuses on the field of RNA (ribonucleic acid) research and how to analyze sequencing data pertaining to it. In addition to performing various other functions in the cell, RNA acts as a messenger molecule, carrying instructions from DNA and acting as a template for protein synthesis.

“As a researcher at an institution focused on developing engineering-driven solutions in medical research, his proposed project supports not only the mission of the Department of Computer Science but also the University as a whole,” said Samir Das, chair of computer science at Stony Brook.

As Patro’s project proposal explains, the goal is “to develop a new generation of accurate, lightweight methods for the analysis of both bulk and single-cell transcriptomic data.” Patro says the project should “push forward the state-of-the-art in terms of both the accuracy and fundamental capabilities of lightweight transcriptome analysis methods.” He hopes the final outcome of the project will provide a new generation of accurate and lightweight transcriptome analysis tools and methods. These advancements in method and software should ultimately reduce costs, enable new analyses, and help contribute to discoveries in future RNA research.

The NSF CAREER funding in the amount of $625,000 supports Patro’s involvement as well as that of several grad and PhD students working in his research lab. The education plan detailed in the CAREER proposal involves working with both students and the campus community and incorporates creating a series of educationally-driven podcasts and videos. He believes that in using a variety of educational methods to accompany his CAREER research he will reach people of both technical and non-technical backgrounds as well as people from diverse communities. In conjunction, Professor Patro also has the support of Stony Brook’s Alan Alda Center for Communicating Science.

Robert Patro is an assistant professor of computer science in the College of Engineering and Applied Sciences at Stony Brook University since 2014. He earned a PhD and BS in computer science from the University of Maryland-College Park. Prior to joining Stony Brook, he was a visiting scholar as well as a Postdoctoral Research Associate at Carnegie Mellon University. Patro’s main academic interests are in the design of algorithms and data structures for processing, organizing, indexing and querying high-throughput genomics data. He is also interested in the intersection between efficient algorithms and statistical inference. Previous to this NSF CAREER award, Patro was the Stony Brook PI on an NSF award shared with Cambridge University entitled Data-driven hierarchical analysis of de novo transcriptomes. Patro and his students develop, maintain and contribute to a number of different open-source bioinformatics software tools.

Mar 22

An international research team including Krishna Veeramah, PhD, Assistant Professor in the Department of Ecology and Evolution at Stony Brook University, has performed the first genomic analysis of populations that lived on the former territory of the Roman Empire from around 500 AD.

The analysis provides a direct look at the complex population movements during the era known as the European Migration Period. The palaeogenomic study, published in PNAS, investigated early human medieval genomic variation in southern Germany, with a specific investigation of the peculiar phenomenon of artificial skull formation, the origins of which scientists have debated for more than 50 years.

While most of the ancient Bavarians looked genetically like modern central and northern Europeans, one group of individuals had a very different and diverse genetic profile. This group was particularly notable in that they were women whose skulls had been artificially deformed at birth. Such enigmatic deformations give the skull a peculiar tower shape and have been found in past populations from across the world and from different periods of time. While the specific origins of this practice have been debated for more than 50 years, scientists think that parents in ancient societies wrapped their children’s heads with bandages for a few months after birth in order to achieve a desired head shape, perhaps to emulate a certain ideal of beauty.

“The presence of these elongated skulls in parts of eastern Europe is most commonly attributed to the nomadic Huns, led by Atilla, during their invasion of the Roman Empire from Asia,” said Veeramah, a population geneticist and first author of the paper titled “Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria.“ “However, the appearance of these skulls in western Europe is more mysterious, as this was very much the fringes of their territory.”

Anthropologist Dr Michaela Harbeck from the State Collection of Anthropology Munich and the Population Geneticist Professor Joachim Burger of the Johannes Gutenberg University Mainz led the team’s work to sequence the genomes of approximately 40 individuals dating the late 5th/early 6th century AD from present-day Bavaria in southern Germany as well as from various locations in the east. They found that while both men and women with normal heads appeared to have local origins, women with elongated heads had genetic ancestry primarily from southeastern Europe rather than Central or East Asia.

According to Veeramah, the team was able to demonstrate by the genomic analysis that in addition to having elongated heads, these women demonstrated darker eyes, hair and even skin compared to the local blond-haired, blue-eyed Bavarians, yet were buried in much the same way as local women. “

“Our data points to Barbarian tribes in Western and Central Europe specifically acquiring exotic looking women with elongated heads born elsewhere, perhaps to form strategic alliances with other entities to the east, but that the Huns likely did not have much of a direct role in this process.”

The research was supported in part by the National Science Foundation.

Mar 22

New York’s U.S. Congressman Lee Zeldin has received the National Sea Grant Award from the National Oceanic and Atmospheric Administration’s National Sea Grant Program for his continued support of this national coastal science association. New York Sea Grant Director and SBU Professor Bill Wise presented the award to him in Washington, DC, on March 7 along with SGA President Jim Hurley. New York Sea Grant is headquartered at Stony Brook University.

New York Sea Grant (NYSG) is a statewide network of integrated research, education and extension services promoting coastal community economic vitality, environmental sustainability and citizen awareness about the state’s marine and Great Lake resources. Last year when federal funding for the non-profit Sea Grant program was eliminated from the budget, Congressman Zeldin was instrumental in securing full funding of $72.5 million for the program through a bipartisan appropriations request. He continued to fight during this year’s budget so that such critical funding will continue to be provided. In addition, he secured more than 100K in funding for NYSG to support the seafood and aquaculture industry and to foster relationships between the industry and next generation of fishermen and other seafood professionals.

“Representing a district almost completely surrounded by saltwater, funding to support our fishermen, our oyster growers, protect our beaches, and support marine science research is essential for our local economy and environment,” said Congressman Zeldin. “The Sea Grant Association plays a critical role in securing and providing this funding to the Long Islanders who rely on it most, and it is such an honor to receive this award from such a worthwhile organization.”

“New York Sea Grant and the coastal residents, businesses and communities our program serves are thankful for Congressman Zeldin’s support,” said NYSG Director Bill Wise. “This national network has existed for over 50 years thanks to Congressional budget support like this.”

Each year NYSG supports millions in university-based research related to a variety of marine, Hudson estuary, and Great Lakes topics and issues. Results and resources from these investigations —conducted by top-notch physical oceanographers, food scientists, benthic ecologists, aquatic toxicologists, fisheries modelers, geochemists, and others — provide useful information to the public, businesses, and managers. Sea Grant research also sets benchmarks within the scientific community, advancing the state of knowledge in many fields.

To learn more about New York Sea Grant, please visit www.nyseagrant.org

Mar 22

As the scientific world mourns the passing of the man many consider a modern-day Einstein, Stony Brook University faculty remembered and reflected on the world-renowned theoretical physicist Stephen Hawking, who died peacefully at his home in Cambridge on March 14.

Martin Roček, a Stony Brook professor of theoretical physics and a member of the C. N. Yang Institute, first met Hawking in the late 1970s, when he was a postdoctoral fellow at Cambridge University. In 1979, Hawking hired Roček to teach him about the concept of supergravity, a significant extension of Einstein’s theory of relativity developed at Stony Brook by Roček’s colleague Peter van Nieuwenhuizen, along with Daniel Freedman and Sergio Ferrara.

“Though I failed to teach Stephen supergravity, it was nevertheless a very productive time for Stephen,” Roček said. “During this time, among many other projects, he explored the effects of gravitational instantons, and performed calculations developing the consequences of his then recently proposed Information Paradox; though his argument that Hawking Radiation implied the breakdown of quantum mechanics is generally not accepted today (Stephen himself rejected it later in life), it stimulated a wealth of important research, some of which is described in Leonard Susskind’s entertaining book The Black Hole War: My Battle with Stephen Hawking to Make the World Safe for Quantum Mechanics.”

Roček spent almost three years with Hawking, and so had the chance to get to know him both as a scientist and as a human being.

Many people have heard of Stephen Hawking, the ‘genius in a wheelchair,’ but far fewer know what he did and what he was like,” said Roček, who has served as a professor of physics at Stony Brook since 1983. “He was a great mentor. Many of his students and postdocs went on to very successful academic careers.

“He was a role model for those overcoming physical adversity, and through his many books, a great popularizer of physics and science in general. He will be missed,” Roček continued.

At the age of 21, Hawking was diagnosed with a rare early-onset, slow-progressing form of motor neurone disease (also known as Amyotrophic Lateral Sclerosis [ALS] or Lou Gehrig’s disease) and was given only a few years to live. While his condition gradually paralyzed him, he remained able to communicate through a speech-generating device, initially through use of a handheld switch, and eventually by using a single cheek muscle.

Hawking was famed for his work with black holes, quantum theory and relativity, and wrote several popular science books, including A Brief History of Time, which has sold more than 10 million copies worldwide and has returned to the top of the Amazon Best Sellers list since his death.

“Stephen’s first big breakthrough was the realization that Penrose’s theorems about the inevitability of singularities in black holes in Einstein’s Theory of Gravitation could be applied in reverse, to imply the inevitability of the Big Bang singularity and the beginning of time,”  Roček recalled.

“His next, and most important, breakthrough was the realization that due to quantum effects, black holes are not black — they emit what is now called ‘Hawking Radiation.’ This shocking discovery implied that, despite the many orders of magnitude of scale that separated them, Einstein’s theory could not ignore the quantum world.”

Luis Álvarez-Gaumé, director of the Simons Center for Geometry and Physics at Stony Brook, noted that despite Hawking’s numerous contributions, he was never awarded a Nobel Prize.

“His seminal contributions are deserving of a Nobel, and it is a pity he was not awarded the medal,” said Álvarez-Gaumé, who obtained his PhD from Stony Brook in 1981.

“One can imagine Stephen, with his great sense of humor saying, ‘That’s right, but on the other hand, how many living Nobel laureates have ever been characters in “The Simpsons” and in “Star Trek”?,’” Álvarez-Gaumé said.

Roger Sher, an associate professor in the Department of Neurobiology & Behavior who researches ALS, was inspired by Hawking’s determination to overcome his illness.

“The death of Dr. Stephen Hawking is a loss not just for the greater scientific community, but also for the community of patients, family members, caregivers, and researchers worldwide impacted by and dedicated to curing the neurodegenerative disease Amyotrophic Lateral Sclerosis,” Sher said.

“In one way, Dr. Hawking was a rare ALS patient, living for more than 50 years with his disease while the majority of patients succumb in fewer than 5 years,” he said.

“In another way, Dr. Hawking was not rare, in that I have seen in my interactions with ALS patients and their families and medical professionals, the same embracing of life, the strong sense of humor, the dedication to making their work and their disease something that motivates them to make others’ lives better.’

Mar 23

Scientists believe that anatomical variation within and between species is the raw material for natural selection. However, the prevalence of convergent evolution, or the repeated evolution of highly similar yet complex forms among distantly related animals, suggests the presence of underlying general principles ( or“rules”) of evolution.

Now Alan Turner, Associate Professor of Anatomical Sciences, along with colleagues at the University and at Oklahoma State University are conducting research they believe will help to unlock the rules of evolution. Their research is funded by a newly awarded $579,000 grant from the National Science Foundation. Professor Turner leads the team, which will use high-tech imaging techniques to assess how the bodies and brains of crocodylomorphs (crocodiles, alligators and their extinct relatives) have changed over the last 230 million years.

The research team will then perform computer analysis of these parts to develop conceptual models of anatomical variation and search for common patterns in how their bodies responded to new environmental transitions.

“Crocodylomorphs have an incredible fossil record, and it is remarkable how often they evolved from living exclusively on land to becoming semi-aquatic and marine,” says Turner, all of which makes them an ideal group for studying the rules that govern extreme changes in animals, he explained. Turner expects that by investigating such a unique and long fossil record, combined with advanced imaging techniques, their research will provide data and insight to how habitat and ecological transitions drive evolution not only in this group but potentially across multiple integrated anatomical systems.

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