Power of 3

Fusheng Wang. Photo from SBU

By Daniel Dunaief

Long Island’s opioid-related use and poisoning, which nearly doubled from 2015 to 2016, was higher among lower income households in Nassau and Suffolk counties, according to a recent study in the American Journal of Preventive Medicine.

Looking at hospital codes throughout New York to gather specific data about medical problems caused by the overuse or addiction to painkillers, researchers including Fusheng Wang, an assistant professor in the Department of Biomedical Informatics at Stony Brook University, George Leibowitz, a professor in Stony Brook’s School of Social Welfare, and Elinor Schoenfeld, a research professor of preventive medicine at the Renaissance School of Medicine at Stony Brook, explored patterns that reveal details about the epidemic on Long Island.

“We want to know what the population groups are who get addicted or get poisoned and what are the regions we have to pay a lot of attention to,” Wang said. “We try to use lots of information to support these studies.”

Data from The Journal

The Stony Brook team, which received financial support from the National Science Foundation, explored over 7 years of hospital data from 2010 to 2016 in which seven different codes — all related to opioid problems — were reported.

During those years, the rates of opioid poisoning increased by 250 percent. In their report, the scientists urged a greater understanding and intervening at the community level, focusing on those most at risk.

Indeed, the ZIP codes that showed the greatest percentage of opioid poisoning came from communities with the lowest median home value, the greatest percentage of residents who completed high school and the lowest percentage of residents who achieved education beyond college, according to the study.

In Suffolk County, specifically, the highest quartile of opioid poisoning occurred in communities with lower median income.

Patients with opioid poisoning were typically younger and more often identified themselves as white. People battling the painkilling affliction in Suffolk County were more likely to use self-pay only and less likely to use Medicare.

In Suffolk County, the patients who had opioid poisoning also were concentrated along the western section, where population densities were higher than in other regions of the county.

The Stony Brook scientists suggested that the data are consistent with information presented by the Centers for Disease Control and Prevention, which has found significant increases in use by women, older adults and non-Hispanic whites.

“The observed trends are consistent with national statistics of higher opioid use among lower-income households,” the authors wrote in their study. Opioid prescribing among Medicare Part D recipients has risen 2.84 percent in the Empire State. The data on Long Island reflected the national trend among states with older residents.

“States with higher median population age consume more opioids per capita, suggesting that older adults consume more opioids,” the study suggested, citing a report last year from the American Journal of Preventive Medicine.

Nationally, between 21 to 29 percent of people prescribed opioids for pain misused them, according to the study, which cited other research. About 4 to 6 percent of people who misuse opioids then transition to heroin. Opioid costs, including treatment and criminal justice, have climbed to about $500 billion, up from $55.7 billion in 2007, according to a 2017 study in the journal Pain Physician.

The findings from the current study on Long Island, the authors suggest, are helping regional efforts to plan for and expand capacity to provide focused and targeted intervention where they are needed most.

Limited trained staff present challenges for the implementation of efforts like evidenced-based psychosocial programs such as the Vermont Hub and Spoke system.

The researchers suggest that the information about communities in need provides a critical first step in addressing provider shortages.

New York State cautioned that findings from this study may underreport the burden of opioid abuse and dependence, according to the study. To understand the extent of underreporting, the scientists suggest conducting similar studies in other states.

Scientists are increasingly looking to the field of informatics to analyze and interpret large data sets. The lower cost of computing, coupled with an abundance of available data, allows researchers to ask more detailed and specific questions in a shorter space of time.

Wang said this kind of information about the opioid crisis can provide those engaging in public policy with a specific understanding of the crisis. “People are not [generally] aware of the overall distribution” of opioid cases, Wang said. Each hospital only has its own data, while “we can provide a much more accurate” analysis, comparing each group.

Gathering the data from the hospitals took considerable time, he said. “We want to get information and push this to local administrations. We want to eventually support wide information for decision-making by the government.”

Wang credited his collaborators Leibowitz and Schoenfeld with making connections with local governments.

He became involved in this project because of contact he made with Stony Brook Hospital in 2016. Wang is also studying comorbidity: He’d like to know what other presenting symptoms, addictions or problems patients with opioid-related crises have when they visit the hospital. The next stage, he said, is to look at the effectiveness of different types of treatment.

A resident of Lake Grove, Wang believes he made the right decision to join Stony Brook. “I really enjoy my research here,” he said.

Brendan Boyce, center, with Xiangjiao Yi, left, and Jinbo Li, who are graduate students at the University of Rochester. Photo by Jianguo Tao.

By Daniel Dunaief

Chances are high you won’t see Dr. Brendan Boyce when you visit a doctor. You will, however, benefit from his presence at Stony Brook University Hospital and on Long Island if you have bone or soft tissue lesions and you need an expert pathologist to diagnose what might be happening in your body.

A professor at the University of Rochester for 20 years, the internationally renowned Boyce joined the Renaissance School of Medicine at SBU in November, splitting his time between Rochester and Long Island.

Dr. Ken Shroyer, the chair of the Department of Pathology, reached out to Boyce with an unusual bone tumor case last spring. After that discussion, the two considered the possibility of Boyce adding his bone and soft tissue pathology expertise to the growing department. Boyce was receptive to the idea, particularly because his daughter Jacqueline lives in Woodbury with two of his seven grandchildren.

For local patients, Boyce adds a relatively rare expertise that could shorten the time for a diagnosis and improve the ability for doctors to determine the best course of action during surgeries.

“While the patient is already undergoing a surgical procedure, the preliminary diagnosis can guide the process of the surgery,” said Shroyer. “That’s difficult to achieve if we are dependent on an outside consultant. It happens, more or less in real time, if Boyce can look at the slides as they are being prepared and while the patient is still on the operating table.”

Prior to Boyce’s arrival, Stony Brook functioned the same way most academic medical centers do around the country when it came to bone and soft tissue cancers or disorders.

“There are only a handful of soft tissue and bone surgical pathology subspecialists around the country,” Shroyer said. “There’s an insufficient number of such individuals to make it practical like this at every medical school in the country.”

Many of these cases are “rare” and most pathologists do not see enough cases to feel comfortable diagnosing them without help from an expert, Boyce explained.

Boyce “was recruited here to help this program at Stony Brook continue to grow,” Shroyer said. “He enhances the overall scope of the training we can provide to our pathology residents through his subspecialty expertise. Everything he does here is integrated with the educational mission” of the medical school.

While bone and soft tissue tumors are relatively rare compared to other common cancers, such as colorectal or breast cancer, they do occur often enough that Stony Brook has developed a practice to diagnose and treat them, which requires the support of experts in pathology. Stony Brook hired Dr. Fazel Khan a few years ago as the orthopedic surgeon to do this work.

“To establish a successful service, there needs to be a mechanism to financially support that service that’s not solely dependent on the number of cases provided,” Shroyer said.

Boyce’s recruitment was made possible by “investments from Stony Brook University Hospital and the School of Medicine, in addition to support from the Department of Orthopedics and Pathology.”

Shroyer was thrilled that Boyce brings not only his expertise but his deep and well-developed background to Stony Brook.

It was “important to me that he was not only a highly skilled surgical pathologist, but also was a physician scientist, which made him a very attractive recruit,” Shroyer said.

Indeed, while Boyce will provide pathology services to Stony Brook, he will continue to maintain a laboratory at the University of Rochester.

Boyce’s research is “focused on the molecular mechanisms that regulate the formation of osteoclasts and their activity,” Boyce said. He emphasizes the effects of pro-inflammatory cytokines and NF-Kappa B, which are transcription factors that relay cytokine signaling from the cell surface to the nucleus.

These factors drive osteoclast formation and activity in conditions affecting the skeleton, which include rheumatoid arthritis, postmenopausal and age-related osteoporosis and cancers affecting the skeleton.

Osteoclasts degrade bone, which carve out deformities or the equivalent of potholes in the bone, while osteoblasts help rebuild the bone, repaving the equivalent of the roads after the osteoclasts have cleared the path. There are over a million sites of bone remodeling in the normal human skeleton and the number of these increases in diseases.

Boyce has studied various aspects of how bone remodeling occurs and how it becomes disturbed in a variety of pathological settings by using animal models. He uses cellular and molecular biological techniques to answer these questions.

On behalf of Boyce and three other researchers, the University of Rochester Medical Center just finished licensing a compound to a company in China that he recently contacted, which will do animal studies that will test the toxicity of a treatment for myeloma.

At this point, Boyce is applying in July for another five-year grant from the National Institutes of Health for research in his Rochester lab. He hopes to renew another NIH grant next year, which he has for four years. After he renews that grant, he will continue writing up papers and studies with residents and collaborating on basic science at Stony Brook as well.

Boyce and his wife Ann, have three children and seven grandchildren. Originally from Scotland, Boyce has participated in Glasgow University Alumni activities in the United States, including in New York City, where he walked in this year’s Tartan Parade with his daughters and their children.

As for his work at Stony Brook, Boyce is enjoying the opportunity to contribute to the community.

“The setting and faculty are very nice and congenial and I’ve been made to feel welcome,” he said.

Many of Madagascar’s iconic lemur species such as this black-and-white ruffed lemur are critically endangered. Photo by Daniel Burgas

By Daniel Dunaief

As a part of an ambitious reforestation plan announced in March, Madagascar’s newly elected president Andry Rajoelina explained that he wanted to change the way his nation off the southwest coast of the African continent was known, from the Red Island to the Green Island.

An international collection of scientists, including lemur expert and award-winning scientist Patricia Wright of Stony Brook University, recently weighed in on other ways Rajoelina can help conservation goals for the country through a five-step solution they outlined in the journal Nature Sustainability.

“We are all very concerned” about the fate of biodiversity in Madagascar, said Wright. “We know that only with a collaborative effort can we push things in the right direction.”

Madagascar, which has numerous species endemic to the island nation, including many of the lemurs Wright studies, is known as the island of red clay in part because deforestation has exposed much of the clay underlying the country. This clay has eroded into rivers, which have washed into the ocean.

“If you flew over the whole island, it would be very sad” because of all the exposed red clay from deforestation, Wright said.

She remains optimistic about Rajoelina’s goals and the potential for achieving them. The president “talked about going on the offensive and reforestation is one of his platforms,” she said. “It’s most important to reforest with endemic species,” as opposed to eucalyptus and pine.

Unlike in other countries, where politicians sometimes view conservation and economic development as forces pulling in opposite directions, Malagasy leaders acknowledge and recognize the benefit of preserving unique habitats that are home to the rare and threatened species of Madagascar.

“If you destroy all the forests, you destroy all the water and they will no longer be able to farm,” Wright said. “The natural wildlife and habitats are closely connected to their well-being. One of the biggest industries is ecotourism, which supports many industries on the ground. It’s not like there’s a line between people and wildlife.”

Indeed, the scientists acknowledge the importance of financial growth for the country that dovetails with their conservation goals.

“Conservation needs to contribute to, and not detract from, national efforts targeting economic development,” Julia Jones of Bangor University, in Wales, who led the study, said in a press release. “It must not make situations worse for the rural poor who are so often marginalized in decision making.”

The people of Madagascar have many of the same needs as those in other countries, as they seek jobs, health care, and good schooling, Wright said. “These families are closer to not having enough food to eat and they are much poorer if the natural resources are all destroyed.”

Concerned about the fate of biodiversity in Madagascar, Jones contacted Wright, who suggested the team enlist the help of Jonah Ratsimbazafy from the University of Antananarivo in Madagascar.

“It was just a matter of bringing together some of the key players in conservation for 20 years,” explained Wright.

The group generated a list of five priorities.

First on the list is tackling environmental crime. The scientists suggest using new technologies, including remote sensing and rapid DNA barcoding, to allow forest rangers and others to identify protected species. To improve this effort, however, the Ministry of Justice also needs to enhance the way it reacts to environmental crimes.

The researchers suggest prosecuting and fining those who traffic in rosewood or the critically endangered species for the pet trade. They see progress in this arena in the northeastern part of the island nation, where prosecutors have effectively charged some people who have sold rosewood.

Second, the group recommends investing in protected areas. The researchers urge greater investment in policy, legal and economic conditions that encourage additional investment in nature, which could include improving infrastructure to develop tourism around protected areas, payment for ecosystem services and debt for nature swaps.

Critically endangered species such as these ploughshare tortoises may be extinct in the wild within the next few years if illegal collection isn’t stopped. Photo by Chris Scarffe

Third, the scientists urge that major infrastructure developments limit the impact on biodiversity. The current environmental impact assessment law is over 20 years old and needs an update to require the use of environmental assessment. This component also includes a greater commitment to enforcement.

Fourth, the scientists suggest strengthening tenure rights for local people over natural resources. Most farmers can’t get certification for their land, which reduces the incentive for them to invest in settled agriculture and potentially exacerbates forest clearance. A review of tenure laws could help local landowners and biodiversity.

Finally, researchers recognize a growing crisis in fuel wood. They urge an investment in reforestation efforts, which could provide environmental and economic benefits.

While these steps are important for Rajoelina and the government in Madagascar, Wright suggests several ways Long Islanders can help. She urges school teachers to cover Madagascar in their classes. Teachers in the area who are interested in gathering information about the island nation can write to Wright at Patricia.Wright@stonybrook.edu.

She also urges people to become involved through social media, which they can use to have fundraisers through organizations like PIVOT, an organization committed to improving health in developing nations like Madagascar and strongly encourages people to visit Madagascar, where they can enjoy the benefits of ecotourism.

Visitors to Madagascar would have the incredible opportunity to witness the varied biodiversity for themselves.“We have charismatic lemurs,” Wright said, although many of them are critically endangered. Even if they can’t travel that far, people can support students who wish to study abroad.

“I don’t think health and wildlife are separated,” Wright said. “The health of the people depends on us preserving natural resources.”

She is looking forward to the Annual Association for Tropical Biology and Conservation meeting in Antananarivo, Madagascar, from July 30 through August 3. “Hopefully, we will be going forward with the next step during or shortly after that meeting.”

Bruce Stillman. Photo courtesy of CSHL

By Daniel Dunaief

Bruce Stillman, the president and CEO of Cold Spring Harbor Laboratory, was recently awarded the prestigious Canada Gairdner International Award for his contributions to research about the way DNA copies itself. The 60-year-old prize, which Stillman will receive in a ceremony in October and that he shares with his former postdoctoral fellow John Diffley, includes a financial award of $100,000 Canadian dollars that he can spend however he’d like.

A native Australian, Stillman, who has been at Cold Spring Harbor Laboratory since 1979, recently shared his thoughts about the award, research at the lab and his concerns about science in society with Times Beacon Record News Media. 

How does it feel winning the Gairdner Award?

It’s one of the most prestigious awards in the life sciences in the world and it’s certainly a great honor to win it and to join the list of spectacular scientists in the history of the award. There are some really fantastic scientists who I very much admire who have received this award.

How does it relate to the research you’ve conducted?

The field of DNA replication and chromosome inheritance was recognized. It is something I’ve devoted my entire career to. There are a lot of people that have made important contributions to this field. I’m pleased to be recognized with [Diffley] who was my former postdoc. [It’s validating] that the field was recognized.

Has CSH Laboratory been at the cutting edge of discoveries using the gene-editing tool CRISPR?

Cold Spring Harbor didn’t discover CRISPR. Like many institutions, we’ve been at the forefront of applying CRISPR and gene editing. The most spectacular application of that has been in the plant field. Zachary Lippman, Dave Jackson and Rob Martienssen are using genetic engineering to understand plant morphogenesis and development, thereby increasing the yield of fruit. Hopefully, this will be expanded into grains and have another green revolution.

CSHL has also been making strides in cancer research, particularly in Dave Tuveson’s lab, with organoids.

Organoids came out of people studying development. Hans Clevers [developed organoids] in the Netherlands … Tuveson is at the forefront of that. The full promise hasn’t been realized yet. From what I’ve seen, we are quite excited about the possibility of using organoids as a tool to get real feedback to patients. It is rapidly moving forward with the Lustgarten Foundation and with Northwell Health.

What are some of the other major initiatives at CSHL?

The laboratory’s investment about 10 or 15 years ago in understanding cognition in the brain has paid off enormously. Neuroscientists here are at the forefront of understanding cognition and how the brain does computation in complicated decisions. [Scientists are also] mapping circuits in the brain. It took a lot of investment and kind of the belief that studying rodent cognition could have an impact on human cognition, which was controversial when we started it here, but has paid out quite well. At the same time, we are studying cognitive dysfunction particularly in autism. 

Any other technological advances?

There’s been a real revolution in the field of structural biology… [Researchers] have the ability to look at single biological molecules in the electron microscope. It shoots electrons through a grid that has individual biological molecules. The revolution, which was done elsewhere by many people actually, led to the ability to get atomic resolution structures of macro molecular complexes. 

Cold Spring Harbor invested a lot of money, well over $10 million to build a facility and staff a facility to operate this new technology. I’ve been working on this area for about 12, 13 years now … Our structural biologists here in neuroscience, including neuroscientists Hiro Furukawa and Leemor Joshua-Tor have really helped introduce a lot of new biology into CSHL.

What are some of the newer efforts at the lab?

One of the big new initiatives we started is in the field of cancer. As you know by looking around, there’s an obesity epidemic in the Western world. We started a fairly large initiative, understanding the relationship between obesity and cancer and nutrition, and we’re not unique in this. We’re going to have some significant contributions in this area. 

Cancer cells and the tumor affect the whole body physiology. The most severe [consequence] is that advanced cancer patients lose weight through a process called cachexia. We hired [new staff] in this new initiative, renovated a historic building, the Demerec building at a fairly substantial expense, which was supported by New York State. 

What will CSHL researchers study related to obesity?

We’re absolutely going to be focusing on understanding mostly how obesity impacts cancer and the immune system, then how cancer impacts the whole body physiology. Hopefully, once we start to understand the circuits, [we] will be able to intervene. If we can control obesity, we will by logic reduce cancer impact.

What worries you about society?

What worries me is that there is a tendency in this country to ignore science in policy decisions … The number of people not getting vaccinated for measles is ridiculous. There is this kind of pervasive anti-science, anti-technology view that a lot of Americans have. They want the benefits of science and everything that can profit for them. 

There are certain groups of people who misuse data, deliberately abuse misinformation on science to promote agendas that are completely irrational. One of the worst is anti-vaccination. … We should as a society have severe penalties for those who choose to go that route. They shouldn’t send their children to schools, participate in public areas where they could spread a disease that effectively was controlled. Imagine if polio or tuberculosis came back?

How is the lab contributing to education?

People need to act like scientists. It’s one of the reasons we have the DNA Learning Center, to teach people to think like scientists. If 99.99 percent of the evidence suggests [something specific] and 0.01 percent suggest something [else], you have to wonder whether those very small and vocal minority are correct.

Gordon Taylor with technician, Tatiana Zaliznyak. A Raman microspectrometer is pictured in the background. Photo by J. Griffin

By Daniel Dunaief

Something is happening in the Twilight Zone of the ocean, but it’s unclear exactly who is involved and how fast the process is occurring. 

Plants and animals are eating, living, defecating and dying above the so-called Twilight Zone and their bodies and waste are falling toward the bottom of the ocean. But most of that matter isn’t making it all the way to the ocean floor.

That’s where Gordon Taylor, a professor and director of the NAno-RAMAN Molecular Imaging Laboratory at the School of Marine & Atmospheric Sciences at Stony Brook University, comes in. 

Taylor and Professor Alexander Bochdansky of Old Dominion University recently received a $434,000 three-year grant to study the way microorganisms eat, process and convert organic carbon — i.e., carbon that’s a part of living organisms like plants, sea birds and whales — into inorganic carbon, which includes carbon dioxide, carbonate, bicarbonate and carbonic acid.

“The inorganic carbon moves back and forth among these four chemical species,” Taylor explained in an email. Understanding the rate at which carbonic acid builds up can and will help lead to a greater awareness of ways the ocean, which used to have a pH around 8.2 — which is slightly basic, as opposed to levels below the neutral 7— is becoming more acidic.

Above, incubators that Alexander Bochdansky has used in Bermuda. The ones Taylor and Bochdansky will analyze will be smaller than these, which won’t require such a large A-frame to deploy. Images courtesy of A. Bochdansky

They will start by deploying the traps at a single depth, about 985 feet, along the ocean off the coast of Virginia. “We are going to look at who the players are,” Bochdansky said. “There might be only a few key players that degrade this organic carbon. With [Taylor’s] great methods, we can measure the uptake rate in single microbes. This is really exciting.”

The Twilight Zone received its name because it is 650 to 3,300 feet below the surface of the water. Some faint light reaches the top of that zone, but most of that region, which includes creatures that use bioluminescence to attract or find prey, is pitch black.

“The directory of which inventories and fluxes decrease [is] still poorly understood,” Taylor said. “Animals eating the material is one mechanism and we don’t know how important that is compared to microbial decomposition or remineralization,” adding that the goal of this project is to “better define the role of microorganisms in returning carbon to the inorganic pool.”

Taylor is exploring this area with new tools that will allow a greater depth of understanding than previously possible. His group has developed new experimental approaches to apply Raman microspectrometry to this problem. The organisms they examine will include bacteria, fungi and protozoans.

Their experiment will explore which organisms are recycling organic carbon, how fast they are doing it and what factors control their activities. Through this approach, Taylor will be able to see these processes down to the level of a single cell as the instrument can identify organisms that have consumed the heavy isotope tracer.

The Raman microspectrometer uses an optical microscope with a laser and a Raman spectrometer. This tool will measure samples that are micrometers thick, which is smaller than the width of a human hair. The microspectrometer can obtain data from a 0.3-micrometer spot in a cell and he has even produced spectra from single viruses.

The scientists will place phytoplankton common to the region in incubators that Bochdansky developed. They will use a heavy carbon isotope, called carbon 13, that is easy to find through these experiments and see how rapidly microorganisms that colonize are incorporating the isotopically labeled carbon.

Taylor and Bochdansky received funding for the project through the Biological Oceanography Program at the National Science Foundation in the Directorate of Geosciences. Twice a year, the division makes open calls for proposals on any topic of interest to researchers. The scientists submit 15 pages of text that the NSF sends to peer reviewers. A panel meets to evaluate the reviews and ratings and decides which projects to fund.

Bochdansky and Taylor have been “acquainted for a long time and have shared similar interests,” Taylor said.

The carbon experiments in the Twilight Zone account for about a quarter of the work Taylor is doing in his lab. The other research also employs Raman microspectrometry. The United States only has one or two other facilities that do environmental research comparable to the one in Taylor’s lab at Stony Brook. Europe also has three such tools, which can look into single cells using lasers.

One of the other projects Taylor hopes to get funded involves studying the distribution of microplastics in the ocean. “The instrument I have is one of the best tools to look at microscopic plastic particles,” because it identifies the plastic polymer and its source, said Taylor, who is awaiting word on funding from the National Oceanic and Atmospheric Administration.

The other work involves exploring viruses that attack plankton.

“We are exploring Raman methods for early detection of viruses that attack plankton,” Taylor explained. Every organism in the ocean has at least one virus that has evolved to attack it.

As for his work on the Twilight Zone, Taylor said the area acts as a filter of sorts because less than 20 percent of the organic material entering at the top exits at the bottom.

Bochdansky added that these microbes are critical to processes that affect oceans and the planet.

“That’s something people often overlook,” Bochdansky said. “We can’t understand the ocean if we don’t understand it at the level or the scale that’s relevant to microbes.”

Bochdansky is thrilled to work with Taylor, who he’s known for years but will collaborate with for the first time on this project.

“In my lab, we have measured the turnover and release of carbon dioxide,” Bochdansky said. In Taylor’s lab, he measures “the actual feeding of microbial cells.”

A rendering of Suskityrannus hazelae by Andrey Atuchin

By Daniel Dunaief

Even the name Tyrannosaurus rex seems capable of causing ripples across a glass of water, much the way the fictional and reincarnated version of the predator did in the movie “Jurassic Park.”

Long before the predatory dinosaur roamed North America with its powerful jaws and short forelimbs, some of its ancestral precursors, whom scientists believed were considerably smaller, remained a mystery.

A team of scientists led by Sterling Nesbitt, an assistant professor at Virginia Tech, shed some light on a period in which researchers have found relatively few fossils when they shared details about bones from two members of T. rex’s extended ancestral family in New Mexico. 

These fossils, which they named Suskityrannus hazelae, help fill in the record of tyrannosauroid dinosaurs that lived between the Early Cretaceous and latest Cretaceous species, which includes T. rex.

Sterling Nesbitt, assistant professor of geosciences at Virginia Tech, with a partial fossil of Suskityrannus hazelae found in New Mexico. Photo courtesy of Virginia Tech

The researchers, which included Alan Turner, an associate professor of anatomical sciences at Stony Brook University, chronicled the history of these fossils from the Late Cretaceous period, or about 92 million years ago.

“Getting a chance to understand the origin of something is compelling,” said Turner. “Having a discovery like Suskityrannus, which helps us understand how the body plan of tyrannosauroids evolved, is super interesting.” The fossils reveal the “humble beginnings” of a group that would “later dominate North American terrestrial ecosystems.”

Indeed, the new dinosaur was considerably more modest in size than future predators. The Suskityrannus, which included one individual that wasn’t fully grown when it died after living at least three years, measured about three feet at the hip, weighed about 100 pounds, and was about nine feet long, which made it more like a full grown male wolf, albeit longer because of its extended tail.

Scientists had found earlier tyrannosaur relatives from the Early Cretaceous as well as T. rex and its closest relatives near the end of the Late Cretaceous. They were missing data about tyrannosaurs from the middle of the group’s history because fossils from this time period are so rare.

The researchers cautioned that this paper, which was published in the journal Nature, Ecology & Evolution, does not suggest that Suskityrannus was a direct ancestor of T. rex. It does, however, fill a fossil gap in the extended T. rex family.

Suskityrannus hazelae,

The Suskityrannus species has a broad mouth and a muscular skull. Additionally, the bones in its foot were built in a way that made it good at absorbing shocks.

As far as fossil specimens, the bones from this finding are “well represented” across various parts of this creature’s anatomy, including a “lot of limb anatomy and a good portion of the skull and vertebral column,” Turner said. 

This collection of bones help define where on the evolutionary map this new species belong. Some of the anatomical characteristics in this new species appear to be well-suited for future predators, even as they likely also provided an adaptive advantage for the Suskityrannus. 

“These are features that were already in place much earlier” than this new species needed them, Turner said. They may have been adaptations that helped with their agility or with the environment in which they lived. Eventually, evolution turned them into the kinds of anatomical features that made them useful when T. rex eventually grew to as large as 16 tons.

“That’s something you see often in evolution: the way a species is using [its anatomy] isn’t always necessarily what the features evolved for,” Turner said. “Evolution can only work with what it has. What we see with Suskityrannus is that it had these things that became important later on.”

Turner’s role was to help compile and analyze the enormous amount of data that came out of this discovery. He explored how the number of species changed along the boundary between the first half of the Late Cretaceous and the second half of the Late Cretaceous periods, adding that the process of exploring and analyzing such a discovery can take years. 

Indeed, Turner first saw the fossil in 2007. “The studies take a long time and you can get lost in the details,” he said. “You do try and keep the big picture in your head. That’s the thing that makes [the work] interesting.”

Alan Turner while conducting fieldwork in Kenya last summer. Photo by Eric Gorscak

Turner became a part of this work through his connection to Nesbitt. The two scientists attended graduate school together at Columbia University. They have been doing field work together since 2005.

Nesbitt explained in an email that he thought of including Turner immediately “because he is an expert on aspects of paleobiology and theropods, plus he is an excellent colleague to work on papers with.”

In the research paper, the scientists have created an artistic rendering of what this new species might have looked like. While Turner acknowledges that the image involves a “bit of an artistic license,” the image is also “bound by what we know.” 

Nesbitt said this finding provides information about the theropods as a whole. “We really don’t know why T. rex and its closest relatives got so big,” he said, but researchers do know this happened at the end of the Cretaceous period, after 80 million years of being relatively small.

Turner lives in Port Jefferson with his wife, Melissa Cohen, who is the graduate program coordinator in the Department of Ecology & Evolution at Stony Brook University. The couple has two children.

Turner, who grew up in a suburb of Cleveland, recalls a field trip when he was 17 that encouraged him to pursue a career in paleontology. He was conducting research in Montana and he was exploring dinosaurs and sharing a sense of camaraderie with others on the expedition.

“I remember feeling like that was an affirming experience,” Turner said.

As for the discovery of Suskityrannus, Turner shared the wonder at finding a new species, something he’s been a part of eight times with dinosaurs in a career that now includes 11 years at Stony Brook.

“It’s always pretty exciting when you get to work on something that’s new,” he said.

Members of the quantum materials team, from left, Gregory Doerk, Jerzy Sadowski, Kevin Yager, Young Jae Shin and Aaron Stein. Photo from BNL

By Daniel Dunaief

Henry Ford revolutionized the way people manufactured cars through automation, speeding up the process, reducing waste and cutting costs.

Similarly, at Brookhaven National Laboratory, researchers like the newly hired Young Jae Shin, who is a staff scientist at the Center for Functional Nanomaterials, hopes to improve the process of automating the handling of thin flakes of material used in a next generation technology called quantum information science, or QIS.

Working with scientists at Harvard University and the Massachusetts Institute of Technology, Shin is looking for ways to handle these flakes, which are one atom thick, of two-dimensional layers from different materials. Stacked together, these flakes can help create structures with specific electronic, magnetic or optical properties that can be used as sensors, in communication, or encryption.

Young Jae Shin at Harvard University, where he was a post doctoral researcher. Photo from Y. Shin

“Researchers are building these kinds of customized structures manually now,” explained Kevin Yager, leader of the CFN Electronic Nanomaterials Group, in an email. “QPress [Quantum Material Press] will allow us to automate this.” At this point, QPress is just starting, but, if it works, it will “absolutely allow us to accelerate the study of these materials, allowing researchers to find optimal materials quickly,” Yager continued.

Theoretically, quantum computers overcome the limitations of other systems, Shin explained.

The flakes come from the exfoliation of thin structures taken from a bulk material. This is akin to a collection of leaves that fall around trees. According to Yager, the structures scientists hope to make would be akin to a collection of leaves from different trees, put together to make a new structure or material with specific properties. “The idea is for the robot to sift through the flakes, and identify the ‘best’ ones and to stack these together into the right structure. The ‘stacking’ will involve combining flakes of different materials,” he said.

The less desirable flakes typically are the wrong size, have tears, ripples or other defects and have contaminants. Groups of scientists are predicting the kinds of layered designs that will have desired properties.

Shin suggested that the CFN supports the needs of the end user community, as CFN is a “user-based facility.”

Physicists at Harvard and MIT plan to use the QPress to study unusual forms of superconductivity. By tapping into materials that conduct electricity without losing energy at lower temperatures, researchers may make progress in quantum computing, which could exceed the ability of the current state-of-the-art supercomputers.

Stacking the flakes can create new materials whose properties not only depend on the individual layers, but also on the angle between the stacks. Scientists can change one of these new structures from having metallic to having insulating properties, just by altering the relative angle of the atoms. The challenge, however, is that putting these fine layers together by hand takes time and generates errors which, BNL hopes, an automated approach can help reduce.

“Ultimately, we would like to develop a robot that delivers a stacked structure based on the 2-D flake sequences and crystal orientations that scientists select through a web interface” to a machine, Charles Black, the head of the Center for Functional Nanomaterials at BNL, explained in a recent BNL feature. “If successful, the QPress would enable scientists to spend their time and energy studying materials, rather than making them.”

Barring unforeseen delays, scientists anticipate that they will be able to build a machine that creates these flakes, catalogs them, stacks them and characterizes their properties within three years. These functions will be available online in stages, to allow the use of the QPress prior to its completion.

Each stage in the QPress process uses computer software to reduce the effort involved in generating and interpreting usable structures.

Minh Hoai Nguyen, an assistant professor in the Department of Computer Science at Stony Brook University and doctoral student Boyu Wang from the Computer Vision Lab at SBU are creating a flake cataloger, which will use image analysis software to scan and record the location of flakes and their properties.

“The flakes that scientists are interested in are thin and thus faint, so manual and visual inspection is a laborious and error-prone process,” Nguyen said in the BNL feature.

At BNL, Shin is one of three scientists the Upton-based facility is hiring as a part of this effort. They are also seeking robot or imaging process experts. Shin has “been in the CFN just a short while, but is already having an impact- — for instance, allowing us to handle classes of two-dimensional materials that we were not working with before,” Yager said.

The field of quantum information science is extremely competitive, with researchers from all over the world seeking ways to benefit from the properties of materials on such a small scale. The United States has been investing in this field to develop leadership science in this area.

The University of Tokyo has developed an automation system, but Shin explained that it is still not perfect.

Yager said that numerous unknown applications are “waiting to be discovered. Researchers are working hard on real quantum computers. Prototypes already exist but creating viable large-scale quantum computers is a major challenge.”

A resident of on-site housing at BNL, Shin was born in the United States and grew up in Korea. He is married to Hyo Jung Kim, who is studying violin at Boston University. 

As for the work Shin and others are doing, Yager suggested that the effort has generated considerable interest at the CFN.

“There is huge excitement at BNL about quantum research broadly and QPress in particular,” said Yager. Shin is “a big part of this — bringing new technical knowledge and new enthusiasm to this ambitious project.”

From left, Megan Crow, Associate Professor Jesse Gillis and postdoctoral researcher Sara Ballouz Photo by Gina Motisi/CSHL

By Daniel Dunaief

Diversity has become a buzz word in the workplace, as companies look to bring different perspectives that might represent customers, constituents or business partners. The same holds true for the human brain, which contains a wide assortment of interneurons that have numerous shapes and functions.

Interneurons act like a negative signal or a brake, slowing or stopping the transmission. Like a negative sign in math, though, some interneurons put the brakes on other neurons, performing a double negative role of disinhibiting. These cells of the nervous system, which are in places including the brain, spinal chord and retina, allow for the orderly and coordinated flow of signals.

One of the challenges in the study of these important cells is that scientists can’t agree on the number of types of interneurons.

“In classifying interneurons, everyone argues about them,” said Megan Crow, a postdoctoral researcher in Jesse Gillis’ lab at Cold Spring Harbor Laboratory. “People come to this question with many different techniques, whether they are looking at the shape or the connectivity or the electrophysiological properties.”

Megan Crow. Photo by Constance Brukin

Crow recently received a two-year grant from the National Institutes of Health to try to measure and explain the diversity of interneurons that, down the road, could have implications for neurological diseases or disorders in which an excitatory stimulus lasts too long.

“Understanding interneuron diversity is one of the holy grails of neuroscience,” explained Gillis in an email. “It is central to the broader mission of understanding the neural circuits which underlie all behavior.”

Crow plans to use molecular classifications to understand these subtypes of neurons. Her “specific vision” involves exploiting “expected relationships between genes and across data modalities in a biologically thoughtful way,” said Gillis.

Crow’s earlier research suggests there are 11 subtypes in the mouse brain, but the exact number is a “work in progress,” she said.

Her work studying the interneurons of the neocortex has been “some of the most influential work in our field in the last two to three years,” said Shreejoy Tripathy, an assistant professor in the Department of Psychiatry at the University of Toronto. Tripathy hasn’t collaborated with Crow but has been aware of her work for several years.

The interactivity of a neuron is akin to personalities people demonstrate when they are in a social setting. The goal of a neuronal circuit is to take an input and turn it into an output. Interneurons are at the center of this circuit, and their “personalities” affect the way they influence information flow, Crow suggested.

“If you think of a neuron as a person, there are main personality characteristics,” she explained. Some neurons are the equivalent of extraverted, which suggests that they have a lot of adhesion proteins that will make connections with other cells.

“The way neurons speak to one another is important in determining” their classes or types, she said.

A major advance that enabled this analysis springs from new technology, including single-cell RNA sequencing, which allows scientists to make thousands of measurements from thousands of cells, all at the same time.

“What I specialize in and what gives us a big leg up is that we can compare all of the outputs from all of the labs,” Crow said. She is no longer conducting her own research to produce data and, instead, is putting together the enormous volume of information that comes out of labs around the world.

Megan Crow. Photo by Daniel Katt

Using data from other scientists does introduce an element of variability, but Crow believes she is more of a “lumper than a splitter,” although she would like to try to understand variation where it is statistically possible.

She believes in using data for which she has rigorous quality control, adding, “If we know some research has been validated externally more rigorously than others, we might tend to trust those classifications with more confidence.”

Additionally she plans to collaborate with Josh Huang, the Charles Robertson professor of neuroscience at Cold Spring Harbor Laboratory, who she described as an interneuron expert and suggested she would use his expertise as a “sniff test” on certain experiments.

At this point, Crow is in the process of collecting baseline data. Eventually, she recognizes that some interneurons might change in their role from one group to another, depending on the stimuli.,

Crow hasn’t always pursued a computational approach to research. 

In her graduate work at King’s College London, she produced data and analyzed her own experiments, studying the sensory experience of pain.

One of the challenges scientists are addressing is how pain becomes chronic, like an injury that never heals. The opioid crisis is a problem for numerous reasons, including that people are in chronic pain. Crow was interested in understanding the neurons involved in pain, and to figure out a way to treat it. “The sensory neurons in pain sparked my general interest in how neurons work and what makes them into what they are,” she said.

Crow indicated that two things brought her to the pain field. For starters, she had a fantastic undergraduate mentor at McGill University, Professor of Psychology Jeff Mogil, who “brought the field to life for me by explaining its socio-economic importance, its evolutionary ancient origins, and showed me how mouse behavioral genetic approaches could make inroads into a largely intractable problem.”

Crow also said she had a feeling that there might be room to make an impact on the field by focusing on molecular genetic techniques rather than the more traditional electrophysiological and pharmacological approaches.

As for computational biology, she said she focuses on interpreting data, rather than in other areas of the field, which include building models and simulations or developing algorithms and software.

In the bigger picture, Crow said she’s still very interested in disease and would like to understand the role that interneurons and other cells play. “If we can get the tools to be able to target” some of the cells involved in diseases, “we might find away to treat those conditions.”

The kind of research she is conducting could start to provide an understanding of how cells interact and what can go wrong in their neurodevelopment.

Gillis praises his postdoctoral researcher for the impact of her research.

“Just about any time [Crow] has presented her work — and she has done it a lot — she has ended up convincing members of the audience so strongly that they either want to collaborate, adapt her ideas, or recruit her,” Gillis wrote in an email. 

Crow grew up in Toronto, Canada. She said she loved school, including science and math, but she also enjoyed reading and performing in school plays. She directed a play and was in “The Merchant of Venice.” In high school, she also used to teach skiing.

A resident of Park Slope in Brooklyn, Crow commutes about an hour each way on the train, during which she can do some work and catch up on her reading.

She appreciates the opportunity to work with other researchers at Cold Spring Harbor, which has been “an incredible learning experience.”

Enyuan Hu with images that represent electron orbitals. Photo from Enyuan Hu

By Daniel Dunaief

Charging and recharging a battery can cause a strain akin to working constantly without a break. Doctors or nurses who work too long in emergency rooms or drivers who remain on the road too long without walking around a car or truck or stopping for food can function at a lower level and can make mistakes from all the strain.

Batteries have a similar problem, as the process of charging them builds up a structural tension in the cathode that can lead to cracks that reduce their effectiveness.

Working with scientists at Brookhaven National Laboratory and the Stanford Synchrotron Radiation Lightsource, Enyuan Hu, an assistant chemist at BNL, has revealed that a doughnut-shaped cathode, with a hole in the middle, is more effective at holding and regenerating charges than a snowball shape, which allows strain to build up and form cracks. 

At this point, scientists would still need to conduct additional experiments to determine whether this structure would allow a battery to hold and regenerate a charge more effectively. Nonetheless, the work, which was published in Advanced Functional Materials, has the potential to lead to further advances in battery research.

“The hollow [structure] is more resistant to the stress,” said Hu. Lithium is extracted from the lattice during charging and changes the volume, which can lead to cracks.

The hollow shape has an effective diffusion lens that is shorter than a solid one, he added.

Yijin Liu, a staff scientist at Stanford’s Linear Accelerator Center (SLAC) and a collaborator on the project, suggested that the result creates a strategic puzzle for battery manufacture.

Enyuan Hu with drawings that represent images of metal 3d orbitals interacting with oxygen 2p obits, forming either sigma bonds (above) or pi bonds (below).
Photo from Enyuan Hu

“On the one hand, the hollow particles are less likely to crack,” said Liu. “On the other hand, solid particles exhibit better packing density and, thus, energy density. Our results suggest that careful consideration needs to be carried out to find the optimal balance.” The conventional wisdom about what caused a cathode to become less effective involved the release of oxygen at high voltage, Hu said, adding that this explanation is valid for some materials, but not every one.

Oxygen release initiates the process of structural degradation. This reduces voltage and the ability to build up and release charges. This new experiment, however, may cause researchers to rethink the process. Oxygen is not released from the bulk even though battery efficiency declines. Other possible processes, like loss of electric contact, could cause this.

“In this specific case of nickel-rich layered material, it looks like the crack induced by strain and inhomogeneities is the key,” said Hu.

In the past, scientists had limited knowledge about cracks and homogeneity, or the consistent resilience of the material in the cathode.

The development of new technology and the ability to work together across the country made this analysis possible. “This work is an excellent example of cross-laboratory collaboration,” said Liu. “We made use of cutting edge techniques available at both BNL and SLAC to collect experimental data with complementary information.”

At this point, Hu estimates that about half the battery community believes oxygen release causes the problem for the cathode, while the other half, which includes Hu, thinks the challenge comes from surface or structural problems. 

He has been working to understand this problem for about three years as a part of a five-year study. His role is to explore the role of the cathode, specifically, which is his particular area of expertise.

Hu is a part of a Battery500 project. The goal of the project is to develop lithium-metal batteries that have almost triple the specific energy currently employed in electric vehicles. A successful Battery500 will produce batteries that are smaller, lighter and less expensive than today’s model.

Liu expressed his appreciation for Hu’s contributions to their collaboration and the field, saying Hu “brings more than just excellent expertise in battery science into our collaboration. His enthusiasm and can-do attitude also positively impacts everyone in the team, including several students and postdocs in our group.”

In the bigger picture, Hu would like to understand how lithium travels through a battery. At each stage in a journey that involves diffusing through a cathode, an anode and migrating through the electrolyte, lithium interacts with its neighbors. How it interacts with these neighbors determines how fast it travels. 

Finding lithium during these interactions, however, can be even more challenging than searching for Waldo in a large picture, because lithium is small, travels quickly and can alter its journey depending on the structure of the cathode and anode.

Ideally, understanding the journey would lead to more efficient batteries. The obstacles and thresholds a lithium ion needs to cross mirror the ones that Hu sees in everyday life and he believes he needs to circumvent these obstacles to advance in his career.

One of the biggest challenges he faces is his comfort zone. “Sometimes, [comfort zones] prevent us from getting exposed to new things and ideas,” he said. “We have to be constantly motivated by new ideas.”

A cathode expert, Hu has pushed himself to learn more about the anode and the electrolyte.

A resident of Stony Brook, Hu lives with his wife, Yaqian Lin, who is an accountant in Port Jefferson, and their son Daniel, who attends Setauket Elementary School.

Hu and Lin met in China, where their families were close friends. They didn’t know each other growing up in Hefei, which is in the southeast part of the country.

Hu appreciates the support Lin provides, especially in a job that doesn’t have regular hours.

“There are a lot of off-schedule operations and I sometimes need to leave home at 10 p.m. and come back in the early morning because I have an experiment that requires my immediate attention. My wife is very supportive.”

As for his work at BNL, Hu said he “loves doing experiments here. It has given me room for exploring new areas in scientific research.”

Lori Chan, standing, in the lab with doctoral student Jiabei He. Photo from SBU

By Daniel Dunaief

It’s like a factory that makes bombs. Catching and removing the bombs is helpful, but it doesn’t end the battle because, even after many or almost all of the bombs are rounded up, the factory can continue to produce damaging products.

That’s the way triple-negative breast cancer operates. Chemotherapy can reduce active cancer cells, but it doesn’t stop the cancer stem cell from going back into the cancer-producing business, bringing the dreaded disease back to someone who was in remission.

Scientists who stop these cancer stem cells would be doing the equivalent of shutting down the factory, reducing the possible return of a virulent type of cancer.

Lori Chan, an assistant professor in the Department of Pharmacological Sciences in the Renaissance School of Medicine at Stony Brook University, recently published research in Cell Death & Disease that demonstrated the role of a specific gene in the cancer stem cell pathway. Called USP2, this gene is overexpressed in 30 percent of all triple-negative breast cancers.

Inhibiting this gene reduced the production of the tumor in a mouse model of the disease.

Chan’s results “suggest a very important role [of this gene] in cancer stem cells,” Yusuf Hannun, the director of the Stony Brook University Cancer Center, explained in an email.

Lori Chan with her dog KoKo. Photo by Joshua Lee

Chan used a genetic and a pharmacological approach to inhibit USP2 and found that both ways shrink the cancer stem cell population. She used RNA interference to silence the gene and the protein expression, and she also used a USP2-specific small molecular inhibitor to block the activity of the USP2 protein.

With the knowledge that the cancer stem cell factory population needs this USP2 gene, Chan inhibited the gene while providing doxurubicin, which is a chemotherapy treatment. The combination of treatments suppressed the tumor growth by 50 percent.

She suggested that the USP2 gene can serve as a biomarker for the lymph metastasis of triple-negative breast cancer. She doesn’t know if it could be used as a biomarker in predicting a response to chemotherapy. Patients with a high expression of this gene may not respond as well to standard treatment.

“If a doctor knows that a patient probably wouldn’t respond well to chemotherapy, the doctor may want to reconsider whether you want to put your patient in a cycle for chemotherapy, which always causes side effects,” Chan said.

While this finding is an encouraging sign and may allow doctors to use this gene to determine the best treatment, the potential clinical benefit of this discovery could still be a long way off, as any potential clinical approach would require careful testing to understand the consequences of a new therapy.

“This is the beginning of a long process to get to clinical trials and clinical use,” Hannun wrote. Indeed, researchers would need to understand whether any treatment caused side effects to the heart, liver and other organs, Chan added. 

In the future, doctors at a clinical cancer center might perform a genomic diagnostic, to know exactly what type of cancer an individual has. Reducing the cancer stem cell population can be critically important in leading to a favorable clinical outcome.

A few hundred cancer cells can give rise to millions of cancer cells. “I want to let chemotherapy do its job in killing cancer cells and let [cancer stem cell] targeted agents, such as USP2 inhibitors, prevent the tumor recurrence,” Chan said. 

She urges members of the community to screen for cancer routinely. A patient diagnosed in stage 1 has a five-year survival rate of well over 90 percent, while that rate plummets to 15 to 20 percent for patients diagnosed with stage 4 cancer.

The next step in Chan’s research is to look for ways to refine the inhibitor to make it more of a drug and less of a compound. She is also interested in exploring whether USP2 can be involved in other cancers, such as lung and prostate, and would be happy to collaborate with other scientists who focus on these types of cancers.

For Chan, the moment of recognition of the value of studying this gene in this form of breast cancer came when she compared the currently used drug with and without the inhibitor compound. With the inhibitor, the drug becomes much more effective.

A resident of Stony Brook, Chan lives with her husband, Joshua Lee, who is working in the same lab. The couple, who have a 1½-year-old rescue dog from Korea named KoKo, met when they were in graduate school.

Concerned about snow, which she hadn’t experienced when she was growing up in Taiwan, Chan started her tenure at Stony Brook five years ago on April 1, on the same day a snowstorm blanketed the area. “It was a very challenging first day,” she recalled. She now appreciates snow and enjoys the seasonal variety on Long Island.

Chan decided to pursue a career in cancer research after she volunteered at a children’s cancer hospital in Taiwan. She saw how desperate the parents and the siblings of the patient were. In her role as a volunteer, she played with the patients and with their siblings, some of whom she felt didn’t receive as much attention from parents who were worried about their sick siblings.

“This kind of disease doesn’t just take away one person’s life,” Chan said. “It destroys the whole family.” When she went to graduate school, she wanted to know everything she could about how cancer works.

Some day Chan hopes she can be a part of a process that helps doctors find an array of inhibitors that are effective in treating patients whose cancers involve the overexpression of different genes. “It would be a privilege to participate in this process,” she said.