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Daniel Dunaief

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Ride For Life presents CSHL with $300,000 for ALS research: from left, CSHL Director of Annual Giving and Donor Relations Karen Orzel, CSHL Assistant Professor Molly Hammell, Ride for Life Founder Chris Pendergast, Stony Brook Associate Professor Josh Dubnau and Ride for Life board member Frank Verdone. Photo by Jessa Giordano, Cold Spring Harbor Laboratory

By Daniel Dunaief

The past can come back to haunt us, even in the world of genetics. Over the course of millions of years, plants and animals have battled against viruses, some of which inserted their genes into the host. Through those genetic struggles, explained Molly Hammell, an assistant professor at Cold Spring Harbor Laboratory, cells develop “elaborate ways to fight back,” even as they continue to make copies of these pieces of DNA.

Sometimes, when our defenses break down, these retrotransposons, or jumping genes, can become active again. Indeed, that appears to be the case in a fly model of amyotrophic lateral sclerosis, also known as ALS or Lou Gehrig’s disease.

Working on a fruit fly model of ALS, Joshua Dubnau, an associate professor at Stony Brook University, Lisa Krug, who earned her doctorate at Cold Spring Harbor Laboratory and is now working at Kallyope in New York, and Hammell showed that these ancient genetic invaders play an important role in the disease amid activation by a protein often linked to ALS called TDP-43.

A recent study, published in PLOS Genetics, “really proves that retroviral reactivation (as a consequence of TDP-activity) is … central to either causing or accelerating neuronal cell death when TDP-43 inclusions are present,” explained Hammell in an email. If TDP-43 plays the same role for humans, this would suggest that targeting this protein or the jumping genes, it activates could lead to potential treatment for ALS.

These collaborators showed that an aggregation of this protein turned on jumping genes. These genes can make copies of themselves and insert themselves in other parts of the genetic code. In this case, TDP-43 expression disrupts the normal immune-like system that silences retrotransposons such as gypsy, which is a particular type of jumping gene in the fruit fly.

When gypsy was activated, the fruit fly exhibited many of the features of ALS, including protein pathology, problems with movement, shortened life span and cell death or glia and neurons in the brain. The scientists were also able to turn gypsy off, which improved the health and extended the life span of the fly.

Mimicking this protein results in broad activation of several retrotransposons. If this also occurs in people, the disease may activate a retrotransposon that is the human analog to gypsy, called HERV-K, as well as other retrotransposons. The study also suggests that DNA damage caused by retrotransposons may active a cell suicide mechanism. Finally, this effort showed a means by which the protein disrupts the normal immune surveillance that keeps retrotransposons quiet.

To be sure, Dubnau cautioned that animal models of a disease may not translate when returning to people. Researchers need to look at more patients at all the retrotransposons in the human genome to monitor its prevalence, Dubnau suggested. If the link between retrotransposon activation and the development of ALS is as evident in humans as it is in the fruit fly, scientists may take an approach similar to that which they took to battle the human immuno-deficiency virus, or HIV. Retrotransposons have an RNA genome that needs to be copied to DNA. This, Dubnau explained, is the step in the process where researchers attacked the virus.

In a small subset of HIV patients who have motor neuron symptoms that are similar to ALS, Avi Nath, a senior investigator at the National Institutes of Health discovered that treating patients with the typical HIV medication cocktail helped relieve their ALS symptoms as well.

“What is not known is whether, for some reason, this subset of patients had an ALS syndrome caused by HIV or they were curing them” by treating HIV, Dubnau said. Nath is currently involved in one of two clinical trials to see if HIV medications help ALS patients. The next step for Dubnau and Hammell is to screen the tissue of numerous ALS patients after their death to see if their retrotransposons were elevated.

In addition to NIH funding, the scientists received financial support from Ride for Life, which is a not-for-profit organization started in 1997 that raises funds for research to find a cure for ALS, supports patients and their families through patient services and raises awareness of ALS. Every May, Ride for Life conducts a 12-day, 100-mile patient wheelchair ride across Long Island. Dubnau and Hammell, who received a $300,000 grant from Ride for Life in 2015, said they have been inspired by Ride for Life founder Chris Pendergast.

Meeting Pendergast “has had a big impact,” Dubnau said. “He’s a force of nature. He’s an incredibly strong and intelligent person.” Receiving funds from Ride for Life created a sense of personal obligation to Pendergast and many other people who “had raised that money through sweat and effort.”

Without funding from the Ride for Life Foundation, “We would not have the resources to obtain these samples and do the sequencing experiments necessary to prove that this is a clinically relevant phenomenon in a large number of ALS patients,” Hammell said.

Through an email, Pendergast explained that Ride for Life chose to fund the work by Dubnau and Hammell because the research met several criteria, including that it might lead to new strategies to treat ALS and the research was on Long Island, which is a “powerful affirmation for our generous donors.”

Pendergast emphasized the importance of funding basic ALS research. “We need to know why it develops, how it progresses [and] how it can be diagnosed and monitored,” he urged.

A resident of Huntington, Dubnau and his wife Nicole Maher, who works at the Nature Conservancy as a climate scientist, have a nine-year-old daughter, Caitlin. Reflecting both of her parents’ professional interests, Caitlin is going to a statewide science fair, where she is presenting her work on how temperature affects the life span of insects.

As for his research, Dubnau hopes a further exploration of TDP-43 might reveal an important step in the progression of ALS. He hopes this discovery may suggest a strategy researchers and clinicians can take that might “stop the cascade of events” in ALS.

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Percy Zahl. Photo courtesy of BNL

By Daniel Dunaief

When he was in high school in Negenborn, Germany, Percy Zahl built his own computer, with some help from one of his father’s friends. Nowadays, Zahl spends considerable time improving the computer capability of an open-source community drive software project that helps researchers see structures and interactions at a subatomic level.

Recently, Zahl, who is an associate scientist in the Proximal Probe Microscopy facility at the Center for Functional Nanomaterials at Brookhaven National Laboratory, completed an extensive upgrade to software called Gnome X Scanning Microscopy, or GXSM, that adds a whole suite of new features. Zahl re-coded about half of the original 300,000 lines of code during this project.

The software, which is used to operate any kind of scanning probe microscopy system which includes atomic force microscopy and scanning tunneling microscopy, has a wide range of applications, from understanding catalysts that facilitate chemical reactions, to capturing gases, to biomedical sensors.

Oliver Monti, a professor of chemistry and biochemistry and a professor of physics at the University of Arizona, has been working with Zahl for over four years and has been using this system to explore atomic and molecular-scale processes that determine efficiency in plastic solar cells and other next-generation low-energy-use technologies. He said he uses the GXSM for data analysis.

Zahl “often introduces modifications and upgrades as instantaneous response to some scientific need,” which has “helped us solve specific problems efficiently,” Monti explained in an email. A former student of Monti’s needed to analyze molecule-to-molecule interactions. The two came up with an algorithm to study that and, unprompted, Zahl “introduced a version of this algorithm to his software.”

Percy Zahl (front of line) during a Tour of Somerville race in 2011. Photo by Anthony Skorochod.

Monti said he is “very much aware of the most recent release,” which he considers a “major upgrade” and he is in the process of installing it. The new software allows the export of images in formats such as PDF and SVG, which are editable and resolution independent, Zahl explained. A PDF output of a graph has publication quality, while the images with high-resolution displays are enhanced and sharper than the previous bitmap PNG files.

The upgrade also includes making a remote control process for automating scanning and manipulation tasks “easy to use,” which is a “big plus for less experienced users,” Zahl explained. It can help automate complex or tedious repetitive jobs. As an example, Zahl said the need to scan an image that takes 10 minutes each for 20 different settings creates a laborious task. “I can either sit there and enter manually a new number every 10 minutes” or he can program a script that he made to use a list of bias voltages and hit execute in the new remote console, he explained, leaving him time to work on other projects for the next two hours and 20 minutes.

Recently, Zahl ran a spectra covering the area of a molecule, which is a task he can do reliably without worrying about user typos or errors. An additional noncontact atomic force microscopy simulation plug-in module provides researchers with a more efficient way to generate data. The new approach measures the force between atoms and molecules of the surface of a sample and a probe smaller than the diameter of an atom. Zahl has calculated and simulated forces between atoms, taking into account all atoms of a molecule and the probe atom and finds the equilibrium position of his probe. Using that three-dimensional force field, he can extract an image that he compares to the model.

Zahl spends about three quarters of his time working with users like Monti, while he dedicates the remaining time to his own projects. He appreciates the opportunity to work with many different systems and with people in a wide range of scientific disciplines.

“It’s really as diverse as it can get in this particular field of fundamental surface science — a specialty of solid state physics,” Zahl explained in an email. He has the experience to work with many different sample types while still continuing to learn “all the tricks on how to get the best images possible.”

Monti appreciates Zahl’s dedication to his work. “Data processing and analysis can be challenging,” he explained. His students often compare a trip to BNL to drinking from a firehose.

Zahl has been “essential in helping us figure out how to sift through the data and quickly focus on the most important observations,” Monti added. That appreciation extends well beyond Monti’s lab. “Whenever I meet colleagues across the world who had the pleasure to interact with [Zahl], they lavish praise on his scientific and technical expertise,” Monti said.

Bruce Koel, a professor in the Department of Chemical and Biological Engineering at Princeton University, appreciated Zahl’s contribution to his research on chemical reactions at surfaces. Zahl has “enabled us to do very high impact research,” Koel explained in an email. This work would “not have been possible without [Zahl’s] technical support and guidance about what experiments could be done.”

A resident of Rocky Point, Zahl rides the 20 miles to work as often as he can on one of several of his bicycles. An avid cyclist, Zahl has a high-end racing bike, a commuter bike and a mountain bike from those “beloved times” riding mountain trails in Switzerland.

In Chile, he reached a top speed of around 56 miles per hour descending the Osorno Volcano. In a YouTube video of his ride, he can be seen passing a car in a clearing along the windy road.

As for his work, Zahl remains committed to continuing to improve the software scientists use to enhance their visual understanding of the small surfaces of the substances they study. “I am pretty much always working on some new details or fixing this and that tiny issue,” he said. “No software is ever done. It’s evolving.”

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At the first meeting of the HiTOP consortium. Kotov is in the center. Photo from HiTOP consortium.

By Daniel Dunaief

Instead of lamenting the shortcomings of a system they felt didn’t work as well as it should, Roman Kotov and a growing group of collaborators whose numbers now exceed 50 decided to do something about it. An associate professor of psychiatry at Stony Brook University, Kotov and his collaborators are building their own mental health tool, which, they hope, will offer specific diagnoses for everything from anxiety to schizophrenia.

Roman Kotov. Photo from SBU School of Medicine

The current resource psychologists and psychiatrists use is called the “Diagnostic and Statistical Manual of Mental Disorders 5,” which came out in 2013. The latest version of the DSM, as the manual that offers psychologists and psychiatrists a way to link a collection of symptoms to a diagnosis is called, “felt far too limited,” Kotov said. “Once we started discussing [an alternative], almost everyone was interested in the scientific community. They thought it was a good and necessary idea.”

Called the Hierarchical Taxonomy of Psychopathology, or HiTOP, the developing classification system uses scientific evidence, illness symptoms and impaired functioning in its diagnoses. Another HiTOP co-creator, David Watson, the Andrew J. McKenna Family professor of psychology at the University of Notre Dame, recognized Kotov’s important early work on the project.

Kotov “deserves sole credit for the idea of putting all of our data together to provide the basis for an alternative model,” Watson explained in an email. “He did some preliminary work along these lines, which convinced us that this was a great idea that was worth pursuing.” Watson, who served as Kotov’s graduate adviser at the University of Iowa, said that his former student leads meetings and conference calls for the HiTOP group.

The HiTOP system, which was recently described in the Journal of Abnormal Psychology, views mental disorders along a spectra, while also using empirical evidence to understand overlap among disorders and classify different symptoms within a given diagnosis. As an example, Kotov said that depression in the DSM is “treated as one thing. We know that depression is heterogeneous.”

Indeed, some people with depression may have lost their appetite and have trouble sleeping, while others may be eating and sleeping considerably more than they would if they weren’t depressed. “In some ways, these are opposite presentations, yet they get the same diagnosis” in the DSM, Kotov said.

HiTOP unpacks this variability into seven dimensions, which describe symptom types. That is helpful not only for a diagnosis but also for a treatment. HiTOP also goes beyond the binary description of the presence or absence of a particular symptom, offering clinicians a way of indicating the severity of a problem. At this point, HiTOP is a developing prototype and not a completed diagnostic tool. The scientists developing this tool have made inroads in four primary areas: anxiety and depression, substance use problems, personality problems and psychotic disorders.

“The HiTOP system currently is incomplete, as it primarily focuses on more common and widely studied forms of psychopathology,” Watson suggested, “but mental health professionals certainly could use it to assess/ diagnose a broad range of conditions.” Mental health professionals can view this new resource at the website https://medicine.stonybrookmedicine.edu/HITOP.

Kotov hopes this new paradigm will “focus on science and do everything we can to keep unpolitical, nonscientific considerations out of it,” he said. “We hope that it provides the most up-to-date alternative” to the DSM. The HiTOP approach, Kotov said, relies more heavily on scientific evidence, which can include genetic vulnerabilities, environmental risk factors and neurobiological abnormalities.

Kotov, who is working on several projects, said HiTOP takes about a quarter of his time. He is also involved with a long-term study of schizophrenia and bipolar disorders, which was started in the early 1990s, before he arrived at Stony Brook in 2006.

Kotov is following up on this cohort, looking at outcomes for treatment and analyzing risk factors and processes that determine the course of an illness. He is also leading a study on first responders to the 9-11 attack on the World Trade Center, which is exploring the physical and emotional consequences of participating in the response to the unprecedented attack.

Kotov and his collaborators are investigating the health of responders in their daily life using mobile technology. They are also studying how personalities affect their health, which may soon help guide personalized treatment.

Another project involves the study of children who are 14 to 17 years old and explores the emotional growth and personality development. This study includes reports, surveys and interviews. During those years, “much happens as far as personality development,” Kotov said.

Colleagues at Stony Brook praised Kotov’s scientific contributions. Kotov is a “rising star” and is “perhaps best known for his work on the role of personality in psychopathology and, increasingly, for work on classification of psychiatric disorders,” Daniel Klein, a distinguished professor in the Department of Psychology at Stony Brook, wrote in an email.

A resident of Port Jefferson, Kotov lives with his wife Tatiana, who is a controller for a small company in Manhattan. The couple has two young daughters. Kotov grew up in Russia in a small town near Moscow. He was always interested in science and developed a particular curiosity about psychology when a high school psychology teacher sparked his interest when he was 15.

As for the HiTOP effort, Kotov is convinced this endeavor will offer the mental health community a valuable tool. “We believe that describing patients more accurately, precisely and reliably will help provide better and more personalized care,” he said.

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Jun Wang in her laboratory with a transmission x-ray microscope. Photo from BNL

By Daniel Dunaief

The first time is most definitely not the charm. That’s what Jun Wang and her colleagues at Brookhaven National Laboratory discovered about sodium ion batteries.

Wang, a physicist and lead scientist at the facility, looked deep into the inner workings of a sodium ion battery to determine what causes structural defects as the battery functions. As it turns out, the first time a sodium ion battery charges and discharges, it develops changes in the microstructure and chemical composition of iron sulfide. These changes, which degrade the performance of the battery, are irreversible during the first charging cycle.

“We found that the cracks happened during the first cycle, then, after that, the structure kind of reached equilibrium,” said Wang, who published her research in the journal Advanced Energy Materials. “All these changes happen during the first cycle.”

Collaborators from Brookhaven’s Photon Sciences and Sustainable Energy Technologies groups stand behind the new transmission x-ray microscope (TXM) at BNL’s National Synchrotron Light Source. From left: Yu-chen Karen Chen-Wiegart, Can Erdonmez, Jun Wang (team leader), and Christopher Eng. Photo from BNL

Sodium ion batteries are considered an alternative to lithium ion batteries, which are typically found in most consumer electronics. Like lithium, sodium is an alkali metal, which means that it is in the same group in the periodic table. Sodium, however, is more abundant and, as a result, considerably less expensive than lithium.

Using a synchrotron-based hard X-ray full-field microscope, Wang was able to see what happened when sodium ions moved into and out of an iron sulfide electrode through 10 cycles. “We can see this microstructure evolution,” she said.

Wang monitored the evolution as a function of time while the battery is charging and discharging. The results are the first time anyone has studied a sodium-metal sulfide battery with these tools, which provides information that isn’t available through other methods. “It is challenging to prepare a working sodium ion battery for the in operandi/in situ TXM study to correlate the microstructural evolution with its electrochemical performance,” she said.

Other researchers suggested that Wang has developed a following in the scientific community for her ground-breaking research. “She has a very good reputation in the area of X-ray nanotomography, applied to a wide range of different materials,” Scott Barnett, a professor of materials science and engineering at Northwestern University, explained in an email. “I am most familiar with her work on fuel cell and battery electrodes — I think it is fair to say that this work has been some of the best pioneering research in this area,” he said.

Barnett, who started collaborating with Wang in 2010 on measuring fuel cell and battery electrodes with X-ray tomography, suggested that Wang’s work on capacity loss “could certainly lead to new breakthroughs in improved batteries.”

In her most recent work with sodium ion batteries, Wang found that the defects start at the surface of the iron sulfide particles and move inward toward the core, Wang said. The microstructure changes during the first cycle and is more severe during sodiation. The particles don’t return to their original volume and shape. After the first cycle, the particles reach a structural equilibrium with no further significant morphological changes, she said.

In other cycles, the material does not show further significant morphological changes, reach a structural equilibrium and electrochemical reversibility. Wang and her colleagues confirmed these observations with X-ray nanotomography, which creates a three-dimensional image of the battery material while recording the change in volume.

Wang suggested that a way to reduce these structural defects could be to reduce the size of the iron sulfide particles to create a one-phase reaction. She will work with other collaborators on modeling and simulations that will enhance the design of future battery materials.

In addition to conducting research on batteries, Wang is an industrial program coordinator in the Photon Science Directorate at BNL. She works with industrial researchers and beamline staff to find and explore new opportunities in industrial applications using synchrotron radiation. She leads the industrial research program, interacting with user groups through consultation, collaboration and outreach.

To manage her research, which includes a lab of three other researchers, and to accomplish her mission as manager of an industrial research program, Wang jokes that she “spends 100 percent of her time” with each responsibility. “I try to do my best for the different things” she needs to do with her time, she said.

Jun Wang with her husband Qun Shen and their 11-year old son Sam in Waikiki last year. Photo from Jun Wang

A native of Wuhu, China, Wang earned her bachelor’s degree in physics from Anhui University in China and her doctorate in physics from the Chinese Academy of Sciences in Beijing. She worked at the Beijing Synchrotron Radiation Facility, which was the first synchrotron light source in China. During her doctoral training, she studied multilayer films using X-ray diffraction and scattering.

A resident of Poquott, Wang is married to Qun Shen, who is the deputy director for science at the NSLS-II. The couple has an 11-year-old son, Sam, who is a sixth-grade student at Setauket Elementary School. Shen and Wang met at an international X-ray crystallography conference in the early 1990s.

Shen trained in the United States after he graduated from Beijing University in 1980, when he went to Purdue University for his doctorate through the China-US Physica Examination and Application Program. The couple have worked together a few times over the years, including publishing a paper in Nature Communications. Wang is hoping that her work with battery research will lead to improvements in the manufacture and design of sodium ion batteries.

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Beetles, which thrive in warmer temperatures, are threatening pine trees

Residents from Cutchogue work together to place sand bags at the edge of the Salt Air Farm before Hurricane Sandy in 2012. Photo by Prudence Heston

While surrounded by salt water, Long Island is in the midst of a drought that is heading into its third year. Amid a trend towards global warming, the New York State Department of Environmental Conservation sent a letter to water district superintendents throughout Suffolk and Nassau County to ask them to lower their water consumption by 15 percent in the next three to four years.

“The primary area that is ripe for reduction is summertime watering,” said Bill Fonda, a spokesman for the DEC. The department has asked the water districts to reduce consumption, but it’s up to the districts to determine how they will reach those goals, he said.

The letter, written by Tony Leung, the regional water engineer, indicated that “results for 2015 show both Nassau and Suffolk County have exceeded the safe yield as cited in the 1986 Long Island Groundwater Management Program,” and that “a concerted effort is needed to reduce peak season water demand.”

The letter, which doesn’t cite global warming, indicates that salt water intrusion, contaminant plumes migration, salt water upconing and competing demand have raised concerns about a need to reduce peak season water demand.

Observers suggested the demand was likely rising for a host of reasons, including increased use of underground irrigation systems and a rise in the population of Long Island.

Water experts welcomed the DEC’s initiative, which is one of many steps Long Islanders can and are taking to respond to a changing environment.

“Most people have no clue how much water they use…They get their water bill, it is what it is, and then they write a check and send it in.”

— Sarah Meyland

Sarah Meyland, the director of the Center for Water Resources Management and associate professor at the New York Institute of Technology, commended the DEC for asserting control over water withdrawals.

“Most people have no clue how much water they use,” Meyland said. “They get their water bill, it is what it is, and then they write a check and send it in.”

She admitted changing consumer behavior will be challenging.

The first step in ensuring water suppliers meet this request, Meyland suggested, is to inform the public about the need for less water use, particularly during the summer months. One possible solution is for irrigation systems that turn off automatically after a rainstorm.

The change in climate has posed a threat to trees that commonly grow on Long Island.

Pine trees have faced an invasion from the southern pine beetle, which extended its range onto Long Island in 2014 and is now a pest that requires routine managing and monitoring.

Long the scourge of pine trees in southern states, the pine beetle, which is about the size of a grain of rice, has found Long Island’s warmer climate to its liking.

“We’re assuming either [Hurricane] Irene or Sandy brought it in,” said John Wernet, a supervising forester at the DEC. “Because it’s getting warmer, the beetle has been able to survive farther north than they have historically.”

Forestry professionals in the south have waged a battle against the beetle for years, trying to reduce the economic damage to the timber market. On Long Island, Wernet said, they threaten to reduce or destroy the rare Pine Barrens ecosystem.

The beetle can have three or four generations in a year and each generation can produce thousands of young.

The first step relies on surveying trees to find evidence of an infestation. Where they discover these unwanted pests, they cut down trees and score the bark, which creates an inhospitable environment for the beetle.

“If left alone, the beetle is like a wildfire and will keep going,” Wernet said. Without direct action, that would be bad news for the pine warbler, a yellow bird that lives near the tops of pine trees, he said.

Wernet added Long Island’s drought also increases the risk of
wildfires.

Farmers, meanwhile, have had to contend with warmer winters that trick their crops into growing too soon while also handling the curveballs created by unexpected cold snaps, frosts, and the occasional nor’easter.

Dan Heston and Tom Wickham survey waters that entered Salt Air Farm after Hurricane Sandy. Photo by Prudence Heston

Last year, the colored hydrangeas of Salt Air Farm in Cutchogue budded early amid warmer temperatures in March, only to perish amid two eight-degree nights.

“We lost [thousands of dollars] worth of hydrangeas in two nights,” said Dan Heston, who works on the farm with his wife Prudence, whose family has been farming on Long Island for 11 generations. “Our whole colored hydrangea season was done.”

Heston said he’s been a skeptic of climate change, but suggested he can see that there’s something happening with the climate on Long Island, including the destructive force of Hurricane Sandy, which flooded areas that were never flooded during large storms before.

“I think the climate is shifting on Long Island,” Prudence Heston explained in an email. “Farmers are constantly having to adapt to protect their crops. In the end, pretty much every adaptation a farmer makes boils down to climate.”

Changes on Long Island, however, haven’t all been for the worse. Warmer weather has allowed some residents to grow crops people don’t typically associate with Long Island, such as apricots and figs. For three generations, Heston’s family has grown apricots.

Other Long Islanders have attempted to grow figs, which are even more sensitive to Long Island winters, Heston said. This was not an economically viable option, as each plant required individual wrapping to survive. That hasn’t stopped some from trying.

“People are now finding our winters to be warm enough to make [figs] a fun back yard plant,” Prudence Heston said.

In other positive developments, the Long Island Sound has had a reduction in hypoxia — low oxygen conditions — over the last decade, according to Larry Swanson, the interim dean of the School of Marine and Atmospheric Sciences at Stony Brook University.

“The state and the Environmental Protection Agency have agreed to a nitrogen reduction program,” Swanson said. “It appears that the decline in nitrogen may be having a positive effect.”

Brookhaven Town took a similar step in 2016.

The town board approved a local law proposed by Supervisor Ed Romaine (R) last summer that established nitrogen protection zones within 500 feet of any body of water on or around Long Island. The zones prohibit new structures or dwellings being built in that range from installing cesspools or septic systems.

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Scientists, like those who work out of the Stony Brook University School of Marine and Atmospheric Sciences’ Marine Sciences Center, are constantly asking questions, as the desire grows to find links between correlation and causation. File photo

Researchers often desire more data to help make the distinction between correlation — it rained the last three Tuesdays — and causation — dumping nitrogen into the lake caused the growth of algae that robbed the lake of oxygen.

Scientists don’t like to get ahead of their information, preferring to take the painstaking steps of going that extra mile to control for as many mitigating or confounding variables as they can.

Researchers are often “reluctant to say with certainty that they are correct,” Larry Swanson, the interim dean of the School of Marine and Atmospheric Sciences at Stony Brook University said.

This hesitation to indicate a certain conclusion can raise challenges for politicians, who would like to rely on scientific proof in developing plans for their constituents.

“Policy people want to create a law or regulation that is definitive and will have the desired outcome,” Swanson added.

File photo.

Since he began working in and around Long Island waters in 1960, he started his work collecting data at wetlands around New Haven, and has since studied hypoxia — the process through which oxygen levels are depleted in waterways.

Swanson urges a more extensive collection of data around Long Island.

“I believe we need to monitor the physical environment for changes not just for time series data, such as temperature, but in order to understand how ecological processes are being altered as a consequence of warming,” Swanson said.

Henry Bokuniewicz, a distinguished service professor of oceanography at Stony Brook, said there was a coastline monitoring program in place in 1995 after nor’easters and hurricanes in 1992, but that the effort petered out.

“This should be re-established if [New York State is] serious about coastal impact of shoreline changes,” he said.

Bokuniewicz also suggests measuring and recording waves that are close to shore, and water levels at the ocean coast and interior bays.

Stony Brook had an initiative for additional hires in a cluster for coastal engineering and management, but never completed the hires for budgetary reasons, Bokuniewicz said. “We could do much better with a new generation of scientists dedicated to the Long Island shore,” he said.

Scientists acknowledge that the study of climate change rarely involves establishing the kind of linear connection between action and reaction that turning up the thermostat in a house would provide.

Scientists distinguish between the weather — is it raining today, tomorrow or next week — and the climate — how does March in New York compare to March in North Carolina?

File photo

The climate, generally, remains consistent with a long-term outlook, even if Long Island might experience an unseasonably hot July, an unusually cool September and a heavier-than-normal snowfall in December.

With climate change, scientists collect as much data as they can to determine how the climate is shifting. That presents significant challenges: how do researchers pick data to feed into their models and the patterns to explore?

The broader trend in March could be that spring starts earlier, extending the growing season and creating opportunities for insects, plants or animals to affect the habitat. That could be slightly different this year, amid a cold snap that lasts more than a few days, or in the wake of an unexpected blizzard days before spring.

Indeed, until, and even after there is a scientific consensus, researchers debate long into the night about their interpretations, conclusions and simulation models.

More often than not, scientists crave more information to help them interpret evolving conditions.

“While we know in general why hypoxia will be bad, we can’t really predict it,” Swanson said. “When will it start? How long will it last? This is because we do not understand all the processes — things like the role of bacteria, phytoplankton and the blooming processes and water circulation.”

Science, as it turns out, is often more about collecting more information to ask better questions and developing more precise theories.

As researchers often point out, they can be wrong for the right reasons and right for the wrong ones, all of which, they hope, helps them understand more about the inevitable next set of questions. And, as scientists have offered, it’s a never-ending discussion, as the best answers lead to more questions.

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At the ribbon cutting of the Kavita and Lalit Bahl Center for Metabolomics and Imaging last December, from left, Lina Obeid; Yusuf Hannun; Kavita and Lalit Bahl; Samuel Stanley, President of Stony Brook University; and Kenneth Kaushansky, dean of Stony Brook University’s School of Medicine. Photo from SBU

By Daniel Dunaief

Many ways to kill cancer involve tapping into a cell’s own termination system. With several cancers, however, the treatment only works until it becomes resistant to the therapy, bringing back a life-threatening disease.

Collaborating with researchers at several other institutions, Dr. Lina Obeid, the director of research at Stony Brook University School of Medicine, has uncovered a way that cancer hides a cell-destroying lipid called ceramide from treatments. The ceramide “gets co-opted by fatty acids for a different species of fats, namely acylceramide, and gets stored side by side with the usual triglycerides,” Obeid explained in an email about her recent finding, which was published in the journal Cell Metabolism. “It makes the ceramide inaccessible and hence the novelty.” The ceramide gets stored as a lipid drop in the cell.

“We describe a completely new metabolic pathway and role in cell biology,” Obeid said. Other researchers suggested that this finding could be important in the battle against cancer. “That acylceramides are formed and deposited in lipid droplets is an amazing finding,” George Carman, the director of the Rutgers Center for Lipid Research, explained in an email. “By modifying the ceramide molecule with an acyl group for its deposit in a lipid droplet takes ceramide out of action and, thus, ineffective as an agent to cause death of cancer cells.”

Carman said Obeid, whom he has known for several years, visited his campus in New Jersey to share her results. “All of us at Rutgers were so excited to hear her story because we knew how important this discovery is to the field of lipid droplet biology as well as to cancer biology,” he said. Obeid conducted some of the work at the Kavita and Lalit Bahl Center for Metabolomics and Imaging at Stony Brook University. The center officially opened on Dec. 1 of last year on the 15th floor of the Health Sciences Center and will move to the Medical and Research Translation Building when it is completed next year. “This study is exactly the kind of major questions we are addressing in the center that [the Bahls] have generously made possible,” she explained.

Obeid discovered three proteins that are involved in this metabolic pathway: a ceramide synthesizing protein called CerS, a fatty acyl-CoA synthetase protein called ACSL and an enzyme that puts them together, called DGAT2, which is also used in fatty triglyceride synthesis. Her research team, which includes scientists from Columbia University, Northrop Veterans Affairs Medical Center and Mansoura University in Egypt is looking into implications for the role of this novel pathway as a target for cancer and obesity.

Indeed, obesity enables more frequent conversion of ceramide into acylceramide. “Fats in cells and in diets increase and predispose to obesity,” Obeid suggested. “This new pathway we found occurs when fatty acids are fed to cells or as high-fat diets are fed to mice.” In theory, this could explain why obesity may predispose people to cancer or make cancer resistance more prevalent for some people. According to Obeid, a high-fat diet can cause this collection of proteins to form in the liver of mice, and she would like to explore the same pathways in humans. Before she can begin any such studies, however, she would need numerous approvals from institutional review boards, among others.

Obeid and her collaborators hypothesize that a lower-fat diet could reduce the likelihood that this lipid would be able to evade cancer therapies.

These kinds of studies “provide the justification for looking at the effect of diet on acylceramide production,” Daniel Raben, a professor of biological chemistry at Johns Hopkins University School of Medicine, explained in an email. Further research could include “isocaloric studies with [high-fat diets] and [low-fat diets] in animals that are age and gender matched.”

Obeid was a part of the first group to describe the lipid’s role in cancer cell death in 1993. “We have been studying its metabolism and looking at how it’s made and broken down,” she said. “We found recently that it associates with these proteins to metabolize it.”

While the lipid provides a way to tackle cancer’s resistance to chemotherapy, it also has other functions in cells, including as a membrane permeability barrier and in skin. A therapy that reduced acylceramide could affect these other areas but “as with hair loss [with chemotherapy treatment], this will likely be easily managed and reversible,” Raben explained.

Obeid and Yusuf Hannun, the director of the Cancer Center at Stony Brook, are searching for other scientists to work at the Kavita and Lalit Bahl Center for Metabolomics and Imaging. “We are actively recruiting for star scientists” at the center, Obeid said. Other researchers suggested that the history of the work Obeid and Hannun have done will attract other researchers.

Hannun and Obeid are “considered the absolute leaders in the area of sphingolipid biochemistry and their clinical implications,” Raben said. “Simply put, they are at the top of this academic pile. Not only are they terrific scientists, they also have an outstanding and well-recognized reputation for training and nurturing young investigators.” Carman asked, “Who wouldn’t want to be associated with a group that continues to make seminal contributions to cancer biology and make an impact on the lives of so many?”

As for the next steps in this particular effort, Carman foresaw some ways to extend this work into the clinical arena. “I can imagine the discovery of a drug that might be used to combat cancer growth,” Carman said. “I can imagine the discovery of a drug that might control the acylation of ceramide to make ceramide more available as a cancer cell inhibitor. Clearly, [Obeid’s] group, along with the outstanding colleagues and facilities at Stony Brook, are positioned to make such discoveries.”

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Image courtesy of Disney Dan Stevens as the Beast and Emma Watson as Belle star in Disney’s ‘Beauty and the Beast.’ Image courtesy of Disney

By Daniel Dunaief

The latest version of “Beauty and the Beast,” which broke box office records when it opened last weekend, offers a visually stunning montage, as one magnificent set blends into the next in a familiar story that, not much of a spoiler here, tracks the well-known story.

The sets, cinematography and songs take center stage in this live-action remake, as Disney spared no expense to make the enchanted castle, the quiet village where every day is like the one before, and the journey through the forest between them as detailed and lavish as the animated version. The script and main actors, including Emma Watson as Belle and Dan Stevens as the Beast, are fine, but not extraordinary.

Disney may not have wanted to tinker too much with a classic film and its well-known dialog, leaving the original script largely unchanged. That is both for the better and the worse, as this current incarnation lacks a novel flavor, a new Disney humor and charm, or the opportunity to explore much more about the characters. There are a few welcome moments when the audience learns more about unfortunate events in Belle and the Beast’s past, but those are short-lived in a film that is over two hours.

Luke Evans does a serviceable job as Gaston, conveying the narcissistic brute who seems more in love with his own reflection than he is with Belle or anyone else. The charm or the irresistibility the villagers feel for him is not evident to Belle or to the audience.

Josh Gad provides welcome comic relief as Gaston’s companion LeFou, fawning over him and calming him down when things don’t go his way. Gad takes his character further than the animated version of LeFou, becoming impish and playful.

Like the Broadway version of the classic animated film “Aladdin” and its “Never Had a Friend Like Me” song, “Beauty and the Beast” somehow equals and, in some ways, exceeds the original film with its “Be Our Guest” feature. While Belle prepares for her meal, the creatures of the castle surround her with food, song and spectacle.

While the script and the characters stay true to the Broadway and animated versions of the story, the visual details truly make the film memorable. The finale in the castle looks like the kind of details an eager bride would include if she had an unlimited budget, with symmetrical floral arrangements, magnificent lighting, perfectly spaced dancers and a cast of characters delighted to share in the space.

For parents, the scenes of peril with the wolves outside the Beast’s castle are familiar and filled with the same kind of potential for danger. Young children will likely be as concerned for the welfare of Belle and the Beast in the wolf scenes of this film as they would be watching the animated version.

The fight scene between the Beast and Gaston also involves some peril, with Gaston displaying a combination of cowardice and villainy. At the same time, the fight scene between the villagers incited by Gaston to battle and the members of the enchanted castle who are defending themselves also contains some of the few moments of humor in a film that otherwise takes its tale and the retelling of it seriously.

Some of the other cast members, including Emma Thompson as Mrs. Potts, have a tough act to follow, repeating familiar phrases and songs from Angela Lansbury. Thompson holds her own, regaling the audience with the lyrics from a tale as old as time.

The three-dimensional version of the film included a few noticeable effects, including when Belle and the Beast engage in a snowball fight. It also adds some depth to the image of the castle and the trek through the woods. The additional expense, however, didn’t seem especially necessary, given an elaborate attention to other visual details.

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Line Pouchard at the Great Smoky Mountains National Park in 2013. Photo by Allan Miller

By Daniel Dunaief

They produce so much information that they can’t keep up with it. They use the latest technology to gather data. Somewhere, hidden inside the numbers, might be the answer to current questions as well as the clues that lead to future questions researchers don’t know how to ask yet.

Scientists in almost every facility, including at Brookhaven National Laboratory, Cold Spring Harbor Laboratory and Stony Brook University, are producing information at an unprecedented rate. The Center for Data-Driven Discovery at Brookhaven National Laboratory can help interpret and make sense of all that information.

Senior researcher Line Pouchard joined BNL’s data team early this year, after a career that included 15 years at Oak Ridge National Laboratory (another Department of Energy facility) and more than two-and-a-half years at Purdue University. “The collaborations at the [DOE] lab are highly effective,” she said. “They have a common purpose and a common structure for the scientist.” Pouchard’s efforts will involve working with metadata, which adds annotations to provide context and a history of a file, and machine learning, which explores large blocks of information for patterns. “As science grows and the facility grows, we are creating more data,” she said.

Scientists can share large quantities of information, passing files through various computer systems. “You may want to know how this data has been created, what the computer applications or codes are that have been used, who developed it and who the authors are,” she said.

Knowing where the information originated can help the researchers determine whether to trust the content and the way it came together, although there are other requirements to ensure that scientists can trust the data. If the metadata and documentation are done properly “this can tell you how you can use it and what kind of applications and programs you can use to continue working with it,” Pouchard said. Working in the Computational Science Initiative, Pouchard will divide her time between responding to requests for assistance and conducting her own research.

“At Purdue, [Pouchard] was quite adept at educating others in understanding metadata, and the growing interest and emphasis on big data in particular,” explained Jean-Pierre Herubel, a professor of library science at Purdue, in an email. Herubel and Pouchard were on the research council committee, and worked together with other members to shepherd their research agendas for the Purdue University library faculty.

Pouchard “has a capacity to participate well with colleagues; regarding national and international venues, she will be a strong participating member,” Herubel continued. “She does well working and integrating with others.”

Pouchard recently joined a team that submitted a proposal in the area of earth science and data preservation. She has also worked on something called the Semantic Web. The idea, which was proposed by Tim Berners-Lee, who invented the World Wide Web, is to allow the use of data items and natural language concepts in machine readable and machine actionable forms. As an example, this could include generating rules for computers that direct the machines to handle the multiple meanings of a word.

One use of the Semantic Web is through searches, which allows people to look for information and data and, once they’re collected, gives them a chance to sort through them. Combined with other technologies, the Semantic Web can allow machines to do the equivalent of searching through enormous troves of haystacks.

“When I first started talking about the Semantic Web, I was at Oak Ridge in the early days,” Pouchard said. Since then, there has been considerable progress, and the work and effort have received more support from scientists.

Pouchard was recently asked to “work with ontologies [a Semantic Web technology] in a proposal,” she said, which suggests they are getting more traction. She is looking forward to collaborating with several scientists at BNL, including Kerstin Kleese van Dam, the director of the Computational Sciences Initiative and the interim director of the Center for Data-Driven Discovery.

Kleese van Dam has “an incredible vision of what is needed in science in order to improve computational science,” said Pouchard, who met the director about a decade ago when van Dam was working in England. Pouchard has an interest in data repositories, which she explored when she worked at Purdue University.

Living temporarily in Wading River, Pouchard bought a home in Rocky Point and hopes to move in soon. Her partner Allan Miller, from Knoxville, Tennessee, owned and managed the Disc Exchange in Knoxville for 26 years. He is starting to help small business owners and non-profit organizations with advertising needs. Pouchard experienced Long Island when she was conducting her Ph.D. research at the City University of New York and took time out to visit a friend who lived in Port Jefferson.

When she’s not working on the computer, Pouchard, who is originally from Normandy, France, enjoys scuba diving, which she has done in the Caribbean, in Hawaii, in Mexico and a host of other places.

When Pouchard was young, she visited with her grandparents during the summer at the beach in Normandy, in the town of Barneville-Carteret. Her parents, and others in the area, lectured their children never to go near or touch metal objects they found in the dunes because unexploded World War II devices were still occasionally found in remote areas. The environment on Long Island, with the marshes, reminds her of her visits years ago.

Pouchard has an M.S. in information science from the University of Tennessee and a Ph.D. in comparative literature from the City University of New York.

As for her work, Pouchard said she is “really interested in the Computational Science Initiative at BNL, which enables researchers to collaborate. Computational science is an integral part of the facilities,” at her new research home.

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From left, Catherine Keener, Bradley Whitford, Allison Williams and Daniel Kaluuya in a scene from ‘Get Out,’ now playing at local theaters. Photo courtesy of Universal

By Daniel Dunaief

Race permeates Jordan Peele’s directorial debut “Get Out” so thoroughly that the film is like a battery, with the white people on one side and the African-Americans on the other. Between them, the electricity of an unusual horror film flows with a shocking effect.

The film starts off with the feel of Sidney Poitier’s masterpiece, “Guess Who’s Coming to Dinner,” with Rose Armitage, played by Allison Williams, bringing her African-American boyfriend Chris Washington (Daniel Kaluuya) home to meet her parents. Even though she says he’s the only African-American man she’s dated, she makes it clear that her parents will be totally cool with her choice and that they’ll support the biracial couple. And yet, the film quickly disposes of any notion of a simple meeting between an African-American man and potentially liberal white America.

Daniel Kaluuya in a hypnotic scene from ‘Get Out’. Photo courtesy of Universal

While Chris meets several African-American people around his girlfriend’s parents’ house, each encounter has a Hitchcock quality, with an eerie disconnect that suggests an unexplained distance.

On the other hand, Rose’s parents and her over-the-top creepy brother Jeremy (Caleb Landry Jones), who wants to fight with Chris at dinner, introduce a terrifying blend of personalities. Catherine Keener is at her creepy best, playing Rose’s hypnotist mother Missy while Bradley Whitford as Rose’s father Dean seems on the verge of supporting and attacking Chris at the same time.

Chris’s best friend Rod (Lil Rel Howery), who spends much of the movie talking to Chris by cell phone, threatens to steal the movie. A TSA agent, Rod provides comic relief, infusing the movie with humorous lines that seem straight out of a paranoid playbook, until he seems like the only one who might have a clue about what could be going on at Rose’s house.

The movie is a true horror film, which means there’s gore and an undercurrent of violence. Each scene, which occurs in upstate New York, could easily have been filmed in Salem, Massachusetts, home of mass hysteria and witch trials.

As the movie progresses, Peele gradually reviews details about the Armitage family, and the people who share the upstate neighborhood, that blur the line between mundane and creepy. When the plot unfolds, all the details about how Chris and the audience got there become clear.

The final 20 minutes of the film blend horror, gore, comedy and social satire. Some of the particular details of the plot reside in the willing suspension of disbelief. Thinking through the specifics detracts from the film’s value as entertainment and social commentary.

The audience in the packed theater reacted to the climactic scenes of “Get Out” in a way that would likely please Peele, as they shared the drama of a gruesome experience that strays from customary plot points to shocking drama and horror.

While the film offers a disturbing take on race, it also tells a dramatic story that drives the viewer through to the chilling end. While it’s not Mark Twain’s “Huckleberry Finn,” it does reveal a captivating, literally at times, story that keeps the audience guessing and at times horrified.

The best element of “Get Out” is the balance between horror and comedy, provided primarily by Rod, whose fast-talking, high-pitched responses to situations he senses aren’t what they seem are endearing and amusing.

While “Get Out” offers the audience plenty to ponder after the movie ends, the action and the plot won’t appeal to everyone. It earns its R rating with violence, horror, foul language and dangerous, suspenseful situations. Still, the movie exposes a fresh look at the races, albeit with novel plot devices, and it seemed to satisfy its viewers with unexpected and jarring visuals, music and close-ups.

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