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From left, Shawn Serbin, Scott Giangrande and Chongai Kuang. Photo from Brookhaven National Laboratory

By Daniel Dunaief

Chongai Kuang is doing considerably more than standing in the middle of various fields throughout the southeast, looking up into the sky, sticking his finger in the air and taking notes on the potential appeal of the area.

Entrusted with finding the right spot for the third ARM Mobile Facility, or AMF3, Kuang, who is an Atmospheric Scientist in the Environmental & Climate Sciences Department at Brookhaven National Laboratory, is gathering considerable amounts of information about different areas in the southeast.

In March of 2023, the ARM3 mobile facility, which has been operating in Oliktok Point, Alaska, will have a new home, where it can gather information about atmospheric convection, land-atmosphere interactions and aerosol processes.

In addition to finding the right location for this facility, Kuang will coordinate with the larger science community to make recommendations to ARM for observations, measurements, instruments and sampling strategies. Observations from these fixed and mobile facilities will improve and inform earth system models.

Kuang would like to find a strategic place for the AMF3 that is “climactically relevant to provide important observations on clouds, aerosols, and land atmosphere interactions that are needed to answer science drivers” important in the southeastern United States, Kuang said. These facilities will help researchers understand how all these atmospheric phenomena interact with solar radiation and the Earth’s surface.

The AMF3 should provide information that informs climate, regional and weather models.

In 2018, the Department of Energy, which funds BNL and 16 other national laboratories, held a mobile facility workshop to determine where to move the AMF3. The group chose the Southeastern United States because it has atmospheric convection, high vegetative-driven emissions and strong coupling of the land surface with the atmosphere. This area also experiences severe weather including tornadoes and hurricanes, which have significant human and socioeconomic impacts, said Kuang.

The most violent weather in the area often “tests the existing infrastructure,” Kuang said. “This deployment can provide critical observations and data sets,” in conjunction with regional operational observational networks.

Atmospheric phenomena as a whole in the southeastern United States includes processes and interactions that span spatial scales ranging from nanometers to hundreds of kilometers and time scales spanning seconds to days.

Kuang’s primary research interests over the past decade has focused on aerosol processes at nanometer scales, as he has studied the kinds of miniature aerosol particles that form the nuclei for cloud formation. These aerosols affect cloud lifetime and spatial distribution.

“Our research is challenged by disparate scales relevant to phenomena we’re trying to characterize, from nanometers to the length scale of convective systems, which are tens of kilometers or even larger,” Kuang said. These scales also present opportunities to study coupled science with convection, aerosol and land-atmosphere interactions.

The ARM observatories around the world provide atmospheric observations of aerosols, clouds, precipitation and radiation to inform and improve Earth system models.

“We are going to leverage as much as we can of the existing networks,” Kuang said. The ARM has a fixed site in Oklahoma, which provides data for the Southern Great Plains Site, or SGP. The Southeastern site, wherever it winds up, will provide a context for large-scale atmospheric phenomena.

The way aerosols, clouds and weather systems form and change presents a challenge and an opportunity for research stations like AMF3, which will seek to connect phenomenon at spatial and time scales that affect where Kuang and his team hope to locate the site.

Kuang is also staying abreast of the latest technology and is also contributing to the development of these capabilities. The technology the AMF3 may use could be developed between now and when the site starts gathering data.

“We have the opportunity now to start thinking about what the next generation measurement capabilities and emerging technologies are that could be operational in 2023,” he said. “We are in conversations with the broader community and with different vendors and with a number of different investigators who are developing new technologies.”

Researchers hope to understand the coupling between the land surface and atmospheric phenomenon. “That will have feedback on radiation and precipitation and the impact on land-surface interactions,” Kuang explained. The current plan is for the new facility to operate for about five years.

While Kuang is focused on the scientific drivers for the site selection, he has also been exploring the dynamic with potential research partners, including universities, seeking ways to add educational partners.

“We have hopes and plans for this kind of deliberate, targeted outreach within the region,” Kuang said. “We want to organize activities like summer school, to provide young scientists with primers and an introduction about how observations are made within their backyard.”

The work he’s trying to do now is “setting the table and preparing the soil for the eventual siting” of the station.

Kuang will measure his success if the new site improves poorly represented model processes.

Once the DOE chooses a site, Kuang plans to develop and execute an initial science plan that uses AMF3 observations. As an ARM instrument mentor, he will also be responsible for a set of instruments that measure aerosol size and concentration.

A resident of Wading River, Kuang started working at BNL in 2009 as a postdoctoral researcher. When he’s not working, he describes cooking as “therapeutic,” as he and his wife, Anyi Hsueh, who is a psychiatric nurse practitioner, have explored Southeastern Asian and Middle Eastern cuisines.

Kuang is working with Associate Ecologist Shawn Serbin and Meteorologist Scott Giangrande, in site selection. The work presents an “important responsibility and our site science team envisions the AMF3 southeastern united States [site] to enable transformational science,” he said.

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From left, Environmental Director David Barnes, Supervisor Ed Wehrheim, Smithtown artist Susan Buroker, Smithtown CSD Art Teacher Timothy Needles talk with students about stormwater runoff. Photo from Town of Smithtown

The Town of Smithtown, in partnership with the Smithtown Central School District, has begun a unique partnership in time for the 2021-2022 school year. Town officials will begin to coordinate hands-on experiential learning opportunities with school science teachers, which focus on real world environmental issues affecting the community. The new programming will focus on the branches of science and how to apply the curriculum to real world issues such as solid waste, invasive species, and water quality.

“We’re absolutely thrilled at the prospect of getting our youth more engaged in critical environmental issues, like protecting the watershed, and Long Island’s impending waste crisis. I can remember back to my school days, always asking ‘When am I ever going to use this in the real world?’ This programming takes studies from the chalk board to the real world, so kids witness the benefits of their hard work unfold before their eyes… I’m especially grateful for the School Districts partnership in what will undoubtedly be a phenomenal learning experience for our youth,” said Supervisor Ed Wehrheim.

Over the Summer, town department experts at Environment and Waterways, and Municipal Services Facility will begin coordinating with school district science teachers to help perfect the programming. Real world topics include the impending solid waste crisis, shellfish and water quality, invasive species census and stormwater runoff. Each class will hear expert presentations from Smithtown’s environmental authorities, in addition to participating in eco-adventure field trips. Students will then learn how to apply STEM related solutions to real world issues.

While still in the planning phase, the new partnership program is slated to launch in the fall.

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Katherine Liang of Paul J. Gelinas Junior High School with the bridge that earned her first place in BNL’s annual Bridge Building Contest

Sometimes the term building bridges takes on a more literal meaning. 

David Liang of Ward Melville High School placed second in the bridge building contest.

The Office of Educational Programs (OEP) at the U.S. Department of Energy’s Brookhaven National Laboratory announced local students who earned the top spots in both the  2021 Bridge Building Contest and 2021 Maglev Competition during an online awards ceremony on April 16.

Each competition, held virtually this year, offers students a hands-on opportunity to apply math, science, and technology principles as they design and build bridges and magnetic levitation cars.

“Conceiving, designing, and building the one-of-a-kind facilities at Brookhaven National Laboratory takes extraordinary vision on the part of our scientists and our engineers to advance our science mission,” said OEP Manager Kenneth White. 

“These two competitions test the design and analytical skill of contestants to create bridges and vehicles to exacting specifications and performance expectations much like our facilities demand of our staff. We hope some of these contestants will be our staff one day to take on another engineering challenge supporting extraordinary discoveries.”

Bridge Building Competition

Victor Prchlik of Ward Melville High School took third place in the bridge building contest.

In the annual Bridge Building Contest, high school students became engineers competing to construct the most efficient model bridge out of lightweight wood. Efficiency is calculated from the bridge’s weight and the weight the bridge can hold before breaking or bending more than one inch. The higher the efficiency, the better the design and construction.

Dedicated Brookhaven Lab staff engineers and technicians tested 40 qualifying structures during a live online event on April 8.

Katherine Liang, a 9th grade student of Paul J. Gelinas Junior High School earned first place with a bridge that weighed 18.7 grams, supported 38.6 pounds. The bridge earned an efficiency of 936.29.

For some students, a trial-and-error process was key to solidifying a design. Liang said she built and tested five bridges by weighing them down with a bucket of sand before submitting her final winning structure.

Second place went to David Liang of Ward Melville High School, whose bridge weighed 19 grams, held 36.4 pounds had an efficiency of 868.98.

Victor Prchlik, also from Ward Melville High School, placed third with a bridge that weighed 23.7 and supported 44.5 pounds with an efficiency of 851.87

Jonathan Chung of Smithtown East High School won this year’s Aesthetic Award.

“The whole process was fun from start to finish,” Chung said. “One of the most challenging parts was getting the glue to stick the wood together. I ended up solving that problem by using a hairdryer to dry it.”

This year’s Bridge Building Contest Aesthetic Award went to Jonathan Chung of Smithtown East High School, pictured with physics teacher Dr. Gillian Winters.

Brookhaven Lab staff tested magnetic levitation cars built by students from Island Trees Middle School and Bay Shore Middle School to see who came up with the fastest design.

MAGLEV Contest

This year’s Maglev Contest for 6th, 7th, and 8th grade students included two main categories for speed and appearance. Brookhaven Lab staff tested 21 maglev cars for speed on a fixed gravity track–13 of which reached the finish line.

Brady Leichtman of Bay Shore Middle School won first place in the speed category.

Second place went to Isabella Rouleau of Bay Shore Middle School. Jesse Bonura of Island Trees Middle School placed third and also won the top spot in the competition’s appearance category with a futuristic blue car. Bay Shore Middle School students Amber Marquez and Andrea Romero, placed second and third in the appearance category, respectively.

Brookhaven Lab staff tested magnetic levitation cars to see who came up with the fastest design. Bonura found that part of the fun was testing and reengineering the maglev’s design. “We’d make it quicker and test it over and over again to make it perfect,” Bonura said.

The maglev contest is based on research by two Brookhaven engineers, the late Gordon Danby and James Powell, who invented and patented maglev technology—the suspension, guidance, and propulsion of vehicles by magnetic forces.

Magnetic properties give the maglev trains their extraordinary capabilities for speed and stability. These same principles—using magnetic forces to move matter — are used in world-class research facilities at Brookhaven Lab, including the Relativistic Heavy Ion Collider (RHIC) and the National Synchrotron Light Source II (NSLS-II) — which are both DOE Office of Science user facilities. Magnetic properties allow the machines to move particles at nearly the speed of light for research purposes.

Brookhaven National Laboratory is supported by the U.S. Department of Energy’s Office of Science. For more information, visit https://energy.gov/science.

Photos courtesy of BNL

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Photo courtesy of the Vanderbilt Museum

The Suffolk County Vanderbilt Museum, 180 Little Neck Road, Centerport will celebrate Astronomy Day on May 15 from  10 a.m. to 2 p.m. Astronomy educators will perform earth science and astronomy demonstrations free for visitors with admission to the museum.

“Although the planetarium theater remains closed, we are happy to be able to share these Earth and space science toolkits with families,” said Dave Bush, director of the Reichert Planetarium. 

“This is yet another opportunity to explore, learn and have fun while visiting the museum. [Saturday’s] event at the Vanderbilt is part of a nationwide celebration of educational programs designed to engage audiences in the awe-inspiring fields of Earth and space science,” he said. 

Enjoy exciting science, take-home materials, and engaging discussion about science and society. Participants will make clouds, create nebula spin art, investigate Moonquakes, explore craters, and much more! These fun activities introduce guests to the ongoing research happening at NASA in the fields of Earth science, planetary science, and astrophysics.

For more information, call 631-854-5579.

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Linda Van Aelst. Photo from CSHL

By Daniel Dunaief

Different people respond to the same level of stress in a variety of ways. For some, a rainy Tuesday that cancels a picnic can be a minor inconvenience that interrupts a plan, while others might find such a disruption almost completely intolerable, developing a feeling of helplessness.

Scientists and clinicians have been working from a variety of perspectives to determine the cause of these different responses to stress.

From left, graduate student Nick Gallo, Linda Van Aelst and Postdoctoral Researcher Minghui Wang. Photo by Shanu George

Cold Spring Harbor Laboratory Professor Linda Van Aelst and a post doctoral researcher in her lab, Minghui Wang, recently published a collaborative work that also included graduate student Nicholas Gallo, postdoctoral researcher Yilin Tai and Professor Bo Li in the journal Neuron that focused on the gene Oligophrenin-1, which is also implicated in intellectual disability.

As with most X-linked diseases, the OPHN1 mutation primarily affects boys, who have a single X chromosome and a Y chromosome. Girls have two X chromosomes, giving them a backup gene to overcome the effect of an X-linked mutation.

In addition to cognitive difficulties, people with a mutation in this gene also develop behavioral challenges, including difficulty responding to stress.

In a mouse model, Wang and Van Aelst showed that the effect of mutations in this gene mirrored the stress response for humans. Additionally, they showed that rescuing the phenotype enabled the mouse to respond more effectively to stress.

“For me and [Wang], it’s very exciting,” Van Aelst said. “We came up with this mouse model” and with ways to counteract the effect of this mutated analogous gene.

As with many other neurological and biological systems, Oligophrenin1 is involved in a balancing act in the brain, creating the right mix of excitation and inhibition.

When oligophrenin1 was removed from the prelimbic region of the medical prefrontal cortex, a specific brain area that influences behavioral responses and emotion, mice expressed depression-like helpless behaviors in response to stress. They then uncovered two brain cell types critical for such behavior: the inhibitory neurons and excitatory pyramidal neurons. The excitatory neurons integrate many signals to determine the activity levels in the medial prefrontal cortex.

The inhibitory neurons, meanwhile, dampen the excitatory signal so they don’t fire too much. Deleting oligophrenin1 leads to a decrease in these inhibitory neurons, which Van Aelst found resulted from elevated activity of a protein called Rho kinase.

“The inhibitor keeps the excitatory neurons in check,” Van Aelst said. “If you have a silencing of the inhibitory neurons, you’re going to have too much excitatory response. We know that contributes to this maladaptive behavior.”

Indeed, Wang and Van Aelst can put their metaphorical finger on the scale, restoring the balance between excitation and inhibition with three different techniques.

The scientists used an inhibitor specific for a RhoA kinase, which mimicked the effect of the missing Oligophrenin1. They also used a drug that had the same effect as oligophrenin1, reducing excess pyramidal neuron activity. A third drug activated interneurons that inhibited pyramidal neurons, which also restored the missing inhibitory signal. All three agents reversed the helpless phenotype completely.

Japanese doctors have used the Rho-kinase inhibitor fasudil to treat cerebral vasospasm. which Van Aelst said does not appear to produce major adverse side effects. It could be a “promising drug for the stress-related behavioral problems” of oligophrenin1 patients, Van Aelst explained in an email. “It has not been described for people with intellectual disabilities and who also suffer from high levels of stress.”

From left, graduate student Nick Gallo, Linda Van Aelst and Postdoctoral Researcher Minghui Wang. Photo by Shanu George

Van Aelst said she has been studying this gene for several years. Initially, she found that it is a regulator of rho proteins and has linked it to a form of intellectual disability. People with a mutation in this gene had a deficit in cognitive function that affected learning and memory.

From other studies, scientists learned that people who had this mutation also had behavioral problems, such as struggling with stressful situations.

People with intellectual difficulties have a range of stressors that include issues related to controlling their environment, such as making decisions about the clothing they wear or the food they eat.

“People underestimate how many [others] with intellectual disabilities suffer with behavioral problems in response to stress,” Van Aelst said. “They are way more exposed to stress than the general population.”

Van Aelst said she and Wang focused on this gene in connection with a stress response.

Van Aelst wanted to study the underlying cellular and molecular mechanism that might link the loss of function of oligophrenin1 with the behavioral response to stress.

At this point, Van Aelst hasn’t yet studied how the mutation in this gene might affect stress hormones, like cortisol, which typically increase when people or mice are experiencing discomfort related to stress. She plans to explore that linkage in future studies.

Van Aelst also plans to look at some other genes that have shown mutations in people who battle depression or other stress-related conditions. She hopes to explore a genetic link in the brain’s circuitry to see if they can “extend the findings.” She would also like to connect with clinicians who are studying depression among the population with intellectual disabilities. Prevalence studies estimate that 10 to 50 percent of individuals with intellectual disability have some level of behavioral problems and/or mood disorders.

Reflecting the reality of the modern world, in which people with various conditions or diseases can sequence the genes of their relatives, Van Aelst said some families have contacted her because their children have mutations in oligophrenin1.

“It’s always a bit tricky,” she said. “I don’t want to advise them yet” without any clinical studies.

A resident of Huntington, Van Aelst arrived at CSHL in the summer of 1993 as a post doctoral researcher in the lab of Michael Wigler. She met Wigler when he was giving a talk in Spain.

After her post doctoral research ended, she had planned to return to her native Belgium, but James Watson, who was then the president of the lab, convinced her to stay.

Outside of work, Van Aelst enjoys hiking, swimming and running. Van Aelst speaks Flemish, which is the same as Dutch, French, English and a “bit of German.” 

She is hopeful that this work may eventually lead to ways to provide a clinical benefit to those people with intellectual disabilities who might be suffering from stress disorders.

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Eszter Boros. Photo from SBU

By Daniel Dunaief

And the winner is … Eszter Boros. An Assistant Professor in the Department of Chemistry at Stony Brook University, Boros recently won the 2021 Stony Brook Discovery Prize, which includes $200,000 in new funding.

The prize, which was established in 2013, is designed to fund higher-risk research for scientists who are no more than five years beyond tenure and promotion at the Associate Professor level or who are on a tenure track as an Assistant Professor. The research might not otherwise receive financial support from agencies like the National Institutes of Health.

Eszter Boros. Photo from SBU

Stony Brook awards the prize to a faculty member who is considered a rising star.

Boros’s proposal suggests using a radioactive light switch to activate anticancer molecules.

The goal behind Boros’s work is to target cancer cells in particular, while avoiding the kinds of painful side effects that typically accompany chemotherapy, which can lead to gastrointestinal discomfort and hair loss, among others.

Boros, who has been at Stony Brook since 2017, was pleased to win the award. “It’s really exciting,” she said. “I’m kind of in disbelief. I thought all the finalists had convincing and exciting projects.”

The four finalists, who included Eric Brouzes in biomedical engineering, Gregory Henkes in geosciences and Kevin Reed in climate modeling, went through three rounds of screening, culminating in a Zoom-based 10-minute presentation in front of four judges.

Bruce Beutler, the Director of the Center for the Genetics of Host Defense at the University of Texas Southwestern Medical Center, served as one of the four judges.

In an email, Beutler wrote that Boros’s work had an “inventive approach” and was “high risk, but potentially high impact.”

Beutler, who won the 2011 Nobel Prize in Physiology and Medicine, suggested that the Discovery Prize may give a start to “a bright person with relatively little track record and a risky but well reasoned proposal.”

The success from such a distinction “does build on itself,” Beutler wrote. “Other scientists hear of such awards or read about them when evaluating future proposals. This may influence decisions about funding, or other awards, in the future.”

Boros said she would use the prize money to fund work from graduate students and post doctoral fellows, who will tackle the complexities of the work she proposed. She will also purchase supplies, including radioactive isotopes. She hopes to stretch the funds for two and a half or three years, depending on the progress she and the members of her lab make with the work.

The idea behind her research is to send radioactive materials that emit a light as they decay and that bind to the cancer cell. The light makes the chemotherapy toxic. Without that light, the chemotherapy would move around the body without damaging non-cancerous cells, reducing the drug’s side effects.

She is thinking of two ways to couple the radioactive light-emitting signal with an activated form of treatment. In the first, the two parts would not be selectively bound together.

The chemotherapy would diffuse into tissues around the body and would only become activated at the target site. This may affect healthy neighbors, but it wouldn’t cause as many side effects as conventional chemotherapy. This could take advantage of already clinically used agents that she can combine.

In the second strategy, she is taking what she described as a “next level” approach, in which she’d make the radioactive agent and the chemotherapy react with one another selectively. Once they saw one another, they would become chemically linked, searching to find and destroy cancer cells. This approach would require new chemistry which her lab would have to develop. 

Beutler suggested that Boros’s work might have other applications, even if cancer might currently be the best one. Some focal but infectious diseases can be treated with antimicrobial therapy which, like cancer directed chemotherapy, is toxic, he explained.

The same principle of using a drug activated by light that is connected to a site-specific marker “could be used in such cases,” he said.

While the potential bench-to-bedside process for any single treatment or approach can seem lengthy and filled with unexpected obstacles, Beutler said he has seen certain cancers that were formerly fatal yield to innovation. “People who are battling cancer can at least be hopeful that their cancer might fall into this category,” he said.

Boros appreciated the opportunity to apply for the award, to bond with her fellow finalists and to benefit from a process that included several sessions with experts at the Alan Alda Center for Communicating Science, who helped prepare her for the presentation in front of the judges. She developed her full proposal during the course of a week, over the December holiday, when her lab had some down time.

In the final stage, she met weekly for an hour with Louisa Johnson, an Improvisation Lecturer at the Alda Center and Radha Ganesan, an Assistant Professor of Medicine, to hone her presentation.

Boros said she appreciated how the Alda Center guides helped her focus on the obsession she and other scientists sometimes have of putting too much text in her slides. “I put text and conclusions on every slide,” she said. Ganesan and Johnson urged her to focus on what she wants to say, while letting go of this urge to clutter her presentation with the same words she planned to use in her presentation. “That was a huge shift in mindset that I had to make,” she said.

As for the work this prize will help fund, Boros said she’ll start with targets she knows based on some research she’s already done with prostate, breast and ovarian cancers.

Boros, who was born and raised in Switzerland, described herself as a chemist at heart.

Outside of work, she enjoys spending time with her husband Labros Meimetis, Assistant Professor of Radiology at the Renaissance School of Medicine at Stony Brook, and their nine-month-old son.

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Above, a humpback whale breaks the surface of the water. Photo from Eleanor Heywood/National Marine Fisheries Service permit no. 21889

By Daniel Dunaief

The waters off the South Shore of Long Island have become a magnet, attracting everything from shipping vessels, recreational boaters, fishermen and women, potential future wind farms, and humpback whales.

While the commercial component of that activity can contribute to the local economy, the whale traffic has drawn the attention of scientists and conservationists. Whales don’t abide by the nautical rules that guide ships through channels and direct traffic along the New York Bight, a region from the southern shore of New Jersey to the east end of Long Island.

Left, Julia Stepanuk with a drone controller. Photo by Kim Lato

Julia Stepanuk, a PhD student at Stony Brook University in the laboratory of Lesley Thorne, Assistant Professor in the School of Marine and Atmospheric Sciences, is focusing her research efforts on monitoring the humpback whale’s use of this habitat.

“This can help us understand how we focus our energy for monitoring and conservation,” she explained in an email. If the whales are traveling, it helps to know where to minimize human impact.

Ultimately, the work Stepanuk, who also earned her Master’s degree at Stony Brook in 2017, does provides ecological context for how whales use the waters around New York and how old the whales are that are feeding in this area.

In her dissertation, Stepanuk is “looking at the biological and ecological drivers, the motivators of where the whales are, when they’re there, specifically, from the lens of how human activity might be putting whales at risk of injury or mortality.”

Each summer, whales typically arrive in the area around May and stay through the end of October.

When she ventures out on the water, Stepanuk uses drones to gather information about a whale’s length and width, which indicates the approximate age and health of each individual. Since 2018, she has been gathering information to monitor activity in the area to track it over time.

With the research and data collected, she hopes to help understand the ecology of these whales, which will inform future policy decisions to manage risk.

Stepanuk’s humpback whale work is part of a 10-year monitoring study funded by the New York State Department of Environmental Conservation, which includes four principal investigators at the School of Marine and Atmospheric Sciences. The study looks at carbonate chemistry, physical oceanography, fish distribution, and top predator abundance, distribution and body condition, Thorne explained.

“My lab is leading the seabird and marine mammal aspect of this project,” said Thorne.

The grid over the whale demonstrates how members of Thorne’s lab measure the size of the whale from drone images. Photo by Julia Stepanuk

By documenting the ecological ranges of whales of different ages, Stepanuk may provide insight into the age groups that are most at risk. Many of the humpback whales that travel closer to shore are juveniles, measuring below about 38 feet.

Stepanuk has seen many of these whales, either directly or from the drones she flies overhead. She has also gathered information from events in which whales die after boats hit them.

Mortality events off the east coast have been increasing since 2016 as numerous whales have washed up along the coast. About half of the humpbacks in these mortality events have evidence of human interaction, either ship strike or entanglement, Stepanuk said.

“There have been many more strandings than usual of humpback whales along the east coast” in the last five years, Thorne explained.

Humpback whales likely have appeared in larger numbers in New York waterways due both to the return of menhaden in nearshore waters, which comes from changes in the management of this fish stock and from environmental management more broadly, and from an overall increase in the humpback whale population after 40 years of protection, Thorne suggested.

Ultimately, Stepanuk said she hopes to use the scientific inquiry she pursued during her PhD to help “bridge the gap between academic, policymakers, conservationists, interested parties and the public.” 

A part of Stony Brook’s STRIDE program, for science training and research to inform decisions, Stepanuk received training in science communication, how to present data in a visual and accessible way, and how to provide science-based information to policymakers.

For Thorne, this study and the analysis of the vessel strikes on humpback whales could be helpful for understanding similar dynamics with other cetaceans.

Julia Stepanuk and Matt Fuirst, a previous master’s student in Lesley Thorne’s lab, release a drone. Photo by Rachel Herman

“Understanding links between large whales and vessel traffic could provide important information for other studies, and could provide methods that would be useful for studies of other species,” said Thorne.

Stepanuk offers some basic advice for people on a boat in the New York Bight and elsewhere. She suggests driving more slowly if visibility is limited, as people would in a car in foggy weather. She also urges people to pay close attention to the water. Ripples near the surface could indicate a school of fish, which might attract whales.

“Slow down if you see dolphins, big fish schools and ripples,” she said. “There’s always a chance there could be a whale.”

If people see a whale, they shouldn’t turn off their engines: they should keep the engine in neutral and not approach the whale head on or cut them off. For most species, people can’t get closer than 300 feet. For North Atlantic right whales, which are critically endangered, the distance is 1,500 feet.

She suggests people “know the cues” and remember that whales are eagerly feeding.

Stepanuk has been close enough to these marine mammals to smell their pungent, oily fish breath and, when they exhale, to receive a residue of oil around her camera lens or sunglasses. She can “loosely get an idea of what they’re feeding on in terms of how bad their breath is.”

When she was younger, Stepanuk, who saw her first whale at the age of eight, worked on a whale watching boat for six years in the Gulf of Maine. An adult female would sometimes leave her calf near the whale watching boat while she went off to hunt for food. The calf stayed near the boat for about 45 minutes. When the mother returned, she’d slap the water and the calf would race to her side.

“Experiences like that stuck with me and keep me excited about the work we do,” Stepanuk said.

Video: Humpback whale lunge feeding off the south shore of Long Island

 

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From left, atmospheric scientists Andrew Vogelmann, Edward Luke, Fan Yang, and Pavlos Kollias explored the origins of secondary ice — and snow. Photo from BNL

By Daniel Dunaief

Clouds are as confounding, challenging and riveting to researchers as they are magnificent, inviting and mood setting for artists and film makers.

A team of researchers at Brookhaven National Laboratory and Stony Brook University recently solved one of the many mysteries hovering overhead.

Some specific types of clouds, called mixed-phase clouds, produce considerably more ice particles than expected. For those clouds, it is as if someone took an empty field, put down enough seeds for a thin covering of grass and returned months later to find a fully green field.

Ed Luke, Atmospheric Scientist in the Environmental Sciences Department at Brookhaven National Laboratory, Andy Vogelmann, Atmospheric Scientist and Technical Co-manager of the BNL Cloud Processes Group, Fan Yang, a scientist at BNL, and Pavlos Kollias, a professor at Stony Brook University and Atmospheric Scientist at BNL, recently published a study of those clouds in the journal Proceedings of the National Academy of Sciences.

“There are times when the research aircraft found far more ice particles in the clouds than can be explained by the number of ice nucleating particles,” Vogelmann wrote in an email. “Our paper examines two common mechanisms by which the concentrations of ice particles can substantially increase and, for the first time, provides observational evidence quantifying that one is more common” over a polar site.

With a collection of theoretical, modeling and data collecting fire power, the team amassed over six years worth of data from millimeter-wavelength Doppler radar at the Department of Energy’s Atmospheric Radiation Measurement facility in the town of Utqiagvik, which was previously called Barrow, in the state of Alaska.

The researchers developed software to sort through the particles in the clouds, grouping them by size and shape and matching them with the data from weather balloons that went up at the same time. They studied the number of secondary ice needles produced under various conditions.

The scientists took about 100 million data points and had to trim them down to find the right conditions. “We culled the data set by many dimensions to get the ones that are right to capture the process,” Luke explained.

The dataset required supercooled conditions, in which liquid droplets at sub-freezing temperatures came in contact with a solid particle, in this case ice, that initiated the freezing process.

Indeed, shattering ice particles become the nuclei for additional ice, becoming the equivalent of the venture capitalist’s hoped for investment that produces returns that build on themselves.

“When an ice particle hits one of those drizzle drops, it triggers freezing, which first forms a solid ice shell around the drop,” Yang explained in a press release. “Then, as the freezing moves inward, the pressure starts to build because water expands as it freezes. That pressure causes the drizzle drop to shatter, generating more ice particles.”

Luke described Yang as the “theory wizard on the ice processes and nucleation” and appreciated the opportunity to solve the mechanism involved in this challenging problem.

“It’s like doing detective work,” said Luke. The pictures were general in the beginning and became more detailed as the group focused and continued to test them.

Cloud processes are the biggest cause for differences in future predictions of climate models, Vogelmann explained. After clouds release their precipitation, they can dissipate. Without clouds, the sunlight reaches the surface, where it is absorbed, particularly in darker surfaces like the ocean. This absorption causes surface heating that can affect the local environment.

Energy obtained from microscopic or submicroscopic processes, such as the absorption of sunlight at the molecular level or the energy released or removed through the phase changes of water during condensation, evaporation or freezing, drive the climate.

“While something at microscales (or less) might not sound important, they ultimately power the heat engine that drives our climate,” said Vogelmann.

To gather and analyze data, the group had to modify some processes to measure particles of the size that were relevant to their hypothesis and, ultimately, to the process.

“We had to overcome a very serious limitation of radar,” Kollias said. They “started developing a new measurement strategy.”

When the cost of collecting large amounts of data came down, this study, which involved collecting 500 times more data points than previous, conventional measures, became feasible.

Luke “came up with a very bright, interesting technique of how to quantitatively figure out, not if these particles are there or how often, but how many,” Kollias said.

Luke found a way to separate noise from signal and come up with aggregated statistics.

Kollias said everyone in the group played a role at different times. He and Luke worked on measuring the microphysical properties of clouds and snow. Yang, who joined over two and a half years ago and was most recently a post doctoral research associate, provided a talented theoretical underpinning, while Vogelmann helped refine the study and methodology and helped write up the ideas.

Kollias said the process begins with a liquid at temperatures somewhere between 0 and 10 degrees below zero Celsius. As soon as that liquid touches ice, it explodes, making it a hundred times more efficient at removing liquid from the cloud.

Kollias described the work as a “breakthrough” because it provided real measurements, which they can use to test their hypotheses.

In the next few months, Kollias said the group would make sure the climate modeling community sees this work.

Luke was hoping the collaboration would lead to an equation that provided the volume of secondary ice particles based on specific parameters, like temperature and humidity.

From the data they collected, “you can almost see the equation,” Luke said. “We wanted to publish the equation. That’s on the to-do list. If we had such an equation, a modeler could plug that right in.”

Even though they don’t yet have an equation, Luke said that explicit descriptions of the dataset, in the form of probability density functions, are of value to the modeling community.

The group would like to see how broadly this phenomenon occurs throughout the world. According to Kollias, this work is the “first step” and the team is working on expanding the technique to at least three more sites.

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Dr. Kenneth Kaushansky
Stony Brook, NY; Stony Brook University: School of Medicine 2018 Convocation Photo by Arthur Fredericks
Stony Brook, NY; Stony Brook University Medical Center: The White Coat Ceremony in the Student Activities Center. (8/14/2016)
Stony Brook, NY; Stony Brook University MART & Children's Hospital Pavilion: MART ribbon cutting, November 1, 2018. Left to right: New York State Assemblyman Steve Englebright; SUNY Trustee and Stony Brook Foundation board member Cary Staller; Stony Brook University President Samuel L. Stanley Jr., MD; New York State Senator Kenneth P. LaValle; SUNY Chancellor Kristina Johnson; Jim and Marilyn Simons; New York State Senate Majority Leader John Flanagan; Kevin Law, President of the Long Island Association and Chair of the Stony Brook Council; Kenneth Kaushansky, MD, Senior Vice President for Health Sciences and Dean of the School of Medicine; Director of the Stony Brook University Cancer Center Yusuf Hannun, MD; representing Governor Andrew Cuomo, Marta Santiago-Jones, Consultant Nurse Hospital Services Administrator at the New York State Department of Health.
Stony Brook, NY; Stony Brook University Medical Center: Donors David and Cynthia Lippe and Dean, School of Medicine and Senior Vice President of Health Sciences Ken Kaushansky outside of the garden area of the MART/Hospital Pavilion
Stony Brook, NY; Stony Brook University Hospital: Stony Brook Medicine rolled out new Mobile Stroke Units on March 18, 2019, to treat people who are having a stroke. Left to right: Kimberly Noel, MD, Director, Telehealth, Stony Brook Medicine, Michael Guido III, MD, Neurologist, Director, Stony Brook Neurology Stroke Program, Ken Kaushansky, MD, Dean, Renaissance School of Medicine at Stony Brook University, David Fiorella, MD, PhD, Neurointerventionalist, Director, Stony Brook Cerebrovascular Center, Trevor Marshall, MD and Eric Niegelberg, Associate Director, Operations, Emergency Services and Internal Medicine
Stony Brook, NY; Stony Brook University: Chancellor Jim Malatras and Stony Brook University President McInnis Announce Partnership with SUNY Upstate Medical University to Launch Pooled Surveillance Testing for COVID-19. Stony Brook to Test 5200 Students Each Week. Testing Expansion Follows FDA Approval of Groundbreaking Saliva Swab Test Developed at Upstate Medical University

By Daniel Dunaief

Like so many others, Ken Kaushansky had to alter his plans when the pandemic hit last March. Kaushansky had expected to retire after over 10 years as Dean of the Renaissance School of Medicine at Stony Brook University and the Senior Vice President of Health Sciences, but the public health needs of the moment, particularly on Long Island which became an early epicenter for the disease, demanded his attention.

“Now that COVID hopefully is coming under control, it seems more logical” to retire this year, Kaushansky said in a wide-ranging interview about the pandemic, his career, and the medical school. In January, he stepped down as the dean, while he plans to retire as Senior Vice President of Health Sciences at the end of June.

Views on the Pandemic

Dr. Kenneth Kaushansky

Looking back at the immediate challenges in the first few months, Kaushansky said SBU did “extremely well” in caring for patients who were battling COVID-19 and was gratified by the school’s effort to catalog and understand the disease. “I’m very proud that we’ve been able to study this infection on all sorts of levels and make a real impact that has helped others,” he said.

Early on, as the medical team at Stony Brook met, Kaushansky urged the hospital to study COVID “to the hilt” and to “extract every little bit of data we can. We must keep all that data on all these patients.”

Indeed, Stony Brook has created a database that continues to grow of close to 10,000 people, which includes 3,000 inpatients, 4,000 who weren’t sick enough for hospital admission, and around 3,000 who thought they had the disease, but had other illnesses. “We’ve learned a ton from that, and it’s not just learning for learning’s sake,” Kaushansky said. The demand for the use of the database is so high that a steering committee is reviewing proposals. 

Stony Brook had heard from doctors in Italy that COVID patients were having problems with blood clotting. This symptom was particularly meaningful to Kaushansky, who is a hematologist.

SBU studied the symptoms and “did a trial to see if aggressive anticoagulants would produce better outcomes” than the standard of care at the time, he said. “Our [intensive care unit] patients who were on this more aggressive anticoagulation protocols had half the mortality” of other patients, so the hospital “quickly adopted all of our care” to the more effective approach.

The hospital preemptively used biomarkers to determine who should and should not get aggressive anticoagulation. A subsequent study using the database confirmed the school’s early conclusion. Stony Brook published over 150 papers on the structure of the virus, clinical observations, sociological interventions, and a host of other areas, according to Kaushansky.

Carol Gomes, Chief Executive Officer of Stony Brook University Hospital, appreciated Kaushansky’s hands on approach, which included participating in daily calls as part of the hospital incident command center.

She likened Kaushansky to an orchestra leader, coordinating the research and patient care, making sure there was “no duplication of effort.”

Kaushansky believes federal research funding agencies and policy makers will recognize the importance of gathering information about this pandemic to treat future patients who might battle against variants and to provide a playbook for other health threats. “We really do need to prepare for the next one” as this is the third and deadliest of three coronaviruses, including SARS and MERS, he said.

Vaccines

As for vaccines, Kaushansky said Stony Brook was making it as “convenient as we can” to get a vaccination for health care workers. As of about a month ago, over 80 percent of Stony Brook’s health care workers had been vaccinated.

The black and brown communities have benefited from seeing leaders and role models receiving the vaccine. “This is beginning to erode the mistrust,” said Kaushansky, which developed as a byproduct of the infamous Tuskegee experiment, in which black men with syphilis did not receive penicillin despite its availability as an effective treatment.

Kaushansky added that a concern he’s heard from a range of people is that the vaccine was developed too quickly and that the side effects could be problematic. He cited the simultaneous steps doctors, pharmaceutical companies and others took to accelerate a process that didn’t leave out any of those steps.

Kaushansky participates in a group email interaction with prominent European hematologists. Looking at the data for the Astrazeneca vaccine, these researchers have calculated that anywhere from one in 500,000 to one in a million have developed blood clots.

“Not a single person on this mass email believes that they should stop the Astrazeneca vaccines for that kind of incident,” he said.

What He Helped Build

Kaushansky has been such a supporter of expanding the facilities and expertise at Stony Brook that he said the campus developed a joke about him.

“What’s the dean’s favorite bird?” he asked. “A crane.”

Fixtures on the campus for years, those cranes — the construction vehicles, not the birds — have changed the university, adding new teaching, research and clinical space on the campus.

That includes the Medical and Research Translational building and Bed Tower, which started in 2013 and opened in 2018, and the Hospital Pavilion, which has an additional 150 beds. Those extra beds were especially important a year after the pavilion opened, providing much-needed space for patients battling against COVID.

Gomes appreciated what Kaushansky built physically, as well as the interactive collaborations among different parts of the university. “An active collaboration and communication between researchers, clinicians and academics is a very different model” from the typical separation among those groups, she said. The work “reaped great rewards on the front end with the ability to collaborate to bring new ideas forward.”

As for the type of care patients received at Stony Brook, Kaushansky recalled a discussion over six years ago about central line infections. The data came from a 12 month period, starting six months prior to the meeting and going back to 18 months earlier.

“How are we going to know why all those central line infections occurred by looking at data” from so much earlier, Kaushansky recalled asking. The hospital created real time dashboards, which is an effort that has “paid huge dividends.”

Kaushansky cited the hospitals’ top 100 health grade for three years running. These grades assess whether patients survive a procedure, have complications or need to be readmitted.

“You’re going to get the best care possible when you come to Stony Brook,” Kaushansky said, as the top 100 rating puts Stony Brook in the top 2 percent of hospitals in the country.

Apart from the buildings Kaushansky helped develop, he’s proud of the program he helped build for medical school students.

About six years ago, Stony Brook instituted a new medical school curriculum that had translational pillars. The school starts students in the clinical realm considerably earlier than the classic program that involves two years of basic studies, followed by two years of clinical work.

Stony Brook provides basic science, followed by earlier exposure to the clinic, with a return to basic science after that

“It’s much more effective if you teach the basic science after the student has witnessed the clinical manifestation,” Kaushansky said. These approaches are part of translational pillars in areas such as cancer, physiology and infectious diseases.

As for what he’ll miss after he leaves, Kaushansky particularly appreciated the opportunity to speak with students. He used to hold a monthly breakfast with four or five students, where he learned about each student, their career goals and their medical journey.

A former colleague at the University of California at San Diego, John Carethers, who is the Chair in the Department of Internal Medicine at the University of Michigan, visited Kaushansky as a speaker twice at Stony Brook.

Carethers saw “first hand the wonderful impact he had on students — knowing their names, and providing wonderful advice,” he wrote in an email.

The Next Steps

For a decade, Kaushansky said he wanted to create a course about the future of medicine.

“There are a lot of great innovations in medicine that are fascinating from a scientific and clinical perspective,” Kaushansky said.

He will work on a course for use at Stony Brook in the main campus, the medical campus and for whichever program is interested in sharing these innovative medical and scientific steps in medicine.

He also plans to continue to be the lead editor of the primary textbook in hematology, called Williams Hematology. The textbook has gone through 10 editions.

Kaushansky and his wife Lauren, who is an author and education professor at Stony Brook, aren’t likely to remain on Long Island in the longer term. The couple has a getaway home in Santa Fe and may go there.

Kaushansky’s hobbies include wood working and running. He made a sofa when he was an undergraduate at UCLA, while his second significant work was a 16-foot sailboat he made as a second-year resident. He estimates he has made 40 pieces of furniture.

Kaushansky runs four miles a day four to six times a week. In 1990, he ran the Seattle Marathon which was the Goodwill Games Marathon, finishing in a time of around three hours and twenty-five minutes.

Culturally, Kaushansky hopes the school continues to embrace his focus on generosity.

“You’ve got to be generous with your time,” he said. 

“No more can you say that you are too busy to talk. You have to be of a personality that takes pride and that gets the endorphins going from seeing the people you have brought, the people you have entrusted in leadership roles, succeed.”

Photos courtesy of Stony Brook University

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F. William Studier

By Daniel Dunaief

People around the world are lining up, and in some cases traveling great distances, to get vaccinations to COVID-19 that will provide them with immune protection from the virus.

An important step in the vaccinations from Pfizer-BioNTech and Moderna, the two messenger RNA vaccinations, originated with basic research at Brookhaven National Laboratory in the 1980’s, close to 40 years before the pandemic infected millions and killed close to three million people.

At the national laboratory, scientists including F. William Studier, Alan Rosenberg, and the late John Dunn, among others, worked on another virus, called the T7 bacteriophage, which infects bacteria. T7 effectively corrupts a bacteria’s genetic machinery, turning it into a machine that makes copies of itself.

From top graphic, the T7 virus uses RNA polymerase and a promoter to start a process inside a bacteria that makes copies of itself; researchers use copies of the promoter and the polymerase to insert genes that code for a specific protein; the mRNAs are injected into our arms where human ribosomes make COVID-19 spike proteins. Those spike proteins train the attack dog cells of our immune system to recognize the virus if it attempts to invade.

Back in the 1980’s, Studier and Dunn in BNL’s Biology Department were trying to do something no one else had accomplished: they wanted to clone the T7 RNA polymerase. The use of this genetic region, along with a promoter that starts the process of transcription, enabled scientists to mimic the effect of the virus, directing a cell to make copies of genetic sequences or proteins.

The BNL researchers perfected that process amid a time when numerous labs were trying to accomplish the same molecular biological feat.

“Although there were several labs that were trying to clone the T7 RNA polymerase, we understood what made its cloning difficult,” said Alan Rosenberg, who retired as a senior scientist at BNL in 1996. The patented technology “became the general tool that molecular biologists use to produce the RNA and proteins they want to study.”

The scientists who worked on the process, as well as researchers who currently work at BNL, are pleased that this type of effort, which involves a desire for general knowledge and understanding before policy makers and funders are aware of all the implications and benefits, led to such life-saving vaccinations.

“This is an excellent example of the value of basic science in that the practical applications were quite unanticipated,” John Shanklin, Chair of BNL’s Biology Department, wrote in an email. 

“The goal of the work Studier and his team did was to understand fundamental biological principles using a virus that infects bacteria. Once discovered, those principles led to a transformation of how biochemists and biomedical researchers around the world produce and analyze proteins in addition to providing a foundational technology that allowed the rapid development of mRNA vaccines,” he wrote.

Shanklin described Studier, who recruited him to join BNL 30 years ago from Michigan, as a mentor to numerous researchers, including himself. Shanklin credits Studier for helping him develop his career and is pleased that Studier is getting credit for this seminal work.

“I am tremendously proud that the basic research done in the Biology Department has been instrumental in accelerating the production of a vaccine with the potential to save millions of lives worldwide,” Shanklin wrote. “I couldn’t be happier for [Studier] and his team being recognized for their tremendous basic science efforts.”

Steve Binkley, Acting Director of the Department of Energy’s Office of Science, acknowledged the importance of the earlier work.

“The fact that scientific knowledge and tools developed decades ago are now being used to produce today’s lifesaving mRNA vaccines for COVID-19 is a great example of how the Department of Energy’s long-term investments in fundamental research at our National Laboratories can improve American lives today and into the future,” Binkley said in a statement.

Studier explained that his interests were more modest when he started studying this particular virus, which infects the bacteria E. coli.

“T7 was not a well-studied bacteriophage when I came to Brookhaven in 1964,” Studier, who is a senior biophysicist Emeritus, said in a statement. “I was using it to study properties of DNA and decided also to study its molecular genetics and physiology. My goal, of course, was to understand as much as possible about T7 and how it works.”

In an email, Studier said he did not realize the connection between his work and the vaccinations until Venki Ramakrishnan, a Nobel-Prize winning structural biologists from the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, told him.

“I am pleased that our work with T7 is relevant for fighting this world-wide pandemic,” Studier wrote. “History shows that some of the most useful discoveries come from basic research that could not have been predicted.”

While BNL is one of 17 Department of Energy facilities, it has conducted scientific research in numerous fields.

Several translational achievements originated at BNL, Shanklin wrote, including the thalium stress test for evaluating heart function, the development of Fluoro Deoxy Glucose for Positron Emission Tomography and the first chemical synthesis for human insulin, which allowed human insulin to replace animal insulin.

As for the effort that led to the T7 discoveries, Studier worked with Parichehre Davanloo, who was a postdoctoral fellow, Rosenberg, Dunn and Barbara Moffatt, who was a graduate student.

Rosenberg appreciated the multi-national background of the researchers who came together to conduct this research, as Moffatt is Canadian and Davanloo is Iranian.

Rosenberg added that while the group had “an inkling” of the potential usefulness of the processes they were perfecting, they couldn’t anticipate its value over the next 40 years and, in particular, its current contribution.

“Nobody really understood or thought just how widely spread its use would be,” Rosenberg said. “We certainly had no idea it would be an important element in the technology” that would lead to the Pfizer and Moderna vaccinations.

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