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Power of 3

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By Daniel Dunaief

A problematic atmospheric greenhouse gases, methane comes from natural gas, agriculture, and swamps. 

John Mak

Recently, John E. Mak, a Professor in the School of Marine and Atmospheric Sciences at Stony Brook University worked with an international group of scientists to demonstrate a process that removes methane from the atmosphere.

A mixture of dust from the Sahara and sea spray reacts with methane to form carbon monoxide and a small amount of hydrochloric acid.

In a recent paper published in the prestigious journal Proceedings of the National Academy of Sciences, Mak, corresponding author Matthew Johnson, who is a Professor in the Department of Chemistry at the University of Copenhagen, and others showed how a novel process removes 5 percent, plus or minus 2 or 3 percent, of the methane from the atmosphere in specific areas.

“What we are showing is that some methane in the middle of the tropical Atlantic Ocean region may be removed” through this process, Mak said from the Gordon Research Conference on Atmospheric Chemistry in Sunday River, Maine.

The research validates a mechanism Mak had proposed in the late 1990’s, when he conducted studies funded by the National Science Foundation in Barbados. “When I first made the observations, I proposed that what we were seeing was a chlorine mediated removal of methane,” Mak explained.

At that time, he didn’t have the ability to make those measurements. The technology, however, has evolved over the years and researchers can now measure chlorine radical precursors such as Cl2 and other chlorine compounds.

Indeed, Maarten van Herpen, first author on the study and a member of Acacia Impact Innovation, approached Mak with a new theory and a new mechanism that he thought could explain Mak’s results from decades earlier.

“They were excited to hear that no one had solved the problem,” said Mak.

By working together through this international team, the group was able to take new measurements and utilize advances in their understanding of atmospheric processes.

‘New, but old’

Mak had conducted his studies towards the beginning of his time at Stony Brook University in the late 1990’s as a part of one of his first federally funded projects. 

“It’s a little unusual for people to make use of observations so far in the past,” said Mak. “It opens up a new, but old avenue of research.”

Mak, who is conducting studies in other areas including a recent project in New York to investigate air quality and air chemistry mechanisms specific to the greater New York City region, believes the research on this PNAS paper takes him almost full circle back to this earlier work.

“There’s a feeling of satisfaction that good measurements are useful for a longer period of time,” he said. 

In this study, Mak helped interpret some of the data his collaborators generated.

The reactions

The process of removing methane starts with sea spray, which is aerosolized by bubbles bursting at the contact point between the ocean and the air. The chlorine comes from that sea spray, while iron comes from the continental crust.

Saharan dust can traverse the globe, but scientists are not sure of the spatial extent of this process. They believe it could be throughout the tropical Atlantic, but it could be in other dust laden ocean regions in the Indian and Pacific Oceans as well.

That process creates what is described as a reactive chlorine species, which is on the hunt for a positively charged particle, such as one of the four hydrogen atoms attached to carbon in methane.

Once the chlorine removes a hydrogen, it creates a methyl group, or CH3, and an incredibly small amount of hydrochloric acid, or HCl, at about one part per quadrillion.

The acid, in fact, is so low that it doesn’t cause any acidification of the oceans. Ocean acidification primarily comes from the absorption of carbon dioxide gas, which reacts with seawater and eventually increases the amount of positively charged hydrogen atoms, decreasing the ocean’s pH.

Meanwhile in the atmosphere, the remaining methyl group is oxidized to carbon monoxide, which eventually becomes carbon dioxide. That is also a greenhouse gas, but is not as potent at trapping heat in the atmosphere as methane.

Now that the group has explored this process, Mak explained that the next step will involve proposing a field campaign in the tropical Atlantic with state of the art instruments.

Mak believes the journal PNAS likely found the subject matter compelling on a broader scale, particularly because this process affects weather and climate.

Outside work

When he’s not working, Mak enjoys boating and fishing. A native of Southern California, Mak is a commercial pilot, who also does some flying as a part of his research studies.

As for climate change, Mak suggested that the weather extremes from this year, which include record high temperatures in the ocean near the Florida Keys and high temperatures in areas in Arizona, are a part of a pattern that will continue.

“What we have been and will continue to observe are changes to the broad equilibrium of energy balance of the Earth ocean atmosphere system,” he explained. “There’s a lot of inertia in the system. But when you change the input by changing the forcing, you upset that equilibrium.” That, he explained, could alter the weather, which is generated as a response to differences in energy from one place to another.

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Maurizio Del Poeta. File photo from SBU

By Daniel Dunaief

Maurizio Del Poeta is taking another approach to battling fungal infections that can be deadly, particularly for people who are immunocompromised.

Maurizio Del Poeta. Photo from SBU

A Distinguished Professor at Stony Brook University in the Department of Microbiology and Immunology at the Renaissance School of Medicine at Stony Brook University, Del Poeta has made progress in animal models of various fungal infections in working on treatments and vaccines.

After receiving an additional $3.8 million from the National Institutes of Health for five years, Del Poeta is expanding on some findings that may lead to a greater understanding of the mechanism that makes some fungal infections problematic.

The Stony Brook Distinguished Professor is studying “what makes people susceptible to fungal infections,” he said. “It’s something I’m really passionate about.”

Del Poeta explained that researchers and medical professionals often focus on the people who get sick. Understanding those people who are not developing an infection or battling against a fungus can provide insights into ways to understand what makes one population vulnerable or susceptible and another more resistant.

Expanding such an approach outside the realm of fungal infections could also provide key insights for a range of infections in the future.

Indeed, the awareness of specific signals for other infections could help protect specific populations, beyond those who had general categories like underlying medical conditions, who might be more vulnerable amid any kind of outbreak.

“It’s possible that the study we are doing now with fungi could stimulate interest” in other areas of infectious disease, Del Poeta said.

He suggested that this was “pioneering work” in terms of fungal infections. At this point, his lab has produced “strong preliminary data.”

An important drug treatment side effect as a signal

This investigation arises out of work Del Poeta had done to understand why some people with multiple sclerosis who took a specific drug, called fingolimid, developed fungal infections during their drug treatment.

Del Poeta observed that the drug inhibits a type of immunity that involves the movement of lymphocytes from organs into the bloodstream.

Fingolimid mimics a natural lipid, called a sphingolipid. Del Poeta showed that this sphingolipid is important to contain the fungus Cryptococcus neoformans in the lung. When its level decreases, the fungus can move from the lung to the brain.

Indeed, Fingolimid mimics sphingosin-1-phosphate (S1P) and binds to several S1P receptors.

Del Poeta believes that the pathway between S1P and its receptor regulates the immunity against Cryptococcus. Blocking a specific receptor is detrimental for the host and may lead to reactivation of the fungus.

Putting a team together

Nathália Fidelis Vieira de Sá. Photo by Futura Convites studio

Del Poeta has been working with Iwao Ojima, a Distinguished Professor and the Director of the Institute of Chemical Biology and Drug Discovery in the Department of Chemistry at Stony Brook, to create compounds that energize, instead of block, the target of fingolimid.

Del Poeta has recruited two scientists to join his lab in this effort, each of whom has educational experience in nursing.

Nathália Fidelis Vieira de Sá, who is a registered nurse at the Federal University of Minas Gerais and a chemistry technician at Funec- Contagem City, will join the lab as a technician in the second week of September.

Fidelis Vieira de Sá, who currently lives in her native Brazil, is an “expert on collecting and analyzing organs for mice,” explained Del Poeta in an email.

For her part, Fidelis Vieira de Sá is thrilled to join Del Poeta’s lab at Stony Brook. “I’m very excited,” she said in an email. She is eager to get started because the research is “of such great relevance to public health” and is occurring at such a “renowned institution.”

Fidelis Vieira de Sá believes this is a public health issue that could have a positive impact on people with immunodeficiency conditions who need effective treatment so they live a better, longer life. When she was a peritoneal dialysis nurse, she had a few patients who had fungal infections.

“This is very serious and challenging, detection is difficult, and the life expectancy of these patients drops dramatically with each episode of infection,” she explained. 

Fidelis Vieira de Sá, who has never lived outside Brazil, is eager for new experiences, including visiting Central Park, the Statue of Liberty, Times Square, and the One World Trade Center Memorial.

As for the work, she hopes that, in the near future, Del Poeta will “be able to explain this mechanism deeply and to develop new drugs that will act on this receptor.”

Dr. Marinaldo Pacífico Cavalcanti Neto

Dr. Marinaldo Pacífico Cavalcanti Neto, who is an Assistant Professor at Federal University of Rio de Janeiro, will be arriving at Stony Brook University on August 6. Dr. Neto earned his bachelor of science in nursing and has a PhD in biochemistry from the Medical School of Ribeirão Preto at the University of São Paulo.

Del Poeta described Dr. Neto as an “expert on animal handling and genotyping,”

Dr. Neto recognizes the burden of fungal infections around the world and hoped to work with someone with Del Poeta’s credentials and experience in immunology and infection.

Understanding how cells eliminate infection, how cells might have a lower capacity to control an infection, and looking for how cells respond to treatments such as fingolimid could be a “great strategy to understand why these are so susceptible,” he said.

While Dr. Neto’s background is in immunology, he hopes to learn more about molecular biology.

Unlike Fidelis Vieira de Sá, Dr. Neto, who will live in Centereach, has worked previously in the United States. He has experience at the National Institutes of Health and at the University of California at San Diego and has been attending Del Poeta’s lab meetings from a distance for about a month.

Dr. Neto, whose interest in science increased while he watched the TV show Beakman’s World while he was growing up, is eager to work in an area where he can apply his research.

He appreciates that his work may one day “be used in the generation of protocols in a clinic.

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From left, graduate students Thomas Reilly and Hanxiao Wu with Weisen Shen. Wu and Shen are holding two of the 183 sensors they will place in the Antarctic. The team is shipping the sensors in the black container, which will travel through Port Hueneme, California and New Zealand before reaching the South Pole. Photo by Maeve McCarthy/ Angela Gruo

By Daniel Dunaief

While it’s easy to see and study materials in valleys or on the tops of bare mountains, it’s much more difficult to know what’s beneath 2.7 kilometers of ice. Turns out, that kind of question is much more than academic or hypothetical.

At the South Pole, glaciers sit on top of land that never sees the light of day, but that is relevant for the future of cities like Manhattan and Boston.

The solid land beneath glaciers has a strong effect on the movement of the ice sheet, which can impact the melting rate of the ice and sea level change.

Weisen Shen, Assistant Professor in the Department of Geosciences at Stony Brook University, recently received over $625,000 over the course of five years from the National Science Foundation to study the unexplored land beneath the East Antarctic Ice Sheet at the South Pole.

The subglacial water and hydrosystems, together with geology such as sediment or hard rocks, affect the dynamics and contribute to the movement speed of the ice sheet.

Once Shen provides a better understanding of the material beneath the ice, including glacial water, he can follow that up with other researchers to interpret the implications of ice sheet dynamics.

“We can predict better what’s the contribution of the Antarctic ice sheet to the sea level change” which will offer modelers a way to gauge the likely impact of global warming in future decades, he said.

Using seismic data

Starting this November, Shen and graduate students Siyuan Sui, Thomas Reilly and Hanxiao Wu will venture for two months to the South Pole with seismic monitors.

By placing 183 seismic nodes and installing an additional eight broad-band seismic stations, Shen and his team will quantify the seismic properties and, eventually, use them to infer the composition, density and temperature structure of the crust and the uppermost mantle.

The temperature when they place these monitors will be 10 to 30 degrees below 0 degrees Fahrenheit. They will need to do some digging as they deploy these sensors near the surface.

While the South Pole is believed to be geologically stable, signs of sub-glacial melting suggest the crust may bear a higher concentration of highly radioactive elements such as uranium, thorium and potassium.

Those natural elements “produce heat all the time,” said Shen. 

The process and analysis of seismic waves works in the same way it would for the study of a prism. Looking at the refraction of light that enters and leaves the prism from various angles can help researchers differentiate light with different frequencies, revealing clues about the structure and composition of the prism.

Earth materials, meanwhile will also cause a differentiation in the speed of surface waves according to their frequencies. The differentiation in speeds is called “dispersion,” which Shen and his team will use to quantify the seismic properties. The area has enough natural waves that Shen won’t need to generate any man-made energy waves.

“We are carefully monitoring how fast [the seismic energy] travels” to determine the temperature, density and rock type, Shen said.

The water beneath the glacier can act like a slip ’n slide, making it easier for the glacier to move.

Some large lakes in Antarctica, such as Lake Vostok, have been mapped. The depth and contours of sub glacier lakes near the South Pole, however, are still unclear.

“We have to utilize a lot of different methods to study that,” said Shen.

The Stony Brook researcher will collaborate with colleagues to combine his seismic results with other types of data, such as radar, to cross examine the sub ice structures.

The work will involve three years of gathering field data and two years of analysis.

Educational component

In addition to gathering and analyzing data, Shen has added a significant educational component to the study. For the first time, he is bringing along Brentwood High School science teacher Dr. Rebecca Grella, A PhD graduate from Stony Brook University’s Ecology and Evolutionary Biology program, Grella will provide lectures and classes remotely from the field.

In addition to bringing a high school teacher, Shen will fund graduate students at Stony Brook who can help Brentwood students prepare for the Earth Science regents exam.

Shen is working with Kamazima Lwiza, Associate Professor in the School of Marine and Atmospheric Sciences at Stony Brook, to bring Earth Science, including polar science, to schools in New York City and on Long Island with a bus equipped with mobile labs.

Lwiza, who is the Principal Investigator on the EarthBUS project, will work together with Shen to build a course module that includes a 45-minute lecture and exhibition.

Shen feels that the project will help him prepare to better educate students in graduate school, college, and K-12 in the community.

He feels a strong need to help K-12 students in particular with Earth Science.

As for students outside Brentwood, Shen said he has an open door policy in which the lab is receptive to high school and undergraduate students who would like to participate in his research all year long.

Once he collects the first batch of data from the upcoming trip to the South Pole, he will have to do considerable data processing, analysis and interpretation.

While Shen is looking forward to the upcoming field season, he knows he will miss time in his Stony Brook home with his wife Jiayi Xie, and his four-and-a-half year old son Luke and his 1.5 year old son Kai.

“It’s a huge burden for my wife,” Shen said, whose wife is working full time. When he returns, he “hopes to make it up to them.”

Shen believes, however, that the work he is doing is important in the bigger picture, including for his children.

Record high temperatures, which are occurring in the United States and elsewhere this summer, will “definitely have an impact on the dynamics of the ice sheet.” At the same time, the Antarctic ice sheet is at a record low.

“This is concerning and makes [it] more urgent to finish our work there,” he added.

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Timothy Glotch. Photo from SBU

By Daniel Dunaief

It’s almost easier to figure out what makes Earth unique among the planets than it is to list the ways humans are unique among Earth’s inhabitants. Earth is, after all, the only blue planet, filled with water from which humans, and so many other creatures, evolved. It is also the only planet on which seven enormous plates deep beneath the surface move. These unique features have led scientists to expect certain features that give Earth its unique geological footprint.

Not so fast.

According to a recent paper in the high-profile journal Nature in which Timothy Glotch, Professor of Geosciences at Stony Brook University, was a co-author, the moon has a vast swath of over 50 kilometers of granite in the Compton-Belkovich Volcanic complex, which is on the its far side. 

Usually formed from plate tectonics of water bearing magma, the presence of this granite, which appears in greater quantities around the Earth, is something of a planetary mystery.

“Granites are extremely rare outside of Earth,” said Glotch. “Its formation process must be so different, which makes them interesting.”

The researchers on this paper, including lead author Matt Siegler, a scientist at the Planetary Science Institute, suggest a range of possibilities for how the granite formed. Over three billion years ago, the moon, which, like the Earth, is over 4.5 billion years old, had lava that erupted to form the Compton-Belkovich Volcanic Complex, or CBVC. Researchers think most volcanic activity on the moon ended about two billion years ago.

This illustration shows the Compton-Belkovich Volcanic Complex (CBVC) on the Moon’s far side and the boxed area indicated a large granite zone, which could not be picked up by topography. Image courtesy of Matthew Siegler/Planetary Science Institute/Nature

The magma formed as a result of a melting of a small portion of the lunar mantle. Melting could have been caused by the addition of water or the movement of hot material closer to the surface. Scientists are not completely sure about the current nature of the lunar core.

As for the granite, it might have come from fractionation, in which particles separate during a transition from different phases, in this case from a hot liquid like magma to a solid.

Additionally, the presence of granite could suggest that some parts of the moon had more water than others.

“There are other geochemical arguments you could make,” Glotch said. “What we really need are to find more samples and bring them back to Earth.”

The analysis of granite on the moon came from numerous distant sources, as well as from the study of a few samples returned during the Apollo space missions. The last time people set foot on the moon was on the Apollo 17 mission, which returned to Earth on Dec. 19, 1972.

A 10-year process

The search and study of granite on the moon involved a collaboration between Glotch and Siegler, who have known each other for about 18 years. The two met when Glotch was a postdoctoral researcher and Siegler was a graduate student.

In 2010, Glotch published a paper in the journal Science in which he identified areas that have compositions that are similar to granite, or rhyolite, which is the volcanic equivalent.

Since that paper, Glotch and others have published several research studies that have further characterized granitic or rhyolitic materials, but those are “still relatively rare,” Glotch said.

Long distance monitoring

Led by Siegler and his postdoctoral researcher Jiangqing Feng, the team gathered information from several sources, including microwave data from Chinese satellites, which are sensitive to the heat flow under the surface.

The team also used the Diviner Lunar Radiometer Experiment, which is a NASA instrument on the Lunar Reconnaissance Orbiter, that measures surface temperatures.

Part of the discovery of the silicic sites on the moon comes from the identification of the element thorium, which the Lunar Prospector Gamma Ray Spectrometer found. Similar to uranium or plutonium, thorium is radioactive and decays.

Another piece of data came from the Grail mission, which measures the lunar gravity field.

Glotch suggested that the study involved a “daisy chain of observations.” In his role, he tried to identify sites that might be rich in granite, while Siegler applied new data to these areas to learn more about the underground volcanic plumbing.

In addition to doing long distance monitoring, Glotch engages in long distance recreational activities. The Stony Brook professor is preparing for a November 11th run in Maryland that will cover 50 miles. He expects it will take him about 10 or 11 hours to complete. 

Looking at other planets

By analyzing granite on the moon, which could reveal its early history, geologists might also turn that same analysis back to the Earth.

“Can we use the results of this study to take a more nuanced view of granite formations on Earth or other bodies in our solar system?” Glotch asked. “We can learn a lot, not just about the moon, but about planetary evolution.”

NASA is planning a DAVINCI+ mission to Venus in the coming decade, while a European mission is also scheduled for Venus. Some researchers have suggested that Venusian terrains, which are referred to as Tesserae, might be granitic.

“If Venus has continent-like structures made of granite, that’s interesting, because Venus does not appear to have plate tectonics either,” Glotch said.

Closer to Earth, some upcoming missions may offer a better understanding of lunar granite. The first is a small orbiter called Lunar Trailblazer that will have sensitive remote instruments. The second is a part of NASA’s Commercial Lunar Payload Services program, which will include a small lander and rover that will land on the Gruithuisen Domes.

Conference in Italy

In the shorter term, Glotch and Siegler plan to attend the 10th Hutton Symposium in Italy.

Glotch is eager to discuss the work with researchers who are not planetary scientists to “get their take on this.”

He is excited by the recent planetary decadal survey, which highlighted several priorities, which include lunar research.

In his opinion, Glotch believes the survey includes more high priority lunary science than in previous such surveys.

Countries including India, China, Israel and Japan have a renewed national interest in the moon. South Korea currently has an orbiter at the moon.

All this attention makes the moon a “really good target for U.S. science to maintain our leadership position, as well as providing a tool for geopolitical cooperation,” Glotch added.

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Clare Flynn conducts a census count of gentoo penguins at Neko Harbour in Antarctica in January 2023.

By Daniel Dunaief

Humans may have nothing on penguins when it comes to viral marketing. Almost immediately after the Covid pandemic shut down tourism in parts of Antarctica, some gentoo penguins likely altered their choice of nesting sites.

Clare Flynn with her award- winning poster at the Pacific Seabird Group annual meeting in Feb. 2023. Photo by William Kennerly

As if the penguins got an avian email alert indicating that tourists eager to send a post card from the only post office in Antarctica weren’t coming, these flightless birds quickly divvied up desirable real estate, which, for a gentoo penguin, means bare rock on which they make nests out of pebbles.

“Antarctica is seen as a mostly pristine place where humans have very little impact,” said Clare Flynn, a PhD student in the lab of Heather Lynch, the Institute for Advanced Computational Sciences Endowed Chair for Ecology & Evolution at Stony Brook University.

Flynn used a combination of ground counts from researchers and drone footage to tally the nests during the Covid years. Based on these numbers, she concluded that tourism has been “depressing the population sizes at Port Lockroy” and nearby Jougla Point.

The study suggests that even limited human visits to remote locations can alter decisions by wildlife, affecting the kind of reproductive choices that could, over time and with greater numbers of people coming, affect population sizes.

Pomona College Biology Professor Nina Karnovsky, who is an undergraduate thesis advisor and mentor for Flynn but didn’t participate in this research, suggested that this kind of analysis highlights the need for greater awareness of human influence.

“It shows that people even visiting the colony can have impacts,” Karnovsky said. “Tourism is a double-edged sword. You want people to experience Antarctica and see how precious life there is.” At the same time, researchers don’t want any such visits to have negative side effects.

Nest numbers

The number of penguin nests in Port Lockroy surged to 978 in the 2021/ 2022 breeding season. That is considerably higher than the 535 nesting pairs in the 2018/2019 season, according to data compiled and analyzed by Flynn. What’s more, when the post office returned to normal operations, bringing back tourists in 2022 and 2023, the nest number at Port Lockroy returned to its earlier levels, at 529.

The overall number of nesting gentoo penguins didn’t change dramatically in a cluster of gentoo penguin colonies around Wiencke Island during Covid, as many of these birds likely shifted their breeding locations from nearby sites that don’t have as much human activity, such as Damoy Point.

“It’s shocking how quickly [the changed nesting sites] happened,” Flynn said, occurring over the course of two years, not generations. “Tourism is just ramping up when the penguins are choosing nesting sites.” The shifting nest sites accounted for most of the increase in Port Lockroy and Jougla Point. Some of the gentoo penguins who may have skipped a breeding season, however, also might have decided to give it a go amid the pandemic closure.

Post office attraction

Flynn and Lynch have a few theories about what caused these nesting patterns.

Flynn suggested the nesting sites at Damoy Point and Dorian Beacon, where the number of nesting colonies declined during the lockdown, may have been close to carrying capacity, which means that prospective penguin parents found the equivalent of No Vacancy signs when they searched for places to build their nest.

Sites near the post office were not at carrying capacity prior to the pandemic. From visual inspection of the drone images, these sites had available bare rock, which is a limiting factor for gentoo penguins.

Flynn believes that pedestrian traffic may have dissuaded penguins from creating nests.

Human disturbance

Boat traffic may also be dissuading gentoo penguins from nesting. While there is a limit to the number of people who can land at any given time, people often cruise around the area in zodiacs, which increases the noise and could create a physical barrier for swimming penguins.

Last month, Lynch brought Flynn’s analysis of nesting numbers during the pandemic to the Antarctic Treaty Consultative Meeting in Finland. Policy makers are considering implementing a no-wake zone in Port Lockroy harbor as a first step to reduce disturbance.

While the number of nests typically varies by year at these sites, the dramatic increases and decreases lie outside that normal range, Flynn said. She called the numbers “eye popping,” as Port Lockroy had the largest population size ever recorded in 2021/ 2022 and Jougla Point saw the largest population size in 2021/2022 in over 20 years. Damoy Point and Dorian Beacon, by contrast, had huge drops.

Understanding the effects of tourism is becoming increasingly important, particularly as the appetite for travel to this area increases.

While gentoo penguins are doing well overall, an increase in the kind of tourism that exists at Port Lockroy could affect their breeding success.

“We need to understand how increasing levels of tourism affect these species so that the effects in conjunction with climate change effects don’t cause a disaster” for several penguin species, Flynn added.

Rewarding pivot

Flynn hadn’t intended to study the effects of Covid on the gentoo penguin. Instead, she was using drone images to identify whether penguins nested in the same place from one year to the next.

While Flynn was annotating images from 2018 through 2021, Lynch noticed the changes at Port Lockroy during those years. After Flynn took a deeper dive into the numbers, she made a new poster just one week before presenting her results at the Pacific Seabird Group annual meeting in February.

The “exhausting” effort, as Flynn put it, paid off, as she won runner up honors for best PhD poster at the conference. She has since sent the results out to Biological Conservation for publication.

Ecology spark

Flynn grew up near Baltimore and attended Pomona College, where she anticipated exploring her interest in math. She switched her focus to ecology. An ecology and evolution class she took with Karnovsky cemented her decision and brought her into the world of seabirds.

Karnovsky recalled how Flynn “loved collecting data,” which, in Southern California is “not a walk in the park, literally.” Flynn had to contend with cactus and poison ivy on an owl project.

Karnovsky believes her former student could “go on and do great things in this field.”

At one point about five years ago, Karnovsky told Flynn she might “go to Antarctica one day to study penguins,” Flynn recalled. At the time, Flynn thought the idea sounded “crazy.”

Karnovsky’s suggestion about Flynn’s future was less crazy than it was prescient.

When she’s not following her research calling, Flynn enjoys following recipes. She makes baked goods and is particularly fond of a blueberry muffin recipe she found in Bon Appétit magazine. Instead of putting in too many blueberry, which sink in the muffin, she makes a blueberry compote and sprinkles lemon zest sugar on top.

As for her future, Flynn hasn’t decided on a post PhD plan. This could include becoming a professor or pursuing a data science career.

“I could see her becoming a really wonderful professor because she also sees mentoring as really important,” Karnovsky said.

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Sam Kleeman. Photo by Caryn Koza/CSHL
From left, Sam Kleeman, Assistant Professor Tobias Janowitz, Miriam Ferrer Gonzalez and Emma Davidson. Photo by Caryn Koza/CSHL
Sam Kleeman at Lake Tahoe
Sam Kleeman in front of a sequoia grove at Yosemite.

By Daniel Dunaief

This is part 2 of a two-part series.

Cancers not only compromise human health, but they can also suppress the body’s immune response. A little studied small protein called cystatin C, which is secreted by numerous cells, may render the immune system less effective in its response to tumors.

Sam Kleeman, a PhD student in Cold Spring Harbor Laboratory Assistant Professor Tobias Janowitz’s lab, recently published results in the journal Cell Genomics that demonstrate a link between elevated levels of this protease inhibitor, the suppression of the immune system, and the development of cancer.

Kleeman was able to demonstrate a potential role “Cystatin C might play in damping down the immune response to tumors,” he said.

Cystatin C is a known cysteine protease inhibitor, but the biological and organ-level relevance of this has not been characterized in detail. This protein could be one of many mechanisms by which glucocorticoids can reduce the effectiveness of the immune system.

Cystatin C could drive the progression of the disease, which could explain why Kleeman has found evidence that higher levels coordinate with worse outcomes.

Starting with the data

Pursuing an interest in data- driven research, Kleeman, who has a Bachelor of Medicine and Surgery from New College at the University of Oxford, searched the UK Biobank, which provides health data for numerous people in the United Kingdom. 

In this Biobank, Kleeman, who joined Cold Spring Harbor Laboratory in August of 2020, found that cystatin C was the best prognostic indicator of cancer deaths.

“I was a little surprised by this,” Kleeman said as he had heard of cystatin C as a marker of kidney function, but was not aware of any association with cancer mortality. Some studies had found evidence for this previously, but those were in small cohorts and were poorly understood, he explained.

A healthy kidney clears most proteins quickly, pumping it out into urine. A kidney that’s not functioning optimally, however, allows it to accumulate.

In his research, Kleeman removed cystatin C selectively in cancer cells, causing the tumors to grow more slowly. The main changes in the architecture of the tumor was that it reduced the frequency of macrophages with expression of a protein called Trem2. While the exact mechanism is not known, it’s likely that immune control of the tumor increases without cystatin C.

Kleeman also demonstrated a similar effect on the connection between levels of Covid-19 and mortality in a paper published in iScience.

The biological mechanism explaining the correlation is nuanced. Patients with higher levels of glucocorticoids can be associated with poor outcomes. It is not a simple relationship, he said, which makes causality difficult to assess.

Kleeman believes cystatin C secretion in response to glucocorticoids has context dependency. Not all cells posses inducible cystatin C secretion.

The research primarily found that only macrophages and cancer cells can secrete cystatin C in response to glucocorticoids.

He describes a “two hit” model, by which glucocorticoids plus an inflammatory stimulus recruit macrophages. The model applies to all inflammatory stores, but is co-opted in the case of cancer.

At this point, drugs aren’t available to inhibit or reduce cystatin C. Instead, Kleeman suggested that a viable research target route might involve creating a specific antibody.

Some researchers have created so-called knockout mice, which don’t have this protein. These mice can survive without it, although eliminating all cystatin C creates other problems.

Kleeman speculated that the protein could play a role in preventing significant immune reaction against sperm.

Indeed, this protein is secreted at high levels in the testes. Males without it have lower sperm function and production.

Kleeman hopes this work acts as a starting point to understand the mechanism better by which glucocorticoids modify immune response to cancer, and to investigate cystatin C as a possible therapeutic target.

Long standing partnership

As an undergraduate, Kleeman took a class with Janowitz, which kicked off a mentorship that now spans two continents.

Kleeman appreciates the comfort level Janowitz has in working on higher-risk, higher-reward topics or on ideas that haven’t already attracted considerable attention from other scientists.

“There’s a tendency in science towards group think,” Kleeman said. In the history of medicine and science, many widely accepted theories turn out to be wrong. “Patients undoubtedly benefit from a diversity of thought in science and medicine,” he explained.

When he completes his PhD, Kleeman said it would be a “dream to have a dual appointment” in which he could conduct research and work in the clinic with patients. To get there, he knows he needs to establish his research profile that includes a genuine track record of achievement while demonstrating that he can function as a reliable and effective clinician.

Kleeman’s thesis research lies outside the field of cystatin C, which started out as a curiosity and developed into the recent publication. He wanted to “understand what UK Biobank could teach us about cancer patients.” With Janowitz and Cold Spring Harbor Laboratory Professor Hiro Furukawa, Kleeman is working to understand how a specific type of cancer could cause an auto-immune disease.

A resident of Forest Hills, Kleeman lives about 45 minutes from the lab. Outside of work, he enjoys visiting national parks. He has visited 10 so far, including Yosemite National Park, Zion and Rocky Mountain National Park. 

Professionally, Kleeman feels it is a privilege to be a PhD student. He appreciates that he can explore his interests without too many restrictions and is eager to make the most of the opportunity.

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From left, Sam Kleeman, Assistant Professor Tobias Janowitz, Miriam Ferrer Gonzalez and Emma Davidson. Photo by Caryn Koza/CSHL

By Daniel Dunaief

This part one of a two part series.

It’s a bit like shaking corn kernels over an open flame. At first, the kernels rustle around in the bag, making noise as they heat up, preparing for the metamorphosis.

That’s what can happen in any of the many laboratories scattered throughout Long Island, as researchers pursue their projects with support, funding and guidance from lab leaders or, in the science vernacular, principal investigators.

Sometimes, as happened recently at the benches of Cold Spring Harbor Laboratory Assistant Professor Tobias Janowitz, several projects can pop at around the same time, producing compelling results, helping advance the careers of developing scientists and leading to published papers.

PhD graduate Miriam Ferrer Gonzalez and MD/ PhD student Sam Kleeman recently published separate studies.

In an email, Janowitz suggested the work for these papers is “time consuming and requires a lot of energy.” He called the acceptance of the papers “rewarding.” 

In a two-part series, Times Beacon Record News Media will describe the research from each student. This week, the focus is on Ferrer Gonzalez. Check back next week for a profile of the work of Kleeman.

Miriam Ferrer Gonzalez

Miriam Ferrer Gonzalez. Photo by Caryn Koza/CSHL

Miriam Ferrer Gonzalez was stuck. She had two results, but couldn’t seem to figure out how to connect them. First, in a mouse model of the ketogenic diet — heavy on fats, without including carbohydrates —cancer tumors shrunk. That was the good news.

The bad news, which was even more pronounced than the good, was that this diet was not only starving the tumors, but was triggering an earlier onset of cachexia, in which bodies weaken and waste away. The cachexia overpowered the mice, causing them to die sooner than if they had a normal diet.

Ferrer, a student in residence from Spain who was conducting her research at Cold Spring Harbor Laboratory while earning her PhD at the University of Cambridge in the UK, thought the two discoveries were paradoxically uncoupled. A lower tumor burden, she reasoned, should have been beneficial.

In presenting and discussing her findings internally to the lab group, Ferrer received the kind of feedback that helped her hone in on the potential explanation.

“Finding out the mechanism by which a ketogenic diet was detrimental for both the body and the cancer was the key to explaining this uncoupling,” Ferrer explained.

The adrenal glands of mice fed a ketogenic diet were not producing the necessary amount of the hormone corticosterone to sustain survival. She validated this broken pathway when she discovered higher levels of corticosterone precursors that didn’t become functional hormones.

To test this hypothesis, she gave mice dexamethasone, which boosted their corticosterone levels. These mice had slower growing tumors and longer lives.

Ferrer recently published her paper in the journal Cell Metabolism.

To date, the literature on the ketogenic diet and cancer has been “confusing,” she said, with studies that show positive and negative effects.

“In our study, we go deeper to explain the mechanism rather than only talking about glucose-dependency of cancer cells and the use of nutritional interventions that deprive the tumor of glucose,” said Ferrer. She believed those factors are contributing to slower tumor growth, but are not solely responsible.

Thus far, there have been case studies with the ketogenic diet shrinking tumors in patients with cancer and, in particular, with glioblastoma, but no one has conducted a conclusive clinical trial on the ketogenic diet.

Researchers have reported on the beneficial effects of this diet on epilepsy and other neurological diseases, but cancer results have been inconclusive.  For the experiments in Janowitz’s lab, Ferrer and technician Emma Davidson conducted research on mouse models.

Ferrer, who is the first author on the paper, has been working with this system for about four years. Davidson, who graduated from the College of Wooster in Ohio last year and is applying to MD and MD/PhD programs, contributed to this effort for about a year.

Next steps

From left, Emma Davidson, Assistant Professor Tobias Janowitz, Sam Kleeman and Miriam Ferrer Gonzalez. Photo by Caryn Koza/CSHL

Now that she earned her PhD, Ferrer is thinking about the next steps in her career and is considering different institutions across the country. Specifically, she’s interested in eating behavior, energy homeostasis, food intake and other metabolic parameters in conditions of stress. She would also like to focus on how hormonal cycles in women affect their eating behavior.

Originally from a small city in Spain called Lleida, which is in the western part of Catalonia, Ferrer appreciated the opportunity to learn through courses and conferences at Cold Spring Harbor Laboratory.

Until she leaves the lab in the next few months, Ferrer plans to work with Davidson to prepare her to take over the project for the next year.

The follow up experiments will include pharmacologically inducing ferroptosis of cancer cells in mice fed a ketogenic diet. They hope to demonstrate that early induction of ferroptosis, or a type of programmed cell death, prevents tumor growth and prevents the tumor-induced reprogramming of the rest of the body that causes cachexia.

These experiments will involve working with mice that have smaller and earlier tumors than the ones in the published paper. In addition, they will combine a ketogenic diet, dexamethasone and a ferroptosis inducing drug, which they didn’t use in the earlier experiments.

Janowitz has partnered with Ferrer since 2018, when she conducted her master’s research at the University of Cambridge. As the most senior person in Janowitz’s lab, Ferrer has helped train many of the people who have worked in his lab. She has found mentoring rewarding and appreciates the opportunity to invest in people like Davidson.

Ferrer, who is planning a wedding in Spain in September, is a fitness and wellness fan and has taken nutrition courses. She does weight lifting and running.

Ferrer’s parents don’t have advanced educational degrees and they supported their three children in their efforts to earn their degrees.

“I wanted to be the best student for my parents,” said Ferrer, who is the middle child. She “wanted to make my parents proud.

The hand off

Emma Davidson and Miriam Gonzalez Ferrer examine an adrenal gland sample section from a cachectic mouse. Photo by Caryn Koza/CSHL

For her part, Davidson is looking forward to addressing ways to implement further treatment methods with a ketogenic diet and supplemental glucocorticoids to shrink tumors and prevent cachexia. 

Davidson appreciated how dependable Ferrer was during her time in the lab. Just as importantly, she admired how Ferrer provided a “safe area to fail.”

At one point, Davidson had taken all the cells she was planning to use to inject in mice. Ferrer reminded her to keep some in stock.

“Open lines of communication have been very beneficial to avoid more consequential failures,” Davidson said, ”as this mistake would have been.”

Davidson developed an interest in science when she took a high school class called Principles in Biological Science and Human Body Systems. When she was learning about the cardiovascular system, her grandfather had a heart attack. In speaking with doctors, Davidson acted as a family translator, using the language she had studied to understand what doctors were describing.

Like Ferrer, Davidson lives an active life. Davidson is preparing for the Jones Beach Ironman Triathlon in September, in which she’ll swim 1.2 miles, bike 56 miles and run a half marathon. She plans to train a few hours during weekdays and even more on weekends for a competition she expects could take about six hours to complete.

Davidson started training for these events with her father Mark, an independent technology and operations consultant and owner of Exoro Consulting Group.

Longer term, Davidson is interested in medicine and research. After she completes her education, she will try to balance between research and clinical work.

 

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Above, a photo of Turkana taken from a single engine plane shows the Koobi Fora spit and Lake Turkana alongside a time map. Photo from Bob Raynolds

By Daniel Dunaief

In a wide-ranging interview, Louise Leakey, Director of Public Education and Outreach for the Turkana Basin Institute and a Research Professor in the Department of Anthropology at Stony Brook University shared her thoughts on numerous topics in the field of paleontology.

Louise Leakey at the Richard Leakey Memorial Conference on June 5. Photo by John Griffin/SBU

Leakey, who earned her PhD at the University College London, suggested that the process of finding fossils hasn’t changed that much, although other options beyond scouring a landscape for fragments of the world’s former occupants may be forthcoming.

“It may very well change if we can implement machine learning with high resolution imagery, using drones,” she said. “That’s one of the things we’re looking at the moment.”

What’s really changed, however, is the accuracy field scientists have in marking where, and, importantly, when new discoveries originated, she said.

Geologists like Bob Raynolds, Research Associate at the Denver Museum of Nature & Science, have created time maps that indicate the approximate age of sediments around a fossil in some select areas of the Turkana Basin.

These maps “can be uploaded onto an iPad app for use in the field that shows you in real time where you are on the geological map,” Leakey explained. “This is a game changer for field work in the basin.”

A time map created by Bob Raynolds in collaboration with Geologic Data Systems, a Littleton, Colorado company.

The maps represent the work of many people, Raynolds explained.  Originally, teams of Master’s students used air photographs, tracing paper and ink to make a map. These students spent many weeks walking systematically on the ground and tracing the patterns on the photos.

The rugged and isolated nature of the ground in Northern Kenya makes the work done on foot difficult, Raynolds explained.

The original maps, which were made in the 1970’s, took months to make and were presented as paper copies in unpublished Master’s theses. After numerous enhancements, Raynolds, working with companies including Geologic Data Systems in Littleton, Colorado, created time maps.

The internal GPS on an iPhone enables a blue dot to indicate a person’s location on the map.

“I have worked on the maps to make a new set of derived products that are maps of the age of the rocks,” said Raynolds who created these time maps earlier this year. “The resolution of the time maps is 100,000 years” which is an “astonishingly detailed resolution for us who are accustomed to million year packages of time.”

The maps cover the entire Turkana Basin at various scales, Raynolds added.

More broadly, Bernard Wood, University Professor of Human Origins in the Center for the Advanced Study of Human Paleontology at George Washington University and the first speaker at a recent Stony Brook University conference to honor Richard Leakey, explained that dating fossils has become increasingly accurate.

The first dates of fossils in the KBS Tuff, which is an ash layer in the Koobi Fora Formation east of Lake Turkana, was estimated within 260,000 years of a specific date. Using improved methods, a study published this year has reduced that range to 600 years.

Publishing pace

In the meantime, the pace of publishing has slowed considerably.

“There’s so much more material” that can serve as a frame of reference for new discoveries, Leakey said. “The rate of publication is frustratingly slow for some of these specimens.” This contrasts dramatically with the experience of Leakey’s father Richard.

When the elder Leakey submitted his letters or paper to the prestigious journal Nature, the late editor John Maddox never sent them out for review. “[Maddox] explained that he couldn’t see the point, because they concerned fossils so recently discovered” that few had seen them, Wood explained in his presentation.

Louise Leakey also differed from Richard in earning her bachelor’s degree and PhD, while her father dropped out of high school and never received any additional formal education.

Wood suggested that, next to marrying Meave, the elder Leakey described leaving school as one of the best decisions he’d ever made.

For his daughter, though, Leakey “encouraged me to go and do that,” Louise Leakey said. The education helped “in terms of being able to be [principal investigator] on grant applications,” she said.

Leakey suggested it was a “real privilege to be able to spend time” earning her PhD. She also found that the educational experience gave her the opportunity to “stand on my own two feet” in her research.

Like her father, Louise Leakey is concerned about conservation and declining biodiversity. When she was younger, she saw areas that were teeming with wildlife. On a recent three-hour drive, she only saw a golden jackal and a dik-dik, which is a type of small antelope, compared with the much wider variety of creatures she would have seen decades ago, such as Grévy’s zebra, Burchell zebra, lesser kudu, ostriches, warthogs, topi, gerenuk, oryx and, possibly lions and cheetah. 

She attributes this decline to hunting as some have exterminated these species as result of competition for grazing areas and hunting the animals for meat. Record droughts are also threatening their survival.

Leakey is working with the next generation to get “kids to care about nature” so they can “think about what they’re doing and the real impact it has.”

In addition to preserving biodiversity, Leakey remains passionate about studying the past, which could help the current and future generations tackle climate change. “We might be able to learn lessons” from those who survived during such challenging conditions, she said.

Leakey is able to maintain her involvement and commitment to numerous efforts by working with talented collaborators.

“If you don’t have teams to really hold it together, you can’t do any of it,” she said.

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Ali Khosronejad in front of the Santa Maria Cathedral, which is considered the first modern cathedral in Madrid.

By Daniel Dunaief

An approaching weather front brings heavy rains and a storm surge, threatening to inundate homes and businesses with dangerous water and potentially undermining critical infrastructure like bridges.

Once officials figure out the amount of water that will affect an area, they can either send out inspectors to survey the exact damage or they can use models that take time to process and analyze the likely damage.

Ali Khosronejad

Ali Khosronejad, Associate Professor in the Department of Civil Engineering at Stony Brook University, hopes to use artificial intelligence to change that.

Khosronejad recently received $550,000 from the National Science Foundation (NSF) for four years to create a high-fidelity model using artificial intelligence that will predict the flood impact on infrastructure.

The funds, which will be available starting on June 20, will support two PhD students who will work to provide an artificial intelligence-based program that can work on a single laptop at a “fraction of the cost of more advanced modeling approaches,” Khosronejad said during an interview in Madrid, Spain, where he is on sabbatical leave under a Fulbright U.S Senior Scholar Award. He is doing his Fulbright research at Universidad Carlos III de Madrid.

Stony Brook University will also provide some funding for these students, which will help defray the cost of expenses related to traveling and attending conferences and publishing papers.

In the past, Stony Brook has been “quite generous when it comes to supporting graduate students working on federally funded projects,” Khosronejad explained and he hopes that continues with this research.

Khosronejad and his students will work with about 50 different flooding and terrain scenarios, which will cover about 95 percent of extreme flooding. These 50 possibilities will cover a range of waterways, infrastructure, topography, and coastal areas. The researchers will feed data into their high fidelity supercomputing cluster simulations to train artificial intelligence to assess the likely damage from a flood.

As they build the model, Khosronejad explained that they will collect data from floods, feed them into the computer and test how well the computer predicts the kind of flooding that has can cause damage or threaten the stability of structures like bridges. Over the next four years, the team will collect data from the Departments of Transportation in California, Minnesota and New York.

Nearly six years ago, his team attempted to use algorithms available in ChatGPT for some of his AI development. Those algorithms, however, didn’t predict flood flow prediction. He tried to develop new algorithms based on convolutional neural networks. Working with CNN, he attempted to improve its capabilities by including some physics-based constraints.

“We are very enthusiastic about this,” Khosronejad said. “We do think that this opportunity can help us to open up the use of AI for other applications in fluid mechanics” in fields such as renewable energy, contaminant transport predictions in urban areas and biological flow predictions, among others.

Planners working with groups such as the California Department of Transportation could use such a program to emphasize which infrastructure might be endangered.

This analysis could highlight effective mitigation strategies. Artificial intelligence can “provide [planners and strategists] with a tool that is not that expensive, can run on a single laptop, can reproduce lots of scenarios with flooding, to figure out which infrastructure is really in danger,” Khosronejad said.

Specifically, this tool could evaluate the impact of extreme floods on bridge foundations. Floods can remove soil from around the foundation of a bridge, which can cause it to collapse. Civil engineers can strengthen bridge foundations and mitigate the effect of future floods by using riprap, which is a layer of large stones.

This kind of program can reduce the reliance on surveying after a flood, which is expensive and sometimes “logistically impossible and unsafe” to monitor areas like the foundations of bridges, Khosronejad said. He plans to build into the AI program an awareness of the changing climate, so that predictions using it in three or five years can provide an accurate reflection of future conditions.

“Floods are getting more and more extreme” he said. “We realize that floods we feed into the program during training will be different” from the ones that will cause damage in subsequent years.

Floods that had a return period of every 100 years are now happening much more frequently. In one or two decades, such a flood might occur every 10 years.

Adding updated data can allow practitioners to make adjustments to the AI program a decade down the road, he suggested. He and his team will add data every year, which will create a more versatile model.

What it can’t do

While the AI programs will predict the damage to infrastructure from floods, they will not address storm or flood predictions.

“Those are different models, based on the movement of clouds” and other variables, Khosronejad said. “This doesn’t do that: if you give the program a range of flood magnitudes, it will tell you what will happen.”

High fidelity models currently exist that can do what Khosronejad is proposing, although those models require hundreds of CPUs to run for five months. Khosronejad has developed his own in house high fidelity model that is capable of making similar predictions. He has tested it to examine various infrastructures and used it to study various flooding events. These models are expensive, which is why he’s trying to replace them with AI to reduce the cost while maintaining fidelity.

AI, on the other hand, can run on a single CPU and may be able to provide the same result, which will allow people to plan ahead before it happens. The NSF approved the single principal investigator concept two months ago.

Khosronejad has worked with Fotis Sotiropoulos, former Dean of the College of Engineering and Applied Sciences at Stony Brook and current Provost at Virginia Commonwealth University, on this and other projects.

The two have bi-weekly discussions over the weekend to discuss various projects.

Sotiropoulos was “very happy” when Khosronejad told him he received the funds. Although he’s not a part of the project, Sotiropoulos will “provide inputs.”

Sotiropoulos has “deep insights” into fluid mechanics. “When you have him on your side, it always pays off,” Khosronejad said.

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Chengfeng Yang Photo by Zhishan Wang

By Daniel Dunaief

This is part two of a two-part series.

As Erin Brockovich (the real life version and the one played by Julia Roberts in the eponymous movie) discovered, some metals, such as hexavalent chromium can cause cancer in humans.

Chengfeng Yang and Zishan Wang

Environmental exposure to a range of chemicals, such as hexavalent chromium, benzo(a)pyrene, arsenic, and others, individually and in combination, can lead to health problems, including cancer.

In March, Stony Brook University hired Chengfeng Yang and Zhishan Wang, a husband and wife team to join the Cancer Center and the Pathology Departments from Case Western Reserve University.

The duo, who have their own labs and share equipment, resources and sometimes researchers, are seeking to understand the epigenetic effect exposure to chemicals has on the body. Yang focuses primarily on hexavalent chromium, while Wang works on the mechanism of mixed exposures.

Last week, the TBR News Media highlighted the work of Wang. This week, we feature the work of Yang.

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When he was young, Chengfeng Yang was using a knife to make a toy for his younger brother. He slipped, cutting his finger so dramatically that he almost lost it. Doctors saved his finger, impressing him with their heroic talent and inspiring him to follow in their footsteps.

Indeed, Yang, who earned an MD and a PhD from Tongji Medical University, is focused not only on answering questions related to cancer, which claimed the life of his mother and other relatives, but also in searching for ways to develop new treatments.

A Professor in the Department of Pathology at the Renaissance School of Medicine at Stony Brook University and a member of the Stony Brook Cancer Center, Yang has his sights set on combatting cancer.

“Our research always has a significant clinical element,” said Yang. “This is related to our medical background.”

He is interested in studying the mechanism of cancer initiation and progression and would like to develop new strategies for treatment.

Yang and his wife Zhishan Wang recently joined the university from Case Western after a career that included research posts at the University of Pennsylvania, Michigan State University, and the University of Kentucky.

The tandem, who share lab resources and whose research staffs collaborate but also work independently, are focused specifically on the ways exposures to carcinogens in the environment cause epigenetic changes that lead to cancer.

Specifically, Yang is studying how hexavalent chromium, a metal commonly found in the environment in welding, electroplating and even on the double yellow lines in the middle of roads, triggers cancer. It is also commonly used as a pigment to stain animal leather products.

Yang is focused mainly on how long cancer develops after exposure to hexavalent chromium.

People can become exposed to hexavalent chromium, which is also known as chromium 6, through contaminated drinking water, cigarette smoking, car emissions, living near superfund sites and through occupational exposure.

Yang has made important findings in the epigenetic effect of metal exposure. His studies showed that chronic low-level chromium six exposure changed long non-coding RNA expression levels, which contributed to carcinogenesis. Moreover, his studies also showed that chronic low level exposure increased methylation, in which a CH3 group is added to RNA, which also contributed significantly to chromium 6 carcinogenesis.

“It is now clear that metal carcinogens not only modify DNA, but also modify RNA,” Yang explained. Metal carcinogen modification of RNAs is an “exciting and new mechanism” for understanding metal carcinogenesis.

By studying modifications in RNA, researchers may be able to find a biomarker for the disease before cancer develops.

Yang is trying to find some specific epigenetic changes that might occur in response to different pollutants.

Stony Brook attraction

Yang was impressed with the dedication of Stony Brook Pathology Chair Ken Shroyer, whom he described as a “really great physician scientist. His passion in research and leadership in supporting research” helped distinguish Stony Brook, Yang said.

Yang is confident that Stony Brook has the resources he and Wang need to be successful, including core facilities and collaborative opportunities. “This is a very great opportunity for us, with strong support at the university level,” he said.“We plan to be here and stay forever.”

Yang is in the process of setting up his lab, which includes purchasing new equipment and actively recruiting scientists to join his effort.

“We need to reestablish our team,” he said. “Right now, we are trying to finish our current research project.”

He hopes to get new funding for the university in the next two to three years as well. After he establishes his lab at Stony Brook, Yang also plans to seek out collaborative opportunities at Cold Spring Harbor Laboratory, which is “very strong in RNA biology,” he added.

A return home

Returning to the Empire State brings Yang full circle, back to where his research experience in the United States started. About 23 years ago, his first professional position in the United States was at New York University.

Outside of work, Yang likes to hike and jog. He is looking forward to going to some of Long Island’s many beaches.

He and Wang live in an apartment in South Setauket and are hoping to buy a house in the area. The couple discusses science regularly, including during their jogs.

Working in the same area provides a “huge opportunity” for personal and professional growth, he said.

Yang suggested that his wife usually spends more time training new personnel and solving lab members’ technical issues. He spends more time in the lab with general administrative management and support. Wang has “much stronger molecular biology skills than I have,” Yang explained in an email, whereas he has a solid background in toxicology.

Growing up, Yang said he had an aptitude in math and had dreamed of becoming a software engineer. When he applied to college, he received admission to medical school, which changed his original career path.

Once he started running his own experiments as a researcher, he felt he wanted to improve human health.“Once humans develop disease, in many cases, it’s very expensive to treat and [help] people recover,” he said. “Prevention could be a more cost effective way to improve health.”

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