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Power of 3

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Evan Musterman at the SRX beamline. Photo by Kevin Coughlin/Brookhaven National Laboratory

By Daniel Dunaief

It’s everywhere, from holding the water we drink to providing a cover over the Norman Rockwell painting of “The Three Umpires” to offering a translucent barrier between our frigid winter backyards and the warm living room.

While we can hold it in our hands and readily see through it, glass and its manufacture, which has been ongoing for about 4,000 years, has numerous mysteries.

Indeed, given enough temperature and time, glass crystallizes. Controlling the process has been used to increase strength and chemical durability, tailor thermal properties and more over the last several decades.

Evan Musterman, who studied the way lasers served as a localized heat source to induce single crystal formation in glass when he was a graduate student at Bethlehem, Pennsylvania-based Lehigh University, joined Brookhaven National Laboratory in September as a postdoctoral researcher.

Musterman, who received funding for nine months at the end of his PhD program through the Department of Energy’s Office of Science Graduate Student Research program when he was at Lehigh that enabled him to work at BNL, is adding scanning x-ray diffraction mapping as a more user-ready technique at the Submicron Resolution X-ray Spectroscopy beamline (or SRX) that he used as a graduate student. 

The beamline looks at x-ray fluorescence measurements, which provide information about the elemental distribution and chemical information, such as oxidation state and bond distances, in an experimental sample. The next component scientists are looking for is using diffraction to inform the crystal structure of the material and to gather information about strain, explained Andrew Kiss, the lead beamline scientist for the SRX.

Musterman hopes to build on the electron diffraction mapping he did during his PhD work when he studied the crystals he laser-fabricated in glass. X-rays, he explained, are more sensitive to atomic arrangements than electrons and are better at mapping strain.

Musterman’s “background in materials science and crystal structures made him an excellent candidate for a post-doc position,” Kiss said.

The SRX has applications in material science, geological science and biological imaging, among other disciplines. 

Glass questions

For his PhD research, Musterman worked to understand how glass is crystallizing, particularly as he applied a laser during the process. He explored how crystal growth in glass is unique compared with other methods, leading to new structures where the crystal lattice can rotate as it grows.

Musterman finds the crystallization of glass ‘fascinating.” Using diffraction, he was able to watch the dynamics of the earliest stages after a crystal has formed. In his PhD work, he used a spectroscopy method to understand the dynamics of glass structure before the crystal had formed.

Musterman started working at the SRX beamline in June of 2022. He was already familiar with the beamline operation, data collection and types of data he could acquire, which has given him a head start in terms of understanding the possibilities and limitations.

In his postdoctoral research, he is developing diffraction mapping and is also finishing up the experiments he conducted during his PhD.

Himanshu Jain, Musterman’s PhD advisor at Lehigh who is Professor of Materials Science and Engineering, was pleased with the work Musterman did during his five years in his lab. Jain sees potential future extensions and applications of those efforts.

Musterman’s research “forms a foundation for integrated photonics, which is expected to revolutionize communications, sensors, computation and other technologies the way integrated circuits and microelectronics did 50-60 years ago,” Jain explained in an email. The goal is to “construct optical circuits of single crystal waveguides in a glass platform.”

Musterman’s work “showed details of these optical elements made in glass by a laser,” he added.

Jain, who is an alumnus of BNL, indicated that his lab is continuing to pursue the research Musterman started, with his former graduate student as a collaborator and guide.

Musterman appreciates the opportunity to work with other scientists from different academic and geographic backgrounds. In addition to working with other scientists and helping to refine the functionality of the SRX beamline, he plans to continue glass and glass crystallization research and their interactions with lasers. As he refines techniques, he hopes to answer questions such as measuring strain.

As glass is heated, atoms form an ordered crystalline arrangement that begins to grow. The nucleation event and crystal growth occurs at the atomic scale, which makes it difficult to observe experimentally. Nucleation is also rare enough to make it difficult to simulate.

Most theories describe crystal nucleation and growth in aggregate, leaving several questions unanswered about these processes on single crystals, Musterman explained.

As they are for most material processing, temperature and time are the most important factors for glass formation and glass crystallization.

Historically, studies of glass structure started shortly after the discovery of x-ray diffraction in 1913. In the 1950’s, S. Donald Stookey at Corning discovered he could crystallize glass materials to improve properties such as fracture resistance, which led to a new field of studies. Laser induced single crystal formation is one of the more recent developments.

Musterman and his colleagues found that laser crystallization does not always produce the same phase as bulk crystallization, although this is an active area of research.

Musterman created videos of the earliest stages of crystal growth under laser irradiation by direct imaging and with electron and x-ray diffraction.

Kiss anticipates that Musterman, who is reporting to him, will build infrastructure and understanding of the detection system in the first year, which includes building scanning routines to ensure that they know how to collect and interpret the data.

Once Musterman demonstrates this proficiency, the beamline scientists believe this expanded technical ability will interest scientists in several fields, such as materials science, energy science, Earth and environmental science and art conservation.

Pitching in with former colleagues

While Musterman is not required to work with other beamline users, he has helped some of his former colleagues at Lehigh as they “try to get their best data,” he said. He has also spoken with a scientist at Stony Brook University who has been collecting diffraction data.

A native of Troy, Missouri, Musterman lives in an apartment in Coram. When he was younger, he said science appealed to him because he was “always curious about how things worked.” He said he frequently pestered his parents with questions.

His father John, who owns a metal fabrication and machining business, would take various ingredients from the kitchen and encourage his son to mix them to see what happened. 

As for the future, Musterman would like to work longer term in a lab like Brookhaven National Laboratory or in industrial research.

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Jin Koda and Amanda Lee at the recent 243rd annual meeting of the American Astronomical Society in New Orleans. Photo by Jenny Zhang

By Daniel Dunaief

Hollywood is not the only place fascinated with the birth of stars. Indeed, researchers at Stony Brook University, among many other academic institutions, have focused considerable time, energy and effort into understanding the processes that lead to the creation of stars.

Astronomers had tried, unsuccessfully, to detect molecular clouds in the galaxy outskirts, which is how stars form in the inner part of galaxies.

About 18 years ago, a NASA satellite called GALEX discovered numerous newly formed stars at the edges of a spiral galaxy M83, which is 15 million light years from Earth. 

Leading an international team of scientists, Jin Koda, Professor in the Department of Physics and Astronomy at Stony Brook University, together with his former undergraduate student Amanda Lee, put together data and information from a host of sources to describe how these stars on the outer edge of the galaxy formed.

Their work demonstrated star-forming molecular clouds in this outer area for the first time.

“These molecular clouds at the galaxy edge are forming stars as much as the molecular clouds in normal parts of galaxies” such as molecular clouds around the sun, Koda explained.

Before their discovery, Koda said astronomers had considered that new-born stars at galaxy edges could have formed without molecular clouds.

Koda recently presented this work at the 243rd annual meeting of the American Astronomical Society in New Orleans.

Indeed, partnering with scientists from the United States, Japan, France and Chile, Koda, who is the Principal Investigator on the study, and Lee found evidence of 23 of these molecular clouds on the outskirts of the M83 galaxy.

Combining data from a host of telescopes for this research, Koda and Lee found “higher resolution than before,” Lee said. “We could see a peak of atomic hydrogen in that region, which we didn’t know before.”

While helium also exists in the molecular clouds in the galaxy edges as well as in the atomic gas and in stars, it does not emit light when it’s cold, which makes its signature harder to detect.

Scientists are interested in “why we weren’t able to detect these molecular clouds for such a long time,” Lee said. “We ended up using a different tracer than what is normally used.”

The group came up with a hypothesis for why the molecular clouds were difficult to find. Carbon monoxide, which typically helps in the search for such clouds, is dissociated in the large envelopes at the galaxy edges. Only the cores maintain and emit this gas.

A collaboration begins

When Lee, who grew up in Queens, started at Stony Brook University, she intended to major in physics. In her sophomore year, she took an astronomy class that Koda taught.

“I was very interested in studying galaxies and the evolution of galaxies,” Lee said.

After the course ended, she started working in Koda’s lab.

“Her tireless efforts made her stand out,” Koda explained in an email. Koda appreciates how speaking with students like Lee helps him think about his research results.

Lee is “particularly good at identifying and asking very fundamental questions,” he added.

At one point about two years before she graduated in 2022, Lee recalled how Koda shared a picture of M83 and described the mystery of star formation at the outskirts of galaxies.

Two years later, by delving into the data under Koda’s supervision, she helped solve that mystery.

“I didn’t know my work would end up contributing to this project,” Lee said. “It’s really exciting that I was able to contribute to the big picture of star formation” in distant galaxies.

Since graduating from Stony Brook, Lee has been a PhD student for the last year and a half at the University of Massachusetts at Amherst.

At this point, Lee is still working towards publishing a paper on some of the work she did in Koda’s lab that explores the formation of stars in the inner disk of M83.

“Broadly,” she said, the two research efforts are “all related to the same picture.”

For her part, Lee was pleased with the opportunity to work with such a geographically diverse team who are all contributing to the goal of understanding star formation.

Future focus

The area they observed is relatively small and they would like to see more regions in M83 and other galaxies, Koda explained.

Finding so many molecular clouds at once in the small region “encourages us to hypothesize that the process is universal,” although scientists need to verify this, Koda said.

The researchers also discovered more atomic gas than they would expect for the amount of molecular clouds. A compelling discovery, this observation raised questions about why this abundant atomic gas wasn’t becoming molecular clouds efficiently.

“We need to solve this mystery in future research,” Koda explained. He is pleased with the level of collaboration among the scientists. “It’s very interesting and stimulating to collaborate with the excellent people of the world,” he said.

A resident of Huntington, Koda grew up in Tokyo, where he earned his bachelor’s, master’s and PhD degrees. When he moved to the United States, Koda conducted post doctoral studies for six years at Cal Tech. 

About 15 years ago, he moved to Stony Brook, where he replaced Professor Phil Solomon, who was one of the pioneers of molecular cloud studies in the Milky Way galaxy.

Science appeals to Koda because he is “interested in how things work, especially how nature works,” he said.

In this work, Koda suggested that the molecular clouds have the same mass distribution as molecular clouds in the Milky Way, indicating that star formation is the same, or at least similar, between the Milky Way and galaxy edges.

Koda made the discovery of the molecular clouds and the hypothesis about the carbon monoxide deficient cloud envelope in 2022. Since then, he and his team have obtained new observations that confirmed that what they found were the “hearts of molecular clouds,” he said.

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James Konopka. Photo by Susan Watanabe

By Daniel Dunaief

Most of the time, the fungus Candida albicans, which is ubiquitous on the skin, inside people’s mouths, throat, and guts, among other places, doesn’t cause problems. It can, however, be an opportunistic infection, particularly in people who are immunocompromised, leading to serious illness and even death.

Antifungal infections work best during the early stage of an infection. Once a severe infection becomes established, it responds less well to drugs, as resistance can become a problem.

James “Jamie” Konopka, Professor in the Department of Microbiology and Immunology in the Renaissance School of Medicine at Stony Brook University, is working to find the mechanism that enables C. albicans to resist attack by the immune system. His long term goal is to identify ways to make the fungus more vulnerable to immune defenses.

In a paper published recently in the journal mBio, which is published by the American Society of Microbiology, Konopka identified the mechanism by which hypochlorous acid, which is produced by cells in the immune system, attacks C. albicans.

He expanded this by testing forms of the fungus that lack specific genes. These mutants can be more vulnerable to attack by hypochlorous acid, which is produced by neutrophils and is also called “human bleach.” Longer term, Konopka hopes to find ways to sensitize the fungus to this acid, which would bolster the ability of the immune system to respond to an infection.

His study showed that hypochlorous acid disrupts the plasma membrane, which is a layer of lipids that surround the cell. Once this is breached, parts of the cell leak out, while more bleach can damage the fungus.

Hypochlorous acid reacts with proteins, lipids and DNA.

The activated immune system produces several chemicals known as “reactive oxygen species.” In some cells, particularly neutrophils, hydrogen peroxide is converted into hypochlorous acid to strengthen and diversify the attack.

To be sure, the discovery of the mechanism of action of hypochlorous acid won’t lead to an immediate alternative therapeutic option, as researchers need to build on this study.

Future studies will examine how some genes promote resistance, and which are likely to be the most promising targets for drug development, Konopka explained.

Increase sensitivity

These are C. albicans cells growing invasively into tissue in a mouse model of an oral infection. The candida hyphae are stained black, and the tissue is stained a blue/green. Image from James Konopka

Konopka suggested that increasing the sensitivity of the fungus to hypochlorous acid would likely prove more effective and less potentially toxic than increasing the amount of the acid, which could also damage surrounding tissue.

“Our idea is to sensitize fungal pathogens” to hypochlorous acid “rather than upping the dose of bleach, which could lead to negative consequences,” Konopka said. Ideally, he’d like to “take the normal level and make it more effective” in eradicating the fungus.

Other scientists funded by the National Institutes of Health created a set of about 1,000 different strains of the fungus, which provides a valuable resource for Konopka and others in the scientific community.

In a preliminary screen of plasma membrane proteins, Konopka and his team found that most of the mutants had at least a small increase in sensitivity. Some, however, had stronger effects, which will guide future experiments.

One of the challenges in working with a fungus over pathogens like bacteria or viruses is that fungi are more closely related biologically to humans. That means that an approach that might weaken a fungus could have unintended and problematic consequences for a patient.

“Although they may look very different on the outside, the inner workings of fungi and humans are remarkably similar,” Konopka explained in an email. This has made it difficult to find antifungal drugs that are not toxic to humans.

An ‘overlooked’ ally

Konopka suggested that scientists have been studying hydrogen peroxide, which is also made by immune system combatants like macrophages and neutrophils.

“It seemed to us that somehow bleach had been overlooked,” Konopka said. “It hadn’t been studied in the fungal world, so we launched” their research.

Konopka also believes the plasma membrane represents an effective place to focus his efforts on developing new drugs or for making current drugs more effective. 

Hydrochlorous acid “fell into our wheel house,” he said. In initial tests, Konopka discovered that human bleach caused damage to the membrane within minutes if not sooner, allowing outside molecules to enter freely, which could kill the potentially dangerous infection.

Considering the ubiquitous presence of the fungus, immunocompromised people who might conquer an infection at any given time could still be vulnerable to a future attack, even after an effective treatment. Even people with a healthy immune system could be reinfected amid a large enough fungal load from a biofilm on a medical device or catheter.

Providing vulnerable people with a prophylactic treatment could lower the risk of infection. When and if those patients develop an ongoing and health-threatening infection, doctors could use another set of drugs, although such options don’t currently exist.

In other work, Konopka has identified proteins in C. albicans that help CoQ, or ubiquinone, protect the plasma membrane from oxidation by agents such as hydrogen peroxide and hypochlorous acid.

People can purchase ubiquinone at local stores, although Konopka urges residents to check with their doctors before taking any supplement.

Fish and beer

An organizer of a department wide Oktoberfest, Konopka was pleased that faculty, post doctoral researchers and students were able to decompress and enjoy the fall festival together for the first time since 2019.

In addition to a range of beer, attendees at the event, which occurred half way between the start of the semester and final exams, were able to partake in German food from Schnitzels in Stony Brook Village, which was a big hit.

An avid fly fisherman who catches and releases fish, Konopka said he caught some bigger striped bass this year than in previous years.

When he’s fishing, Konopka appreciates the way the natural world is interconnected. He pays attention to variables like the weather, water temperature, bait fish and the phases of the moon.

He particularly enjoys the wind and fresh air. This year, Konopka marveled at the sight of a bald eagle.

As for his work, Konopka said basic research may have an immediate effect or may contribute longer term to helping others in the scientific community build on his results, which could lead to the next breakthrough.

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Dima Kozakov. Photo from SBU
Michael Zingale. Photo by John Griffin/SBU

By Daniel Dunaief

They have little in common. One studies deep inside cells to understand the difference between diseased and healthy states. The other explores models that represent distant thermonuclear reactions.

What Stony Brook University’s Dima Kozakov, Professor in the Department of Applied Mathematics and Statistics, and Michael Zingale, Professor in the Department of Physics and Astronomy, share, however, is that both led teams that recently won a Department of Energy grant that will allow them to use the fastest publicly available supercomputer in the world, at DOE’s Oak Argonne and Oak Ridge National Laboratories.

Kozakov and Zingale, who are both members of the Institute for Advanced Computational Sciences, are recipients of the DOE’s grants through its Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program.

“It’s a huge recognition of computation” not just at the IACS, but also for Stony Brook in general, said Robert Harrison, Director of the IACS and Professor in the Department of Mathematics & Statistics. Kozakov and Zingale are the “point persons on world-class teams [which] positions Stony Brook at the forefront of the scientific community.”

Harrison suggested that the astrophysics group at Stony Brook was already world class when he arrived a decade ago and the university has been pushing to move Stony Brook to take advantage of all the modern powerful tools for simulation and data driven discovery.

Disease states

Kozakov, who is also an affiliate of the Laufer Center for Physical and Quantitative Biology,  plans to model enormous numbers of molecular interactions to compare how they function in diseased cells with how they work in healthy cells.

He and his team will get the data on important proteins and interactions in disease compared with healthy cells from high throughput but noisy experiments and validate those computationally.

By studying diseases such as cancer, diabetes and Alzheimer’s, Kozakov plans to look for clues about what occurs at the level of the atomic structure of protein interactions, hoping such an analysis points to the creation of new types of therapies.

Kozakov will use a combination of publicly available data and information from some of his experimental collaborators to identify new targets that small molecules may alter amid a diseased state. He feels the tight integration between the theoretical and the experimental nature of the team will enhance its effectiveness.

A supercomputer “allows you to try many approaches in parallel” such as training deep learning models that require trying many options to get the best possible ones, he said.

The pilot work the team has done created the kind of momentum that increased the chance of securing funds and time through the INCITE program.

Kozakov and co-investigators including Assistant Professor Pawel Polak at Stony Brook, Professor Andrew Emili at OHSU, Associate Professor Matthew Torres at Georgia Tech and Julie Mitchell, the Director of Biosciences Division at Oak Ridge National Laboratory, were “very happy” when they learned they’d won the award. he said. “It’s good to know that people appreciate the [work] we are doing.”

Starry, starry explosion

In the meantime, Zingale’s project, called “Exascale Models of Astrophysical Thermonuclear Explosions,” was renewed for a second year in the INCITE program.

Zingale leads a team that explores two types of astrophysical thermonuclear explosions to understand these physical processes and their broader implications. The computational work is focused mostly on whether a particular model for a thermonuclear explosion is viable.

“We really want to just understand: does it explode or not?” Zingale explained. His work focuses on the explosion mechanism and on the design of algorithms that can efficiently model these explosions.

Graduate students Zhi Chen, Alexander Smith Clark, Eric Johnson, Melissa Rasmussen, and Khanak Bhargava will be working with the supercomputer in the next year, Zingale added.

“Each student is working on separate questions, both on this problem and on related problems (novae and x-ray bursts),” said Zingale. “The goals are the same — in each case, we want to produce a realistic model of the burning that takes place in these events to understand how these explosions unfold.”

Models help connect to the observations astronomers make. While the work doesn’t produce new physics, it allows researchers to gain a greater understanding of supernovae.

Numerous other groups around the world are pursuing similar simulations, which Zingale explained is favorable for the science.

“If we all get the same result using different codes and techniques, then it gives us confidence that we might be understanding what is actually taking place in nature,” he said.

The explosions Zingale is studying differ from those on Earth because they are far larger and can reach higher densities in stars, which produces elements up to iron in explosions. The tools he uses to model these explosions have “similarities to the techniques used to model chemical combustion on Earth,” he said. “We work with applied mathematicians that study terrestrial flames and can use the techniques” in the astrophysical setting.

Zingale explained that he was always interested in astronomy and computers, so this field of work serves as the bridge between the two.

For students interested in the field, Zingale added that it teaches people how to solve complex problems on computers.

“Even if you don’t stay in the field, you build skills that are transferable to industry (which is where many of my graduate students wind up),” he said. He urges people to study something they enjoy. The main code he uses is called Castro and is freely available online, which means that “anyone can look at what we’ve done and run it for themselves,” he explained.

Student opportunities

For Stony Brook graduate students, these INCITE awards offer opportunities for additional learning and career advancement.

“The excitement is infectious,” said Harrison. “The students see not just the possibility to be at the frontier of discovery and the frontier of technology [but also to have] the career opportunities that lie beyond that.”

Students trained to make effective use of these platforms of cutting-edge science are “heavily recruited, going into industry, national labs, working for the likes of Google and so on,” Harrison added.

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Photo courtesy of SBU

By Daniel Dunaief

Predicting extreme heat events is at least as important as tracking the strength and duration of approaching hurricanes.

Ping Liu

Extreme heat waves, which have become increasingly common and prevalent in the western continental United States and in Europe, can have devastating impacts through wildfires, crop failures and human casualties.

Indeed, in 2003, extreme heat in Europe caused over 70,000 deaths, which was the largest number of deaths from heat in recent years.

Recently, a trio of scientists at Stony Brook University’s School of Marine and Atmospheric Sciences (SoMAS) received $500,000 from the National Oceanographic and Atmospheric Administration to study heat events by using and analyzing NOAA’s Seamless System for Prediction and EArth System Research, or SPEAR, to understand heat waves and predict future such events.

The first objective is to evaluate simulations in the SPEAR model, by looking at how effectively this program predicts the frequency and duration of heat events from previous decades, said Ping Liu, who is the Principal Investigator on the project and is an Associate Professor at SoMAS.

Liu was particularly pleased to receive this funding because of the “urgent need” for this research, he explained in an email.

The team will explore the impact of three scenarios for increases in overall average temperature from pre-Industrial Revolution levels, including increases of 1.5 degrees Celsius, 2 degrees Celsius and four degrees Celsius, which are the increases the IPCC Assessment Reports has adopted.

Answering questions related to predicting future heat waves requires high-resolution modeling products, preferably in a large ensemble of simulations from multiple models, for robustness and the estimation of uncertainties, the researchers explained in their proposal.

“Our evaluations and research will provide recommendations for improving the SPEAR to simulate the Earth system, supporting NOAA’s mission of ‘Science, Service and Stewardship,’” they explained.

Kevin Reed, Professor, and Levi Silvers, research scientist, are joining Liu in this effort.

Liu and Reed recently published a paper in the Journal of Climate and have conducted unfunded research on two other projects. Liu brought Silvers into the group after Reed recommended Silvers for his background in climate modeling and dynamics.

Reed, who is Interim Director of Academic, Research and Commercialization Programs for The New York Climate Exchange, suggested that the research the heat wave team does will help understand the limitations of the SPEAR system “so that we can better interpret how the modeling system will project [how] blocking events and heat will be impacted by climate change.”

An expert in hurricanes, Reed added that blocking events, which can cause high pressure systems to stall and lead to prolonged heat waves, can also lead to unique hurricane tracks, such as Hurricane Sandy in 2012.

“A longer term goal of many of my colleagues at Stony Brook University is to better understand these connections,” said Reed, who is Associate Provost for Climate and Sustainability Programming and was also recently appointed to the National Academies’ Board on Atmospheric Sciences and Climate.

Liu will use some of the NOAA funds to recruit and train a graduate student, who will work in his lab and will collaborate with Reed and Silvers.In the bigger picture, the Stony Brook researchers secured the NOAA backing in the same year that the university won the bidding to develop a climate solutions center on Governors Island.

Reed suggested that the “results of the work can be shared with our partners and can help to inform future societally relevant climate research projects.”

Focus on two regions

The systems that have caused an increase in heat waves in the United States and Europe are part of a trend that will continue amid an uneven distribution of extreme weather, Liu added.

Heat waves are becoming more frequent and severe, though the magnitude and impact area vary by year, Liu explained.

The high pressure systems look like ridges on weather maps, which travel from west to east.

Any slowing of the system, which can also occur over Long Island, can cause sustained and uncomfortable conditions.

Over the past several years, Liu developed computer algorithms to detect high pressure systems when they become stationary. He published those algorithms in two journal papers, which he will use in this project.

Personal history

Born and raised in Sichuan, China, Liu moved to Stony Brook from Hawaii, where he was a scientific computer programmer, in November of 2009.

He and his wife Suqiong Li live in East Setauket with their 16-year old daughter Mia, who is a student at Ward Melville High School and  a pianist who has received classical training at the Manhattan School of Music. Mia has been trained by award-winning teacher Miyoko Lotto.

Outside of the lab, Liu, who is five-feet, seven-inches tall, enjoys playing basketball on Thursday nights with a senior basketball team.

Growing up in China, Liu was always interested in weather phenomenon. When he was earning his PhD in China at the Institute for Atmospheric Physics at the Chinese Academy of Sciences in Beijing, he had limited computer resources, working in groups with IBM and, at times, Dell computer. He built several servers out of PC parts.

With air trapped inside the basin surrounded by tall mountains, Sichuan is particularly hot in the summer, which motivated him to pursue the study of heat waves.

Liu appreciated how Stony Brook and Brookhaven National Laboratory had created BlueGene, which he used when he arrived.

As for the future of his work, Liu believes predicting extreme heat waves is increasingly important “to help planners from local to federal levels cope with a climate that is changing rapidly and fostering more frequent and more severe heat events,” he explained.

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Zhe Qian

By Daniel Dunaief

Addition and subtraction aren’t just important during elementary school math class or to help prepare tax returns.

As it turns out, they are also important in the molecular biological world of healthy or diseased cells.

Some diseases add or subtract methyl groups, with a chemical formula of CH3, or phosphate groups, which has a phosphorous molecule attached to four oxygen molecules.

Nicholas Tonks. Photo courtesy of CSHL

Adding or taking away these groups can contribute to the progression of a disease that can mean the difference between sitting comfortably and watching a child’s performance of The Wizard of Oz or sitting in a hospital oncology unit, waiting for treatment for cancer.

Given the importance of these units, which can affect the function of cells, researchers have spent considerable time studying enzymes such as kinases, which add phosphates to proteins.

Protein tyrosine phosphatases, which Professor Nicholas Tonks at Cold Spring Harbor Laboratory purified when he was a postdoctoral researcher, removes these phosphate groups.

Recent PhD graduate Zhe Qian, who conducted research for six years in Tonks’s lab while a student at Stony Brook University, published a paper in the journal Genes & Development demonstrating how an antibody that interferes with a specific type of protein tyrosine phosphatase called PTPRD alters the way breast cancer spreads in cell cultures.

“The PTPs are important regulators of the process of signal transduction — the mechanisms by which cells respond to changes in their environment,” explained Tonks. “Disruption of these signal transduction mechanisms frequently underlies human disease.”

To be sure, Tonks cautioned that the study, which provides a proof of concept for the use of antibodies to manipulate signaling output in a cancer cell, is a long way from providing another tool to combat the development or spread of breast cancer.

The research, which formed the basis for Qian’s PhD project, offers an encouraging start on which to add more information.

Blocking the receptor

Qian, who goes by the name “Changer,” suggested that developing a compound or small molecule to inhibit or target the receptor for this enzyme was difficult, which is “why we chose to use an antibody-based method,” he said.

By tying up a receptor on the outside of the cell membrane, the antibody also doesn’t need to enter the cell to reach its target.

The Antibody Shared Resource, led by Research Associate Professor Johannes Yeh, created antibodies to this particular receptor. Yeh created an antibody is shaped like a Y, with two arms with specific attachments for the PTPD receptor.

Once the antibody attaches, it grabs two of these receptors at the same time, causing a dimerization of the protein. Binding to these proteins causes them to lose their functionality and, ultimately, destroys them.

Cell cultures of breast cancer treated with this antibody became less invasive.

Limited presence

One of the potential complications of finding a new target for any treatment is the side effects from such an approach.

If, for example, these receptors also had normal metabolic functions in a healthy cell, inhibiting or killing those receptors could create problematic side effect.

In this case, however,  the targeted receptor is expressed in the spine and the brain. Antibodies normally don’t cross the blood-brain barrier.

Qian and Tonks don’t know if the antibody would affect the normal function of the brain. Further research would help address this and other questions.

Additionally, as with any possible treatment, future research would also need to address whether cancer cells developed resistance to such an approach.

In the time frame Qian explored, the cells in culture didn’t become resistant.

If the potential therapeutic use of this antibody becomes viable, future researchers and clinicians might combine several treatments to develop ways to contain breast cancer.

Eureka moment

In his research, Qian studied the effect of these antibodies on fixed cell, which are dead but still have the biochemical features of a living cell He also studied living cells.

When the antibody attaches to the receptor, it becomes visible through a staining process. Most antibody candidates stain living cells. Only the successful one showed loss-of-signal in living staining.

The antibody Qian used not only limited the ability of the receptor to send a signal, but also killed the receptor. The important moment in his research occurred when he discovered the antibody suppressed cancer cell invasion in cell culture.

Outside of the lab, Qian enjoys swimming, which he does between four and five times per week. Indeed, he combined his athletic and professional pursuits when he recently raised funds for Swim Across America.

“I not only want to do research, but I also want to call more attention to cancer research in the public,” said Qian.

The Swim Across America slogan suggests that each stroke is for someone who “couldn’t be with us” because of cancer. In the lab, Qian thinks each time he pipettes liquids during one of his many experiments it is for someone who couldn’t make it as well.

Qian, who currently lives in Hicksville, grew up in Suchow City, which is a village west of Shanghai and where Cold Spring Harbor Asia is located. 

Qian has been living on Long Island since he arrived in the United States. Qian graduated from Stony Brook University in October and is currently looking for a job in industry.

Looking back, Qian is pleased with the work he’s done and the contribution he’s made to breast cancer research. He believes the antibody approach offers a viable alternative or complement to searching for small molecules that could target or inhibit proteins or enzymes important in the development of cancer.

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From left, Daisy Zavala, Stacey Scott and Krishna Veeramah Photo by John Griffin/Stony Brook University

By Daniel Dunaief

They can’t tell you whether the leading current presidential Republican and Democratic candidates demonstrate signs of cognitive decline or, for that matter whether any real or perceived cognitive decline is greater for one than the other.

Researchers at Stony Brook University, however, have conducted recent studies that may act as a platform to generate a measure of cognitive age that differs from chronological age.

Associate Professors Krishna Veeramah and Stacey Scott and graduate student Daisy Zavala recently published research in the Journal of Gerontology: Biological Sciences in which they studied a combination of cognitive testing done over different time periods and blood tests.

Indeed, the combination of looking at signs of epigenetic changes, or alterations in the environment that affect the way genes work, and studying the effectiveness and variability of tests of memory has the potential to offer some clues about how chronological age may differ from cognitive age. At this point, the scientists have been exploring that relationship, while future work may address not just what is happening, but also why.

Among the data from 142 subjects who took a host of learning tests from 2012 to 2016 during different time periods in the day, increasing epigenetic age was linked with poorer average processing speed and working memory, as well as with greater variability in test performance.

While the statistical analysis accounted for the fact that increasing chronological age had an effect, biological age had an even bigger impact, Veeramah, who is in the Department of Ecology and Evolution and a population geneticist at Stony Brook University, explained.

The study, which Veeramah described as an “early/pilot study,” and will require further follow up, offers another perspective on the different impacts the aging process can have on cognitive function.

The results matched the scientists’ prediction, which was that people who had greater epigenetic age acceleration processed information more slowly and had poorer memory performance on average across the study.

These individuals were not only performing more poorly on average, but were also more variable in their performance.

“This should give us pause about making judgments about people related to their age and what that means about their abilities,” said Scott, who is in the Psychology department.

This study suggests that “how old you are doesn’t tell you so much about how well you’re doing in your cognitive function,” said Scott. Theoretically, the extent to which a person’s body is older than a chronological age could be an indication of what might accelerate or decelerate cognitive function, although longitudinal studies will test this.

The researchers believe this study will contribute to a body of work that is trying to see if researchers can reliably identify biological age acceleration and, if so, how to slow it down.

Testing design

The researchers gathered data from participants who took tests on smartphones provided to them. These phones didn’t receive calls or messages and didn’t have access to the web.

Participants took tests during different times in the day. About 60 percent of study participants were African American and 20 percent were Hispanic/Latino. They also varied in household income, with most participants earning between $20,000 to $60,000.

In one test, people saw symbols at the top of the screen that they had to match with symbols at the bottom as quickly as possible. In another test, people viewed three red dots on a grid for a few seconds. They were distracted by searching for “E’s” and “F’s” on a screen and then had to place the dots back in their original place on the grid.

Participants completed dozens of tests over two weeks, offering a profile of their performance during different times of the day, situations and activities.

By testing people under various conditions, the researchers could get a more comprehensive, complete and realistic understanding of their cognitive state, which also reflects the way people experience a range of competing stimuli.

The scientists were profiling people “in terms of good and bad days” to get an understanding of their “typical performance,” explained Scott.

The SBU scientists suggested that inconsistency was increasingly proposed as a potential early indicator of dementia.

The “unique aspect” of what these scientists did is comparing epigenetic data to ambulatory cognitive measurements, rather than cognitive tests in a lab setting, Veeramah said.

To test the epigenome, Veeramah explored the degree of methylation of DNA from a single blood sample from each participant using a microarray to look at about a million positions in the human genome.

Adding a CH3 group, or methylating, genes tends to make the DNA coil more tightly, making it less likely to interact with other molecules that might turn it on.

Some parts of DNA show changes in methylation that correlate with age, while others are dependent on other things like the environment or specific cell type.

The underlying assumption is that cells pick up more damage and this includes the DNA sequence with time.

Zavala’s dissertation extends this work to look at more long term implications on cognitive health.

Zavala’s research “looks forward,” Scott explained in an email. “Does someone’s epigenetic age acceleration now at the beginning of the study predict their cognitive performance up to three years later?”

Dinner and a hypothesis

Veeramah and Scott, who got married in 2020, decided to combine their expertise for a research project.

“We were talking about our work over dinner and we thought about what I do and the kind of data we have from this existing sample of people” who participated in this cognitive study, said Scott.

The couple wrote a small grant to the research foundation at Stony Brook, which provided seed funding for this study.

Veeramah, whose research covers a broad scope of topics, suggested that the concept of studying these clocks is a fairly new area.

Researchers have been testing whether obesity, Alzheimer’s, and other factors could correlate with the internal environments that cause the kind of wear and tear often associated with aging.

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From left, Joshua Rest and Jackie Collier. The blurred image in the background shows the genome structure of Aurantiochytrium limacinum, including the arrays of rDNAs at the chromosome ends, and the two mirusvirus elements that were discovered. Photo by Donna DiGiovanni

By Daniel Dunaief

They were trying for two years to solve a puzzle that didn’t make sense. Then, a combination of another discovery, some extensive analysis, and a deep dive into the past helped them put the pieces together.

Jackie Collier, Associate Professor at the School of Marine and Atmospheric Sciences at Stony Brook University and Joshua Rest, also an Associate Professor in the Department of Ecology and Evolution at Stony Brook, had been looking closely at the genetic sequence of a marine protist called Aurantiochytrium limacinum. A circular section and pieces at the end of the chromosome seemed inconsistent with the rest of the genes and with the specific type of single-celled organism.

But then, they saw a preprint of a paper in 2022 that the prestigious journal Nature published earlier this year that described a new type of virus, called a mirusvirus, which appeared to have genetic similarities and a signature that matched what they saw in their protist.

Mirus means “strange” or unknown in Latin, which was a way to describe the unusual evolutionary traits of these viruses.

Collier and Rest, working with a group of collaborators, found that a high copy circular structure and genetic elements that integrated at the end of one chromosome resembled this mirusvirus.

“From the perspective of the virus folks, ‘mirus’ was apt because the mirusviruses contain features of the two very distinct ‘realms’ of viral diversity,” Collier explained. “Our results confirm that strangeness, and add more strangeness in terms of two different ways to maintain themselves (circular episomes or integrated into a chromosome) in the same host genome.”

Researchers had discovered the mirusvirus by sequencing DNA they took from the ocean. “What our findings do is connect to a host and hopefully eventually prove that there is a protist that contains a mirusvirus genome,” said Collier.

The Aurantiiochytrium protist, which is part of the Thraustochytrids order, intrigues researchers in part because it produces essential omega-3 fatty acids and carotenoids, which enhances its biotechnology potential. This protist also intrigues Collier because it is involved in decomposing dead mangrove leaves in mangrove forests.

Dormant virus

The Stony Brook scientists have been working on analyzing the genome for a paper they recently published in the journal Current Biology since 2019.

“We had been struggling to figure out what that was,” said Collier. “We had a lot of hints that it had some relationship to some kind of viruses, but it wasn’t similar enough to any known virus. We were struggling to figure out what to call this thing,” which they had tentatively designated CE1, for circular element one.

Identifying viral elements provided the “hook” for the paper.

Rest suggested that the different confounding elements in the protist genome came from two different viruses.

At this point, Collier and Rest think the virus may be something like the herpesvirus, which hides out in human nerve cells. That virus enters a latent phase, remaining quiescent until a host becomes stressed.

John Archibald, Lucie Gallot-Lavallee and others from Dalhousie University in Canada, who are collaborators on this study, are creating the kind of conditions, such as lower food or colder temperatures, that might reactivate the viral DNA, causing it to release viral particles.

The research team has detected similar mirusvirus proteins in other Aurantiochytrium isolates and in four other Thraustochytrid genomes. 

Focusing on this protist

Collier started working on thraustochytrids in 2002, after the first outbreak of QPX disease in Raritan Bay hard clams.

Bassem Allam, who is now the Marinetics Endowed professor in Marine Sciences at SBU asked Collier if she would help understand what was going on with the clams which had QPX disease. That was caused by another Thraustochytrid.

The organism that caused QPX is a relative of the protist that interested Collier.  She chose Aurantiochytrium in part because it was the easiest to grow.

When the Gordon and Betty Moore Foundation started a program to develop molecular genetic methods for diverse marine protists about seven years ago, Collier approached Rest for a potential collaboration.

A key piece, half a century old

In her informatics work, Collier followed a path that Google or artificial intelligence might otherwise have missed.

Like traveling back hand over hand in time through older research, Collier pulled up the references from one study after another. Finally, she found an intriguing study from 1972 that had overlaps with their work.

Scientists had isolated a Thraustochytrid from an estuary in Virginia using the same kinds of methods Collier and Rest used to grow Aurantiochytrium. Using electron microscopy, these earlier researchers characterized its ultrastructure. Along the way, these 1970’s scientists noticed that starved cells released viral particles, which Collier and Rest believe might be the first record of a mirusvirus.

The researchers wrote a short paper that the prestigious journal Science published.

A cat connection

While Collier, who lives in Lake Grove, and Rest, who is a resident of Port Jefferson, are collaborators at Stony Brook, they have also have a feline connection.

In the beginning of the pandemic, a feral cat delivered kittens in Rest’s garage. Rest’s family initially tried to raise them, but allergies made such a pet arrangement untenable. 

A cat lover, Collier was searching for kittens. She adopted two of the kittens, bottle feeding them starting at three days old. When Collier and Rest speak by zoom, Rest’s children Julia, nine, and Jonah, five, visit with the cats virtually.

As for their work, Collier and Rest are intrigued by the possibility of gathering additional pieces to answer questions about this virus.

“For me, the most intriguing question is how common our observations will turn out to be — do many Thraustochytrids have latent mirusviruses?” she explained.

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Christopher Vakoc with graduate student Junwei Shi. Photo by Gina Motisi/ CSHL.

By Daniel Dunaief

It is the type of miraculous conversion that doesn’t involve religion, and yet it may one day lead to the answer to passionate prayers from a group of people on a mission to help sick children.

Researchers in the lab of Professor Christopher Vakoc at Cold Spring Harbor Laboratory have been working tirelessly to understand the fundamental biology of Rhabdomyosarcoma, or RMS, which is a type of connective tissue cancer that afflicts between 400 and 500 people each year in the United States, with more than half receiving the diagnosis before they turn 10 years old.

As a part of her PhD research, Martyna Sroka searched for a way to convert the processes involved in this cancer into something benign.

Using a gene editing tool enhanced by another former member of Vakoc’s lab, Sroka disrupted a signal she had spent years trying to find in a protein called NF-Y, causing cancerous cells in a dish to differentiate into normal muscle cells, a conversion that offers future promise for treatment.

Sroka, who is now working as a scientist in a biotechnology company focused on the development of oncology drugs, described how RMS cells look small and round in a microscope. After disrupting this protein, the “differentiated cells become elongated and spindle-like, forming those long tubular structures,” she explained.

She often grew cells on plastic dishes and the differentiated RMS cells spanned the entire diameter of a 15 centimeter plate, providing a striking visual change that highlighted that conversion.

While this research represents an important step and has created considerable excitement in the scientific community and among families whose philanthropic and fundraising efforts made such a discovery possible, this finding is a long way from creating a new treatment.

Other research has indicated that disrupting NF-Y could harm normal cells. A potential therapeutic alteration in NF-Y could be transient and would likely include follow ups such as a surgical, radiation or biological approach to remove the converted RMS cells, Vakoc explained.

Nonetheless, the research, which was published in August in the prestigious Proceedings of the National Academy of Sciences, offers a potential roadmap for future discoveries.

“It was a long journey and being able to put the pieces of the puzzle together into a satisfying mechanism, which might have broader implications not only for our basic understanding of the biology of the disease but also for potential novel therapeutic approaches, was extremely exciting and rewarding,” said Sroka.

“It’s great to see so much excitement in the pediatric cancer field, and I am hoping that with time it will translate to much-needed novel therapeutic options for pediatric patients.”

The search

Cancer signals typically involve rewiring a cell’s genetic material, turning it into a factory that creates numerous, unchecked copies of itself.

Sroka and Vakoc were searching for the kind of signal that might force those cells down what they hope is a one-way differentiation path, turning those otherwise dangerous cells into more normal muscle cells that contract.

To find this NF-Y gene and the protein it creates, Sroka, who started working in Vakoc’s lab in the summer of 2017, screened over a 1,000 genes, which Vakoc described as a “heroic effort.”

Encouraged by this discovery and as eager to find new clinical solutions as the families who helped support his research, Vakoc recognizes he needs to strike a balance between trumpeting this development and managing expectations.

Interactions with the public, including families who have or are confronting this health threat, “comes with a lot of responsibility to make sure we’re being as clear as possible about what we’ve done and what have yet to do,” said Vakoc. “It’s going to be a long and uncertain road” to come up with new approaches to this cancer.

Funding families

Some of the families who provided the necessary funding for this work shared their appreciation for the commitment that Vakoc, Sroka and others have made.

“We are very excited about the newest paper [Vakoc and Sroka] published,” said Phil Renna, the Senior Director of Communications at CSHL and Director of the Christina Renna Foundation, which he and his wife Rene formed when their daughter Christina, who passed away at the age of 16, battled the disease. The Christina Renna Foundation has contributed $478,300 to Vakoc’s lab since 2007.

“In just a few short years, he has made a major leap forward. This lights the path of hope for us and our cause,” said Renna.

Renna explained that the lab has had numerous inquiries about this research. He and others recognize that the search for a cure or treatment involves “tough, grinding work” and that considerable basic research is necessary before the research can lead to clinical trials or new therapeutics.

Paul Paternoster, whose wife Michelle succumbed to the disease and who has raised funds, called Vakoc and Sroka “brilliant and incredibly hard working,” and suggested the exciting results “came as no surprise.”

He is “extremely pleased” with the discovery from the “standpoint of what it can lead to, and how quickly it was discovered.”

Paternoster, President of Selectrode Industries Inc., which manufactures welding products and has two factories in Pittsburgh, suggested that this strategy can have implications for other soft tissue sarcomas as well.

The next steps

To build on the discoveries Sroka made in his lab, Vakoc plans to continue to use a technique Junwei Shi, another former member of his lab, developed after he left CSHL and joined the University of Pennsylvania, where he is now a tenured professor.

Shi, whom Vakoc called a “legend” at CSHL for honing the gene editing technique called CRISPR for just this kind of study, is also a co author in this paper.

In future research, Vakoc’s lab plans to take the screens Sroka used to find NF-Y to search to the entire human genome.

“That’s how the family tree of science operates,” said Vakoc. Shi “made a big discovery of CRISPR and has since continued to create new technology and that he is now sharing back” with his lab and applying it to RMS. Additionally, Vakoc plans to expand the testing of this cellular conversion from plastic dishes to animal models

Shi, who worked in Vakoc’s lab from 2009 to 2016 while he earned his PhD at Stony Brook University, expressed satisfaction that his work is paying dividends for Vakoc and others.

“It just feels great that [Vakoc] is still using a tool that I developed,” said Shi in an interview. Many scientists in the field are using it, he added.

For Shi, who was born and raised in southern China, working at Cold Spring Harbor Laboratory fulfilled a lifelong dream.

He recalled how he retrieved data one Saturday morning that indicated an interesting pattern that might reveal the power of a new methodology to improve CRISPR screening.

When Vakoc came to the lab that morning, Shi shared the data, which was a “whole turning point,” Shi said. 

Shi said he appreciates how CSHL has been “a home for me,” where he learned modern molecular biology and genetics.

When he encounters a problem in his lab, he often thinks about how Vakoc would approach it. Similarly, Vakoc suggested he also reflects on how his mentor Gerd Blobel, who is a co-author on the recent paper and is at the Children’s Hospital of Philadelphia, would respond to challenges.

As for the family members of those eager to support Vakoc, these kinds of scientific advances offer hope.

When he started this journey, Renna suggested he would feel satisfied if researchers developed a cure in his lifetime. This paper is the “next step in a marathon, but it makes us very excited,” he said.

To share the encouraging results from Vakoc’s lab with his daughter, Renna tacked up the PNAS paper to the wall in Christina’s bedroom.

 

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A Jamaican fruit bat, one of two bat species Scheben studied as a part of his comparative genomic work. Photo by Brock & Sherri Fenton

By Daniel Dunaief

Popular in late October as Halloween props and the answer to trivia questions about the only flying mammals, bats may also provide clues about something far more significant.

Despite their long lives and a lifestyle that includes living in close social groups, bats tend to be resistant to viruses and cancer, which is a disease that can and does affect other mammals with a longer life span.

Armin Scheben

In recent work published in the journal Genome Biology and Evolution, scientists including postdoctoral researcher at Cold Spring Harbor Laboratory and first author Armin Scheben, CSHL Professor and Chair of the Simons Center for Quantitative Biology Adam Siepel, and CSHL Professor W. Richard McCombie explored the genetics of the Jamaican fruit bat and the Mesoamerican mustached bat.

By comparing the complete genomes for these bats and 13 others to other mammals, including mice, dogs, horses, pigs and humans, these scientists discovered key differences in several genes.

The lower copy number of interferon alpha and higher number of interferon omega, which are inflammatory protein-coding genes, may explain a bat’s resistance to viruses. As for cancer, they discovered that bat genomes have six DNA repair and 33 tumor suppressor genes that show signs of genetic changes.

These differences offer potential future targets for research and, down the road, therapeutic work.

“In the case of bats, we were really interested in the immune system and cancer resistance traits,” said Scheben. “We lined up those genomes with other mammals that didn’t have these traits” to compare them.

Scheben described the work as a “jumping off point for experimental validation that can test whether what we think is true: that having more omega than alpha will develop a more potent anti-viral response.”

Follow up studies

This study provides valuable potential targets that could help explain a bat’s immunological superpowers that will require further studies.

“This work gives us strong hints as to which genes are involved, but fully understanding the molecular biology will require more work” explained Siepel.

In Siepel’s lab, where Scheben has been conducting his postdoctoral research since 2019, he is using human cell lines to see whether adding genetic bat elements makes them more effective in fighting off viral infections and cancer. He plans to do more of this work with mice, testing whether these bat variants help convey the same advantages in live mice.

Armin Scheben won the German Academic International Network Science Slam competition with his presentation on bat genomics.

Siepel and Scheben have discussed improving the comparative analysis by collecting information across bats and other mammals of tissue-specific gene expression and epigenetic marks which would help reveal changes not only in the content of DNA, but also in how genes are being turned on and off in different cell types and tissues. That could allow them to focus more directly on key genes to test in mice or other systems.

Scheben has been collaborating with CSHL Professor Alea Mills, whose lab has “excellent capabilities for doing genome editing in mice,” Scheben said.

Scheben’s PhD thesis advisor at the University of Western Australia, Dave Edwards described his former lab member’s work as “exciting.”

Edwards, who is Director of the UWA Centre for Applied Bioinformatics in the School of Biological Sciences, suggested that Scheben stood out for his “ability to strike up successful collaborations” as well as his willingness to mentor other trainees.

Other possible explanations

While these genetic differences could reveal a molecular biological mechanism that explains the bat’s enviable ability to stave off infections and cancer, researchers have proposed other ways the bat might have developed these virus and cancer fighting assets.

When a bat flies, it raises its body temperature. Viruses likely prefer a normal body temperature to operate optimally. 

Bats are “getting fevers without getting infections,” Scheben said.

Additionally, flight increases the creation of reactive oxygen species, which the bat needs to control on an ongoing basis.

At the same time, bats produce fewer inflammatory cytokines, which helps prevent them from having a runaway immune reaction. Some researchers have hypothesized that bats clear reactive oxygen species more effectively than humans.

A ‘eureka’ moment

The process of puzzling together all the pieces of DNA into individual chromosomes took considerable time and effort.

A Mesoamerican mustached bat, one of two bat species Scheben studied as a part of his comparative genomic work. Photo by Brock & Sherri Fenton

Scheben spent over 280,000 CPU hours chewing through thousands of genes in dozens of species on the CSHL supercomputer called Elzar, named for the chef from the cartoon “Futurama.” Such an effort would have taken eight years on a modern day personal computer.

During this effort, Scheben saw this “stark effect,” he said. “We had known that bats had lost some interferon alpha. What astounded me was that some bats had lost all alpha” while they had also raised interferon omega. That was the moment when he realized he found something novel and bat specific.

Scheben recognized that this finding could be one of many that lead to a better understanding of the processes that lead to cancer.

“We know that it’s unlikely that a single set of genes or a small set of genes such as we identified can fully explain the diversity of outcomes when it comes to a complex disease like cancer,” said Scheben.

A long journey

A resident of Northport, Scheben grew up in Frankfurt, Germany. He moved to London for several years, which explains his use of words like “chuffed” to describe the excitement he felt when he received a postdoctoral research offer at Cold Spring Harbor Laboratory.

When he was young, Scheben was interested in science despite the fact that classes were challenging for him.

“I was pretty poor in math and biology, but I liked doing it,” he said.

Outside of work, Scheben enjoys baking dense, whole wheat German-style bread, which he consumes with cheese or with apple, pear and nuts, and also hiking.

As for his work, which includes collaborating with CSHL Professor Rob Martienssen to study the genomes of plants like maize that make them resilient amid challenging environmental conditions, Scheben suggested it was the “best time to be alive and be a biologist” because of the combination of new data and the computational ability to study and analyze it.

Scheben recognized that graduate students in the future may scoff at this study, as they might be able to compare a wider range of mammalian genomes in a shorter amount of time.

Such a study could include mammals like naked mole rats, whales and elephants, which also have low cancer incidence and long lifespans.

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