Science & Technology

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.

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.

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.

Maggie Sullivan (Kevin Coughlin/Brookhaven National Laboratory)

Maggie Sullivan, an experienced leader and manager of the Talent Management group at the U.S. Department of Energy’s Brookhaven National Laboratory, was recently named Chief Human Resources Officer and Assistant Laboratory Director for Human Resources. Sullivan took over the position from Bob Lincoln, who transitioned to an advisory role after serving more than 12 years in the position.

Since joining the Lab in 2011, Sullivan has progressively assumed more responsibility, most recently leading a multidisciplinary team of HR professionals and administrators in training, recruitment, leadership development, and HR systems.

“Throughout her 12 years at Brookhaven, Maggie has demonstrated a strong ability to work with constituents across the Laboratory and to appreciate the role that each member of the Lab community plays in achieving our mission,” said Laboratory Director JoAnne Hewett. “She has also worked closely with senior leadership on major Lab initiatives and institutional-level processes, giving her insight into how the Lab and its senior leadership team operate.”

Sullivan has implemented best-in-class leadership development programs, including mentoring, the Lab’s Science and Engineering Development Program, and LEADER program for supervisory development. Most recently, she co-led the multi-year effort to modernize the Lab’s human capital management system. Sullivan has also served as the co-leader of the Lab’s recent engagement survey and continues to support that effort. Sullivan has also played a lead role in the design and delivery of supervisory and leadership training programs across the Battelle laboratory complex.

Sullivan partners closely with Brookhaven’s Chief Diversity Officer to promote a diverse, equitable, and inclusive work culture and is a key contributor to the Lab’s annual diversity, equity, and inclusion (DEI) plan. She is also a member of the Lab’s Executive DEI Council and the DEI Management Council, and she serves on the Human Resources Diversity, Equity, and Inclusion Council.

“I’m excited and looking forward to working closely with Lab leadership and staff as we continue to build our future workforce, advance DEI efforts, and review and modernize our HR processes and functions to best serve the Laboratory and our current and future staff,” said Sullivan. “We have a very talented HR team in place, and together we will create positive change for the Lab.”

Prior to her current role, the Hampton Bays resident was the Lab’s learning and development manager from 2011 to 2017. From 1989 to 2011, she worked for the Applied Research Corporation in Metuchen, NJ, first as a consultant, then senior consultant, then executive vice president.

Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit science.energy.gov.

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.

Dr. Alexander Orlov. Photo by John Griffin/SBU

Alexander Orlov, PhD, Professor of Materials Science and Chemical Engineering at Stony Brook University, has been elected chair of the American Chemical Society’s (ACS) Environmental Division. With a four-year term starting January 1, 2024, Orlov will lead the Division’s extensive community of scientists toward the goal of applying concepts in chemistry to address the world’s leading environmental and sustainability issues.

Orlov, a Middle Island resident and professor at Stony Brook since 2008, has contributed significantly to environmental protection and sustainability efforts throughout his career. His work as an educator earned him the 2017 ACS Award for Incorporating Sustainability into Chemistry Education and the 2018 American Institute of Chemical Engineers Sustainable Engineering Forum Education Award. He is a member of the US-EU working group on Risk Assessment of Nanomaterials supported by the U.S. White House and European Commission cooperative program on nanotechnology research. In 2022, he was a chair of the Environmental Division at the American Institute of Chemical Engineers.

For years Orlov has contributed to the United Nations Environmental Program and has helped lead several reports coming out of the program. From 2007 to 2014, he was appointed by two UK Secretary of States to advise the government on environmental issues such as hazardous substances and environmental impact of nanotechnology.

Orlov’s interdisciplinary research seeks to develop new materials for clean energy generation, structural applications, and environmental protection. He currently co-directs two Centers at Stony Brook — the Center for Laser Assisted Advanced Manufacturing and the Center for Development and Validation of Scalable Methods for Sustainable Plastic Synthesis and Processing.

At more than 150,000 members, the ACS is one of the largest scientific societies in the U. S. Approximately 3,000 scientists nationally and internationally are in the Environmental Division. The Division is dedicated to addressing all 17 Sustainable Development Goals outlined by the United Nations with an emphasis on issues surrounding climate change.

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.

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.

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. Photo by James Konopka

A study that assesses the effects of hypochlorous acid (HOCI), commonly known as bleach, as it is generated during the immune response of a cell (phagocytosis) when fighting a common fungal pathogen, Candida albicans, reveals that HOCI is a potent killing agent. The laboratory finding, highlighted in a paper published in the coming issue of the American Society of Microbiology’s mBio, also uncovers some of HOCI’s mechanisms of actions in that killing process. The work could be a significant step toward using HOCI as a novel therapeutic strategy against C. albicans, and potentially other pathogens.

C albicans causes much infection worldwide. It is particularly virulent in immunocompromised patients and the cause of dangerous systemic infections in this population. There have been many effective treatments against the fungal pathogen, but for decades drug resistance has been problematic when treating infections cause by C. albicans.

Most studies looking at this immune response against the fungal pathogen have focused on hydrogen peroxide (H2O2), not HOCI. Phagocytes capture the fungal invader and in the process two oxidants are created – H202 and HOCI. Myeloperoxidase converts H2O2 created during the oxidative burst in the phagosome into HOCI, the more potent killing agent.

“We discovered that hypochlorous acid kills cells by targeting the plasma membrane and oxidizing cellular components in a very different way than hydrogen peroxide,” says James Konopka, PhD, lead author and Professor in the Department of Microbiology and Immunology in the Renaissance School of Medicine at Stony Brook University. “It disrupts the C. albicans plasma membrane, produces a very different transcriptional response than hydrogen peroxide, is more effective and disruptive to the plasma membrane, and therefore has a more distinct effect on killing these fungal cells.”

Konopka explains that neutrophils are the critical cell type for controlling infections by C. albicans and other fungal pathogens. They are distinct because they make high levels of myeloperoxidase compared to other phagocytes, such as macrophages. This study shows the important aspect of the neutrophil response, essential to the oxidative process that produces this fungal killing HOCI or bleach.

While the laboratory results will not have any immediate impact on new treatments against C. albicans infections,  Konopka believes the findings provide a basis for designing new therapeutic strategies against this pathogen that causes infections worldwide.

The research was supported by a grant from the National Institutes of Health’s Institute of Allergies and Infectious Disease (grant number RO1AI047837), and in collaboration with researchers at Seoul National University in South Korea.

 

 

The 2023 Double Helix Medals Dinner was once again held under the American Museum of Natural History's iconic blue whale model. Photo from CSHL

By Nick Wurm

On November 15, Cold Spring Harbor Laboratory (CSHL) held its 18th annual Double Helix Medals dinner (DHMD) at the American Museum of Natural History in New York City. CBS journalist Lesley Stahl returned to emcee the awards dinner, which honored Neri Oxman & William Ackman and 2018 Nobel laureate Jim Allison. Thanks to the event chairs and donors, the event raised more than $10 million. After receiving the Double Helix Medal, Oxman and Ackman announced an extraordinary gift, further breaking the event’s fundraising record to support scientific research and education at CSHL.

William Ackman & Neri Oxman

Neri Oxman & William Ackman are co-trustees of the Pershing Square Foundation. The organization empowers scientists to take on important social causes, including the environment, cancer, and cognitive health. Ackman is also the CEO of Pershing Square Capital Management and chairman of the Howard Hughes Corporation. Oxman is an innovative designer whose fusions of technology and biology have been featured in museums around the world. Her work has yielded over 150 scientific publications and inventions.

“Something we continue to this day is backing young, talented entrepreneurs who are on a mission to solve an important societal problem,” Ackman says. “We believe in taking risks with incredible scientists who have the ability to tackle these complex problems,” Oxman adds.

Dr. Jim Allison

Dr. Jim Allison is regental professor and chair of the MD Anderson Cancer Center’s Department of Immunology. He won the 2018 Nobel Prize in Physiology or Medicine for pioneering the field of cancer immunotherapy. Since then, his research has led to the development of ipilimumab, an FDA-approved therapy for metastatic melanoma, renal cell carcinoma, and lung cancer.

“The perception of immunology has shifted,” Dr. Allison says. “People used to say, ‘Will immunotherapy ever work?’ We now know it works. Immunotherapy is going to be a part of all cancer therapies for almost every kind of cancer.”

The 2023 DHMD was chaired by Ms. Jamie Nicholls and Mr. O. Francis Biondi, Ms. Barbara Amonson and Dr. Vincent Della Pietra, Drs. Pamela Hurst-Della Pietra and Stephen Della Pietra, Mr. and Mrs. John M. Desmarais, Mr. and Mrs. Jonathan Gray, Mr. and Mrs. Jeffrey E. Kelter, Dr. and Mrs. Tomislav Kundic, Mr. and Mrs. Robert D. Lindsay, Ms. Ivana Stolnik-Lourie and Dr. Robert Lourie, Dr. Marcia Kramer Mayer, Dr. and Mrs. Howard L. Morgan, Drs. Marilyn and James Simons, and Mr. and Mrs. Paul J. Taubman.

Since the inaugural gala in 2006 honoring Muhammed Ali, the DHMD has raised over $60 million to support CSHL’s biological research and education programs.

Author Nick Wurm is a Communications Specialist at Cold Spring Harbor Laboratory.