CLOSE
Power of 3

by -
0 510
Katie Engel submitted a video of her spinning on the ice to demonstrate the work of Emmy Noether.

*This article was updated  Feb. 13 to reflect a change in the Jocelyn Bell Burnell lecture from Feb. 13 to Feb. 14 due to the weather.

By Daniel Dunaief

And the winner is … women in science! 

While Stony Brook University’s Institute for Advanced Computational Science (IACS) announced the winners of its inaugural challenge to celebrate the scientific and engineering achievement of women on Feb. 7, the organizers and participants feel like they’ve already come out ahead.

The inaugural competition, which 195 students kindergarten through 12th grade in schools on Long Island entered by submitting a one-minute video, included prizes for the 13 finalists. The winner received $1,000 prize, the runner up got $750 and the third-place finisher collected $500.

Marivi Fernández-Serra

“The goal of it was to celebrate the International Day of Women and Girls in Science, while simultaneously promoting the important role that women had in science in the last century,” explained Marivi Fernández-Serra, Professor in the Physics and Astronomy Department and at the Institute for Advanced Computational Science.

In their videos, the students selected one of nine scientists that included experiments showcasing the work of these researchers by using computers or household products to demonstrate the search for dark matter, explore the laws of conservation, create homemade telescopes, simulate a volcano with lava and many more.

Fernández-Serra, who had helped with a similar effort at the Institute for Theoretical Physics in Madrid, Spain, brought the idea for the competition to Mónica Bugallo, Professor of Electrical and Computer Engineering, Vice Provost for Faculty Affairs and Diversity, Equity and Inclusion and affiliated member of the IACS  Faculty Director of the Women in Science and Engineering Honors Program, who immediately supported it.

Fernández-Serra thought the competition might attract 10 entrants in its inaugural year while Bugallo, who reached out to Long Island schools to showcase the competition, was confident local students would embrace the opportunity.

“Wait for a tsunami of participants,” Bugallo said she told Fernández-Serra, with whom she’s been a colleague and friend for years. “I was not surprised” by the contributions from the 103 teams, which included entrants from individual students and groups of as many as three students.

Bugallo, who recommended computer scientists Grace Hopper and mathematician and writer Ada Lovelace as important scientists for the competition, was impressed with the student effort.

“It was extremely tough to come up with the finalists,” said Bugallo.

Stony Brook plans to share the videos from the finalists after naming the winners.

Figure skating and conservation

One of the finalists, Katie Engel, a senior at Cold Spring Harbor High School, chose to demonstrate the work of Emmy Noether.

A German mathematician, Noether contributed to theoretical physics and abstract algebra. A theorem named after her, the Noether Theorem, explains that any continuous symmetry in a system has an associated conservation law. That helps explain how the speed of someone spinning in a chair changes depending on how far their arms re-extended.

Mónica Bugallo

An ice skater since she was six who is also interested in studying computer science or engineering, Engel had never heard of Noether but was intrigued with the physics and with the person who helped discover ways to characterize it.

In her entry, Engel explained the mathematical principals on a white board and then recorded a video of herself spinning on ice. When she learned about Noether’s life, Engel discovered that Noether was an important contributor to her field, despite some resistance to her work from men. “Reading about her stories is really inspiring,” said Engel.

Engel is stunned at the conclusions Noether reached with the tools at her disposal.

Currently working as an intern for Peter Koo at Cold Spring Harbor Laboratory, Engel suggested she is committed to pursuing her interest in science, technology, engineering and math fields during and after college.

Engel was also a member of the robotics team at Cold Spring Harbor High School that won the regional conference and went to the World Championships in Houston last year. In robotics, Engel said the number of girls on the team declined from 10th through 12th grades. 

She is, however, heartened to learn that 180 boys and 200 girls attended a recent research fair at her school.

New teaching tools

Fernández-Serra and Bugallo are hoping that teachers at all levels can use the videos to inspire students and help them connect with scientists whose contributions continue to resonate with current researchers. The purpose of activities like the competition is to “spark interest, so students want to investigate more,” said Bugallo.

Stony Brook plans to build on this experience in future years through either similar efforts or ongoing programs or initiatives. “Our intent was to have these challenges year after year if this was successful, and it obviously was,” said Bugallo.

In the immediate future, Fernández-Serra encourages students in the area to attend the upcoming talks given by University of Oxford astrophysicist Jocelyn Bell Burnell, who discovered the pulsar, as a part of the Della Pietra lecture series at the Simons Center for Geometry and Physics on Stony Brook University’s West Campus from February 13 through Feb. 15.

Bell Burnell is giving a general public lecture on Feb. 14 at 5 p.m., with a reception at 4:15 p.m. in the Simons Center Lobby. The lecture will also be livestreamed at scgp.stonybrook.edu/live.

Bell Burnell will also offer a special talk for high school students titled You Are Made of Star Stuff! on Feb. 15 at 11 a.m. that examines how and where elements in the human body were created in the cosmos. Both lectures will be held in the Della Pietra Family Auditorium (room 103).

A curiosity outside the classroom

For scientists, what they learn and study often stays with them long after they finish an assignment or submit or publish a paper.

Fernández-Serra, who studies the fundamental properties of liquid water using quantum mechanical simulations, thinks about how amazing water atoms are that are holding her when she swims.

As for Engel, thoughts of Noether will stay with her when she figure skates. “I probably can’t do a spin without thinking about her,” she said.

Heroes with staying power

For Fernández-Serra, Mildred Dresselhaus, one of the celebrated scientists of the past who was a part of the contest, was a “number one hero” in condensed matter physics.

Called the “Queen of Carbon,” Dresselhaus earned numerous awards, including the Presidential Medal of Freedom and the National Medal of Science and Engineering.

“She was a positive and brilliant scientist who never lost her enthusiasm and curiosity,” Fernández-Serra explained.

Stony Brook’s IACS team hopes this competition, the Bell Burnell lecture, and other efforts ignite such enthusiasm in the next generation of STEM students.

by -
0 391
The new species named, Booralana nickorum, may play a crucial role in maintaining the health of the ecosystem. Photo courtesy of OceanX

By Daniel Dunaief

Oliver Shipley recently shared one of the mysteries of the heavily photographed but lightly explored deep sea areas near the Bahamas’ Exuma Sound.

Oliver Shipley

A Research Assistant Professor at Stony Brook University, Shipley and his colleagues published a paper in the journal Zootaxa describing a new species of isopod they named Booralana nickorum.

A few inches long, this isopod, which was found at a depth of about 1,600 feet, sheds light on some of the mysteries in these waters, offering a glimpse into areas mostly too deep for sunlight to penetrate.

“The level of knowledge on deep sea biodiversity anywhere in the Caribbean is very poor,” said Shipley. The scientists were specifically studying the biomass housed areas around The Exuma Sound.

In the Bahamas, the researchers are interested in preserving species biodiversity and identifying links between the shallow and deep-sea ecosystems, which can inform management of marine resources and help conserve biodiversity.

Shipley suggested it was “exciting” and, perhaps, promising that this area has already produced two isopods that are new species, both of which he described with low-cost technologies deployed off small boats.

“We haven’t even genetically sequenced 95 percent of the creatures that we’ve captured” which includes fish and sharks, Shipley said.

Brendan Talwar, a co-author on the paper describing the isopod and a Postdoctoral Scholar at Scripps Institution of Oceanography at UC San Diego, added that “this discovery is representative of the lack of knowledge” in this area. “You can swim from one environment, where almost every species is known or has been studied, to a place where almost nothing is known and almost nothing is studied.”

Finding new species could have numerous benefits, including in the world of drug discovery. To be sure, such findings require “many years of work and analysis” he said.

Still, such a possibility for future benefits exist, particularly as researchers catalog and study these creatures.

In the meantime, understanding individual species and the ecosystems in which they live can reveal information about how, depending on the biomass of various species, different places affect the cycling of gases such as carbon dioxide.

“When you find high biomass of a new species, it could have potentially huge implications for mitigating climate change,” said Shipley. “We have a primitive understanding of the Caribbean deep sea ecosystem. We don’t know the full effects or benefits and services of organisms that live in the deep ocean environment.”

In addition to finding organisms that might provide various benefits, scientists are also hoping to understand the “food web dynamics of the eastern Bahamas,” said Talwar.

Long road to identification

Shipley first saw an individual of this isopod species in 2013. Over time, he has since identified numerous other individuals.

Dorsal views of the newly described Booralana nickorum on left and previously known Booralana tricarinata highlight distinguishing characteristics between the two species. Image courtesy of Oliver Shipley

The region in which Shipley identified this isopod has several potential food or energy sources. The deep sea area is in close proximity to shallower sea grass beds, which are closer to the surface and use light to generate food and energy through photosynthesis.

The tides and currents wash that sea grass into the deeper territory, sending food towards the deeper, darker ocean.

Energy also likely comes from coral reef productivity as reefs line the edge of the drop off.

Additionally, animals that traverse the shallower and deeper areas, whose poop and bodies sink, can provide food sources to the ecosystem below.

“There may be multiple sources of productivity which combines to promote a high level of biodiversity” in the ecosystem below, said Shipley.

The isopod Shipley and his collaborators identified lives in a pressure that is about 52 times the usual atmospheric pressure, which would be extremely problematic for organisms like humans. Isopods, however, have managed to live in most major ecosystems around the planet, including on mountains, in caves and in the deep sea.

“There’s something about that lineage that has supported their ability to adapt to a variety of environments,” said Shipley.

To bring the creatures back to the surface for study, researchers have used deep sea traps, including crustacean and eel traps, that are attached to a line. People working on boats then retrieve those traps, which can take one to two hours to pull to the surface. 

When they are brought to the surface, many animals suffer high mortality, which is a known sensitivity of deep-sea fisheries.

“We must gain as much knowledge as possible from each specimen,” Shipley explained

Scratching the surface, at depth

Talwar and Shipley have each ventured deep into the depths of The Exuma aboard a submersible.

The journey, which Talwar described as remarkably peaceful and calm and akin to an immersive aquarium experience, is “like a scavenger hunt,” he said.

When scientists or the sub pilot see a new species of sea cucumber, the pilot can move the sub closer to the organism and deploy the manipulator arm to store it in a collection box. Shipley and others hope to explore deep sea creatures under conditions akin to the ones in which they live in high pressure tanks on land.

Talwar described Shipley as “an extremely productive scientist” who works “incredibly hard.” Talwar also appreciates how Shipley will put collaborative projects at the top of his list, which is “fairly unique in a field where people are so busy with their own stuff.”

Shipley, who lives in Austin, Texas with his girlfriend Alyssa Ebinger, explained that researchers are pushing to support scientific leadership by Bahamians to conserve marine resources threatened by climate change.

Looking under rocks

As a child, Shipley, who grew up in York, England, spent about three years in Scotland, where they spent time at a beach called Trune.

“I remember looking in rock pools, picking up stuff and inspecting it,” he said. He was naturally inquisitive as a child.

While Shipley enjoys scuba diving and is a committed soccer fan — his favorite team is Leeds United — he appreciates the opportunity to build on his childhood enthusiasm to catalog the unknowns of the sea. He’s so inspired by the work and exploration that it “doesn’t feel like a job,” he said. He’s thrilled that he gets paid “to do all this exciting stuff.”

 

by -
0 517
Evan Musterman with lead SRX beamline scientist Andrew Kiss at the SRX beamline. Photo by Kevin Coughlin/Brookhaven National Laboratory

By Daniel Dunaief

When he took over to lead the sub micron resolution X-ray spectroscopy, or SRX, beamline at Brookhaven National Laboratory on January 1, 2020, Andrew Kiss expected to balance between improving the machinery and helping visiting scientists use it. The pandemic, however, altered that balance.

BNL received components for the beamline in December 2019, when the researchers were going to try to take a fraction of the available x-ray time to install and commission it, all while still running experiments. The pandemic, however, kept scientists from visiting the site. That meant Kiss and his colleagues could dedicate more time to technical enhancements.

“Since the pandemic shut down the user program, this gave us an opportunity to focus all of our time on the new equipment” that visiting researchers could tap into when they returned, he explained in an email.

The beamline, which postdoctoral researcher Evan Musterman is enhancing further with diffraction techniques to reveal information about strain (see related story here), is in high demand. During the current cycle, 324 researchers applied for beamline time, while 99 time slots were allocated.

Scientists have a range of ways of discovering which beamline might best suit their research needs, including word of mouth. Kiss has had conversations with researchers who describe how they read something in a research paper and have similar goals.

Scientists “usually have a good idea of what instrument/ facility to use and why it is good for their research so informal conversations at conferences and seminars can be very useful,” Kiss said.

Most of Kiss’s time is dedicated to ensuring the stability and reliability of the beamline, as well as extending its capabilities to scan larger regions with less overhead, he explained.

“All of this is to help the researchers that come to the beamline, but my hope is that with this baseline of reliable and fast data acquisition, I can focus more on scientific topics such as metal additive manufacturing,” Kiss wrote.

With the SRX, Kiss can explore applied questions related to corrosion effects or how a material is modified by exposure to different gases, liquids or other parameters.

Working at the beamline has given Kiss an unusual perspective outside the lab. A few years ago, he received a notification about a recall on baby food he purchased that could have elevated levels of something unhealthy in it. His second thought, after making sure he didn’t give any to the child, was to wonder how much was in the food and if he could measure it. Before he could bring it to the lab, the contaminated food was already taken away with the garbage.

Kiss enjoys his work and suggested that the field attracts a “certain type of person and, once you are there, it is tough to pull yourself away from the instrument and the community of researchers around you,” he explained.

In addition to making basic discoveries in fields such as materials science, Earth science and biological sciences, the SRX beamline has played an important role in studies that have affected public policy.

Indeed, a study in 2022 showed that veterans who worked in Iraq and Afghanistan near burn pits had oxidized particles of iron and titanium in their lungs. “This is not direct evidence it came from a burn pit, but these were not seen in healthy lungs,” Kiss said. Only a few places in the world had the kind of machinery with a bright enough source and high enough resolution to discover these particles.

Kiss and collaborators from other laboratories, universities and medical institutions appreciated the opportunity to have a “positive impact on these soldiers’ lives by providing the measurements to get them help,” he said. The discovery of these elements in the lungs of veterans who lived near burn pits and suffered health consequences, which the study at SRX and other facilities helped demonstrate, led to the Pact Act, which President Joe Biden signed into law in 2022 and which provides $280 billion in federal funding for the health effects veterans suffer after exposure to such toxins.

SRX has high spatial resolution and is highly sensitive to trace concentrations for elemental mapping and chemical composition. SRX is an x-ray fluorescence microscope with “high spatial resolution and highly sensitive to trace concentrations for elemental mapping and chemical composition,” Kiss said. “If that can be used to help people’s lives, that is a wonderful thing.”

by -
0 632
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.

by -
0 559
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.

by -
0 720
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.

by -
0 661
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.

by -
0 798
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.

by -
0 714
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.

by -
0 725
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.

Prev123...60Next Page 2 of 60
TBR News Media is your local news and entertainment website.
We provide you with the latest breaking news and information for your community.
Contact us: [email protected]

Most Viewed

©