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Daniel Dunaief

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

By Daniel Dunaief

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

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

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

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

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

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

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

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

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

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

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

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

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

A collaboration begins

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

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

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

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

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

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

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

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

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

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

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

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

Future focus

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

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

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

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

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

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

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

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

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

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

Some historical phrases help shape and define the country the way landmarks like the Grand Canyon, Statue of Liberty, and Mt. Rushmore provide a distinct national identity.

One of those expressions, for me, is “rugged individualism.” The combination of the two words suggest independent thought, an ability to decide for ourselves, and a willingness to eschew tradition in favor of something more personal, practical and self-directed.

We don’t need kings and monarchs to tell us how to behave or to dictate from on high. We favor the stories of Americans whose humble origins offered hope to anyone born in a log cabin, a la Abraham Lincoln, or whose compassion inspired them to build houses for others, Jimmy Carter, perhaps, long after they were no longer the most powerful person on the planet.

We think for ourselves, we live with the view that we have unlimited potential and that we don’t need to have the right name or address to realize our dreams. Our self confidence allows us to imagine that we can become the next “Cinderella Man” or “Working Girl.”

And yet, we the people of the United States sometimes appear to be living lives that are filled with paint-by-the-numbers decisions and that involve following other people’s footprints in the snow.

Why? Have we and our children become so accustomed to group think that we don’t want to separate ourselves from the pack? Are we living in a world where we are desperate to conform?

Part of our collapse in independent thinking comes from corporate America. That faceless, nameless, profit churning machine, with its fake wooden boardrooms and its army of handlers and focus groups, has encouraged us to believe that buying their products, supporting their stores and following the trends is a way of asserting our independence.

It’s a clever ploy, my friends. They convince you that eating what everyone else eats, saying the same words everyone else says and wearing what everyone else wears helps you realize your potential.

The argument is an easy one to make, especially as you drive through Anytown USA. You see the same collection of franchised stores, with their predictable food and products and their well-oiled experiences, where it takes 5.6 minutes from the time you entered the store to get exactly the same soggy french fries in Dubuque, Iowa as it would in Setauket, New York.

We resist risk. Going into a restaurant with an unknown name means we might consume food that doesn’t taste familiar or good to us and that might give us indigestion as we move, like cattle, to the next predictable destination and engage in an echo of the same conversation we had last week, last month and last year.

I get it: it’s hard to decide to go to a unique store or restaurant in a town, particularly when the parking lot in the franchise chain next door is packed with people driving the same model and color cars we see on our roads back home.

Well, it’s 2024, and not 1984. We can and should make our own decisions. I would encourage you, your children and your friends to decide who you are and what that means. Yes, it’s hard and yes, people might hide behind the cloak of conformity to encourage you to do as they and everyone else does. They might even peck at you verbally, uncomfortable with differences and unsure of how to react to “the real you.”

If we fit in too well everywhere we go, we run the risk of disappearing. As Frank Sinatra suggests, it’s time to do things “My Way.” Yes, we might hate tuna fish with peanut butter, but at least we’ll be listening to our own voice and getting off a nonstop conveyor belt of conventional thought in which we follow the same roads, the same thoughts, and the same routines. Different? Different is good and, best of all, it’s up to you to decide what that means.

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James Konopka. Photo by Susan Watanabe

By Daniel Dunaief

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

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

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

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

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

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

Hypochlorous acid reacts with proteins, lipids and DNA.

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

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

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

Increase sensitivity

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

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

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

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

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

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

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

An ‘overlooked’ ally

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

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

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

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

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

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

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

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

Fish and beer

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

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

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

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

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

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

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

The reality of aging is that we sometimes wake up feeling like we’ve got less than a full tank of gas, or, for those of you driving electric vehicles, a fully charged battery, with which to maneuver through the day.

Maybe our ankles are sore from the moment we imagined we could still dive across the grass to catch a foul ball. Perhaps, less ambitiously, we twisted our ankle when we took a bad step on a sidewalk as we did something much less heroic, like texting an old friend or playing a mindless video game. Or it hurts because it, like our jobs, our cars, and our homes, inexplicably needs attention.

What’s the antidote to the numerous headwinds that slow us down and make us feel exhausted earlier each day?

The start of a new year can provide that energy and inspiration. We get to write 2024 on our checks, if we’re still writing them, we can imagine a blank canvas on which we can reinvent ourselves, find new friends, get new jobs, travel to new places, live our values and contribute meaningfully to the world.

We can start jotting activities into that new calendar, smiling as we imagine seeing friends we haven’t seen in years or decades or fulfilling long-held desires to shape our lives, our bodies or both into what we’ve always imagined.

On a more immediate scale, we have other ways to boost our energy. We can grab a steaming hot cup of hot chocolate or coffee, loading our nervous system up with caffeine, which can wake us up and help us power through the next few hours.

We can also grab a donut, a cookie, or some other food loaded with sugar, knowing, of course, that we run the risk of emptying that short-energy tank quickly after the sugar rush ends.

I have discovered plenty of places I can go, literally and figuratively, to feel energized and inspired. My list includes:

Our children: Yes, they are draining and can be demanding and needy, but their youth and energy can be restorative. They take us to places we hadn’t been before, give us an opportunity to share books we might have missed in our own education and offer insights about themselves and their world that amaze us. Their different interests and thoughts keep us on our toes, focused and, yes, young, as we try to meet them where they live. As we relate to them, we can also imagine our own lives at that age.

Our pets: Watching a dog chase a ball, its tail or a frisbee, or observing a cat push a ball of string across the floor can be invigorating. If we threw that ball or tossed that string, we become a human partner in their games, giving us a role to play even as they expend considerably more effort in this entertaining exchange.

Nature: Energy surrounds us. Water lapping on the shores of Long Island at any time of year, small leaf buds responding to the cues of spring, and birds calling to each other through the trees can inspire us and help us feel alert, alive and aware of the symphony of life that serenades us and that invites us to participate in the evolving narrative around us.

Science: I have the incredible privilege of speaking with scientists almost every day. Listening to them discuss their work, when they don’t travel down a jargon rabbit hole filled with uncommon acronyms, is inspirational. The insatiable curiosity of scientists at any age  and any stage of their careers makes each discovery a new beginning. Each of their answers raises new questions. Scientists are always on the verge of the next hypothesis, the next great idea and the next adventure. Their energy, dedication and unquenchable thirst for knowledge invites listeners to participate in the next chapter in the evolving knowledge story.

Sunrises: Okay, if you’ve read this column often enough, you know I’m a morning person. I try to be quiet in the morning, for my family and for anyone else who stayed up late into the night. Sunrises, however, bring a welcome introduction to something new and original.

History: reading about or studying history puts our world into perspective. We not only can contrast previous time periods with today, but we also can enjoy and appreciate that we have the opportunity to share in and shape this moment.

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

By Daniel Dunaief

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

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

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

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

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

Disease states

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

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

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

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

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

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

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

Starry, starry explosion

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

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

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

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

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

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

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

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

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

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

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

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

Student opportunities

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

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

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

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METRO photo

By Daniel Dunaief

Daniel Dunaief

Here we are, poised on the precipice of 2024, or, if you’d prefer, at the bottom of the mountain, looking up at the year ahead.

What a privilege to start 2024 together, to share the same air, to enjoy or brace for the same weather, to root for or against the same teams and to revel in the miracle of our children, grandchildren, nieces, nephews and neighbors.

As we venture into the days, weeks and months ahead, we can all see certain patterns continuing because, let’s face it, we know the familiar playbook people use. I would love to figure out how to capitalize on some coming certainties. If, for example, we had a dime for every time the song “Jingle Bells” came on in department stores around the country in the last few weeks of each year, we’d have enough money to buy our own one-horse open sleigh and fill it with presents. With that in mind, I’d like to consider certainties or near certainties in various realms.

Political:

Let’s start with former president Donald Trump. A dime for every time he insulted someone could pay for an enjoyable and deluxe vacation to Europe or, if you prefer, a week or more at a Disney resort.

A dime for each time he uttered the words “rigged,” “witch hunt,” or “socialist,” would also net some nice cash.

Collecting money when he referred to himself in the third person, as in “only Donald Trump can fix that” would also prove profitable.

President Biden, of course, has his go-to approaches and idiosyncrasies as well. Collecting money when he misspoke or stepped in the wrong direction would turn gaffes into cash.

Or, perhaps, adding money each time he became angry or annoyed with someone would also provide considerably more change than the typical back of the couch.

Collecting cash each day that goes by without the president taking questions from the Press Corps or reacting to unscripted moments would also build wealth.

A dime for each time Chris Christie insults Trump would help build a college fund.

Oh, and some change for each time Jim Jordan (R-OH) takes off his coat, MTG scowls, Ron DeSantis uses the word “woke” or attacks Disney, AOC insults NYC, or Nikki Haley smiles when she’s insulted would also make real money.

Sports:

Ah, yes, the world of sports not only is filled with cliches, but also has predictable patterns.

Fans and sports talk radio hosts always know better. Monday morning quarterbacking has become something between a religion and a profession.

The next day, everyone else always claims to have known exactly when to take a pitcher out of a ballgame, when to run the ball and when to take a time out. 

The pundits on the sidelines always know better about the Big Game than the people who are paid to make the decisions.

And, of course, with the Olympics coming in Paris this year, we can anticipate the back stories about athletes who are competing in memory of a cherished dead relative who inspired them. If we the viewers had a dime for every tear shed during these serious and melodramatic moments, we’d be able to afford the plane ticket to Paris to watch the Games in person.

I’m not minimizing the inspiration these athletes take from their relatives, coaches and friends. I’m reflecting on the types of stories, with their sad, moving slow guitar background music, these networks share, combining loss and grief with determination and the quest for glory.

Random but predictable moments:

As a coach for many teams, I am sure parents throughout the country are convinced that their children are being short changed. A dime for each parent complaint could provide a down payment for a new field.

I’d also like to collect money each time someone who talks all the time “breaks their silence” on something. It’s amusing when headline writers suggest that, say, Britney Spears or one of the Kardashians breaks their silence on anything. I thought these non-stop celebrities shared every thought in their heads. Ah yes, a dime for each deep internal secret of people who would do well to be more discrete would also build wealth.

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Photo courtesy of SBU

By Daniel Dunaief

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

Ping Liu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Focus on two regions

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

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

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

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

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

Personal history

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

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

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

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

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

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

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

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Shohei Ohtani. Photo by Mogami Kariya/Wikimedia Commons

By Daniel Dunaief

Daniel Dunaief

You know when you were younger and your parents, grandparents, teachers and adults in general urged you to “make every second count.”

“A second,” you’d scoff incredulously. “How much could I do in a second? It took me longer than a second just to say those words, and those, and those, and they don’t seem to count for much.”

While that may be true most of the time for most of us, it’s certainly not the case for sport’s best paid athlete, the baseball sensation Shohei Ohtani, who signed a $700 million contract to play for the Los Angeles Dodgers over the next decade.

To borrow from the Tom Cruise movie “Jerry Maguire,” the Dodgers showed him the money!

Wait, don’t go if you’re not a sports fan. This isn’t about baseball. It’s about money!

Just for fun, let’s take a closer look at the approximately $33.5 million Sports Insider Andrew Petcash estimates Ohtani will earn per year after taxes and fees.

Assuming he’s paid for every second of each year, that means, he earns $1.06 each second. That’s what he’ll earn each second he sleeps, eats, sits in traffic, brushes his teeth or waits for an announcer to say his name so he can run on the field.

Assuming he has a healthy 60 beats per minute heart rate, that means each time his heart goes “lub-dub,” he earns about a dollar.

According to a website called covers.com, the average time to sing “The National Anthem” is 115.4 seconds, which means Ohtani makes $122.32 each time he listens to the national anthem of a country where he’s earning much more than a living.

Extending the math a bit, Ohtani clears $3,824.74 per hour.

As for each day, he’ll make $91,780.82. At that rate, it will take the star pitcher and home run hitter (yes, he can do both) 11 days to make a million dollars.

Each month, his after tax take home pay will be $2.79 million. Assuming Ohtani, who is single, follows the General Rule for engagement rings, namely, that he should spend at least two months of salary on the ring, some lucky future partner may be in line for a ring that costs $5.58 million. That assumes the value of the ring comes from what he’s taking home and not his overall salary. If he chose a ring based on his gross pay, he’d spend a whopping $11.7 million, which is the equivalent of 16 average priced homes in Setauket.

So, speaking of cash, what does $33.5 million look like? If you stacked dollar bills, which are 0.0043 inches wide, one on top of the other without any extra space between the bills, the pile of money would reach 12,004 feet. That would stretch 2.3 miles into the sky. 

Now, if he were to try to hold that money — and no one uses cash anymore, so why would he – he would need more than a few teammates. There are $454 dollar bills in a pound, which means that $33.5 million weighs 73,788 pounds. 

Realistically, dollar bills aren’t the most likely currency for someone who earns over $1 for every second. Maybe you’d prefer to stack $1,000 bills? That would still present a pile of money that’s about 12 feet tall. Imagine how much money you’d make if you were standing downwind of that pile during a sudden gust? That sounds like the winner’s circle for a future game show. 

Of course, you say, the first player since Babe Ruth to demonstrate proficiency as a pitcher and a home run hitter is not getting paid for every second, but, rather, for the magic he works on the field.

If we want to break it down just to the time he’s paid during games, the average time for a baseball game in 2023 was two hours and 42 minutes. The season has 162 games. Let’s throw in 19 additional games, assuming his Dodgers win each series in the maximum number of games and become World Series champions. That means, he’s a part of 29,322 minutes of baseball or 1.8 million seconds. Assuming his paycheck covers games and not all the practice time and spring training, he clears $38.88 per second. So, depending on how you look at it, he earns somewhere between $1.06 for every second of each year and $38.88 for each second he plays. 

Yeah, and you thought your lawyer was charging you a pretty penny!

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Zhe Qian

By Daniel Dunaief

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

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

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

Nicholas Tonks. Photo courtesy of CSHL

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

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

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

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

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

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

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

Blocking the receptor

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

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

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

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

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

Limited presence

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

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

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

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

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

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

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

Eureka moment

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

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

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

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

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

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

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

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

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

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

We have friends who live close to us who are pregnant. Okay, that sounds weird, right? She’s pregnant, and he looks sheepish, like he’s not sure what’s coming.

That’s not entirely fair. He was socially awkward before he brought his small package of genetic material to the pregnancy party. Why would anyone imagine he would be any different in the months before he makes a head first dive down the rabbit hole into the wonders and challenges of parenthood?

Now, if their families are anything like others I’ve known, they are bound to have a wide range of pre and post delivery discussions.

“Are you going to name the baby after my side of the family?”

“Make sure you put sugar, spice and everything nice in the crib or the baby will become colicky like your Aunt Michelle. She was one of the most miserable babies we’ve ever seen and that’s because her mother forgot about the sugar and spice under the crib.”

One of the most fascinating and sometimes confounding parts of the baby discussion, which can extend well into the years that follow, is the family credit for various traits.

To wit, “He’s incredibly serious and focused just like his Uncle Oswald. That Oswald was a man with a purpose from the time he was born, just like your little baby Joey.”

Or maybe, “Morgan has the same broad smile, laugh or sense of humor as her Aunt Carol.”

Each family can dig in, sharing ways that the developing child has characteristics they are convinced come from one side of the family, often from the speaker who has a proprietary interest in propagating the enduring myth of a family heritage.

Such talk suggests somehow that heredity is much more important than environment. The credit can go beyond physical characteristics such as long eyelashes, rounded shoulders, or sparkling eyes: they can include artistic talent, an ability to relate to other people, or a proficiency for languages.

That somehow seems un-American. After all, we the people generally believe that hard work can help people become proficient in any area, developing the kind of talent that differentiates them in their field and allowing them to control their destiny.

Such strong genetic links, while providing an appealing way to connect to ancestors and to those who aren’t around to smile and play with their descendants, is akin, if you’ll pardon the pun, to linking someone’s last name to their profession.

“Oh, the Jones family? Sure, they all became teachers. The Berringtons went into the clothing business, while the Shimmers all became dentists. They all have such gifted dental hands.”

Such blanket statements about where someone’s exceptionalism originated also throws the other sides of the family into the shadows, as if their only role were to ensure the ongoing survival of the dominant and more important family tree.

Family trees, however, like the trees that people decorate around this time of year, have bilateral symmetry, with people decorating each side in popcorn, cranberries and/or holiday lights.

Rarely does anyone do a deep dive into the other side of a family, learning whether the Jones family had faster legs, a quicker wit, better grades or a stronger work ethic.

Then again, the point of these claims isn’t to be scientific, thorough or even fair. It’s a way to connect the children of today with those who came before. Even if people don’t believe in reincarnation, focus on genes, or contemplate the enduring qualities of any family culture, they might feel tremendous joy and comfort hoping that this person’s unwritten life includes future chapters that reflect a familial past that need not be exclusive to one branch, one side or one person.

Story weaving may help give a developing life context and meaning. Ideally, those attributes and connections may remind the family and this new person about the kind of strong and accomplished roots that can help him or her develop into the kind of person he or she chooses to be, which would be a win for everyone.

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