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Daniel Dunaief

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Martyna Sroka. Photo by Sofya Polyanskaya

By Daniel Dunaief

Part 1:

A group of people may prove to be the guardian angels for the children of couples who haven’t even met yet.

After suffering unimaginable losses to a form of cancer that can claim the lives of children, several families, their foundations, and passionate scientists have teamed up to find weaknesses and vulnerabilities in cancers including rhabdomyosarcoma and Ewing sarcoma.

Rhabdomyosarcoma affects about 400 to 500 people each year in the United States, with more than half of those patients receiving the diagnosis before their 10th birthday. Patients who receive diagnoses for these cancers typically receive medicines designed to combat other diseases.

 

Christopher Vakoc. Photo from CSHL

A group of passionate people banded together using a different approach to funding and research to develop tools for a different outcome. Six years after the Christina Renna Foundation and others funded a Banbury meeting at Cold Spring Harbor Laboratory, the grass roots funders and dedicated scientists are finding reasons for optimism.

“I wish I could run up to the top of a hill and scream it out: ‘I’m more hopeful than I’ve ever been,’” said Phil Renna, director of operations, communications department at CSHL and the co-founder of the Christina Renna Foundation. “I’m really excited” about the progress the foundation and the aligned group supporting the Sarcoma Initiative at the lab has made.

Renna and his wife Rene started the foundation after their daughter Christina died at the age of 16 in 2007 from rhabdomyosarcoma. Renna’s optimism stems from work Cold Spring Harbor Laboratory’s Christopher Vakoc, a professor and Cancer Center co-director and his research team, including PhD candidate Martyna Sroka have performed.

The cause for optimism comes from the approach Vakoc has taken to cancers, including leukemia.

Vakoc has developed a way to screen the effects of genetic changes on the course of cancer.

“Usually, when you hear about a CRISPR screen, you think of taking out a function and the cell either dies or doesn’t care,” Sroka said, referring to the tool of genetic editing. Sroka is not asking whether the cell dies, but whether the genetic change nudges the cellular processes in a different direction.

“We are asking whether a loss of a gene changes the biology of a cell to undergo a fate change; in our case, whether cancer cells stop growing and differentiate down the muscle lineage,” she explained.

In the case of sarcoma, researchers believe immature muscle cells continue to grow and divide, turning into cancer, rather than differentiating to a final stage in which they function as normal cells.

Through genetic changes, however, Sroka and Vakoc’s lab are hoping to restore the cell to its non cancerous state.

Cold Spring Harbor Laboratory has had success with other diseases and other types of cancer, which is where the optimism comes from, explained Paul Paternoster, President of Selectrode Industries, Inc. and the founder of the Michelle Paternoster Foundation for Cancer Research.

As a part of her doctoral research which she’s been conducting for four years, Sroka is also working with Switzerland-based pharmaceutical company Novartis AG to test the effect of using approved and experimental drugs that can coax cells back into their muscular, non-cancerous condition.

The work Sroka and Vakoc have been doing and the approach they are taking could have applications in other cancers.

“The technology that we’ve developed to look at myodifferentiation in rhabdomyosarcoma can be used to study other cancers (in fact, we are currently applying it to ask similar questions in other cancer contexts),” said Sroka. “In addition, our findings in RMS might also shed light on normal muscle development, regeneration and the biology of other diseases that impact myodifferentiation, e.g. muscular dystrophy.”

Martyna Sroka’s journey

Described by Vakoc as a key part of the sarcoma research effort in his lab, Martyna Sroka, who was born and raised in Gdańsk, Poland, came to Long Island after a series of eye-opening medical experiences.

In Poland, when she was around 16, she shadowed a pediatric oncology doctor who was visiting patients. After she heard the patient’s history, she and the doctor left the room and convened in the hallway.

Martyna Sroka. Photo by Sofya Polyanskaya

“He turned to me and said, ‘Yeah, this child has about a month or two tops.’ We moved on to the next case. I couldn’t wrap my head around it. That’s as far as we could go. There’s nothing we could do to help the child and the family,” said Sroka.

Even after she started medical school, she struggled with the limited ammunition modern medicine provided in the fight against childhood cancer.

She quit in her first year, disappointed that “for a lot of patients diagnosed with certain rare types of tumors, the diagnosis is as far as the work goes. I found that so frustrating. I decided maybe my efforts will be better placed doing the science that goes into the development of novel therapies.”

Sroka applied to several PhD programs in the United Kingdom and only one in the United States, at Cold Spring Harbor Laboratory, where she hoped to team up with Vakoc.

Sroka appreciated Vakoc’s approach to the research and his interest in hearing about her interests.

“I knew that we could carve out an exciting scientific research project that tries to tackle important questions in the field of pediatric oncology, [the] results of which could potentially benefit patients in the future,” she explained in an email.

The two of them looked at where they could make a difference and focused on rhabdomyosarcoma.

Sroka has “set up a platform by which advances” in rhabdomyosarcoma medicines will be possible, Vakoc said. “From the moment she joined the sarcoma project, she rose to the challenge” of conducting and helping to lead this research.

While Sroka is “happy” with what she has achieved so far, she finds it difficult at times to think about how the standard of care for patients hasn’t changed much in the last few decades.

“Working closely with foundations and having met a number of rhabdomyosarcoma patients, I do feel an intense sense of urgency,” she wrote.

Read Part 2 here.

 

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Maurizio Del Poeta in his laboratory at Stony Brook University. Photo by Antonella Rella

By Daniel Dunaief

Researchers at Stony Brook University, the University of Arizona and Wake Forest University School of Medicine in North Carolina may have found an enzyme that drives the worst COVID-19 symptoms. Secreted phospholipase A2 group IIA, or sPLA2-IIA may lead to severe symptoms and death, making this enzyme a potential therapeutic target.

P116, Maurizio DelPoeta, Microbiology

In an examination of plasma samples from 127 patients hospitalized at Stony Brook University Medical Center between January and July 2020 and a mix of 154 patient samples from Stony Brook and Banner University Medical Center in Tucson between January and November 2020, scientists including Distinguished Professor Maurizio Del Poeta of the Renaissance School of Medicine at Stony Brook University found that 63 percent of people with concentrations of the enzyme that were over 10 nanograms/ milliliter generally died. Most healthy people have circulating levels of the enzyme around 0.5 nanograms/ milliliter.

“It is possible that sPLA2 levels represent a tipping point and when it reaches a certain level, it is a point of no return,” said Del Poeta.

The collaborators involved in the study, which was published this week in the Journal of Clinical Investigation, were encouraged by the finding.

“This is exciting as it is leading to really novel connections for COVID-19,” Yusuf Hannun, Director of the Cancer Center at Stony Brook and a contributor to the research who participated in the discussion and data analysis, explained in an email. “It may lead to both diagnostics (for risk prediction) and therapeutics.”

Looking closely at the levels of sPLA2-IIA together with blood urea nitrogen, or BUN, which is a measure of the performance of the kidney, the researchers in this study found that the combination of the two measures predicted mortality with 78 percent accuracy.

“That is an opportunity to stratify patients to those where an inhibitor” to sPLA2-IIA could help patients, said Floyd Chilton, director of the University of Arizona Precision Nutrition and Wellness Initiative and senior author on the paper, said.

While they found a difference in the amount of the enzyme between healthier and sicker patients, the scientists recognize that this could reflect a correlation rather than a causation. The progression of the disease and the threat to people’s lives may come from other contributing factors that also intensify the severity of the illness.

“These studies do not establish causality at the moment, but the strength of the correlation and the known functions of this enzyme raise the possibility of participating in the pathology of the disease,” Del Poeta explained.

Floyd Chilton. Photo from University of Arizona

Indeed, Chilton has studied sPLA2-IIA for over three decades and has described some patterns in other diseases, including sepsis.

The enzyme performs an important role in fighting off bacterial infection by destroying microbial cell membranes. When the concentration of sPLA2-IIA rises high enough, however, it can threaten the health of the patient, as it can attack and destroy cells in organs including the kidney.

The enzyme “plays a critical role in host defense,” said Chilton. “These same systems can really turn on the host.”

In order to determine a causative link between sPLA2-IIA and the progression of the disease, Chilton, Del Poeta and others will need to increase their sample size.

“We’ve been very fortunate at getting individuals at some of the top global organizations… who have connected me with medical centers” that have a larger patient population, Chilton said. These executives may be able to expedite the process of expanding this study.

In the 1990’s, scientists studied an inhibitor that had the ability to act on the enzyme. 

That effort had mixed results in phase 2 clinical trials.

“In 2005, the first phase of the phase 2 clinical trials were highly encouraging,” Chilton said. “It really inhibited mortality at 18 hours” by reducing severe sepsis. The second part of those tests, which used a slightly different protocol, failed.

While he’s not a clinical trials expert, Chilton is hopeful that researchers might find success with this same drug to treat COVID-19.

Only clinical trials would reveal whether inhibitors would work with COVID-19, scientists said.

As with many drugs, inhibitors of sPLA2-IIA have side effects.

By blocking the activity of these enzymes, “we do also decrease the production of arachidonic acid, which is a precursor of prostaglandins,” said Del Poeta. “In condition of hyperinflammation, this is a good thing, but prostaglandins are also important in a variety of cellular functions” including blood clots and starting labor.

Chilton pointed out that sPLA2-IIA is similar to the active enzyme in rattlesnake venom. It can bind to receptors at neuromuscular junctions and disable the function of these muscles, he explained.

In nature, some animals have co-evolved with snakes and are no longer susceptible to these toxins. Researchers don’t yet understand those processes.

While copying such evolutionary solutions is intriguing, Chilton said he and his collaborators are “much more interested in the inhibitors” that were taken through clinical trials in 2005 because that might present a quicker solution.

The research collaboration started with Chilton, who partnered with Arizona Assistant Research Professor Justin Snider. The first author on the paper, Snider earned his PhD at Stony Brook, where he knew Del Poeta well.

Snider “knew what a great researcher [Del Poeta] was. I also knew [Hannun] in a former life. We were both working on similar biochemistry 20 to 25 years ago,” Chilton said.

Chilton called the efforts of his Stony Brook collaborators, including Research Assistant Karen You, Research Associate Professor Chiara Luberto and Associate Professor Richard Kew,  “heroic” and explained that he and his colleagues recognize the urgency of this work.

“I’ve been continuously funded by the [National Institute of Health] for 35 years, and I’m very grateful for that,” Chilton said. “There is nothing in my life that has felt this important,” which is why he often works 18 hour days, including on weekends.

After studying the effects of variants on the population, Chilton recognized that building a firewall against COVID-19 through vaccinations may not be enough, especially with the combination of lack of access to the vaccine for some and an unwillingness to take the vaccine from others.

“We may have to go to the other side of the equation,” HE said. “We’ve got to move to specific therapeutics that are agnostic to the variant.”

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METRO photo

By Daniel Dunaief

Daniel Dunaief

We packed our bags full of dreams, hopes, clothing and cliches and took our son to college. We pondered the journey, which is really what’s it’s all about, and not the destination.

My wife and I were bursting with pride, thinking about the shining light that is our son.

We wondered what advice we could offer before we returned to a house that would feel so empty without him. We thought a good rule of thumb might be to avoid harebrained ideas, although we knew we could do better at preparing him for future dark and stormy nights.

As he took his first steps onto his new campus, we encouraged him to discover the world and himself at the same time.

We shared the butterflies that fluttered among our four stomachs. Like a good soldier in our family’s mission, his sister joined us for this momentous occasion, prepared to offer her version of older sibling advice and to help find whatever item he might need in a college dorm he is sharing with a stranger he’d chosen from a grab bag of potential roommates.

As we followed the move-in directions to a tee, we could feel the electricity in the air. We drove up to an official behind a desk, who was all ears listening to him spell a last name chock full of vowels.

With bated breath and sweaty palms, we waited with every fiber of our beings until she found him on the list. We breathed a sigh of relief when she found his name and handed him a key that would open his dorm room to a new world of possibilities. As a freshman, he knew he was no longer the big man on campus he had been during his pandemic-altered senior year.

Once inside his dorm, we got down to the business of unpacking. We debated where to put his shoes even as he stared out the window, considering where he might plant his feet.

Recognizing that time was of the essence, we spring to life while unpacking his room. Standing apart in a small room full of wonders, we drew strength from our collective mission.

Slowly but surely, we removed the contents of his boxes, creating order from the chaos despite a few moments when we felt like we were all thumbs. We lined all his ducks in a row, creating neat rows of pencils, pens and notebooks on his desk and boxers, shorts, tee shirts and socks in his drawers.

After we prepared his room, we wiped the sweat from our brow, reminding him that this effort was but a drop in the bucket of the work he’d need to do in college.

We assured him he could bet his bottom dollar he wouldn’t feel like a babe in the woods or a fish out of water for long.

We could almost hear the angelic chords as the sun set in the west, where it always sets because that’s the way the cookie crumbles, or, rather, the earth rotates.

Before we left him in his new home away from home, we exchanged embraces and urged him to dance to the beat of his own drum.

We also suggested he find a healthy way to blow off steam, to recognize that a rising tide lifts all boats, to swim when it was time to sink or swim, and to play his cards right.

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BNL LECTURE: ZHANGBU XU

By Daniel Dunaief

Gregory Breit and John Wheeler were right in the 1930s and Werner Heisenberg and Hans Heinrich Euler in 1936 and John Toll in the 1950s were also right.

Breit, who was born in Russia and came to the United States in 1915, and Wheeler, who was the first American involved in the theoretical development of the atomic bomb, wrote a paper that offered theoretical ideas about how to produce mass from energy.

Breit and Wheeler suggested that colliding light particles could create pairs of electrons and their antimatter opposites, known as positrons. This idea was an extension of one of Albert Einstein’s most famous equations, E=mc2, converting pure energy into matter in its simplest form.

Zhangbu Xu in front of the time-of-flight detector, which is important for identifying the electrons and positrons the STAR Collaboration measured. Photo from BNL

Working at the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory, a team of scientists in the STAR Collaboration has provided experimental proof that the ideas of some of these earlier physicists were correct.

“To create the conditions which the theory predicted, even that process is quite exhausting, but actually quite exciting,” said Zhangbu Xu, a senior scientist at BNL in the physics department.

The researchers published their results recently in Physics Review Letters, which provides a connection to Breit and Wheeler, who published their original work in a predecessor periodical called Physics Review.

While Breit and Wheeler wrote that the probability of two gamma rays colliding was “hopeless,” they suggested that accelerated heavy ions could be an alternative, which is exactly what the researchers at RHIC did.

The STAR team, for Solenoidal Tracker at RHIC, also proved another theory proposed decades ago by physicists Heisenberg, who also described the Heisenberg Uncertainty Principle, and Hans Heinrich Euler in 1936 and John Toll, who would later become the second president at Stony Brook University, in the 1950s.

These physicists predicted that a powerful magnetic field could polarize a vacuum of empty space. This polarized vacuum should deflect the paths of photons depending on photon polarization.

Researchers had never seen this polarization-dependent deflection, called birefringence, in a vacuum on Earth until this set of experiments.

Creating mass from energy

Xu and others started with a gold ion. Without its electrons, the 79 protons in the gold ion have a positive charge, which, when projected at high speeds, triggers a magnetic field that spirals around the particle as it travels.

Once the ion reaches a high enough speed, the strength of the magnetic field equals the strength of the perpendicular electric field. This creates a photon that hovers around the ion.

The speeds necessary for this experiment is even closer to the speed of light, at 99.995%, than ivory soap is to being pure, at 99.44%.

When the ions move past each other without colliding, the photon fields interact. The researchers studied the angular distribution patterns of each electron and its partner positron.

“We also measured all the energy, mass distribution, and quantum numbers of the system,” Daniel Brandenburg, a Goldhaber Fellow at BNL who analyzed the STAR data, said in a statement.

Even in 1934, Xu said, the researchers realized the cross section for the photons to interact was so small that it was almost impossible to create conditions necessary for such an experiment.

“Only in the last 10 years, with the new angular distribution of e-plus [positrons] and e-minus [electrons] can we say, ‘Hey, this is from the photon/ photon creation,’” Xu said.

Bending light in a vacuum

Heisenberg and Euler in 1936 and Toll in the 1950’s theorized that a powerful magnetic field could polarize a vacuum, which should deflect the paths of photons. Toll calculated in theory how the light scatters off strong magnetic fields and how that connects to the creation of the electron and positron pair, Xu explained. “That is exactly what we did almost 70 years later,” he said.

This is the first experiment on Earth that demonstrates experimentally that polarization affects the interactions of light with the magnetic field in a vacuum.

Xu explained that one of the reasons this principle hasn’t been observed often is that the effect is small without a “huge magnetic field. That’s why it was predicted many decades ago, but we didn’t observe it.”

Scientists who were a part of this work appreciated the connection to theories their famous and successful predecessors had proposed decades earlier.

“Both of these findings build on predictions made by some of the great physicists in the early 20th century,” Frank Geurts, a professor at Rice University, said in a statement. 

The work on bending light through a vacuum is a relatively new part of the research effort.

Three years ago, the scientists realized they could study this, which was a surprising moment, Xu said.

“Many of our collaborators (myself included) did not know what vacuum birefringence was a few years ago,” he said. “This is why scientific discovery is exciting. You don’t know what nature has prepared for you. Sometimes you stumble on something exciting. Sometimes, there is a null set (empty hand) in your endeavor.

Xu lives in East Setauket. His son Kevin is earning his bachelor’s degree at the University of Pennsylvania, where he is studying science and engineering. His daughter Isabel is a junior at Ward Melville High School.

As for the recent work, Xu, who earned his PhD and completed two years of postdoctoral research at Yale before coming to BNL, said he is pleased with the results.

“I’ve been working on this project for 20 years,” he said. “I have witnessed and participated in quite a few exciting discoveries RHIC has produced. These are very high on my list.”

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Brandpoint photo

After seeing enough cases of vaccinated people testing positive amid a surge in the Delta variant that has become the dominant strain of the virus in Suffolk County, local health officials support the federal government’s plan to provide booster doses eight months after the first course of vaccination.

Several studies have pointed to the benefit of boosters, highlighting how people who are vaccinated have lower antibody levels over time and are more susceptible to the highly transmissible Delta variant.

Centers for Disease Control and Prevention Director Rochelle Walensky and Food and Drug Administration Acting Commissioner Janet Woodcock said in a joint statement on Wednesday, Aug. 18, that the government is prepared to offer booster shots for all Americans beginning the week of Sept. 20 and starting eight months after people received their second shots.

A recent study by Mayo Clinic researchers looked at records for 25,0000 vaccinated and unvaccinated patients in Minnesota. The study showed 76% effectiveness in the Pfizer vaccine protecting them from infection, but 42% effectiveness in July during COVID, Sunil Dhuper, chief medical officer at St. Charles Hospital, explained in an email.

At the same time, Health Ministry of Israel data showed a similar progressive decline in the effectiveness of the vaccination in protecting patients from infection over a six-month period, particularly amid Delta variant surges.

Still, the vaccinations continued to provide protection against more serious forms of the disease, with a much smaller 10% decline in the effectiveness of vaccines in protecting people against hospitalizations, Dhuper said.

In physician practices, urgent care centers and emergency departments, doctors are seeing a “sizable number” of breakthrough cases, Dhuper continued.

Adrian Popp, chair of Infection Control at Huntington Hospital/ Northwell Health, said Huntington Hospital has seen breakthrough cases, although most of them are “mild” and are “diagnosed incidentally when patients get admitted for other issues.”

Dhuper urged residents to take precautions similar to the ones they took last year before vaccines were available, including social distancing, wearing masks and washing hands carefully, especially in indoor settings.

At this point, boosters will likely be available for the Pfizer/ BioNTech and Moderna vaccinations. The Food and Drug Administration is still looking at data for people who received the Johnson & Johnson shot.

Once the FDA provides Emergency Use Authorization for a booster for the general population, medical health experts anticipate a much smoother roll out than the initial struggle with finding vaccinations.

“As all who have been vaccinated in New York State have a [Centers for Disease Control and Prevention] vaccine card,” Sharon Nachman, chief of the Division of Pediatric Infectious Diseases at Stony Brook Children’s Hospital, said in an email, “It should be straightforward to each person to get a booster at the eight-month mark.”

At the same time, parents are focused on the timing and availability of vaccines for children under the age of 12. Results from the trial are “expected in December 2020,” wrote Popp.

Medical experts continue to urge residents to receive their shots.

“It is hoped that the booster will cut down on these infections and thus transmissions,” Nachman said.

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Image from Pixabay

By Daniel Dunaief

Daniel Dunaief

Welcome to Dan Dunaief HS or DDHS. I know it’s an odd time to start a new high school, but children need to learn, even during a pandemic.

Originally, I was planning to have everyone come to a pep rally on the first day of school. After all the restrictions of last year, it only seemed fitting to bring the kids together in the gym and celebrate the chance to sit in 1950s style wooden bleachers that rock when someone walks a few steps.

But, then, I realized we don’t have a basketball, football or squash team, we haven’t picked school colors, we don’t have a school song and, most importantly, we are in a difficult spot with the pandemic.

I know your kids are exhausted from dealing with the virus. Who can blame them? Aren’t we all?

At first, I thought we’d avoid the whole topic and stick to the basics in school.

But, then, it occurred to me that avoiding a virus that has now affected three school years wouldn’t make it better. We can try not to think about it, but that doesn’t make it go away. Information and knowledge will help these students understand the strange world that surrounds them and might empower them to feel as if they’re doing something about it, even if it’s just learning more about a time that future generations will no doubt study carefully, scrutinizing our every move as if we were some kind of early laboratory experiment.

With that in mind, I gave the curriculum serious consideration. I thought about all the standard ways students have learned.

Ultimately, I decided to turn toward the academic vortex. At DDHS, at least for the first year or so, we’re going to encourage students to study the real challenges of the world around them.

For starters, in our art class, we’re going to have design competitions for the front and back of masks. The winners will provide masks that the entire school will wear each week.

Then, in an engineering class, we’ll work on creating masks that are more comfortable and just as effective as the ones that make our faces sweat. Maybe this class can also figure out how to provide words that flash across the mask when we talk, giving people a better idea of what we’re saying behind our masks. Maybe enterprising students can design masks that cool our faces when we sweat and warm them when we’re cold, that shave or bleach unwanted hair or that act like dry-fit shirts, covering our faces without clinging to them.

In history, we’ll spend at least a semester on the Spanish Influenza. We’ll explore what leaders throughout the world did in 1918 during the last pandemic. We’ll see what worked best and what disappointed.

Our psychology class will devote itself to the conflicts between people’s perceptions of infringements on their individual freedoms and their desire to protect themselves and each other by wearing masks.

Our political science course will delve into how politics became enmeshed in the response to the virus. This class will look at which side gains, politically, amid different public health scenarios.

Science classes will explore why some people get incredibly sick from the virus, while others show no symptoms. We will also study the way the virus works, look at similar viruses and try to understand and track the development of variants.

Math will work with the science department to understand the spread of the virus and to plot various scenarios based on human behavior. Eager students in math will have the chance to demonstrate how sicknesses spread depending on the wearing of masks, the use of vaccines, and the creation of new variants.

Our language arts class will provide an outlet for students to express their hopes, dreams and concerns amid the unique challenges in their lifetime created by the pandemic.

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A screenshot of the app created by Christopher Gobler and Sung-Gheel Jung of Stony Book University.

Stony Brook University’s Christopher Gobler, endowed chair of Coastal Ecology and Conservation, and Sung-Gheel Jang, faculty director in the Geospatial Center at Stony Brook University, have created a free app that provides information on water quality on Long Island.

Through the downloadable Long Island Beach and Water Quality App, also known as LIBAWQA, residents can gather information that can connect to a person’s location, indicating the health and safety of beaches, bays, estuaries or waterways near them.

Gobler’s lab provides the water quality data, which comes from measures they make in 30 locations from East Hampton to Hempstead.

The New York State Department of Health provides updates on about 200 beaches across the Island, while the NYS Department of Environmental Conservation offers shellfishing data for more than 500,000 acres of bays, harbors and estuaries.

Jang, whose expertise is in the mapping related to geographic information systems, or GIS, helped build a service he targeted for the general public.

Instead of calling the county to find out if their favorite summer destination is open, residents can “use the app and you will know the current water quality,” Jang said.

Shellfishing and bathing restrictions use different criteria to determine the safety of swimming or pulling up clams and other shellfish.

“This is the beauty of the app,” Gobler said. One day last week, he noticed that a site in Center Moriches allowed swimming but not shellfishing. “The beach right next to it” allows shellfishing. “Which one would you rather go to?”

The app, which is available by installing ArcGIS AppStudio Player from Google Play, the App Store or the Microsoft Store and using a QR code on a camera, can show the health history of a beach.

While the system, which Gobler described as being in “version 1.0” doesn’t have text alerts, it does provide real-time information.

Users can track their location on the map in the app, checking on the shellfish or bathing status of nearby waterways.

The idea for this app came about a couple of years ago when Jang visited Gobler’s lab and the two Stony Brook researchers talked about collaborating.

“I was impressed by [Gobler’s] work,” Jang said. “His lab collected water quality data for many, many years.”

Jang suggested creating an easy-to-use mobile app. Gobler wanted to add other information beyond the water quality data his lab collected regularly.

Gobler and Jang expect to modify and enhance the information by next summer, when it could include a crowdsourcing opportunity, in which participants share updated information, including limitations on parking or beach closures.

Gobler and Jang said they would need to provide a filter before posting information to ensure it contains quality data.

The service isn’t available in the Google or Apple app stores yet.

“By next summer we hope we can release a new version,” Jang added. “We wanted to show we have a working app first.”

Scientists of any age, from primary school through postdoctoral researchers, can use the information for their own research papers or studies, Jang said.

Anyone who is interested in accessing and using the data for their own research projects can contact Jang through his email at [email protected].

The scientists have received funding from the Rauch Foundation and The Chicago Community Trust. The pair will seek renewals from both sources this fall.

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Stony Brook University's played in the summer Olympics with Team Puerto Rico's women's basketball team. Photo from India Pagan

Stony Brook University’s India Pagan, competing in the Olympics for Puerto Rico, took several shots against China in the preliminary round of the basketball tournament, but none of them went in.

India Pagan at the summer Olympics opening ceremony. Photo from India Pagan

Against Belgium, the 6-foot-1-inch forward finally put the ball through the hoop, something she’d done so frequently at Stony Brook that she scored over 1,000 points as a Seawolf.

“I remember the first one I made” at the Olympics, said Pagan. “I didn’t have to stress anymore. I couldn’t stop smiling.”

Pagan, who was on Puerto Rico’s first women’s Olympic basketball team, scored two baskets and sank two free throws, scoring six points in that game.

Despite the challenges and restrictions created by the Delta variant of COVID-19 and the three losses the Puerto Rican team had in games against China, Belgium and Australia, Pagan had plenty of reasons to smile as she enjoyed everything from the opening ceremonies to taking selfies with some of the best athletes in the world to some limited sightseeing.

After a lengthy journey to the other side of the world, Pagan cheered her way through an opening ceremony full of familiar pageantry, but devoid of its customary shouting spectators.

“It was surreal to me,” Pagan said. “I watched this on TV a couple of years ago. Walking with the flag, with the whole delegation of Puerto Rico, seeing the stage, the torch, the dances, the acts of music, everything, it was just so beautiful.”

Pagan said she cried three or four times during the ceremonies.

Behind the scenes, Pagan said the time spent waiting for the ceremonies to begin and the hours on their feet amid the excitement took their toll.

“By the end of the night, all of our backs hurt, our feet hurt,” she laughed. “Thankfully, we didn’t have practice the next day, so we had a little time to recover.”

Around the games, Pagan soaked in the atmosphere and reveled in the moment on one of the world’s largest, albeit emptiest, athletic stages.

One of the big stories to come out of the Olympics involved American gymnast Simone Biles, who pulled out of most of the competition amid concerns about her mental health and her ability to get her bearings while flying and twisting through the air.

“We understood the mental health aspects” of Biles’s decision, Pagan said. “She’s got to do what’s best for her. We did feel for her.”

Pagan said the Puerto Rican basketball team met with their coach, who told them they could speak with a doctor or a psychologist if they needed support.

Pagan missed her family and friends but didn’t need those mental health services during her time in Tokyo.

Pagan was thrilled to run into several superstars in their sports, taking selfies with National Basketball Association star Jayson Tatum from the Boston Celtics, and with Spanish basketball sensations Marc Gasol, who currently plays for the Los Angeles Lakers and his brother Pau, who retired from the NBA in 2019 after an 18-year career. She also ran into Serbian tennis great Novak Djokovic.

“Seeing those people was cool for me,” Pagan said.

Pagan takes a photo with Spanish basketball sensation Pau Gasol. Photo from India Pagan

Everyone had to wear face shields in the dining hall which made conversations, even among teammates, challenging.

“It was tough to interact” while she was eating, Pagan said.

She did, however, have the opportunity to speak and play games with other masked athletes in a recreational area. Pagan and teammates Jada Stinson and Jacqueline Benitez visited with athletes from the South African soccer and track teams, and several teams from Ireland, Italy and Iran while playing table tennis, pool and darts.

During her stay in Tokyo, Pagan recalled the lives of two people she and her family recently lost. She wrote the names of Tatiana Mayas, one of her closest childhood friends, and Gloria Sotomayor, a friend of her mother’s, on a white ribbon and pinned them on a memorial tree.

While the athletes couldn’t explore Tokyo on their own or travel much outside the Olympic village, they took a bus tour to Mt. Fuji, which, at 12,380 feet, is the tallest mountain in Japan.

“If we got off the bus and the [International Olympic Committee] found out, they would have kicked us out of the Olympics,” Pagan said.

Pagan remained appreciative of an opportunity she didn’t take for granted, especially since she has no guarantee that she or the Puerto Rican team will return for the 2024 Olympics in Paris.

“I was ready for anything and I was grateful for anything,” Pagan said.

In addition to returning with a collection of memories, photos and selfies, Pagan brought back numerous souvenirs for herself and her family.

She purchased a letterman jacket that she said she “had to have,” because it was a once-in-a-lifetime opportunity.

She also purchased shoes, shirts, key chains, umbrellas, pins and notebooks.

“It was like Christmas,” she laughed. The gifts were worth the money, as her family’s faces “lit up” when she produced their presents.

During her Olympics, she appreciated the outpouring of support for her and for the team.

“My phone has never blown up as much as it did when I was at the Olympics,” said Pagan, who is returning to Stony Brook to earn her master’s this fall and to use a fifth year of eligibility the National Collegiate Athletic Association granted to athletes amid the pandemic.

She left North America with 6,000 Instagram followers and returned with 11,000.

One of the first things she did when she returned, after sharing presents, crying and catching up with family, was to get behind the wheel.

“I couldn’t wait to drive my car and be free and go wherever I wanted to, instead of being restrained and told to stay in one place or being locked up in a room,” Pagan said.

She hopes the team will return to the next Olympics in Paris in 2024.

“Hopefully, we’ll be back,” she said. “This experience will definitely help us grow as a program. We’re on our way up.”

As for what’s next, she plans to rest and recover from the exhausting and exhilarating trip and to add the Olympic rings tattoo to her leg.

Pagan appreciates the opportunity to play a game she loves at the Olympic level.

“It was a blessing and an honor,” Pagan said.

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From left, postdoctoral researcher Yunjun Zhao and Brookhaven Lab biochemist Chang-Jun Liu in a greenhouse with poplar trees. Photo from BNL

By Daniel Dunaief

Plants not only make our food, produce the oxygen we breathe, and provide key ingredients in medicines, but they could also contribute chemicals that might otherwise require fossil fuels to produce.

Scientists have known since 1955 that poplar trees produce small amounts of a product called p-hydroxybenzoic acid that they attach to the lignin in their cell walls. What they didn’t know, however, was how they were attached.

After years of cloning genes and, more recently, using the gene editing tool CRISPR, Chang-Jun Liu, a plant biochemist at Brookhaven National Laboratory, and collaborators in Japan discovered the gene that codes for an enzyme that catalyzes the attachment of pBA to the lignin.

Up to now, companies have produced pBA by using fossil fuels as raw materials and for the energy required to generate enough heat and pressure for the catalytic reactions.

This discovery, which Liu published in the journal Nature Plants, could provide a more eco-friendly way to produce a chemical involved in the manufacture of toothpaste, shampoos, commercial moisturizers, shaving gels, and spray tanning solutions, among other products.

The global market value of p-hydroxybenzoic acid was $59 million in 2020 and is expected to climb to $80 million in the next five years.

“We wanted to identify the enzyme that is responsible for attaching pBA into lignin and reconstitute this pathway and promote its storage in the cell wall,” Liu said. Ideally, he’d like to combine the pathways that produce the donor molecule containing pBA with their enzyme to promote pBA storage in cell walls.

Once Liu found the gene responsible for that enzyme, he did what scientists typically do to check on the importance of a genetic sequence: first, he knocked it out and second, he overexpressed it.

By knocking out the genetic sequence, he found that poplar trees stopped producing pBA. Overexpressing the gene, on the other hand, not only increased the amount of this chemical by about 48 percent, but also raised the strength of the lignin and, consequently, the durability of the cell wall.

Aside from the benefit of increasing the natural production of the chemical, changing the amount of pBA could have implications for the environment and industry. Less durable lignin, which has a lower amount of pBA, could be useful in producing pulp, paper and biofuel, making it easier to access the biomass of the wood.

More durable lignin could be useful in the timber industry, while also enabling the plant to remove more carbon, mostly in the form of carbon dioxide, from the air.

“If we can engineer the plant to produce more of this carbon-dense compound, … particularly in the root, we can fix more carbon into the underground fraction, which will absorb more carbon from the air to promote carbon sequestration,” Liu said.

A long process

The work that led to identifying the gene that codes for the enzyme that attaches pBA to lignin took about 15 years.

Liu knew this enzyme worked to attach pBA, among other chemicals, in a test tube, but the journey to prove its importance in the poplar trees took considerable work.

Liu cloned 20 genes that are expressed in woody tissues and encoded enzymes called acyltransferases. While expressing these enzymes, he mixed them with an isotope-labeled carbon, which allowed him to check to see whether the enzyme contributed to the process of attaching pBA to lignin.

He tried using RNA interference to knock down the targeted gene, but that didn’t work.

The breakthrough that established the importance of this gene came when Liu used CRISPR. 

Next steps

Scientists aren’t sure of the specific steps or even why plants produce pBA in the first place.

Plants produce pBA through the shikimate pathway, but the exact routes leading to pBA formation are still undiscovered. 

As for why plants produce pBA, one hypothesis is that the plant uses a higher amount as a defense mechanism, making its lignin harder to remove for an insect. It could also provide resistance to mechanical stress caused by wind or snow.

“We do not have solid evidence to prove that,” he said, but “we need to explore that further.”

Liu also hopes to take a synthetic biology approach to build a more effective pathway by using the enzyme to make the plant a partner in producing pBA and in capturing and storing organic carbon.

The biochemist hopes to find a commercial partner who might be interested in exploring the development of a process that occurs naturally in poplar trees.

The environmental impact of increasing pBA in plants on the ecology of the areas in which these poplar trees might grow is unclear.

“We do not know at this moment whether this will benefit or be harmful to the soil microbial community,” he said. “In some cases, it can help the plant absorb more nutrients. It potentially can also kill other microbial life.”

For the plant, it’s unclear what the effect of higher pBA might be. The enzyme Liu identified moves pBA from inside the cell to the cell where, which would likely mitigate any toxicity because that is dead material. 

“We expect the increase of cell wall-bound pBA should promote the trees’ ability in withstanding environmental changes,” he explained.

Altering the cell’s metabolic processes by rebuilding a new pathway that produces high amounts of pBA could negatively affect a tree’s normal growth. Liu would need to conduct more experiments to explore this possible effect.

A resident of Rocky Point, Liu lives with his wife Yang Chen, who is a special education teacher assistant at Rocky Point Middle School. Their son Allen is in his third year at Purdue University, while Bryant is in his second year at the University of Southern California. The family enjoys skiing and hiking trips.

The work to confirm the link between the gene and the production of pBA involved numerous post doctoral researchers.

Liu appreciates the effort of his research team over the years. “I’m very happy that we were finally able to resolve this issue,” he said.

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

Years ago, restaurants had smoking and non-smoking sections. Airlines reserved parts of the plane for people who smoked and those who didn’t.

How, after all, were people addicted to nicotine supposed to get through a meal or a plane ride, especially one that could take hours, without lighting up?

Society knew back then that smoking was harmful for the smoker. We knew that each person ran the risk of lung, mouth and throat cancers, among others, from inhaling the toxins in cigarettes.

Slowly, we also started to learn about the dangers of second-hand smoke. People who didn’t light up cigarettes and cigars couldn’t simply move away from that smoke, especially if they were in the same house, the same car, or even, for several hours, on a plane together.

Over time, health officials started to piece together the kind of information that made it clear that non smokers needed protection.

Slowly, restaurants and planes banned smoking. And yet, despite the years of no-smoking policies on planes, the flight attendants or the videos we watch before take off include threats about the consequences of disabling or dismantling smoke detectors in bathrooms.

We also knew, at great cost, that drinking and driving was enormously problematic. People getting behind the wheel after having a few drinks at dinner or while watching a sporting event with their buddies risked the lives of those in their own car, as well as anyone else unfortunate enough to be on the road at the time.

Groups like Mothers Against Drunk Driving and Students Against Drunk Driving came together to fight against habits that put others at risk. While drunk driving still occurs throughout the world, the awareness of the dangers of drinking and driving and, probably just as importantly, the vigilance with which police forces cracked down on people while they were driving impaired has helped to reduce the threat. In 2018, alcohol-impaired driving fatalities was 3.2 per 100,000, which is a drop of 65% since 1982, according to Responsibility.org.

Drunk driving remains a public health threat, with advertisements encouraging people not to let friends drive drunk and organizations like MADD continuing to fight to reduce that further.

While risking the potential for false equivalence, the current pandemic presents similar challenges, particularly regarding wearing masks. Yes, masks are a nuisance and we thought we were done with them, particularly in the early part of the summer when the infection rate declined and vaccinations increased.

With the Delta variant raging throughout the country, the Centers for Disease Control and Prevention recommends masks for anyone indoors and for those in larger, outdoor settings, regardless of their vaccination status.

Now, living without a mask and drinking or smoking are not the same. Drinking and smoking are riskier activities adults engage in and that are not a basic necessity, like breathing.

At the same time, however, people opting not to wear masks because they don’t want to or because that was so 2020 are risking more than their own health. They are sharing whatever virus they may have, in some cases with people whose health might be much more at risk.

When I’m sweating at the gym, I find the masks uncomfortable and distracting. I do, however, continue to wear them because they are a way to protect other people in the room.

I hope I don’t have COVID-19, but I can’t be sure because I have been vaccinated and I could be an asymptomatic carrier.

Students, many of whom can’t receive the vaccine, are better off learning at school than at home or, worse, in a hospital bed. If you’re not wearing a mask for you, consider putting one on for everyone else. 

Together, we can and will get through what seems like a viral sequel no one wanted. Until there’s a better way, consider wearing a mask to protect others. If people could do it during the Spanish Influenza in 1918 and 1919, we can do it, too.

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