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Daniel Dunaief

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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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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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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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H. Reşit Akçakaya during a recent bird watching expedition. Photo by T. Lybvig

By Daniel Dunaief

In the world of conservation, scientists and policy makers have relied on the International Union for Conservation of Nature Red List of Threatened Species to understand just how likely species are to go extinct, often as a result of human actions.

When a species moves from one threat level to another, conservationists typically spring into action, taking steps to protect individuals within a species and the habitat in which that species lives.

A team of over 200 scientists in 171 institutions tested a new measure, called the Green Status, that is designed to measure how effective those conservation efforts have been.

“There are always stories about conservation successes,” said H. Reşit Akçakaya, one of the leaders of the effort who helped develop the methodology for this new metric. The scientists wanted to “create a standard, objective way of recognizing the success and effectiveness of conservation measures. That is very important. We need optimism. People don’t act unless there is hope.”

The Green Status monitors a species recovery, measuring the impact of past and future conservation efforts. Researchers including Akçakaya, who is a Professor in the Department of Ecology and Evolution at Stony Brook University, came up with a formula to determine Green Status. 

The formula includes elements conservations consider important: it should be safe from extinction, it should have a large enough population to have all its natural interactions with the other parts of the ecosystem, and it should be represented in every ecosystem in which it naturally exists and has existed.

The scientists considered the trade-offs between practicality in aiming for a system that is feasible to apply to many species and comprehensiveness, which incorporates relevant aspects of, and factors involved in, species recovery, Akçakaya explained in an email.

The International Union for Conservation of Nature Green Status of Species will join the IUCN Red List to provide a more complete update on a species’ conservation condition, which includes their extinction risk and recovery process.

In a new paper, published in Conservation Biology, scientists from around the world contributed to creating preliminary Green Status for 181 species.

It took seven years from the time the scientists came up with the method, developed it further to make it applicable to all species, published papers, organized workshops and other consultations to get feedback and tested the method.

Akçakaya, who has been involved with the Red List since 1999, said the new system provides information about the status of the species that goes beyond the risk of extinction.

“It’s not sufficient to prevent extinction,” Akçakaya said. “We want them to recover as well.”

One of the challenges in developing this method was in deriving definitions that apply across all species and that are not specific to the conditions and threats any one species faces.

Extinction is difficult to measure but easy to conceptualize, he explained. Recovery, on the other hand, is “not as clear cut.”

The first goal of this enterprise was to come up with ways of standardizing how to measure the recovery of a species that would reflect whether conservation efforts were working.

A species on the Red List might have been critically endangered over a decade earlier. After considerable conservation effort, that species may still be critically endangered, according to the same Red List.

That, however, does not indicate anything specific about whether the conservation efforts are working.

The Red List “doesn’t tell us how much more we need to work to get to a level that we can call recovered,” Akçakaya explained.

The Green Status is not currently a part of conservation policy decisions, particularly because it has only been applied to 181 species. The IUCN, however, which is the world’s largest network of conservationists and conservation scientists, has approved it.

Getting from 181 to tens of thousands will take several years, although Akçakaya said he “has a good start” and he has interest from different people who are involved in conservation.

“We are on our way” towards creating a metric that affects conservation policy, he said. “It will take several years to be used” to affect conservation policies for threatened species.

When the Green Status is more broadly available for a wider collection of species, Akçakaya believes it will provide a way for government officials to make informed decisions.

The IUCN, however, does not tell local and national officials what to do with the information provided with the Red List or with the Green Status.

In developing the Green Status, Akçakaya worked with numerous scientists and conservationists. For this methodology, the researchers received hundreds of comments from people who  shared insights online. They also announced the work within the IUCN network, through which they received feedback.

Part of the larger advances in the context of the Green Status came from looking not only at the resilience of the species, but also at what the species is doing in the ecosystem. “Is it fulfilling its ecological role and its function in the ecosystem?” Akçakaya asked.

The Stony Brook scientist is pleased with the Green Status work. The intelligence of the group is larger than the intelligence of any one person, he said.

The group “had the same goal,” he added. “It was a really satisfying experience in terms of how we came up with a system.”

The Green Status can help balance the conservation news. While conserving biodiversity is urgent, one of the things this measure can achieve is to formalize the successes.

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

Welcome to the casino. Just by being alive today, you’ve all punched your ticket to the worldwide slot machine.

Now, the machines operate the way people expect, most of the time. They follow their programming, they make the loud noises as the three wheels inside of them spin and then show images on those three wheels.

The machine doesn’t cost anything to play. You don’t have to put in quarters or tokens or anything else. You just sit down and a machine starts spinning.

In fact, when you sit in one of our relatively unclean chairs, because we’re much more about playing the game than we are about cleanliness or safety, the process begins.

The chairs are close together, so you and your neighbor can compare notes on how you’re doing in this game, can share stories about your lives and can enjoy time out, away from the limitations of quarantine and all the other frustrations that you’ve had to endure for so long.

We do everything we can to discourage masks. We want you to be able to share the freedom that comes from seeing each other’s faces clearly.

And, if you should happen to need to use the bathroom, we don’t have any annoying signs about washing your hands. In fact, we don’t even recommend soap. What is the value of soap, after all? It’s probably some corporate scheme to boost profits somewhere.

We mean, come on, right? The cavemen didn’t have soap and they lived long enough to become fossils. That should be good enough for you, too, right? Before they died, they drew cool things on the wall, sharing stories that survived years after they did.

Now, we want to share a few details about our cool slot machines. You want to know a secret? We didn’t build these machines. We know, it’s hard to believe, but they just appeared one day, as if a stork or another kind of flying creature brought them. Well, not all of them. That’s the incredible thing. A few of them appeared and, after we started playing them, they copied themselves. The more we played them, the more they produced new copies.

Now, you might have heard that these machines can be bad for you. But, hey, so many other things are bad for you, too, and you still do them, right? You have a little too much to eat or drink now and then, and you maybe put a recycling bottle in the wrong trash can, but who pays attention to those things?

Anyway, so, these original machines built themselves the same way, most of the time. Each time a new machine appeared, they worked the same way, with images flying across the screen.

Every so often, when the machines made enough copies of themselves, they changed slightly. We’re not exactly sure why or how that happened, but it’s perfectly normal, we think.

The newest versions of these machines spin at a faster rate and also copy themselves more rapidly. One of them, which is now the most common type, has a big D on its side. That’s the dominant machine.

Actually, at this point, we’d kind of prefer people stop playing the game. You see, each time you play the game, not only does that D version copy itself, but our people are telling us that we run the risk of creating other types of the machine that might have worse features.

But, wait, how can you stop playing? What can keep you out of a casino that’s everywhere? Well, there’s a special thing you can get at any local drug store that someone puts in your arm. After you get it, you become almost invisible to the machine. That may be the best way to get away from these monsters.

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Attendees at a conference at CSHL, an in-person tradition started in 1933. These conferences were suspended from 1943 to 1945 during WWII and were virtual during the pandemic in 2020 and for most of 2021. Photo by Miriam Chuai/CSHL

By Daniel Dunaief

For scientists, meetings and conferences aren’t just a chance to catch up on the latest research, gossip and see old friends: they can also provide an intellectual spark that enhances their careers and leads to new collaborations.

Amid the pandemic, almost all of those in-person conferences stopped, including the annual courses and meetings that Cold Spring Harbor Laboratory hosts. The internationally renowned lab has run meetings since 1933, with a few years off between 1943 and 1945 during World War II.

CSHL’s David Stewart. Photo by Gina Motisi/CSHL

While scientists made progress on everything from basic to translational research, including in laboratories that pivoted towards work on the SARS-CoV-2 virus, which causes COVID-19, they missed out on the kinds of opportunities that come from in-person interactions.

Assuming COVID infection rates are low enough this fall, CSHL is hoping to restart in-person conferences and courses, with the first conference that will address fifty years of the enzyme reverse transcriptase scheduled for Oct. 20th through the 23rd. That event was originally scheduled for October of 2020.

One of the planned guest speakers for that conference, David Baltimore, who discovered the enzyme that enables RNA to transfer information to DNA and is involved in retroviruses like HIV, won the Nobel Prize.

“I am hoping that there will be significant participation by many eminent scientists, so that is in itself somewhat [of] a ceremonial start,” wrote David Stewart, Executive Director of meetings and courses at Cold Spring Harbor Laboratory.

To attend any of the seven in-person meetings on the calendar before the end of the year, participants need to have vaccinations from either Pfizer, Moderna, Johnson & Johnson or AstraZeneca.

Attendees will have to complete an online form and bring a vaccination card or certificate. Scientists who don’t provide that information “will not be admitted and will not get a key to their room or be able to attend the event,” Stewart said.

CSHL also plans to maintain the thorough and deep cleaning procedures the lab developed. 

Stewart hopes that 75 to 80 percent or more of the talks presented will be live, with a virtual audience that could be larger than the in-person attendance.

“It is important to have a critical mass of presenters and audience in-person, but there’s no real limit on how large the virtual audience could be,” he explained.

Typically, the courses attract participants from over 50 countries. Even this year, especially with travel restrictions for some countries still in place, Stewart expects that the majority of participants will travel from locations within the United States.

The Executive Director explained that CSHL was planning to introduce a carbon offset program for all travel to conferences and courses that the facility reimburses starting in 2020. After evaluating several options, they plan to purchase carbon offsets from Cool Effect and will encourage participants paying their own way to do the same or through a similar program.

The courses, meanwhile, will begin on October 4th, with macromolecular crystallography and programming for biology. CSHL hopes to run six of these courses before the end of the year, including a scientific writing retreat.

“We are looking to 100 percent enrollment for our courses, so likely this year that will largely be domestic,” Stewart explained.

The courses, which normally have 16 participants, may have 12 students, as the lab tries to run these training opportunities safely without masks or social distancing.

From March of 2020 through the end of last year, the lab had planned 25 meetings and 25 courses. As the pandemic spread, the lab pivoted to virtual meetings. “I felt like a car salesman trying to sell virtual conferences,” Stewart recalled. For the most part, the lab was able to keep to its original schedule of conferences, albeit through a virtual format.

In addition to the scheduled meetings, CSHL decided to add meetings to discuss the latest scientific information related to COVID research. 

Stewart approached Hung Fan, a retired virologist at the University of California at Irvine, to help put together these COVID exchanges. Those meetings occurred in June, July, August, October, and January. The sixth one recently concluded.

The meetings addressed “everything around the science of the virus,” Stewart said, which included the biology, the origin, the genomics, the immune response, vaccines, therapeutics and diagnostics, among other scientific issues.

“There was a lot of excellent work being done around SARS-CoV-2,” Stewart said. “We were trying to identify that early on. It was helpful to have people who knew the field well.”

Fan said he combed through preprints like the CSHL-based bioRxiv and related medRxiv every day for important updates on the disease.

Fan described the scientific focus and effort of the research community as being akin to the Manhattan Project which built the atomic bomb during World War II, where “everybody said, ‘We have a common enemy and we want to apply all our capabilities to combating that.”

While Fan is pleased with the productive and valuable exchanges that occurred amid the virtual conferences, he recognized the benefit of sharing a room and a drink with scientific colleagues.

“A lot of the productive interactions at meetings take place in a social setting, at the bar, over dinner” and in other unstructured gatherings, he said. “People are relaxed and can share their scientific thoughts.”

After presentations, Fan described how researchers discuss the work presented and compare that to their own efforts. It’s easier to talk with people in person “as opposed to making a formalized approach through letters and emails.”

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METRO photo

By Daniel Dunaief

Daniel Dunaief

One day, you wake up and your kids who called noodles “noonies” are getting ready for college.

No, not exactly. It’s a long journey filled with skinned knees, ripped tee shirts — don’t ask — eye rolling and muttering between clenched teeth. Still, here we are, as our kids prepare to move on from the educational minor leagues. Along the way, we went through numerous milestones. Please find below a few of the phases in our journey.

— Deer in the headlights. I’ve seen deer in my headlights. The only difference between them and us when we first brought our children home is that the deer’s eyes are open much wider. We almost instantly became sleep-deprived. Other than that, we had that frozen not-sure-where-to-move feeling, knowing we had to do something, but not exactly sure what or in what order to take care of those needs.

— Hating everyone. People meant well back in the days when our children were young and cried. Numerous people, who didn’t live with or even know our needy infants, offered unsolicited advice about what this scream or that scream meant. Strangers would tell us how our daughter’s cry meant she had gas, was hungry, needed her diaper changed, or was hot or cold. Yes, thanks, those are the options. Thanks for the help!

— Cooking the plastics. Yup, back in the early days, I was so sleep deprived that I put plastic bottles in a pot of boiling water to sterilize them and fell asleep. It wasn’t until I smelled the burning plastic that I realized how long I’d been out.

— Carrying everything: We couldn’t go four blocks without a diaper bag filled with everything, including the special toy each of them needed, diapers, wipes, ointment, sunscreen, bug spray, rain jackets, boots, and extra clothing.

— Straining our backs: Picking the kids up and playing with them was fun when they were under 20 pounds. When they reached 50 and above, holding them the entire length of a ski slope became impossible.

— Crazy sports parents: This phase lasted much longer than it should have. It was only when the kids reached late middle school that I appreciated the fresh air, the sparkling sunlight and the excitement of the moment. Exercise and making friends are the goal. Everything else, including winning, is gravy.

— Giving them space (aka, it’s not about us). As they reached adolescence, our children needed to make their own decisions. Tempting as it was to jump in and redirect them or even to kiss them before they left the car for middle school, we bit our tongues as often as we could, leaving us feeling lonely and nostalgic in our cars as they joined their friends.

— Beautiful naps: Giving them space allowed us to do what we wanted. After years of living our lives while monitoring and helping theirs, we had a chance to do exactly what we wanted, which started with restorative naps.

— Sending them into space. We aren’t putting them in a Jeff Bezos rocket ship or sending them to the International Space Station, but we are preparing to give them an opportunity to explore the world outside our house.

— Looking at the calendar differently. With both of them on the way to their futures, we can choose places to visit that didn’t interest them. We can visit these places when school is in session, which should mean lower costs for us.

— Telling other people how to take care of their kids: With our free time, we see parents struggling with young children. We, of course, know better. Or maybe not.

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