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Power of 3

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Above, microscopic image showing brown, antibody-based staining of keratin 17 (K17) in bladder cancer. Image from Shroyer Lab, Stony Brook University

By Daniel Dunaief

Detectives often look for the smallest clue that links a culprit to a crime. A fingerprint on the frame of a stolen Picasso painting, a shoe print from a outside a window of a house that was robbed or a blood sample can provide the kind of forensic evidence that helps police and, eventually, district attorneys track and convict criminals.

Kenneth Shroyer MD, PhD                  Photo from SBU

The same process holds true in the world of disease detection. Researchers hope to use small and, ideally, noninvasive clues that will provide a diagnosis, enabling scientists and doctors to link symptoms to the molecular markers of a disease and, ultimately, to an effective remedy for these culprits that rob families of precious time with their relatives.

For years, Ken Shroyer, the Marvin Kuschner Professor and Chair of Pathology at the Renaissance School of Medicine at Stony Brook University, has been working with a protein called keratin 17.

A part of embryological development, keratin 17 was, at first, like a witness who appeared at the scene of one crime after another. The presence of this specific protein, which is unusual in adults, appeared to be something of a fluke.

Until it wasn’t.

Shroyer and a former member of his lab, Luisa Escobar-Hoyos, who is now an Assistant Professor at Yale, recently published two papers that build on their previous work with this protein. One paper, which was published in Cancer Cytopathology, links the protein to pancreatic cancer. The other, published in the American Journal of Clinical Pathology, provides a potentially easier way to diagnose bladder cancer, or urothelial carcinoma.

Each paper suggests that, like an abundance of suspicious fingerprints at the crime scene, the presence of keratin 17 can, and likely does, have diagnostic relevance.

Pancreatic cancer

A particularly nettlesome disease, pancreatic cancer, which researchers at Stony Brook and Cold Spring Harbor Laboratory, including CSHL Cancer Center Director David Tuveson, have been studying for years, has a poor prognosis upon diagnosis.

During a process called surgical resection, doctors have been able to determine the virulence of pancreatic cancer by looking at a larger number of cells.

Shroyer and Escobar Hoyos, however, used a needle biopsy, in which they took considerably fewer cells, to see whether they could develop a k17 score that would correlate with the most aggressive subtype of the cancer.

“We took cases that had been evaluated by needle biopsy and then had a subsequent surgical resection to compare the two results,” Shroyer said. They were able to show that the “needle biopsy specimens gave results that were as useful as working with the whole tumor in predicting the survival of the patient.”

A needle biopsy, with a k17 score that reflects the virulence of cancer, could be especially helpful with those cancers for which a patient is not a candidate for a surgical resection.“That makes this type of analysis available to any patient with a diagnosis of pancreatic cancer, rather than limiting it to the small subset of cases that are able to undergo surgery,” Shroyer said. 

Ultimately, however, a k17 score is not the goal for the chairman of the pathology department.

Indeed, Shroyer would like to use that score as a biomarker that could differentiate patient subtypes, enabling doctors to determine a therapy that would prove most reliable for different groups of people battling pancreatic cancer.

The recently published report establishes the foundation of whether it’s possible to detect and get meaningful conclusions from a needle biopsy in terms of treatment options.

At this point, Shroyer isn’t sure whether these results increase the potential clinical benefit of a needle biopsy.

“Although this paper supports that hypothesis, we are not prepared yet to use k17 to guide clinical decision making,” Shroyer said.

Bladder cancer

Each year, doctors and hospitals diagnose about 81,000 cases of bladder cancer in the United States. The detection of this cancer can be difficult and expensive and often includes an invasive procedure.

Shroyer, however, developed a k17 protein test that is designed to provide a reliable diagnostic marker that labs can get from a urine sample, which is often part of an annual physical exam.

The problem with bladder cancer cytopathology is that the sensitivity and specificity aren’t high enough. Cells sometimes appear suggestive or indeterminate when the patient doesn’t have cancer.

“There has been interest in finding biomarkers to improve diagnostic accuracy,” Shroyer said. 

Shroyer applied for patent protection for a k17 assay he developed through the Stony Brook Technology Transfer office and is working with KDx Diagnostics. The work builds on “previous observations that k17 detects bladder cancer in biopsies,” Shroyer said. He reported a “high level of sensitivity and specificity” that went beyond that with other biomarkers.

Indeed, in urine tests of 36 cases confirmed by biopsy, 35 showed elevated levels of the protein.

KDx, a start up biotechnology company that has a license with The Research Foundation for The State University of New York, is developing the test commercially.

The Food and Drug Administration gave KDx a breakthrough device designation for its assay test for k17.

Additionally, such a test could reveal whether bladder cancer that appears to be in remission may have recurred.

This type of test could help doctors with the initial diagnosis and with follow up efforts, Shroyer said.“Do patients have bladder cancer, yes or no?” he asked. “The tools are not entirely accurate. We want to be able to give a more accurate answer to that pretty simple question.”

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Matt Damon in a scene from ‘The Martian’

By Daniel Dunaief

One of the seminal, and realistic, scenes from the movie “The Martian” involves astronaut Mark Watney, played by Matt Damon, clearing the dust from a solar panel.

The cleaning process not only made it possible for the space station on Mars to continue to generate solar energy, but it also alerted the National Aeronautics and Space Administration staff on Earth to the fact that Watney somehow survived a storm and was alive and stranded on the Red Planet.

Alexander Orlov Photo from SBU

Back in 1967, engineers from NASA proposed a system to remove dust from solar panels, which can deprive space stations of energy and can cause rovers and other distant remotely operated vehicles to stop functioning. Washing these solar cells on dried out planets with water is not an option.

That’s where Alexander Orlov, a Professor of Materials Science and Chemical Engineering in the College of Engineering and Applied Science, his graduate student Shrish Patel, Victor Veerasamy, Research Professor of Materials Science and Chemical Engineering at Stony Brook University, and Jim Smith, Chief Technology Officer at Bison Technologies and a board member at the Clean Energy Business Incubator Program at SBU, come in.

Working at a company Orlov founded called SuperClean Glass, Orlov, Patel and other colleagues tried to make an original effort started by NASA feasible. The particles have an electric charge. An electric field they created on the solar glass lifts the particles and then throws them away.

The process recently became a finalist in the Department of Energy’s American-Made Solar Prize for 2021. The 10 companies who are finalists get a $100,000 prize and $75,000 in vouchers from the Department of Energy to test their technology.

The DOE will announce two winners in September of 2021, who will each get an additional half a million dollars and $75,000 in vouchers to develop and test their prototypes.

Orlov, who was delighted that this effort received the recognition and the funds, said the company would use the money to develop prototypes and verify that ‘this technology works at the National Renewable Energy Lab.”

SuperClean Glass is creating prototypes of larger scale to show that turning on a power supply will cause dust to levitate and be removed within seconds.

At this point, Orlov estimates that companies can recoup the additional cost of using this technology within four to five years. The average lifespan of a solar panel is about 25 years, which means that companies could increase their energy efficiency for the 20 years after the initial investment in the technology.

Orlov said the current state of the art for cleaning solar panels typically involves using either water, getting people to dust off the surface, or deploying robots.

This device used for experiments is a highly transparent electrodynamic shield deposited on glass to repel dust from solar panels. Image courtesy of SuperClean Glass Inc

In Egypt, where labor costs are lower, companies can pay people to remove dust with brushes. While robots reduce the cost of labor, they are not always efficient and can break down.

Some companies put a coating on the panels that allows rainwater to wash the dust away more easily. That, however, relies on rain, which is scarce in desert conditions.

Orlov originally became involved in trying to develop an alternative to these methods when Sam Aronson, the former director of Brookhaven National Laboratory, contacted him following a visit to the Turkana Basin Institute in Kenya.

When he visited the archeological site in Kenya, Aronson saw that dust frequently reduced the efficiency and effectiveness of the solar panels. The dust problem is not specific to Kenya or the United States, as many of the most attractive sites for solar panels are in regions with considerable sun and little rainfall. The benefit of minimal precipitation is that it provides access to critical sunlight, which generates energy.

The downside of these sites, however, is that the dry, sunny climates often produce dust.

Orlov researched the NASA technology, where he discovered that it wasn’t efficient and couldn’t be scaled up.

Using $150,000 he received from the New York State energy Research and Development Authority, or NYSERDA, Orlov and Patel started reaching out to solar panel manufacturers to determine the price point at which such a dust cleaning removal service might be viable.

“We conducted interviews with 180 people who use solar panels to find out the particular price point where this technology becomes attractive,” Orlov said. That was the steep curve, to do economic analysis, financial projections and to understand what the market wants. All that is not present in [typical] academic research.”

They reduced the power consumption for electrodes by a factor of five. They also explored commercial methods for scaling up their manufacturing approach.

Dust isn’t the same throughout the world, as it is a different color in various areas and has different mineral contents.

“In the future, depending on where this might be deployed, there needs to be some tweaking of this technology,” Orlov said.

As a part of the technology roadmap for the work they are proposing, the SuperClean effort includes a self-monitoring system that would activate the electrodes on the shield if needed to repel an accumulation of dust.

Orlov described the market for such a self-cleaning and efficient process as “very significant.” He is hoping to provide a field demonstration of this approach later this year. If the process continues to produce commercially viable results, they could license the technology within two to three years.

In the near term, Orlov is focused on producing results that could enhance their positioning for the DOE’s grand prize.

“There are a lot of steps before September to be eligible” to win the $500,000, he said. The biggest hurdle at this point is to get positive results from the National Renewable Energy Lab and demonstrate that the technology is effective and also durable.

“Our expectation is that it should last for 25 years, but the lab, which is going to do the testing, is the gold standard to verify that claim,” he said.

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From left, John Inglis and Richard Sever. Photo from CSHL

By Daniel Dunaief

Scientists rarely have people standing at their lab door, waiting eagerly for the results of their studies the way the public awaits high-profile verdicts.

That, however, changed over the last 16 months, as researchers, public health officials, school administrators and a host of others struggled to understand every aspect of the basic and translational science involved in the Sars-Cov2 virus, which caused the COVID-19 pandemic.

With people becoming infected, hospitalized and dying at an alarming rate, businesses closing and travel, entertainment and sporting events grinding to a halt, society looked to scientists for quick answers. One challenge, particularly in the world of scientific publishing, is that quick and answers don’t often mesh well in the deliberate, careful and complicated world of scientific publishing.

The scientific method involves considerable checking, rechecking and careful statistically relevant analysis, which is not typically designed for the sharing of information until other researchers have reviewed it and questioned the approach, methodology and interpretation.

The pandemic changed that last year, increasing the importance of preprint servers like bioRxiv and medRxiv at Cold Spring Harbor Laboratory, which provide a way for researchers to share unfiltered and unchecked information quicker than a scientific review and publishing process that can take months or even years.

The pandemic increased the importance of these preprint servers, enabling scientists from all over the world to exchange updated research with each other, in the hopes of leading to better basic understanding, diagnosis, treatment and prevention of the spread of the deadly virus.

The importance of these servers left those running them in a bind, as they wanted to balance between honoring their mission of sharing information quickly and remaining responsible about the kinds of information, speculation or data that might prove dangerous to the public.

Richard Sever and John Inglis, Assistant Director and Executive Director of Cold Spring Harbor Laboratory Press, created pandemic-specific criteria for work reporting potential Covid-19 therapies.

“Manuscripts making computational predictions of COVID-19 therapies are accepted only if they also include in vitro [studies in test tubes or with live cells] or in vivo [studies in live subjects] work,” the preprint directors wrote in a recent blog. “This restriction does not apply to non-covid-19 work.”

Inglis and Sever continue to decline research papers that might cause people to behave in ways that compromise public health.

“We are simply doing our best to tread carefully in the early days of clinical preprints, as we gain experience and bias our actions toward doing no harm” the authors wrote in their blog.

In the first few months after the pandemic hit the United States, the pace at which scientists, many of whom pivoted from their primary work to direct their expertise to the public health threat, was the highest bioRxiv, which was founded in November of 2013, and medRxiv, which was started in June of 2019, had ever experienced.

These preprint servers published papers that wound up leading to standards of care for COVID-19, including a June research report that appeared on June 22nd in medRxiv on the use of the steroid dexamethasone, which was one of the treatments former President Donald Trump received when he contracted the virus.

The rush to publish information related to the virus has slowed, although researchers have still posted over 16,000 papers related to the virus through the two pre-print servers. MedRxiv published 12,400 pandemic-related papers since January of 2020, while bioRxiv published over 3,600.

At its peak in late March of 2020, medRxiv’s abstract views reached 10.9 million, while downloads of the articles were close to five million.

Currently, bioRxiv is publishing about 3,500 papers a month, while medRxiv put up about 1,300 during a month. Close to 60 percent of the medRxiv papers continue to cover medical issues related to the pandemic.

The numbers of page views are “not anywhere near the frenzy of last year,” Inglis said in an interview. 

With the volume of papers still high, people can receive alerts from the preprint servers using parameters like their field of interest or word searches.

“The real question is how to sort out the gold from the dross,” Inglis said. While some people have suggested a star system akin to the one shopping services use, Inglis remained skeptical about the benefit of a scientific popularity contest.

“Have you looked at the stuff [with four or five stars] on Amazon? It’s one thing if you’re buying a widget, but it’s different if you’re trying to figure out what’s worthwhile science,” he said.

Other organizations have reviewed preprints, including the Bloomberg School of Public Health at Johns Hopkins.

“By sheer diligence, the [Johns Hopkins team] go into medRxiv mostly and simply pick out things they think are striking,” Inglis said. 

At the same time, a team of researchers led by Nicolas Vabret, Robert Samstein, Nicolas Fernandez, and Miriam Merad created the Sinai Immunology Review Project, which provides critical reviews of articles from the Cold Spring Harbor Laboratory preprint sites. The effort ranks COVID-related preprints according to their immunological relevance. Fernandez created a dedicated website to host and integrate the reviews. The group also worked with Nature Reviews Immunology to publish short weekly summaries of preprints, according to a comment piece in that journal.

BioRxiv and medRxiv were founded on the belief that early sharing of results as preprints would speed progress in biomedical research, better equipping scientists to build on each other’s work.

“My team is proud to have contributed to the response to this worldwide human tragedy,” Inglis said. “We’re also glad we made the decision to set up a separate server for health science, in which the screening requirements are different and more stringent.”

Inglis explained that the pre-print servers have “learned a lot in the past year” about providing information during a crisis like the pandemic. “If another pandemic arose, we’d apply these learnings and respond immediately in the same way.”

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Xiaoning Wu at her recent PhD graduation with Kevin Reed. Photo by Gordon Taylor

By Daniel Dunaief

If they build it, they will understand the hurricanes that will come.

That’s the theory behind the climate model Kevin Reed, Associate Professor at the School of Marine and Atmospheric Sciences at Stony Brook University, and his graduate student Xiaoning Wu, recently created.

Working with Associate Professor Christopher Wolfe at Stony Brook and National Center for Atmospheric Research scientists, Reed and Wu developed an idealized computer model of the interaction between the oceans and the atmosphere that they hope will, before long, allow them to study weather events such as tropical cyclones, also known as hurricanes.

In his idealized program, Reed is trying to reduce the complexity of models to create a system that doesn’t require as much bandwidth and that can offer directional cues about coming climate change.

“When you’re trying to build a climate model that can accurately project the future, you’re trying to include every process you know is important in the Earth’s system,” Reed said. These programs “can’t be run” with university computers and have to tap into some of the biggest supercomputers in the world.

Reed’s work is designed to “peel back some of these advances that have happened in the field” which will allow him to focus on understanding the connections and processes, particularly between the ocean and the atmosphere. He uses fewer components in his model, reducing the number of equations he uses to represent variables like clouds.

“We see if we can understand the processes, as opposed to understanding the most accurate” representations possible, he said. In the last ten years or so, he took a million lines of code in a climate model and reduced it to 200 lines.

Another way to develop a simpler model is to reduce the complexity of the climate system itself. One way to reduce that is to scale back on the land in the model, making the world look much more like something out of the 1995 Kevin Costner film “Waterworld.”

About 30 percent of the world is covered by land, which has a variety of properties.

In one of the simulations, Reed reduced the complexity of the system by getting rid of the land completely, creating a covered aqua planet, explaining that they are trying to develop a tool that looks somewhat like the Earth.

“If we could understand and quantify that [idealized system], we could develop other ways to look at the real world,” he said.

The amount of energy from the sun remains the same, as do the processes of representing oceans, atmospheres and clouds.

In another version of the model, Reed and Wu represented continents as a single, north-south ribbon strip of land, which is enough to change the ocean flow and to create currents like the Gulf Stream.

The expectation and preliminary research shows that “we should have tropical cyclones popping up in these idealized models,” Reed said. By studying the hurricanes in this model, these Stony Brook scientists can understand how these storms affect the movement of heat from around the equator towards the poles.

The weather patterns in regions further from the poles, like Long Island, come from the flow of heat that starts at the equator and moves to colder regions.

Atlantic hurricanes, which pick up their energy from the warmer waters near Africa and the southern North Atlantic, transfer some of that heat. Over the course of decades, the cycling of that energy, which also reduces the temperature of the warmer oceans, affects models for future storm systems, according to previous studies.

Reed said the scientific community has a wide range of estimates for the effect of hurricanes on energy transport, with some researchers estimating that it’s negligible, while others believing it’s close to 50 percent, which would mean that hurricanes could “play an active role in defining” the climate.

Reed’s hypothesis is that a more rapid warming of the poles will create less of an energy imbalance, which will mean fewer hurricanes. This might differ in various ocean basins. He has been studying the factors that control the number of tropical cyclones.

Reed and Wu’s research was published in the Journal of Advances in Modeling Earth Systems in April.

Wu, who is completing her PhD this summer after five years at Stony Brook, described the model as a major part of her thesis work. She is pleased with the work, which addresses the changing ocean as the “elephant in the room.”

Oftentimes, she said, models focus on the atmosphere without including uncertainties that come from oceans, which provide feedback through hurricanes and larger scale climate events.

Wu started working on the model in the summer of 2019, which involved considerable coding work. She hopes the model will “be used more widely” by the scientific community, as other researchers explore a range of questions about the interaction among various systems.

Wu doesn’t see the model as a crystal ball so much as a magnifying glass that can help clarify what is happening and also might occur in the future.

“We can focus on particular players in the system,” she said.

A native of central China, Wu said the flooding of the Yangtze River in 1998 likely affected her interest in science and weather, as the factors that led to this phenomenon occurred thousands of miles away.

As for her future, Wu is intrigued by the potential to connect models like the one she helped develop with applications for decision making in risk management.

The range of work she has done has enabled her to look at the atmosphere and physical oceanography and computational and science communication, all of which have been “useful for developing my career.”

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From left, Shawn Serbin, Scott Giangrande and Chongai Kuang. Photo from Brookhaven National Laboratory

By Daniel Dunaief

Chongai Kuang is doing considerably more than standing in the middle of various fields throughout the southeast, looking up into the sky, sticking his finger in the air and taking notes on the potential appeal of the area.

Entrusted with finding the right spot for the third ARM Mobile Facility, or AMF3, Kuang, who is an Atmospheric Scientist in the Environmental & Climate Sciences Department at Brookhaven National Laboratory, is gathering considerable amounts of information about different areas in the southeast.

In March of 2023, the ARM3 mobile facility, which has been operating in Oliktok Point, Alaska, will have a new home, where it can gather information about atmospheric convection, land-atmosphere interactions and aerosol processes.

In addition to finding the right location for this facility, Kuang will coordinate with the larger science community to make recommendations to ARM for observations, measurements, instruments and sampling strategies. Observations from these fixed and mobile facilities will improve and inform earth system models.

Kuang would like to find a strategic place for the AMF3 that is “climactically relevant to provide important observations on clouds, aerosols, and land atmosphere interactions that are needed to answer science drivers” important in the southeastern United States, Kuang said. These facilities will help researchers understand how all these atmospheric phenomena interact with solar radiation and the Earth’s surface.

The AMF3 should provide information that informs climate, regional and weather models.

In 2018, the Department of Energy, which funds BNL and 16 other national laboratories, held a mobile facility workshop to determine where to move the AMF3. The group chose the Southeastern United States because it has atmospheric convection, high vegetative-driven emissions and strong coupling of the land surface with the atmosphere. This area also experiences severe weather including tornadoes and hurricanes, which have significant human and socioeconomic impacts, said Kuang.

The most violent weather in the area often “tests the existing infrastructure,” Kuang said. “This deployment can provide critical observations and data sets,” in conjunction with regional operational observational networks.

Atmospheric phenomena as a whole in the southeastern United States includes processes and interactions that span spatial scales ranging from nanometers to hundreds of kilometers and time scales spanning seconds to days.

Kuang’s primary research interests over the past decade has focused on aerosol processes at nanometer scales, as he has studied the kinds of miniature aerosol particles that form the nuclei for cloud formation. These aerosols affect cloud lifetime and spatial distribution.

“Our research is challenged by disparate scales relevant to phenomena we’re trying to characterize, from nanometers to the length scale of convective systems, which are tens of kilometers or even larger,” Kuang said. These scales also present opportunities to study coupled science with convection, aerosol and land-atmosphere interactions.

The ARM observatories around the world provide atmospheric observations of aerosols, clouds, precipitation and radiation to inform and improve Earth system models.

“We are going to leverage as much as we can of the existing networks,” Kuang said. The ARM has a fixed site in Oklahoma, which provides data for the Southern Great Plains Site, or SGP. The Southeastern site, wherever it winds up, will provide a context for large-scale atmospheric phenomena.

The way aerosols, clouds and weather systems form and change presents a challenge and an opportunity for research stations like AMF3, which will seek to connect phenomenon at spatial and time scales that affect where Kuang and his team hope to locate the site.

Kuang is also staying abreast of the latest technology and is also contributing to the development of these capabilities. The technology the AMF3 may use could be developed between now and when the site starts gathering data.

“We have the opportunity now to start thinking about what the next generation measurement capabilities and emerging technologies are that could be operational in 2023,” he said. “We are in conversations with the broader community and with different vendors and with a number of different investigators who are developing new technologies.”

Researchers hope to understand the coupling between the land surface and atmospheric phenomenon. “That will have feedback on radiation and precipitation and the impact on land-surface interactions,” Kuang explained. The current plan is for the new facility to operate for about five years.

While Kuang is focused on the scientific drivers for the site selection, he has also been exploring the dynamic with potential research partners, including universities, seeking ways to add educational partners.

“We have hopes and plans for this kind of deliberate, targeted outreach within the region,” Kuang said. “We want to organize activities like summer school, to provide young scientists with primers and an introduction about how observations are made within their backyard.”

The work he’s trying to do now is “setting the table and preparing the soil for the eventual siting” of the station.

Kuang will measure his success if the new site improves poorly represented model processes.

Once the DOE chooses a site, Kuang plans to develop and execute an initial science plan that uses AMF3 observations. As an ARM instrument mentor, he will also be responsible for a set of instruments that measure aerosol size and concentration.

A resident of Wading River, Kuang started working at BNL in 2009 as a postdoctoral researcher. When he’s not working, he describes cooking as “therapeutic,” as he and his wife, Anyi Hsueh, who is a psychiatric nurse practitioner, have explored Southeastern Asian and Middle Eastern cuisines.

Kuang is working with Associate Ecologist Shawn Serbin and Meteorologist Scott Giangrande, in site selection. The work presents an “important responsibility and our site science team envisions the AMF3 southeastern united States [site] to enable transformational science,” he said.

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Linda Van Aelst. Photo from CSHL

By Daniel Dunaief

Different people respond to the same level of stress in a variety of ways. For some, a rainy Tuesday that cancels a picnic can be a minor inconvenience that interrupts a plan, while others might find such a disruption almost completely intolerable, developing a feeling of helplessness.

Scientists and clinicians have been working from a variety of perspectives to determine the cause of these different responses to stress.

From left, graduate student Nick Gallo, Linda Van Aelst and Postdoctoral Researcher Minghui Wang. Photo by Shanu George

Cold Spring Harbor Laboratory Professor Linda Van Aelst and a post doctoral researcher in her lab, Minghui Wang, recently published a collaborative work that also included graduate student Nicholas Gallo, postdoctoral researcher Yilin Tai and Professor Bo Li in the journal Neuron that focused on the gene Oligophrenin-1, which is also implicated in intellectual disability.

As with most X-linked diseases, the OPHN1 mutation primarily affects boys, who have a single X chromosome and a Y chromosome. Girls have two X chromosomes, giving them a backup gene to overcome the effect of an X-linked mutation.

In addition to cognitive difficulties, people with a mutation in this gene also develop behavioral challenges, including difficulty responding to stress.

In a mouse model, Wang and Van Aelst showed that the effect of mutations in this gene mirrored the stress response for humans. Additionally, they showed that rescuing the phenotype enabled the mouse to respond more effectively to stress.

“For me and [Wang], it’s very exciting,” Van Aelst said. “We came up with this mouse model” and with ways to counteract the effect of this mutated analogous gene.

As with many other neurological and biological systems, Oligophrenin1 is involved in a balancing act in the brain, creating the right mix of excitation and inhibition.

When oligophrenin1 was removed from the prelimbic region of the medical prefrontal cortex, a specific brain area that influences behavioral responses and emotion, mice expressed depression-like helpless behaviors in response to stress. They then uncovered two brain cell types critical for such behavior: the inhibitory neurons and excitatory pyramidal neurons. The excitatory neurons integrate many signals to determine the activity levels in the medial prefrontal cortex.

The inhibitory neurons, meanwhile, dampen the excitatory signal so they don’t fire too much. Deleting oligophrenin1 leads to a decrease in these inhibitory neurons, which Van Aelst found resulted from elevated activity of a protein called Rho kinase.

“The inhibitor keeps the excitatory neurons in check,” Van Aelst said. “If you have a silencing of the inhibitory neurons, you’re going to have too much excitatory response. We know that contributes to this maladaptive behavior.”

Indeed, Wang and Van Aelst can put their metaphorical finger on the scale, restoring the balance between excitation and inhibition with three different techniques.

The scientists used an inhibitor specific for a RhoA kinase, which mimicked the effect of the missing Oligophrenin1. They also used a drug that had the same effect as oligophrenin1, reducing excess pyramidal neuron activity. A third drug activated interneurons that inhibited pyramidal neurons, which also restored the missing inhibitory signal. All three agents reversed the helpless phenotype completely.

Japanese doctors have used the Rho-kinase inhibitor fasudil to treat cerebral vasospasm. which Van Aelst said does not appear to produce major adverse side effects. It could be a “promising drug for the stress-related behavioral problems” of oligophrenin1 patients, Van Aelst explained in an email. “It has not been described for people with intellectual disabilities and who also suffer from high levels of stress.”

From left, graduate student Nick Gallo, Linda Van Aelst and Postdoctoral Researcher Minghui Wang. Photo by Shanu George

Van Aelst said she has been studying this gene for several years. Initially, she found that it is a regulator of rho proteins and has linked it to a form of intellectual disability. People with a mutation in this gene had a deficit in cognitive function that affected learning and memory.

From other studies, scientists learned that people who had this mutation also had behavioral problems, such as struggling with stressful situations.

People with intellectual difficulties have a range of stressors that include issues related to controlling their environment, such as making decisions about the clothing they wear or the food they eat.

“People underestimate how many [others] with intellectual disabilities suffer with behavioral problems in response to stress,” Van Aelst said. “They are way more exposed to stress than the general population.”

Van Aelst said she and Wang focused on this gene in connection with a stress response.

Van Aelst wanted to study the underlying cellular and molecular mechanism that might link the loss of function of oligophrenin1 with the behavioral response to stress.

At this point, Van Aelst hasn’t yet studied how the mutation in this gene might affect stress hormones, like cortisol, which typically increase when people or mice are experiencing discomfort related to stress. She plans to explore that linkage in future studies.

Van Aelst also plans to look at some other genes that have shown mutations in people who battle depression or other stress-related conditions. She hopes to explore a genetic link in the brain’s circuitry to see if they can “extend the findings.” She would also like to connect with clinicians who are studying depression among the population with intellectual disabilities. Prevalence studies estimate that 10 to 50 percent of individuals with intellectual disability have some level of behavioral problems and/or mood disorders.

Reflecting the reality of the modern world, in which people with various conditions or diseases can sequence the genes of their relatives, Van Aelst said some families have contacted her because their children have mutations in oligophrenin1.

“It’s always a bit tricky,” she said. “I don’t want to advise them yet” without any clinical studies.

A resident of Huntington, Van Aelst arrived at CSHL in the summer of 1993 as a post doctoral researcher in the lab of Michael Wigler. She met Wigler when he was giving a talk in Spain.

After her post doctoral research ended, she had planned to return to her native Belgium, but James Watson, who was then the president of the lab, convinced her to stay.

Outside of work, Van Aelst enjoys hiking, swimming and running. Van Aelst speaks Flemish, which is the same as Dutch, French, English and a “bit of German.” 

She is hopeful that this work may eventually lead to ways to provide a clinical benefit to those people with intellectual disabilities who might be suffering from stress disorders.

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Eszter Boros. Photo from SBU

By Daniel Dunaief

And the winner is … Eszter Boros. An Assistant Professor in the Department of Chemistry at Stony Brook University, Boros recently won the 2021 Stony Brook Discovery Prize, which includes $200,000 in new funding.

The prize, which was established in 2013, is designed to fund higher-risk research for scientists who are no more than five years beyond tenure and promotion at the Associate Professor level or who are on a tenure track as an Assistant Professor. The research might not otherwise receive financial support from agencies like the National Institutes of Health.

Eszter Boros. Photo from SBU

Stony Brook awards the prize to a faculty member who is considered a rising star.

Boros’s proposal suggests using a radioactive light switch to activate anticancer molecules.

The goal behind Boros’s work is to target cancer cells in particular, while avoiding the kinds of painful side effects that typically accompany chemotherapy, which can lead to gastrointestinal discomfort and hair loss, among others.

Boros, who has been at Stony Brook since 2017, was pleased to win the award. “It’s really exciting,” she said. “I’m kind of in disbelief. I thought all the finalists had convincing and exciting projects.”

The four finalists, who included Eric Brouzes in biomedical engineering, Gregory Henkes in geosciences and Kevin Reed in climate modeling, went through three rounds of screening, culminating in a Zoom-based 10-minute presentation in front of four judges.

Bruce Beutler, the Director of the Center for the Genetics of Host Defense at the University of Texas Southwestern Medical Center, served as one of the four judges.

In an email, Beutler wrote that Boros’s work had an “inventive approach” and was “high risk, but potentially high impact.”

Beutler, who won the 2011 Nobel Prize in Physiology and Medicine, suggested that the Discovery Prize may give a start to “a bright person with relatively little track record and a risky but well reasoned proposal.”

The success from such a distinction “does build on itself,” Beutler wrote. “Other scientists hear of such awards or read about them when evaluating future proposals. This may influence decisions about funding, or other awards, in the future.”

Boros said she would use the prize money to fund work from graduate students and post doctoral fellows, who will tackle the complexities of the work she proposed. She will also purchase supplies, including radioactive isotopes. She hopes to stretch the funds for two and a half or three years, depending on the progress she and the members of her lab make with the work.

The idea behind her research is to send radioactive materials that emit a light as they decay and that bind to the cancer cell. The light makes the chemotherapy toxic. Without that light, the chemotherapy would move around the body without damaging non-cancerous cells, reducing the drug’s side effects.

She is thinking of two ways to couple the radioactive light-emitting signal with an activated form of treatment. In the first, the two parts would not be selectively bound together.

The chemotherapy would diffuse into tissues around the body and would only become activated at the target site. This may affect healthy neighbors, but it wouldn’t cause as many side effects as conventional chemotherapy. This could take advantage of already clinically used agents that she can combine.

In the second strategy, she is taking what she described as a “next level” approach, in which she’d make the radioactive agent and the chemotherapy react with one another selectively. Once they saw one another, they would become chemically linked, searching to find and destroy cancer cells. This approach would require new chemistry which her lab would have to develop. 

Beutler suggested that Boros’s work might have other applications, even if cancer might currently be the best one. Some focal but infectious diseases can be treated with antimicrobial therapy which, like cancer directed chemotherapy, is toxic, he explained.

The same principle of using a drug activated by light that is connected to a site-specific marker “could be used in such cases,” he said.

While the potential bench-to-bedside process for any single treatment or approach can seem lengthy and filled with unexpected obstacles, Beutler said he has seen certain cancers that were formerly fatal yield to innovation. “People who are battling cancer can at least be hopeful that their cancer might fall into this category,” he said.

Boros appreciated the opportunity to apply for the award, to bond with her fellow finalists and to benefit from a process that included several sessions with experts at the Alan Alda Center for Communicating Science, who helped prepare her for the presentation in front of the judges. She developed her full proposal during the course of a week, over the December holiday, when her lab had some down time.

In the final stage, she met weekly for an hour with Louisa Johnson, an Improvisation Lecturer at the Alda Center and Radha Ganesan, an Assistant Professor of Medicine, to hone her presentation.

Boros said she appreciated how the Alda Center guides helped her focus on the obsession she and other scientists sometimes have of putting too much text in her slides. “I put text and conclusions on every slide,” she said. Ganesan and Johnson urged her to focus on what she wants to say, while letting go of this urge to clutter her presentation with the same words she planned to use in her presentation. “That was a huge shift in mindset that I had to make,” she said.

As for the work this prize will help fund, Boros said she’ll start with targets she knows based on some research she’s already done with prostate, breast and ovarian cancers.

Boros, who was born and raised in Switzerland, described herself as a chemist at heart.

Outside of work, she enjoys spending time with her husband Labros Meimetis, Assistant Professor of Radiology at the Renaissance School of Medicine at Stony Brook, and their nine-month-old son.

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Above, a humpback whale breaks the surface of the water. Photo from Eleanor Heywood/National Marine Fisheries Service permit no. 21889

By Daniel Dunaief

The waters off the South Shore of Long Island have become a magnet, attracting everything from shipping vessels, recreational boaters, fishermen and women, potential future wind farms, and humpback whales.

While the commercial component of that activity can contribute to the local economy, the whale traffic has drawn the attention of scientists and conservationists. Whales don’t abide by the nautical rules that guide ships through channels and direct traffic along the New York Bight, a region from the southern shore of New Jersey to the east end of Long Island.

Left, Julia Stepanuk with a drone controller. Photo by Kim Lato

Julia Stepanuk, a PhD student at Stony Brook University in the laboratory of Lesley Thorne, Assistant Professor in the School of Marine and Atmospheric Sciences, is focusing her research efforts on monitoring the humpback whale’s use of this habitat.

“This can help us understand how we focus our energy for monitoring and conservation,” she explained in an email. If the whales are traveling, it helps to know where to minimize human impact.

Ultimately, the work Stepanuk, who also earned her Master’s degree at Stony Brook in 2017, does provides ecological context for how whales use the waters around New York and how old the whales are that are feeding in this area.

In her dissertation, Stepanuk is “looking at the biological and ecological drivers, the motivators of where the whales are, when they’re there, specifically, from the lens of how human activity might be putting whales at risk of injury or mortality.”

Each summer, whales typically arrive in the area around May and stay through the end of October.

When she ventures out on the water, Stepanuk uses drones to gather information about a whale’s length and width, which indicates the approximate age and health of each individual. Since 2018, she has been gathering information to monitor activity in the area to track it over time.

With the research and data collected, she hopes to help understand the ecology of these whales, which will inform future policy decisions to manage risk.

Stepanuk’s humpback whale work is part of a 10-year monitoring study funded by the New York State Department of Environmental Conservation, which includes four principal investigators at the School of Marine and Atmospheric Sciences. The study looks at carbonate chemistry, physical oceanography, fish distribution, and top predator abundance, distribution and body condition, Thorne explained.

“My lab is leading the seabird and marine mammal aspect of this project,” said Thorne.

The grid over the whale demonstrates how members of Thorne’s lab measure the size of the whale from drone images. Photo by Julia Stepanuk

By documenting the ecological ranges of whales of different ages, Stepanuk may provide insight into the age groups that are most at risk. Many of the humpback whales that travel closer to shore are juveniles, measuring below about 38 feet.

Stepanuk has seen many of these whales, either directly or from the drones she flies overhead. She has also gathered information from events in which whales die after boats hit them.

Mortality events off the east coast have been increasing since 2016 as numerous whales have washed up along the coast. About half of the humpbacks in these mortality events have evidence of human interaction, either ship strike or entanglement, Stepanuk said.

“There have been many more strandings than usual of humpback whales along the east coast” in the last five years, Thorne explained.

Humpback whales likely have appeared in larger numbers in New York waterways due both to the return of menhaden in nearshore waters, which comes from changes in the management of this fish stock and from environmental management more broadly, and from an overall increase in the humpback whale population after 40 years of protection, Thorne suggested.

Ultimately, Stepanuk said she hopes to use the scientific inquiry she pursued during her PhD to help “bridge the gap between academic, policymakers, conservationists, interested parties and the public.” 

A part of Stony Brook’s STRIDE program, for science training and research to inform decisions, Stepanuk received training in science communication, how to present data in a visual and accessible way, and how to provide science-based information to policymakers.

For Thorne, this study and the analysis of the vessel strikes on humpback whales could be helpful for understanding similar dynamics with other cetaceans.

Julia Stepanuk and Matt Fuirst, a previous master’s student in Lesley Thorne’s lab, release a drone. Photo by Rachel Herman

“Understanding links between large whales and vessel traffic could provide important information for other studies, and could provide methods that would be useful for studies of other species,” said Thorne.

Stepanuk offers some basic advice for people on a boat in the New York Bight and elsewhere. She suggests driving more slowly if visibility is limited, as people would in a car in foggy weather. She also urges people to pay close attention to the water. Ripples near the surface could indicate a school of fish, which might attract whales.

“Slow down if you see dolphins, big fish schools and ripples,” she said. “There’s always a chance there could be a whale.”

If people see a whale, they shouldn’t turn off their engines: they should keep the engine in neutral and not approach the whale head on or cut them off. For most species, people can’t get closer than 300 feet. For North Atlantic right whales, which are critically endangered, the distance is 1,500 feet.

She suggests people “know the cues” and remember that whales are eagerly feeding.

Stepanuk has been close enough to these marine mammals to smell their pungent, oily fish breath and, when they exhale, to receive a residue of oil around her camera lens or sunglasses. She can “loosely get an idea of what they’re feeding on in terms of how bad their breath is.”

When she was younger, Stepanuk, who saw her first whale at the age of eight, worked on a whale watching boat for six years in the Gulf of Maine. An adult female would sometimes leave her calf near the whale watching boat while she went off to hunt for food. The calf stayed near the boat for about 45 minutes. When the mother returned, she’d slap the water and the calf would race to her side.

“Experiences like that stuck with me and keep me excited about the work we do,” Stepanuk said.

Video: Humpback whale lunge feeding off the south shore of Long Island

 

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From left, atmospheric scientists Andrew Vogelmann, Edward Luke, Fan Yang, and Pavlos Kollias explored the origins of secondary ice — and snow. Photo from BNL

By Daniel Dunaief

Clouds are as confounding, challenging and riveting to researchers as they are magnificent, inviting and mood setting for artists and film makers.

A team of researchers at Brookhaven National Laboratory and Stony Brook University recently solved one of the many mysteries hovering overhead.

Some specific types of clouds, called mixed-phase clouds, produce considerably more ice particles than expected. For those clouds, it is as if someone took an empty field, put down enough seeds for a thin covering of grass and returned months later to find a fully green field.

Ed Luke, Atmospheric Scientist in the Environmental Sciences Department at Brookhaven National Laboratory, Andy Vogelmann, Atmospheric Scientist and Technical Co-manager of the BNL Cloud Processes Group, Fan Yang, a scientist at BNL, and Pavlos Kollias, a professor at Stony Brook University and Atmospheric Scientist at BNL, recently published a study of those clouds in the journal Proceedings of the National Academy of Sciences.

“There are times when the research aircraft found far more ice particles in the clouds than can be explained by the number of ice nucleating particles,” Vogelmann wrote in an email. “Our paper examines two common mechanisms by which the concentrations of ice particles can substantially increase and, for the first time, provides observational evidence quantifying that one is more common” over a polar site.

With a collection of theoretical, modeling and data collecting fire power, the team amassed over six years worth of data from millimeter-wavelength Doppler radar at the Department of Energy’s Atmospheric Radiation Measurement facility in the town of Utqiagvik, which was previously called Barrow, in the state of Alaska.

The researchers developed software to sort through the particles in the clouds, grouping them by size and shape and matching them with the data from weather balloons that went up at the same time. They studied the number of secondary ice needles produced under various conditions.

The scientists took about 100 million data points and had to trim them down to find the right conditions. “We culled the data set by many dimensions to get the ones that are right to capture the process,” Luke explained.

The dataset required supercooled conditions, in which liquid droplets at sub-freezing temperatures came in contact with a solid particle, in this case ice, that initiated the freezing process.

Indeed, shattering ice particles become the nuclei for additional ice, becoming the equivalent of the venture capitalist’s hoped for investment that produces returns that build on themselves.

“When an ice particle hits one of those drizzle drops, it triggers freezing, which first forms a solid ice shell around the drop,” Yang explained in a press release. “Then, as the freezing moves inward, the pressure starts to build because water expands as it freezes. That pressure causes the drizzle drop to shatter, generating more ice particles.”

Luke described Yang as the “theory wizard on the ice processes and nucleation” and appreciated the opportunity to solve the mechanism involved in this challenging problem.

“It’s like doing detective work,” said Luke. The pictures were general in the beginning and became more detailed as the group focused and continued to test them.

Cloud processes are the biggest cause for differences in future predictions of climate models, Vogelmann explained. After clouds release their precipitation, they can dissipate. Without clouds, the sunlight reaches the surface, where it is absorbed, particularly in darker surfaces like the ocean. This absorption causes surface heating that can affect the local environment.

Energy obtained from microscopic or submicroscopic processes, such as the absorption of sunlight at the molecular level or the energy released or removed through the phase changes of water during condensation, evaporation or freezing, drive the climate.

“While something at microscales (or less) might not sound important, they ultimately power the heat engine that drives our climate,” said Vogelmann.

To gather and analyze data, the group had to modify some processes to measure particles of the size that were relevant to their hypothesis and, ultimately, to the process.

“We had to overcome a very serious limitation of radar,” Kollias said. They “started developing a new measurement strategy.”

When the cost of collecting large amounts of data came down, this study, which involved collecting 500 times more data points than previous, conventional measures, became feasible.

Luke “came up with a very bright, interesting technique of how to quantitatively figure out, not if these particles are there or how often, but how many,” Kollias said.

Luke found a way to separate noise from signal and come up with aggregated statistics.

Kollias said everyone in the group played a role at different times. He and Luke worked on measuring the microphysical properties of clouds and snow. Yang, who joined over two and a half years ago and was most recently a post doctoral research associate, provided a talented theoretical underpinning, while Vogelmann helped refine the study and methodology and helped write up the ideas.

Kollias said the process begins with a liquid at temperatures somewhere between 0 and 10 degrees below zero Celsius. As soon as that liquid touches ice, it explodes, making it a hundred times more efficient at removing liquid from the cloud.

Kollias described the work as a “breakthrough” because it provided real measurements, which they can use to test their hypotheses.

In the next few months, Kollias said the group would make sure the climate modeling community sees this work.

Luke was hoping the collaboration would lead to an equation that provided the volume of secondary ice particles based on specific parameters, like temperature and humidity.

From the data they collected, “you can almost see the equation,” Luke said. “We wanted to publish the equation. That’s on the to-do list. If we had such an equation, a modeler could plug that right in.”

Even though they don’t yet have an equation, Luke said that explicit descriptions of the dataset, in the form of probability density functions, are of value to the modeling community.

The group would like to see how broadly this phenomenon occurs throughout the world. According to Kollias, this work is the “first step” and the team is working on expanding the technique to at least three more sites.

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F. William Studier

By Daniel Dunaief

People around the world are lining up, and in some cases traveling great distances, to get vaccinations to COVID-19 that will provide them with immune protection from the virus.

An important step in the vaccinations from Pfizer-BioNTech and Moderna, the two messenger RNA vaccinations, originated with basic research at Brookhaven National Laboratory in the 1980’s, close to 40 years before the pandemic infected millions and killed close to three million people.

At the national laboratory, scientists including F. William Studier, Alan Rosenberg, and the late John Dunn, among others, worked on another virus, called the T7 bacteriophage, which infects bacteria. T7 effectively corrupts a bacteria’s genetic machinery, turning it into a machine that makes copies of itself.

From top graphic, the T7 virus uses RNA polymerase and a promoter to start a process inside a bacteria that makes copies of itself; researchers use copies of the promoter and the polymerase to insert genes that code for a specific protein; the mRNAs are injected into our arms where human ribosomes make COVID-19 spike proteins. Those spike proteins train the attack dog cells of our immune system to recognize the virus if it attempts to invade.

Back in the 1980’s, Studier and Dunn in BNL’s Biology Department were trying to do something no one else had accomplished: they wanted to clone the T7 RNA polymerase. The use of this genetic region, along with a promoter that starts the process of transcription, enabled scientists to mimic the effect of the virus, directing a cell to make copies of genetic sequences or proteins.

The BNL researchers perfected that process amid a time when numerous labs were trying to accomplish the same molecular biological feat.

“Although there were several labs that were trying to clone the T7 RNA polymerase, we understood what made its cloning difficult,” said Alan Rosenberg, who retired as a senior scientist at BNL in 1996. The patented technology “became the general tool that molecular biologists use to produce the RNA and proteins they want to study.”

The scientists who worked on the process, as well as researchers who currently work at BNL, are pleased that this type of effort, which involves a desire for general knowledge and understanding before policy makers and funders are aware of all the implications and benefits, led to such life-saving vaccinations.

“This is an excellent example of the value of basic science in that the practical applications were quite unanticipated,” John Shanklin, Chair of BNL’s Biology Department, wrote in an email. 

“The goal of the work Studier and his team did was to understand fundamental biological principles using a virus that infects bacteria. Once discovered, those principles led to a transformation of how biochemists and biomedical researchers around the world produce and analyze proteins in addition to providing a foundational technology that allowed the rapid development of mRNA vaccines,” he wrote.

Shanklin described Studier, who recruited him to join BNL 30 years ago from Michigan, as a mentor to numerous researchers, including himself. Shanklin credits Studier for helping him develop his career and is pleased that Studier is getting credit for this seminal work.

“I am tremendously proud that the basic research done in the Biology Department has been instrumental in accelerating the production of a vaccine with the potential to save millions of lives worldwide,” Shanklin wrote. “I couldn’t be happier for [Studier] and his team being recognized for their tremendous basic science efforts.”

Steve Binkley, Acting Director of the Department of Energy’s Office of Science, acknowledged the importance of the earlier work.

“The fact that scientific knowledge and tools developed decades ago are now being used to produce today’s lifesaving mRNA vaccines for COVID-19 is a great example of how the Department of Energy’s long-term investments in fundamental research at our National Laboratories can improve American lives today and into the future,” Binkley said in a statement.

Studier explained that his interests were more modest when he started studying this particular virus, which infects the bacteria E. coli.

“T7 was not a well-studied bacteriophage when I came to Brookhaven in 1964,” Studier, who is a senior biophysicist Emeritus, said in a statement. “I was using it to study properties of DNA and decided also to study its molecular genetics and physiology. My goal, of course, was to understand as much as possible about T7 and how it works.”

In an email, Studier said he did not realize the connection between his work and the vaccinations until Venki Ramakrishnan, a Nobel-Prize winning structural biologists from the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, told him.

“I am pleased that our work with T7 is relevant for fighting this world-wide pandemic,” Studier wrote. “History shows that some of the most useful discoveries come from basic research that could not have been predicted.”

While BNL is one of 17 Department of Energy facilities, it has conducted scientific research in numerous fields.

Several translational achievements originated at BNL, Shanklin wrote, including the thalium stress test for evaluating heart function, the development of Fluoro Deoxy Glucose for Positron Emission Tomography and the first chemical synthesis for human insulin, which allowed human insulin to replace animal insulin.

As for the effort that led to the T7 discoveries, Studier worked with Parichehre Davanloo, who was a postdoctoral fellow, Rosenberg, Dunn and Barbara Moffatt, who was a graduate student.

Rosenberg appreciated the multi-national background of the researchers who came together to conduct this research, as Moffatt is Canadian and Davanloo is Iranian.

Rosenberg added that while the group had “an inkling” of the potential usefulness of the processes they were perfecting, they couldn’t anticipate its value over the next 40 years and, in particular, its current contribution.

“Nobody really understood or thought just how widely spread its use would be,” Rosenberg said. “We certainly had no idea it would be an important element in the technology” that would lead to the Pfizer and Moderna vaccinations.

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