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Power of 3

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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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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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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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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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A group of gelada monkeys in Ethiopia. Photo from Jacob Feder

By Daniel Dunaief

Timing can mean the difference between life and death for young geladas (an Old World monkey species). Geladas whose fathers remain leaders of a social group for as much as a year or more have a better chance of survival than those whose fathers are displaced by new males under a year after they’re born. 

New males who enter a social group can, and often do, kill the young of other males, giving the new male leaders a chance to impregnate the female members of their social group who might otherwise be unable to conceive.

Jacob Feder

 

The odds of a new male leader killing a young gelada are about 60 percent at birth, compared to closer to 15 percent at around a year of age, according to researchers at Stony Brook University (SBU).

Additionally, pregnant gelada monkeys often spontaneously abort their unborn fetuses once a new male enters the group, as the mother’s hormones cause a miscarriage that enables them to dedicate their resources to the future progeny of the next dominant male.

At the same time, the survival of females depends on becoming a part of a group that is just the right size.

Jacob Feder, a graduate student at SBU, and Amy Lu, Assistant Professor in the Department of Anthropology in the College of Arts and Sciences at Stony Brook, recently published a paper in Proceedings of the Royal Society B that explores the ideal group size that optimizes the longevity of females and the number of their offspring.

The researchers discovered a Goldilocks effect. By studying the behavioral and group data for over 200 wild geladas over the course of 14 years, they determined that a mid-size group with five to seven females has the greatest benefit for their own fitness and for the survival of their offspring.

“There tends to be a trade off” in the dynamics that affect female geladas in different groups, Feder said. Females in the biggest groups face a higher risk of takeovers and takeover-related infanticide, since males are more likely to try to dominate a part of larger social groups where they have greater reproductive opportunities.

By contrast, individuals in the smaller groups may live on the periphery of a multi-group dynamic. These females are less protected against predators.

In their native Ethiopia, geladas are vulnerable to leopards, hyenas, and jackals, among others.

For the females, the survival of their offspring depends on the ability of males to remain in the group long enough.

“The male turnover is one of the major drivers of their reproductive success,” explained Feder.

Researchers have seen new males enter a group and kill infants born from another father. The infants, for their part, don’t often recognize the need to avoid new males, Lu said.

When males enter big groups, females often have to reset their reproduction.

Groups with about nine to 11 females often split into units of four to seven, Feder said. A new male might become the leader for half of the females, leaving the remaining male with the other half. Alternatively, new males may take over each group.

The pregnant females who are part of a group with a new male will spontaneously abort their offspring about 80 percent of the time, as females “cut their losses,” Feder said

About 38 percent of females live in a mid-sized group that is close to optimum size.

Gelada charm

According to Feder and Wu, geladas are a compelling species to research, Feder and Wu said.

Feder found his visits to the East African nation rewarding, especially when he had the opportunity to watch a small female named Crimson.

An important part of daily life for these primates involves grooming, where primates comb through each other’s hair, remove insects and, in many cases, eat them.

Crimson, who was a younger member of the group when Feder started observing geladas, didn’t have much grooming experience with this activity. Instead of running her hands over the body of her grooming partner, she focused on her mouth. Her partner’s wide eyes reflected surprise at the unusual grooming choice.

One of the favorites for Lu was a monkey who has since passed away named Vampire. A part of the V group, Vampire was taller and bigger than most adult females. She displaced male geladas, some of whom were larger than she, almost as often as they displaced her.

“If you go out in the field enough, you know the individuals pretty well,” Lu said. “They all have their own personalities. Some of them walk in a different way and react to situations differently.”

A resident of Centereach, Feder grew up in northern Connecticut, attending Wesleyan University as an undergraduate, where he majored in music and biology. A bass guitar player, Feder said he “dabbles in anything with strings.”

In fourth grade, Feder read a biography of Dian Fossey, which sparked his interest in biology.

While he has yet to combine his musical and science interests with geladas, Feder said these monkeys have a large vocabulary that is almost as big as chimpanzees.

Lu, meanwhile, started studying geladas as a postdoctoral researcher. They’re a great study species that allow scientists to ask compelling questions about reproductive strategies. “At any point, you can follow 20 social groups,” Lu said.

Lu, whose two children are four years old and 16 months old, said she has observed the similarities between human and non-human primate young.

“Babies throw tantrums, whether it is my child or a gelada infant protesting being put on the ground,” she described in an email. Gelada infants use a sad “cooing” sound. Sometimes, the sad cooing sound is real and sometimes “they just get what they want.”

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Rebecca Smith at the Sólheimajökull glacier in Iceland, where the scientist did field work during the 2015 Astrobiology Summer School. Photo from Rebecca Smith

By Daniel Dunaief

Rocks may not speak, move or eat, but they can and do tell stories.

Recognizing the value and importance of the ancient narrative rocks on Earth and on other planets provide, NASA sent vehicles to Mars, including the rover Perseverance, which landed on February 18 of this year.

Perseverance brought seven instruments, most of them identified by the acronym-loving teams at NASA, that carry out various investigations, such as searching for clues about a water-rich environment that may have sustained life about 3.5 billion years ago.

Several instrument teams developed and monitor these pieces of equipment, including Joel Hurowitz, Associate Professor in the Department of Geosciences at Stony Brook University and Deputy Principal Investigator on the Planetary Instrument for X-ray Lithochemistry, or PiXL.

In addition to the instrument leads, NASA chose participating scientists who can contribute to several teams, providing scientific support for a host of questions that might arise as the rover explores the terrain of the Red Planet 128 million miles from Earth.

Rebecca Smith, a post-doctoral researcher at Stony Brook in Geosciences Professor Scott McLennan’s lab, is one such participating scientist.

“I get to move around between all these different groups, which is fun,” said Smith, whose appointment will last for three years. While the Mars2020 program takes up about 20 percent of Smith’s time, the remainder is focused on the Mars Science Laboratory mission. Smith is likely to spend almost all of her time on Mars2020 starting this September.

Smith has helped make the science plans for the rover. The scientist and other researchers help select targets for the instruments that will help answer specific science questions. For this work, they collaborate with different science teams. Smith plans to get more involved with specific instrument teams soon, including SuperCam, PiXL and Sherloc.

For Smith’s own research, the scientist has a suite of rock samples that include lacustrine carbonates and hydrothermally altered volcanic rocks. The volcanic rocks formed under conditions that might be analogous to those once present in Jezero crater, where the rover landed and is currently maneuvering. The crater is just north of the Martian equator and has a delta that once long ago contained water and, potentially, life.

On Earth, Smith is using versions of the SuperCam, PiXL, and Sherloc to understand how these rocks would look to different instruments and determine what baseline measurements they need to tell the different types of rocks apart using the instruments aboard the rover.

Smith has studied rocks on Earth located in Hawaii, Iceland and the glaciers in the Three Sisters Volcanic Complex in Oregon.

Many planetary geologists use Earth as an analog to understand geologic processes on other planets. It is still uncertain if the climate of early Mars was warn and wet or cold and icy and wet, Smith explained in an email, adding, “It is possible the minerals we see with the rovers and from orbit can help us answer this question.” 

Most of the work the scientist been involved with is trying to understand how Mars-like volcanic rocks chemically weather under different climates.

Through previous research on Mars, scientists discovered that large regions had poorly crystalline materials. The poorly crystalline nature of the materials makes them difficult to identify using rover-based or orbiter-based instruments.

“The fact that they could have formed in the presence of water makes them important to understand,” Smith explained.

Part of the work Smith is doing is to understand if poorly crystalline material formed by water have specific properties that relate to the environment or climate in which they formed.

Smith said the bigger picture question of the work the teams are doing is, “was there life on Mars? If not, why not? We think that Mars, for the first billion years or so, was pretty similar to Earth around the same time and Earth developed life.”

Indeed, Earth had liquid water on its surface, which provided a habitat for microbial life about 3.5 billion years ago.

The ancient rock record on Mars provides a better-preserved history because the Red Planet doesn’t have plate tectonics.

“Based on what we know about Earth, if life ever developed on early Mars, it would likely have been microbial,” Smith wrote.

Other goals of Mars2020 include characterizing the climate and the geology. Both goals focus on looking for evidence of ancient habitable environments and characterizing those to understand a host of details, such as the pH of the water, the temperature and details about how long the water was on the surface.

Part of the reason NASA put out a call for participating scientists is to “bridge instrument data” from different pieces of equipment, Smith explained.

“I love the collaborative nature of working on a team like this,” Smith offered. “Everybody is interested in getting the most important information and doing the best job that we can.”

Smith enjoys the opportunity to study potentially conflicting signals in rocks to determine what they indicate about the past.“Geology is just so complex. It’s a big puzzle. Forces have been acting over a very long period of time and forces change over time. We are trying to tease apart what happened and when.”

While Smith works at Stony Brook, the post-doctoral scientist returned to California during the pandemic to live closer to her family. After finishing the current research program, Smith plans to remain open to various options, including teaching.

Smith appreciates the opportunity to work on the Mars 2020 mission, adding, “I’m really grateful for that during this past year in particular.”

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Pixabay photo

By Daniel Dunaief

Rain can put a damper on life, as the two children at the beginning of Dr. Seuss’s The Cat in the Hat shared and as the itsy bitsy spider that went up the water spout only to get washed out again discovered.

As it turns out, rain, clouds, wind and foul weather can reduce the trading decisions of people who buy and sell large sums of money in stocks, as they grapple with their own reactions to clouds that they’d like to go away and come again some other day.

Danling Jiang

Danling Jiang, associate dean of research and faculty development in Stony Brook University’s College of Business; Lin Sun, Assistant Professor at George Mason University; and Dylan Norris, Assistant Professor at Troy University recently published a study in which they explored the effect of cloudy or inclement weather in the two weeks before an earnings surprise on investor reactions.

Every three months, public companies provide a detailed disclosure of their profits and losses, giving investors a chance to look over the equivalent of a quarterly report card.

Like helicopter parents who monitor every line, sentence and word in a report card, institutional investors tend to have a stronger reaction, either positively or negatively, if those numbers are considerably different than they expected. An “A” in advanced calculus might be like profits that exceed estimates by 10 percent, while a “C” might be the equivalent of an unexpected loss in a business that had been doing well.

As it turns out, institutional investors are less likely to react as strongly, at least initially, to an earnings surprise if the skies in the two weeks before they review the earnings announcements are cloudy or unpleasant.

“We find strong supporting evidence in our empirical tests which reveal increases in the pre-announcement unpleasant weather of institutional investors results in muted immediate market responses to earnings news and amplified port-earnings-announcement drifts,” Jiang explained in an email.

Over the course of two to three months, the stock price reflects a more typical pattern that aligns with the direction of the earnings surprise.

The researchers published their work in the Journal of Corporate Finance.

These results, which came from an analysis of reactions to earnings surprises from 1990 to 2016, validate and extend previous efforts to understand how weather affects investor decisions.

Earlier studies revealed the effects of weather on individuals’ psychological and physiological states, according to Jiang.

“These effects have also been shown to influence financial decisions and security prices, even through the actions of sophisticated market participants such as market makers and security analysts,” she said.

The three academics started working together when Lin and Jiang were faculty and Norris was a PhD student at Florida State University.

“We were fascinated by the idea present in prior research that weather seems a perfect exogenous shock to investor psychology and physiology,” said Jiang. “This exogenous feature allows us to draw some causality of psychology on market pricing in a new setting with institutional investors and earnings announcements.”

The researchers chose the years 1990 to 2016 because they had the data in their possession.

“We tried to ensure that our sample period was long enough to confirm the weather effect was a persistent force throughout time and not merely a phenomenon of a small segment in time,” said Jiang who added that solving the weather-related muted effect by adding brighter lights to a trading floor could backfire, as excessive bright lights can have negative effects.

“Overillumination can cause fatigue, stress and anxiety,” she explained. “It is also likely that most traders are subject to the weather at some point during the day” through arriving at work, leaving for lunch or glancing out the window. That means the weather still likely influences them even when they may be in a brightly-lit indoor setting.

The researchers used two measures of weather conditions. One integrated wind, cloud and rain, and the other used cloud cover only. Both measures produced similar findings.

Using earlier studies and their own research, it appears accounting for the combined effect of simultaneous weather parameters or focusing on cloud cover better captures any physiological or psychological effects as opposed to using wind or rain alone, said Jiang.

Public companies are unlikely to trigger a more muted response to earnings surprises by recruiting investors from areas with greater cloud cover, as prior research demonstrated that seasonal climate norms don’t appear to affect the behavior of investors once they acclimate, so to speak, to the weather.

In addition to the 14-day window to create the weather measures, the researchers generated a seven-day measure that showed similar results.

Announcement day weather may also affect market reactions to earnings news and “we do not discredit its importance,” Jiang said. Indeed, other research has shown that the weather in New York City at the time of an earnings announcement impacts market reactions.

The explanation for the muted reaction to earnings is based on psychological and physiological reactions of institutional investors to weather, including anxiety and sadness as well as fatigue and decreased activity.

“In addition to causing delayed information processing, weather could cause a reduction in energy amongst some traders,” said Jiang

That means institutional investors may struggle with the same factors that made the boy and Sally from The Cat in the Hat struggle while it was “too wet to go out and too cold to play ball. So we sat in the house, we did nothing at all,” Dr. Seuss wrote.

While institutional investors don’t do nothing at all, they are less active, at least according to the recent research, than they are when the sun shines brightly, reliably and more consistently.

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Photo courtesy of CSHL

By Daniel Dunaief

Cold Spring Harbor Laboratory’s DNA Learning Center and the Red Cloud Indian School recently launched a program called Students Talk Science in which high school students could ask questions from several senior scientists about the vaccine for COVID-19 and healthcare disparities in minority communities.

Dr. Eliseo Pérez-Stable

 

The talks are a component of a program called STARS, for Science, Technology & Research Scholars, an effort the group started in 2019 to build interest and experience in STEM for minority students. The Students Talk Science program engaged the STARS participants and students from the Red Cloud Indian School on the Pine Ridge Indian Reservation.

Jason Williams, Assistant Director of Inclusion and Research Readiness at the DNA Learning at CSHL; Brittany Johnson, an educator at the DNA Learning Center; Katie Montez, a teacher at the Red Cloud Indian School ;and Carol Carter, Professor in the Department of Microbiology and Immunology at the Renaissance School of Medicine at Stony Brook University, wanted to connect minority students with practicing physicians and scientists in leadership positions at the National Institutes of Health to allow them to ask questions of concern regarding the vaccines.

Dr. Monica Webb-Hooper

“We did this to empower them to function as trusted resources for their families, friends and network,” Carter, who participated as an individual rather than as a formal representative of Stony Brook University, explained in an email.

The conversations included interactions with Dr. Eliseo Pérez-Stable, Director of the National Institute on Minority Health and Health Disparities, or NIMHD at the National Institutes of Health; Dr. Monica Webb Hooper, Deputy Director of the NIMHD; Dr. Gary Gibbons, Director of the National Heat, Lung and Blood Institute; and Dr. Eugenia South, Assistant Professor in Emergency Medicine at the Hospital of the University of Pennsylvania and the Presbyterian Medical Center of Philadelphia.

The high school students prepared informed questions.

Dr. Gary Gibbons

“The students were encouraged to do their own research” on the interview subjects, Williams explained. “We asked students not to look just at [each] interviewee’s science work, but also any personal background/ biography they could find. Students had multiple opportunities for follow up and were largely independent on their choices of questions.”

Samantha Gonzalez, a student at Walter G. O’Connell Copiague High School, asked South about her initial skepticism for the vaccine.

South acknowledged that she had no interest in taking the vaccine when she first learned she was eligible. “I almost surprised myself with the fierceness with which I said, ‘No,’” South said. “I had to step back and say, ‘Why did I have this reaction?’”

Some of the reasons had to do with mistrust, which includes her own experiences and the experiences of her patients, whom she said have had to confront racism in health care. In addition, she was unsure of the speed at which the vaccine was developed. She had never heard of the mRNA technology that made the vaccines from Moderna and Pfizer/ BioNTech possible.

“I had to do my own research to understand that this wasn’t a new technology,” she said.

Dr. Eugenia South

South went through a learning process, in which she read information and talked to experts. After she received answers to her questions and with the urging of her mother, she decided to get the vaccine.

“I’m so thankful that I was able to do that,” South said.

The team behind Students Talk Science not only wanted to empower students to make informed decisions, but also wanted to give them the opportunity to interact with scientists who might serve as personal and professional role models, providing a pathway of information and access that developed amid an extraordinary period.

“We wanted to engage high school students in something unique going on in their lifetime,” Carter said.

To be sure, Carter and Williams said the scientific interactions weren’t designed to convince students to take the vaccine or to urge their parents or families to get a shot. Rather, they wanted to provide an opportunity for students to ask questions and gather information.

“We purposely did not participate in the discussions because our goal was not to convince or ‘preach,’ but to enable students and their networks to make informed decisions,” Carter said.

Parents had to read and sign off on the process for students to participate. The organizers didn’t want a situation where they were doing something that conflicts with a parents’ decisions or views.

Williams added that the purpose of the conversations was never to say, “you must get the vaccine. Our purpose is to talk about information.”

The objective of these interactions is to help minority students find a track for a productive career in ten years.

In addition to questions about hesitancy, Williams said some of the high school students expressed concerns about access to vaccines. He is pleased with the result of this effort to connect students with scientists and doctors.

The group was “able to get some of the most important scientists in the country to sit with high school students,” he said. “It was very powerful to give students access to these role models.”

The goal is to stay with these students, mentor them and stay in touch with them until they graduate from college and, perhaps, return as research scientists.

Even for students who do not return, this type of interaction could provide an “impactful experience that prepares them for other opportunities,” Williams explained, adding that the STARS program would incorporate the Students Talk Science Series into the program more formally in the future, with new students and topics most likely during the school year.

The interviews are available at the following website: https://dnalc.cshl.edu/resources/students-talk-science/.

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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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