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Nivea Pereira de Sa Photo by Rodrigo Carvalho da Silva

By Daniel Dunaief

When people are immunocompromised, exposure to what might ordinarily be a harmless fungus can cause significant health problems.

Researchers in the laboratory of Maurizio del Poeta, Distinguished Professor in the Department of Microbiology and Immunology at the Renaissance School of Medicine at Stony Brook University, have been looking to create new treatments and develop vaccines against these fungi.

Working with a team of scientists at Stony Brook, research scientist Nivea Pereira de Sa, who joined del Poeta’s lab in 2018 as a postdoctoral researcher, recently published research in the journal mBio about potential anti-fungal drugs that target a key enzyme in the fungus Aspergillus fumigatus. 

Without the enzyme, the fungus can’t cause disease and the host defenses have time to eliminate it even if the host is immunodeficient.

Working with Michael Airola, Assistant Professor in the Department of Biochemistry and Cell Biology at SBU, Pereira de Sa started out by trying to find the structure of sterylglucosidase, an enzyme that is a molecular key for the fungus during infection and that aids in its ability to adapt to environmental changes such as low oxygen levels and changes in pH.

Pereira de Sa learned how to do x-ray crystallography from Airola, a process that reveals the structure of compounds.

In an email, Airola described Pereira de Sa as an “expert” in the technique.

Airola called the research “one of the most exciting projects” he’s worked on and hopes the group can translate the results into the clinic. A talented biochemist, Pereira de Sa is also an “expert in so many different scientific areas,” Airola wrote, which he described as “rare.”

Pereira de Sa also determined the structure of the same enzyme for Cryptococcus, another invasive and potentially harmful fungus. The enzymes in both fungi have a high degree of similarity.

Pereira de Sa expressed satisfaction at the application of such work. “Every time I get a crystal structure, it’s so amazing,” she said. “I love doing that.”

Pereira de Sa started screening potential compounds to inhibit sterylglucosidase in Aspergillus,

Del Poeta’s lab coordinated the design and testing of these inhibitors with Iwao Ojima, Distinguished Professor in the Department of Chemistry and Director of the Institute of Chemical Biology and Drug Discovery at Stony Brook.

Refining potential drugs

Ojima’s group is synthesizing derivatives of the hits Pereira de Sa found and she will start tests outside a living organism, or in vitro, soon.

Ojima has synthesized several compounds using computer-assisted drug design. He is currently developing several inhibitors that scored high on his computational molecular docking analysis and will synthesize two to three dozen potential small molecules.

Ojima, who partnered with Pereira de Sa in this study, “greatly appreciates her and her seminal contributions to this project,” he wrote in an email. She made critical contributions to the study that ensured its success and Stony Brook is “very fortunate to have her as a leader in this project.”

Ojima plans to identify highly potent inhibitors individually for Aspergillus and Cryptococcus separately, and then will try to find and develop broad spectrum inhibitors based on those compounds.

The need for a treatment has increased dramatically as the number of immunocompromised patients has increased.

Invasive aspergillosis can have mortality rates above 90 percent. The World Health Organization last October released its first ever list of health threatening fungi, which includes Aspergillus.

Pereira de Sa suggested two possible uses for this inhibitor. It could work as a treatment, knocking down the virulence of the fungus or it could contribute to the development of a vaccine.

In strains with a mutated enzyme, a mouse model has full protection against infection.

Getting a vaccine approved through the Food and Drug Administration for immunocompromised individuals might be challenging, she said. Several studies would be needed to confirm its safety.

Del Poeta added that the vaccine his lab has developed is effective alone when heat killed, reducing the threat a live virus with a defective enzyme might pose to an immunocompromised patient. Del Poeta has been developing a vaccine for cryptococcus and aspergillus and is testing it for other fungal infections as well.

‘A beautiful cause’

Del Poeta described Pereira de Sa as a key contributor to his lab, who is methodical, systematic and hard working.

The program she is developing will take years to go to clinical trials, he added.

Del Poeta met Pereira de Sa in 2017, when he visited Brazil and spoke with her mentor, Daniel de Assis Santos, who gave her an enthusiastic reference.

After meeting with her for only five minutes, del Poeta offered her a job.

“I will never forget her face: surprised, joyful, excited and she could not hold back some tears,” del Poeta described.

Del Poeta is thrilled with his choice, as she has gone above and beyond his expectations.

Born and raised in Belo Horizonte, Brazil, Pereira de Sa lives in East Setauket with her husband Rodrigo Carvalho da Silva, who is an airplane mechanic.

She enjoys Long Island, particularly during the summer, when she goes hiking, visits parks, kayaks and goes paddle boarding.

Pereira de Sa is encouraged by the progress in her work and is hoping her research contributes to future treatments.

“We are developing tools to help people,” she said. “It’s a beautiful cause I’m fighting for.”

She said the mortality rate from these fungal infections is “very high,” especially because a fungus like Aspergillus is ubiquitous.

“The fungus is present everywhere,” she said. “We are inhaling the spores of it every day.”

The invasive fungal disease starts in the lungs and spreads to the rest of the body, including in the brain, which can cause seizures.

Pereira de Sa recognizes the urgency of developing an effective treatment.

“We need some solutions and we need it now,” she said. “We are not prepared to fight fungal infections” on a large scale.

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Victoria Greening at the Grotte Mandrin site in France. Photo by Svenya Drees

By Daniel Dunaief

Last summer, the Anthropology Department at Stony Brook University brought 13 students to the south of France to help gather information from a rich archaeological site called the Grotte Mandrin.

Asa Wong-Gómez at the Grotte Mandrin site in France. Photo by Nicholas Gonzalez

The trip with the Field School through SBU Study Abroad enabled the students to work in the field and gather information from a site that has provided a treasure trove of information about Neanderthals and Homo sapiens from 54,000 years ago.

The students found the trip successful, inspirational and, at times, exhausting.

“I did archeology all summer,” said Asa Wong-Gómez, a senior anthropology major at Stony Brook, who spent time in Kenya before joining the team in France. “It was really cool.”

Wong-Gómez recalled the thrill of finding teeth and stones in the dirt. “The first day, everyone’s first find was super exciting,” he said.

The field expedition, which was the first Stony Brook ran at this site, enabled students to forge connections with each other and with the site’s leaders, including Stony Brook Lecturer Jason Lewis, Ludovic Slimak, cultural anthropologist at the University of Toulouse-Jean Jaurès, and Laure Metz, an archaeologist at Aix-Marseille University.

Victoria Greening at the Zooarcheological Training and Research Laboratory. Photo by Nicholas Gonzalez

“Working with everyone so closely for that month definitely builds really strong connections that have lasted since,” said Victoria Greening, who graduated from Stony Brook in the winter and is planning to start a Master’s program in the fall at the University of Oxford.

She appreciated the opportunity to be a part of new discoveries.

“Working with something that’s not in the written records and discovering it yourself was a privileged feeling,” said Greening, who grew up in Yaphank.

A happy grown up

Echoing Gollum from the “Lord of the Rings” series, Slimak would look at something a student found and say, “my precious, this goes in a special bag,” Wong-Gómez recalled.

Slimak reflected the joy he took in discovering compelling finds. “It was amusing, watching a grown adult be so happy,” Wong-Gomez said.

Eva Marsh, who is a senior at Stony Brook in the anthropology department, appreciated the excitement of finding flint. A couple of students, she recalled, also found teeth, including a horse’s tooth. The group discovered a massive core, from which early Homo sapiens would chip off pieces to construct arrows they would shoot from a bow to bring down buffalo or horses.

On the first night gathering at their summer accommodations, Marsh said the group looked up at a star-filled sky.

“There was not a lot of pollution there” or other lights, which was “really amazing,” Marsh said.

Marsh was nervous on her first day, as she didn’t know what to expect. The team played games for the first few nights and discussed why they all signed up for the field experience. Each night at dinner, they discussed the events of the day, Marsh recalled.

Svenya Drees at the Grotte Mandrin site. Photo by Victoria Greening

For Svenya Drees, who grew up in Port Jefferson and is a Master’s Student in Lewis’s lab, the experience was familiar, as she had conducted field work during the summer of 2021. “I knew what to expect,” she said. Still, she found the discovery of pebbles from a distant river intriguing.

“There’s this whole mystery at the site about pebbles that made it into the assemblage,” Drees said. “These rocks were brought there from the local river. I thought that was pretty awesome.”

The theory about the pebbles is that Neanderthals or Homo sapiens, who had lived in the cave at different times, deployed the pebbles to help remove flakes from the rock cores these ancient ancestors used to create weapons.

Some challenges

While the students enjoyed the experience, with many of them planning to continue in their anthropological studies, the summer included some challenges.

The students stayed in a house at the top of a hill. At the same time, the cave was also on a hill. Each morning, they walked down the hill to a car that drove them to the bottom of the Grotte Mandrin site, where they walked about 15 minutes up to the field station. At the end of the day, they had to climb back up to their temporary home.

“After digging holes all day, walking up the hill was not my favorite part,” Wong-Gómez said. Greening suggested that future participants in the program, which will also run this summer, bring sturdy shoes.

The students also sometimes carried heavy containers filled with sand. The physical challenges notwithstanding, most of the students eagerly anticipate future such explorations.

“It’s definitely the right field for me,” said Greening. “Working at Mandrin solidified that for me.”

Wong-Gómez hopes to continue his field work at the University of Florida. The university has accepted him as a PhD student, although he is awaiting word on whether he gets funding.

“When I got the email that I was accepted, it didn’t feel real,” Wong-Gómez said. “I really want to do this.”

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A reconstruction by Ludovic Slimak of the arrows Homo sapiens likely used 54,000 years ago in France. Credit: Ludovic Slimak

By Daniel Dunaief

Have bow and arrow, will travel, even in Eurasia 54,000 years ago.

An archaeological site in the south of France that’s 70 miles from the coastline called Grotte Mandrin not only provided evidence that Homo sapiens and Neanderthals lived in this area around the same time, but also offered proof that early humans used bow and arrows to hunt for prey like bison and wild horses.

Jason Lewis. Photo from SBU

In research published in the journal Science Advances, Jason Lewis, a Lecturer in the Department of Anthropology at Stony Brook University; Ludovic Slimak, cultural anthropologist at the University of Toulouse-Jean Jaurès; and Laure Metz, an archaeologist at Aix-Marseille University, shared an extensive analysis of stone artifacts that demonstrated the use of bows and arrows.

These hunting tools, which inhabitants of the cave could use to pursue herd animals migrating between the Mediterranean region and the plains of Northern Europe, provide the earliest evidence of mechanically propelled projectile technology from Eurasia.

“We looked for diagnostic evidence of a very powerful impact once the stone tip hits something,” said Lewis. “We can see experimentally what type of damage” is produced on the tips of the arrows. The damage to these arrows is in line with everything that modern archers are doing because the tools human ancestors used were so light, Lewis added.

The collaborative effort to study these arrows in labs across two continents involved an extensive analysis of the flaking pattern around the tips of the arrows. The researchers didn’t find any of the organic materials that the early hunters would have used to create the bow.

This technology, which likely took about an hour to make, likely enabled Homo sapiens to bring down prey. Effective hunting from about 10 to 20 yards likely would have required more than one arrow, particularly with the size and strength of the targets.

At an archaeological site in the Middle East, scientists described stone tools around the same time that look similar to the bows and arrows humans in Eurasia used.

“The evolving modern humans were developing and using projectile technology,” Lewis said.  

Cultural differences

Lewis, Slimak and Metz showed in a seminal paper last year that Homo sapiens and Neanderthals had lived in the same cave, sometimes separated by a year or even a season.

While these two types of humans lived around the same time and in the same place, they didn’t share the same technology or have the type of cultural exchange that would enable Neanderthals, who typically hunted with hand-thrown spears, to use the same hunting tools.

“There’s no evidence of learning exchange,” Lewis said. Neanderthals did not start using the smaller points typical of the arrows or that would have been used as projectiles.

“It doesn’t look like there was a cultural exchange between the two groups,” Lewis said, as the artifacts from the time Neanderthals occupied the cave didn’t include any arrows.

Cultures sometimes develop identities that preclude using technology from other groups. Such cultural differences existed in the Maale and neighboring Tsamai people in Southwestern Ethiopia.

“Even though [bows and arrows] might be logically or objectively advantageous, some cultures suggest that ‘that’s not what we do,’” Lewis said.

Indeed, cultural differences have occurred in other areas that groups haven’t bridged, despite the availability of similar resources and the chance to learn the technology.

At the cave in Grotte Mandrin, researchers found a large collection of stone tools in Layer E of the cave.

The scientists believe the numerous arrows could have been the early equivalent of a munitions dump.

While bows and arrows would have provided a hunting advantage to Homo sapiens, the technology doesn’t explain why the two groups of early humans occupied the cave or dominated the area at different times.

“I doubt it comes down strictly to stone tool technology,” Lewis said. “There’s not a continuous march of occupation and expansion” as the interactions between the two populations were long lasting and complex.

Homo sapiens and Neanderthals moved up into a region and then moved back. This is akin to the way European settlers interacted with Native Americans when ships first crossed the Atlantic.

The Europeans moved into the region, interacted with people who already in the country, returned home, and then, at a later point crossed the ocean again.

Arrow studies

To understand the technology used to create these arrows, Metz and Slimak have spent years studying the way rocks flake off or get damaged in response to contact with animals or objects they hit when shot through the air.

Working for over a decade, Metz has been conducting experimental replication of the effect of use on these stone tools.

Scientists who shoot these stone arrows into carcasses from butcher shops can see the flaking pattern and scratches on the arrows.

Lewis explained that the flaking on the arrow heads could not have been made during the creation of the arrows themselves.

“Only high velocity strikes” could produce such markings, Lewis said.

These kinds of studies combine geology, physics and natural science. Lewis said John Shea, Anthropology Professor in the College of Arts and Sciences at Stony Brook University, has pioneered the study of such technology during the Pleistocene Ice Ages.

Lewis explained that his primary role is to bring the contextual understanding about how various types of early humans were using the landscape and interacting with the animals.

He also brings the context of work he does in Africa around the same time period as a comparator.

Lewis explained that more research would be forthcoming from this site.

“This is part of a larger modern human ability to conceptualize the world,” Lewis said. Early humans were trying to change their environment to match their needs, with boats, clothing, dwelling structures and other elements of their lives.

Such tool use could reduce hunting time and could enable a greater division of labor, suggesting that “each person didn’t have to do everything” to meet basic needs. 

 

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Turnersuchus hingleyae. Image by Júlia d’Oliveira

By Daniel Dunaief

Nature plays a slow game, drawn out over millions of years, of hide and seek. First, spectacular and elaborate creatures lived hunted, reproduced, and avoided predators millions of years ago. After they died in places like Dorset in the United Kingdom, their bodies became preserved in the muddy, shallow marine environment. The sediment was then covered over by rock layers and safely preserved.

Eric Wilberg in Coyote Buttes, Utah in 2018

Fast forward about 185 million years, after waves crashing upon the shore erode those rocks on a beach and expose those fossils.

Indeed, in 2017, in a UNESCO World Heritage site where scientists and fossil hunters and paleontologists like 19th century star Mary Anning made key discoveries, archeology enthusiasts Paul Turner and Lizzie Hingley found the head, backbone and limbs of a creature scientists had imagined, but hadn’t, until then, discovered.

Called a thalattosuchian, which is an ancient sister of modern day crocodile ancestors, this finding extended the timeline of when these coastal marine crocodiles lived.

In late 2019, Dr. Roger Benson, who was then at the University of Oxford, reached out to Pedro Godoy, a postdoctoral researcher at Stony Brook who Benson co-supervised during his PhD, and Eric Wilberg, Assistant Professor at the Department of Anatomical Sciences at Stony Brook University. The team, which included Alan Turner, Professor in the Department of Anatomical Sciences at the Renaissance School of Medicine at Stony Brook, planned to describe and characterize the fossil.

Benson said he had never met Wilberg before but had “read his work on croc evolution and really admired his systematic approach.”

This ancient crocodilian creature, which was about six feet long and was likely either a sub adult or an adult, is the first “thalattosuchian fossil complete enough to definitively identify as a member of the group of rocks older than about 180 million years ago,” Wilberg explained.

Wilberg, Godoy (who is now a postdoctoral researcher at the University of Sao Paolo), Turner and Benson (who is currently Macaulay Curator of Dinosaur Paleobiology at the American Museum of Natural History), recently published their study on this fossil in the Journal of Vertebrate Paleontology.

Godoy said that Wilberg is “an expert in this group of animals and it was great working with him on this.” Godoy added that this was an “important finding, which helps us fill a gap in the evolution of thalattosuchians.”

Benson suggested that this fossil provides a glimpse into the origin of thalattosuchians, indicating that the group originated before this fossil. The particular organism is the first discovered in a new species gathered by the two fossil hunters (see related story on right).

The Thalattosuchian group lived until the Early Cretaceous period, about 130 million years ago. These predators likely fed on fish or cephalopods like ancient octopi or squid.

Recently, another team of scientists discovered a thalattosuchian skull in Morocco, which is about five to 10 million years older than the Turnersuchus Wilberg described.

The discoveries “support our prediction that thalattosuchians evolved millions of years earlier —probably in the late Triassic” around 200 million or more years ago, Wilberg added. His analysis determined that the thalattosuchian lineage diverged from its last common ancestor with crocodile-relatives during the Triassic period.

Wilberg and other researchers will be on the lookout for additional specimens which can add details to the understanding of this species. This specimen was missing most of the front of the skull, all of the hindlimb and pelvis and most of the tail.

Specific features

By examining the spinal column and part of the forelimb, Wilberg explained that this species did not have forelimbs that evolved into flippers, like later descendants in the group. It would have been similar in overall body form to living crocodiles, which means that it likely had similar swimming capabilities. 

The specimen included a couple of partial teeth. Like all living crocodiles, it likely continually replaced its teeth throughout its life. Its bite force would have been less than a similar sized modern crocodile. The modern crocodylian skull evolved structural reinforcements to allow it to withstand the massive bite forces it generated.

Thalattosuchians skulls were “not as well reinforced, so they were probably not able to bite as hard,” Wilberg wrote. It seems likely that the “muscles that generate fast bites were large in this group, so they may have evolved for fast bites to capture small-moving prey.”

The Turnersuchus probably lived close to the coast in relatively shallow water. Like living crocodiles, it also likely spent time out of the water to bask in the sun (it was also cold blooded) and lay eggs. The climate of the region when this species lived would have been warmer than the current climate of the United Kingdom.

This creature was likely not an apex predator, with larger hunters like ichthyosaurs, pleiosaurs and probably sharks likely preying on it.

“We don’t have any direct evidence of predation from these groups on thalattosuchians, but it probably happened,” Wilberg added.

This particular fossil, like many other discoveries, has numerous unknowns. The gender of the individual (which scientists often determine by comparing body sizes) is unclear.

This particular find will “continue to be important moving forward in determining how thalattosuchians are related to other fossil crocodiles — every new species discovered is a chance to test existing hypotheses of how they are related to one another” which is important in determining how evolution occurred in the group, Wilberg explained.

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The fossil hunters who lent their names to an ancient crocodile

By Daniel Dunaief

The beaches along the southern shore of the United Kingdom have rich and ancient stories to share.

Lizzie Hingley and Paul Turner. Photo from Lizzie Hingley

Lizzie Hingley and Paul Turner — friends who met on the beach and started working together in 2016 — are eager to gather clues about the past. Fossil hunters at the UNESCO World Heritage Site in Charmouth in the United Kingdom, which is about a three-hour drive southwest from London, Hingley and Turner discovered fragments of an unusual fossil starting in 2017. “Initially, we just saw random bones,” explained Hingley, who finds, prepares and sells some of the fossils on her website. Some fragments appeared to be a jaw in the clay next to an initial stone block containing multiple bones.

Hingley, who lives a ten minute walk from a beach that is also referred to as the Jurassic Coast, said that it’s “very unusual to come across anything with lots of bones in it on the beaches.” She took the find to her workshop, where she used an air abrasive and pneumatic chisel. She noticed it was semi-articulated, which means the bones were arranged in something resembling a natural order.

It took about one and a half years for Hingley and Turner to collect all the pieces of this fossil. Turner found the first main block, Hingley discovered the jaw next to it, Turner uncovered the next two and she found the last piece.

“It was quite difficult to collect as it was coming out of a huge glacial landscape,” said Hingley.  It likely fell out of the cliff 50 years earlier and had been traveling to the front of the slip over the years. “This meant that, although we did try to dig for it, the best way to recover it was to wait for nature to uncover it for us,” she added.

Lizzie Hingley holding the ichthyosaur jaw she found when she was eight. Photo by Craig Chivers

Hingley and Turner visited daily to make sure they didn’t miss any pieces. The Charmouth Heritage Centre staff found a few loose vertebrae and reunited them with the rest of the fossil.

Hingley, who is one of about 15 people who regularly search parts of the seven miles of beaches almost daily, wanted to do more than collect this fossil — she wanted to know its history. Through her network, she found Roger Benson, who was a Professor of Paleobiology at the University of Oxford.

“It was great to work with him and see the scans being done,” she said. “He was instrumental” in bringing together a team of researchers who could analyze the finding and put it into historical context.

Indeed, Benson reached out to several researchers at Stony Brook University, including his former postdoctoral researcher Pedro Godoy, Assistant Professor Eric Wilberg and Professor Alan Turner (see related story on left) to gather information.

Close-up of ichthyosaur jaw. Photo by Lizzie Hingley

Their work concluded that this was a new species of marine crocodile. The ancient crocodile relative was named Turnersuchus hingleyae, after the fossil hunters who discovered it.

“It’s wonderful to have my name go down in history,” said Hingley, who also has a gastropod named after her.

Hingley, who is 35, started looking for fossils when she was six in Dorset, first on family holidays and then at every opportunity she could get. Over the years, she has found ichthyosaur skulls, ammonites measuring half a meter across, shark skin and teeth and numerous blocks containing hundreds of ammonites. When she was eight, she found a 20 centimeter ichthyosaur jaw, which is still part of her own collection.

Hingley is thrilled with her job, in which “every day is different and you never know what you are going to find or be working on,” she wrote. “I get to spend a lot of time in nature on the beach; the tide changes the beach every day, too.”

Benson described the beaches where Hingley and Turner search for new fossils as a European “pilgrimage for paleontologists.”

Hingley added that the process of erosion, which reveals fossils hidden in the cliffs along the beach, is something of a double edged sword, revealing fossils and threatening to carry them away.

A storm can decimate a beach and destroy fossils when the tide is too high to collect examples of creatures that lived as many as 185 million years ago. At the same time, erosion along the coast, caused by some of these same storms, reveals new fossils.

Walking along the beach, Hingley explained that it is almost incomprehensible to imagine the time scale separating her from the creatures who died so long ago.

The environment on the Jurassic Coast didn’t change much over those millennia.

“It is odd to think that you are collecting from the sea bed when it’s coming out of the cliff many meters above you,” she wrote. “The distance and time that these fossils have travelled to be found is incredible.”

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Christopher Gobler. Photo by Conor Harrigan

By Daniel Dunaief

When they can’t stand the heat, bay scallops can’t get out of the proverbial kitchen.

A key commercial shellfish with landings data putting them in the top five fisheries in New York, particularly in the Peconic Bay, bay scallops populations have declined precipitously during a combination of warmer waters and low oxygen.

In a study published in the journal Global Change Biology, Christopher Gobler, Stony Brook University Endowed Chair of Coastal Ecology and Conservation and Stephen Tomasetti, a former Stony Brook graduate student, along with several other researchers, showed through lab and field experiments as well as remote sensing and long-term monitoring data analysis how these environmental changes threaten the survival of bay scallops.

Stephen Tomasetti. Photo by Nancy L. Ford/ Hamilton College

Bay scallops are “quite sensitive to different stressors in the environment,” said Tomasetti, who completed his PhD last spring and is currently Visiting Assistant Professor of Environmental Studies at Hamilton College in Clinton, New York. Of the regional shellfish, bay scallops are the most sensitive to environmental stress.

Indeed, since 2019, bay scallops have declined by between 95 and 99 percent amid overall warming temperatures and extended heat waves. These declines have led to the declaration of a federal fishery disaster in the Empire State.

Tomasetti used satellite data to characterize daily summer temperatures from 2003 to 2020, which showed significant warming across most of the bay scallop range from New York to Cape Cod, Massachusetts. He monitored four sites with sensors in the water in addition to satellite data during a field deployment with scallops.

At the warmest site, which was in Flanders Bay, New York, the temperature was above the 90th percentile of its long term average during an eight-day period that overlapped with the scallop deployment. The bay scallops in Flanders Bay were “all dead by the end of the heat wave event,” Tomasetti said.

At the same time, low levels of oxygen hurt the bay scallops which, like numerous other shellfish, feed on phytoplankton. Oxygen levels are declining in some of these bays as nitrogen from fertilizers and septic systems enter these waterways. High nitrogen levels encourage the growth of algae. When the algae die, they decay, which uses up oxygen and releases carbon dioxide into the water.

Field and lab studies

In the field, Tomasetti measured the heartbeat of bay scallops in East Harbor, Massachusetts by putting optical infrared sensors on them that took heartbeat readings every 15 minutes for a month.

Stephen Tomasetti conducts field work in East Harbor during the summer of 2020.

When the average daily temperature increased, their average heart rate climbed, which the scientists used as a proxy for their respiration rate. A higher respiration rate meant that the scallop was expending energy more rapidly, potentially leading to reductions of energy reserves.

Additionally, Tomasetti measured how quickly the scallops fed on algae in the lab under warm temperatures and low oxygen.  These conditions caused the scallops to stop feeding or to feed slowly. Tomasetti interpreted this as a sign that they were waiting out the stress.

In the lab, bay scallops in the same conditions as the bays from Long Island to Massachusetts had the same reactions.

While a collection of fish and invertebrates feed on bay scallops, the effect of their die off on the food web wasn’t likely severe.

“I think there are other prey items that are likely redundant with scallops that cushion the impact,” Gobler explained in an email.

Solutions

Stephen Tomasetti with his wife Kate Rubenstein in East Harbor during the summer of 2020.

As for solutions, global warming, while an important effort for countries across the planet, requires coordination, cooperation and compliance to reduce greenhouse gases and lower the world’s carbon footprint.

On a more local and immediate scale, people on Long Island can help with the health of the local ecosystem and the shellfish population by reducing and controlling the chemicals that run off into local waters.

Waste management practices that limit nutrients are “super helpful,” Tomasetti said. “Supporting restoration (like the clam sanctuaries across Long Island that are increasing the filtration capacities of bays) is good.”

Gobler is encouraged by county, state and federal official responses to problems such as the decline in bay scallops, including the declaration of a federal disaster.

Long Island experience

A graduate student at Stony Brook for five years, Tomasetti was pleasantly surprised with the environment.

He had lived in New York City, where he taught high school biology for five years, before starting his PhD.

His perception was that Long Island was “a giant suburb” of New York. That perspective changed when he moved to Riverhead and enjoyed the pine forest, among other natural resources.

He and his wife Kate Rubenstein, whom he met while teaching, enjoyed sitting in their backyard and watching wild turkeys walking through their property, while deer grazed on their plant life.

Initially interested in literature at the University of Central Florida, Tomasetti took a biology course that was a prerequisite for another class he wanted to take. After completing these two biology classes, he changed his college and career plans.

Teaching high school brought him into contact with researchers, where he saw science in action and decided to contribute to the field.

At Hamilton College, Tomasetti has started teaching and is putting together his research plan, which will likely involve examining trends in water quality and temperature. He will move to the University of Maryland Eastern Shore in Princess Anne, MD this fall, where he will be an assistant professor in coastal environmental science.

As for his work with bay scallops and other shellfish on Long Island, Tomasetti looked at the dynamics of coastal systems and impacts of extreme events on economically important shellfish in the area.

Tomasetti is not just a scientist; he is also a consumer of shellfish.  His favorite is sea scallops, which he eats a host of ways, although he’s particularly fond of the pan seared option.

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CSHL Associate Professor Stephen Shea and Postdoc Yunyao Xie in Shea’s lab. Photo from CSHL/2020

By Daniel Dunaief

Good parenting, at least in mice, is its own reward.

No, mice don’t send their offspring to charter schools, drive them to endless soccer and band practices or provide encouragement during periods of extreme self doubt.

What these rodents do, however, protects their young from danger.

When a young mouse wanders, rolls or strays from the nest, it becomes distressed, calling out mostly to its mother, who is the more effective parent, to bring it back to safety.

Responding to these calls, the mother mouse carries the young back to the safety of the nest.

This behavior involves a reward system in a region of the mouse brain called the ventral tegmental area, or VTA. When the mouse effectively retrieves its young, the VTA releases the neurotransmitter dopamine, which is the brain’s way of saying “well done!”

In a paper published in December in the journal Neuron, Cold Spring Harbor Laboratory Associate Professor Stephen Shea and his postdoctoral researcher Yunyao Xie, who worked in the lab from 2019 to 2021, likened the release of dopamine in this area to a neurological reward for engaging in the kind of behavior that protects their young.

The research “proposes a mechanism that shapes behavior in accordance with that reward,” Shea said. The connection between dopamine in a reward system is an established paradigm.

“There was plenty of smoke there,” he said. “We didn’t pull this out of thin air.”

Indeed, in humans, mothers with postpartum depression have disrupted maternal mood, motivation and caregiving. PPD is linked to dysfunction of the mesolimbic dopamine system, which is a neural circuit that involves the VTA, Xie explained.

“Studies using functional magnetic resonance imaging (fMRI) revealed that the reward brain areas including VTA in healthy mothers have higher response to their own babies’ smiling faces than those in mothers with PPD,” Xie added.

What’s new in this research, however, is that it is “a study of how these signals use mechanisms to shape behavior and social interaction,” Shea said.

How the process works

The feedback loop between dopamine in the VTA and behavior involves a cumulative combination of dopamine interactions.

Dopamine is not at its highest level when the mouse mom is engaging in effective pup retrieval.

“Dopamine is shaping future, not current behavior,” Shea said. “If dopamine was driving the mouse on a current trial, a high dopamine level would be associated with high performance. The trial found the opposite: a low dopamine level was associated with high performance in a given trial, and vice versa.”

Like a skater laying her blades down effortlessly and gracefully across the ice after spending hours exerting energy practicing, the mother mouse engaged in the kind of reinforcement learning that required less dopamine to lead to effective pup saving behavior.

As the performance increases, dopamine diminishes over time, as the reward is “more expected,” reflecting a nuanced dynamic, Shea said.

To test the correlation between dopamine levels in the VTA and behavior, Shea and Xie created an enclosure with two chambers. They put a naive virgin female mouse, which they called surrogates, on one side and played specific sounds behind a door on each side of the chamber. The test mice initially had “no experience in maternal behaviors,” Xie explained.

As these surrogates became more experienced by either observing mothers or practicing on their own, the amplitude of the VTA dopamine signals got smaller.

To provide a control for this experiment, Xie monitored a group of naive virgin female mice who spent less time with pups and had to figure out how to retrieve them on their own under similar neurological monitoring conditions. The dopamine signals in this group stayed elevated over days and their performance in maternal behaviors remained poor.

Through these experiments, Xie and Shea concluded that “there is a negative correlation between the dopamine signals in the VTA and their performance in maternal behaviors,” explained Xie.

‘Mind blowing’ moment

In her experiments, Xie used optogenetic tools that allowed her to inhibit the activity of dopaminergic neurons in the VTA with high temporal precision.

Shea appreciated Xie’s hard work and dedication and suggested the discoveries represent a “lot of her creativity and innovation,” he said.

A native of China, Xie said her grandparents used to have a garden in which they taught her the names and morphologies of different plants during her childhood. She enjoyed drawing these plants.

In graduate school, she became more interested in neuroscience. She recalls how “mind-blowing” it was when she learned about the work by 1963 Nobel laureates Alan Hodgkin, Sir Andrew Fielding Huxley and John Eccles, who established a mathematical model to describe how action potentials in neurons are initiated and propagated.

In the study Xie did with Shea, she found that the dopamine signals in the VTA encoded reward prediction errors in maternal behaviors that was consistent with the mathematical model.

In the bigger picture, Xie is interested in how neural circuits shape behaviors. The neural circuits of most natural behaviors, such as defensive behaviors and maternal behaviors are hard-wired, she added.

Mice can also acquire those behaviors through learning. She is interested in how pup cues are perceived as rewards and subsequently facilitate learning maternal behavior. She found a great fit with Shea’s lab, which focuses on the neural mechanism of maternal behavior.

Xie enjoyed her time at Cold Spring Harbor Laboratory, where she could discuss science with colleagues by the bench, at the dining room or at one of the many on site seminars. She also appreciated the opportunity to attend neuroscience seminars with speakers from other schools, which helped expand her horizons and inspire ideas for research.

Next steps

As for the next steps, Shea said he believes there is considerable additional follow up research that could build on these findings. He would like to apply methods that measure the activity in individual neurons. Additionally, with a number of targets for dopamine, he wants to figure out what areas the neurotransmitter reaches and how the signals are used when they get there. More broadly, he suggested that the implications for this research extend to human diseases. 

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From left, Alea Mills and Xueqin Sun Photo from CSHL

By Daniel Dunaief

People have natural defenses against cancer. Proteins like P53 search for unwelcome and unhealthy developments. 

Sometimes, mutations in P53, which is known as the “guardian of the genome,” rob the protein of its tumor fighting ability. In more than seven out of ten cases, the brain tumor glioblastoma, which has a grim prognosis for people who develop it, has an intact P53 protein.

So what happened to P53 and why isn’t it performing its task?

That’s what Cold Spring Harbor Laboratory Professor and Cancer Center member Alea Mills and postdoctoral researcher Xueqin “Sherine” Sun wanted to know.

Starting with the idea that something epigenetic was somehow blocking P53, Sun conducted numerous detailed experiments with the gene editing tool CRISPR-Cas9.

She knocked out parts of the chromatin regulating machinery, which determines whether factors for DNA replication, gene expression, and the repair of DNA damage can access genes and perform their tasks.

The researchers wanted to find “something specific to glioblastoma,” Mills said in an interview. Working with a team of researchers in Mills’s lab, Sun focused on the protein BRD8.

In experiments with mice, Sun and her colleague inhibited this specific protein by destroying the gene that encodes it. That step was enough to stop the tumor from growing and allowed the mouse to live longer.

Mills and Sun published their work in the prestigious journal Nature just before the holidays.

The article generated considerable buzz in the scientific community, where it was in the 99th percentile among those published at the same time in attracting attention and downloads. It also attracted attention on social media platforms like Twitter and LinkedIn.

“We see this as a major discovery, and are not surprised that many others think that the impact is extraordinary,” Mills said. The paper “has the potential of having a significant impact in the future. The work is completely novel.”

While finding a connection between BRD8 and glioblastoma suggests a target for researchers to consider in their search for new glioblastoma treatments, a potential new approach for patients could be a long way off.

“We cannot predict how long it will take to be able to help patients” who have glioblastoma, Mills said.

A promising step

From left, Alea Mills and Xueqin Sun Photo from CSHL

Still, this finding provides a promising step by showing how knocking out the BRD8 protein can enable P53 to gain access to a life threatening tumor.

Sun and Mills said BRD8 and its partners lock down genes that are normally turned on by P53.

“What you inherit from mom and dad is one thing,” said Mills. “How it’s packaged, the epigenetic mechanism that keeps it wrapped up or open, is key in how it’s all carried out within your body.”

By targeting BRD8, Mills and her team opened the chromatin, so P53 could bind and turn on other cancer fighting genes.

After receiving patient samples from Northwell Health, Stanford and the Mayo Clinic, the team studied tissue samples from patients battling glioblastoma. Those patients, they found, had higher concentrations of BRD8 than people without brain cancer.

Researchers and, down the road, pharmaceutical companies and doctors, are careful to make sure removing or reducing the concentration of any protein doesn’t have so-called “off target effects,” which would interfere with normal, healthy processes in cells.

Mills said they tested such actions in the context of neural stem cells in the brain. At this point, removing BRD8 didn’t have any “deleterious consequence,” she said. 

Her lab is working to see the effect of reducing or removing the mouse version, also called Brd8, during development by engineering mice that lack this protein.

Future research

An important next step in this research involves searching for and developing viable inhibitors of the BRD8 protein.

For histone readers like BRD8, researchers look for an active domain within the protein. The goal is to interrupt the interface in their interactions with histones.

In creating molecules that can block the action of a protein, researchers often start with the structure of the protein or, more specifically, the active site.

Sun, who is currently applying for jobs to run her own lab after working at Cold Spring Harbor Laboratory for over eight years, is hoping to purify enough of the protein and determine its structure.

Sun is working on x-ray crystallography, in which she purifies the protein, crystallizes it and then uses x-rays to determine the atomic structure.

Sun described the search for the structure of the protein as an “important direction” in the research. “Once we solve the structure” researchers can focus on drug design, testing and other experiments.

She suggested that the search for a small molecule or compound that might prove effective in inhibiting BRD8 would involve optimizing efficiency and activity.

There is a “long way to go” in that search, Sun added.

She is working to generate a chemical compound in collaboration with other groups.

A long, productive journey

Born and raised in China, Sun has been an active and important contributor to Mills’s lab.

“I’ll miss [Sun] personally as well as in the lab,” Mills said. “She’s been a really good role model and teacher across the Cold Spring Harbor campus and in my lab.”

Mills is “really excited about [Sun’s] future,” she said. “She’ll be really great” at running her own lab.”

For her part, Sun enjoyed her time on Long Island, where she appreciated the natural environment and the supportive culture at Cold Spring Harbor Laboratory.

Sun described her time on Long Island as a “very exciting and satisfying journey.” 

She is determined to study and understand cancer for a number of reasons.

“I know people who died of cancer,” she said. “It’s a terrible disease and it’s urgent to find more efficient therapeutic strategies to stop cancers and improve human heath.”

Sun is also eager to embrace the opportunity to mentor and inspire other students of science.

“Teaching is very important,” she said. She looks forward to helping students grow as professionals to create the “next generation of scientists.”

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From left, Darren Martin and Benjamin Hsiao during a visit to Ram’s Head Inn on Shelter Island. Photo from Darren Martin

By Daniel Dunaief

One person’s garbage is another’s treasure.

Benjamin Hsiao

Benjamin Hsiao has plans to convert garbage — from dog poop to food waste and even cardboard boxes — into the kind of low cost materials and fertilizers that can help combat climate change. His primary target is agricultural residues because of their volume and collectability.  

A Distinguished Professor of Chemistry at Stony Brook University, Hsiao and collaborator Darren Martin at the University of Queensland in Australia recently were awarded one of 16 multidisciplinary grants totaling $11.4 million from the National Science Foundation’s Convergence Accelerator program.

Hsiao, who is the primary investigator, will receive $570,000 over the next nine months in Phase I of the research effort while Martin will collect $180,000 from the Commonwealth Scientific and Industrial Research Organisation in Australia.

The researchers plan to take a zero waste approach to create a circular system that will generate efficiencies, reduce pollution and combat climate change.

The research is focused on creating immediate solutions for current problems, Hsiao said.

The NSF received “many quality submissions” and chose the winners after a rigorous review process, the NSF said.

The proposal from Hsiao and Martin stood out as it is “based on strong science” and make a clear connection to climate change,” NSF officials said.

Hsiao and Martin were delighted with the award and the opportunity not only to make contributions through their own research, but also to work with some of the other recipients.

“I am so pleased on many counts,” Martin explained in an email from Australia. First, Martin and Hsiao, who met at a conference in 2014, followed through on long standing plans to work together. Second, this program, which the NSF started in 2019, is about “early engagement with the market to get feedback on new technologies and platforms.”

Martin suggested it was akin to a “business model boot camp” that includes support and opportunities to pressure test ideas early. “This approach could really accelerate and compress the number of years traditionally taken to see helpful new technologies out in society sooner.”

If they are successful and effective, the scientists can apply for competitive Phase II funding within the year, which includes $5 million for two years and which four or five of the Phase I recipients, who are from a host of A-list research institutions, will receive.

Solids and liquids

Hsiao has been working with solid plant-based waste to create filters that can purify water at a low cost since 2009.

“Nanoscale cellulose materials can be used for water purification,” said Hsiao.

The needles of plants, from shrubs to bushes to feedstock, all have the same cellulosic nanostructure. Hsiao’s technology can convert these different feedstock into similar carboxy-cellulose nanofibers that can be used as purifying agents with negative charge. These filters can remove oppositely charged impurities.

Additionally, Hsiao plans to use solid plant based biomass to create a biogel. Rich in nutrients, the biogel is like the naturally occurring residue that is at the bottom of streams, which is a nutrient-rich mix of dead trees and grass.

The biogel, which is also funded by the NSF, has three applications. First, it can replace soil to grow food or for seed germination, which could be useful to grow food in space. It can also reduce the impact of drought.

Second, it can make a farm more resistant to drought because the material in biogel retains water for a longer period of time and amid drier conditions.

Third, the biogel can induce vegetation or plant growth in drier or sandier areas. Such growth, which could occur along the shoreline of Long Island, could help reduce erosion, Hsiao said. The biogel can also reduce desertification.

Martin explained that Stony Brook University and the University of Queensland have two different biogel platforms that they may hybridize.

Hsiao’s team is “very strong in the chemistry and physical chemistry side,” Martin wrote. “Being based in a Chemical Engineering School, we have been pretty good over the years at finding the most efficient, cost-effective ways to manufacture bio-based materials and composites at scale.”

Fertilizer

Building and expanding on this work, Hsiao is focusing on the liquid waste from biomass as well.

“With the new thinking, we have a circular design,” he said.

Using a nitric acid treatment that is similar to composting and that removes human pathogens, liquid biomass can become an effective fertilizer, which sanitizes animal and human waste.

Nitric acid also releases the existing nutrients in feedstock, which provides more nitrogen and phosphorous to help plants grow.

The ideal treatment would involve providing a controlled amount of fertilizer each day, Hsiao explained.

Farmers, however, can’t put that kind of time and resources into spraying their fields. Instead, they spray a fertilizer that becomes run off when it rains. Artificial intelligence and robots can deploy fertilizer in a more cost effective manner.

The nitrogen from the run off winds up in streams and other water bodies, where it can cause a process called eutrophication, leading to the kind of algal blooms that rob oxygen of water, making it more difficult for desirable marine life to survive and close beaches to swimming.

By using an efficient process for producing fertilizer that includes taking the inedible parts of plants, and making them a part of the circular process, run off could decrease by “half or even more,” Hsiao said.

Martin added that he and Hsiao have, in the back of their minds, a plan to create scalable fertilizer for single family farms in developed and developing nations.

“Our modeling may indeed show that ‘distributed manufacturing’ of the biogels from agricultural residues using a ‘mobile factory placed on the farm’ may be the smartest way to get there,” Martin explained. “This is exactly the sort of question the Convergence Accelerator is designed to test.”

Martin said that he hopes this technology lead to an array of jobs that support farming under a variety of circumstances.

Sorghum, which is one of his favorite crops, is ultra resilient and is of increasing global importance. Its ability to withstand environmental stress and thrive on low input marginal farmland make it the ‘golden crop of the future,’ Martin added.

This crop makes it an “attractive option to transform infertile land into profitable agrivoltaic farms supplying raw materials for emerging non-foo markets such as these biogels,” Martin wrote.

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Kaushik Mitra. Photo from SBU

By Daniel Dunaief

From over 66 million miles away, they take pieces of a puzzle and try to fill in the picture. In addition to looking at what’s there now, they also use clues to look back in time.

For the last eight years, researchers suspected that the presence of manganese oxide suggested that Mars had atmospheric oxygen billions of years ago. That’s because, on Earth and in water, oxygen converts manganese to manganese oxide.

Such a process whets the appetite in the search for prehistoric life on Mars that, like so many creatures on Earth, breathed oxygen.

The Martian story, however, involves puzzle pieces that came together in a different way.

In a paper published last month in Nature Geosciences, Kaushik Mitra, a postdoctoral researcher at Stony Brook University in the Department of Geosciences, suggested through geochemical modeling that oxygen on Mars, even if it was abundant billions of years ago, wouldn’t have created manganese oxide.

That’s because the water on Mars was acidic, with a pH of less than 5.5, which is below the neutral 7 level. Under those conditions, oxygen wouldn’t oxidize manganese.

Using experiments, Mitra showed that the manganese oxide could form in acidic water in other ways.

“Mars and Earth fluid conditions are very different,” Mitra said. “What I showed in my experiments is that oxygen in acidic fluids will not be able to oxidize manganese.”

Mitra conducted research that were part of his PhD work in Jeffrey Catalano’s lab at Washington University in St. Louis, MO. 

Taking oxygen out of the picture, Mitra also detailed previous efforts that might explain the presence of manganese oxide, such as ultraviolet light. The manganese oxides formed in sub surface fractures, which this light couldn’t reach.

So, what happened?

“If the originally proposed (and plausible) oxidants were not the cause, there had to be some culprit,” Mitra explained in an email. “So there had to be some other oxidant.”

Bromine and chlorine

Enter chlorine and bromine, which are both halogens, or reactive non-metallic elements.

No one had looked into the potential of oxyhalogen compounds to produce manganese oxides in Mars-like conditions.

Bromate, which is a bromine atom attached to three oxygen atoms, can oxidize manganese in orders of magnitude faster than other oxidants, particularly in acidic conditions. Chlorate, which is also a chlorine atom attached to three oxygen atoms, alone can’t do it, but, with a small quantity of bromate, can create quantities of manganese oxide.

The oxygen attached to chlorine and bromine can come from water or any other ingredient, and doesn’t need oxygen gas to form.

“People didn’t really appreciate until [Mitra’s] paper came along that [manganese] is highly reactive towards these oxyhalogen compounds that he has been working with, so it gives us a whole new way to think about how [manganese-oxides] might form on Mars,” Joel Hurowitz, Associate Professor in Geosciences at Stony Brook University, explained in an email. Mitra has been working as a postdoctoral researcher in Hurowitz’s lab since November of 2021.

While oxygen may not have caused the change in manganese, the search for Martian life doesn’t end here. Some organisms, including on Earth, don’t need oxygen to survive.

Extremophiles, which can survive in the Great Salt Lake, the Dead Sea, and around hydrothermal vents at the bottom of the ocean, do not need oxygen.

Mitra’s research “teaches us to be cautious in our astrobiology strategy and consider all the alternative possibilities,” Hurowitz explained. “It is entirely possible that Martian life did not depend on [oxygen] or produce [oxygen] as a by-product of its metabolism.”

For the first two billion years of life on Earth, high concentrations of oxygen would have been toxic to microbial life, Hurowitz added.

To be sure, just because halogens like chlorine and bromine can explain the presence of manganese oxide instead of oxygen doesn’t rule out the possibility that Mars had oxygen.

Paradigm shift

Mitra has continued his exploration of the importance of oxyhalogen species in Hurowitz’s lab to improve the understanding of how they interact with various mineral phases that are considered key records of paleoenvironmental conditions on Mars.

On a more immediate scale, Mitra’s approach to his work has created something of a paradigm shift in Hurowtiz’s lab. When the postdoctoral researcher arrived at Stony Brook, he immediately started between 30 and 40 separate experiments within the span of a month. 

This effort contrasts with the attempt to create one perfect, completely controlled experiment that can take months of time that might be lost if something went wrong.

“It has actually changed the way that I think about experimental project methods,” Hurowitz wrote. “It’s a great new way to explore geochemistry and my students are adopting many of the approaches he’s brought into the lab.”

Hurowitz described Mitra as a “great addition” to the group.

A passion for science

A native of Bhagalpur, India, which is in the state of Bihar, Mitra had a strong interest in chemistry during his youth.

He attended the Indian Institute of Technology Kharagpur, where he earned an integrated Bachelors and Masters of Science Degree in Applied Geology.

Mitra, who currently lives in Centereach, is fluent in English, Hindi and Bengali and is learning Nepali, the native language of his spouse Priyanka Sharma who is from Nepal.

Sharma, who is an Indian Nepali, is applying for graduate school in English Literature and Comparative Literature.

An avid reader whose favorite genre is philosophy, Mitra is currently reading Fyodor Dostoesky and Friedrich Nietzsche.

A long distance runner, Mitra ran a 10K in Queens last year and would like to run a half marathon in the spring.

He will likely finish his postdoctoral research by next year, at the latest, at which point he will apply for a faculty job.

Passionate about teaching, Mitra has been a committed mentor to other students at Stony Brook, Hurowitz said.

Mitra created a YouTube channel for geology and geochemistry undergraduates and graduates in which he shares lessons about geoscience and chemistry in English and Hindi, which is available at https://www.youtube.com/@kmicalmindset6322.

“I am trying to inspire more people to come into planetary geoscience,” he said, especially undergraduates.

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Nandita Kumari at the 53rd Lunar and Planetary Science Conference in Woodlands, Texas in March of 2022. Photo by Delia Enriquez Draper from the Lunar and Planetary Institute

By Daniel Dunaief

Some day in the not too distant future, an astronaut may approach rocks on the moon and, with a handheld instrument, determine within minutes whether the rock might have value as a natural resource or as a source of historical information.

That’s the vision Nandita Kumari, a fourth-year graduate student in the Department of Geosciences in the College of Arts and Sciences at Stony Brook University, has.

In the meantime, Kumari was part of a multi-institutional team that recommended two landing sites in the moon’s south polar region for future Artemis missions. 

Nandita Kumari at a San Francisco Volcanic Field, where she was doing stress and strain measurements of cinders. Photo by Saurabh Subham.

The group, which included students from the University of Arizona, the University of California Los Angeles, and the University of Buffalo, used several criteria to recommend these two sites.

They looked at the resources that might be available, such as water and rocks, at how long the areas are in sunlight and at how the features of the land, from the slope of hills to the size of boulders, affects the sites accessibility.

“These two sites ended up fulfilling all these criteria,” Kumari said. Models suggest water might be present and the regions are in sunlight more than 80 percent of the time, which is critical for solar-powered devices.

The group used high-resolution data from the Lunar Reconnaissance Orbiter to create a map of all the rocks and to model the geological diversity of the site. They used infrared images to gather data from areas when they were dark. They also added temperature readings.

To the delight of the team, NASA selected both of the sites as part of a total of 13 potential landing locations.

Planetary scientist David Kring advised the group during the process. Kring has trained astronauts and worked on samples brought back from the Apollo missions.

At the end of the first year of her PhD, Kumari received encouragement to apply for the virtual internship with Kring from Stony Brook Geosciences Professor Tim Glotch, who runs the lab where she has conducted her PhD work.

Putting a number on it

Kumari said her thesis is about using machine learning to understand the composition of resources on the moon. She would like to use artificial intelligence to delve deeply into the wealth of data moon missions and observations have been collecting to use local geology as a future resource.

“Instead of saying something has a ‘little’ or a ‘lot’” of a particular type of rock that might have specific properties, she would like to put a specific numerical value on it.

An engineer by training, Kumari said she is a “very big fan of crunching numbers.”

Since joining the lab, Kumari has become “our go-to source for any type of statistical analysis me or one of my other students might want to conduct,” Glotch explained.

The work Kumari has done provides “large improvements over traditional spectroscopic analysis techniques,” Glotch added.

In examining rocks for silicic properties, meaning those that contain silicon, most scientists describe a rock as being less or more silicic, Kumari said.

“It’s difficult to know whether 60 percent is high or 90 percent is high,” she added. Such a range can make an important difference, and provides information about history, formation and thermal state of the planet and about potential resources.

With machine learning that trains on data collected in the lab, the model is deployed on orbiter data.

The machine learning doesn’t stop with silica. It can also be extended to search for helium 3 and other atoms.

Understanding and using the available natural resources reduces the need to send similar raw materials to the moon from Earth.

“There has to be a point where we stop” transporting materials to the moon, said Kumari. “It’s high time we use modern practices and methods so we can go through really large chunks of data with limited error.”

The machine learning starts with a set of inputs and outputs, along with an algorithm to explain the connection. As it sorts through data, it compares the outputs against what it expects. When the data doesn’t match the algorithm, it adjusts the algorithm and compares that to additional data, refining and improving the model’s accuracy.

A love for puzzles

Kumari, who grew up in Biharsharif, India, a small town in the northern state of Bihar, said this work appeals to her because she “loves puzzles that are difficult to solve.” She also tries to find solutions in the “fastest way possible.”

Kumari was recently part of a field exploration team in Utah that was processing data. The team brought back data and manually compared the measurements to the library to see what rocks they had.

She wrote an algorithm that provided the top five matches to the spectroscopic measurements the researchers found. Her work suggested the presence of minerals the field team didn’t anticipate. What’s more, the machine provided the analysis in five minutes.

The same kind of analysis can be used on site to study lunar rocks.

“When astronauts go to the moon, we shouldn’t require geology experts to be there to find the best rocks” she said. While having a geologist is the best-case scenario, that is not always possible. “Anyone with a code in their instruments should be able to decide whether it is what they’re looking for.”

As for her interest in space travel, Kumari isn’t interested in trekking to the moon or Mars.

While she believes the moon and Mars should be a base for scientific experiments, she doesn’t think people should focus on colonizing either place.

Such colonization ideas may reduce the importance of working on the challenges humans have created on Earth, including climate change.

“You can’t move to Mars,” Kumari said. The litmus test for that occurred during Covid, when people had to isolate.

“If we couldn’t stay in our homes with all the comfort and everything, I do not see a future where this would be possible with stringent constraints on Mars,” she added.

An advocate for women in STEM fields, Kumari said women should pursue scientific careers even if someone else focuses on their mistakes or tries to break their confidence.

“The only way to stop this from happening is to have women in higher places,” she explained. “We should also be supportive of each other and grow together.”

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