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Power of 3

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Arkarup Banerjee. Photo ciourtesy of CSHL

By Daniel Dunaief

Brain cells don’t always have easily discovered roles, the way various instruments do in an orchestra.

Sometimes, different cells share a function, making it possible to perform various tasks or to process information from the environment, while other times, different cells play their own part in making it possible for an organism to optimize its circuitry to act and react on the world.

So it is for the tufted and mitral cells of land based vertebrates, which are part of the olfactory system, sending signals to the brain about the odors and triggering thoughts about moving towards a desired food or away from the scent of a predator. In many studies, the names have been used interchangeably, as scientists were not sure how to separate them.

Florin Albeanu. Photo courtesy of CSHL

Researchers have spent considerable time studying mitral cells, which project into a region of the brain called the piriform cortex. These cells are nicely organized into one layer, which makes them easy to identify and are bigger in size compared to tufted cells.

Mitral cells, which have been the celebrated stars of the olfactory system, are easier to see and sort out than their nasal cousins, the tufted cells which, by contrast, are slightly smaller.

Recently, two scientists at Cold Spring Harbor Laboratory, Florin Albeanu, an Associate Professor, and Arkarup  Banerjee, an Assistant Professor, published a study that suggested there’s more than meets the eye, or, maybe, the nose, with these tufted cells.

Tufted cells, it turns out, are better at recognizing smells than mitral cells and are critical for one of two parallel neural circuit loops that help the brain process different odor features, according to a study the scientists published in the journal Neuron at the end of September.

“People had assumed mitral cells were very good at” differentiating odor, but “tufted cells are better,” Albeanu said. “How they interact with each other and what the mitral cells are computing in behaving animals remains to be seen.”

Albeanu and Arkarup, who had performed his PhD research in Albeanu’s lab before returning to CSHL in 2020, exposed mice to different odors, from fresh mint to bananas and at different concentrations. They chose these compounds because there are no known toxic effects. The scientists also screened for compounds that elicited strong responses on the dorsal surface of the olfactory bulb that they could access using optical imaging tools.

It is hard to distinguish mitral and tufted cells when doing recordings. Optical imaging, however, enabled them to see through layers and shapes, if they were recording activity in a particular type of cell.

So, Albeanu asked rhetorically, “why is this exciting?”

As it turns out, these two types of cells project to different regions of the brain. Mitral cells travel to the piriform cortex, while tufted cells travel to the anterior olfactory nucleus.

It appears at this point that tufted cells are more likely to share information with other tufted cells, while mitral cells communicate with other mitral cells, as if the olfactory system had two parallel networks. There may yet be cross interactions, Albeanu said.

Mitral cells may be part of a loop that helps enhance and predict smells that are important for an animal to learn. Tufted cells, however, appear superior to mitral cells in representing changes in odor identity and intensity. By flagging the tufted cells as sources of olfactory information, the researchers were able to suggest a different combination of cells through which animals detect smells.

“A large fraction of people in the field would expect that mitral cells and the piriform complex are representing odor identity more so than the tufted cells and the anterior olfactory nucleus, so this is the surprise,” Albeanu explained in an email. Thus far, the reaction in the research community has been positive, he added. 

Throughout the review process, the researchers encountered natural skepticism.

“It remains to be determined how the findings we put forward hold when mice are engaged in odor trigger behavior” as odors are associated with particular meaning such as a reward, an lead to specific actions,” Albeanu explained. “This is what we are currently doing.”

Albeanu added that a few different streams of information may be supported by tufted and mitral cells, depending on the needs of the moment.

Arkarup Banerjee. Photo ciourtesy of CSHL

The study that led to this work started when Banerjee was a PhD student in Albeanu’s lab. Albeanu said that a postdoctoral fellow in his lab, Honggoo Chae, provided complementary work to the efforts of Banerjee in terms of data acquisition and analysis, which is why they are both co-first authors on the study.

For Banerjee, the work with these olfactory cells was an “echo from the past,” Albeanu added. 

As for where the research goes from here, Albeanu said future questions and experiments could take numerous approaches.

Researchers are currently looking for markers or genes that are expressed specifically and differentially in mitral or tufted cells and they have found a few potential candidates. While some markers have been found, these do not sharply label all mitral only versus all tufted cells only.

One of the confounding elements to this search, however, is that these cells have subtypes, which means that not every mitral cell has the same genetic blueprint as other mitral cells.

Another option is to inject an agent like a virus into the piriform cortex and assess whether boosting or suppressing activity in that region in the midst of olfaction alters the behavioral response.

Additionally, researchers could use tools to alter the activity of neurons during behavior using optogenetic approaches, inducing or suppressing activity with cell type specificity and millisecond resolution.

Albeanu would like to test speculation about the roles of these cells in action, while a mice is sampling smells he presents.

By observing the reactions to these smells, he could determine an association between rewards and punishment and anything else he might want to include.

The upshot of this study, Albeanu said, is that an objective observer would have much less trouble extracting information about the identity and intensity of a smell from a tufted cell as compared with a mitral cell.

Tufted cells had been “slightly more mysterious” up until the current study.

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Mercy Baez. Photo by Joseph Rubino/ BNL

By Daniel Dunaief

She is a greeter, a corporate concierge, a facilitator, a point of contact for people traveling thousands of miles, a Spanish translator, an important contact in case of emergencies, and whatever else visitors need.

While Mercy Baez, who was promoted to User Program Coordinator for the National Synchrotron Lightsource II and the Laboratory for BioMolecular Structure at Brookhaven National Laboratory early in October, wears many hats, one of the only ones she doesn’t wear is scientist, although that doesn’t keep her from appreciating and taking pride in the research conducted at the Department of Energy facility.

“We’re helping them and they are helping the world,” Baez said.

BNL has a steady stream of users who apply for time at the various research facilities at the national laboratories. 

Baez is specifically responsible for providing a wide range of support and services to the NSLS II and the LBMS. Users, which is how BNL describes potential visiting scientists who conduct research at the lab’s facilities, submit proposals to her office, which then distributes them to a proposal review panel.

When visiting scientists learn that their work, which includes monitoring batteries as they function and searching for fine structural sites in the molecular battle against pathogens, has earned a high enough score to receive coveted time on the lab’s instruments, they prepare for their visit by interacting with Baez and her current team of four by getting registered and approved for access.

Baez offers soup to nuts guidance that often also includes helping users literally find soup, nuts and numerous other items. Baez ensures that users take any necessary training courses, provides guidance regarding registering for on site access to BNL, provides information on the steps or items necessary when they arrive, helps find nearby hotels, coordinate travel to and from the lab and, if necessary, secures places to stay if they miss their planes, get snowed in or have other unforeseen changes in their schedules.

As of October 1st, visitors also have to have some type of active shooter training to access the lab’s facilities. Currently, users are required to take five training courses. Last week, the lab decided to incorporate active shooter training into one of these other training courses.

The lab has always had routine emergency training courses and drills for lab employees. With the changing times and current events, the lab is looking to equip users for such emergencies. The lab hopes never to have to use this training, but if such an event occurs, staff and users will know how to handle such a situation.

In addition to training to help users prepare to visit the facility, Baez provides visitors with a host of on site facilities, including adaptors in case they are using European electronics that don’t connect with the outlets, laptops in case the computer a scientist brought isn’t working, conference rooms for impromptu meetings, and dorm rooms for a respite while running time-intensive experiments.

BNL hosts employee resource groups including the African American Advancement Group, the Asian Pacific American Association, the Brookhaven Veterans Association, Brookhaven Women in Science, the Early Career Resource Group, the Pride Alliance and the Hispanic Heritage Group. Baez said the lab tries to involve users and visitors in as many cultural and social events as possible, which include outings to dinners, plays and cultural virtual cooking classes.

In September, Baez participated in the Port Jefferson Dragon Boat Race Festival which the Asian Pacific  American Association sponsored. 

Baez, whose mother is from Puerto Rico and whose father is from Ecuador, is a member of the Hispanic Heritage Group.

A people person

A member of the user offices since 2003, Baez had recently been responsible for coordinating conferences, workshops, and training courses, including financial and logistical aspects of the events for NSLS-II and the LBMS. She had been functioning as the user program coordinator since January, when Gretchen Cisco retired. Baez feels fortunate to have worked with Cisco since she joined NSLS in 2005.

A self-described “people person,” Baez said she loves the opportunity to interact with scientists from all over the world. She particularly appreciates the chance to get to know about other cultures and has added destinations to her travel itinerary from speaking with visitors. She is hoping to travel to Morocco and Peru next year and is hoping to travel to Japan and a few other countries in the near future.

Coming from a Latina family that tends to be loud and outspoken and whose family gatherings often includes more than 30 people, she has learned to speak in a softer voice, particularly with people from other cultures or backgrounds.

She also has a tendency to speak quickly and has learned to slow the pace down so visitors who haven’t interacted with her can understand what she’s saying.

A resident of Medford, which is a ten-minute drive from the lab, Baez has a son Xzavier and a granddaughter Francesca. She is excited for the upcoming arrival of her second granddaughter in November.

When she’s not at the lab, she uses her leisure time to go hiking, fishing and camping.

With her then teenage son in tow, she went to the jungle of Belize for a survival course, where they learned how to catch their own food, build shelters, and harpoon fish. She also learned which plants are safe to eat and which are poisonous.

While her work responsibilities can be hair-raising, particularly in emergencies, she “loves the feeling that I was able to help a scientist, whether to get him or her on site or in an emergency,” she said. Knowing that she’s a part of making all this science happen makes her day and job rewarding, she said.

Baez has had some requests from scientists who have wanted cultural foods, such as Turkish or vegan dishes, that might be harder to find, particularly during off hours.

Around Thanksgiving each year, some visitors have asked if they can hunt wild turkeys at BNL, which is located within the Pine Barrens and has turkeys and deer wandering on site. She has told those users that the lab does not allow hunting.

Hunting aside, Baez said she is “here to help [users] do what they need to do.”

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From left, K. Barry Sharpless and John Moses. Photo from CSHL

By Daniel Dunaief

K. Barry Sharpless changed John Moses’s life. And that’s before Moses even started working as a postdoctoral researcher in Sharpless’s lab.

When Moses, who is the first chemist to work at Cold Spring Harbor Laboratory in its 132-year history, was earning his PhD in chemistry at Oxford, he read an article that Sharpless co-authored that rocked his world.

Nicknamed the “click manifesto” for introducing a new kind of chemistry, the article, which was published in Angewandte Chemie in 2001, was “one of the greatest I’ve ever read,” Moses said, and led him to alter the direction of his research.

Moses walked into the office of the late chemist Sir Jack Baldwin at Oxford, who was Moses’s PhD advisor, and announced that Sharpless, a colleague of Baldwin’s at the Massachusetts Institute of Technology, was the only chemist he wanted to work with in the next phase of his career.

Baldwin looked at Moses and said, in a “very old-fashioned gangster English, ‘That shows you’ve got some brains,’” recalled Moses.

Sharpless was important not only to Moses’s career, but also to the world.

Recently, Sharpless, who is the W.M. Kepp Professor of Chemistry at Scripps Research, became only the fifth two-time recipient of the Nobel Prize.

Sharpless will share the most recent award, which includes a $900,000 prize, with Carolyn R. Bertozzi, the Anne T. and Robert M. Bass Professor in the School of Humanities and Sciences at Stanford University, and Morten P. Meldal, professor at the University of Copenhagen, for the invention of a type of chemistry that has implications and applications from drug discovery and delivery, to making polymers, to developing anti cancer treatments.

The way click chemistry works is that chemists bring together catalysts and reagents, often attached to sulfur or carbon, that have a high level of specific attraction for each other. The click is like the sound a seat belt makes when secured, or the click a bike helmet lock makes when the two units are connected.

Scientists have often described the click reaction as being akin to LEGO blocks coming together, with an exact and durable chemical fit.

Natural product synthesis is generally challenging and often requires complex chemistries that are not always selective. This type of chemistry can produce side reactions that create unwanted byproducts and require purification.

Click reactions, by contrast, are selective and reliable and the products are generally easy to purify. Sometimes, purification is as simple as a water wash.

“It’s a democratization of synthetic chemistry,” Moses said.

Moses said biologists have performed click reactions. Chemists have developed click tablets that can be added to a reaction to create a plug and play system.

Moses described the reactions in click chemistry as “unstoppable” and suggested that they are part of a “domino rally” in which a latent build up of reactivity can create desired products with beneficial properties.

Moses, who arrived at CSHL in 2020, has collaborated with several researchers at the famed lab. He is submitting his first collaborative paper soon with Dr. Michael Lukey, who also started in 2020 and performed his PhD at Oxford, and Dr. Scott Lyons. He is also working on a New York State Biodefense funded project to create shape shifting antibiotics that can keep up with drug resistance pathogens. 

He has collaborated with Cancer Center Director David Tuveson to develop a new ligand to target a protein important in pancreatic cancer. Moses said they have a “very exciting” lead compound.

Early resistance

While the Nobel Prize committee recognized the important contribution of this approach, the concept met with some resistance when Sharpless introduced it.

“When [Sharpless] submitted this, the editor called colleagues and asked, ‘Has Barry gone crazy?’” Moses said.

Some others in the field urged the editor to publish the paper by Sharpless, who had already won a Nobel Prize for his work with chirally catalyzed oxidation reactions.

Still, despite his bona fides and a distinguished career, Sharpless encountered “significant resistance” from some researchers. “People were almost offended by it” with some calling it “old wine in new bottles,” Moses said.

In 2007, Moses attended a faculty interview at a “reasonably good” university in England,. where one of his hosts told him that click chemistry is “just bulls$#t!”

Moses recognized that he was taking a risk when he joined Sharpless’s lab. Some senior faculty advised him to continue to work with natural product synthesis.

In the ensuing years, as click chemistry produced more products, “everyone was using it and the risks diminished quickly,” Moses added.

Unique thought process

So, what is it about Sharpless that distinguishes him?

Moses said Sharpless’s wife Janet Dueser described her husband as someone who “thinks like a molecule,” Moses said.

For Moses, Sharpless developed his understanding of chemistry in a “way that I’ve never seen anyone else” do.

Moses credits Dueser, who he described as “super smart,” with coining the term “click chemistry” and suggested that their partnership has brought together his depth of knowledge with her ability to provide context.

Moses believes Sharpless “would admit that without [Dueser], his career would have been very different! In my opinion, [Dueser] contributed immeasurably to click chemistry in so many ways.”

Indeed, click chemistry won a team prize from the Royal Society of Chemistry last year in which Dueser was a co-recipient.

As for what he learned from working with a now two-time Nobel Prize winner, Moses said “relinquishing control is very powerful.”

Moses tells his research team that he will never say “no” to an innovative idea because, as with click chemistry, “you never know what’s around the corner.”

Moses said Sharpless is a fan of the book “Out of Control” by Kevin Kelly, the co-founder of Wired Magazine. The book is about the new biology of machines, social systems and the economic world. Sharpless calls Kelly “Saint Kevin.”

On a personal level, Sharpless is “humble and a nice person to talk to” and is someone he would “want to go to a pub with.”

Moses believes Sharpless isn’t done contributing to chemistry and the world and anticipates that Sharpless, who is currently 81 years old, could win another Nobel Prize in another 20 years.

An inspirational scientist, Sharpless ” is “that kind of person,” Moses said.

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Peter Westcott, on right, in the lab with technicians Zakeria Aminzada, on left and Colin McLaughlin, center. Photo by Steven Lewis

By Daniel Dunaief

When Peter Westcott was growing up in Lewiston/Auburn, Maine, his father Johnathan Harris put the book “Human Genome” on his bed. That is where Westcott, who has a self-described “obsessive attention to detail,” first developed his interest in biology.

Westcott recently brought that attention to detail to Cold Spring Harbor Laboratory, where he is an assistant professor and Cancer Center member. He, his wife Kathleen Tai and their young children Myles and Raeya moved from Somerville, Massachusetts, where Westcott had been a postdoctoral fellow at the Koch Institute of Integrative Cancer Research at the Massachusetts Institute of Technology.

Westcott will take the passion and scientific hunger he developed and honed to the famed lab, where he plans to continue studies on colon cancer and the immune system.

“A lot of things attracted me to Cold Spring Harbor Laboratory,” said Westcott who had been to the lab during conferences, joining three Mechanisms and Models of Cancer meetings, and appreciated that the small size of the lab encourages collaboration and the sharing of ideas across disparate fields.

At this point, Westcott, who purchased a home in Dix Hills and started on campus on September 1st, has two technicians, Zakeria Aminzada and Colin McLaughlin working with him. He will be taking on a graduate rotation student from Stony Brook University soon and would also like to add a postdoctoral researcher within about six months. He plans to post ads for that position soon. 

Research directions

Westcott said his research has two major research directions.

The first, which is more translatable, involves looking at how T cells, which he described as the “major soldiers” of the immune system, become dysfunctional in cancer. These T cells balance between attacking unwanted and unwelcome cells relentlessly, disabling and destroying them, and ignoring cells that the body considers part of its own healthy system. When the T cells are too active, people develop autoimmunity. When they aren’t active enough, people can get cancer.

“Most cancers, particularly the aggressive and metastatic ones, have disabled the immune response in one way or another, and it is our focus to understand how so we can intervene and reawaken or reinvigorate it,” he explained.

During cancer development, T cells may recognize that something on a tumor is not healthy or normal, but they sometimes don’t attack. Depending on the type of genetic program within the T cells that makes them tolerant and dysfunctional, Westcott thinks he can reverse that.

A big push in the field right now is to understand what the genetic programs are that underlie different flavors of dysfunction and what cell surface receptors researchers can use as markers to define T cells that would allow them to identify them in patients to guide treatment.

Westcott is taking approaches to ablate or remove genes called nrf4a 1, 2 and 3. He is attacking these genes individually and collectively to determine what role they play in reducing the effectiveness of the body’s immune response to cancer.

“If we knock [some of these genes] out in T cells, we get a better response and tumors grow more poorly,” he said.

Westcott is exploring whether he can remove these genes in an existing T cell response to cause a regression of tumor development. He may also couple this effort with other immunotherapies, such as vaccines and agonistic anti-CD40 antibody treatment.

As a second research direction, Westcott is also looking more broadly at how tumors evolve through critical transitions. Taking an evolutionary biology perspective, he hopes to understand how the tumors start out as more benign adenoma, then become malignant adenocarcinoma and then develop into metastatic cancer. He is focusing in particular on the patterns of mutations and potential neoantigens they give rise to across the genome, while concentrating on the immune response against these neoantigens.

Each tumor cell is competing with tumor cells with other mutations, as well as with normal cells. “When they acquire new mutations that convey a selective advantage” those cells dominate and drive the growth of a tumor that can spread to the rest of the body, Westcott said.

Using a mouse model, he can study tumors with various mutations and track their T cell response.

T cells tend to be more effective in combating tumors with a high degree of mutations. These more mutated tumors are also more responsive to immunotherapy. Westcott plans to study events that select for specific clones and that might shift the prevalence, or architecture, of a tumor.

Some of the work Westcott has done has shown that it is not enough to have numerous mutations. It is also important to know what fraction of the cancer cells contain these mutations. For neoantigens that occur in only a small fraction of the total cells in the tumor, the T cell responses aren’t as effective and checkpoint blockade therapy doesn’t work.

He wants to understand how the T cell responses against these neoantigens change when they go from being subclonal “to being present in most or all of the tumor cells,” he explained. That can occur when a single or few tumor cells acquire a selective advantage. His hypothesis is that these selective events in tumor progression is inherently immunogenic. \

By exploring the fundamental architecture of a tumor, Westcott hopes to learn the mechanisms the tumor uses to evade the immune system.

Ocean breeze

As Westcott settles in at CSHL, he is excited by the overlap between what he sees around the lab and the Maine environment in which he was raised.

“Looking out the window to the harbor feels like New England and Maine,” he said. “It’s really nostalgic for me. Being near the ocean breeze is where I feel my heart is.”

Before his father shared the “Human Genome” book with him, Westcott was interested in rocks and frogs. In high school, his AP biology teacher helped drive his interest in the subject by encouraging discussions and participation without requiring her students to repeat memorized facts. The discussions “brought to life” the subject, he said.

As for his work, Westcott chose to study colon cancer because of its prevalence in the population. He also believes colon cancer could be a model disease to study all cancers. By understanding what differentiates the 12 percent of cases that are responses to immunotherapy from the remainder that don’t respond as well to such approaches, he hopes to apply these lessons to all cancer.

“There is a huge, unmet need,” he said.

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Caroline Mota Fernandes Photo by Jonas Nascimento Conde

By Daniel Dunaief

Fungal infections represent a significant health risk for some patients, killing about 1.5 million people globally each year. Doctors struggle to provide medical help for some of these patients, especially those whose weakened immune systems offer insufficient protection against developing pathogens.

Invasive fungal infections, which people typically contract by inhaling them as spores, account for about half of all AIDS-related deaths.

Maurizio del Poeta, Distinguished Professor at the Renaissance School of Medicine at Stony Brook University, has been studying ways to boost the body’s defenses against these potentially deadly infections, even among people with weakened immunities.

Recently, Caroline Mota Fernandes, a postdoctoral researcher in del Poeta’s lab, published research in the journal mBIO, a publication of the American Society for Microbiology, that demonstrated that a heat-killed, mutated version of the fungus Aspergillus conveyed protection in an animal model of an immunocompromised individual.

“The biggest news is that we can simply use the ‘autoclaved’ mutated version,” explained del Poeta in an email. “This version cannot be more dead!”

An autoclave is like a scientific oven: it raises the temperature or pressure. In this case, it can kill the mutated fungus, leaving only the mutated signal that primes the immune system.

The mutated and heat-killed version of the fungus, however, still provided full protection in a condition in a model of a weakened immune system.

“That means this formulation is highly stable and resistant to heat degradation,” del Poeta added.

Del Poeta’s lab had conducted similar research with another fungus called Cryptococcus.

By demonstrating that this approach also works with Aspergillus, del Poeta said the result “validates the cryptococcal vaccine (after all, it uses a mutant of the homolog gene, Sg11 in Crypto and SglA in Aspergillus.”

It also shows that protection exists under an additional type of immunodepression that is different from the one used in the cryptococcal vaccine.

The encouraging results, while in the preliminary stages, are relevant not only for immunocompromised people in general, but also for those who have been battling Covid, as Aspergillus was the cause of death for many patients during the worst of the pandemic.

Homologous genes

Del Poeta’s lab has focused on genes that catalyze the breakdown of steryl glucosides, which scientists have also studied in the context of plants. Crops attacked by various fungi become less productive, which increases the need to understand and disrupt these pathways.

“Folks working with plants started observing that these molecules had some kind of immunomodulatory property,” said Fernandes. “That’s where the idea of this steryl glucosides, which also is medicating fungal virulence, came from.”

The mutation Fernandes studied removed the sterylglucosidase gene sglA. Without the enzyme that breaks up the steryl glucose, the fungus had less hypha, which are necessary for the growth of the fungus. The mutation also changed the cell wall polysaccharides. Mice vaccinated with this heat-killed mutation had a one hundred percent survival rate in response to exposure to the live fungus.

“What was a very great achievement of our work was getting 100 percent protection,” said Fernandes. For immunocompromised people for whom a live attenuated fungus might threaten their health, the effectiveness of the heat-killed mutation proved especially promising.

In the experiment, she administered the vaccine 30 days before exposure, while providing boosters as often as every 10 days.

Fernandes, who started her post doctoral research in del Poeta’s lab in 2018, said several questions remain. “After this study, we are going to try to characterize exactly how this strain induces the immunity and protection to a secondary challenge of Aspergillus,” she said. Dr. Veronica Brauer, another post doctoral researcher in del Poeta’s lab, is conducting this research.

At this point, it’s unclear how long protection against a fungal infection might last.

“For us to estimate the duration of the protection, we have to have a more specific understanding of which immune components are involved in the response,” said Fernandes.

As of now, the mice vaccinated with the mutated and heat-killed fungus had no off target effects for up to 75 days after vaccination.

Fernandes is also working to characterize the mechanism of action of a new class of antifungal drugs previously identified by the lab, called acylhydrazones. She hopes to identify a new virulence protein in Cryptococcus as well.

Collaboration origins

Fernandes, who was born and raised in Rio de Janeiro, Brazil, first worked in del Poeta’s lab in 2013, while she was conducting her PhD research at Federal University of Rio de Janeiro. She was studying antifungal peptides and explained to the Brazilian government why coming to Stony Brook would contribute to her research.

Fernandes started studying fungi when she was in her second year of college at Federal University of Rio de Janeiro.

The daughter of two chemists, Fernandes said she grew up in a house in which she had pH strips, which she used to test the acidity of shampoo, water and anything else she could test. She also entered numerous science fairs.

Fernandes met her husband Jonas Conde, who is a virologist at Stony Brook University and who has studied Covid-19, when they were in nearby labs during their PhD research.

Residents of Port Jefferson, Fernandes and Conde have a four-month-old son named Lucas.

Having a child “motivates me to be better in my work and to set an example for him to be committed in doing some good for other people,” Fernandes said.

Del Poeta described Fernandes as being “extremely effective” in managing her time and has “extraordinary motivation.” He appreciates her commitment to her work, which is evident in the extra papers she reads.

Fernandes appreciates being a part of del Poeta’s lab. She described him as an “amazing” researcher and supervisor and said being a part of his group is “an honor.”

Del Poeta said Fernandes will continue to make mutants for additional fungi, including Mucorales and Rhizopous, for which antifungal therapy is not particularly effective.

Del Poeta added that the urgency of this work remains high. With several other Stony Brook faculty, he has submitted grants to study Sgl1 as a vaccine and antifungal target.

“Imagine [making] a drug that not only can treat the primary infection, but, by doing so, can potentially prevent the recurrence of a secondary infection?” he asked rhetorically. “Exciting!”

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Dr. John Clarke. Photo from BNL

By Daniel Dunaief

Live from Upton, New York, it’s … Dr. John Clarke.

While the arrival of the new Occupational Medicine Director and Chief Medical Officer at Brookhaven National Laboratory doesn’t involve late-night comedy, or a live studio audience, it does bring a medical doctor with a passion for bringing his rap and musical skills to a health care audience.

Dr. John Clarke. Photo from BN

Formerly the director of occupational medicine at Cornell University, Dr. Clarke joined the Department of Energy lab as Occupational Medicine Director and Chief Medical Officer for BNL in June..

“My role is to help maintain safety and wellness among the workers,” said Dr. Clarke. “If we have employees who start coming in for some sort of complaint and we see a pattern, that may help us identify who could be at risk of something we didn’t know about that we are detecting.”

A doctor who served as chief resident at New York Medical College in family residency and Harvard University in occupational & environmental medicine, Dr. Clarke said he plans to support a range of preventive efforts.

“I’m excited about the potential to engage in what’s considered primary prevention,” said Clarke, which he defined as preventing a disease from occurring in the first place.

Through primary prevention, he hopes to help the staff avoid developing chronic illnesses such as cancer, while also ensuring the health and responsiveness of their immune systems.

Through physical fitness, a plant-based diet including fruits and vegetables, adequate sleep and hydration with water, people can use lifestyle choices and habits to reduce their need for various medications and enable them to harness the ability of their immune systems to mount an effective response against any threat.

“Modifying your lifestyle is the therapy,” he said. “If you engage [in those activities] in the right way, that is the treatment.”

Dr. Clarke added that the severity and stage of a disease may impact the effectiveness of such efforts. For any vaccine and for the body’s natural immunity to work, people need a healthy immune system.

When Dr. Clarke practiced family medicine, he saw how patients lost weight through a diet that reduced the need for medication for diabetes and high blood pressure.

“Losing weight and staying active does provide a therapeutic impact, where you could be medication free,” he said.

To be sure, living a healthier lifestyle requires ongoing effort to maintain. After reaching a desired weight or cholesterol level, people can backslide into an unhealthier state or condition, triggering the occurrence or recurrence of a disease.

In the vast majority of cases, Clarke said, “you have to make a permanent lifestyle change” to avoid the need for pharmaceutical remedies that reduce the worst effects of disease.

BNL has an exercise physiologist on staff who “we hope to engage in consultations with employees,” said Clarke. He would like the exercise physiologist to go to the gym with staff to show them how to use equipment properly to get the maximum benefit.

BNL already has some classes and various initiatives that promote wellness. “One of the things we’d like to do is coordinate and try to publicize it enough where employees are aware” of the options available at the lab to live a healthier and balanced life, he added.

BNL also has a dietician on staff. Dr. Clarke has not worked with the dietician yet, but hopes it will be part of an upcoming initiative. As he and his staff respond to the demand, they will consider bringing on other consultants and experts to develop programs. 

Covid concerns

Like others in his position in other large employers around Long Island, Dr. Clarke is focused on protecting workers from any ongoing threat from Covid-19.

“We’re still learning more as [SARS-CoV2, the virus that caused the pandemic] evolves,” he said. BNL does a “great job about monitoring the prevalence and the numbers of cases in Suffolk County and among workers.”

Dr. Clarke said he and others at BNL are following the Department of Energy, New York State and Centers for Disease Control and Prevention guidance on these issues.

If the numbers of infections and hospitalizations increase in the coming months, as people move to more indoor activities, BNL may consider deploying a strategy where the lab provides more opportunities for staff to work remotely.

Prior to his arrival at BNL, Dr. Clarke worked as a consultant for a company that was looking to create numerous permanent jobs that were remote.

He suggested that workers need to remain aware of their remote surroundings and shouldn’t work near a furnace or any heater that might release dangerous gases like carbon monoxide. 

Additionally, people should avoid working in areas that aren’t habitable, such as in an attic. Dr. Clarke urges people to notify and consult their employer if they have concerns about working safely at home or on site.

Music vs. medicine

A native of Queens who spent three years of his childhood in Barbados, Dr. Clarke attended Columbia University, where he majored in sociology and music while he was on a pre-med track.

While he was an undergraduate, Dr. Clarke wrote, produced and performed original music. An independent label was going to help secure a major label deal.

He chose to attend medical school at Icahn School of Medicine at Mount Sinai.

Dr. Clarke has championed a program he calls “health hop,” in which he has used rap to reach various audiences with medical care messages. In 2009, he won a flu prevention video contest sponsored by the Department of Health and Human Services for an “H1N1 rap.”

Train commuters may also recognize him from his work for the Long Island Railroad, for which he created a “gap rap.” The public service announcement was designed to protect children from falling into or tripping over the gap between the train and the platform.

Dr. Clarke has produced music for numerous genres, including for a children’s album and a Christian album.

As for life outside BNL, Dr. Clarke is married to Elizabeth Clarke, who is a nurse practitioner and is in the doctorate of nursing practice and clinical leadership program at Duke University.

When he’s not spending time with his wife or their children, he enjoys home projects like flooring and tiling.

Dr. Clarke is pleased to be working at the national Department of Energy lab.“BNL is a great place, because the science and the work they do has an impact,” he said.

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Babak Andi holds a 3-D model of the coronavirus responsible for the COVID-19 pandemic. Photo courtesy of BNL

By Daniel Dunaief

For close to two and a half years, the world has had a microbial enemy. The SARS-CoV2 virus, which causes Covid-19, has resulted in close to 6.5 million deaths, caused lockdowns, restricted travel, closed businesses, and sickened millions. The key to fighting such a dangerous enemy lies in learning more about it and defeating its battle plan.

Working with principal investigator Daniel Keedy, Assistant Professor at the City University of New York and Diamond Light Source in the United Kingdom, Babak Andi, who is a beamline scientist from the structural biology group at Brookhaven National Laboratory, spent over two years studying a key viral enzyme.

Recently, the researchers revealed the structure at five temperatures of an enzyme called Mpro, for main protease. This enzyme, which separates proteins the virus makes, is critical for the maturation of the SARS-CoV-2 virus particles. They published their work in the Journal of the International Union of Crystallography (IUCrJ).

Using the Frontier Macromolecular Crystallography (FMX) beamline at the National Synchrotron Light Source II at BNL, Andi collected data on the structure of the enzyme at temperatures ranging from 100 degrees Kelvin, which is about negative 280 degrees Fahrenheit, all the way up to 310 degrees Kelvin, which is normal body temperature. “Nobody had done that, specifically for this protein,” said Andi.

Keedy, who guided the data collection, processed the information and wrote most of the paper, described the effort as a “great collaboration.” The gradual change in the conformation of the enzyme helped the scientists learn how it may move or shape-shift in general, he explained.

Keedy had worked with BNL in the past and pursued research at the FMX beamline because the scientists at BNL had “been working with Mpro on site, and were very approachable and open to the idea.”

Finding the specific structure of important proteins like Mpro can help researchers, pharmaceutical companies and doctors search for inhibitors or small molecules that could be specific to these proteins and that might interfere with their function.

Andi and other scientists at this beamline worked through the pandemic shutdown because of the potential practical application of what they were doing.

“We almost had all the infrastructures in place to allow other scientists to connect and operate the beamlines remotely, enabling them to collect data on Covid-19 virus proteins,” said Andi. “In my opinion, being able to support all the academic and industrial scientists to collect data for Covid-19 research was our greatest achievement during the worst period of the pandemic.”

While coming into the lab in those early months raised concerns about their own health, Andi and his colleagues, who developed safety protocols, felt an urgency to conduct this research.

“When Covid hit, we had a sense that this is our duty, this is our job to contribute to this field, to make sure that every scientist who works on Covid-19 had easy access to our beamlines, facilities and all the tools [necessary] to make new drugs,” said Andi. 

How they solved the structure

The technology for the beamline enables Andi and other scientists to collect data quickly and even remotely. Speed helps because the longer x-rays hit a protein, the more likely they are to cause the kind of damage that makes determining the structure difficult, particularly at higher temperatures.

The first step in this research was in producing this protein, which Andi’s collaborators at BNL in the biology department provided. The biology department also helped with crystallization.

Andi prepared the beamline and aligned the x-ray beam, which are necessary to collect data.

The scientists rotated and moved the crystal through the x-ray, distributing the beam over the length of the crystal to minimize radiation damage.

The small size of the x-ray beam made it possible to keep the beam focused on the smallest dimension of the structure. The researchers studied the crystal at five different temperatures, starting at cryogenic all the way up to physiological.

Of the 195,000 structures listed in the Protein Data Bank, or PDB, only five had been determined at body temperature. That includes two from the group of collaborators who participated in this study.

Andi collected three or four data sets at each temperature.

“The different conformations we saw may inspire a new twist on antiviral drug development that targets a different place in the protein, but with a similar or better effect,” Keedy explained.

The researchers did not include other factors that might affect the conformation of the protein, such as pH, pressure, the number of ions or salts in the environment, among others. For the Mpro protease to work, it has to bond to another similar protein, forming a dimer.

Andi said the Pfizer treatment Paxlovid binds to the active site of this enzyme, inactivating it.

The drugs he is looking for are similar, although he is also searching for other places on the enzyme besides its active site.

Keedy hopes to try to make a monomeric form of the enzyme through a mutation. He could then find drug-like small molecules that target the exposed interface between the two copies.

BNL origins

After he completed his PhD and post doctoral work at the University of Oklahoma, Andi started his career at BNL 11 years ago as a post doctoral researcher.

During his childhood, Andi was initially interested in astronomy. When he enrolled at a university outside the United States, he took an entrance exam.

“Based on your score, it tells you which discipline of science you can go into,” he said. His score directed him to the field of cell and molecular biology.

“I’m happy this happened,” he said. “I find that I’m actually more interested in molecular biology than in astronomy.”

Outside of work, Andi enjoys do-it-yourself projects. Astronomy also continues to appeal to him, as he is fascinated with astrophotography and reads astronomy articles.

As for the work with a Covid enzyme, Andi hopes he has other opportunities to contribute. 

“I am interested [in continuing] the research in this field,” he explained. “That depends on time, resources and current or future priorities.”

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From left, Chang Kee Jung, Barry Barish and Carl Lejuez. Photo by John Griffin/Stony Brook University

By Daniel Dunaief

Albert Einstein predicted gravitational waves existed, but figured interference on the Earth would make them impossible to observe. He was right on the first count. On the second, it took close to a century to create an instrument capable of detecting gravitational waves. The first confirmed detection, which was generated 1.3 billion light years away when two black holes collided, occurred in September of 2015.

For his pioneering work with gravitational waves, which now include numerous other such observations, Barry Barish shared the Nobel Prize in 2017 with physicists Rainer Weiss and Kip Thorne.

In the fall of 2023, Barish is bringing his physics background and knowledge to Stony Brook University, where he will be the inaugural President’s Distinguished Endowed Chair in Physics. Barish will teach graduate students and serve as an advisor to Chang Kee Jung, Chair of the Department of Physics and Astronomy and Distinguished Professor.

From left, Barry Barish and Chang Kee Jung. Photo by John Griffin/Stony Brook University

“I’m really happy,” said Jung in an interview. “Nobel Prize winning work is not all the same. This work [Barish] has done with LIGO [the Laser Interferometer Gravitational-Wave Observatory] is incredible.”

Jung suggested the discovery of these two merging black holes “opened up a completely new field of astronomy using gravitational waves.” The finding is a “once-in-a-generation discovery.”

Gravitational waves disrupt the fabric of spacetime, a four-dimensional concept Einstein envisioned that combines the three dimensions of space with time. These waves are created when a neutron star with an imperfect spherical shape spins, and during the merger of two black holes, the merger of two neutron stars, or the merger of a neutron star and a black hole.

Jung suggested a way to picture a gravitational wave. “Imagine you have a bathtub with a little rubber ducky,” he said. In the corner of the bathtub, “you slam your hand into the water” which will create a ripple that will move the duck. In the case of the gravitational wave Barish helped detect, two black holes slamming into each other over 1.2 billion light years ago, when life on Earth was transitioning from single celled to multi celled organisms, started that ripple.

While Barish, 86, retired after a lengthy and distinguished career at CalTech in 2005, Stony Brook has no plans to create a team of physicists who specialize in this area. “The most important thing is that people together exchange ideas and figure out what to do next that’s interesting,” Barish said in an interview. “I’ll keep doing gravitational waves.”

Instead of encouraging graduate students and even undergraduates to follow in his footsteps, Barish hopes to “help stimulate the future here and help educate students,” he said.

An important call

Jung, who became chair of the department in the fall of 2021, has known Barish for over three decades. On a periodic informal zoom call, Jung reached out to Barish to tell him Stony Brook had offered Jung the opportunity to become chair. Barish suggested he turn it down. As Jung recalled, Barish said, “Why do you want to do that?”

On another informal call later on, Jung told Barish he decided to become chair, explaining that he wanted to serve the university and the department. Barish asked him what he would do as chair. Jung replied, “‘I would like guys like you to come to Stony Brook. It took [Barish] about 10 seconds to think about it and then he said, ‘That’s possible.’”

That, Jung said, is how a Nobel Prize winning scientist took the first steps towards joining Stony Brook.

Last week, Barish came to Stony Brook to deliver an inaugural lecture as a part of the newly created C.N. Yang Colloquium series in the Department of Physics and Astronomy.

Stony Brook officials were thrilled with Barish’s appointment and the opportunity to learn from his well-attended on-site lecture.

In remarks before Barish’s packed talk at the Simons Center Della Pietra Family Auditorium, Carl Lejuez, Executive Vice President and Provost, said he hears the name C.N. Yang “all the time,” which reflects Yang’s foundational contribution to Stony Brook University. “It’s fitting that we honor his legacy with a speaker of Dr. Barish’s character who, like Yang, is also a Nobel Prize winner. It’s a really nice synergy.”

Indeed, Yang, who won his Nobel Prize in 1957, coming to Stony Brook “instantaneously raised the university profile,” said Jung, whose department is the largest on campus with 75 faculty.

Surrounded by a dedicated team of scientists, and with the addition of another Nobel Prize winner to the fold, Jung believes the team will continue to thrive. 

“If you put together great minds, great things will happen,” he said.

Seeing the bigger picture

Barish is eager to encourage undergraduates and graduate students to consider the bigger picture in the realm of physics.

“[In general] we train graduate students to do something really important by making them narrower and narrower and narrower, so they can concentrate on doing something that’s worthy of getting a thesis and is as important as possible,” Barish said. “That works against creating a scientist who can look beyond something narrow. That’s bothered me for a long time.”

The problem, Barish continued, is that once researchers earn their degree, they continue on the same path. “Why should you happen to have had a supervisor in graduate school determine what you do for the rest of your life?” he asked.

Once students have the tools of physics, whether they are experimental or theoretical, they shouldn’t be so locked in, he urged. “It’s possible to use these same tools to do almost any problem in physics,” Barish added.

His goal in a course he plans to teach to advanced graduate students (that’s also open to undergraduates) is to provide exposure to the frontiers of science.

A few years ago, Barish recalled how the New York Times ran a picture of a black hole above the fold. He taught a class how scientists from around the world combined radio telescopes to make it act like one radio telescope the size of the Earth.

Helping students understand how that happened “pays off in the long run in making our physics students that we turn out be broader and more interesting and more interested in physics,” Barish said.

When Barish arrives next September, Jung said he plans to have some assignments for interactions with undergraduates. “Undergraduate research is critically important,” Jung said. Barish will also interact with various student groups, as well as the community outside the university.

“We will create those opportunities,” Jung said.

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Aleida Perez during BNL's virtual teaching sessions this summer

By Daniel Dunaief

For well over two years, herd immunity, vaccination status, social distancing, masking and airborne particles became regular topics of conversation. 

People have a range of understanding of these terms and how to apply them to understanding the fluid conditions that are an evolving part of the pandemic.

Aleida Perez

This summer, with funding from the National Science Foundation, a group of scientists and doctors from Brookhaven National Laboratory, Stony Brook University, New York University and MoMath, the National Museum of Mathematics, worked together with middle school and high school teachers around Long Island to prepare lesson plans on how to use and understand the application of statistics to the pandemic.

“It was a wildly successful summer,” said Dr. Sharon Nachman, Chief of the Division of Pediatric Infectious Diseases at Stony Brook Children’s Hospital. “We spent hours and hours of time” working with teachers who developed lessons that addressed a host of issues related to COVID-19.

It was “an amazing experience” and the teachers “were the best part,” said Dr. Nachman.

Allen Mincer, Professor of Physics at New York University, has been working on and off with BNL for over two decades on various educational programs. He has been more actively engaged in the last four years.

As he and his collaborators were discussing possible educational outreach topics, they focused on the disruptive disease that changed the world over the last few years.

“This year, we were talking about it and, instead of doing random applications of statistics, we figured, why not do something that’s very practical in everyone’s mind,” Mincer said.

The projects and discussions, which were all conducted virtually, centered on numerous misconceptions people have about the pandemic. Teachers focused on questions including: what is the “efficiency” of a vaccine and how is it determined, what does a positive virus test result mean, if I am vaccinated, why do I care if others are, why take a vaccine when there are side effects, and I have to go to school and mix with people, so why shouldn’t I also let down my guard in other ways, among others.

“The challenges that this virus brings concerning topics like herd immunity was very interesting,” said Scott Bronson, manager of outreach to K-12 teachers and student for BNL’s Office of Educational Programs.

Scott Bronson during the BNL virtual teaching sessions this summer.

For teachers and their students, the realities of the pandemic were the backdrop against which these teachers were seeking to provide guidance. “It was happening live,” said Bronson. “What is herd immunity? That’s where the work of [Dr. Nachman and Mincer] came together beautifully.”

Bronson added that students will have a chance to explore the kinds of questions pharmaceutical companies are addressing, such as “What would you want the next vaccine to do” and “What would you do to make the vaccine better at preventing infection.”

The organizers put together teams of three to four high school and middle school teachers who created statistics lessons plans for the group.

“The way we worked it out, we put teachers in groups,” said Aleida Perez, supervisor of student research and citizen science programs for Brookhaven National Laboratory’s Office of Educational Programs. “We wanted to have different teachers with different courses and different perspectives on how to do things.”

One of the overarching goals was to help students understand such lessons as what it means to have a negative result on a virus test or what it meant when scientists and pharmaceutical companies described a vaccine’s efficacy.

The teachers explored the probability of side effects like myocarditis and whether the “benefit outweighs the risk of taking the vaccine,” Perez said.

For many of the teachers, the discussion expanded beyond COVID to an analysis of any infectious agent. Indeed, one of the groups of teachers described a zombie apocalypse.

The teachers provided a “nice overview to look at the education of public students,” said Perez.

The group hopes to make these lessons available for other teachers, although they haven’t determined where or how to post them.

The scientific team also hasn’t determined yet how to measure the long term impact or effectiveness of these lessons.

ATLAS project

As a part of the team involved in the ATLAS physics program at the Large Hadron Collider in Geneva, Switzerland, Mincer uses statistics to design, test and implement the tools to pick and choose from numerous reactions and then to study the data collected.

“We actually keep about a billion events out of the 100 trillion or so interactions the LHC produces in a year,” Mincer explained.

In previous years, Mincer has taught about statistics in general and its use in ATLAS. This year, he focused on statistics and its application to pandemic questions.

Several years ago, Mincer taught a freshman seminar called “Great science, fabulous science and voodoo science,” in which he described what students could learn from statistics, how the media covers science, science and government policy and how lawyers use science in the courtroom.

“After explaining statistics [and sharing] why we can only say we have evidence down to this level, I had a student tell me he’s dropping out of science as a major because he wanted certainty and I disillusioned him,” Mincer said.

As for the work with the high school teachers, Mincer said it was “great what they have been able to do” in preparing lessons for their students and sharing information about statistics.

Mincer has received some additional funds from the NSF to support two more such educational outreach programs, one of which will tentatively cover climate change.

“Statistics can be used to quantify the likelihood of events in the absence of climate change,” he explained.

Statistics provide a tool to document subtle but potentially significant changes in climate.

While Bronson wouldn’t commit to a discussion of climate change for the next group of teachers, he said he “wouldn’t be surprised if we look at climate change” and that “there’s a lot of interesting areas to explore in this field.”

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Arjun Venkatesan is testing an enhanced coagulation approach to treat contaminated water. Photo by John Griffin/Stony Brook University

By Daniel Dunaief

One person’s toilet flush is another’s pool of information.

Arjun Venkatesan, Associate Director for the New York State Center for Clean Water Technology at Stony Brook University, has gathered information from wastewater plants to search for traces of opioids and other chemicals.

Such monitoring is a “great tool” and relies on the sensitivity of the method, Venkatesan said.

Indeed, other scientists, including Professor Christopher Gobler, Endowed Chair of Coastal Ecology and Conservation at the School of Marine and Atmospheric Sciences at Stony Brook, have used wastewater monitoring to collect information about the prevalence of Covid-19 in a community.

Gobler explained that such monitoring has proven to be an “ideal way to track community infections. Through early to mid 2022, positive test rates and wastewater virus levels tracked perfectly. Since then, people began home testing and now, wastewater epidemiology is probably our best sign of community infection rates.”

In a joint effort through the Center for Cleanwater Technology, Venkatesan’s team monitors for chemicals, including opioids and other drugs. Such tracking, which college campuses and local governments have done, does not involve gathering information from any specific home. Instead, the scientists take anonymous samples from a larger dorm or a neighborhood, hoping to track changes in the presence of chemicals or a virus to enable health care mitigation efforts.

Venkatesan has been looking at common over-the-counter drugs and anti-viral treatments that residents used to treat Covid-19 infection, particularly before the development and distribution of several vaccines. He noticed an increase in over the counter use that matched the increase of Covid cases, which suggested that the infected people took these pain medicines for their symptoms first.

Venkatesan’s group monitored the use of these drugs over the last two years to confirm the trends. This baseline allowed him to “see increasing trends” in usage, he said. The increase “clearly indicates something more than what the drugs are regularly used for.”

Opioids

Venkatesan’s group has been working with the Department of Health to develop standard protocols to measure drugs at these sewage treatment plants. The testing needs to be updated to account for changes in consumption of new drugs that are being synthesized.

Each sample Venkatesan and his colleagues collect typically has hundreds of thousands of people in it, because the treatment plants process sewage for a large collection of communities. “This keeps anonymity,” he said. “We don’t want to dig up [information] from a single family home.”

The method is also cost effective when a single sample represents a larger population. This kind of information, however, could help public health professionals monitor the presence of drugs broadly in a community, providing them with a way to track the prevalence of addictive and potentially harmful drugs.

Venkatesan is developing methods to track fentanyl, a highly addictive drug linked to numerous deaths throughout the country and the world. Studies in other regions have demonstrated elevated levels of this drug.

Venkatesan said New York State responded to the pandemic by developing surveillance over the last few years. The approach was not well known and was limited mostly to illicit drugs. The pandemic made a significant impact, which helped officials appreciate the value of such a tool.

The state could also theoretically monitor for any chemicals that are stable enough in sewage.

While Venkatesan hasn’t measured traces of alcohol at sewage treatment plants, researchers and public health officials could create a screen to measure it. He was involved in a study that monitored for alcohol and nicotine consumption in many cities. “We could get interesting trends and understand community and population health in a better way,” he said. The pandemic has “helped establish the importance of this network.”

Surveys in which people call and ask about the consumption of drugs or alcohol can contain self-reporting error, as respondents may not know exactly how much they drink or may be reluctant to share those details.

Wastewater monitoring could capture trends, including whether communities have a spike in the use of drugs or alcohol on Friday nights or on weekends.

The Centers for Disease Control and Prevention created standardized methods for monitoring Covid-19 in the wastewater of cities and states.

Wastewater monitoring techniques are different for detecting viruses compared to chemicals. Venkatesan’s group is developing different method to screen for opioids. “We are excited about it,” he said. “Hopefully, next year, we should be able to monitor communities.”

As long as the sampling doesn’t cross any predetermined ethical line, monitoring could provide an effective way of looking at the trends and data, he said.

With so much water flowing through pipes and treatment plants, one of the biggest challenges in these efforts is to understand variables that affect what the scientists are monitoring.

The time between when a toilet is flushed in an apartment to the time when it reaches a plant can vary, depending on numerous variables, which creates uncertainty in the data.

To reduce this variability, scientists could do some sampling in manholes, between treatment plants.

Scientific roots

Venkatesan took an elective at the end of college in environmental science when he attended Anna University in Chennai, India. It was the first time he observed a wastewater treatment plant.

Fascinated by the process, he earned a Master’s in Environmental Engineering at the University of Nevada, Las Vegas and then went on to get a PhD at Arizona State. He also did his post doctoral research in Arizona.

Stony Brook was looking for a scientist to screen for contaminants in drinking water, including PFAS chemicals, which is a group of chemicals that are stable, hard to break down and are linked to thyroid cancer, among others.

PFAS chemicals are used in cleaners, textiles, fire-fighting foam and other applications.

Venkatesan leads drinking water efforts, while waste water epidemiology remains an ongoing project of interest.

Gobler hired Venkatesan five years ago to help run and then to exclusively run the drinking water initiative at Stony Brook.

Through the process, Venkatesan has “brought new insights and research programs related to wastewater epidemiology, bisolids and many other topics,” Gobler explained. Venkatesan has “exceeded expectations,” as he transitioned from a postdoctoral researcher to become Associate Director for Drinking Water Initiatives.”

Gobler called his colleague a “complete professional” who is “very positive and a good person to work with.”

In his research, Venkatesan develops technologies to remove these PFAS chemicals, while monitoring is also a part of that effort. Activated carbon filters can remove these chemicals from groundwater. These filters, however, require frequent replacement. Venkatesan is exploring ways to improve the life of the carbon filter.

PFAS chemicals make rain water unsafe to drink. Removing PFAS chemicals is an “important research topic locally and globally.”

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