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Daniel Dunaief

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From left, CSHL’s Bruce Stillman, Double Helix Medal recipients Leonard Schleifer and Reggie Jackson, Chair of the CSHL Board of Trustees Marilyn Simons, and Double Helix Medal recipient George D. Yancopoulos. Photos by Constance Brukin
Above, NYC Mayor-elect Eric Adams speaks at the 16th Annual Double Helix Medals dinner with CSHL President and CEO Bruce Stillmanon and television journalist Lesley Stahl. Photos by Constance Brukin
The guests, including scientists from CSHL, and the honorees shared stories and hors d’oeuvres beneath the dinosaurs at the Museum of Natural History. Photo by Tobias Janowitz
Above, NYC Mayor-elect Eric Adams speaks at the 16th Annual Double Helix Medals dinner with CSHL President and CEO Bruce Stillmanon and television journalist Lesley Stahl. Photos by Constance Brukin
Double Helix Medal recipient George Yancopoulos takes a selfie with CSHL President and CEO Bruce Stillman, Regeneron Chairman of the Board P. Roy Vagelos, Double Helix Medal recipients Leonard Schleifer and Reggie Jackson, and Chair of the CSHL Board of Trustees Marilyn Simons. Photo by Constance Brukin
Dinner was served under the Blue Whale at the Natural History Museum. Photo by Sara Roncero-Menendez
CSHL Trustee Robert W. Lourie, CSHL President and CEO Bruce Stillman, and County Executive Steve Bellone. Photo by Constance Brukin
From left, Assistant Professor Tobias Janowitz, Professor Leemor Joshua-Tor, Assistant Professor Peter Koo, and Professor Linda Van Aelst. Photo by Constance Brukin
Dessert at the awards dinner was caramel tart dessert with chocolate ganache and vanilla ice cream. Photo by Sara Roncero-Menendez

By Daniel Dunaief

This November, Cold Spring Harbor Laboratory celebrated baseball’s Mr. October.

The research facility that specializes in studying cancer, neuroscience, quantitative and plant biology hosted its 16th annual Double Helix Medals dinner at the Museum of Natural History on Nov. 17.

The evening, which was emceed by television journalist Lesley Stahl, honored Hall-of-Famer Reggie Jackson, as well as Leonard Schleifer and George Yancopoulos, the founders of Regeneron, the pharmaceutical company that has provided a life-saving antibody treatment for COVID-19.

The evening, which featured a dinner beneath the blue whale at the museum, raised a record $5 million for research.

“When we were standing in the hall of dinosaurs at the museum, it was fantastic,” said CSHL President and CEO Bruce Stillman. “It was one of the first events where people went out like the old days” prior to the pandemic.

Stillman said guests had to have received their COVID vaccinations to attend the celebration.

In addition to establishing a career as a clutch hitter in the playoffs, Reggie Jackson has dedicated considerable energy through his Mr. October Foundation to improve education around the country.

“His Mr. October foundation complements and parallels the DNA Learning Center programs, particularly now that we’ve opened a large DNA Learning Center in downtown Brooklyn that is serving underserved students in lab-based science,” said Stillman.

In his acceptance speech, Jackson said he found it “significant” that he received an honor for his educational efforts off the baseball field.

Yancopoulos, meanwhile, described his roots as the son of first generation immigrant parents from Greece. Yancopoulos highlighted the need for more funding in research and suggested that science helped pull the world through the pandemic. Yancopoulos said the National Institutes of Health should increase its budget 10-fold to meet the research and clinical needs of the population.

“Biotechnology offers the promise of really solving some of the most difficult problems that we face if we want our citizens to live not only longer, but healthier lives,” Schleifer said in a statement.

Mayor-elect Eric Adams, meanwhile, gave a speech about his vision for the future of the city which included, after some prompting from Stillman, increasing science in the education system.

The Double Helix gala, which started in 2006 when the lab honored the late boxer Muhammed Ali, raises money that goes into CSHL’s operating budget to support research and education.

This year, the donations included a generous gift from Astros owner Jim Crane, who introduced his friend Jackson.

Stillman helps direct the funds raised through the dinner to support scientists who are making what he termed “breakthrough discoveries.”

Many of the most significant discoveries come through philanthropic support, Stillman said, which makes it possible for researchers to design high-risk, high-reward experiments.

CSHL Chair of the Board of Trustees Dr. Marilyn Simons, a previous winner, attended the festive evening.

Senior leadership at the lab chooses the honorees. Stillman said CSHL already has two honorees for the event next year.

Previous honorees include actor Michael J. Fox, basketball legend Kareem Abdul-Jabbar, actor and science educator Alan Alda, and newscasters including Tom Brokaw and Katie Couric.

“It is a really spectacular list,” Stillman said. The winners, who receive a medal, have all contributed in some significant way to science or to science education.

The dinner provides an opportunity for supporters of the mission of CSHL, which has had eight Nobel Prize winners work at the lab during their careers, to invite others to hear about research at the lab.

“It was a very inspiring evening,” Stillman said.

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

Ah, the benefits of an older bladder.

Granted, that’s not generally the case. Usually, I get up in the middle of the night, realizing that the dream that involves the search for a bathroom is my brain’s way of telling me that I need to urinate in real life.

I shift my weight slightly toward the floor, hoping that the rocking motion of my body doesn’t move the bed so much that I wake my wife or the cat sleeping on her, who sometimes sees my movement as a starter’s gun to race toward the table in the laundry room to devour another can of the same food he eats every day.

I slide my feet off the bed and try not to step on our huge dog, who moves around often enough that he could easily be that furry thing under my feet. My toes can’t always tell whether that’s him or just the softer part of the inside-out sweatpants I’ve been wearing for a week. I also try to avoid the other cat, whose tail is like a spring waiting for me to step on so he can shriek loudly enough to wake my wife and terrify the other cat and the dog.

When I reach the bathroom, I try to urinate into the bowl but away from the water to avoid any splashing sound. I retrace my steps back to the bed, hoping the safe places to step on the way out from the bed are still safe on the return.

This past week, the bathroom routine gave me the opportunity to look at a rare event. I watched the extended lunar eclipse, which was the longest it’s been in 580 years. I crept out to the hallway to view it through a window, hoping I didn’t have to go out in the cold to catch a glimpse of Earth’s shadow. I was also concerned that the dog, even at 3 a.m., would fear that he was missing out on something and bark, negating my efforts to enjoy the eclipse in silence.

I was amazed at the shadow that slipped slowly across the moon. I took an unimpressive photo that captured the yin and yang of the light and shadow.

The next morning, I ran into some neighbors on my routine walk with my dog.

After saying how they’d stayed up all night to watch this rare event — they are retired and don’t have any time pressure most days — they started to recount their evening.

“I was tempted to dress in black and howl while I watched it,” the man said.

“Excuse me?” I asked.

“Well, you know, I figured as long as I was up, the neighbors on the other side who think it’s OK to play basketball at 11:30 p.m. should know I was awake and active.”

“Hmm,” I said.

“Yeah, and the other day, they had a party and threw beer bottles over the fence into our backyard. It took until late in the day for them to pick them up.”

“That’s terrible,” I said. “Sorry to hear that.”

As I walked back with my dog, who was eager for his post-walk breakfast, I realized we had never discussed the sights from the night before.

Sleep deprivation overshadowed a discussion of the observation of the Earth’s long shadow.

As for me, I was, for the first time, grateful for the momentary need to pee. The evening and the morning interaction that followed brought to the fore a collision of the mundane and the magnificent.

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Above, DeLorenzo (in blue) at a Multiple Sclerosis benefit in which she and a group of friends climbed the stairs at Rockefeller Center. Photo from C. DeLorenzo

By Daniel Dunaief

Her colleagues highlight the joy, passion and optimism she brings to her work, which can be the opposite of the way people she is eager to help feel. 

Dr. Christine DeLorenzo, Professor of Psychiatry and Biomedical Engineering at Stony Brook University, studies depression.

A disease with numerous symptoms that likely has a wide range of causes, depression presents an opportunity for Dr. DeLorenzo to bring not only a relentless energy to her work, but also an engineer’s perspective.

“Engineering is all about examining a complex problem and thinking, ‘I bet we can fix that,’” explained Dr. DeLorenzo in an email. “Biomedical engineering takes it to a new level.”

Indeed, Dr. DeLorenzo specializes in brain imaging, using positron emission tomography, among other techniques, to understand and differentiate the factors that might contribute to depression and to develop ways to treat specific subtypes of the mental health disease.

Dr. Ramin Parsey, who mentored Dr. DeLorenzo and is professor and Della Pietra Chair of Biomedical Imaging at Stony Brook, believes she will help define the subtypes of depression by imaging the brain.

For Dr. DeLorenzo, the abundance of discussion in the popular and scientific literature that currently attributes the progression of depression to a host of causes, from eating the wrong foods to not exercising enough to not getting the right amount of sleep, doesn’t offer much clarity.

“We see a million articles about what causes depression and they don’t all agree,” said Dr. DeLorenzo. “Depression is caused by a bunch of different things, which is not all that helpful when you’re the person suffering.”

In her brain studies, Dr. DeLorenzo has looked at inflammation and neurotransmitter systems. The goal of her work is to find “whatever is outside the normal range in the person with depression and treat” that potential cause, she said. High levels of inflammation might suggest an anti-inflammatory treatment.

When people receive a major depressive disorder diagnosis, they often are prescribed a selective serotonin reuptake inhibitor, or SSRI. This enables the neurotransmitter serotonin to remain in the brain for a longer period of time.

“It’s great that it works in a subset of people” for whom it is effective, Dr. DeLorenzo said. “We would like to know beforehand if we give this medication will it work for you, specifically.”

In one of her studies, Dr. DeLorenzo uses positron emission tomography, or PET scans, to search for signs of inflammation. She is looking for translocator proteins, which is a marker of inflammation. Reactive glial cells in the brain, which are an important supporting part of the nervous system that don’t have axons and dendrites like nerve cells, increase the production of these proteins during some depression and other disorders.

The level of these translocator proteins increase in glial cells when the brain is having an inflammatory response, which likely occurs in a subtype of depression as well as in other diseases.

Dr. DeLorenzo has a PET tracer that sticks to that protein and that gives off a signal to the camera, which enables her to quantify the inflammation.

At this point, she and her collaborators, including co-Principal Investigator Dr. Parsey and Dr. Stella Tsirka, Professor of Pharmacological Sciences at Stony Brook, are recruiting a collection of patients with depression. They are testing the idea that people with higher inflammation are better treated with an anti-inflammatory. They are using PET to see who has high or low inflammation prior to treatment. During the study, the researchers will determine if those with the highest inflammation had the best response.

Dr. Tsirka’s lab uses animal models to understand mechanisms of disease and experiment on treatment, while Dr. DeLorenzo uses neuro-imaging in human patients to understand and treat pathology.

“Our preclinical results certainly support the idea of the neuro-inflammation hypothesis of depression” and suggest potential ways to interfere with the process in preclinical models, Dr. Tsirka explained in an email.

Dr. Tsirka, who has been working for Dr. DeLorenzo for over three years, described her colleague as “enthusiastic, rational creative and hard working” and believed imaging could provide a way to verify efficient treatment of depression.

By understanding the biology of the brain, Dr. DeLorenzo hopes to address a range of questions that might affect the disease.

In other work, Dr. DeLorenzo is exploring the possibility that a disruption in glutamate leads to circadian and mood dysfunction in a subtype of depression.

In some studies with glutamate, researchers assessed mood before and after sleep deprivation. They found that sleep deprivation provided an antidepressant effect in about 40 percent of patients with Major Depressive Disorder.

A healthy person would typically become tired and angry after staying awake for 36 straight hours. Some people with this form of depression, however, see an improvement in their mood after staying up for so many hours.

“Something about sleep deprivation causes an antidepressant effect in some people,” Dr. DeLorenzo said. “We don’t know what that is.”

The antidepressant effect can be short lived, although about 10 percent of people have benefits that last as long as a few weeks.

To be sure, Dr. DeLorenzo cautioned that no one is “advocating just doing sleep deprivation” or even a continuous cycle of partial sleep deprivation.

Born and raised in Bay Ridge, Brooklyn, Dr. DeLorenzo earned her undergraduate and Master’s Degrees at Dartmouth College. She earned her PhD from Yale University, where she started her brain imaging work.

When Parsey left Columbia to join Stony Brook in 2012, Dr. DeLorenzo moved with him, even though her commute from Queens was three hours each way.

“She never complained” about her travels, Dr. Parsey marveled. In fact, Dr. DeLorenzo uses the commuting time to read papers and prepare emails.

Dr. Parsey admired Dr. DeLorenzo’s dedication to teaching and mentoring students in her lab. In her first summer, she took on 17 interns. “This is the kind of stuff that nobody else I know does,” Dr. Parsey marveled.

As for her work, Dr. DeLorenzo believes understanding sub-categories of mental health will follow the same pattern as cancer research. “Back in the day, we used to say, ‘Someone has cancer or a tumor.’ Now, we say that that tumor has this genetic marker, which is what we’re going to target when we treat it.”

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METRO photo

By Daniel Dunaief

Daniel Dunaief

Flying? Are we really flying? Well, sure, why not, right? Everyone else is flying.

Wait, then again, everyone else seems to be flying. What if one of those other people is sick? Don’t think too much about it and breathe through your nose. Oh, you can’t because the two masks you’re wearing are pinching your nose? Well, tough! 

They’re serving drinks and cookies? People have to lower their masks to eat and drink, right? So, doesn’t that defeat the purpose of mandatory masks? Look away from everyone who’s breathing. Yeah, that’ll help.

Okay, finally, we’re on the ground. 

Hey, this is a nice campus. The sidewalks are packed and filled with so much energy, not all of which is positive.

“Why are all these $#@! parents here this weekend? I have several tests and I don’t need them all staring at me!”

That girl is sharing her academic anxiety with her friend and anyone else within 100 feet of her. Subtle, real subtle! Tempted as I am to let her know that parents, likely including her own, make this sometimes miserable experience possible, I refrain. She might be my son’s current or future friend.

I ask two students for the location of a building. The first shrugs and points me in the wrong direction and the second nearly draws a map. Okay, one for two.

I sit just in time for the start of a talk by successful alumni, who connect their careers to the lessons they learned at school. Clever marketing! Other parents chuckle at the jokes. I imagine these parents as college students. In my mind, the presenters onstage become Broadway performers. Each of the two men and two women, which I presume is a well-planned balance of genders, does his or her rendition of “how I succeeded,” with the subtext, just feet from the school president, of, “keep paying those tuitions!”

When the session ends, the phone rings. It’s my son! He’s strolling across a lawn. Wait, is that really him? Much as I want to run over and squeeze him, I play it cool, congratulating myself on my impulse control. Well done, Dan. You haven’t embarrassed him so far, but the weekend is young yet, even if you are not. He adjusts his hair, a move I’ve seen him and almost all his friends do frequently, even while running back and forth on a basketball court. What’s with all the hair adjustment? I quietly ask for permission to hug him. Yay! He agrees. I wrap my arms around his shoulders and fight the urge to pick him up, which is probably best for my back.

As we head to his dorm, he tells me he hasn’t done laundry in nine days. I don’t know whether that’s a hint, as in, “Dad, while you’re here…” or a statement of fact.

We part company and I learn about the evolving world of the commercialization of college athletes, who can use their name, image and likeness to make money. He’s listening to a psychology lecture about, who else, Sigmund Freud.

At a football game, I wonder how it can be this cold in Louisiana. Aren’t we in the deep south? We leave before it’s over, waiting in the cool air for 11 minutes for an expensive Uber — they must know it’s parents weekend — to take two families who are heading back to the same hotel.

10 pm. Who eats this late? I’m usually half way to sleep by now. My older brother is undoubtedly already in REM sleep. My stomach is going to hate this. Shut up stomach!

Looking around the table at these families, one thing is clear: these parents adore their children.

This is part of the story of how these boys got here and, hopefully, will help them continue to learn lessons, like how to dress for a cold football game and how to make reservations in advance before a busy parents weekend so we can eat earlier.

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Three long-finned pilot whales. Photo by Andrew Sutton/ Shutterstock
From left, Lesley Thorne, Eleanor Heywood and Julia Stepanuk. Photo by Julia Stepanuk
Lesley Thorne on a research ship in the Antarctic. Photo from Lesley Thorne
Lesley Thorne in the Antarctic. Photo from Lesley Thorne
Lesley Thorne with black-browed albatross in the Falkland Islands. Photo from Lesley Thorne

By Daniel Dunaief

Long-finned pilot whales can’t stand the heat, so they are heading north.

Amid increases in ocean temperatures caused by global warming, long-finned pilot whales have moved the center of their range to the north, according to a 25-year study Lesley Thorne, Assistant Professor in the School of Marine and Atmospheric Sciences at Stony Brook University and Janet Nye, Associate Professor at the University of North Carolina Institute of Marine Sciences and Adjunct Professor of SoMAS, recently published in the journal Scientific Reports.

What’s more, these whales are swimming farther north despite the fact that some of their prey, including fish and invertebrates such as squid, aren’t shifting as far north, while others are moving into deeper offshore waters.

That could have broad ecological consequences for both regions, as whales may head towards areas to compete against other predators for the same prey, while some fish populations in deeper waters offshore may increase, putting pressure on the creatures that live in those areas.

“We know that different species are responding in different ways to climate change,” Thorne said. “That will impact all the dynamics” including food webs and competition. 

Climate change may change the predator-prey dynamics in unexpected ways, Nye explained in an email. “We know that it would be wrong to assume that all species would shift at the same rate in response to changing environmental patterns, but this is one of a growing number of papers to illustrate that the rate at which individual species” in different feeding groups changes can be different, which alters the way ecosystems function.

Nye explained that researchers don’t yet have a good sense of how such mismatches would affect productivity of fisheries or the ecosystem as a whole, but they are “working on answering those questions with food web models and climate models.”

To be sure, Thorne indicated that the researchers would need considerably more data to validate any ecological conclusions, as they only looked at one species of whale and four main prey species.

“Understanding the specifics of the broader implications for a location would require looking at a range of important predator and prey species and assessing how the strength of interactions” might be affected by their responses to climate change, she said.

According to Thorne, this study and others suggested that species characteristics such as body size, mobility, thermoregulatory strategy and longitudinal range, in addition to the speed of change in the climate, can help predict the responses of marine species to climate change.

Whales such as the long-finned pilot whale examined in this study are challenging to observe because they have wide geographic ranges, could be difficult to track, and spend most of their time underwater, where they are difficult to see or track.

Additionally, even people with considerable maritime experience sometimes have difficulty differentiating between the long finned pilot whale and the short finned pilot whale, which are different species.

To address the central range of these long-finned pilot whales, Thorne and Nye used two data points: strandings, when whales strand on land, and bycatches, when people catching other fish with bottom trawls also bring up these whales in their nets.

Bycatches occur in part because pilot whales and other cetaceans depredate fishing gear, removing fish from fishing lines or trawls, which presents an easier meal than searching for food themselves. These whales, however, sometimes get caught in the nets themselves. 

People in the fisheries business sometimes use acoustic deterrents to keep the whales away. These efforts, however, can backfire, as the whales hear these sounds as something akin to a dinner bell and head for nets that could inadvertently trap them.

Strandings data is useful for looking at trends in the distribution of cetaceans because networks provide standardized observations throughout the coastline, dating back for decades.

Thorne is in the process of looking at strandings data more broadly. Her team is also looking at strandings of odontocete, or toothed whale, species along the east coast of the United States more broadly. She will also examine whether short-finned pilot whales, which are adapted to warmer waters, show similar trends.

“We are already examining the strandings data and testing our hypothesis that fish species may be shifting both horizontally (latitudinally or north-south) and/or shifting vertically (in depth),” Nye wrote. “I suspect that are doing a bit of both.”

Strandings represented about two thirds of the data in this study, while bycatch constituted the rest.

The shift in the central range represents a fairly dramatic geographic change in the center of the whale range and was considerably higher than that observed for their prey species.

Nye, who worked at Stony Brook from 2012 to 2020, said she was “shocked” that pilot whales were shifting much faster than the fish species, mostly because she knows how much the distribution of many species has changed over the last half century in the northeastern United States.

Whales are heading in the opposite direction that Thorne took in her career path. Thorne grew up in Kingston, Ontario and did her undergraduate work at the University of Guelph. She earned her PhD from Duke University and started as a lecturer at Stony Brook and was offered a tenure track position three years later.

During college. Thorne spent three years at the Huntsman Marine Science Center on the Bay of Fundy. Seeing the impact of the tides in the bay and taking field courses was “amazing,” she said. She first started working with whales at a research station on Grand Manan Island in the Bay of Fundy in future years.

Married to Bernd Distler, who is a surface materials engineer, Thorne and her husband have a four-year- old daughter Annika and two-year- old daughter Franka.

As for what her work tells her about the changing world, Thorne said it was sobering to see first hand the rapid changes in temperature occurring in the Northeast and, specifically, in New York.

This kind of study, along with others that highlight the increases in temperature, should be “more than enough information” to encourage action, she said.

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METRO photo

By Daniel Dunaief

Daniel Dunaief

Have you ever watched someone who was cheering for their team at a sporting event?

Aside from the potential enormous and mindless consumption of calories in the form of hot dogs, chips and beverages, superfans scream at the players, tilt their heads when they want a ball to move in a particular direction, or beg a higher power to help their player outperform people on the other team whose fans are pleading for the opposite outcome.

As fans, we have little control over the result of a game, especially if we’re watching it on television. Sure, home field advantage likely helps some teams and players, as fans urging their favorites on, standing and shouting at the tops of their lungs could inspire athletes to raise their level of play.

But, really, all of that pleading, begging and cheering into the ether or at the blinking lights on our screens gives us the illusion of control, as if we have some way to influence games.

We generally don’t accept or give up control because we like to think that, somewhere, somehow, our wishes, goals and desires mean something to a deity, a guardian angel, or a fairy godmother. To be human is to hope to control the uncontrollable.

Give me the inspiration to pick the right lotto numbers, please! Let me ride the subway with my future spouse. Keep me from hitting the curb on my driver’s test!

Millions of Americans sit each night with a remote control in their hands, surfing channels, changing the volume and traveling, without getting up from the couch, from a program about ospreys to a fictional story about a female secretary of state who becomes an embattled president. We sometimes revel in the excitement that comes at the point that teeters between control and a lack of control. When we’re young, we ride a bike with both hands. At some point, we take one hand off the bike. Eventually, we learn to balance the bike with no hands, as we glide down the street with our hands on our hips or across our chest.

In our entertainment, we imagine people who have higher levels of control, like wizards with wands or superheroes who use the force to move objects.

When we become parents, we realize the unbelievable joy and fear that comes from trying to control/ help/ protect and direct the uncontrollable.

When our children are in their infancy, we might determine where they go and what they wear, but we generally can’t control the noises they make, even by finding and replacing their pacifiers. These noises are their way of preparing us for the limited control we have as they age.

They make numerous choices, some of which we feel might not be in their longer term best interest. We can see the bigger picture, which can be as simple as recognizing that taking eight classes while working part time at night and joining the marching band is likely creating an  unsustainable schedule. We know how important the basics — sleeping, eating, exercising — are to their lives, even if they make impulse driven choices.

One of the hardest parts of parenting may be knowing when to give them the space and opportunity to make decisions for themselves and to encourage them to learn from their choices.

Parents are lifetime fans of their children, supporting and encouraging them, leaning to the left to keep a ball in play, to the right to keep it out of a goal, or higher when we want their voices to hit the highest notes in their range during a performance of “West Side Story.”

It’s no wonder so many parents are exhausted and exhilarated after a big moment in their children’s lives: we might not have done anything but sit in a seat and clap our hands, but we tried, from a distance and in our own way, to control the uncontrollable.

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David McCandlish, center, with postdoctoral researchers Anna Posfai and Juannan Zhou. Photo by Gina Motisi, 2020/ CSHL

By Daniel Dunaief

If cancer were simple, scientists would have solved the riddle and moved on to other challenges.

Often, each type of the disease involves a combination of changes that, taken together, not only lead to the progression of cancer, but also to the potential resistance to specific types of treatment.

Using math, David McCandlish, Assistant Professor at Cold Spring Harbor Laboratory, is studying how the combination of various disruptions to the genome contribute to the development of cancer.

McCandlish recently published a study with colleagues at Cold Spring Harbor Laboratory in the journal Proceedings of the National Academy of Sciences.

David McCandlish. Photo by Gina Motisi, 2020/CSHL

The research didn’t explore any single type of cancer, but, rather applied the method looking for patterns across a range of types of cancers. The notion of understanding the way these genetic alterations affect cancer is a “key motivating idea behind this work,” McCandlish said.

So far, the method has identified several candidates that need further work to confirm.

“Cancer would be a lot easier to treat if it was just one gene,” said Justin Kinney, Associate Professor at CSHL and a collaborator on the work. “It’s the combination that makes it so hard to understand.”

Ultimately, this kind of research could lead researchers and, eventually, health care professionals, to search for genetic biomarkers that indicate the likely effect of the cancer on the body. This disease playbook could help doctors anticipate and head off the next moves with various types of treatments.

“This could potentially lead to a more fundamental understanding of what makes cancer progress and that understanding would very likely open up new possibilities in cancer treatments,” Kinney said.

To be sure, at this point, the approach thus far informs basic research, which, in future years, could lead to clinical improvements.

“We are working on this method, which is very general and applicable to many different types of data,” McCandlish said. “Applications to making decisions about patients are really down the road.”

McCandlish described how he is trying to map out the space that cancer evolves in by understanding the shape of that space and integrating that with other information, such as drug susceptibility or survival time.

“We are trying to ask: how do these variables behave in different regions of this space of possibilities?” he said.

McCandlish is making this approach available to scientists in a range of fields, from those scientists interpreting and understanding the effects of mutations on the development of cancer to those researchers pursuing a more basic appreciation of how such changes affect the development and functioning of proteins.

“This is accessible to a wide array of biologists who are interested in genetics and, specifically in genetic interactions,” said McCandlish.

The main advance in this research is to take a framework called maximum entropy estimation  and improve its flexibility by using math to capture more of the underlying biological principals at work. Maximum entropy estimation is based on the idea of inferring the most uniform distribution of behaviors or outcomes with the least information that’s compatible with specific aspects of experimental observations.

Using this philosophy, scientists can derive familiar probability distributions like the bell curve and the exponential distribution. By relaxing these estimates, scientists can infer more complicated shapes.

This more subtle approach enhances the predictive value, which captures the distributions of data better, McCandlish explained. “We’re trying to capture and model cancer progression in a new and more expressive way that we hope will be able to tell us more about the underlying biology.”

The idea for this paper started when McCandlish, Kinney and  Jason Sheltzer, a former fellow at Cold Spring Harbor Laboratory and a current Assistant Professor of Surgery at Yale School of Medicine, discussed the possibilities after McCandlish attended a talk by Wei-Chia Chen, a post doctoral researcher in Kinney’s lab.

Chen will continue to pursue questions related to this effort when he starts a faculty position in the physics department at National Chung Cheng University in Taiwan this spring.

Chen will use artificial intelligence to handle higher dimensional data sets, which will allow him “to implement effective approximations” of the effect of specific combinations of genetic alterations, Kinney said.

Kinney believes teamwork made this new approach, which the high-impact, high-profile journal PNAS published, possible.

“This problem was an absolutely collaborative work that none of us individually could have done,” Kinney said. He described the work as having a “new exploratory impact” that provides a way of looking at the combination of genomic changes that “we haven’t had before.”

Working at Cold Spring Harbor Laboratory, which McCandlish has done since 2017, enables collaborations across different disciplines.

“We have this quantitative biology group, we also have people working on neuroscience, cancer, and plant biology,” McCandlish added.

McCandlish is also currently also working with Professor Zachary Lippman and his graduate student Lyndsey Aguirre to understand how multiple mutations interact to influence how the fruit on tomato plants develop.

“The idea is that there are these huge spaces of genetic possibilities where you can combine different mutations in different ways,” McCandlish explained. “We want to find those key places in that space where there’s a tipping point or a fork in the road. We want to be able to identify those places to follow up or to ask what’s special about this set of mutations that makes it such a critical decision point.”

A native of Highland Park, New Jersey, McCandlish was interested in math and science during his formative years. 

As for the work, McCandlish appreciates how it developed from the way these collative researchers interacted.

“This would never have happened if we weren’t going to each other’s talks,” he said.

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Downtown Port Jefferson flooded during Superstorm Sandy. File photo

By Daniel Dunaief

Daniel Dunaief

Nine years ago, Superstorm Sandy came roaring through the area, causing flooding, knocking out power and disrupting work and school.

All these years later, New York is not prepared for other significant storms, despite studies suggesting that future, slow moving hurricanes with heavy rain could overwhelm infrastructure in and around Long Island.

“While we have dithered, New Orleans, Houston and other U.S. cities have gained federal support for regional protection strategies — which will be funded with our tax dollars,” according to an information packet created by the New York New Jersey Storm Surge Working Group. “We can’t waste another decade pursuing local responses to regional threats.”

In a ninth anniversary boat tour designed to address the challenges from a future Sandy or even a Hurricane Ida, the working group, which is chaired by School of Marine and Atmospheric Sciences Distinguished Professor at Stony Brook University Malcolm Bowman, outlined four messages.

First, the group suggested that coastal flooding presented a significant danger. Storm surge, sea level rise and storm water from extreme rain present an “existential threat” to the area.

Second, the group concluded that coastal flooding is a regional challenge that requires a regional solution. These scientists urge the two middle Atlantic states to consider creating a layered defense system, which they argue would be cost effective to protect property and the environment.

Third, and perhaps most damaging, the group concludes that the area is as vulnerable now as it was nine years ago in the days before Hurricane Sandy arrived. The group wrote that “no regional costal resilience plan” is in place to protect over 1,000 miles of the New York and New Jersey metropolitan coastline.

Fourth, the changing political climate presents an opportunity to do something. The group highlighted how a new governor of New York, the start of a new term or releected governor in New Jersey, a new mayor of New York City and the restarting of the $20 million New York and New Jersey Harbor and Tributaries Focus Area Feasibility Study, or HATS, presents a “once in a lifetime opportunity to act now to address the existential threat of costal flooding with a regional coastline resilience system that meets our social justice, environmental justice, quality of life and economic development goals.”

Bowman urged New York and New Jersey residents to consider the progress other states and countries have made.

“Houston is going ahead,” Bowman said, even while New York hasn’t taken any significant steps.

Bowman said part of the challenge in creating any change that protects the area comes from the lack of any enduring focus on a vulnerability that isn’t evident to residents on a daily basis.

“People have short memories,” Bowman said. “It’s not on their minds” even if they endured the disruption and devastation from storms like Sandy and Ida.

Necessity and the lack of deep pockets in other countries is the mother of invention.

“A lot of countries can’t afford” to rebuild the way New York and New Jersey did after Hurricane Sandy,” Bowman said. “They are forced to be more careful.”

Bowman said any major project to protect the area needs a hero who can tackle the details, navigate through the politics and execute on viable ideas.

The late Daniel Patrick Moynihan had “that kind of charisma,” Bowman said. “We need somebody who everybody sees as the hero. I don’t see that person” at this point.

For New York and New Jersey, the longer time passes without any protective measures, “the more the danger will increase,” Bowman cautioned.

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Qingyun Li. Photo by Xuecheng Chen

By Daniel Dunaief

Qingyun Li has a plan for carbon dioxide.

The newest hire in the Department of Geosciences at Stony Brook University, Li, who is an assistant professor, is a part of a team exploring carbon capture and storage.

“My work is expected to help reduce the amount of carbon dioxide released into the atmosphere,” Li said. It will “help people find ways to promote carbon dioxide mineralization for safer carbon dioxide storage” below the ground. While her work will help promote carbon storage, it doesn’t include capturing and transporting the gas.

By selecting sites carefully, researchers can store carbon dioxide for geologically long periods of time.

While carbon sequestration occurs on the scale of kilometers, Li often works on a minuscule level, at the nanometer to centimeter scale. Smaller scale alterations affect properties such as the permeability of the rock formation.

Li is trying to predict nucleation of a certain mineral in her computer models. She has done that for carbonate minerals, which could be what carbon dioxide becomes after it is stored in geologic formations.

A similar process of nucleation occurs in clouds, when fine particles form the nuclei around which gases condense to form water or ice.

Li used a small angle x-ray scattering synchrotron to explore important details about each particle. This technique, which doesn’t look directly at the particles, reveals through data analysis the particle’s shape, size and surface morphology and, eventually, the rate at which nucleation occurs.

For carbon dioxide sequestration, the minerals that provide nucleation start at the nanoscale, which give them a high specific surface area.

“That matters for later reactions to generate carbonate minerals,” Li said. “That’s one reason we care about the nanoscale phenomenon. The bulk minerals are generated starting from the nanoscale.” 

A larger surface area is necessary in the beginning to lead to the next steps.

Li’s work involves exploring how carbonate starts to form. Her earlier efforts looked at how calcium carbonate forms in the aqueous or water phase.

Carl Steefel, Head of the Geochemistry Department at the Lawrence Berkeley National Laboratory in California, worked with Li during her PhD research at Washington University in St. Louis. Steefel believes her research will prove productive.

“She has an approach to science that combines that one-of-its-kind capabilities for studying nucleation with a deep understanding of modeling and how these open systems involving flow and transport work,” Steefel said. “The combination of these unique capabilities, in nucleating and in understanding reactive transport modeling, will put her a very good position.”

As of now, Li plans to study carbon sequestration in natural gas formations in shale, which has nanometer sized pores. The particles can change the permeability of the rock.

Some companies, like British Petroleum and ExxonMobil, have started to explore this method as a way to reduce their carbon footprint.

While geologic carbon sequestration has shown promising potential, Li believes the process, which she said is still feasible, could be decades away. She said it may need more policy support and economic stimuli to come to fruition.

Part of the challenge is to incorporate such carbon sequestration in the established market.

Scientists working in this field are eager to ensure that the stored carbon dioxide doesn’t somehow return or escape back into the atmosphere.

“People are actively investigating possible leakage possibilities,” Li wrote in an email. “We try to design new materials to build wells that resist” carbon dioxide deterioration.

Controlling pressure and injection rates could prevent various types of leaks.

In her earlier studies, Li explored how cement deteriorates when contacted with carbon dioxide-saturated brine. She hoped to find cracks that had self-healing properties. Other studies investigated this property of concrete.

It’s possible that a mineral could form in a fracture and heal it. In natural shale, scientists sometimes see a fracture filled with a vein of carbonate. Such self healing properties could provide greater reassurance that the carbon dioxide would remain stored in rocks below the surface. Li hopes to manage that to inhibit carbon dioxide leakage.

The assistant professor grew up in Beijing, China, studied chemistry and physics in college. She majored in environmental sciences and is eager to apply what she learned to the real world.

For her PhD, Li conducted research in an engineering department where her advisor Young-Shin Jun at Washington University in St. Louis was working on a project on geologic carbon dioxide sequestration. 

In her post doctoral research at SLAC National Accelerator Laboratory, which is operated by Stanford University, Li explored mineral reactions in shale, extending on the work she did on mineral reactions in concrete as a graduate student. She sought to understand what happens after hydraulic fracturing fluids are injected into shale. These reactions can potentially change how easily the mix of gas and oil flow through a formation.

With Stony Brook building a lab she hopes is finished by next spring, Li plans to hire one graduate student and one post doctoral researcher by next fall.

She is teaching a course related to carbon sequestration this semester and is looking for collaborators not only within geoscience but also within material science and environmental engineering.

Li is looking forward to working with other researchers at the National Synchrotron Lightsource 2 at Brookhaven National Laboratory, which provides beamlines that can allow her to build on her earlier research.

Li and her husband Xuecheng Chen, who are renting an apartment in South Setauket and are looking for a home close to campus, have a three-year old son and an 11-month old daughter.

Outside the lab, Li enjoys quality time with her family. A runner, Li also plays the guzheng, which she described as a wooden box with 21 strings.

Steefel, who wrote a letter to Stony Brook supporting Li’s candidacy to join the Geosciences Department, endorsed her approach to science.

“She’s very focused and directed,” Steefel said. “She’s not running the computer codes as black boxes. She’s trying to understand what’s going on and how that relates to her experiments and to reality.”

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From left, 8 1/2-year-old Dan Barsi, Jennifer Barsi, Maggie Barsi (age 4), James Barsi, and Lily Barsi (age 7)

By Daniel Dunaief

Daniel Dunaief

If your children are under the age of 12 and the Food and Drug Administration soon approves a COVID-19 vaccine, you’ll have many people to thank for the opportunity to return them to a more normal, and safer, childhood, including four-year-old Maggie, seven-year-old Lily and eight-and-a-half-year-old Dan Barsi.

The three siblings, who live in East Setauket with their parents James and Jennifer Barsi, recently participated in a clinical trial for the COVID-19 vaccine at Stony Brook Hospital. While the children don’t know whether they received vaccinations for the virus or the placebo, they are three of numerous children who volunteered to test the Pfizer-BioNTech vaccine to make sure it was safe before health care providers administer it to the broader population.

Their children “knew what they were signing up for,” said Dr. James Barsi, a pediatric orthopedic surgeon. “It’s something to help other people.”

Indeed, the community benefits from volunteers like the Barsis, who participate in clinical trials that evaluate the effectiveness of the treatment, help determine the correct doses, and reveal potential side effects before the rest of the population gets the COVID-19 vaccine or any other medicine or therapeutic intervention.

“We would never make advances in medicine without families — adults and children — volunteering to participate in clinical trials,” said Dr. Sharon Nachman, Chief of the Division of Pediatric Infectious Diseases at Stony Brook Children’s Hospital.

Some treatments for a range of illnesses or conditions look promising in the earlier stages of clinical development, such as phase 1 or phase 2. When they reach phase 3, during which researchers provide medicine to a much larger volunteer population, they sometimes fall short of expectations.

“Companies will tout drugs as the next best thing,” Dr. Nachman said. “When they get into phase 3, they are not better than standard therapy.”

Clinical trials on even an ineffective drug or one that produces side effects, however, can help pharmaceutical companies and health care providers by signaling what these professionals should look for in future treatments, Dr. Nachman added.

While volunteers of any age take risks by participating in these studies, they also have considerable medical oversight.

“They are well protected,” Dr. Nachman said. “When you participate in a clinical trial, you don’t just have two sets of eyes on you; you have 100 sets of eyes.”

Volunteers for clinical trials not only take some risk before everyone else in the community, but they also experience regular testing and monitoring.

The Barsi children, for example, had to have blood work and nose swabs. “We call it a brain swab,” Jennifer Barsi said. “The kids are so excited about getting a treat afterwards, but they still have to do the hard thing.”

Health care professionals throughout Long Island shared their appreciation for clinical trial volunteers. Without them “none of these innovative therapies and drugs would exist,” said Stephanie Solito, Research Manager of the Oncology Service Line at Catholic Health, which includes Smithtown-based St. Catherine of Siena and Port Jefferson-based St. Charles Hospital.

When Daniel Loen, Catholic Health’s Vice President of Oncology Services, takes any medicine, he appreciates that patients were “willing to sacrifice something or take on some kind of increased risk to get on a trial for the good of humanity and medicine.”

As for the specific COVID-19 pediatric trials, Dr. Nachman said parents and children have to approve to participate. Doctors talk with children in an age-appropriate way about these clinical trials.

Dan Barsi was born at 25 weeks old. He stayed in the hospital for several months and is now a healthy child.

Jennifer and James felt that this was their opportunity to give back to the next generation. The children who participated in clinical research before Dan was born helped make it possible for him to get the best treatment, and now they feel they’re doing the same thing.

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