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Daniel Dunaief

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Photo from SBU

By Daniel Dunaief

Daniel Dunaief

Isaiah Nengo recalled a day years ago when he was working in a field station in Kenya, searching for fossils.

A man who had a tremendous influence on his life was on the way to alter his horizons yet again, although this time the visit would have nothing to do with science.

Richard Leakey, the late founder of the Turkana Basin Institute (TBI) and a famed paleoanthropologist and conservationist, was bringing food from his home on the coast of Kenya in Lamu to the field station.

Leakey “prepared this lobster meal,” said Nengo, who is native of Nairobi, Kenya, and is currently associate director of TBI. “It was my first seafood meal. It was fantastic. I was like, ‘I’m sitting almost 600 miles from the ocean, it’s hot as hell and I’m eating lobster.’ That always stuck in my mind.”

Leakey, who died on Jan. 2 (see a tribute to the Stony Brook legend in this week’s Arts & Lifestyles page B12), left behind a lasting scientific legacy that filled science textbooks of people around the world, while he left an enduring food legacy that filled the stomachs of family, friends, coworkers and colleagues.

People fortunate enough to dine with him shared tales of Leakey’s culinary prowess and refined tastes.

Sonia Harmand, associate professor in the Anthropology Department at Stony Brook, took a long flight with Leakey to Kenya. Leakey had a salmon meal on the plane that didn’t meet his standards.

“He called the staff, and even the pilot came by to say hi because everybody knows about him,” Harmand said. Amid the introductions, he expressed his displeasure with the salmon.

When he returned to Kenya, he wrote to the airline and complained about the food.

As a host, Leakey went out of his way to make sure all of his guests enjoyed the food he purchased, prepared and served.

Harmand said her daughter Scarlett, who will turn nine in February, enjoyed eating at Leakey’s house because he prepared mussels and oysters he knew appealed to her.

“Every time you had a meal with him, he kept on asking if you liked it,” Harmand said.

Harmand also appreciated the unexpected gifts of incongruous foods at TBI. One day, Leakey arrived with ice cream and fresh strawberries.

“We had to eat it quickly,” she recalled with a laugh.

Another long time friend and colleague, Lawrence Martin, the director of TBI, said Leakey had a fondness for some Long Island foods. He particularly enjoyed ducks, as well as oysters and mussels from Long Island’s waterways.

“He said mussels were never as good in the warm water as they were in Stony Brook,” Martin said.

When he first got to know Leakey, Martin said Leakey cooked all the meals they shared, whether they were in Stony Brook or Kenya.

Martin called Leakey a “great chef” and said his late colleague “loved good food and loved going food shopping.”

While Leakey shared important information with former Stony Brook President Shirley Kenny, he also dined on memorable meals.

When they were on their own on Long Island without their spouses, Kenny invited Leakey over to her home for a meal.

After the dinner, he thanked her and promised he would return, providing she allowed him to do the cooking.

Sharing food with Leakey often meant benefiting from his storytelling prowess and his sense of humor.

Kenny and her family went on a safari with Jim and Marilyn Simons, co-founders of the Simons Foundation and supporters of science throughout Long Island.

“At the end of the day, we would sit in a circle and have drinks and [Leakey] would regale us with stories that were absolutely wonderful,” Kenny said. “You can’t even imagine how they made these [incredible] meals when there’s nothing out there to do it with.”

With hyenas howling at night and hot showers created with water heated by the sun during the day, the entire experience was “so exotic and so elegant at the same time,” Kenny added.

Harmand said Leakey didn’t cook with the goal of winning over people, but, rather, to share a connection.

“I don’t think he needed to impress anyone,” Harmand said. “He wanted to please you through food.”

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Sean Clouston. Photo by Rachel Kidman

By Daniel Dunaief

The same wind that powers sailboats, makes kites dart through the air, and causes flags to flutter can make being outdoors in a group safer, particularly during the pandemic.

While public health officials have suggested that being outdoors with others amid the pandemic is safer than remaining inside, the strength of the wind can affect the level of protection provided by wide open spaces.

That’s the conclusion Sean Clouston, Associate Professor in the Program in Public Health and the Department of Family, Population and Preventive Medicine at the Renaissance School of Medicine at Stony Brook University, reached after studying public health data from 96,000 cases of COVID in Suffolk County from March 16, 2020 to December 31, 2020.

By combining public health data with the daily reports from the National Oceanic and Atmospheric Administration, Clouston found that days in which the temperature was between 60 and 84 degrees Fahrenheit and in which the wind was about 5 miles per hour or less had higher COVID-19 transmission than those days in which the wind speed was faster.

This kind of study, which was recently published in the journal BMC Infectious Disease, might affect the guidance policy makers provide to reduce the risk of COVID transmission during outdoor gatherings.

“If you’re imaging yourself as a policy maker and you want to contain COVID, what do you do?” Clouston asked rhetorically. Vaccines and masks are established tools. Ensuring airflow is higher might also be important, he suggested.

Indeed, amid the early days of the pandemic in 2020, public officials closed parks in Suffolk County for a while and eventually reopened them.

An alternative could be to provide access to parks where wind speed is also protective, or to reduce the use of parks where social distancing is difficult and where wind speed is lower.

At the same time, residents might want to protect themselves by putting out fans in their backyard or some other airflow devices to keep the flow of air moving during a social gathering, reducing the chance of transmitting the virus. People might want to avoid using tents that reduce the flow of air around them.

Additionally, people could eat out at restaurants where the airflow is stronger. 

Diners can search for places where the air “moves around, so the outdoor experience is as protective as possible,” Clouston said. He recognized that the data had some variability between when people who went outside might have contracted COVID. The air flow could increase and then decrease and the average length of time from exposure to symptoms and testing could differ between people.

“Any time we deal with humans, this is the problem,” Clouston said. Researchers can’t control for everything. Instead, they have to assume people make decisions in a consistent, but variable, way.

The larger data set, with close to 100,000 cases, enabled Clouston and his colleagues to average out the effects of the time when people reported their positive COVID tests.

For numerous cases, people had a good idea where and how they contracted COVID. Even when they were at outdoor events, such as a barbecue, some people had indoor parties where they ate together.

In addition, merely being outdoors didn’t reduce the risk if people were standing in the equivalent of stale air, where wind couldn’t reach them and help carry viral particles away from others who attended these events.

Being outside if the air isn’t moving is similar to being indoors in a space with a very large ceiling and a wide space between walls, he explained. It is safer than a small room, but it is not inherently safe on its own.

As for air circulation indoors, Clouston said people have suggested that moving air in buildings could reduce the spread of the virus.

Testing the effects of having HEPA filters or air filtration systems run continuously in hospitals  compared to areas that don’t have such units could reveal the benefit of having these air flow systems. Some studies have been done on this, although more work is ongoing, he said. 

Clouston suggested that other environmental conditions could also impact the transmissibility of the virus. The heat index, for example, might explain why wind speed might be important.

The heat index “might diminish the effect or make it stronger,” Clouston said. “It can push people indoors.”

Clouston worked on this study with Stony Brook colleagues in the Department of Family, Population and Preventive Medicine Assistant Professor Olga Morozova and Professor Jaymie Meliker. The team has worked with the Suffolk County Department of Health since 2020 on different aspects of COVID modeling.

Clouston was surprised that the research revealed a threshold model wind speed. He was also surprised to see that the speed was so low. “You only need a little airflow,” he explained.

The Stony Brook scientist looked at where the positive cases were located by zip code. The summer distribution and the spatial distribution was somewhat unclear, he said.

The spread of COVID was distributed by population size and density. Population size and density are likely more important than alterations in microclimate in the summer.

The analysis is important for places when and where outdoor exposures are most common, he explained.

“This may be true in the summer on Long Island or in the winter in southern states like Louisiana when outdoor activities are more comfortable,” he wrote in an email.

Clouston has several ongoing projects. He has papers discussing the role of social inequalities and COVID, a paper looking at clinical risk factors for COVID at Stony Brook Hospital, and one describing the initial wave of COVID in World Trade Center responders.

He would like to look at the effect of outdoor protests during 2020 on the spread of COVID, which would require data on attendance at those events and at the ones in New York City.

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Pixabay photo

By Daniel Dunaief

I am a terrible loser.

Daniel Dunaief

I blame John McEnroe, Billy Martin, Lou Piniella, Pete Rose, and a host of politicians who couldn’t, or wouldn’t, accept defeat.

All of those people hated to lose. McEnroe had temper tantrums that were so epic that he’s spoofed himself many times, complaining in movies that “you can’t be serious” when things don’t go his way.

Frustrated with the umpiring in a game, Martin would kick dirt on home plate or have an epic meltdown in front of over 50,000 people.

I don’t ever remember any of those tirades or temper tantrums when they or their teams were winning.

Being American means winning. To borrow from the cliche, it means giving 110%.

I can’t tolerate losing, just as CEOs, politicians, athletes and sports coaches and managers can’t stand it, either. Many people hate losing as much if not more than they enjoy winning.

The fans who pay to see their teams win, not just to see them play, boo mercilessly when stars like the New York Knicks Julius Randle don’t live up to their contracts and don’t lead the team to more victories than defeats.

Randle recently expressed his frustration in response to the fans’ disappointment by giving them the thumbs down in a game.

Unconditioned positive regard, however, doesn’t come with having your name in lights or being a star on a celebrated team.

We get that from family members, sometimes, and from psychologists or psychiatrists.

As Americans, we have expectations of ourselves that have been set, in some cases, by role models like athletes, politicians and other popular icons.

At the end of the year, sports networks don’t focus on the best concessions speeches and the most gracious losers.

They are much more likely to replay the greatest rants and epic press conferences when athletes or coaches completely lose their composure in response to a question. We watch in rapt fascination as these superstars have a tantrum or glumly express disappointment.

Being a sore loser is also good business. The media empires on the left and the right long ago figured that out. During the Trump administration, nothing the former president said or did was good enough. The outrage factor over his thoughts, actions, gaffes and verbal inadequacies were attacked mercilessly.

Fox, which spent the last four years laughing at the liberal crying machine, has now turned its attention to attacking President Joe Biden (D) in a similar fashion, mocking everything he says or does or doesn’t do. 

People in the sports world describe muscle memory. They train their bodies and minds to react to evolving situations instantly, so they know where to go, what to do, and how to advance their cause.

That preparation almost never includes lessons on what to do when you lose or are losing. No one plays to lose, and yet, every game has a loser.

Maybe this year, we should prepare ourselves better for the moment we lose. We don’t have to be miserable, stare out blankly at the field, the way baseball players always do after the last game of the World Series, wishing they could have been that team that’s dogpiling near the pitcher’s mound.

Maybe this year, when people are continuing to struggle with a third year of the pandemic, we can hope for a celebration of great competition from both teams. 

We can take comfort and feel joy in the recognition that we brought out the best in each other.

Even when we lose, we can, to borrow from Lou Gehrig, still feel like the “luckiest people on the face of the Earth” for having been a part of something we know is special, regardless of the outcome.

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Ramana Davuluri

By Daniel Dunaief

Ramana Davuluri feels like he’s returning home.

Davuluri first arrived in the United States from his native India in 1999, when he worked at Cold Spring Harbor Laboratory. After numerous other jobs throughout the United States, including as Assistant Professor at Ohio State University and Associate Professor and Director of Computational Biology at The Wistar Institute in Philadelphia, Davuluri has come back to Long Island. 

As of the fall of 2020, he became a Professor in the Department of Biomedical Informatics and Director of Bioinformatics Shared Resource at Stony Brook Cancer Center.

“After coming from India, this is where we landed and where we established our life. This feels like our home town,” said Davuluri, who purchased a home in East Setauket with his wife Lakshmi and their six-year-old daughter Roopavi.

Although Davuluri’s formal training in biology ended in high school, he has applied his foundations in statistics, computer programming and, more recently, the application of machine learning and deep algorithms to the problems of cancer data science, particularly for analyses of genomic and other molecular data.

Davuluri likens the process of the work he does to interpreting language based on the context and order in which the words appear.

The word “fly,” for example, could be a noun, as in an insect at a picnic, or a verb, as in to hop on an airplane and visit family for the first time in several years.

Interpreting the meaning of genetic sentences requires an understanding not only of the order of a genetic code, but also of the context in which that code builds the equivalent of molecular biological sentences.

A critical point for genetic sequences starts with a promoter, which is where genes become active. As it turns out, these areas have considerable variability, which affects the genetic information they produce.

“Most of the genetic variability we have so far observed in population-level genomic data is present near the promoter regions, with the highest density overlapping with the transcription start site,” he explained in an email.

Most of the work he does involves understanding the non-coding portion of genomes. The long-term goal is to understand the complex puzzle of gene-gene interactions at isoform levels, which means how the interactions change if one splice variant is replaced by another of the same gene.

“We are trying to prioritize variants by computational predictions so the experimentalists can focus on a few candidates rather than millions,” Davuluri added.

Most of Davuluri’s work depends on the novel application of machine learning. Recently, he has used deep learning methods on large volumes of data. A recent example includes building a classifier based on a set of transcripts’ expression to predict a subtype of brain cancer or ovarian cancer.

In his work on glioblastoma and high grade ovarian cancer subtyping, he has applied machine learning algorithms on isoform level gene expression data.

Davuluri hopes to turn his ability to interpret specific genetic coding regions into a better understanding not only of cancer, but also of the specific drugs researchers use to treat it.

He recently developed an informatics pipeline for evaluating the differences in interaction profiles between a drug and its target protein isoforms.

In research he recently published in Scientific Reports, he found that over three quarters of drugs either missed a potential target isoform or target other isoforms with varied expression in multiple normal tissues.

Research into drug discovery is often done “as if one gene is making one protein,” Davuluri said. He believes the biggest reason for the failure of early stage drug discovery resides in picking a candidate that is not specific enough.

Ramana Davuluri with his daughter Roopavi. Photo by Laskshmi Davuluri

Davuluri is trying to make an impact by searching more specifically for the type of protein or drug target, which could, prior to use in a clinical trial, enhance the specificity and effectiveness of any treatment.

Hiring Davuluri expands the bioinformatics department, in which Joel Saltz is chairman, as well as the overall cancer effort. 

Davuluri had worked with Saltz years ago when both scientists conducted research at Ohio State University.

“I was impressed with him,” Saltz said. “I was delighted to hear that he was available and potentially interested. People who are senior and highly accomplished bioinfomaticians are rare and difficult to recruit.”

Saltz cited the “tremendous progress” Davuluri has made in the field of transcription factors and cancer.

Bioinformatic analysis generally doesn’t take into account the way genes can be interpreted in different ways in different kinds of cancer. Davuluri’s work, however, does, Saltz said.

Developing ways to understand how tumors interact with non-tumor areas, how metastases develop, and how immune cells interact with a tumor can provide key advances in the field of cancer research, Saltz said. “If you can look at how this plays out over space and time, you can get more insights as to how a cancer develops and the different part of cancer that interact,” he said.

When he was younger, Davuluri dreamt of being a doctor. In 10th grade, he went on a field trip to a nearby teaching hospital, which changed his mind after watching a doctor perform surgery on a patient.

Later in college, he realized he was better in mathematics than many other subjects.

Davuluri and Lakshmi are thrilled to be raising their daughter, whose name is a combination of the words for “beautiful” and “brave” in their native Telugu.

As for Davuluri’s work, within the next year he would like to understand variants. 

“Genetic variants can explain not only how we are different from one another, but also our susceptibility to complex diseases,” he explained. With increasing population level genomic data, he hopes to uncover variants in different ethnic groups that might provide better biomarkers.

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Pexels photo

By Daniel Dunaief

Daniel Dunaief

He was a part of my wife’s family’s inner circle for years. He appeared at summer gatherings and at significant family events and celebrations.

With his white hair, his signature smile and a Polish accent that seemed as fresh in each conversation as it likely was the first time he arrived in the United States, Carl wandered in and out of conversations and rooms, often smiling and always listening.

He seemed as comfortable in his own skin as anyone I’d ever met, paying close attention to his wife, interacting with his children and grandchildren and soaking up life the way everyone around him soaked up the warm rays of the sun.

Carl watched one day almost 20 years ago when my daughter got too close to the pool’s edge, falling in before she could swim. I immediately jumped off the diving board and brought her back up, where, as I dried her off, she protested that it took too long for me to get her.

When my daughter felt comfortable and confident enough to walk away from me, Carl waited for me to make eye contact.

“That’s what you do when you’re a father,” he smiled.

I nodded and sighed while my blood pressure and pulse returned to normal.

Several times over the years, Carl and I sat next to each other, sharing buffet-style meals of chicken kebobs, pasta, and filets.

Carl didn’t have the numbers tattooed on his arm, but I knew some of the story of his life. I didn’t want to bother him or upset him with a discussion of what was a painful and difficult period.

Once, when we were alone inside a screened-in area, I raised the topic.

“Hey, Carl, I understand you survived the holocaust,” I said.

When he looked me in the eyes, he narrowed his lids slightly, processing what I said and, likely, trying to figure out whether he wanted to talk.

“It’s okay,” I said, immediately backing off. As a journalist, I have a tendency to ask questions. I recognize, however, the boundaries that exist during social interactions and with family and friends. I wanted to speak with him to hear about what had been an unspoken part of his life.

“Yes, I survived,” I said.

“How? Where?”

“In the woods,” he said. “I lived in the woods when the Nazis came.”

He described how he was so hungry that he ate leaves, bugs and bark. That, however, was far preferable to being caught by the Nazis, who had murdered the rest of his family. Carl had been a teenager when he escaped to the woods, avoiding Nazi guards who were always searching for people they deemed enemies and who they readily killed.

Surrounded by a collection of other people who might, at any given time, vanish forever, Carl survived for several years, emerging at the end of the war to try to restart a life shattered by violence and cruelty.

After a brief description of his experience, he told me how important he felt it was that people study the specifics of World War II and understand what really happened to him, his family and people in so many other countries. It angered him that people tried to ignore a history that took so much from him.

All those years later, Carl seemed so easy going and relaxed, so prepared to laugh and smile and to enjoy another bite of lunch or dinner.

Carl recently died. I’m sorry for the loss to his family. I’m glad to have known him and to have shared a few meals, a few smiles and a few stories. All those days, months and years of life, like initials carved into a tree, showed that he was, indeed, here and, having seen his family react and interact with him, that his life had meaning.

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Pixabay photo

By Daniel Dunaief

While wind is nice and effective, moving water is even more promising, especially in the future of alternative energies.

Ali Khosronejad. Photo from SBU

That’s because water is almost 1,000 times more dense than air, which means that the movement of the wet stuff due to tides or storms could produce a considerable amount of energy.

Indeed, “if we can effectively harness the energy from moving waters in our national waterways alone, it could provide enough energy to power the whole country,” said Ali Khosronejad, Assistant Professor in the Department of Civil Engineering at Stony Brook University.

Khosronejad recently received $2 million as part of a $9.7 million four-year Department of Energy grant to study and develop ways to turn the movement of water into usable energy.

“I’m very optimistic about the future of this” approach, he said.

The DOE funds, which will involve a collaboration with East Carolina University, the University of New Hampshire, and Lehigh University, is a part of the new Atlantic Marine Energy Center, for which Khosronejad is a co-director.

The funds at Stony Brook will support hiring researchers at numerous levels, from post doctoral scientists, to graduate students and undergraduates. The money will also support adding new computer modules and expanding storage at the supercomputer. 

Stony Brook will also tap into these funds to enable travel for these new hires, to help them interact in person with their collaborators from other universities.

The combined effort at these academic centers will be dedicated to researching ocean energy technology, education and outreach. 

Researchers will work in the field, the laboratory and with computers on these ocean energy projects. They will seek to use wave energy and tidal energy conversion through such efforts as wave energy converters and tidal turbine farms.

This image depicts simulated turbulence in a waterway where a virtual tidal farm can be installed. The Stony Brook research team will use such simulations to investigate potential renewable ocean energy options. Image from Ali Khosronejad

The wave-energy converter floats on the seawater surface and uses the energy from the up and down motion of the water surface to produce electrical energy.

Researchers around the world are working to improve the efficiency of tidal turbine farms. Khosronejad described the effort as being in its infancy.

A good portion of the current project involves finding ways to optimize the positioning and layout of turbines in tidal farms. In his team, Khosronejad will work on the development of new artificial intelligence approaches to optimize the positioning and layout of turbines in tidal farms.

Stony Brook’s role in this project will involve working with computers.

In his research group, Khosronejad will work with supercomputers. His effort involves working to develop high-fidelity mathematical models that can address sediment transport and sediment-laden flows in tidal farms. 

Scientists at the University of New Hampshire and ECU are involved in addressing environmental concerns.

In the Department of Electrical Engineering at Stony Brook, co-principal investigators Fang Luo, Associate Professor and Peng Zhang, Professor in the Department of Electrical Engineering will work with computers and laboratories for micro-grid software and hardware research, respectively.

Ali Khosronejad, right, with former graduate student Kevin Flora, who earned his PhD in 2021

Working with Lehigh University, Khosronejad is doing high fidelity simulations, to replicate what researchers in the field at the University of New Hampshire and the Coastal Studies Institute at ECU are studying.

“We validate and develop artificial intelligence for design optimization of these tidal farms,” Khosronejad explained. The goal is to optimize the design of hydrokinetic turbines in estuaries and coastal areas that can create tidal farms.

The collaboration will coordinate with the National Renewable Energy Laboratory, Sandia National Laboratories, Pacific Northwest National Laboratory, European Marine Energy Centre and Old Dominion University.

The first year of the project involves hiring, training graduates and undergraduates, setting up the foundation, and beginning the infrastructure upgrade.

“The training part is important,” Khosronejad said. “This will be the next workforce. The infrastructure will stay there for the next 10 years” so the university can use it in a host of other projects.

Khosronejad is encouraged by the financial commitment from the Department of Energy. “They understand how important it is, which is why they are investing a lot in this,” he said. Some of these tidal farms are already working in the East River, between Manhattan and Roosevelt Island.

Wind turbines

At the same time, Khosronejad is continuing a wind turbine project he started with Fotis Sotiropoulos, the former dean of the College of Engineering and Applied Sciences at Stony Brook who is now Provost at Virginia Commonwealth University.

Khosronejad is now the principal investigator on that $1.1 million project and is continuing to work with Sotiropoulos, who officially left the project but is still volunteering to participate in its research activities. The scientists are working on how to use artificial intelligence to enhance the design of wind turbines.

Computer programs can alter the angle of the blades for the offshore wind farms where they attempt to use a control system to pitch the blades automatically to reduce the wind load during highly turbulent wind flows.

Changing the angle of attack of the blade can lower the loads and save money that would otherwise go to repairing blades that cracked or developed weaknesses amid strong winds, Khosronejad said.

The researchers presented their results at the American Physical Society meeting in Phoenix just before Thanksgiving. 

The researchers are trying to balance between using the turbine to generate energy and preventing the force of the winds from damaging the system.

When wind speeds are up to 25 miles per hour, the system uses the full power of the wind to maximize energy production. At speeds above that, the turbulent wind can damage the rotor and gearbox. The blades are pitched to reduce the angular velocity, which is known as self-preservation mode. At speeds over 55 miles per hour, the turbine stops working to produce no energy and avoid significant damage to the rotors and gearbox.

Generally, such federal research projects involve sharing results publicly and with the industry sector. The goal is to share science that enables the production of reliable energy.

 

 

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

Dogs need to go outside, regardless of the temperature. My dog, who has a thick coat of hair, loves the winter and is perfectly happy to linger outside, especially when it’s close to freezing. When the grass is covered with frost, he slowly lowers his right cheek and does a lawn dive, bringing the rest of his body piece by piece down onto the cold, wet surface.

Once he’s completely on the ground, he rolls onto his back, using the blades of grass and the water and ice to scratch his back, while snorting with delight. With the eye that isn’t pressed into the ground, he stares at me, waiting for me to give up the ghost on getting some exercise or coming back inside quickly. When I reach down to pet him, I can almost see him smirk as he wags his tail triumphantly.

This month, he and I have seen some unusual sights. When I see something unusual, I try to take out my phone, but my reaction time, and all the extra material in my pocket, makes that a largely ineffective effort.

Even when I do manage to take out the camera and point it in the general direction of something interesting, the pictures typically disappoint, because my dog who hates to move suddenly gets the urge to pull just as I’m snapping the photo, leaving me with a blurry image of the road.

A few days ago, we were at the top of our street at dusk, near one of my dog’s favorite places to poop. In fact, I can take him on a four-mile walk and, within a tenth of a mile of our home, he finds his favorite blades of grass, takes his usual tentative steps, turns away from me — he needs privacy — and does his business.

This time, though, just as he was approaching his familiar spot, a hawk passed by only a few feet from my head, giving me a chance to look him, and the object he was carrying, squarely in the eyes.

The hawk was holding a squirrel, which seemed especially odd to me given the relative size of the two animals. The squirrel wasn’t moving but was clearly alive. When I told my family about it, they were sympathetic to the squirrel.

A few days later, walking toward the other end of the block, my dog and I observed a blow-up Frosty on one end of a lawn and a blow-up Santa on the other rise slowly from the ground as air flowed slowly into them.

My dog, whose fear of unusual inanimate objects builds around Halloween and the December holidays, stood at attention and considered announcing his presence with authority to objects that can’t, and don’t, react to his deep bark.

Fortunately, he only pulled his lips back slightly and lifted his tail, allowing the neighbors to enjoy their dark, quiet evening without the sound of a panicked pooch on a poop walk.

A few minutes later, I studied the stars at a distance when a light appeared in the sky, flashed toward the horizon and disappeared. Never having seen a shooting star before, I was mesmerized.

When I returned and shared the story, my son, who doesn’t seem too keen on superstition but is clearly aware of pop culture, asked if I made a wish. Not wanting to pass up the opportunity for help from anywhere, I did. Maybe by next December, I’ll let you know if it came true!

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From left, Daniele Rosado and Ullas Pedmale examine a sample of the model plant Arabidopsis. Photo courtesy of Ullas Pedmale

By Daniel Dunaief

Many plants are in an arms race akin to the developers of skyscrapers eager to get the most light for their prized penthouse apartments. Only, instead of trying to collect rent from well-heeled humans, these plants are trying to get the most sun, from which they create energy through photosynthesis.

Plants are so eager to get to the coveted sunlight that the part growing towards the light sends a distress signal to the roots when they are in the shade. While that might help an individual plant in the short term, it can create such shallow and ineffective roots that the plant becomes vulnerable to unfavorable weather. They also can’t get as many nutrients and water from the ground.

This is problematic for farmers, who want plants that grow in the sun, but that don’t sacrifice the development of their roots in the shade. Ullas Pedmale, Assistant Professor at Cold Spring Harbor Laboratory, is working to lend a hand.

Pedmale, who recently published research in the journal Plant Physiology, is studying the signals the shoots, or the parts of the plants either in the sunlight or the shade, send to the roots.

Pedmale and postdoctoral researcher Daniele Rosado, who is the first author on the recent paper, explored the genes that turned on in the roots of the model plant Arabidopsis and tomato plants when these plants were in the shade.

When plants are in the shade, they “prioritize shoot growth and try to outcompete the neighboring plants,” said Rosado. “That’s when root development is compromised.”

Among the genes that are active when plants are in the shade is a family of genes called WRKYs, which affect gene expression and cause stunted growth in the roots.

WRKY genes respond to stress. Keeping WRKY genes on all the time, even when a plant is in the sun, caused stunted growth of the roots. WRKY proteins turn on or off other genes.

This can be problematic for farmers, who tend to try to increase yield by putting more plants in an area. At that point, the plants shade each other, which is “bad for the root system. If we can find a way to get the roots to grow normally, we can potentially increase yield,” Rosado said.

This could also remove more carbon dioxide from the air and store it in the developing roots, helping to mitigate the effect of global warming. “Our study can give a roadmap on how to make longer, deeper roots,” Pedmale said.

At this point, researchers still don’t know how the plant transfers information about the amount of sunlight it receives in the green chloroplasts where photosynthesis occurs to the WRKY genes, which are in the nucleus.

Researchers have been studying the shade response in the shoots of plants for over five decades. They have not, however, focused as much attention on the effect of less sunlight on the roots.

“We want to tackle this problem,” Pedmale said.

WRKY genes are a generalized stress signal, which is not just involved when a plant isn’t getting enough light. They are also turned on during pathogen attacks, stress and amid developmental signals.

Indeed, plants in the shade that have turned on these signals are especially vulnerable to attacks. Caterpillars, for example, can eat most of a shaded plant because the plant is so focused on growing its shoot that its defenses are down.

When that same plant is in the sunlight, it is more effective at defending itself against caterpillars.

At this point, Pedmale doesn’t know whether these genes and signals occur across a broad species of plants beyond tomatoes and Arabidopsis. He and others are hoping to look for these genes in grasses and grains.

Pedmale is also searching for other signals between the shoot and the root. “Plants are masters of adaptation,” he said. “They might have redundant systems” that signal for roots to slow their growth while the shoots tap into the available energy to grow.

Plants may also have natural molecules that serve as brakes for the WRKY signal, preventing the shoot from taking all the available energy and rendering the plant structurally fragile.

A scientist at CSHL for five years, Pedmale came to the lab because of the talent of his colleagues, the reputation and opportunity at CSHL and the location.

Born and raised in Bangalore, India, Pedmale enjoys reading fiction and autobiographies and wood working when he’s not in the lab. He recently made a book shelf, which provides him with a chance to “switch off” from science, which, he said, is a 24-hour job. He has taken wood pieces from his workshop and brought them to PhD classes at CSHL, where he can show them plant biology and genetics at work.

Pedmale and his wife Priya Sridevi, who also works at CSHL, have a mini golden doodle named Henry.

A native of São Paulo, Brazil, Rosado is married to plant biologist Paula Elbl, who is the co-founder of a start up called GALY, which is trying to produce cotton in a lab instead of in a field.

Rosado is the first in her family to attend a public university. She has been working in Pedmale’s lab for two years and plans to continue her research on Long Island for at least another year.

Rosado knew Pedmale had worked as a post doctoral researcher in the lab of celebrated plant biologist Joanne Chory at the Salk Institute for Biological Studies. She met Pedmale at a plant conference, where she expressed an interest in his research.

Longer term, Rosado hopes her research has a broader impact.

“If I’m lucky, I’ll be able to see the fruits of my work being applied to make a difference and help feed people,” she said.

As for his work, Pedmale is eager to understand and use the signals from one part of a plant to another, given that the plant lacks a nervous system. “Once we can understand their language,” he said, “we can manipulate it to increase yield.”

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Jessica Tollkuhn Photo courtesy of CSHL

By Daniel Dunaief

They are like directors in a carefully choreographed production, instructing certain groups that become active, while giving others a five-minute break.

In the case of the human body, directors take many forms, including hormones; the same hormones that can transform adorable, sweet and well-behaved children into smelly, strong-willed teenagers.

Hormones like estrogen, testosterone and progesterone affect people at various ages and in different ways.

Recently, Cold Spring Harbor Laboratory Assistant Professor Jessica Tollkuhn and her graduate student Bruno Gegenhuber teamed up with University of California at San Francisco Herzstein Professor of Molecular Physiology Holly Ingraham to link the way estrogen in a specific area of the brain turns on particular genes.

For mice that are representative of post-menopausal women, the lower activity of a gene called melanocortin-4, or MC4R causes these mice to become less active.

By activating MC4R neurons in the ventrolateral ventromedial hypothalamic nucleus of the brain in the absence of estrogen, researchers caused a dramatic increase in physical activity and 10 percent body weight loss after one day.

Additionally, turning up the MC4R gene increased their bone density over time.

Linking the gene activated by estrogen in a part of the brain that affects how adult females use energy, the scientists provided a causative link that explains lower energy in this population.

Tollkuhn said her contribution showed that the estrogen receptor binds DNA in the presence of hormones.

The scientists published their research in the journal Nature.

“If anything, this paper is a study of how just one gene can show this exquisite behavioral response,” Tollkuhn added.

The MC4R gene is also found in the male brain, although not in the same area. Experimentally, turning up the gene also increases physical activity in males.

Numerous drugs currently target this gene in connection with increasing libido in post-menopausal women. Using these treatments for other issues, like weight gain and activity level, would require additional study.

Estrogen affects numerous other areas of the body, including some that may cause other problems. Hormone replacement therapy has contributed to the development or worsening of other cancers, such as breast cancer, although it is not clear why or how this happens.

“There’s evidence that there can be positive benefits [like bone and mental health], but also evidence that it can increase the risk of cancers,” Tollkuhn said.

Ingraham knew Tollkuhn from their overlapping research experiences at the University of California at San Diego and, later at UCSF.

Ingraham had reached out to Tollkuhn to see if the experiments in Tollkuhn’s lab could determine the link between the hormone and the MC4R gene.

“It’s always a challenge in biology to get a direct causality” because numerous factors in a living system could contribute to the development of a condition or a behavior, Tollkuhn said.

Tollkuhn suggested that the bulk of the experiments were done in Ingraham’s lab.

Ingraham recognized early on the benefit of finding these direct binding sites.

“We are saying, ‘Here is a hormone and it is acting through this molecule and it’s causing this change … that we know is really important for eliciting this behavior,” Ingraham said.

Ingraham, who worked with Tollkuhn when she was a post doctoral researcher and Tollkuhn was a graduate student in Geoffrey Rosenfeld’s lab at UC San Diego, called her colleague “really talented” and said she “spent years working this whole system out. It’s heroic and nobody else has done it.”

Ingraham sent Rosenfeld a message after the journal Nature accepted their paper, indicating his trainees had “hit pay dirt on this one.”

Ingraham hopes the paper motivates other researchers to think about entering this area and tackling this challenge, which is so important for women’s health.

“The only way we’re going to move forward for women’s health is to understand all these different facets of what estrogen is doing in the brain,” she added.

In press coverage of the research, Ingraham described the comments as falling into two categories. In the first, women suggest that they’re past menopause and have never been more active. In the second, women indicate that getting hormone replacement therapy genuinely helped them, including with brain fog.

Other scientists have sent Ingraham congratulatory emails about the paper. They have “appreciated that this had such a great molecular story,” she said.

In a broader research context, Tollkuhn is interested in determining how hormones affect the brain during sexual differentiation.

She is now focused on identifying a new repertoire that she and others can explore in future studies.

Tollkuhn’s lab is also investigating how estrogen influences brain development. She has found dozens of genes she would like to understand in the kind of detail with which she explored MC4R. Estrogen receptors also are connected to HTR1A and HTR1D, which are genes for serotonin receptors and may connect estrogen to mood.

Studies in scientific literature have shown that numerous psychiatric and neurological conditions have sex differences in terms of their impacts on men and women.

“We have these pieces and we can try to put together this puzzle,” Tollkuhn said. “We can try to understand why this would be the case. The long term goal is to figure out why there is a greater increase in [certain diseases] in men or women, which could lead to the development of better treatment.”

Tollkuhn is also interested in understanding the progression of neurodegenerative conditions like Alzheimer’s, which is twice as likely in women as in men. The symptoms for this disease develops more rapidly in post menopausal women, who typically have a more precipitous decline in estrogen than older men do in their levels of testosterone.

“I’m interested in what hormone receptors are doing in the brain,” she said.

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

When she was little, my daughter loved to build sand castles. She’d put wet sand in a bucket, gently pull the bucket back and marvel at the details in the castles that came out.

My son wasn’t as interested in building castles. He derived special pleasure out of stomping on the castles she made. It wasn’t just that it gave him power over the sand: he also felt power over his older sister, who was furious with him for crushing her castles.

While I tried to reason with him, which is almost as effective today as it was when he was two, I came up with an alternative plan that required additional energy from me, but that created peace on the beach. I’d quickly put together a ring of 15 castles, grabbing wet sand and dumping it several feet from where my daughter was working on her creation.

Like a young Olympic sprinter, my son would race over to the collection of castles and stomp all over them, while my daughter slowly built her own city of sand.

These days, it seems, we are surrounded by people eager to stomp on everyone else’s sandcastles.

Sure, it’s satisfying to feel the figurative sand in our toes and to revel in tearing down what other people have created.

But, really, given all the challenges of the world, I think we should ask a few questions of all those people who are so eager to belittle, attack and undermine others. What’s your solution? What are you doing better? How would you fix the problem?

Insulting others for their efforts, their awkwardness or their perceived flaws often seems like a form of ladderism. No one wants to be on the bottom rung of a ladder, so people try to push others down or to shout to anyone who will listen about how much better they are than the people below them. That seems to be a sign of weakness or insecurity, reflecting the notion that other people are below them.

In addition to dumping on others, we live in a society of people for whom hearing views that differ from their own somehow turns them into victims. Surely we have more choices than simply, “I’m right and you’re wrong.” If someone doesn’t agree with you, maybe it’s worth finding out why.

Anger, frustration and hatred, while they may make us feel slightly better in the moment, aren’t solutions and they don’t improve our world. They are a form of destructive energy, like stomping on sand castles.

We should ask more of ourselves and from our leaders. I’m tired of hearing about politicians who will fight for me. I don’t want to send people into office to fight against others who are trying to do the best they can for the country. I want leaders who will learn, listen and, gasp, reach across the aisle in the search for solutions.

While platforms aren’t as sizzling as slogans or take downs, they include ideas and potential solutions.

Civility makes it possible for us to hear and learn.

We have enough threats to our lives without needing to turn against other people or to give in to the urge to crush other people’s sandcastles to feel better. We don’t all have to be best friends, but it’d be nice to look forward to a holiday season and the start of a new year that focused on a shared sense of purpose. We need better ideas, not better ways to attack.

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