Babak Andi holds a 3-D model of the coronavirus responsible for the COVID-19 pandemic. Photo courtesy of BNL
By Daniel Dunaief
For close to two and a half years, the world has had a microbial enemy. The SARS-CoV2 virus, which causes Covid-19, has resulted in close to 6.5 million deaths, caused lockdowns, restricted travel, closed businesses, and sickened millions. The key to fighting such a dangerous enemy lies in learning more about it and defeating its battle plan.
Working with principal investigator Daniel Keedy, Assistant Professor at the City University of New York and Diamond Light Source in the United Kingdom, Babak Andi, who is a beamline scientist from the structural biology group at Brookhaven National Laboratory, spent over two years studying a key viral enzyme.
Recently, the researchers revealed the structure at five temperatures of an enzyme called Mpro, for main protease. This enzyme, which separates proteins the virus makes, is critical for the maturation of the SARS-CoV-2 virus particles. They published their work in the Journal of the International Union of Crystallography (IUCrJ).
Using the Frontier Macromolecular Crystallography (FMX) beamline at the National Synchrotron Light Source II at BNL, Andi collected data on the structure of the enzyme at temperatures ranging from 100 degrees Kelvin, which is about negative 280 degrees Fahrenheit, all the way up to 310 degrees Kelvin, which is normal body temperature. “Nobody had done that, specifically for this protein,” said Andi.
Keedy, who guided the data collection, processed the information and wrote most of the paper, described the effort as a “great collaboration.” The gradual change in the conformation of the enzyme helped the scientists learn how it may move or shape-shift in general, he explained.
Keedy had worked with BNL in the past and pursued research at the FMX beamline because the scientists at BNL had “been working with Mpro on site, and were very approachable and open to the idea.”
Finding the specific structure of important proteins like Mpro can help researchers, pharmaceutical companies and doctors search for inhibitors or small molecules that could be specific to these proteins and that might interfere with their function.
Andi and other scientists at this beamline worked through the pandemic shutdown because of the potential practical application of what they were doing.
“We almost had all the infrastructures in place to allow other scientists to connect and operate the beamlines remotely, enabling them to collect data on Covid-19 virus proteins,” said Andi. “In my opinion, being able to support all the academic and industrial scientists to collect data for Covid-19 research was our greatest achievement during the worst period of the pandemic.”
While coming into the lab in those early months raised concerns about their own health, Andi and his colleagues, who developed safety protocols, felt an urgency to conduct this research.
“When Covid hit, we had a sense that this is our duty, this is our job to contribute to this field, to make sure that every scientist who works on Covid-19 had easy access to our beamlines, facilities and all the tools [necessary] to make new drugs,” said Andi.
How they solved the structure
The technology for the beamline enables Andi and other scientists to collect data quickly and even remotely. Speed helps because the longer x-rays hit a protein, the more likely they are to cause the kind of damage that makes determining the structure difficult, particularly at higher temperatures.
The first step in this research was in producing this protein, which Andi’s collaborators at BNL in the biology department provided. The biology department also helped with crystallization.
Andi prepared the beamline and aligned the x-ray beam, which are necessary to collect data.
The scientists rotated and moved the crystal through the x-ray, distributing the beam over the length of the crystal to minimize radiation damage.
The small size of the x-ray beam made it possible to keep the beam focused on the smallest dimension of the structure. The researchers studied the crystal at five different temperatures, starting at cryogenic all the way up to physiological.
Of the 195,000 structures listed in the Protein Data Bank, or PDB, only five had been determined at body temperature. That includes two from the group of collaborators who participated in this study.
Andi collected three or four data sets at each temperature.
“The different conformations we saw may inspire a new twist on antiviral drug development that targets a different place in the protein, but with a similar or better effect,” Keedy explained.
The researchers did not include other factors that might affect the conformation of the protein, such as pH, pressure, the number of ions or salts in the environment, among others. For the Mpro protease to work, it has to bond to another similar protein, forming a dimer.
Andi said the Pfizer treatment Paxlovid binds to the active site of this enzyme, inactivating it.
The drugs he is looking for are similar, although he is also searching for other places on the enzyme besides its active site.
Keedy hopes to try to make a monomeric form of the enzyme through a mutation. He could then find drug-like small molecules that target the exposed interface between the two copies.
BNL origins
After he completed his PhD and post doctoral work at the University of Oklahoma, Andi started his career at BNL 11 years ago as a post doctoral researcher.
During his childhood, Andi was initially interested in astronomy. When he enrolled at a university outside the United States, he took an entrance exam.
“Based on your score, it tells you which discipline of science you can go into,” he said. His score directed him to the field of cell and molecular biology.
“I’m happy this happened,” he said. “I find that I’m actually more interested in molecular biology than in astronomy.”
Outside of work, Andi enjoys do-it-yourself projects. Astronomy also continues to appeal to him, as he is fascinated with astrophotography and reads astronomy articles.
As for the work with a Covid enzyme, Andi hopes he has other opportunities to contribute.
“I am interested [in continuing] the research in this field,” he explained. “That depends on time, resources and current or future priorities.”
From left, Chang Kee Jung, Barry Barish and Carl Lejuez. Photo by John Griffin/Stony Brook University
By Daniel Dunaief
Albert Einstein predicted gravitational waves existed, but figured interference on the Earth would make them impossible to observe. He was right on the first count. On the second, it took close to a century to create an instrument capable of detecting gravitational waves. The first confirmed detection, which was generated 1.3 billion light years away when two black holes collided, occurred in September of 2015.
For his pioneering work with gravitational waves, which now include numerous other such observations, Barry Barish shared the Nobel Prize in 2017 with physicists Rainer Weiss and Kip Thorne.
In the fall of 2023, Barish is bringing his physics background and knowledge to Stony Brook University, where he will be the inaugural President’s Distinguished Endowed Chair in Physics. Barish will teach graduate students and serve as an advisor to Chang Kee Jung, Chair of the Department of Physics and Astronomy and Distinguished Professor.
From left, Barry Barish and Chang Kee Jung. Photo by John Griffin/Stony Brook University
“I’m really happy,” said Jung in an interview. “Nobel Prize winning work is not all the same. This work [Barish] has done with LIGO [the Laser Interferometer Gravitational-Wave Observatory] is incredible.”
Jung suggested the discovery of these two merging black holes “opened up a completely new field of astronomy using gravitational waves.” The finding is a “once-in-a-generation discovery.”
Gravitational waves disrupt the fabric of spacetime, a four-dimensional concept Einstein envisioned that combines the three dimensions of space with time. These waves are created when a neutron star with an imperfect spherical shape spins, and during the merger of two black holes, the merger of two neutron stars, or the merger of a neutron star and a black hole.
Jung suggested a way to picture a gravitational wave. “Imagine you have a bathtub with a little rubber ducky,” he said. In the corner of the bathtub, “you slam your hand into the water” which will create a ripple that will move the duck. In the case of the gravitational wave Barish helped detect, two black holes slamming into each other over 1.2 billion light years ago, when life on Earth was transitioning from single celled to multi celled organisms, started that ripple.
While Barish, 86, retired after a lengthy and distinguished career at CalTech in 2005, Stony Brook has no plans to create a team of physicists who specialize in this area. “The most important thing is that people together exchange ideas and figure out what to do next that’s interesting,” Barish said in an interview. “I’ll keep doing gravitational waves.”
Instead of encouraging graduate students and even undergraduates to follow in his footsteps, Barish hopes to “help stimulate the future here and help educate students,” he said.
An important call
Jung, who became chair of the department in the fall of 2021, has known Barish for over three decades. On a periodic informal zoom call, Jung reached out to Barish to tell him Stony Brook had offered Jung the opportunity to become chair. Barish suggested he turn it down. As Jung recalled, Barish said, “Why do you want to do that?”
On another informal call later on, Jung told Barish he decided to become chair, explaining that he wanted to serve the university and the department. Barish asked him what he would do as chair. Jung replied, “‘I would like guys like you to come to Stony Brook. It took [Barish] about 10 seconds to think about it and then he said, ‘That’s possible.’”
That, Jung said, is how a Nobel Prize winning scientist took the first steps towards joining Stony Brook.
Last week, Barish came to Stony Brook to deliver an inaugural lecture as a part of the newly created C.N. Yang Colloquium series in the Department of Physics and Astronomy.
Stony Brook officials were thrilled with Barish’s appointment and the opportunity to learn from his well-attended on-site lecture.
In remarks before Barish’s packed talk at the Simons Center Della Pietra Family Auditorium, Carl Lejuez, Executive Vice President and Provost, said he hears the name C.N. Yang “all the time,” which reflects Yang’s foundational contribution to Stony Brook University. “It’s fitting that we honor his legacy with a speaker of Dr. Barish’s character who, like Yang, is also a Nobel Prize winner. It’s a really nice synergy.”
Indeed, Yang, who won his Nobel Prize in 1957, coming to Stony Brook “instantaneously raised the university profile,” said Jung, whose department is the largest on campus with 75 faculty.
Surrounded by a dedicated team of scientists, and with the addition of another Nobel Prize winner to the fold, Jung believes the team will continue to thrive.
“If you put together great minds, great things will happen,” he said.
Seeing the bigger picture
Barish is eager to encourage undergraduates and graduate students to consider the bigger picture in the realm of physics.
“[In general] we train graduate students to do something really important by making them narrower and narrower and narrower, so they can concentrate on doing something that’s worthy of getting a thesis and is as important as possible,” Barish said. “That works against creating a scientist who can look beyond something narrow. That’s bothered me for a long time.”
The problem, Barish continued, is that once researchers earn their degree, they continue on the same path. “Why should you happen to have had a supervisor in graduate school determine what you do for the rest of your life?” he asked.
Once students have the tools of physics, whether they are experimental or theoretical, they shouldn’t be so locked in, he urged. “It’s possible to use these same tools to do almost any problem in physics,” Barish added.
His goal in a course he plans to teach to advanced graduate students (that’s also open to undergraduates) is to provide exposure to the frontiers of science.
A few years ago, Barish recalled how the New York Times ran a picture of a black hole above the fold. He taught a class how scientists from around the world combined radio telescopes to make it act like one radio telescope the size of the Earth.
Helping students understand how that happened “pays off in the long run in making our physics students that we turn out be broader and more interesting and more interested in physics,” Barish said.
When Barish arrives next September, Jung said he plans to have some assignments for interactions with undergraduates. “Undergraduate research is critically important,” Jung said. Barish will also interact with various student groups, as well as the community outside the university.
Aleida Perez during BNL's virtual teaching sessions this summer
By Daniel Dunaief
For well over two years, herd immunity, vaccination status, social distancing, masking and airborne particles became regular topics of conversation.
People have a range of understanding of these terms and how to apply them to understanding the fluid conditions that are an evolving part of the pandemic.
Aleida Perez
This summer, with funding from the National Science Foundation, a group of scientists and doctors from Brookhaven National Laboratory, Stony Brook University, New York University and MoMath, the National Museum of Mathematics, worked together with middle school and high school teachers around Long Island to prepare lesson plans on how to use and understand the application of statistics to the pandemic.
“It was a wildly successful summer,” said Dr. Sharon Nachman, Chief of the Division of Pediatric Infectious Diseases at Stony Brook Children’s Hospital. “We spent hours and hours of time” working with teachers who developed lessons that addressed a host of issues related to COVID-19.
It was “an amazing experience” and the teachers “were the best part,” said Dr. Nachman.
Allen Mincer, Professor of Physics at New York University, has been working on and off with BNL for over two decades on various educational programs. He has been more actively engaged in the last four years.
As he and his collaborators were discussing possible educational outreach topics, they focused on the disruptive disease that changed the world over the last few years.
“This year, we were talking about it and, instead of doing random applications of statistics, we figured, why not do something that’s very practical in everyone’s mind,” Mincer said.
The projects and discussions, which were all conducted virtually, centered on numerous misconceptions people have about the pandemic. Teachers focused on questions including: what is the “efficiency” of a vaccine and how is it determined, what does a positive virus test result mean, if I am vaccinated, why do I care if others are, why take a vaccine when there are side effects, and I have to go to school and mix with people, so why shouldn’t I also let down my guard in other ways, among others.
“The challenges that this virus brings concerning topics like herd immunity was very interesting,” said Scott Bronson, manager of outreach to K-12 teachers and student for BNL’s Office of Educational Programs.
Scott Bronson during the BNL virtual teaching sessions this summer.
For teachers and their students, the realities of the pandemic were the backdrop against which these teachers were seeking to provide guidance. “It was happening live,” said Bronson. “What is herd immunity? That’s where the work of [Dr. Nachman and Mincer] came together beautifully.”
Bronson added that students will have a chance to explore the kinds of questions pharmaceutical companies are addressing, such as “What would you want the next vaccine to do” and “What would you do to make the vaccine better at preventing infection.”
The organizers put together teams of three to four high school and middle school teachers who created statistics lessons plans for the group.
“The way we worked it out, we put teachers in groups,” said Aleida Perez, supervisor of student research and citizen science programs for Brookhaven National Laboratory’s Office of Educational Programs. “We wanted to have different teachers with different courses and different perspectives on how to do things.”
One of the overarching goals was to help students understand such lessons as what it means to have a negative result on a virus test or what it meant when scientists and pharmaceutical companies described a vaccine’s efficacy.
The teachers explored the probability of side effects like myocarditis and whether the “benefit outweighs the risk of taking the vaccine,” Perez said.
For many of the teachers, the discussion expanded beyond COVID to an analysis of any infectious agent. Indeed, one of the groups of teachers described a zombie apocalypse.
The teachers provided a “nice overview to look at the education of public students,” said Perez.
The group hopes to make these lessons available for other teachers, although they haven’t determined where or how to post them.
The scientific team also hasn’t determined yet how to measure the long term impact or effectiveness of these lessons.
ATLAS project
As a part of the team involved in the ATLAS physics program at the Large Hadron Collider in Geneva, Switzerland, Mincer uses statistics to design, test and implement the tools to pick and choose from numerous reactions and then to study the data collected.
“We actually keep about a billion events out of the 100 trillion or so interactions the LHC produces in a year,” Mincer explained.
In previous years, Mincer has taught about statistics in general and its use in ATLAS. This year, he focused on statistics and its application to pandemic questions.
Several years ago, Mincer taught a freshman seminar called “Great science, fabulous science and voodoo science,” in which he described what students could learn from statistics, how the media covers science, science and government policy and how lawyers use science in the courtroom.
“After explaining statistics [and sharing] why we can only say we have evidence down to this level, I had a student tell me he’s dropping out of science as a major because he wanted certainty and I disillusioned him,” Mincer said.
As for the work with the high school teachers, Mincer said it was “great what they have been able to do” in preparing lessons for their students and sharing information about statistics.
Mincer has received some additional funds from the NSF to support two more such educational outreach programs, one of which will tentatively cover climate change.
“Statistics can be used to quantify the likelihood of events in the absence of climate change,” he explained.
Statistics provide a tool to document subtle but potentially significant changes in climate.
While Bronson wouldn’t commit to a discussion of climate change for the next group of teachers, he said he “wouldn’t be surprised if we look at climate change” and that “there’s a lot of interesting areas to explore in this field.”
Arjun Venkatesan is testing an enhanced coagulation approach to treat contaminated water.
Photo by John Griffin/Stony Brook University
By Daniel Dunaief
One person’s toilet flush is another’s pool of information.
Arjun Venkatesan, Associate Director for the New York State Center for Clean Water Technology at Stony Brook University, has gathered information from wastewater plants to search for traces of opioids and other chemicals.
Such monitoring is a “great tool” and relies on the sensitivity of the method, Venkatesan said.
Indeed, other scientists, including Professor Christopher Gobler, Endowed Chair of Coastal Ecology and Conservation at the School of Marine and Atmospheric Sciences at Stony Brook, have used wastewater monitoring to collect information about the prevalence of Covid-19 in a community.
Gobler explained that such monitoring has proven to be an “ideal way to track community infections. Through early to mid 2022, positive test rates and wastewater virus levels tracked perfectly. Since then, people began home testing and now, wastewater epidemiology is probably our best sign of community infection rates.”
In a joint effort through the Center for Cleanwater Technology, Venkatesan’s team monitors for chemicals, including opioids and other drugs. Such tracking, which college campuses and local governments have done, does not involve gathering information from any specific home. Instead, the scientists take anonymous samples from a larger dorm or a neighborhood, hoping to track changes in the presence of chemicals or a virus to enable health care mitigation efforts.
Venkatesan has been looking at common over-the-counter drugs and anti-viral treatments that residents used to treat Covid-19 infection, particularly before the development and distribution of several vaccines. He noticed an increase in over the counter use that matched the increase of Covid cases, which suggested that the infected people took these pain medicines for their symptoms first.
Venkatesan’s group monitored the use of these drugs over the last two years to confirm the trends. This baseline allowed him to “see increasing trends” in usage, he said. The increase “clearly indicates something more than what the drugs are regularly used for.”
Opioids
Venkatesan’s group has been working with the Department of Health to develop standard protocols to measure drugs at these sewage treatment plants. The testing needs to be updated to account for changes in consumption of new drugs that are being synthesized.
Each sample Venkatesan and his colleagues collect typically has hundreds of thousands of people in it, because the treatment plants process sewage for a large collection of communities. “This keeps anonymity,” he said. “We don’t want to dig up [information] from a single family home.”
The method is also cost effective when a single sample represents a larger population. This kind of information, however, could help public health professionals monitor the presence of drugs broadly in a community, providing them with a way to track the prevalence of addictive and potentially harmful drugs.
Venkatesan is developing methods to track fentanyl, a highly addictive drug linked to numerous deaths throughout the country and the world. Studies in other regions have demonstrated elevated levels of this drug.
Venkatesan said New York State responded to the pandemic by developing surveillance over the last few years. The approach was not well known and was limited mostly to illicit drugs. The pandemic made a significant impact, which helped officials appreciate the value of such a tool.
The state could also theoretically monitor for any chemicals that are stable enough in sewage.
While Venkatesan hasn’t measured traces of alcohol at sewage treatment plants, researchers and public health officials could create a screen to measure it. He was involved in a study that monitored for alcohol and nicotine consumption in many cities. “We could get interesting trends and understand community and population health in a better way,” he said. The pandemic has “helped establish the importance of this network.”
Surveys in which people call and ask about the consumption of drugs or alcohol can contain self-reporting error, as respondents may not know exactly how much they drink or may be reluctant to share those details.
Wastewater monitoring could capture trends, including whether communities have a spike in the use of drugs or alcohol on Friday nights or on weekends.
The Centers for Disease Control and Prevention created standardized methods for monitoring Covid-19 in the wastewater of cities and states.
Wastewater monitoring techniques are different for detecting viruses compared to chemicals. Venkatesan’s group is developing different method to screen for opioids. “We are excited about it,” he said. “Hopefully, next year, we should be able to monitor communities.”
As long as the sampling doesn’t cross any predetermined ethical line, monitoring could provide an effective way of looking at the trends and data, he said.
With so much water flowing through pipes and treatment plants, one of the biggest challenges in these efforts is to understand variables that affect what the scientists are monitoring.
The time between when a toilet is flushed in an apartment to the time when it reaches a plant can vary, depending on numerous variables, which creates uncertainty in the data.
To reduce this variability, scientists could do some sampling in manholes, between treatment plants.
Scientific roots
Venkatesan took an elective at the end of college in environmental science when he attended Anna University in Chennai, India. It was the first time he observed a wastewater treatment plant.
Fascinated by the process, he earned a Master’s in Environmental Engineering at the University of Nevada, Las Vegas and then went on to get a PhD at Arizona State. He also did his post doctoral research in Arizona.
Stony Brook was looking for a scientist to screen for contaminants in drinking water, including PFAS chemicals, which is a group of chemicals that are stable, hard to break down and are linked to thyroid cancer, among others.
PFAS chemicals are used in cleaners, textiles, fire-fighting foam and other applications.
Venkatesan leads drinking water efforts, while waste water epidemiology remains an ongoing project of interest.
Gobler hired Venkatesan five years ago to help run and then to exclusively run the drinking water initiative at Stony Brook.
Through the process, Venkatesan has “brought new insights and research programs related to wastewater epidemiology, bisolids and many other topics,” Gobler explained. Venkatesan has “exceeded expectations,” as he transitioned from a postdoctoral researcher to become Associate Director for Drinking Water Initiatives.”
Gobler called his colleague a “complete professional” who is “very positive and a good person to work with.”
In his research, Venkatesan develops technologies to remove these PFAS chemicals, while monitoring is also a part of that effort. Activated carbon filters can remove these chemicals from groundwater. These filters, however, require frequent replacement. Venkatesan is exploring ways to improve the life of the carbon filter.
PFAS chemicals make rain water unsafe to drink. Removing PFAS chemicals is an “important research topic locally and globally.”
Victoria Bautch on right with graduate student Danielle Buglak. Photo from UNC McAllister Heart Institute
By Daniel Dunaief
This is part two of a two-part series featuring Cold Spring Harbor Laboratory alums Joanna Wysocka, Robert Tjian, Victoria Bautch, Rasika Harshey and Eileen White.
Often working seven days a week as they build their careers, scientists plan, conduct and interpret experiments that don’t always work or provide clear cut results.
Driven by their passion for discovery, they tap into a reservoir of ambition and persistence, eager for that moment when they might find something no one else has discovered, adding information that may lead to a new technology, that could possibly save lives, or that leads to a basic understanding of how or why something works.
Nestled between the shoreline of an inner harbor along the Long Island Sound and deciduous trees that celebrate the passage of seasons with technicolor fall foliage, Cold Spring Harbor Laboratory has been a career-defining training ground for future award-winning scientists.
Last week two alumni of Cold Spring Harbor Laboratory, Joanna Wysocka and Robert Tjian, shared their thoughts, experiences, and reflections on the private lab that was founded in 1890. This week the article continues with reflections from alumni Rasika Harshey, Victoria Bautch and Eileen White.
Confidence builder
Lunch time presented no break from science for Rasika Harshey, and that was just as she’d hoped.
Rasika Harshey
When she was at Blackford Hall between 1979 and 1983, first as a postdoctoral researcher and then as a staff investigator in the lab of Ahmad Bukhari, Harshey said conversations frequently included discussions about research. “It was wonderful,” she said. “It was just science, 24/7.”
Bukhari was studying a virus that infects bacteria, called mu, for mutator. The viral particle genome was jumping into the host genome. “At that point, transposable elements” of DNA were “entering into our consciousness,” Harshey explained.
In her research, Harshey would induce the virus and, 30 minutes later, get 100 phage particles. Looking in the cytoplasm, however, she didn’t find any of this viral DNA until phage progeny appeared about 50 minutes later. “How is that possible?” she asked. “I wanted to solve this mystery.”
Harshey spent countless hours in the electron microscope room, isolating DNA. She knew mu was replicating, or copying itself, but she couldn’t figure out how or what it was doing. She and Bukhari proposed a model about transposable elements at a meeting called “Movable Genetic Elements” in 1979 at CSHL that generated considerable discussion.
“It was thrilling at the time for me to develop as a scientist,” Harshey said. “It seemed to me that I was saying something and people were listening. I gained a lot of confidence in myself.” The work she did turned out to be only partially correct, but it gave her the sense that she could solve problems.
With CSHL as a backdrop, Harshey enjoyed the opportunity to attend meetings and to interact with other visitors and other scientists on campus. “It was a total immersion” she said. “Summers were magical, with so many meetings one could just walk into.”
Harshey visited Barbara McClintock’s lab, which was down the hall from hers. McClintock, who won the Nobel Prize in Harshey’s final year at CSHL, showed her the maize cells.
McClintock also invited her to her cottage, where she served what Harshey recalled was a “delicious” poppyseed cake.
She described McClintock as “quiet” and a “tough cookie.”
Rasika Harshey at CSHL.Courtesy of Cold Spring Harbor Laboratory Archives, NY.
Harshey thought it was inspiring to be with McClintock, Watson and Richard Roberts, who also won a Nobel Prize. She also appreciated the opportunity to visit with Guenter Albrecht-Buehler and Joseph Sambrook. “I was in and out of Richard Roberts’s lab all the time,” she said.
For her work, Harshey needed restriction enzymes, which Phyllis Myers produced. She had to “beg” Myers for these valuable enzymes that were in short supply.
Harshey felt an urgency to commit herself to her work. When she and her husband Makkuni Jayaram were expecting a baby, she didn’t share the news until it had become obvious. She worked until the last moment before the baby was born in 1982, “but I came back,” she said.
Harshey, who also calls CSHL “home,” described it as a “place time forgot. It’s quiet and beautiful and you can do and think and talk science.” Professor in Molecular Biosciences at The University of Texas at Austin in the College of Natural Sciences, Harshey is grateful for the career and the life she’s led. “A series of accidents got me here,” she said. “I can’t believe my good fortune, that I get to do what I get to do every day.”
As a part of the history of CSHL, Harshey appreciates a culture that she has carried forward in her career. The “deep joy, commitment, excitement for biology, particularly for designing experiments, and looking at a problem from all angles” was embedded into the approach scientists took to the work they did at the lab.
She also believes the tradition at CSHL includes an “appreciation for how easy it is to get things wrong and to continually challenge your own ideas.”
Intense culture
Victoria Bautch came to Cold Spring Harbor Laboratory in the 1983 knowing that she was interested in studying aspects of developmental biology. When she saw the power of the new technology, she started working on genetically modified animals.
She was trying to figure out whether viral genes previously only linked to cancer by association could cause cancer when part of the genome was put into animals. When she inserted genes into a mouse’s DNA, some of these mice developed tumors in their blood vessels. She “didn’t know this was going to happen,” she said. “The type of tumor was a complete surprise.”
Bautch needed to know more about how blood vessels formed and functioned to understand these tumors. That’s what got her excited about studying these blood vessels. These blood vessel tumors “weren’t on my radar,” she said.
While working in the lab of Doug Hanahan, Bautch had the opportunity to interact with Judah Folkman, a Professor at Harvard University. Folkman was excited about the way these blood vessels were developing and encouraged Bautch to continue to work in this field. Folkman championed the idea that new blood vessel formation contributes to the progression of many types of tumors. He was eager to bring new people and technologies into the field.
Bautch also met mouse geneticists Nancy Jenkins and Neal Copeland who were at Jackson Labs at the time and were instrumental in her career progression. She started asking basic questions about how blood vessels forms and how they function.
Folkman was looking to “bring people into the field that had more of a basic science and molecular biology background,” Bautch said. He was hoping to add researchers who would use the new tools to understand blood vessel basics and how they are involved in tumors.
The tumor Bautch worked on was an “entree into the bigger field of blood vessels and vascular biology,” she said.
Cold Spring Harbor Laboratory provided a constructive backdrop for the work Bautch did that proved important in her career. “I was looking for an intense and very high caliber scientific environment and I feel like I found it,” she said.
Indeed, Bautch often worked seven days a week, starting at 10 or 11 in the morning and ending around 1 or 2 in the morning. During the later hours, she had an easier time accessing machines and equipment that others in the lab also needed.
Like Harshey, Bautch has her own McClintock story. “She always would say, ‘Look at your organism very carefully.’ You could learn so much from observing.”
At the time, McClintock’s advice seemed “antiquated” to Bautch, especially with researchers doing molecular biology that was more of a technological breakthrough, but now appreciates the guidance. “A really important piece of being a scientist is being observant,” sheexplained.
Bautch said other scientists were prepared to offer their responses to her work. “People were always telling you what they thought, whether you wanted it or not,” she recalled.
Now a Distinguished Professor of Biology and Co-Director of the McAlister Heart Institute at UNC Chapel Hill, Bautch recalls her time at CSHL as a combination of a “very intense life experience as well as science experience.” As for her hopes for the current crop of scientists at CSHL, Dr. Bautch hopes this generation is “more inclusive.”
An alternateexplanation of cancer
Around the same time that actress Heather Locklear was telling TV audiences about Faberge Organics Shampoo about how people can tell two friends about the shampoo who then tell two friends, researchers knew that a type of gene that promoted cancer did essentially the same thing.
Eileen White. Photo courtesy of Rutgers Cancer Institute of New Jersey
Called an oncogene, these genes caused cells to continue to divide and, as the shampoo commercial suggested “and so on and so on and so on.” Back then, scientists focused on the role oncogenes played in cell proliferation, which, with cancer, involved the runaway copying of itself.
A graduate of Smithtown High School who earned her PhD at Stony Brook University, Eileen White joined Bruce Stillman’s lab as a post doctoral fellow at Cold Spring Harbor Laboratory in 1983. After three years, White became a staff investigator, making the beginning of career-defining discoveries about the development of cancer.
“We knew that certain viruses cause cancer, and we knew that these viruses encoded oncogenes,” said Dr. White. “The whole idea was to understand how.”
Indeed, viral oncogenes, which are small and less complicated than tumor genomes, presented the opportunity to find a shortcut to understand how cancers developed in humans. Even if the human oncogene is small, the genome it sits in is huge, which is not the case of a viral oncogene that sits I a very small viral genome, she explained.
Using a DNA tumor virus that promoted cancer, White discovered that this gene prevented apoptosis, or programmed cell death. After this discovery, which she said she could “see with her own eyes” when she studied the effect of the genes on cells, she asked herself what she’d need to do to push the idea forward for this paradigm shift in thinking about cancer.
As she continued to discover more details about the viral oncogene over the years, she said other researchers discovered that the Bcl-2 human oncogene may function similarly.“I thought, ‘Well, if this is a theme that viral oncogenes and potentially cancer oncogenes are blocking apoptosis, they should be functionally interchangeable,’” White recalled, which is what she showed and published.
She substituted human Bcl2 oncogene of the viral E1B 19K oncogene and showed that they both functioned to block apoptosis interchangeably.
Courtesy of Cold Spring Harbor Laboratory Archives, NY.
These discoveries, which started at Cold Spring Harbor Laboratory, among others, helped pave the way for Dr. White’s career, where she is now professor of Molecular Biology and Biochemistry and Deputy Director at the Rutgers Cancer Institute of New Jersey. She is also Associate Director of the Ludwig Princeton Branch of the Ludwig Institute for Cancer Research at Princeton University.
The discovery also led to some anti cancer treatments. Abbott developed the first FDA approved Bcl-2 inhibitor, which others followed.
These kinds of discoveries, which lead to treatments, are why she and others “work so hard, to make a difference for patients,” she said.
Dr. White describes her time at CSHL as an “enormously enriching experience” in which she was surrounded by people who were of “exceptional scientific caliber,” including some who won the Nobel Prize while she was there.
“I had a fertile environment with people that had similar ways of thinking that was very synergistic in terms of propelling the science forward,” she said.
She appreciated the numerous meetings held at CSHL at which she felt like she could learn about anything from the depth and breadth of the material presented and discussed. During these meetings, which she still attends regularly, she has recruited post doctoral researchers to her lab whom she’s met at poster sessions.
As with other alumni of CSHL, Dr. White was particularly pleased with the robust and valuable feedback she and others received. “Critical and productive insights from the scientific community is important to the process of scientific discovery from beginning to the end,” she explained.
White suggested that the layout of the campus and the proximity of so many families created a unique and tight knit community. She recalled how the lab had Santa Claus at Christmas, hay rides to the pumpkin patch and special dinners for people who lived there.
“That very much builds camaraderie and long term friendships and long term relationships,” she said.
This is part one of a two-part series featuring Cold Spring Harbor Laboratory alums Joanna Wysocka, Robert Tjian, Victoria Bautch, Rasika Harshey and Eileen White. Part two will be in the issue of Aug. 25.
Often working seven days a week as they build their careers, scientists plan, conduct and interpret experiments that don’t always work or provide clear cut results.
Driven by their passion for discovery, they tap into a reservoir of ambition and persistence, eager for that moment when they might find something no one else has discovered, adding information that may lead to a new technology, that could possibly save lives, or that leads to a basic understanding of how or why something works.
Nestled between the shoreline of an inner harbor along the Long Island Sound and deciduous trees that celebrate the passage of seasons with technicolor fall foliage, Cold Spring Harbor Laboratory has been a career-defining training ground for future award-winning scientists.
Five alumni of Cold Spring Harbor Laboratory recently shared their thoughts, experiences, and reflections on the private lab that was founded in 1890.
While they shared their enthusiasm, positive experiences and amusing anecdotes, they are not, to borrow from scientific terminology, a statistically significant sample size. They are also a self-selecting group who responded to email requests for interviews. Still, despite their excitement about an important time in their lives and their glowing description of the opportunities they had to hone their craft, they acknowledged that this shining lab on the Sound may not be paradise for everyone.
Cold Spring Harbor Laboratory is considerably smaller than some of the research universities around the country. Additionally, scientists with a thin skin — read on for more about this — may find their peers’ readiness to offer a range of feedback challenging. Still, the lab can and has been a launching pad.
A suitcase and a dream
Joanna Wysocka’s story mirrors that of other immigrants who came to the United States from their home countries. Wysocka arrived from Poland in 1998 with one suitcase that included mementos from her family, a Polish edition of her favorite book, One Hundred Years of Solitude, and a dream of developing her scientific career.
She was also chasing something else: her boyfriend Tomek Swigut, who had come to Cold Spring Harbor Laboratory. “I was fresh off the boat without any fancy resume or anything,” Wysocka recalls. “They really took a chance on me.”
Joanna Wysocka
While she learned how to conduct scientific experiments, she also recognized early on that she was a part of something bigger than herself. Early on, she found that people didn’t hold back in their thoughts on her work. “You always got critical feedback,” she said. “People felt very comfortable picking apart each other’s data.”
The positive and negative feedback were all a part of doing the best science, she explained.
Wysocka felt the inspiration and exhilaration that comes from a novel discovery several times during her five-year PhD program.
“It’s 11 p.m. in the evening, you’re in the dark room, developing a film, you get this result and you realize you’re a person who knows a little secret that nobody else in the world knows just yet,” she recalled. “That is really wonderful.”
For special occasions, the lab celebrated such moments with margaritas. Winship Herr, her advisor, made particularly strongest ones.
In one of her biggest projects, Wysocka was working with a viral host cell factor, or HCF. This factor is critical for transcription for the Herpes simplex virus. What wasn’t clear, however, was what the factor was doing. She discovered that this factor worked with proteins including chromatin modifiers. “From this moment, it set me up for a lifetime passion of working on gene regulation and chromatin,” she said.
As for the scientific process, Wysocka said Herr offered her critical lessons about science. When she started, Herr expected two things: that she’d work hard and that she’d learn from her mistakes. During the course of her work, she also realized that any work she did that depended on the result of earlier experiments required her own validation, no matter who did the work or where it was published. “You need to repeat the results in your own hands, before you move on,” she explained.
Despite the distance from the lab to New York City and the smaller size of the lab compared with large universities, Wysocka never felt isolated. “Because of all the conferences and courses, the saying goes that ‘if you want to meet somebody in science, go to a Cold Spring Harbor bar and sit and wait.’” That, however, is not something she took literally, as she put considerable hours into her research. While she wishes she had this incredible foresight about choosing Cold Spring Harbor Laboratory, she acknowledges that she was following in Swigut’s footsteps.
The choice of CSHL worked out well for her, as her research has won numerous awards, including the Vilcek Prize for Creative Promise in Biomedical Science, which recognizes immigrant scientists who have made a contribution to U.S. society. She now works as Professor at Stanford University and is married to Swigut.
Swinging for the fences
In 1976, Robert Tjian had several choices for the next step in his developing scientific career after he completed his PhD at Harvard University. James Watson, who had shared the Nobel Prize in 1962 for the double helix molecular structure of DNA with Francis Crick and Maurice Wilkins and was director at Cold Spring Harbor Laboratory, convinced him to conduct his postdoctoral research at CSHL.
Robert Tjian
The contact with Watson didn’t end with his recruitment. Tjian, who most people know as “Tij,” talked about science on almost a daily basis with Watson, which he considered an ‘incredible privilege.”
Although he only worked at CSHL for two years, Tjian suggested the experience had a profound impact on a career that has spanned six decades.
Learning about gene discovery was the main driver of his time at CSHL. An important discovery during his work at CSHL was to “purify a protein that binds to the origin of replication of a tumor virus, which was what [Watson] wanted me to do when he recruited me,” he said. That launched his career in a “positive way.”
Tjian feels fortunate that things worked out and suggested that it’s rare for postdoctoral students to achieve a transformative career experiment in such a short period of time either back then or now. He attributes that to a combination of “being in the right place at the right time,” luck and hard work.
At Berkeley, where he is Professor of Biochemistry, Biophysics and Structural Biology and has been running a lab since 1979, he has observed that the most successful researchers are the ones who are “swinging for the fences. If you don’t swing for the fences and get lucky, you sure as hell aren’t going to hit a home run.”
Tjian learned how to run a lab from his experience at CSHL. He selects for risk takers who are independent and feels the only way to motivate people is to ensure that the work they are pursuing involves questions they want to solve.
One of the most important and hardest lessons he learned during his research career was to “fail quickly and move on.” He tells his student that about 85 percent of their experiments are going to fail, so “get used to it and learn from it.”
Despite his short and effective stay at CSHL, Tjian suggested he made “more than his fair share” of mistakes. Terri Grodzicker, who is currently Dean of Academic Affairs at CSHL, taught Tjian to do cell culture, which he had never done before. He contaminated nearly all the cultures for about a month.
While Tjian described the lab as a “competitive place,” he felt like his colleagues “helped each other.”
When he wasn’t conducting his experiments or contaminating cultures, he spent time on the tennis court, playing regularly with Watson. Watson wasn’t “exactly the most coordinated athlete in the world,” although Tjian respected his “remarkably good, natural forehand.” He was also one of the few people who was able to use the lab boat, which he used to fish for striped bass and bluefish early in the morning. “I would try to drag all kinds of people out there,” he said.
While his CSHL experience was “the best thing” for him, Tjian explained that the lab might not be the ideal fit for everyone, in part because it’s considerably smaller than larger universities. At Berkeley, he has 40 to 55 PhD students in molecular biology and he can interact with 40,000 undergraduates, which is a “very different scale.”
Tjian has returned many times to CSHL and is planning to visit the lab at the end of August for a meeting he’s organizing on single molecule microscopy.
Each time he comes back, he “always felt like I was coming home,” he said.
When Jacqueline Olsen learned the day before her birthday last November that she needed surgery for lung cancer, she felt anxious about a procedure she knew could be painful and could involve a lengthy recovery.
“It’s not only my birthday, it’s Thanksgiving,” said Olsen, who is a resident of St. James and is an agent for personal insurance such as home, auto and umbrella insurance. “Everybody was real tense. It was not a pleasant holiday.”
Olsen’s father, William Leonard, and father-in-law, James Olsen, had died of lung cancer after having open chest surgeries. The pain of what her father went through 48 years ago and father-in-law over 20 years ago was fresh in her mind as she readied herself for her own procedure.
Dr. Ankit Dhamija
Speaking with doctors at Stony Brook University Hospital, Olsen heard about newer, better options.
Dr. Ankit Dhamija, Cardiothoracic Surgeon and Director of Thoracic Robotic Surgery at Stony Brook Medicine, suggested to Olsen that she was a candidate for a robot-assist surgery called the da Vinci Surgical System.
Olsen and her family gathered considerable information about the procedure.
“I did some research on it and it said it would be a faster recovery and I would be up and back to my normal self pretty soon afterward,” said Olsen. “It seemed like a less invasive surgery.”
The robotic surgery does not involve turning over the procedure to a machine, Dr. Dhamija explained.
Instead, the process involves making considerably smaller incisions and guiding the robot through the body to remove the cancerous tissue.
“The robot is a machine that is an extension of our hands,” said Dr. Dhamija, who has performed about 500 such procedures with the help of a robot, including around 70 since he arrived at Stony Brook.
The robotic system allows surgeons like Dr. Dhamija and Dr. Henry Tannous, Cardiothoracic Surgeon and Chief of the Cardiothoracic Surgery Division at Stony Brook Medicine, among others, to sit in the operating room with the patient while the robot enters through an incision. The robot provides a three dimensional view of the inside of the body, magnifying cells by ten times.
The robot assist can also improve the ability of surgeons to perform fine operations.
The system “does have a machine algorithm associated with it that actually is known to reduce tremors in surgeons that have tremors,” said Dr. Dhamija. “Someone that may not be able to do a certain portion of the operation due to their technical limitations can subsequently do it with the robot.”
Dr. Henry Tannous
In the procedure, the surgeon can see and maneuver through the body effectively, searching for the specific cells to remove.
An interventional radiologist can inject a dye which under CT guidance allows the surgeon to “see where the lesion is and to verify that you have adequate margins” or the border between cancerous and non-cancerous cells, Dr. Dhamija said. “Having the dye in there to identify [the cancer] is helpful,” he added.
By using the robot instead of creating a large incision, doctors can reduce the time patients spend in a hospital down to as little as one to three days from the four to eight days after an open chest lobectomy.
“There’s so much to be said about someone [recovering] in their own home,” said Dr. Dhamija. They “get to sleep properly, their bowel habits are more normal, and they get to reengage in their daily life functions sooner. I’m a big proponent of a patient taking charge of their own postoperative care.”
Indeed, Stony Brook doctors have become so confident and comfortable with the robot assist that it has become the main platform for thoracic oncology patients at Stony Brook Medicine, explained Dr. Tannous. Tannous estimates that 90 percent of the lobectomies will be performed robotically in 2022, up from 10 to 20 percent in 2021.
In an email, Dr. Tannous wrote that other specialties that have adopted the robotic platform include gynecology, urology, colorectal, bariatrics, and general surgery.
Stony Brook is also expanding robotic surgery to include cardiac procedures in 2023.
Dr. Tannous said robotic procedures that cut down on recovery time means less risk of hospital-acquired infections, lower extremities blood clots, and numerous other benefits.
Some day, theoretically, the robot may enable remote procedures, with surgeons operating the robot with the help of an on-site local medical team. That could be helpful for astronauts who develop a medical problem far from home where they need emergency surgery.
An important caveat with that, Dr. Dhamija said, is that the staff on site would need to be able to complete a procedure if an open chest surgery became necessary.
Olsen, who was out of the hospital less than 24 hours after she had surgery in late May, has become a fan of the technology and of the team at Stony Brook.
Olsen, who has three scars on her back and two on her side, felt pain for about a week. As she recovered, she never felt the need to fill a prescription for a stronger painkiller, choosing to treat the pain with Motrin. She plans to continue to take blood tests every three months and to get CAT scans every six months.
Olsen was thrilled with the quality of care she received and is pleased she can look forward to sharing quality summer time during the family’s annual beach trip. “It’s heaven to me,” she said, where she can “spoil my grandchildren.
As for a perspective on her surgery, she said the difference between 20 years ago and now is “unbelievable. It was such an awful experience” for her father and father in law. “This was a million times better.”
Katia Lamer during her experiment in Houston. Photo courtesy of U.S. Department of Energy Atmospheric Radiation Measurement user facility
By Daniel Dunaief
Clouds and rain often cause people to cancel their plans and seek alternative activities.
The opposite was the case for Katia Lamer this summer. A scientist and Director of Operations of Brookhaven National Laboratory’s Center for Multiscale Applied Sensing, Lamer was in Houston to participate in ESCAPE and TRACER studies to understand the impact of pollution on deep convective cloud formation.
Katia Lamer during her experiment in Houston. Photo courtesy of U.S. Department of Energy Atmospheric Radiation Measurement user facility
With uncharacteristically dry weather and fewer of the clouds she and others intended to study, she had some down time and created a plan to study the distribution of urban heat. “I am always looking for an opportunity to grow the Center for Multiscale Applied Sensing and try to make the best of every situation,” she said.
Indeed, Lamer and her team launched 32 small, helium-filled party balloons. She and Stony Brook University student Zachary Mages each released 16 balloons every 100 meters while walking a one mile transect from the suburbs to downtown Houston. A mobile observatory followed the balloons and gathered data in real time through a radio link.
While helium-filled party balloons are not the best option, Lamer said the greater good lay in gathering the kind of data that will be helpful in measuring and monitoring climate change and explained that until some better balloon technology was available, this is what they had to use.
“Typically, we launch the giant radiosonde balloons, but you can’t launch them in a city,” she said because of the lack of space for these larger balloons to rise without hitting obstacles. The balloons also might pass through navigable airspace, disturbing flight traffic.
The smaller party balloons carried sensitive equipment that measured temperature and humidity and had a GPS sensor tucked into foam cups.
“If we can demonstrate that there is significant variability in the vertical distribution of temperature and humidity at those scales, then this would suggest that we should push to increase the resolution of our models to improve climate change projections,” she explained.
By following these balloons closely with a mobile observatory, Lamer and her team can avoid interference from other signals and signal blockage by buildings.
The system they used allowed them to select a cut-off height. Once the balloons reached that altitude, the string that connected the sensors to the balloon burns off and the sensors start free-falling while the balloon climbs until it pops.
The sensors collect continuous data on temperature, humidity and horizontal wind during the ascent and descent. Using the GPS, researchers can collect the sensors.
While researchers have studied urban heat using mesoscale models and satellite data, that analysis does not have the spatial resolution to understand community scale variability. Urban winds also remain understudied, particularly the winds above the surface, she explained.
Winds transport pollutants, harmful contaminants, and heat, which may be relieved on some streets and trapped on others.
Michael Jensen, principal investigator for the Tracking Aerosol Convection interaction Experiment, or TRACER and meteorologist at BNL, explained that Lamer is “focused on what’s going on in the urban centers.” Having a truck that can move around and collect data makes the kind of experiment Lamer is conducting possible. Jensen described what Lamer and her colleagues are doing as “unique.”
New York model
Katia Lamer during her experiment in Houston. Photo courtesy of U.S. Department of Energy Atmospheric Radiation Measurement user facility
Lamer had conducted similar experiments in New York to measure winds. The CMAS mobile observatory’s first experiment took place in Manhattan around the One Vanderbilt skyscraper, which is 1,400 feet high and is next to Grand Central Terminal. No balloons were launched as part of that first experiment.She launched the small radiosonde balloons for the first time this summer in Houston around the 990 foot tall Wells Fargo complex.
Of the 32 balloons she and Mages launched, they collected data from 24. The group lost connection to some of the balloons, while interference and signal blockage disrupted the data flow from others.
Lamer plans to use the information to explore how green spaces such as parks and blue infrastructure including fountains have the potential to provide some comfort to people in the immediate area.
Such observations will provide additional insight beyond numerical models into how large an area a park can cool in the context of the configuration of a neighborhood.
This kind of urban work can have numerous applications.
Lamer suggested it could play a role in urban planning and in national security, as officials need to know the dispersement of pollutants and chemicals. Understanding wind patterns on a fine scale can help inform models that indicate areas that might be affected by an accidental release of chemicals or a deliberate attack against residents.
Bigger picture
Katia Lamer during her experiment in Houston. Photo by Steven Andrade/ BNL
Lamer is gathering data from cities to understand the scale of heterogeneity in properties such as heat and humidity, among others. If conditions are horizontally and vertically homogeneous, only a few permanent stations would be necessary to monitor the city. If conditions are much more varied, more measurement stations would be necessary.
One way to perform this assessment is to use mobile observatories that collect data. The ones Lamer has deployed use low-cost, research-grade instruments for street level and column wide observations.
Over the ensuing decades, Lamer expects that the specific conditions will likely change. Collecting and analyzing data now will enable scientists to develop a baseline awareness of typical urban conditions.
Scientific origins
A native of St.-Dominique, a small farmer’s village in Quebec Canada, Lamer was impressed by storms as she was growing up. She would often watch them outside her window, fascinated by what she was witnessing. After watching the Helen Hunt and Bill Paxton movie Twister, she wanted to invent her own version of the Dorothy instrument and start chasing storms.
When she spoke with her high school guidance counselor about her interest in tornadoes, which do not occur in Quebec, the counselor said she was the first person to express such a professional passion and had no idea how to advise her.
Lamer, who grew up speaking French, attended McGill University in Montreal, where she studied earth system science, aspects of geology and geography and a range of earth-related topics.
Instead of studying or tracking tornadoes, she has worked on cloud physics and cloud dynamics. Hearing about how clouds are the biggest wild card in climate change projections, she decided to embrace the challenge.
During her three years at BNL, Lamer, who lives with her husband and children in Stony Brook, has appreciated the chance to “push the envelope and be creative,” she said. “I really hope to stay in the field of urban meteorology.”
The temperatures at the poles are heating up more rapidly than those at the equator. Pixabay photo
By Daniel Dunaief
On any given day, heat waves can bring record-breaking temperatures, while winter storms can include below average cold temperatures or snow.
Edmund Chang. Photo from SBU
Weather and climate experts don’t generally make too much of a single day or even a few days amid an otherwise normal trend. But, then, enough of these exceptional days over the course of years can skew models of the climate, which refers to average temperature and atmospheric conditions for a region.
If the climate is steady, “we should see approximately the same number of hot and cold records being broken,” said Edmund Chang, Professor at the School of Marine and Atmospheric Sciences at Stony Brook University. “Over the past few decades, we have seen many more hot records being broken than cold records, indicating the climate is getting hotter.”
Recent heat
Indeed, just last week, before a heatwave hit the northeastern United States, the United Kingdom reported the hottest day on record, with the temperature at Heathrow Airport reaching above 104 degrees.
Erinna Bowman, who grew up in Stony Brook and has lived in London since 2009, said the temperature felt “like a desert,” with hot, dry heat radiating up in the urban setting. Most homes in London don’t have air conditioning, although public spaces like supermarkets and retail stores do.
“I’m accustomed to the summer getting quite hot, so I was able to cope,” said Bowman. Indeed, London is usually considerably cooler during the summer, with average temperatures around 73 degrees.
Michael Jensen. Photo from BNL
News coverage of the two extraordinarily hot days in London “was very much framed in the context of a changing climate,” Bowman said. The discussion of a hotter temperature doesn’t typically use the words “climate change,” but, instead, describes the phenomenon as “global heating.”
For climate researchers in the area, the weather this summer has also presented unusual challenges.
Brookhaven National Laboratory meteorologist Michael Jensen spent four years planning for an extensive study of convective clouds in Houston, in a study called Tracking Aerosol Convection Interactions, or Tracer.
“Our expectation is that we would be overwhelmed” with data from storms produced in the city, he said. “That’s not what we’re experiencing.”
The weather, which has been “extremely hot and extremely dry,” has been more typical of late August or early September. “This makes us wonder what August is going to look like,” he said.
Jensen, however, is optimistic that his extensive preparation and numerous pieces of equipment to gather meteorological data will enable him to collect considerable information.
Warming at the poles
Broadly speaking, heat waves have extended for longer periods of time in part because the temperatures at the poles are heating up more rapidly than those at the equator. The temperature difference between the tropics and the poles causes a background flow from west to east that pushes storms along, Chang explained.
The North Pole, however, has been warming faster than the tropics. A paper by his research group showed that the lower temperature gradient led to a weakening of the storm track.
When summer Atlantic storms pass by, they provide relief from the heat and can induce more clouds that can lead to cooler temperatures. Weakening these storms can lead to fewer clouds and less cooler air to relieve the heat, Chang added.
Rising sea levels
Malcolm Bowman. Photo from SBU
Malcolm Bowman, who is Erinna Bowman’s father and is Distinguished Service Professor at the School of Marine and Atmospheric Sciences at Stony Brook University, believes the recent ice melting in Greenland, which has been about 10 degrees above normal, could lead to a rise in sea levels of about one inch this summer. “It will slowly return to near normal as the fresh water melt spreads slowly over all the world’s oceans,” he added.
Bowman, who has studied sea level rises and is working on mitigation plans for the New York area in the event of a future major storm, is concerned about the rest of the hurricane season after the level of warming in the oceans this summer.
“Those hurricanes which follow a path over the ocean, especially following the Gulf Stream, will remain strong and may gather additional strength from the heat of the underlying water,” he explained in an email.
Bowman is the principal investigator on a project titled “Long Island South Shore Sea Gates Study.”
He is studying the potential benefit of six possible sea gates that would be located across inlets along Nassau and Suffolk County. He also suggests that south shore sand dunes would need to be built up to a height of 14 feet above normal high tide.
Meanwhile, the Army Corps of Engineers has come up with a tentatively selected plan for New York Harbor that it will release some time in the fall. Bowman anticipates the study will be controversial as the struggle between green and grey infrastructure — using natural processes to manage the water as opposed to sending it somewhere else — heats up.
As for the current heat waves, Bowman believes they are a consistent and validating extension of climate change.
Model simulations
In his lab, Chang has been looking at model simulations and is trying to understand what physical processes are involved. He is comparing these simulations with observations to determine the effectiveness of these projections.
To be sure, one of the many challenges of understanding the weather and climate is that numerous factors can influence specific conditions.
“Chaos in the atmosphere could give rise to large variations in weather” and to occasional extremes, Chang said.
Before coming to any conclusions about longer term patterns or changes in climate, Chang said he and other climate modelers examine collections of models of the atmosphere to assess how likely specific conditions may occur due to chaos even without climate change.
“We have to rule out” climate variability to understand and appreciate the mechanisms involved in any short term changes in the weather, he added.
Still, Chang said he and other researchers are certain that high levels of summer heat will be a part of future climate patterns.
“We are confident that the increase in temperature will result in more episodes of heat waves,” he said.
Stony Brook Breast Cancer Screening mobile truck. (8/24/18)
By Daniel Dunaief
Some groups of people on Long Island have a much higher incidence of a particular type of cancer than others.
On an age adjusted rate, African American men, for example, were almost twice as likely to develop prostate cancer from 2014 to 2018 as Caucasians. Out of 100,000 African American men, 216.6 had prostate cancer compared with 123.9 out of 100,000 white men, according to data from the National Cancer Institute.
Dr. Linda Mermelstein. Photo from Stony Brook Medicine
Dr. Linda Mermelstein, Associate Director of Stony Brook Cancer Center’s Office for Community Outreach and Engagement, is working with her team to address those stark differences and to empower members of the community to protect their health and make informed decisions.
“A lot of our focus is on addressing disparities” in cancer care in various communities throughout Long Island, Dr. Mermelstein said.
The Cancer Center Outreach and Engagement office has taken numerous steps to inform the public about research and care. The center has a Mobile Mammography Unit, which travels into communities to provide access to screening for breast cancer.
On June 5, at the Latina Sisters Support Inc. Spanish Fair in Brentwood, the Cancer Center’s Community Outreach and Engagement staff provided mobile mammography screening and cancer prevention and screening education.
At that event, the Suffolk County Department of Health Services provided human papillomavirus and Covid-19 vaccines and Stony Brook School of Health Professionals offered blood pressure screening.
An information chasm
Dr. Jedan Phillips. Photo from Stony Brook Medicine
Dr. Jedan Phillips, Medical Director for Stony Brook Health Outreach and Medical Education and Associate Professor of Family, Population and Preventive Medicine at the Renaissance School of Medicine, explained that Covid-19 exposed the “chasm” between what the health care profession believed and the reality of what works and what doesn’t.
During the pandemic, Stony Brook University brought a vaccination pod to Uniondale in Nassau County, which is a predominantly African American community. “Because we had no relationship there, we might have wasted over 200 doses of the vaccine” as residents were reluctant to get vaccinated, he said. “Even though [Stony Brook] offered something that would help, people chose against it. It’s not about the vaccine. It’s something deeper.”
Dr. Phillips said East Elmhurst, Queens, where he grew up, was “ravaged by Covid. I know at least 10 people in my community who were regular figures in my life that died. I saw how vulnerable of a position we were in as a group and I felt I needed to get involved.”
Dr. Phillips, who has a family medical practice in East Patchogue, together with Dr. Yuri Jadotte, Assistant Professor and Associate Program Director for the Preventive Medicine Residency in the Department of Family, Population and Preventive Medicine at Stony Brook, created three focus groups to survey the views and understanding of African American men on prostate cancer.
Many African American men don’t get screened for prostate cancer, even though such screenings could lead to earlier treatment and better outcomes.
By listening to what inspires African American men throughout Long Island to take action, Dr. Phillips hopes to tailor information to that type of delivery.
“It’s important to listen and understand,” Dr. Phillips said. Understanding what motivates people and seeking to provide the formats in which they prefer to access information can help establish a community connection and demonstrate cultural compassion.
Part of Dr. Phillips’s focus on preventive medicine comes from his experience with his father, who died from complications related to diabetes. His father, who was an inspiration for him, “didn’t live life in a preventive way,” which made managing his health more difficult, Dr. Phillips said.
With the numerous programs offered by the Office for Community Outreach and Engagement, Dr. Mermelstein said the group has four primary goals.
Dr. Jedan Phillips provides medical care.
“We want to monitor and understand what is the cancer burden in our catchment area” which includes Nassau and Suffolk County, she said. “Much of our activities are identifying the issues in terms of cancer” and understanding any barriers towards cancer care, like education, screening, diagnosis and treatment.
Secondly, she wants to provide cancer prevention services, screening, education and community navigation. Third, the group has a bi-directional engagement, with researchers getting to know the community and community advocates and the community learning about the research process.
Finally, the group seeks to catalyze the research by focusing on disparities, providing research services to the entire community based on specific needs.
One of Dr. Mermelstein’s first actions after heading up this team in 2019 was to create a community advisory council for the Stony Brook Cancer Center.
Janine Logan, Vice President of Communications and Population Health with the Long Island Health Collaborative, serves on that advisory council.“What I’m most excited about is that the committee understands the importance of knowing what your community thinks and needs,” Logan said.
Logan is pleased with the work the Stony Brook Cancer Center has done to educate residents about the lifestyle behaviors that can contribute to cancer, such as smoking, inactivity, and nutrition.
“They’ve done a lot of work in reaching out and educating communities to help them understand that these simple, modifiable behaviors can reduce their risk” of developing cancer, Logan said.
The effort at the Cancer Center to educate the public about the danger’s of the sun dovetails with some of the work she has done at the Long Island Health Collaborative.
Indeed, the Cancer Center Community Outreach and Engagement hosted a “Block the sun, not the fun” gathering on May 7 at the Smith Haven Mall in Lake Grove.
The Stony Brook Cancer Center is also working with the Suffolk County Department of Health Services Cancer Prevention and Health Promotion Coalition to provide information about sunscreen safety.
In addition to the disparity among African American men who develop prostate cancer, the outreach effort also addressed the difference among hispanic women who have a higher incidence of cervical cancer than the non-hispanic Caucasian population.
In Suffolk County, about 10.2 Hispanic and Latino women out of 100,000 Hispanic and Latino women develop cervical cancer, which is higher than the 5.9 per 100,000 for white, non-Hispanic women, according to the National Cancer Institute.
Human papillomarvirus is estimated to cause about 36,500 cases of cancer in men and women every year in the United States. The HPV vaccination, which works best before exposure to the virus, can prevent 33,700 of those cancers. Because the vaccine doesn’t prevent all cancers, women still need screening to protect themselves.
Previously employed for 22 years with the Suffolk County Department of Health Services, Dr. Mermelstein, who has a medical degree and a master’s in public health, briefly retired, before taking this job at Stony Brook.
“I wanted to do something to help address cancer after I retired, and so I contacted Stony Brook Cancer Center and began in this position about four months after I retired,” she explained.
Those interested in reaching out to the Office for Community Outreach and Engagement can call 631-444-4263 or email [email protected].
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