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Brookhaven National Laboratory Director JoAnne Hewett. Photo by Jessica Rotkiewicz/BNL

By Daniel Dunaief

Instead of flying a plane through clouds and gathering data during a three to five second window of time, researchers at Brookhaven National Laboratory are one of three teams proposing constructing a cloud chamber.

This new research facility would allow them to control the environment and tweak it with different aerosols, enabling them to see how changes affect drizzle formation.

“This is fascinating,” said JoAnne Hewett, Director of BNL and a self-professed “science geek.”

Hewett, whose background is in theoretical physics and who came to BNL from SLAC National Accelerator Lab in Menlo Park, California, has been the director of the Upton-based lab since April of 2023.

In a celebrity podcast interview, which will be posted on TBR News Media’s website (tbrnewsmedia.com) and Spotify, Hewett addressed a wide range of issues, from updates on developing new technologies such as the Electron Ion Collider and the construction of buildings, to the return of students to the long-awaited reopening of the cafeteria.

The U.S. Department of Energy is currently considering the proposals for the cloud chamber and has taken the first steps towards initiating the project.

Hewett, who is the first woman to lead the national lab in its 77-year history, is hoping the winner will be announced this year.

More x-ray tools

In a discussion about the National Synchrotron Lightsource II, which is a circular electron accelerator ring that sends x-rays into the specialized beamlines, Hewett described a study at the recently opened High Energy X-ray Scattering beamline, or HEX.

The state-funded HEX, which is designed for battery research, recently hosted an experiment to examine the vertebrae from Triceratops.

The NSLS-II, which opened a decade ago and has produced important results in a range of fields, will continue to add beamlines. BNL recently received approval to build another eight to 12 beamlines, depending on available funding. The lab will add one beamline in 2025 and another two in 2026.

Electron-Ion Collider

BNL, meanwhile, is continuing to take important steps in planning for an Electron-Ion Collider (EIC), an ambitious $2.8 billion project the lab won the rights to construct.

The collider, which will reveal secrets of the quarks and gluons that make up atoms, will start construction in 2026 and is expected to generate data sometime in the early 2030’s.

As groups of scientists develop plans for the EIC, they apply to the government to reach various milestones.

In March of this year, the lab met a hurdle called CD3A, which provided $100 million in funding for long lead procurements for some of the parts for the 2.4 mile circumference particle collider.

The next review, called CD3B, will be in early January and will involve $50 million in funding.

The funding for these steps involves ordering parts that the lab knows will be necessary.

The EIC will address five key questions, including how does a proton acquire its spin, what is the nature of dense gluon matter, how do quarks and gluons interact within a nucleus, what is the role of gluons in generating nuclear binding energy, and how do the properties of a proton emerge from its quark and gluon constituents.

Researchers expect the results to have application in a wide range of fields, from materials science, to medicine, to creating tools for complex simulations in areas including climate change.

Return of students

After the Covid pandemic shut down visits from area primary schools, students are now returning in increasingly large numbers.

In 2023, around 22,000 students had a chance to find scientific inspiration at BNL, which is starting to approach the pre-pandemic levels of around 30,000.

School buses come to the science learning center on the campus almost every day.

In addition, BNL hosted a record number of student internships, which are typically for college-age students.

In addition to inspiring an understanding and potentially building careers in science, BNL is now opening a new facility. The science users and support center, which is just outside the gate for the lab, is a three-story building with meeting room space.

“It’s going to be a one-stop-shop” for visiting scientists who come to the lab, Hewett said. Visiting scientists can take care of details like badging and lodges, which they previously did in separate buildings.

Additionally, for staff and visitors, BNL reopened a cafeteria that had been closed for five years. The cafeteria will serve breakfast and lunch with hot food.

“That’s another milestone for the laboratory,” Hewett said. With the extended time when the cafeteria was closed, just about everything will be new on the menu. The reopening of the facility took years because of “all the legalese” in the contract, she added.

A new vision

Hewett spent the first nine months of her tenure getting to know the people and learning the culture of the lab.

She suggested she has a new vision that includes four strategic initiatives. These are: the building blocks of the universe, which includes the Electron-Ion Collider; leading in discovery with light-enabled science, which includes the National Synchrotron Lightsource II; development of the next generation information sciences, including quantum information sciences, microelectronics and artificial intelligence; and addressing environmental and societal challenges.

As for the political landscape and funding for science, Hewett suggested that new administrations always have a change in priorities.

“We’re in the business of doing science,” she said. “Science does not observe politics. It’s not red or blue: it’s just facts.”

She suggested that generally, traditional basic research tends to do fairly well.

The BNL lab director, however, is “always making a concerted effort to justify why this investment [of taxpayer dollars] is necessary,” she said. “That’s not going to change one bit.”

After a recent visit to Capitol Hill, Hewett described her relationship with the New York delegation as “great.” She appreciates how the division that affects people’s perspectives in different parts of the world and that has led to conflicts doesn’t often infect scientists or their goals.

In the field of particle physics, “you have Israelis and Palestinians literally working together side by side,” she said. “It all comes to down to the people doing the science and not the government they happen to live under.”

Hewett also continues to believe in the value of diverse experience in the workplace. “We need the best and the brightest,” she said. “I don’t care if they’re pink with purple polka dots: we want them here at the laboratory doing science for us. We want to develop the workforce of the future.”

Adding key hires

As Hewett has settled into her role, she would like to fill some important staff functions. “This is really two or three jobs that I have to get done in the time it takes to do one job,” she said. “A chief of staff is very much needed to help move some of these projects along.”

Additionally, she is looking for someone to lead research partnerships and technology transfer. “As you do the great science, you want to be able to work hand in hand with industry in order to do the development of that science,” she said.

She said this disconnect between research and industry was known as the “Valley of Death.” Institutions like BNL “do fundamental science and industry has a product, and you don’t do enough of the work to match the two with each other.”

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Bruce Stillman, CEO of Cold Spring Harbor Laboratory. Photo courtesy of CSHL

By Daniel Dunaief

The Oscars could learn a thing or two from Cold Spring Harbor Laboratory. The facility, which conducts research in cancer, neuroscience, genomics, quantitative biology and plant biology, hosted its 19th annual Double Helix Award Dinner on Nov. 14.

Front row from left, 2024 Double Helix Medals honorees Dr. Katalin Karikó, Daniel and Alisa Doctoroff.
Back row, from left, CSHL Chair Marilyn Simons, President & CEO Bruce Stillman, and Grace Stillman. Photo courtesy of Patrick McMullan Company

Held at the American Museum of Natural History in New York City and emceed by CBS journalist Lesley Stahl, the dinner, so named for the twisting ladder structure of the genetic material DNA, raised $7 million while honoring Nobel Prize winner Katalin Karikó, and Daniel and Alisa Doctoroff, a husband and wife team who are leaders of Target ALS.

Bruce Stillman, CEO of Cold Spring Harbor Laboratory, recently discussed the awards dinner, an innovative and potentially revolutionary study on aging, science funding, and a host of other topics in an exclusive interview.

The honorees at this year’s dinner were “really fantastic,” Stillman said.

Originally from Hungary, Karikó thrived in work that helped lead to BioNTech and Pfizer’s work using messenger RNA to create a vaccine for COVID-19 despite setbacks including four demotions while a scientist at the University of Pennsylvania.

Her experience shows how “a scientist can do Nobel prize winning research despite adversity,” Stillman said. She had an “idea she wanted to stick with.”

Through Target ALS, the Doctoroffs have helped generate progress in research on amyotrophic lateral sclerosis, or Lou Gehrig’s disease.

Daniel Doctoroff, who has ALS, had been Deputy Mayor for Economic Development and Rebuilding and CEO and president of Bloomberg LP.

The dinner has raised over $67 million since its inception and has honored scientists and public figures, including the late boxer and inaugural winner Muhammad Ali, baseball Hall of Fame right fielder Reggie Jackson and Nobel Prize winner and co-discoverer of gene editing tool CRISPR Jennifer Doudna.

As a part of the celebration, the lab produces videos of the honorees, who have made significant contributions to philanthropy or to research or who have been advocates for health.

A week after the dinner, Stillman had written a letter to potential honorees for next year.

“It’s a lot of work to do this properly,” said Stillman. “We have a time limit on the evening. We want everyone out by 9:30 p.m. We timed this whole thing down to the minute and it worked out very well.”

An important aging discovery

While the lab produced a large volume of research studies that could have implications in a range of fields during the year, Stillman highlighted the work of Corina Amor Vegas as being “probably the most impactful down the road.”

Corina Amor Vegas. Photo ourtesy of CSHL

Amor Vegas used a technology developed to treat cancer to address the effects of aging.

She produced chimeric antigen receptors on the surface of the immune system’s T cells to attack senescent cells, which have aged and are not functional but could otherwise cause aging related problems such as diseases.

In a mouse model, Amor Vegas found that treating these aging mice with modified forms of their own T cells, through car-T immunotherapy, improved metabolic dysfunction and exercise capacity. Indeed, even a single treatment was enough to provide long term benefits for these mice.

The work attracted considerable venture capital interest and the lab is in discussions about how to pursue a business approach that taps into the potential use of this discovery.

As for businesses, the lab has a number of companies that are “under the radar screen” but that will have an impact in their fields.

Professor Partha Mitra started a company called Clarapath that will make “a major splash” with its automatic slides for pathology, Stillman said. A machine can do the work automatically that is otherwise labor intensive.

Down the road, scientists could apply artificial intelligence to analyze the samples. The laboratory has several faculty that are doing machine learning or AI in their research in areas such as neuroscience or genetics.

Through a neuro-AI scholars program, CSHL brings in people who have had a high level of training in computer science related to machine learning. The scholars come to CSHL for one or two years, where they work in a neuroscience lab.

Meetings

Stillman was pleased with the meetings on site this year, including one on epigenetics and CRISPR.

At the end of May in 2025, CSHL plans to have a symposium called Senescence and Aging.

The lab has invited scientists to speak from Germany, Israel, Japan and the United Kingdom as well as from Harvard, Brown and Yale. Locally, Amor Vegas, Assistant Professor Semir Beyaz and Professor Lloyd Trotman have also received invitations to share their work.

Stillman anticipates the publication of compelling findings from CSHL next year, including in autism.

At the same time, the lab is building a new Neuroscience Research Complex that should be finished in 2026. The 36,347 square-foot facility will include three modern buildings that focus on neurodegenerative diseases, brain-body physiology and quantitative biology and NeuroAI.

The construction has been going “very well,” Stillman said.

Science and politics

Amid talk of a rationalization of the research budget next year when the former and future president Donald Trump takes office, Stillman cautioned against a heightened focus on translational studies.

“If we knew what basic science would be translational, we would be doing it,” Stillman said. “If you go back and look at fundamental discoveries of how a disease can be cured, like Spinraza, people would have said, ‘Don’t study this or that.’”

Professor Adrian Krainer developed the drug Spinraza at CSHL, which is an effective treatment for an otherwise debilitating childhood disease called spinal muscular atrophy.

The development of CRISPR came from a study of bacteria that grow in a marine environment.

If Trump’s administrators think they can predict that every dollar will be productive, “they are nuts,” Stillman said. “We should have a discussion before they start pronouncing what should be done.”

Converting the National Institutes of Health into a directed translational research institute will push down American competitiveness.

China is planning to spend large sums of money in basic research. If the United States cuts back in these areas, this is a “recipe for the country to become a second class citizen to those that are “investing in basic science.”

The Human Genome Project cost $3 billion over 25 years. The returns exceed $1 trillion, Stillman said.

“That’s an enormous payoff,” he added. 

Despite concerns and a watchful eye on research funding, Stillman shared a positive outlook.

“I’m not pessimistic about the future,” he said. “The United States economy is very strong.”

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A 3D constructed building in Ukraine. Photo courtesy of Utu (Ukraine)

By Daniel Dunaief

Instead of discarding concrete from damaged or destroyed buildings during Russia’s attack on Ukraine, Alexander Orlov, Professor in Materials Science & Chemical Engineering at Stony Brook University wants to try to figure out ways to recycle these materials to create new and desperately needed shelters.

Alexander Orlov. Photo courtesy of SBU

Leading a team of researchers in the United States, Poland and Ukraine, Orlov received about $700,000 worth of funding from the National Science Foundation, the Office of Naval Research, and the Polish National Science Centre to develop ways to create these potentially life-saving structures by using three-dimensional printers.

Far larger than the desktop printers, these three-dimensional printers build one layer of a building at a time, reducing the time and labor needed in construction. 

The idea behind the project is to “turn the tragedy of these damaged buildings into new structures,” said Orlov.

In some cases, these buildings could be cheaper and faster than conventional construction methods.

“This research will address challenges in building resilient and sustainable infrastructure by using novel, inexpensive and energy efficient solutions,” Marija Krstic, assistant professor in the Department of Civil Engineering at Stony Brooks said in a statement.

The family of Ukrainian soldier Yaroslav Berezov, who died during the beginning of the Russian invasion, received the first 3D printed house earlier this year, according to the Odessa Journal.

The walls of the house were printed in 58 machine hours, as the printer laid down the inside and outside of the house at the same time.

The idea of doing 3D printing is becoming more popular in Ukraine. The leader in this type of printing is a company called COBOD, which used the technique to rebuild a school in the city of Lviv. The school, which has weatherproof construction and is expected to last for more than 20 years, has four classrooms with a capacity for 100 students.

One layer at a time

Orlov explained that the 3D printing process acts like an ice cream machine, as it lays down one layer of a building at a time with material squeezed through a cone.

In the design of these structures, the machine pauses for some length of time — five or 10 minutes in some cases — to ensure that the layer is strong enough to support additional weight. The structure also requires some time to settle, which could be about two weeks, before adding heavier objects, such as a roof.

Assistant professor Marija Krstic in the Department of Civil Engineering along with a graduate student. Photo from SBU

The machines use waste and add it to a cement mix to form concrete.

In this project, the research is focused on a proof of concept that Ukrainian construction companies might use to build additional homes or shelters.

The National Science Foundation is providing $300,000 in funding for Orlov’s portion of the work.

Stony Brook University is building a 3D printer and is adding parts to it to make it more efficient and reliable. Poland is also purchasing a printer while Ukraine already has one.

The Office of Naval Research is providing funding directly to Ukraine and the Polish National Science Centre is supporting efforts in that country.

“The Navy supports disaster relief and typically offers assistance in any part of the world” after catastrophes including hurricanes and earthquakes, Orlov said.

It takes about two to three days to build a building the size of a house. The process still requires manual labor to add the roof because it has different materials.

The timing of the research is particularly important because of the escalating scale of Russian attacks and amid the approach of winter. People in the capital of Kyiv endure seven hours of bombing each night. The civilian experience is similar to what people in London experienced during World War II, when they hid in shelters and had to be quiet amid the shattering of buildings.

Ukraine has lost about 50 percent of its energy infrastructure, a number that is likely to climb even as colder weather descends on the country. The estimated cost to repair that energy infrastructure is about $60 billion and is likely to climb as the war continues, Orlov added.

Without energy and heat, “this could be the worst winter in the history of the country,” Orlov said.

In developing ways to build these structures, Orlov hopes to create buildings that are mechanically the same or better than traditional homes and with thermal properties that are increasingly important amid temperature extremes.

The biggest challenge for scientists and engineers is that these buildings may not be reproducible, depending on the different available materials. The researchers need to figure out if they can have high-quality printing from different sources.

Personal experience

For Orlov, the horrors of war and the threat of injury and death are all too real. He extracted his mother Tetiana and his father Mykhailo, out of Kyiv, where their apartment windows were blown out after a Russian rocket leveled a nearby five-story building.

Orlov’s parents are struggling even on Long Island, where the sound from nearby fire station causes them to try to run and hide each time they hear the alarm. Motorcycle noises, which have the same vibrating hum as Iranian drones, also terrify them.

Project origins

The research Orlov is doing started when he was working with a Polish researcher. Orlov saw the funding opportunity and reached out to professors in Kyiv to ask how he could help. The researchers worked together to write the proposal.

Orlov, who works in the Consortium for Inter-Disciplinary Environmental Research and has secondary appointments in the Chemistry Department, the Institute for Advanced Computational Science, the Advanced Energy Center, and the Department of Technology and Society, is spending considerably more time than he expected on this project. That, he said, comes in part from the need to cross cultural barriers in working with people from different countries.

Any construction of 3D printed shelters would face the challenge of finding energy to power these machines. Some of that power could come from mobile generators, while the printers could also use intermittent power.

“There are unique challenges that have to be tested during the war,” Orlov explained.

At each of the research sites, students have the opportunity to contribute to the project. Stony Brook has two faculty members and several graduate students who are involved at this point.

Orlov is hoping to provide Ukrainian companies with recipes that might lead to the construction of these shelters.

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Olaf Kleingbeil at the Pezcoller24 Symposium in Italy in June, 2024. Photo by Claudia Tonelli

By Daniel Dunaief

The wreck-and-check method sometimes works, providing the kind of clues that lead to cures.

In the case of cancer, however, taking out one gene or one protein may not be enough, particularly when a combination contributes to cancer growth or to inactivating the body’s defenses against the disease.

Olaf Klingbeil. Photo courtesy of CSHL

Over the course of seven years, first developing a technique, then searching for possible clues about what the work might reveal, Olaf Klingbeil, a postdoctoral researcher in the lab of Professor Chris Vakoc at Cold Spring Harbor Laboratory, discovered two proteins that work together to do cancer’s bidding.

Called Mark 1 and Mark 2, these two proteins in combination keep a tumor suppressor called Hippo from doing its job, enabling a wide range of cancers from continuing to grow.

The Hippo pathway is one of the most dysfunctional in all human cancer biology.

The journey to this discovery is as compelling as the finding itself.

Klingbeil honed a technique that took out a series of genes, hoping to find out how more than one protein might be involved in the kind of on-off switch geneticists are often seeking to slow or squelch cancer.

Indeed, disrupting either of the proteins on its own would not have been enough, as the disease would have progressed with a singular inhibitor.

“When you manipulate A or B individually” you don’t see much difference in the cancer cells, Vakoc said. “When you manipulate A plus B, you get a massive effect.”

Vakoc suggested that his lab developed a new technology to find cancer targets, enabling them to search for processes and contributors that were otherwise invisible. Klingbeil used lentiviruses to introduce CRISPR gene editing into cancer cells.

“What [Klingbeil] developed, a method where you can introduce two [changes] at the same time, can be engineered to target combinations of genes,” Vakoc said. “It took years to figure out how to do this.”

Klingbeil explored the effect of making these double knockouts through many perturbations.

“It was the largest project in my lab to this point,” said Vakoc.

A eureka moment

Klingbeil examined several potential leads that might provide clues about how to attack cancer cells. He published 1,719 single gene knockouts and 2,529 paralog double knockouts and expected to find a few jewels. 

Christopher Vakoc. Photo courtesy of CSHL

He likens the process to panning for gold at a creek, which involves getting rid of numerous stones before discovering that gold nugget, which, in this case came in the form of two kinases, which add phosphate labels to macromolecules.

When Klingbeil honed in on Mark 2 and Mark 3, he couldn’t immediately understand why inhibiting these enzymes affected some forms of cancer, but not all of them. 

The postdoctoral researcher read a study in which the researchers looked at the tumor suppressive function of Yap/Taz in leukemia and neuroendocrine cancers and realized that these were the cancer types that didn’t show a reaction to inhibiting these kinases.

This was the first hint that Marks 2 and 3 and Yap/Taz might work together, Klingbeil explained.

The affected cancers include liver, lung, colorectal, ovarian, triple negative breast cancer, pancreatic cancer and prostate cancer. That list also includes rhabdomyosarcoma, a rare form of pediatric cancer for which Vakoc, in particular, is eager to develop new treatments.

While numerous scientists are seeking ways to block this pathway directly, the focus on Mark 2 and Mark 3 presents a new potential opportunity.

Marks are “totally overlooked in the community” and are “not a known target,” said Vakoc. “This is the first paper that announces these as cancer targets in a compelling way.”

An existing drug

Once he discovered this link, Klingbeil searched for existing drugs that might target Marks 2 and 3. Fortunately, he found one that Merck had tried to develop for Alzheimer’s disease.

While that didn’t work as well as the pharmaceutical company had hoped, the CSHL researchers are looking to use it as a starting point for a future therapy.

“We are excited that there’s a chemical matter” that might help treat cancer, Vakoc said, adding that such a treatment will likely require “a lot of love by chemists to give them the ideal attributes” for any therapeutic approach.

The drug Merck produced inhibited Marks 1 and 4 as well as 2 and 3, which provides opportunities to tailor it for the most relevant enzymes. By increasing the specificity of the drug for two of the four proteins, researchers and pharmaceutical companies could reduce the side effects of inhibition.

To be sure, Vakoc and Klingbeil cautioned that this discovery, while encouraging, wouldn’t likely provide a magic bullet for cancer, which has a way of becoming resistant to treatments and to tapping into other unknown or unseen pathways to continue to cause harm.

Effective future treatments that involve inhibiting Marks 2 and 3 could require the use of a combination of therapies, which might outmaneuver or slow the progression of cancer.

A personal message

Earlier this year, Klingbeil learned that the journal Cancer Discovery had accepted the paper for publication in an unusual way. He was attending a dinner one night at a conference in Italy when Elizabeth McKenna, the Executive Editor of the journal, approached him.

“She told me she was about to send an email” to Vakoc that the paper was accepted, Klingbeil said. “I was very excited. I’m happy to publish it and that I could convince the most critical reviewers about the value of the work.”

After a productive and rewarding collaboration with Vakoc, Klingbeil is preparing for the next steps in his career. He is speaking with various institutions, particularly in Europe, where he can be closer to his family and his native Berlin, Germany while continuing to advance his scientific career. He plans to continue to work with Vakoc after he leaves.

“The discovery was big enough to carve out a piece for him and me,” Klingbeil said and suggested he would study Mark function in pancreatic cancer in more detail.

On the personal front, fate lent a hand when Klingbeil first arrived on Long Island.

He started his life here in the middle of the winter, without a car or a driver’s license. The lab provided temporary housing on campus. He had a choice to share an apartment with either a French or an Italian postdoctoral researcher.

He chose to live with postdoctoral researcher Claudia Tonelli, who works in the lab of Cancer Center Director David Tuveson and is now his partner. The two researchers, who started dating a few months after living together, have a daughter Lily.

As for his work, he is cautiously optimistic that this discovery may one day help with new and effective therapies.

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Bottom row, from left, Andrew Whitely, VP Business Development and Technology Transfer at CSHL; Dr Susan Poser, President of Hofstra University; students Dimitri Dumontier; Charlie Chung, Yong Lin, Stephen Staklinski and Javier Anduaga; Dr. Janet A. Lenaghan, Dean of the Frank G. Zarb School of Business at Hofstra University; and Erick Hunt, Director of the Institute of Innovation and Entrepreneurship at Hofstra University Top row, from left, students Zifei Wang, Viet Hang Lee, Yujia Li, Jed de Ruiter-Swain, and Eva Lentsch. Photo courtesy of Hofstra University

By Daniel Dunaief

Ten graduate students and postdoctoral researchers stepped outside their familiar surroundings at Cold Spring Harbor Laboratory into a different campus and discipline recently.

As a part of the inaugural Bioscience Business Innovation Program, these developing scientists spent a week working with a collection of business professors at the Frank G. Zarb School of Business at Hofstra University, where they learned a range of subjects such as financial planning, intellectual property, leadership and project management.

The program, which will include a second week of training in March, is designed to teach developing scientists about market validation, Food and Drug Administration processes, and the creation of business models. The program also teaches leadership, team building and communications, which could help researchers who enter the pharmaceutical or biotechnology fields after they leave CSHL.

The goal is to “familiarize these new researchers on several aspects of business, marketing, finance, and management” which will help them consider the potential commercial application of their work, said Anoop Rai, Finance Professor at Zarb and one of the instructors in the Bioscience Business effort.

Indeed, in applying for some grants for startups from agencies like the National Science Foundation, researchers need to answer questions relating to growth, profitability and a target market.

“A knowledge of business is probably very important in that sense,” added Rai.

Scientists often have an interest in developing an innovation that could be useful for society, whether that’s a drug to treat a disease, a test to monitor health, or a new product. Such efforts need to “be marketed to become successful,” Rai said. “This group may, at some point, try and make [their findings] into a successful venture.”

Scientists would benefit from knowing about business in case they move to the next stage in their research or business development. To be sure, a two-week course offers an opportunity to learn and to develop an awareness of the business world, but doesn’t provide a comprehensive formula for success. The students will “get a feel more on the venture funding side, not so much on the complete running of a business,” said Rai.

Still, at the end of the program, the CSHL researchers will have an opportunity to make a pitch alongside a law student and a MBA candidate that a group of experts will evaluate. These pitches will require a basic understanding of business.

Student experience

Some of the students, who put most of their research aside for a week to immerse themselves in intensive training from a host of lecturers and experts, felt they have already benefited from such instruction.

Stephen Staklinski

One of the biggest take-home messages for PhD candidate Stephen Staklinski, who works in the lab of Professor Adam Siepel, involved understanding the consumers of any future product.

In research, Staklinski reads papers and looks for information that’s missing in the field. He rarely communicates directly with people who might be affected by any future discovery until a project is well under way. With a business viewpoint, he gained a new perspective he feels he can integrate effectively into his research.

Staklinski recognized the value of talking to physicians and cancer patients about some of their biggest issues. He sees the benefit of these open communications about how to serve patients who are battling various conditions.

In his current research, Staklinski builds statistical probabilistic models around the human genome. Specifically, he’s looking at molecular sites in RNA and is searching for targets that lead to metastatic processes. In working with experimental collaborator, Staklinski said he can “think about therapeutics to block this.”

Viet Hang Le, a postdoctoral researchers in the lab of Professor Linda Van Aelst, felt she received an introduction on how to develop fundamental research findings towards making new therapies.

“We got to learn about the laws and policies involved” in creating a new company, said Le. On the clinical safety side, she also learned how new products maneuver through health care and reach patients.

Her original curiosity was to see how research findings could lead to real-life treatments. Understanding business fundamentals opens more career options.

Indeed, even if Le and her colleagues continue to conduct research, she feels she can communicate more effectively with industry partners. It also whet her appetite for more business learning.

“It really bridges the gap between our background in fundamental science and the requirement for an MBA course,” Le explained. 

She is working on two projects in Van Aelst’s lab. In the first, she is studying early onset epilepsy, which is a symptom of an X-linked intellectual disability in patients carrying a mutation in the gene Oligophrenin 1.

In the second, she is exploring how the nervous system influences the progression of cancer in main tumors and metastatic tumors.

“We built a hypothesis on how different branches of nerves might increase the growth of cancer,” said Le. In Van Aelst’s lab, they are working with primary breast cancer and liver metastasis.

Originally from Dan Nang, Vietnam, Le spent a number of weeks during several summers as a part of the US Navy Pacific Partnership delivering medical treatment to medically underdeveloped areas in the country.

Through her lab work and any budding business interest, she would like to figure out how to deliver medical care to patients who might struggle with the financial or logistical challenge of affording care.

By connecting with experts who’ve negotiated various obstacles, “I’m gaining a clearer sense of how to streamline the path from discovery to patient care, cutting down unnecessary costs and time without compromising safety,” she said.

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Participants of last year's Human Library event. Photo by Rachael Eyler, Stony Brook University

By Daniel Dunaief

Stony Brook University is providing another opportunity for students and the community to venture beyond the labels that define and, at times, limit our views and understanding of each other.

Chris Kretz

For the second year, the university is hosting the Human Library, which gives participants an opportunity to learn about other people’s lives.

Started in 2000 in Denmark, the Human Library brings “books” (people from different walks of life, which has included a refugee, disabled parent, and person with bipolar disorder) with “readers,” who have a chance to ask questions for 30 minutes with each book.

The chapters these books share has surprised readers and given them a chance to reconsider how they view people whose lives or life experiences are different from their own.

“It’s not meant to teach people something or have them leave being converted to some new thought process,” said Chris Kretz, Head of Academic Engagement at Stony Brook University Libraries. “It gives [readers] an opportunity to speak with someone they may never normally encounter or have a conversation they may not get to have.”

The Human Library event occurs on Wednesday, Nov. 20 from noon to 3 p.m. and from 5 p.m. to 7 p.m. at the Frank Melville Jr. Memorial Library’s Central Reading Room. Participants don’t need to pre-register and can show up at the library, where about 110 readers visited last year.

Kretz recommended the latter session for interested community members, which would allow them to park for free to attend the event.

Following the defined structure created by the original Human Library, attendees won’t know about the specific backgrounds of the books until they arrive. The people that represent the books will all sit at desks wearing the same black t- shirts.

“In the conversation, the colors come out,” Kretz said.

Indeed, Richard Tomczak, Director of Faculty Engagement in the Division of Undergraduate Education at SBU and a reader at last year’s Human Library, can attest to that. Tomczak spoke with a book who grew up in the outer boroughs of New York as a member of the working class.

“When you’re having a conversation about shared experiences or experiences that are new to you, it brings out the human characteristics,” said Tomczak. “I wanted to listen and absorb it all.”

Choosing a book

When readers sit down, the book offers a prologue about their lives, providing some details about their experiences. Readers who aren’t sure where to start asking questions or perusing through different chapters in the book can use prompts at each desk to begin their interaction. Readers who stay for an entire session  will be able to interact with three or four books.

Participants of last year’s Human Library event.
Photo by Rachael Eyler, Stony Brook University

“This is an opportunity for people to hone their conversational skills,” said Kretz, as well as to learn about the lives of the books who are offering details that may surprise and move the readers.

Indeed, this year, the university is stocking tissues near each book for those readers who may feel particularly touched by the stories they hear.

The university would like to ensure that the conversation is respectful and that both sides are comfortable with the discussion.

“We have rules for readers,’ said Kretz. “When they sit down with the book, the pages are in mint condition. We want to make sure everyone is on the same page. Books don’t necessarily have to answer every question.”

Kretz urged attendees to recognize that the interaction is not a debate, but presents ways for people to understand more about their own judgments and, as the Human Library website suggests, to “unjudge” each other. In addition to speaking and asking questions, readers and the books will have a chance to process what they’ve heard.

“By design, it’s a session where you have to listen,” said Kretz. “One of the values is that people get a chance to practice this muscle.”

Second year

In the second iteration of the Human Library, Stony Brook added the later time so people could come after work. The administrators have also reached out to journalism classes and to people in international programs. 

Students from other countries will “have a chance to meet people they wouldn’t have met” during their time abroad, Kretz added.

After speaking with the people who served as books last year, Stony Brook heard that the books also wanted to serve as readers of some of the other people’s lives.

University officials were pleased with the exercise last year.

“I’m impressed by how open our community was,” said Kretz. “People learned a great deal from listening to each other.”

The university is considering making this an ongoing annual tradition and might even bring people together each semester.

Other New York schools and libraries have embraced the Human Library process, including Adelphi and SUNY Albany. The Human Library has also caught on globally, as people in 85 countries on six continents have helped facilitate these conversations.

While the participants engage in meaningful discussion, the exchange isn’t designed to create a lasting social network or lead to ongoing connections between the readers and the books.

“It’s not meant for them at the end of the reading to shake hands and exchange business cards,” explained Kretz.

The event is sponsored by the University Libraries and the DEIA (Diversity, Equity, Inclusion, Accessibility) Team with the Division of Student Affairs, Office of Diversity Inclusion and Intercultural Initiative, Office of Military and Veteran Affairs, and Diversity, Intercultural and Community Engagement, and the Program in Public Health.

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2024 Stony Brook University iGEM team. Photo by Ethan Kim

For the third time ever, Stony Brook University’s International Genetically Engineered Machine (iGEM) team brought home the gold medal from the iGEM Giant Jamboree.

Held in Paris, France from October 23-26, the iGEM Giant Jamboree is a world expo for synthetic biology. This year’s competition featured 438 teams from 45+ countries, competing for medals and awards by designing, building, and testing projects using cutting edge synthetic biology.  Stony Brook University was one of 16 U.S. collegiate teams to earn a gold medal.

Stony Brook University’s project focused on developing a less invasive, more cost effective way to diagnose B-cell lymphoma. The team focused on equipping E.coli with a genetically engineered gene circuit to detect microRNAs as biomarkers for this disease.

“Stony Brook’s participation in iGEM continues to have a profound impact on our students,” said Peter Gergen, SUNY distinguished service professor, Department of Biochemistry and Cell Biology in the College of Arts and Sciences. “This year’s team was extremely cohesive and benefited greatly from the advice and assistance provided by former iGEM team members Chris Helenek, AJ Sillato, Abhishek Cherath, Michelle Yang, Bushra Islam and Zach Don as well as input from Dr. Joshua Rest (Ecology and Evolution) and Melanie Cragan (Biochemistry and Cell Biology).”

This year’s interdisciplinary iGEM team, comprising three juniors, four sophomores, and eight first-year students when they started last January, included those with majors in biochemistry, biology, chemistry, computer science, electrical and computer engineering, information systems, and political science. The team was co-advised by faculty members Peter Gergen and Kathryn Gunn in the Department of Biochemistry and Cell Biology, and Gabor Balazsi, in the Department of Biomedical Engineering and received support from the staff in Undergraduate Biology.

For more information on Stony Brook’s iGEM team and this year’s project, visit https://2024.igem.wiki/stony-brook/index.html

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Cold Spring Harbor Laboratory. Photo courtesy Cold Sping Harbor Laboratory website

By Daniel Dunaief

A stock fund is taking a page out of the Newman’s Own playbook.

The food company which was started by the late actor Paul Newman and author A.E. Hotchner donates its after tax profits to charity through the Newman’s Own Foundation, enabling consumers to feel that they aren’t just covering their salad with tasty dressing but are helping the world through their consumer choices.

Range Cancer Therapeutics, an exchange-traded fund that purchases a broad basket of cancer therapeutic stocks, created a new partnership with Cold Spring Harbor Laboratory to contribute to cancer research.

The fund, which was started in 2015, plans to contribute 23 percent of its revenues, reflecting the 23 pairs of chromosomes in the human genome, each quarter to Cold Spring Harbor Laboratory.

“The contribution from Range will directly benefit the research efforts at CSHL, underscoring our commitment to advancing scientific innovation in oncology therapeutics,” Range ETF’s founder and CSHL Association Board Member Tim Rotolo, said in a statement. The ETF provides “exposure to nearly the entire lifecycle of drug development and distribution, and this new collaboration with CSHL provides an opportunity for investors to also see their money go toward the earliest stages of cancer breakthroughs.”

Revenues collected by the fund are likely to vary by quarter, depending on the amount of money the fund manages. With an estimated $12.1 million in assets under management as of the end of September and an expense ratio of 0.79%, the fund could contribute about $21,850.

“Hopefully, people will feel when they’re buying the ETF that they are in some ways supporting cancer research,” said Charles Prizzi, Senior Vice President for Advancement & Special Advisor to CSHL President Bruce Stillman.

Prizzi anticipates that the funding could support the lab’s efforts to conduct a broad range of research as CSHL’s staff, who come to the site from all over the world, seek to address the kinds of questions that can lead to advancements in a basic understanding of processes as well as to translational breakthroughs that can help in the prevention, diagnosis and treatment of various diseases.

Prizzi hopes this partnership will attract attention and inspire other fund managers or businesses to contribute to the lab, particularly amid periods when the budgets for federal funding agencies that support research rise and fall.

Borrowing from the language of genetics, Prizzi hoped that this kind of arrangement will be “replicated” by others.

 NASDAQ event

The NASDAQ stock market, which is where the Range Cancer Therapeutics Fund trades under the ticker CNCR, will celebrate the partnership on November 14th in New York City.

The Nasdaq tower will feature a visual display, while Range ETFs and CSHL leadership and guests come together at the Nasdaq podium to mark the ongoing contribution.

Dave Tuveson, head of the Cancer Center, Professor Adrian Krainer, who developed an effective treatment for spinal muscular atrophy using antisense oligonucleotide to affect gene splicing, Vice Chair Howard Morgan, and Goldman Sachs’s Roy Zuckerberg, and others will attend the event.

d Spring Harbor Laboratory President Bruce Stillman. File photo

“Cold Spring Harbor Laboratory is one of only seven national basic biological research cancer centers designated by the National Cancer Institute in Washington, DC,” Bruce Stillman, CEO of the lab said in a statement. “The institution is investing heavily in the growth of our cancer program, specifically in multidisciplinary, collaborative ventures as part of our new brain-body physiology initiative.”

Prizzi is often searching for novel ways to support research and was pleased with the contribution and hopeful that it would spur other creative donations and support.

“I hope people will learn from it and copy it,” Prizzi said. “It will benefit the lab for many years to come.”

Rotolo joined the board at CSHL earlier this year and has supported the lab for about a decade.

Rotolo had approached the lab to establish this financial commitment.

The laboratory is a 501c3 nonprofit institution, which means that donations to the lab are tax deductible.

Prizzi suggested that interested donors often reach out to him towards the end of December.

“We would love to have more people support what we’re doing,” said Prizzi.

CSHL is home to eight Nobel Prize winners and employs 1,000 people, including 600 scientists, students and technicians.

The Meetings & Courses Program bring in more than 12,000 scientists from around the world each year, offering opportunities for researchers to meet and establish collaborations and to learn about the latest scientific breakthroughs.

CSHL is in the first phase of a Foundations for the Future project, which is a seven-acre expansion effort that will tackle research in neuroscience, neuro-AI and the brain-body. Scientists will pursue better patient outcomes by exploring cancer’s whole-body impacts.

In the second phase of the project, the lab will create a new conference center and collaborative research center.

As for the connection with Range, Prizzi added that CSHL is a “lab, we like experiments. This is like an experiment. I hope it goes well and other people build off of it.”

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At the Milestones in Microbiology ceremony, standing alongside the Department’s commemorative plaque and a NYS Assembly Proclamation, are, from left: Theresa Koehler, ASM President; Carol Carter, Eckard Wimmer, David Thanassi, Jorge Benach; and Lorraine Findlay, from the ASM Committee on the History of Microbiology and Archives. Photo by Constance Brukin Photography

ASM honors the Department for its decades of work against infectious diseases

The Department of Microbiology and Immunology in the Renaissance School of Medicine (RSOM) at Stony Brook University was named a “Milestones in Microbiology” site for its advancements in the diagnosis and treatment of infectious diseases globally. The designation by the American Society for Microbiology (ASM) recognizes academic and research programs in which “major developments and pivotal discoveries occurred.”

The RSOM Department is only the 20th program nationally to receive this distinction, the third in New York State and second on Long Island. Faculty from the Department and University gathered at a Wang Center Ceremony at Stony Brook University on October 17 to commemorate the honor. They received a plaque from the ASM that commemorates the outstanding research and discoveries by the Department at large, since its inception at Stony Brook in 1972.

“The designation of the Department of Microbiology and Immunology as a Milestones in Microbiology Site is an honor and recognizes the impact the Department has made through its groundbreaking discoveries,” said David Thanassi, PhD, the Zhang Family Endowed Chair of the Department of Microbiology and Immunology. “This distinction not only reinforces the significant contributions of our former and current faculty, students and staff, but also raises the profile of the Department and University to the wider scientific community.”

“ASM is delighted to recognize Stony Brook University’s Department of Microbiology and Immunology as a ‘Milestones in Microbiology’ site for its significant contributions to the microbial sciences,” said Theresa Koehler, PhD, ASM President. “The university’s pioneering work investigating causative agents of human diseases have had far-reaching impacts in the sciences and society at large.” 

The Department was awarded the Milestones distinction for its broad research and many discoveries. Specifically, the ASM recognized the following accomplishments:

  • The landmark discovery by Founding Department Chair Joseph Kates, PhD, that viruses could package enzymes required for their replication, with the first demonstration of the vaccinia virus encapsulating the DNA-dependent RNA polymerase enzyme. This laid the groundwork for targeting viral polymerases as a widespread therapeutic strategy.

 

  • The discovery of Borrelia burgdorferi, the causative agent of Lyme disease, by Jorge Benach, PhD and colleagues, along with its isolation from patients and characterization of its environmental reservoir, paved the way for successful antibiotic therapies.

 

  • The first description of the de-novo chemical-biochemical synthesis of a virus (poliovirus) in the absence of a natural template by Dr. Eckard Wimmer and the co-discovery of the human receptor of polio virus. This marked the beginning of the total synthesis of microorganisms in the absence of natural templates, enabling new strategies in virus vaccine development.

 

“As a member of the faculty for several decades, it has been inspiring to witness the emergence of ideas and findings in which the outcomes have had such tremendous impact,” said Carol Carter, PhD, Distinguished Professor in the Department of Microbiology and Immunology. “Over the years, I have worked with incredible colleagues, students and supporting staff.”

Five decades impacting infectious disease discovery 

 In addition to the highlighted research of Drs. Kates, Wimmer and Benach, the Department during its five decades made other groundbreaking discoveries. These include pioneering work in molecular biology on the structure of DNA and regulatory mechanisms of RNA, foreshadowing research by others leading to the Nobel prize this year on the role of regulatory RNAs in eukaryotic cells.

The Department has contributed major findings related to tumor formation and cancer, and has long been a leader in research on pathogenic viruses, bacteria and fungi, revealing how these organisms cause infections and interact with our immune defenses. This research has yielded fundamental biological insights and provided a foundation for the development of therapeutics for the prevention and treatment of disease.

Some of the more recent work impacting the world of infectious diseases includes the role of how cancer-causing herpesviruses manipulate the host to establish life-long infections, advancing the understanding of Adenovirus replication, and unraveling the structure of bacterial appendages that enable kidney infections.

“Although the Milestones in Microbiology designation commemorates past accomplishments, it also sets the stage for future innovations and motivates the Department to keep pushing boundaries, pursue new questions, and lead the way in solving the challenges of tomorrow,”  said Peter Igarashi, MD, the Knapp Dean of the RSOM, who pointed out that the Department has had consistently strong funding success, including 17 grants totaling more than $8 million in funding from the National Institutes of Health in fiscal year 2024.

During the ceremony the department also received a Certificate of Recognition, a Proclamation by New York State Assemblyman Hon. Ed Flood. 

For more about the ASM Milestones Program and list of other awarded institutions nationally see this link.

The Department of Microbiology and Immunology is one of 25 departments within the RSOM. It is dedicated to advancing the knowledge of the fundamental causes, means of prevention and treatment of human diseases, and to educating the next generation of scientific investigators in infectious diseases and related fields. For more see this link.

 

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Kate Alexander. Photo courtesy of CSHL

By Daniel Dunaief

In the nucleus of the cell, researchers often focus on the genetic machinery, as the double-helical DNA sends signals that enable the creation of everything from my fingers that are typing these words to your brain that is processing what you’ve read.

But DNA, which occupies most of the nucleus, is not alone. Scattered through the nucleus are protein and RNA filled structures that have an influence on their important gene-bearing nuclear cohabitants, including speckles.

One of the newest members of the Cold Spring Harbor Laboratory team, Assistant Professor Kate Alexander, who joined the lab in August, is focused on a range of questions about these speckles, which represent about 10 to 30 percent of the nuclear volume.

Preliminary data from Alexander’s lab support the idea that speckles can signal how a person responds to various types of therapy, although careful extensive follow up studies are needed, Alexander explained. She would like to know how the speckles are affecting the genetic machinery.

While speckles have been known since 1910, the ways they affect healthy cells and diseased cells remains a mystery. In some cases, normal or aberrant speckles can signal how a person responds to various types of therapy.

Normal speckles are in the center of the cell nucleus, while aberrant speckles are more scattered. Aberrant speckles can activate some of the surrounding DNA.

At this point, Alexander and her colleagues have “found that normal or aberrant speckle states correlate with survival of clear cell renal cell carcinoma. This accounts for over 80 percent of all kidney cancers.”

Medical choices

After a patient with clear cell renal cell carcinoma receives a cancer diagnosis, the first line of treatment is usually surgery to remove the tumor in the kidney. In addition, doctors could treat the tumor with a systematic anti-cancer therapy. The treatments themselves can and often do cause difficult side effects, as therapies can harm healthy cells and can disrupt normal biological functioning.

Normal speckles look something like the face of the man on the moon and are more centrally located.

Alexander is hoping speckles will help predict the state of the tumor, offering clues about how it might respond to different types of treatments. She could envision how aberrant speckles could correlate with better responses to one drug, while normal speckles might correlate with better responses to another treatment.

In her research, Alexander is exploring how DNA is organized around speckles, as well as how the speckles affect DNA.

“Speckles can change and impact what’s happening to all the DNA that’s surrounding them,” she said. 

Over 20 tumor types show evidence for both normal and aberrant speckles. Aberrant tumors can occur in many types of cancer.

“The consequence of [speckles] becoming normal or aberrant are starting to become more clear,” she said, although there is “still a lot to learn.”

Alexander is trying to figure out how to alter the conformation of these speckles. During cancer, she suspects these speckles may get trapped in a particular state.

In one of the first experiments in her lab, she’s culturing cells in an incubator and is trying to predict what cues may cause speckles in those cells to switch states. 

‘Speckle club’ leader

Alexander previously did postdoctoral research at the University of Pennsylvania in the laboratory of Shelley Berger, where she was also a Research Associate. She led a subgroup in the lab known as the “speckle club.”

Charly Good, who is now Senior Research Investigator in Berger’s lab, worked with Alexander at Penn from 2017 until this summer.

Aberrant speckles are scattered throughout the nucleus.

Alexander “helped recruit me to the postdoc I ended up doing,” said Good who appreciated Alexander’s computational skills in analyzing big data sets. Speckles represent an “up and coming area” for research, which Alexander and Berger are helping lead, Good suggested.

Alexander’s quick thinking meant she would go to a talk and would email the speaker as soon as she got back to her desk. “Her brain is always spinning,” said Good.

Alexander is building her lab at CSHL. Sana Mir is working as a technician and is helping manage the lab. Recently, Hiroe Namba joined the group as a postdoctoral researcher. In the next few years, Alexander would like to add a few graduate students and, within five years, have about eight people.

Originally from Tigard, Oregon, Alexander attended Carleton College in Northfield, Minnesota. In her freshman year, she tried to get into a physics class that was full and wound up taking a biology class. She was concerned that biology classes were mostly memorization. When she started the course, she appreciated how the science involved searching for missing pieces of information.

Cold Spring Harbor Laboratory appealed to her because she could go in whatever direction the research took her.

For Alexander, scientific questions are like a layer of cloth with a few threads sticking out.

“You see one sticking out and you start to pull,” Alexander said. “You don’t necessarily know what’s going to come out, but you keep getting the urge to pull at that thread. You realize that it is connected to all these other things and you can look at those, too.”

She is excited to cross numerous disciplines in her work and is eager to think about how her research might “interplay across those fields and boundaries.”

Speckle origins

As for speckles, Alexander observed during her postdoctoral research how one factor seemed to influence a neighborhood of genes.

For that to occur, she realized that something had to affect those genes at the same time in the physical space. She hadn’t known about speckles before. A few of her colleagues, including Good, came across speckles in their analysis. That made Alexander curious about what these speckles might be doing.

She saw an opening to pursue connections between changes in these potential gene activators and illnesses.

Researchers know that viruses can use speckles to help them copy themselves.

If they are used by viruses “they must be important” and they “probably go wrong in a lot of diseases,” Alexander said. There are a series of neurodevelopmental disorders called “speckleopathies” that involve mutations in proteins found inside speckles.

“We have the computational and experimental tools to start investigating them across a wide variety of conditions,” she said.

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