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Zhishan Wang. Photo from Chengfeng Yang

By Daniel Dunaief

This is part one of a two-part series.

As Erin Brockovich (the real life version and the one played by Julia Roberts in the eponymous movie) discovered, some metals, such as hexavalent chromium can cause cancer in humans.

Chengfeng Yang and Zhishan Wang

Environmental exposure to a range of chemicals, such as hexavalent chromium, benzo(a)pyrene, arsenic, and others, individually and in combination, can lead to health problems, including cancer.

Recently, Stony Brook University hired Chengfeng Yang and Zhishan Wang, a husband and wife team to join the Cancer Center and the Pathology Departments from Case Western Reserve University in Ohio.

The duo, who have their own labs and share equipment, resources and sometimes researchers, are seeking to understand the epigenetic effect exposure to chemicals has on the body. Yang focuses primarily on hexavalent chromium, while Wang works on the mechanism of mixed exposures. 

In part one, TBR News Media highlights the work of Wang. Next week, we will feature the efforts of Yang.

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In certain areas and specific job sites, people can be exposed to environmental pollutants.

Sometimes, the introduction of a metal or element can cause cancer after long term exposure. The effect of another carcinogen can be synergistic in triggering disease, triggering a stronger progression of cancer than an individual exposure alone.

Zhishan Wang, who joined Stony Brook in March and is a Professor of Research in the Department of Pathology, is trying to understand what changes this mixed exposure creates at a molecular level.

“If we find out some gene or pathway change, we can try to intervene,” said Wang, who is a member of the Stony Brook Cancer Center and earned MD and PhD degrees from her native China.

Among the many possible environmental triggers, Wang chose to study arsenic, which is common in rock soil and water and is present in some places in drinking water.

“People living in high exposure areas to arsenic and [who] are also cigarette smokers have a significantly higher risk of lung cancer,” she said.

Arsenic can cause three different kinds of cancer: skin, bladder and lung cancer. For skin cancer, Wang explained that direct contact can lead to the kind of irritation that promotes the disease. 

As the heavy metal works its way through the body, parts of it get excreted through the urine system, which means that bladder cells come into contact with it as well.

For a long time, scientists knew arsenic exposure through drinking water caused lung cancer. The underlying mechanism for the development of that cancer was not well understood. 

Wang’s lab studies the mechanism by which arsenic and benzo(a)pyrene (or BAP) co-exposure increases lung cancer risk. Exposure to arsenic alone causes cancer, but it takes a long time in animal models. Arsenic and BPA co-exposure significantly increases lung cancer risk.

Wang’s study showed that co-exposure increases lung tumor burden and malignancy. She plans to continue to study the mechanism of how arsenic and BAP co exposure increases lung cancer risk.

“That’s our big goal: to try to find some useful method to prevent this tumor from happening,” she said.

Wang believes the cancer cells caused by the mixed exposure increases the number of cancer stem cell-like cells, which could mediate therapeutic resistance.

Wang explained that generating the mouse model took considerable time and effort. She tried to find the exposures during particular windows of time that lead to cancer.

“By using this model, we can do a lot of data analysis” including single cell analysis and can determine which cluster or pathway will change.

Choosing SBU

Wang suggested she and her husband chose Stony Brook for several reasons. The couple would like to help the University earn a National Cancer Institute (NCI) designation, which would give scientists the ability to compete for ambitious, well-funded, multidisciplinary efforts.

Both Wang and Yang “lead NCI-funded research programs that will enhance the [Cancer Center’s] eligibility for NCI designation,” explained Kenneth Shroyer, chair of the Pathology Department at Stony Brook.

Shroyer, who described both researchers as “highly competitive candidates with the potential to enhance the status of any cancer center,” is looking forward to working with his newest recruits.

Wang is eager to use the tissue bank at Stony Brook, which Shroyer explained has also attracted other cancer research scientists recruited to the Renaissance School of Medicine at Stony Brook.

The new scientists also hope to tap into the expertise at nearby Cold Spring Harbor Laboratory, which has become one of the leading centers in creating organoids. 

In the early years of her training during her MD and PhD years in China, Wang developed her technical skills. Through her career, she has worked on several genes that play important roles in carcinogenesis. Down regulation of the gene known as SOCS3, for suppressor of cytokine signaling 3, plays an important role in arsenic and BAP co-exposure caused lung tumorigenesis.

Early in their careers, Wang worked in her husband’s lab for seven years until she received her own research funding.

Outside of work, Wang enjoys playing badminton and ping pong. She also cooks every day. She and her husband bring her home cooked meals to work.

When she was in high school, Wang had ambitions to become a writer. Her teachers regularly read her work out loud to the class.

Her father, who was a lawyer, had encouraged her to join the legal profession. She had heard that people called others “smart” when they joined the fields of Science, Technology, Engineering and Mathematics. “I want people to call me smart,” she said, so she changed her career and went to medical school at Tongji Medical University where she earned top scores. 

Her father had a stroke, surviving afterwards for seven years. When she was in medical school, Wang hoped to learn ways to help him. Wishing she could have done more, she pursued clinical research in the lab. She passed the tests to become a practicing physician in the United States, but she was more inspired to work as a scientist.

As for her work at Stony Brook University, Wang appreciates the beauty of Long Island. She hopes this is their “last move,” as they continue their careers.

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John Moses. Photo courtesy of CSHL

By Daniel Dunaief

It sounds like something straight out of a superhero origin story.

With resistance to widely used drugs becoming increasingly prevalent among bacteria, researchers and doctors are searching for alternatives to stem the tide.

That’s where shape shifting molecules may help. Cold Spring Harbor Laboratory Professor of Organic and Click Chemistry John Moses and his team have attached the drug vancomycin to a molecule called bullvalene, whose atoms readily change position and configuration through a process called a thermal sigmatropic rearrangement as atoms of carbon break and reform with other carbon atoms.

The combination of the bullvalene and vancomycin proved more effective than vancomycin alone in wax moth larva infected with vancomycin resistant Enteroccoccus bacteria.

“Can I make a molecule that changes shape and will it affect bacteria? That was the question,” Moses said. The promising early answer was, yes!

Moses believes that when the bullvalene core is connected to other groups like vancomycin, the relative positions of the drug units change, which likely change properties related to binding.

The urgency for novel approaches such as this is high, as drug resistant bacteria and fungi infect about 2.8 million people in the United States per year, killing about 35,000 of them. 

In his own life, Moses said his father almost died from a bacterial infection five years ago. Vancomycin saved his father’s life, although the infection became resistant to the treatment. Other drugs, however, conquered the resistant strain.

“We need to work hard and develop new antibiotics, because, without them, there will be a lot more misery and suffering,” Moses explained.

To be sure, an approach like this that shows promise at this early stage with an insect may not make the long journey from a great idea to a new treatment, as problems such as dosage, off target effects, toxicity, and numerous other challenges might prevent such a treatment from becoming an effective remedy.

Still, Moses believes this approach, which involves the use of click chemistry to build molecules the way a child puts together LEGO blocks, can offer promising alternatives that researchers can develop and test out on a short time scale.

“We shouldn’t be restricted with one set of ideas,” Moses said. “We should keep testing hypotheses, whether they are crazy or whatever. We’ve got to find alternative pathways. We’re complementary” to the standard approach pharmaceutical companies and researchers take in drug discovery.

Looking to history, Moses explained that the founders of the Royal Society in 1660 followed the motto “nullius in verba,” or take nobody’s word for it. He believes that’s still good advice in the 21st century.

The shape shifting star

Moses has described this bullvalene as a Rubik’s Cube, with the parts moving around and confounding the bacteria and making the drug more effective.

The CSHL scientist and his team don’t know exactly why shape shifting makes the drug work in this moth model.

He speculated that the combination of two vancomycin units on either side of a bullvalene center is punching holes in the cell wall of the bacteria.

Moses is eager to try to build on these encouraging early developments. “If you can make it, then you can test it,” he said. “The sooner the better, in my opinion.”

Moses acknowledged that researchers down the road could evaluate how toxic this treatment might be for humans. It didn’t appear toxic for the wax moth larvae.

Welcoming back a familiar face

Adam Moorhouse
Photo by Rebecca Koelln

In other developments in his lab, Moses recently welcomed Adam Moorhouse back to his team. Moorhouse, who serves as Chemistry Data Analyst, conducted his PhD research in Moses’s lab at the University of Oxford.

Moorhouse graduated in 2008 and went on to work in numerous fields, including as an editor for the pharmaceuticals business and for his own sales consultancy. In 2020, he had a motorcycle accident (which he said was his fault) in which he broke 16 bones and was hospitalized for a while. During his recovery, he couldn’t walk.

At the time, he was working in the intense world of sales. After the accident, Moorhouse decided to build off his volunteer work with disabled children and become a high school teacher. After about 18 months of teaching, Moorhouse reconnected with Moses.

“It’s nice getting here and thinking about chemistry and thinking about ideas and communicating those ideas,” Moorhouse said.

He has hit the ground running, contributing to grants and helping to translate intellectual property into commercial ventures.

The chance to work on projects that get molecules into humans in the clinic was “really exciting,” Moorhouse said. “I’m back to try and support that.”

Moorhouse will be working to procure funding and to build out the business side of Moses’s research efforts.

“Where I’d like to lend a hand is in driving ongoing business discussions,” Moorhouse said. He wants to “get these small molecules into the clinic so we can see if they can actually treat disease in humans.” The vehicle for that effort eventually could involve creating a commercial enterprise.

Like Moses, Moorhouse is inspired and encouraged by the opportunity for small operations like the lab to complement big pharmaceutical companies in the search for treatments.

Moses believes the work his lab has conducted has reached the stage where it’s fundable. “We’ve done something that says, ‘we checked the box,’” he said. “Let’s find out more.”

Currently living on campus at CSHL, Moorhouse appreciates the opportunity to do some bird watching on Long Island, where some of his favorites include woodpeckers, herons, egrets, robins and mockingbirds.

He is tempted to get back on a motorcycle and to return to mountain biking.

As for his work, Moorhouse is excited to be a part of Moses’s lab.

“Back in my PhD days, [Moses] was always an idea machine,” Moorhouse said. “The aim is to move ideas to the clinic.”

 

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A statue of Charles Darwin (and finch) created by sculptor Pablo Eduardo overlooks the harbor on the campus of Cold Spring Harbor Laboratory. Photo courtesy of CSHL

By Tara Mae

Scientific study is a perpetual testimony to the feats and foibles of human nature, intricately intertwined in ways that continue to be excavated by inquiring minds bold enough to imagine. 

Cold Spring Harbor Laboratory (CSHL), which has largely been a titan in such innovative investigations, will offer a series of walking tours on select weekends from Saturday, May 20, through Sunday, August 27, starting at 10 a.m. The hour and a half long tours will traverse the past, present, and future of the complex and its work therein. 

“We are most excited to get people to the Laboratory who have always wondered what goes on here. So many have heard about us, driven by us, read about us, but they have never dug deeper. This walking tour is the chance to learn who we are,” said Caroline Cosgrove, CSHL’s Community Engagement Manager.

Conducted by trained tour guides, including Cold Spring Harbor Laboratory graduate students and postdoctoral fellows, the walks strive to bridge the gap between the physical realm and scientific theory. 

“These tours encompass the stunning grounds, the Lab’s history, and our current facilities and work. Community members, whether they have a background and interest in science, can come and learn from current graduate students about the world-renowned work going on in their very backyard,” explained Cosgrove. 

Probing CSHL’s ongoing research and program development for plant and quantitative biology, cancer, and neuroscience, the tours will encompass details about its historic and modern architecture, Nobel legacy, and identity evolution. Additionally, these scenic, scholarly strolls explore the practices and procedures of CSHL, with behind-the-scenes sneak peaks into the inner workings of scientific investigation. 

“As long as the tour guide’s laboratory is open and available, folks get a walk through and see the student’s own lab station,” Cosgrove said. “Whether it’s a cancer research lab, a neuroscience lab, a plant research lab, you get to see where all the magic happens.” 

Established in 1890, CSHL’s North Shore campus is a beacon of biology education, with 52 laboratories and more than 1100 staff from more than 60 countries. Eight scientists associated with CSHL have earned a Nobel Prize in physiology or medicine. This internationally recognized center of scientific research is also a local history and education site, where students of all ages and backgrounds come to study. 

“History has been, and will continue to be, made here. Please come get to know us,” said Cosgrove. 

Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor offers walking tours on May 20 and 21, June 24 and 25, July 29 and 30 and Aug. 26 and 27 at 10 a.m. Tours begin in the lobby of the Grace Auditorium. Tickets are $5 per person. To order, visit www.cshl.edu/public-events/tour-cshl/. For more information, call 516-367-8800.

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This image from the Hubble Space Telescope shows the galaxy cluster MACS J1149.5 +2233 and multiple appearances of Supernova Refsdal with time-delay positions. Credit: Patrick Kelly / NASA / ESA

A new technique to measure the expansion rate of the Universe may serve as a tool to help scientists more accurately determine the Universe’s age and better understand the cosmos. An international team of researchers that includes two Stony Brook University professors, Simon Birrer, PhD, and Anja von der Linden, PhD, highlighted their data based on the technique in a paper published in Science.

The research team used images from the Hubble Space Telescope of Supernova Refsdal, discovered by University of Minnesota scientist Patrick Kelly in 2014. It is named after astronomer Sjur Refsdal, who created a theory in 1964 on how to measure the Hubble constant – also known as Hubble’s law, which describes that galaxies are moving away from Earth at speeds proportional to their distance, so the further they are the faster the move away from Earth. Refsdal is the first supernova in which this measurement theory was put into practice.

Professor Kelly led the study, assembling an international team. Birrer was involved with the analysis and overall robustness of the measurement study, specifically working on constraining the small-scale dark matter distribution and the positional constraints on the images of the supernova, and their effect on the time-delay prediction. Von der Linden was part of the team that originally discovered SN Refsdal and prepared the follow-up Hubble observations.

There are two precise measurements of the expansion of the Universe, or Hubble constant: calculations from nearby observations of supernovae, and using cosmic microwave background (radiation) that began to steam freely shortly after the Big Bang. However, these two measurements differ by approximately 10 percent, which is the point of debate on current theories about the makeup and age of the Universe.

The team calculated the expansion rate of the Universe by using data from four different images of the Supernova Refsdal explosion event in 2014. Scientists worldwide had correctly predicted that the supernova would appear at a new position in 2015, and the telescope then captured a fifth image. These multiple images appeared because the supernova was gravitationally lensed by a galaxy cluster, a phenomenon in which mass from the cluster bends  light. By using the time delays between the appearances of the images the research team was able to measure the Hubble Constant.

The study provides a measurement of the expansion rate consistent with expectations from the cosmic microwave background. The measurement technique and findings may also contribute to settling the longstanding debate among scientists regarding their disagreements on measurements of the current expansion rate of the Universe.

“The measurement of the expansion rate of the universe is a rollercoaster,” says Birrer, Assistant Professor in the Department of Physics and Astronomy. “While a few years ago most strong lensing measurements yielded higher values in tension with the cosmic microwave background estimates, more recent estimates and revised methodology has resulted in lower values. Our research corroborates a trend, yet does not provide the last word on the expansion rate.”

Knowing the Hubble Constant is knowing the age of the universe. Birrer explains that the findings described in the Science paper “provide a new and completely independent measurement of the age of the Universe, and that by knowing the absolute scale and relative expansion, we can infer the age of the Universe.”

The age of the Universe is about 13.6 billion years, when the cosmic microwave background inferred value of the Hubble constant is correct, or about 12.6 billion years, if the Cepheid-based local distance ladder value is correct.

“The prediction and subsequent observation of the fifth image of Supernova Refsdal was a great success of our cosmological model based on General Relativity and the mysterious dark matter,” adds von der Linden, Associate Professor in the Department of Physics and Astronomy. “Now, these data have allowed multiple teams to further refine their models of how dark matter is distributed in galaxy clusters, yielding a precise measurement of the Hubble constant from a lensed supernova.”

Central to the research and successful measurement of the Hubble constant is a measurement of the time delay between multiply arriving images of the supernova. The researchers address this point in an accompanying paper published in The Astrophysical Journal, also lead by Kelly. They explain that the time delay is directly proportional to the absolute scales in the observer-deflector-supernovae system. Knowing the time delay precisely and reconstruction the matter distribution of the lens enabled them to constrain a distance. This measurement is completely independent from other approaches in measuring the Hubble constant.

Professor Vivian Miranda from Stony Brook’s C.N. Yang Institute for Theoretical Physics, who was not involved in the current work, but contributed to an earlier, less precise estimate of the Hubble constant from the same supernova, commented: “This team has now established a new, exciting way of measuring the Hubble constant, which will add to our endeavor to understand the cause of the Hubble tension.  I congratulate them on their work.”

Birrer and von der Linden are now working on the Legacy Survey of Space and Time (LSST), to be conducted with the newly built Vera C. Rubin Observatory. The LSST will discover many more lensed quasars and supernovae. Birrer has a leading role in the efforts to measure the Hubble constant from the LSST-discovered systems.

The research was funded primarily by NASA through the Space Telescope Science Institute and the National Science Foundation.

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David Baszucki and Jan Ellison Baszucki. Photo from Baszucki Group

Stony Brook University has announced a philanthropic gift to develop Neuroblox, a software platform developed by biomedical engineer and neuroscientist Lilianne Mujica-Parodi that will model brain circuits to treat brain disorders. The gift was made possible by David Baszucki, founder and chief executive officer of Roblox, and his wife, bestselling author Jan Ellison Baszucki.

Mujica-Parodi took inspiration from Roblox in conceiving Neuroblox as a cutting-edge platform that will open up a world of modeling possibilities for neuroscientists without training in computational sciences. The platform will allow researchers to explore the complexities of brain-based disorders by providing a blueprint for individualized care.

Roblox is an interactive platform that allows users to create their own immersive experiences and release them with one click to smartphones, tablets, desktops, consoles and virtual reality devices. Anyone can use the platform, even those without programming experience.

“Right now, there is a disconnect between the aims of clinical research and the computational tools we have to exploit that research,” said Mujica-Parodi. “Neuroblox is doing something fundamentally different. It’s trying to bridge that gap.”

Brain disorders like bipolar disorder, dementia and schizophrenia impact millions of families who have long struggled to find answers, including the Baszucki family. Jan and David Baszucki reached out to Mujica-Parodi after learning about her first-of-its-kind study exploring the role of ketosis on brain functioning. This was an area of particular significance for the Baszuckis, as it was a ketogenic diet that put their own son’s bipolar disorder into remission.

Fueled by enthusiasm for the potential of this project, Mujica-Parodi quickly assembled a team of the brightest minds in computing, neuroscience, biomedical engineering and beyond to bring the Neuroblox vision to life.

“Here was a neuroscientist unveiling the mechanism by which ketones work to stabilize brain networks,” Jan Ellison Baszucki said. “This explained why a ketogenic diet gave our son his mind and his life back. We had to wonder if building on this knowledge by investing in metabolic neuroscience could be the first step toward helping others suffering from mental illnesses.”

The $6.2 million investment from the Baszucki family includes $3.2 million to help build and launch Neuroblox and $3 million to create the Baszucki Endowed Chair for Metabolic Neuroscience at Stony Brook University. Mujica-Parodi will be the inaugural holder of this chair, which recognizes an exceptional researcher in metabolic neuroscience.

“Lily is building a software platform where neuroscience researchers worldwide can refine, test and share models to help us understand how the brain regulates energy — a critical driver of mental health,” said David Baszucki. “Our family believes Neuroblox’s impact on understanding and treating brain-based disorders, including mental illness, will be transformative.”

The gifts will be enhanced by an additional $550,000 from Stony Brook’s Presidential Innovation and Excellence Fund. This fund is designed specifically to accelerate the university’s highest ambitions.

“Lily’s innovative approach to one of our most pressing societal issues — our mental health and well-being — is inspiring. It underscores our commitment as an institution to advance knowledge that will have a long-term, significant impact on the world,” said President Maurie McInnis. “We could not be prouder of these efforts, and we are thrilled that the Baszuckis have chosen to invest in Lily’s trailblazing work in a way that will undoubtedly change lives.”

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Lucas Cheadle with two pieces of artwork in his office, from left by Porferio Tirador 'Gopher' Armstrong, a Cheyenne-Caddo native from Oklahoma and Oklahoma Kiowa artist Robert Redbird. Photo by Austin Ferro

By Daniel Dunaief

Cold Spring Harbor Laboratory Assistant Professor Lucas Cheadle knows a thing or two about under represented groups in the field of Science, Technology, Engineering and Mathematics.

Of Chickasaw, Choctaw and Cherokee lineage, Cheadle, who was born in Ada, Oklahoma, was recently named one of 31 inaugural Howard Hughes Medical Institute’s (HHMI) Freeman Hrabowski scholars.

Lucas Cheadle. Photo by Steve Ryan/ AP Images for HHMI

The first scholars in this highly competitive and unique program, which drew 1,036 applicants, will receive funding that will last at least five years and could get as much as $8.6 million each for their promising early research and for supporting diversity, equity and inclusion in their labs.

“This is the first time a program of this type and magnitude has been attempted,” said HHMI Vice President and Chief Scientific Officer Leslie Vosshall. The scholars are “doing things that set them in the top one percent in creativity and boldness and we are certain we are going to have really healthy, inclusive, diverse labs.”

Vosshall said the scholars, which include scientists from 22 institutions, including Columbia, Harvard, Duke, Cornell, Princeton, the University of Pennsylvania, and Massachusetts Institute of Technology, hit it “out of the park” in their science and diversity efforts.

HHMI, which has committed $1.5 billion for Freeman Hrabowski Scholars, will award about 30 of these select scholarships every other year for the next 10 years, supporting promising scientists who can serve as mentors for under represented groups while also creating a network of researchers who can provide advice and collaborations.

The first group of scientists to receive this support is “diverse in such a way that it reflects the U.S. population,” Vosshall said.

The program is named after Freeman Hrabowski, who was born in Birmingham, Alabama and was president of the University of Maryland, Baltimore County, from 1992 to 2022. Hrabowski, who was arrested during the civil rights movement, created a tutoring center in math and science for African Americans in high school and college and helped create the Meyerhoff Scholars Program.

Cheadle was celebrating the December holidays in Oklahoma when he learned he was a semifinalist, which was “really surprising and exciting,” he recalled. Becoming an HHMI scholar is “amazing” and “very validating,” he said.

Bruce Stillman, President and CEO of CSHL, suggested that HHMI recognition is “a prestigious achievement” and, in a email, wrote that he was “pleased that [Cheadle] was included in the list of remarkable scientists.”

Stillman predicted that Cheadle’s passion about increasing diversity in science would have a “major influence” on CSHL.”

Scientific questions

Cheadle appreciates how HHMI funds the scientist, not individual projects. With this unrestricted funding, which includes full salary and benefits and a research budget of about $2 million over the first five years and eligibility to participate in HHMI capital equipment purchasing programs, Cheadle and other scholars can pursue higher-risk, higher-reward projects.

“If I have a crazy idea tomorrow, I can do that with this with funding,” Cheadle explained.

Cheadle, who joined CSHL in August of 2020, studies the way the immune system shapes brain development, plasticity and function. He also seeks to understand how inflammatory signals that disrupt neural circuit maturation affect various disorders, such as autism.

Last September, Cheadle and his lab, which currently includes six postdoctoral researchers, two PhD students, one master’s student, a lab manager and two technicians, published a paper in Nature Neuroscience that showed how oligodendrocyte precursor cells, or OPCs, help shape the brain during early development.

Previously, scientists believed OPCs produced cells that surrounded and supported neurons. Cheadle’s recent work shows that they can play other roles in the brain as well, which are also likely instrumental in neural circuit construction and function.

When young mice raised in the dark received their first exposure to light, these OPCs engulfed visual processing circuits in the brain, which suggested that they helped regulated connections associated with experience.

With this new position and funding, Cheadle also plans to explore the interaction between the development of nerves in the periphery of the brain and different organs in the body, as well as how immune cells sculpt nerve connectivity.

He is not only studying this development for normal, healthy mice, but is also exploring how these interactions could explain why inflammation has arisen as such an important player in neurodevelopmental dysfunction.

Stillman explained that Cheadle’s work will “have broad implications.”

A talented, balanced team

Cheadle is committed to creating a balanced team of researchers from a variety of backgrounds.

“As principal investigators,” Cheadle said, “we have to actively work to have a diverse lab.”

He has posted advertisements on women’s college forums to garner more applications from women and under represented groups. He has also adopted a mentorship philosophy that focuses on inclusivity. 

Cheadle explained that he hopes to be adaptable to the way other people work. Through weekly lab meetings, mentorship arrangements and reciprocal interactions, he hopes to provide common ground for each aspiring scientist.

He recognizes that such goals take extra effort, but he feels the benefits outweigh the costs.

During annual events, Cheadle also leans in to the cultural diversity and differences of his staff. He hosts a pre-Thanksgiving pot luck dinner, where everybody brings a food item that’s important and close to them. 

Last year, he made pashofa out of cracked corn that his stepmom sent him from the Chickasaw Nation in Oklahoma. Pashofa is a traditional meat and corn Chickasaw dish. Other lab members brought tropical beverages common in Brazil.

In terms of diversity in science, Cheadle believes such efforts take years to establish. Through an approach that encourages people from different backgrounds to succeed in his lab, Cheadle hopes to share his thoughts and experiences with other researchers.

Cheadle last summer hosted a Chickasaw student on campus to do research. He is working with the Chickasaw Nation to expand that relationship.

As for the Freeman Hrabowski scholars, Vosshall said all HHMI wants to do is “allow everybody to do science.-

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HHMI Chief Scientific Officer Vosshall celebrates benefits of diversity in science

By Daniel Dunaief

It’s not one or the other. She believes in both at the same time. For Leslie Vosshall, Vice President and Chief Scientific Officer at Howard Hughes Medical Institute, science and diversity are stronger when research goals and equity work together.

Leslie Vosshall. Photo by Frank Veronsky

That’s the mission of the new and unique HHMI Freeman Hrabowski Scholars program. HHMI this week named 31 inaugural scholars as a part of an effort designed to support promising scientists who provide opportunities to mentor historically under represented groups in research.

Cold Spring Harbor Laboratory Assistant Professor Lucas Cheadle was among the 31 scientists who became HHMI scholars (see related story above), enabling him to receive financial support for the next five years and up to $8.6 million for the next decade.

In an interview, Vosshall said the “special sauce of this group” of scientists who distinguished themselves from among the 1,036 who applied was that they excel as researchers and as supporters of diversity. Bringing in people who may not have had opportunities as scientific researchers not only helps their careers but also enables researchers to take creative approaches to research questions.

“When you bring in people from the ‘out group’ who have been historically excluded, they have an energy of getting into the playing field,” she said. That innovation can translate into successful risk taking.

As an example, Vosshall cited Carolyn Bertozzi, a chemist at Stanford University who shared the 2022 Nobel Prize in Chemistry for helping to develop the field of bioorthogonal chemistry, which involves a set of reactions in which scientists study molecules and their interactions in living things without interfering with natural processes.

Her lab developed the methods in the late 1990’s to answer questions about the role of sugars in biology, to solve practical problems and to develop better tests for infectious diseases. “This scrappy band of women chemists tried this crazy stuff” which provided “massive innovations in chemical biology,” Vosshall said. Mainstream science often solidifies into a groove in which the same thing happens repeatedly. “Innovation comes from the edges,” she added.

In her own to hire staff in her lab, Vosshall has taken an active approach to find candidates from under served communities. “People who have pulled themselves up have worked so hard to get to where they are,” she said. “It’s important to dig deeper to find talent everywhere.”

Keeping away from the off-ramp

The number of under represented groups in science has improved over the last few decades. Indeed, when Vosshall joined Rockefeller University, where she is the Robin Chemers Neustein Professor, she couldn’t count 10 women faculty. Now, 23 years later, that number has doubled.

The number of people in under represented groups in graduate programs has increased. The problem, Vosshall said, is that they “take the off-ramp” from academic science” because they don’t always feel “welcome in the labs.” Supporting diversity will keep people in academic science, who can and will make important discoveries in basic and translational science.

As a part of the Freeman Hrabowski program, HHMI plans to survey people who were trainees in these labs to ask about their mentoring experience. By tracking how developing scientists are doing, HHMI hopes to create a blueprint for building diversity.

HHMI has hired a consultant who will analyze the data, comparing the results for the results and career trajectories. The research institute will publish a paper on the outcome of the first cohort. Researchers in this first group will not only receive money, but will also have an opportunity to interact with each other to share ideas.

New approach

When Vosshall earned her PhD, she considered an alternative career. She bought a training book for the Legal Scholastic Aptitude Test and considered applying to law school, as she was “fed up with how I was treated and fed up with science”

Nonetheless, Vosshall, who built a successful scientific career in which she conducts research into olfactory cues disease-bearing insects like mosquitoes seek when searching for humans, remained in the field.

To be sure, Vosshall and HHMI aren’t advocating for principal investigators to hire only people from under represented groups. The promising part of this scholarship is that HHMI found it difficult to get the final number down to 31, which “makes me optimistic that the [scientific and mentorship] talent is out there,” she said. Over the next decade, HHMI plans to name about 30 Freeman Hrabowski scholars every other year. If each lab provides research opportunities across different levels, this will help create a more diverse workforce in science, which, she said, benefits both prospective researchers and science.

 

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James Rossie conducting field work at Lake Turkana. Photo by Susanne Cote

By Daniel Dunaief

Dead men might not tell tales but fossilized apes and the soil around them may change a narrative. That’s what happened recently when a large collaboration of researchers gathered clues from an ape fossil in Moroto, Uganda that lived 21 million years ago and from a detailed analysis of the soil.

James Rossie in his lab. Photo by Emily Goble

 

Scientists have long thought apes started climbing upright, which is an important evolutionary step, all those years ago to reach fruit in a habitat dense with trees. Recent evidence from two publications in the journal Science, however, suggest that the habitat included grassland and woodlands.

James Rossie, Associate Professor in the Department of Anthropology at Stony Brook University, studied the teeth of the fossil, called Morotopithecus, to determine what this ancient ape ate.

“The important thing about the teeth of Morotopithecus is a shift towards folivory” or leaf eating, Rossie said. “The surface of the molars were elongated with well-developed crests” which indicate that this primate consumed leaves rather than fruit.

By contrast, molars of animals that eat fruit are more rounded. Additionally, carbon isotope dating of the enamel suggest that they fed on water-stressed plants. This discovery and analysis changes not only the narrative of this particular ape species, but also of the evolutionary progression and habitat of primates.

A rendering of ancient apes foraging in trees. Image courtesy of Corbin Rainbolt

This analysis indicated that apes lived in areas of open woodlands, where there were patches of trees separated by stretches of grassland about 10 million years earlier than scientists originally believed. During the miocene period, they would have had to evade predators such as Simbakubwa, an extinct carnivore that was larger than a lion.

“It was very unexpected that an ape with upright, versatile climbing abilities was living in a seasonal woodland with open, grassy patches, rather than in a closed tropical forest,” said Laura MacLatchy, a Professor in the Department of Anthropology at the University of Michigan and the leader on the study.

“The findings have transformed what we thought we knew about early apes, and the origins for where, when and why they navigate through the trees and on the ground in multiple different ways,” Robin Bernstein, Program Director for Biological Anthropology at the National Science Foundation, said in a statement. “The effort outlines a new framework for future studies regarding ape evolutionary origins.”

The fossils Rossie and his colleagues examined including the lower part of a face, the palate, upper teeth, a couple of vertebrae, the lower jaw, and a complete femur. It’s unclear if these fossils came from one individual or from a collection of apes. With considerable wear and tear on the teeth of the upper jaw, the owner of those bones was an adult, Rossie said.

The mandible of an ancient ape with the left molar enlargement inset. Photo by Laura MacLatchy

By studying the bones as puzzle pieces that fill in a narrative, researchers concluded that the smaller, thick femur, or thigh, bone helped the ape climb quickly and effectively up the trunks of trees.

The longer legs of a human push us away from trees, making it harder to climb, while the shorter, sturdy legs of an ape enable it to get closer to the trunk and reach lower branches quickly. 

Apes that fed on leaves would likely have had larger bodies to accommodate the need for a longer digestive tract. A heavier animal that navigated through trees would run the risk of falling to the ground if their weight caused a branch to break.

By climbing upright, apes could distribute their weight more evenly over several branches, enabling them to maneuver through the trees to the leaves while reducing the strain they put on any one branch.

In a second paper published together as a part of this analysis, soil researchers studied the environment at Moroto and at several other sites of similar age across eastern Africa.  These soil scientists determined that the early habitat included forests and grasslands.

Cooperative work

Rossie believes the work of numerous scientists over a long period of time not only represents a paradigm shift in thinking about ape evolution and the environment in Africa, but also in the way scientists across a wide range of expertise collaborate.

James Rossie conducting field work at Lake Turkana. Photo by Susanne Cote

The researchers who trained Rossie and his colleagues were more competitive and guarded, he said. They didn’t share information with each other about their findings and wanted other researchers to learn about their findings through journal publications.

“We decided to take a different strategy” about a dozen years ago, he said. “It occurred to us that these separate silo attempts to reconstruct these environments were incompatible, with different methods and strategies. We couldn’t put it together into a coherent picture.”

By working together with the same methods, the scientists had comparable data and developed a coherent picture. Such broad collaborations across a range of fields required a “bit of a leap of faith,” he added. The scientists knew and trusted each other.

Indeed, Rossie and MacLatchy have known each other since the early 2000s when MacLatchy first asked Rossie to study other fossils.

Bringing numerous researchers across a range of expertise was a “game theory experiment,” Rossie added. Researchers could have published smaller papers about each site more quickly, but chose to combine them into the more meaningful synthesis.

MacLatchy suggested that the work on this project that involved sharing data across multiple sites, as well as joining forces in a range of expertise, makes it possible to reconstruct habitats with much greater detail.

“We are also able to obtain a regional perspective, which is not possible if interpretations are based on individual fossil sites,” she said. “I’d like to think this kind of collaboration will become standard.”

A resident of Centerport, Rossie is a hockey fan and is pulling for the Islanders.

He enjoys studying teeth because a single tooth can provide considerable information about an animal’s place among other species and about its strategies for getting and processing food.

His professional studies have come full circle. As a college junior at St. Lawrence University, he attended a field school run by Harvard University and the National Museum of Kenya at Lake Turkana. Almost every moment of that experience made him more eager to pursue paleontology as a career.

“As fate would have it, my field project is now centered on an area on the west side of Lake Turkana that I first visited back in 1995,” he explained.

The Turkana Basin Institute serves as his home base during the field season and he is grateful for their ongoing logistical support.

As for future work, Rossie is studying the fossils of at least four different species of apes in Lake Turkana in Kenya.

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Harold Metcalf

Stony Brook University Professor Harold Metcalf has been selected as the Optica (formerly OSA), Advancing Optics and Photonics Worldwide 2023 recipient of the Esther Hoffman Beller Medal. Metcalf, a distinguished teaching professor in the Department of Physics and Astronomy in the College of Arts and Sciences, is being honored for outstanding mentorship of undergraduate students in hands-on optics research and for organizing an annual symposium for students to present their work during the Frontier in Optics/Laser Science (FiO/LS) conference.

The Beller Medal is presented for outstanding contributions to education in optical science and engineering. Consideration is given to the recipient’s outstanding teaching and/or original work in optics education that enhances the understanding of optics. The scope of the award is international, and candidates at every career stage are considered. It is endowed by a bequest from the estate of Esther Hoffman Beller.

“My sincere congratulations to Hal on this momentous achievement,” said Nicole S. Sampson, dean of the College of Arts and Sciences and distinguished professor of chemistry. “His dedication to education – from mentorship of students from the high school to graduate level – in addition to his decades-long committment to advancements in optical science, are testament to the promience and recognition of our Physics and Astronomy program at Stony Brook. We are fortunate to have him among our faculty.”

Metcalf was recognized by Optica for being “a dedicated educator and mentor. He created the Laser Teaching Center (LTC) at Stony Brook University, which provides inquiry- and project-based active learning for students from high school to the graduate level. Another of his significant contributions to education is the annual Symposium on Undergraduate Research/LS [sponsored by the Division of Laser Science (DLS) of the American Physical Society] which takes place as part of Frontiers in Optics (FiO/LS).  During the Symposium, undergraduate students present their research in oral and poster sessions and network with leading professionals in the field.

Metcalf’s research is focused on optical control of atomic motion, and he was one of the leaders in the earliest experiments of Laser Cooling and Trapping. He has published three textbooks, including “Laser Cooling and Trapping.” Metcalf has also held several visiting appointments, including Massachusetts Institute of Technology (MIT); École normale supérieure (ENS) Paris, France; Utrecht University, Netherlands; University of Bonn, Germany and Beijing Institute for Modern Physics, China.

“This is a richly deserved award, as Hal is such a generous contributor to the Department and the Atomic, Molecular and Optical Physics community, particularly to the younger generation,” said Chang Kee Jung, PhD, distinguished professor and chair of the Department of Physics and Astronomy.  “In addition, Hal made seminal contributions to the field of laser cooling and trapping of neutral atoms. The members of our Department appreciate him greatly, and I am very proud of his accomplishments.”

Metcalf earned his Bachelor’s degree in physics from MIT and his PhD in physics from Brown University. He was a postdoc at Stony Brook University before joining their faculty. Metcalf is a recipient of the SUNY Chancellor’s Award for Excellence in Teaching, and is a Fellow of Optica and the American Physical Society.

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Pictured at the Earth Day event, from left, Distinguished Professor Dr. Jeffrey Levinton; Town of Brookaven Supervisor Ed Romaine; WMHO President Gloria Rocchio; Brookhaven Town Councilmember Jonathan Kornreich; former New York Assemblyman Steve Englebright; WMHO Chairman Dr. Richard Rugen; WMHO Trustee Laura Huang-Ernst; and WMHO Education Director Deborah Boudreau. Photo courtesy of WMHO
Megan Frey, Frey Family Foundation speaking about the species inventory and data collection at West Meadow Creek. Image courtesy of the WMHO.
Image of Calanoid captured on microscope courtesy of Megan Frey.
Distinguished Professor Dr. Jeffrey Levinton discussing ways to identify animal and plant species in the wetlands.

The Ward Melville Heritage Organization (WMHO) recently announced the creation of the WMHO West Meadow Field Guide and GCIS Survey. Working hand-in-hand, these creations will allow the public to identify and record environmental and ecological data.

Using the field guide to identify plants and animal species within the preserve, the public can store species and water quality data on the GCIS Survey webpage. The survey will be available soon on the WMHO website (WMHO.org). During preliminary testing, Ms. Megan Frey of the Frey Family Foundation found and recorded calanoid, a microscopic arthropod, within her first sample of wetlands water.

The announcement at the WMHO’s Earth Day event —Wetlands Legacies — at the Dr. Erwin Ernst Marine Conservation Center at West Meadow Creek Preserve on April 22. 

The event included guest speakers Megan Frey and Distinguished Professor of Ecology and Evolution Dr. Jeffrey Levinton, as well as a specially created drone video of the wetlands habitats by Nathan Levinton. The WMHO Youth Corps led exhibits that educated the public on water quality testing, the species of the area, the expeditions and life of world-renowned naturalist and ornithologist Dr. Robert Cushman Murphy, as well as the environmental challenges of WMHO’s pristine 88-acre wetlands preserve. Murphy, along with Dr. Erwin Ernst and Ward Melville, worked together in 1960 to create the West Meadow Creek Preserve.

Elected officials in attendance included former New York State Assemblyman, Steve Englebright,  Town of Brookhaven Supervisor Ed Romaine and Town of Brookhaven Councilmember Jonathan Kornreich, who spoke about the various aspects of Long Island’s ecology and environments, as well as Dr. Murphy’s role in protecting them.  

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Aardvark. Pixabay photo

An international scientific project that compares the genomes of 240 living species of mammals has identified transposable elements (TEs) – genes that can change their position within a genome, creating or reversing mutations and thus altering a cell’s genetic identity – as a crucial area of study to help uncover the evolutionary process of mammals and to better understand biodiversity. Stony Brook University’s Liliana M. Dávalos is a collaborator in the analyses of TEs for the project. Two new papers, one published in the current issue of Science, and the other in Molecular Biology and Evolution, highlight the findings.

This graphic depicts the range of recently accumulated transposable elements (TEs) among sample mammals by proportion of their genome. Image credit: Osmanski et al. 2023 Science

The past 100 million years has caused mammals to adapt to virtually every environment on the planet. The Zoonomia Project, of which Dávalos is a scientific contributor, has cataloged the diversity in mammalian genomes by completing comparative genomic DNA sequences from the 240 species. The team, which consists of more than 150 scientists worldwide, published their multi-year comparative genome analysis in the Science paper.

Dávalos studies how biodiversity changes through time and what biological processes fuel biodiversity. She teamed up with David Ray and his lab at Texas Tech University to qualitatively analyze the dynamics of TEs.

The paper describes the TE repertoires of 248 placental mammals. TEs make up a sizeable proportion of all mammalian genomes, yet there is much variation from one species to the next. The scientific team points out that that relating TEs to biodiversity is far from simple. Additionally, with the ability to move throughout the genome, TEs can contribute to biodiversity or also stymie it.

“Determining how many transposable elements of each kind are in each species is key to figuring out how transposons contribute to biodiversity. It seems simple to relate these counts to the number of species or their ecology, however that is misleading,” explains Dávalos, Professor of Conservation Biology in the Department of Ecology and Evolution, and a co-author of the paper. “Some species , like bats and whales, believe it or not are more closely related to each other than to others, such as bats and primates, so we must factor this related into our statistics within the comparative genomic mammalian analyses.”

The researchers identified more than 25,000 TE sequences in the mammalian set, with some mammals having large portions of TEs in their genome, calculated over time for each species. The average was approximately 45 percent

Overall, they concluded that “considering the wide-ranging effects that TEs impose on genomic architecture, these data are an important resource for future inquiries into mammalian genomics and evolution and suggest avenues for continued study of these important yet understudied genomic denizens.”

In the Molecular Biology and Evolution paper, novel statistical approaches to determining genome sequences in bats developed by Dávalos were used by the authors to describe the place bats hold with regard to TEs in mammals.

According to the lead author, Nicole Paulat, a graduate student in the Ray Lab, the research team found bats uniquely have more events involving TE transfers from one species to another. One mechanism that may explain such excess transfers is through viruses, an important finding on how several bat species have been found to host diverse and sometimes dangerous viruses.

Both papers based on the work from the Zoonomia Project illustrate that TEs are highly active across the genome of most mammal species, and because of this, future studies centering on TEs may help provide answers to mammalian biodiversity worldwide. Such research may also provide further hints as to how and why TEs disrupt mammalian genomes, therefore changing DNA and contributing to evolutionary processes and/or the development of disease.

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