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Jeremy Borniger. Photo from CSHL

By Daniel Dunaief

Much as New Yorkers might want to minimize sleep, even during the pandemic when the need to be active and succeed is hampered by limited options, the body needs rest not only for concentration and focus, but also for the immune system.

Recently, Assistant Professor Jeremy Borniger, who joined Cold Spring Harbor Laboratory in January, collaborated with his former colleagues at Stanford University to publish research in the journal Science Advances that sheds light on the mechanism involved in this linkage.

Doctors and researchers had known for a long time that the release of glucocorticoids like cortisol, a stress hormone, can suppress the ability to fight off an infection. “That happens in people that are chronically stressed, even after surgery,” said Borniger in a recent interview.

A comprehensive understanding of the link between neuronal cells that are active during stress and a compromised immune system could help develop new ways to combat infections. The Stanford-led study provides evidence in a mouse model of the neuronal link between stress-induced insomnia and a weakened immune system.

Ideally, scientists would like to understand the neural pathways involved, which could help them design more targeted approaches for controlling the immune system using natural circuitry, according to Borniger.

Scientists could take similar approaches to the therapies involved with Parkinson’s, depression and obesity to increase or decrease the activity of the immune system in various disease states, instead of relying on a broader drug that hits other targets throughout the body.

In theory, by controlling these neurons, their gene products or their downstream partners, researchers could offer a way to fight off infections caused by stress.

While their studies didn’t look at how to gauge the effect of various types of sleep, such as napping or even higher or lower quality rest, their efforts suggest that sleep can help protect against stress-triggered infections.

The total amount and the structure of sleep play roles in this feedback loop. The variability among people makes any broad categorization about sleep needs difficult, as some people function well with six hours of sleep, while others need closer to eight or nine hours per day.

“Scientists are still working out how the brain keeps track of how much sleep it needs to rest and recover,” Borniger explained. “If we can figure this out, then, in principle, we could mess with the amount of sleep one needs without jeopardizing health.”

Researchers don’t know much about the circuitry controlling sleep amount. Borniger recognizes that the conclusions from this study are consistent with what doctors and parents have known for years, which is that sleep is important to overall health. The research also identifies a brain circuit that may be responsible for the way sleep buffers stress and immune responses.

People who have trouble sleeping because of elevated stress from an upcoming deadline often have a flare up of diseases they might have had under control previously, such as herpes viruses or psoriasis. These diseases opportunistically reemerge when the immune system is weakened.

The major finding in this study is not that the connection exists, but that the researchers, including principal investigator Luis de Lecea and first author Shi-Bin Li at Stanford, found the neural components.

While the studies of these linkages in the hypothalamus of mice were consistent across individuals, the same can’t be said for anecdotal and epidemiological evidence in humans, in part because the mice in the study were genetically identical.

For humans, age, sex, prior experiences, diet, family history and other factors make the linkage harder to track.

Even though researchers can’t control for as many variables with humans as they can with mice, however, several other studies have shown that stress promotes insomnia and poor immune function.

Borniger emphasized that he is the second author on the paper, behind Li and was involved in tracking the immune system component of the work.

Borniger and de Lecea are continuing to collaborate to see if drugs that target the insomnia neurons block the effect of stress on the immune system.

Now that he has moved into the refurbished Demerec Laboratory at CSHL, Borniger plans to work on projects to investigate how to use the nervous system to control anti-tumor immunity in models of breast and colorectal cancer, among others.

By understanding this process, Borniger can contribute to ways to manipulate these cells and the immune system to combat cancer and other inflammatory diseases.

Ideally, he’d like to be a part of collaborations that explore the combination of manipulating nervous and immune systems to combat cancer.

Borniger came to Cold Spring Harbor Laboratory because he was eager to collaborate with fellow scientists on site, including those who look at the immune system and metabolism. He appreciates how researchers at the famed research center look at how bodies and the brain respond to a growing tumor and would like to explore how tumors “influence nerves and then, reciprocally, how nerves influence tumor progression.”

The first few steps towards working at CSHL started in 2018, when Tobias Janowitz, Assistant Professor at CSHL, saw a paper Borniger published on breast cancer and asked him to give a 15-minute talk as a part of a young scholars symposium.

Borniger grew up in Washington, DC, attended college at Indiana University, went to graduate school at Ohio State and conducted his post-doctoral work at Stanford. Coming to CSHL brings him back to the East Coast.

Borniger and his fiancée Natalie Navarez, Associate Director of Faculty Diversity at Columbia University, met when they were in the same lab at Stanford. The couple had planned to get married this year. During the pandemic, they have put those plans on hold and may get married at City Hall.

Borniger and Navarez, who live on campus at Hooper House at CSHL, look forward to exploring opportunities to run, hike and swim on Long Island.

The new CSHL researcher appreciates the new opportunities on Long Island.

“This sort of collaborative atmosphere is what I would have in my Utopian dream,” Borniger said.

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James Misewich Photo from BNL

By Daniel Dunaief

Even as the pandemic continues to cast a pall over the prospects for the economy, the federal government is finding ways to support science. Recently, as a part of a $625 billion award to a host of institutions, the Department of Energy earmarked $115 million over five years for a part of a project led by Brookhaven National Laboratory.

The science, called quantum information systems, could have applications in a wide range of industries, from health care to defense to communications, enabling higher levels of artificial intelligence than the current binary system computers have used for decades. By benefiting from the range of options between the 0s and 1s that typically dictate computer codes, researchers can speed up and enhance the development of programs that use artificial intelligence.

The investment “underscores the confidence the federal government has with respect to how important this technology is,” said James Misewich, the Associate Laboratory Director for Energy and Photon Sciences at BNL. “Despite the challenges of the time, this was a priority.”

Local leaders hailed the effort for its scientific potential and for the future benefit to the Long Island economy.

“I have seen strong support inside of Congress and the administration for funding requests coming out of the Department of Energy for ideas on how to move the DOE’s mission forward,” said U.S. Rep. Lee Zeldin (R-NY-1). “I have also seen a very high level of appreciation and respect for BNL, its leadership, its staff, its mission and its potential.”

Zeldin said the average American spends more time than ever engaging with technologies and other discoveries that were made possible by the first quantum revolution. “Here we are on the verge of a second quantum revolution and BNL is at the forefront of it,” Zeldin said.

Zeldin sees limitless possibilities for quantum information science, as researchers believe these efforts will lead to advancements in health care, financial services, national security and other aspects of everyday life. “This next round of quantum advancements seeks to overcome some of the vulnerabilities that were identified and the imperfections in the first wave,” he said.

State Senator James Gaughran (D-Northport) expects quantum science to provide a significant benefit to the region. “We believe this is going to be a major part of our economic future,” he said. “It is a huge victory for Long Island.”

The return on investment for the state and the federal government will also materialize in jobs growth. This is “going to employ a lot of people,” Gaughran said. “It will help to rebuild the type of economy we need on Long Island. The fact that we are on the front lines of that will lead to all sorts of private sector development.”

While the technology has enormous potential, it is still in early enough stages that research groups need to work out challenges before they can fully exploit quantum technology. BNL, specifically, will make quantum error correction a major part of their effort.

As quantum computers start working, they run into a limitation called a noisy intermediate scale quantum problem, or NISQ. These problems come from errors that lower the confidence of getting the right answer. The noise is a current limitation for the best quantum computers. “They can only go so far before you end up with an error that is fatal” to the computing process, Misewich said.

By using the co-design center for quantum advantage, Misewich and his partners hope to use the materials that “beat the NISQ error by having the combination of folks with a great team that are all talking to one another.”

The efforts will use a combination of classical computing and theory to determine the next steps in the process of building a reliable quantum information system-driven computer.

Misewich’s group is also focusing on communication. The BNL scientists hope to provide a network that enables distributed computing. In classical computing, this occurs regularly, as computer scientists distribute a problem over multiple computers.

Similarly, with quantum computing, scientists plan to distribute the problem across computers that need to talk to each other.

Misewich is pleased with the combination of centers that will collaborate through this effort. “The federal government picked these centers because they are somewhat complementary,” he said. The BNL-led team has 24 partners, which include IBM, Stony Brook University, SUNY Polytechnic Institute, Yale University, Princeton University, the Massachusetts Institute of Technology, Harvard University, Columbia University and Howard University, among others.

“We had to identify the best team and bring in the right people to fill the gaps,” Misewich explained.

Using a combination of federal funds and money from New York State, BNL plans to build a new beamline at the National Synchrotron Lightsource II, which will operate at very low temperatures, allowing scientists to study the way these materials work under real word conditions.

BNL would like the work they are doing to have an application in calculations in three areas: the theory of the nucleus, quantum chemistry, which explores ways to design better materials, and catalysis.

A quantum computer could help make inroads in some challenging calculations related to electron-electron interactions in superconducting materials, Misewich said, adding that the entire team feels a “tremendous sense of excitement” about the work they are doing.”

Indeed, the group has been working together for close to two years, which includes putting the team in place, identifying the problems they want to tackle and developing a compelling strategy for the research to make a difference.

The group is expecting to produce a considerable amount of research and will likely develop various patents that will “hopefully transfer the technology so companies can start to build next generation devices,” Misewich said.

Along with local leaders, Misewich hopes these research efforts will enable the transfer of this technology to a future economy for New York State.

This effort will also train a numerous graduate and post doctoral students, who will be the “future leaders that are going to drive that economy,” Misewich said.

The research will explore multiple levels of improvement in the design of quantum computers which they hope will all work at the same time to provide an exponential improvement in the ability of the computer to help solve problems and analyze data.

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Eric Yee. Photo by Felicia Allard

By Daniel Dunaief

In the second of a two-part series, Times Beacon Record News Media will feature the work of Eric Yee, who, like his wife Felicia Allard who was featured last week, is joining the Pathology Department at Stony Brook University.

Eric Yee

Eric Yee, who started as an Associate Professor and Director of Surgical Pathology at Stony Brook Renaissance School of Medicine on July 1, described the focus of his scientific research as translational.

He consults with and helps science researchers put together ideas for experiments, while he and his wife Felicia Allard focus on bringing that work into the clinical setting.

“We provide expertise mainly in clinical gastrointestinal and hepatobiliary pathology,” Yee explained in an email. “We also give insights and perspectives as practicing pathologists to help [with the] analysis of data and how that data in the lab or in animal models may be relevant to clinical medicine.”

Yee completed a gastrointestinal pathology fellowship, working on collaborative research projects and publishing manuscripts with investigators.

As one of the newest members of the staff at Stony Brook, he has worked on some studies looking at certain kinds of inflammatory diseases in the liver. He collaborated with senior investigator Zhenghui Gordon Jiang of Beth Israel Deaconess Medical Center to look at mediators of inflammation in the disease steatohepatitis. He has also worked on different cancer research projects, which is part of the appeal of Stony Brook.

Stony Brook has “important pancreatic research,” Yee said, adding that. Pathology Department Chair Ken Shroyer is a “renowned investigator whose research team has done great work that has led to important insights into pancreatic cancer biology.”

Pancreatic cancer is of particular interest to Yee in his clinical work and he hopes to explore the variety of research expertise at Stony Brook, to support ongoing efforts and to develop projects of his own.

Relocating to Stony Brook from the College of Medicine at the University of Arkansas for Medical Sciences, where Allard and Yee both worked in the Pathology Department, took some convincing for both of the scientists.

“We were very happy in Little Rock and purchased a home in Arkansas two years prior and were just starting to set down roots,” Yee described in an email. “We made lifelong friendships and very much enjoyed the camaraderie among our peers and other departments.”

Yee and Allard had no plans to leave as they approached their third year and were hesitant to move.

In his first visit, Yee said he was impressed with the amount of research in the Stony Brook department, which, he said, has more researchers compared to other institutions of similar size.

On the other side, however, Yee said he and Allard had to reconcile the higher cost of living in New York. They also weren’t eager to make too many moves in their career, especially when they were happy in Arkansas.

Even after the first visit, Yee said he was hesitant to make a move, which would require time to settle in, build relationships, find a home, learn a new system, and find new opportunities, among other challenges..

Shroyer was “very understanding of my hesitation,” Yee explained. “He’s been one of my mentors since medical school and knew exactly where I was coming from.

Clinically, the couple also believed in the potential for career growth.

“There’s a lot of energy in the department,” Yee said. He also appreciated the opportunity to be the Director of Surgical Pathology, where he could shape the operations that support the clinical mission. He would like to optimize the department by specialization, creating a sub-specialty model.

“This is something I want to do to increase the efficiency in the department,” Yee explained. “I’m hoping as we sub-specialize that we make our clinical work flow more efficient” which will create more consistency. “Part of what I’d like to do is to help [Shroyer] create a department where it’ll allow the clinical faculty to thrive.”

Yee thinks any work efficiencies will provide researchers with more time to build on their teaching efforts, and to develop new lectures and teaching models.

Yee will measure his success through a comprehensive report that includes an analysis of the efficiency of the response to clinical needs. He hopes to create a system that will enable the success of the entire anatomic pathology division. He will also become actively engaged in the academic mission, which is measured in the number of publications as well as in staff appointments to editorial boards or major national societies.

“The more people we can get into the national arena the better it is for the institution,” Yee said. These contributions bring good public relations and expertise to the institution.

Yee and Allard will also contribute to Stony Brook through their efforts in education.

Yee believes the school has an advantage in telepathology and distance learning. He believes the Department of Bioinformatics led by Dr. Joel Saltz facilitates telepathology and distance learning.

With the uncertainty caused by COVID-19, Yee believes maintaining social distancing and finding innovative ways for communication and education will provide valuable alternatives to communicate and collaborate.  Radiology has had digital methods in place to send MRIs and CAT scans for a longer period of time than pathologists, who still produce glass slides.

“There will always be some challenges and limitations that are unique to pathology,” Yee suggested.

A native of San Francisco, where he and his older brother, who now works in Boston, grew up, Yee was interested in medicine during the middle of his college career.

Yee and Allard met in medical school and, among numerous other parts of their lives they have in common, discovered they were both fans of the Star Wars films. Early on when they were dating, the pathology couple saw Star Wars: Episode III – Revenge of the Sith together.

Yee enjoys tennis, table tennis, riding road bikes and hiking. He has also developed an appreciation for bird watching, which has allowed him to practice amateur photography.

The couple also shares an interest in music, as Yee grew up playing the piano, while Allard played the trumpet.

When he was in medical school, Yee published his first  paper with Shroyer. He has remained in touch with the pathology chair over the years and appreciates the advice Shroyer has offered.

Yee described Shroyer as an “inspirational leader” and appreciates his energy, selflessness and passion, among other qualities.

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the U.S. Department of Energy awarded a 10-year multi-billion project to build a new electron-ion collider at Brookhaven National Laboratory in Upton. Provide photo from Brookhaven National Lab

By Daniel Dunaief

Through answers to basic questions, scientists develop new technology that changes the world, leading to medical breakthroughs, energy applications and national security devices.

That’s the theory behind the U.S. Department of Energy’s decision last week to award a 10-year project that will cost between $1.6 billion and $2.6 billion to build a new electron-ion collider at Brookhaven National Laboratory in Upton. 

For the scientists, the discoveries will flow from answers to questions about the nature of visible matter.

“The big science we’re excited about, the hundred-year-old questions, are things like where does the mass of a proton come from,” said Robert Tribble, the deputy director for science and technology at Brookhaven National Laboratory and a nuclear physicist. The EIC is like a microscope to look at quarks and gluons, he explained.

With support from numerous New York State and Long Island leaders, BNL recently won a competition against Thomas Jefferson National Accelerator in Virginia to build an electron-ion collider. Members of the Jefferson Accelerator, as well as over 1,000 scientists from 30 nations, will partner with BNL staff to conceptualize and build the new collider, which will be the most advanced ever constructed.

In addition to understanding atomic nuclei, we will be able to generate a better view of the universe writ large [with discoveries from the EIC].”

– Robert Tribble

“We do not understand very dense matter that exists in the universe in objects like neutron stars and black holes,” Tribble explained in an email. “In addition to understanding atomic nuclei, we will be able to generate a better view of the universe writ large [with discoveries from the EIC].”

Over the next decade, the construction of the new EIC will employ 4,000 people, said Doon Gibbs, the laboratory director at BNL. That number represents the workforce that will, at one time or another, contribute to the construction of this new facility. 

The new EIC will expand on the technology of the Relativistic Heavy Ion Collider, which has been operating since 2000 and will stop running experiments in 2024. Indeed, part of the appeal of BNL as a site for this new facility arose out of the ability to extend the resources by building a new electron storage ring and electron accelerator elements.

Researchers will collide electrons and protons and numerous atomic nuclei to study the strong nuclear force. These collisions will reveal how the subunits of protons and neutrons in the nucleus, namely the quarks and gluons, come together to help generate mass in visible matter.

The staff at BNL is “delighted and excited” that the site for the EIC will be on Long Island, said Gibbs. “Our design has the capability of using many existing technologies and extending them farther than they’ve been before.”

Indeed, even the conception of the EIC has led to some new scientific breakthroughs, some of which the lab and its partners will share with the public in the next few weeks.

While the application of research at the EIC will likely lead to breakthroughs in fields including materials science, researchers at BNL are excited about basic questions about the nature of nuclear matter.

A typical experiment at the EIC will likely follow the same pattern as it has with RHIC, in which hundreds of researchers from around the world collaborate to understand physics properties. In the next few years, researchers will develop a detailed design before they start construction.

“We love challenges at BNL, we like building big machines. We’re good at it. We have a whole class of staff who, in particular, are experts at this kind of activity and they are pretty excited.”

– Doon Gibbs

Gibbs said the facility has a strong handle on the safety features of the new collider, which will build on the protocols and designs developed at the RHIC as well as with the National Synchrotron Light Source II, also at the lab in Upton.

“We love challenges at BNL,” Gibbs said. “We like building big machines. We’re good at it. We have a whole class of staff who, in particular, are experts at this kind of activity and they are pretty excited.”

Area politicians are also excited about discoveries in basic science, translational benefits in areas like medicine and the expected boost to the local economy.

“Establishing the electron-ion collider on Long Island might be focused on particles, but it will add some serious mass — nearly $1 billion worth — to the local economy,” U.S. Sen. Chuck Schumer (D) said in a statement. BNL has the “talent, the technology and the track record to make the most of this national project.”

Schumer believes this project will guarantee that BNL continues to be a “world class research facility for the next generation.”

U.S. Rep. Lee Zeldin (R-Shirley) praised the leadership at BNL.

“I congratulate BNL Director Doon Gibbs for leading this exceptional organization and all of its scientists who have worked incredibly hard every step of the way to make this possible, and can’t wait to see what they do next,” Zeldin said in a statement.

 

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Nicholas Gladman with a harvest of sorghum at Cornell University’s Long Island Horticultural Research Lab in Riverhead. Photo by Sendi Mejia

By Daniel Dunaief

When people buy a bag of potato chips, they often find that half of the bag is filled with air. The same is true of a sorghum plant, which produces livestock feed and is converted into ethanol, part of many gases that power cars.

Nicholas Gladman

In a typical sorghum plant, half of the flowers become grain, while the other half remain infertile. As the world grapples with food shortages and scientists seek ways to increase the yield of a wide array of plants, researchers at Cold Spring Harbor Laboratory wondered whether they could increase that yield.

Building on previous work done in the lab of Doreen Ware, an adjunct professor at CSHL, postdoctoral fellow Nicholas Gladman characterized a mutation for a single gene that lowered the level of a hormone. The effect of the lower hormone, or jasmonic acid, at a specific time and place within plant development doubled the fertility of the sorghum plant.

“When we don’t have a functional version of this enzyme, it releases this form of development that wouldn’t normally occur,” Gladman said. “You get increased fertility in flowers.”

The gene they studied is called MSD2. The researchers published their work in International Journal of Molecular Sciences. Another gene, MSD1, which Ware’s lab characterized in 2018, is a likely regulator for MSD2. Other genes may also serve as regulators of MSD2, Gladman said. Disruptions in either gene leads to altered flower development and seed production.

Gladman’s postdoctoral research adviser Zhanguo Xin collaborated on the work. Xin, who is a research molecular biologist at the United States Department of Agriculture’s Agricultural Research Service, explained that Gladman characterized the mutants, identified the interaction between MSD1 and MSD2 and identified the regulatory sequences of MSD1.

This research could extend to other cereal crops, which have the same conserved sets of genes that affect their growth and fertility.

A concern in altering any gene resides in the overall effect on the health of the plant. Creating a super plant that falls over and dies in a slight wind, can’t fend off common infections, or requires a perfect blend of soil would likely offset the benefit of the increased fertility. Plant geneticists would like to ensure any mutation doesn’t make the plant less viable in the long run.

“Sometimes there can be a trade off between an agriculturally beneficial genetic change by introducing other detrimental effects,” Gladman explained in an email. “Optimally, plant geneticists will try to ensure the side effects of any mutation are insignificant to farmers; sometimes, this is more difficult and the downsides may not always present themselves at the early stages of lab investigation.”

This particular gene is narrowly and spatially expressed within the plant, Gladman said, and the researchers haven’t been able to identify or quantify the effect of this gene on anything else other than flowers and floral architecture.

The gene and the hormone would be a concern if it were expressed more broadly and at high levels throughout other plant tissues, but that doesn’t seem to be the case, he said.

The researchers have looked at other tissues, such as the leaf and stem, and have found that MSD2 is expressed in low levels in these other areas. Plants that have the MSD2 mutation do not demonstrate any noticeable differences in growth compared to nonmutants in the field or in greenhouse conditions. If this mutated gene had an agricultural benefit, farmers would likely crossbreed a plant that had this gene with an elite sorghum hybrid line

Ideally, the benefits of the increased fertility would combine with benefits of all the genetic components of the hybrid lines as well. The way the researchers involved in this study produced this more fertile version of sorghum is an “acceptable type of breeding for organic or conventional farming,” Gladman said.

While the plant increases the grain number per seed head, it doesn’t necessarily produce greater overall yield in part because the seeds are smaller. Researchers haven’t been able to confirm that yet in a field condition, although they hope that’s the case.

Gladman was grateful for the opportunity to work in Ware’s lab and to collaborate with Xin. The effects of disrupting similar genes in maize and Arabidopsis, which is a plant in the mustard family that scientists often use in genetic studies, influences flower fertility.

He said researchers in Ware’s lab can perform additional developmental analysis. The researchers in Ware’s lab may seek additional collaborators for other analyses down the road as well.

“How this particular pathway is triggered and cross-communicates with other developmental pathways is very complex, but influences so much about traits that control grain production and yield that it is essential for further investigations,” he explained.

Gladman arrived at Cold Spring Harbor Laboratory in 2017. Prior to conducting research on Long Island, he finished his doctorate at the University of Wisconsin at Madison, where he worked on Arabidopsis. He decided he wanted to get more involved with crop species and explored research opportunities at United States Department of Agriculture labs. He was working with Xin in Lubbock, Texas, before transitioning to Cold Spring Harbor Laboratory.

Gladman has been delighted by the “wonderful place to learn,” where he is surrounded by “people who are always willing to talk and engage and collaborate.”

A resident of Greenlawn, Gladman enjoys hiking along the Hudson and in the Adirondacks. He credits a high school biology class he took in Grandview Heights High School in Columbus, Ohio, with instilling in him and his three brothers an appreciation and love of science. He particularly enjoyed a unit on the “genetics of disease” that inspired him to pursue a career in the sciences.

As for his work, Gladman is excited to be a part of research that may, one day, increase the productivity of crop species. He said thoughts about food shortages are “a constant concern and driver of our research.”

 

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Interns Nylette Lopez (rear) and Stephanie Taboada characterize catalysts as they attempt to convert carbon dioxide and methane into synthesis gas this past summer at Brookhaven National Laboratory. Photo from BNL.

By Daniel Dunaief

This article is part two in a two-part series.

Local medical and research institutions are aware of the challenges women face in science and are taking steps to ensure that women receive equal opportunities for success in science, technology, engineering and mathematics (or STEM). Times Beacon Record News Media reached out to members of each institution and received an overview of some initiatives.

Brookhaven National Laboratory 

The Department of Energy-funded research facility has created a number of opportunities for women, including Brookhaven Women in Science. This effort has been active for over four decades and its mission, according to Peter Genzer, a BNL spokesman, is to support the development of models, policies and practices that enhance the quality of life for BNL employees and emphasize the recruitment, hiring, promotion and retention of women.

BWIS offers annual awards, outreach events and various networking opportunities in the lab and community, while the lab’s Talent Management Group partners with BWIS to bring classes and speakers to discuss issues specific to women.

In October, the group hosted Kimberly Jackson, a vice chair and associate professor of chemistry and biochemistry at Spelman College, who gave a talk titled “Realigning the Crooked Room in STEM.”

The Leona Woods Distinguished Postdoctoral Lectureship Award at BNL, meanwhile, celebrates the scientific accomplishments of female physicists, physicists from under-represented minority groups and LGBTQ physicists and to promote diversity and inclusion. BNL awarded the lectureship this year to Kirsty Duffy, a fellow at Fermi National Accelerator Laboratory.

For the past five years, BNL has also partnered with a local chapter of Girls Inc., which helps to “encourage young women towards careers” in STEM, Genzer explained in an email.

BNL has also collaborated with the Girl Scouts of Suffolk County to organize a new patch program that encourages Girl Scouts to work in scientific fields. As of September, county Girl Scouts can earn three new Brookhaven Lab patches, and the lab hopes to extend the program nationwide across the Department of Energy complex.

BNL also provides six weeks of paid time off at 100 percent of base pay for a primary caregiver after birth or adoption and one week of full pay for a secondary caregiver. BNL is exploring plans to enhance support for primary and secondary caregivers, Genzer said.

Cold Spring Harbor Laboratory

Cold Spring Harbor Laboratory has taken several recent steps as part of an ongoing effort to encourage gender diversity.

In October, a group of four CSHL administrators traveled to the University of Wisconsin in Madison to discuss mentoring. The goal was to train them on how to design and deliver mentoring training regularly to the faculty, postdocs and graduate students on campus, said Charla Lambert, the diversity, equity and inclusion officer for research at CSHL. The first version of the training will occur next spring. The ultimate goal is to ensure the research environment at CSHL emphasizes good mentoring practices and is more inclusive for all mentees.

CSHL has also hosted a three-day workshop in leadership practices for postdoctoral researchers and junior faculty since 2011. The workshop, which is run through the Meetings & Courses Program, trains about 25 postdoctoral researchers and junior faculty each year and has about one per year from CSHL, addresses how to hire and motivate people, while providing constructive feedback.

Lambert said family-friendly policies were already a part of CSHL policies, which include a child care facility. Members of the faculty receive extra funding when they travel to conferences to provide additional child care.

Lambert, who is a program manager for extramural Meetings & Courses overseeing diversity initiatives, has worked to get the demographic data for participants centralized, analyzed and used in developing policies. She believes this kind of data centralization is an area for potential improvement in the research division, where she is working to ensure an equitable distribution of resources among CSHL scientists.

Throughout her nine-year career at CSHL, Lambert said she has worked with the meetings and courses division to make sure the 9,000 scientists who visit the facility each year include women as invited speakers. She also works to reach course applicants from a wide range of institutions, including outside of prestigious research schools.

Ultimately, Lambert is hoping to help change the culture of science among the researchers with whom she interacts from a wide range of institutions. She feels that those people who leave the STEM fields because something about the culture of science didn’t work for them represent a “huge loss” to the field and creates a “survivorship bias.”

Stony Brook University 

For Stony Brook, gender diversity is “very important,” said Latha Chandran, the vice dean for Academic and Faculty Affairs at the Stony Brook University Renaissance School of Medicine. 

Chandran said more men entered the field of medicine 14 years ago. That has completely changed, as women have outnumbered their male counterparts in medicine for the last three or four years.

Chandran cited a number of statistics to indicate changes at the medical school. For starters, women faculty constituted 38 percent of the total in 2011. This April, that number climbed to 48.1 percent. That puts Stony Brook in the top 79th percentile of medical schools in terms of female representation.

While the overall numbers are higher, women are still underrepresented in the top tiers of the medical school, as 18 percent of the department chairs are women. She hopes more women can lead departments and that they can serve as role models that others can aspire to follow.

As for harassment, Chandran said Stony Brook was above the national mean in 2011. For almost all categories, Stony Brook is now below the national mean.

In 2011, Stony Brook created We Smile, which stands for We can Eradicate Student Mistreatment in the Learning Environment. The goal of this program is to educate people about harassment and to ensure that any mistreatment is reported. Through this effort, Stony Brook medical students are aware of the policies and procedures surrounding reporting.

Stony Brook is also addressing any bias in admission procedures by prospective applicants, who receive a standardized scenario to address with an admissions officer. In 2025, admissions officers will not have any information about the qualifications of the individual and will evaluate his or her response during interviews only based on response to scenarios.

Stony Brook University has almost finalized its search for a chief diversity candidate. Chandran expects that the medical school will “continue to make progress.”

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Peter Koo. Photo by ©Gina Motisi, 2019/ CSHL

By Daniel Dunaief

We built a process that works, but we don’t know why. That’s what one of the newest additions to Cold Spring Harbor Laboratory hopes to find out.

Researchers have applied artificial intelligence in many areas in biology and health care. These systems are making useful predictions for the tasks they are trained to perform. Artificial intelligence, however, is mostly a hands-off process. After these systems receive training for a particular task, they learn patterns on their own that help them make predictions.

How these machines learn, however, has become as much of a black box as the human brains that created these learning programs in the first place. Deep learning is a way to build hierarchical representations of data, explained Peter Koo, an assistant professor at the Simons Center for Quantitative Biology at CSHL, who studies the way each layer transforms data and the next layer builds upon this in a hierarchical manner.

Koo, who earned his doctorate at Yale University and performed his postdoctoral research at Harvard University, would like to understand exactly what the machines we created are learning and how they are coming up with their conclusions.

“We don’t understand why [these artificial intelligence programs] are making their predictions,” Koo said. “My postdoctoral research and future research will continue this line of work.”

Koo is not only interested in applying deep learning to biological problems to do better, but he’s also hoping to extract out what knowledge these machines learn from the data sets to understand why they are performing better than some of the traditional methods.

“How do we guide black box models to learn biologically meaningful” information? he asked. “If you have a data set and you have a predictive model that predicts the data well, you assume it must have learned something biologically meaningful,” he suggested. “It turns out, that’s not always the case.”

Deep learning can pick up other trends or links in the data that might not be biologically meaningful. In a simplistic example, an artificial intelligence weather system that tracked rain patterns during the spring might conclude, after seven rainy Tuesdays, that it rains on Tuesdays, even if the day of the week and the rain don’t have a causative link.

“If the model is trained with limited data that is not representative, it can easily learn patterns that are correlative in the training data,” Koo said. He tries to combat this in practice by holding out some data, which is called validating data. Scientists use it to evaluate how well the model generalizes to new data.

Koo plans to collaborate with numerous biologists at Cold Spring Harbor Laboratory, as well as other quantitative biologists, like assistant professors Justin Kenney and David McCandlish.

In an email, Kenney explained that the Simons Center is “very interested in moving into this area, which is starting to have a major impact on biology just as it has in the technology industry.”

The quantitative team is interested in high-throughput data sets that link sequence to function, which includes assays for protein binding, gene expression, protein function and a host of others. Koo plans to take a “top down” approach to interpret what the models have learned. The benefit of this perspective is that it doesn’t set any biases in the models.

Deep learning, Koo suggested, is a rebranding of artificial neural networks. Researchers create a network of simple computational units and collectively they become a powerful tool to approximate functions.

A physicist by training, Koo taught himself his expertise in deep learning, Kenney wrote in an email. “He thinks far more deeply about problems than I suspect most researchers in this area do,” he  wrote. Kenney is moving in this area himself as well, because he sees a close connection between the problem of how artificial intelligence algorithms learn to do things and how biological systems mechanistically work.

While plenty of researchers are engaged in the field of artificial intelligence, interpretable deep learning, which is where Koo has decided to make his mark, is a considerably smaller field.

“People don’t trust it yet,” Koo said. “They are black box models and people don’t understand the inner workings of them.” These systems learn some way to relate input function to output predictions, but scientists don’t know what function they have learned.

Koo chose to come to Cold Spring Harbor Laboratory in part because he was impressed with the questions and discussions during the interview process.

Koo, daughter Evie (left) and daughter Yeonu (right) during Halloween last year. Photo by Soohyun Cho

He started his research career in experimental physics. As an undergraduate, he worked in a condensed matter lab of John Clarke at the University of California at Berkeley. He transitioned to genomics, in part because he saw a huge revolution in next-generation sequencing. He hopes to leverage what he has learned to make an impact toward precision medicine. 

Biological researchers were sequencing all kinds of cancers and were trying to make an impact toward precision medicine. “To me, that’s a big draw,” Koo said, “to make contributions here.”

A resident of Jericho, Koo lives with his wife, Soohyun Cho, and their 6-year-old daughter Evie and their 4-year old-daughter Yeonu.

Born and raised in the Los Angeles area, he joined the Army Reserves after high school, attended community college and then transferred to UC Berkeley to get his bachelor’s degree in physics.

As for his decision to join Cold Spring Harbor Laboratory, Koo said he is excited with the opportunity to combine his approach to his work with the depth of research in other areas. 

“Cold Spring Harbor Laboratory is one of those amazing places for biological research,” Koo said. “What brought me here is the quantitative biology program. It’s a pretty new program” that has “incredibly deep thinkers.”

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Anne Churchland with former postdoctoral fellow Matt Kaufman at Cold Spring Harbor Laboratory. The microscope is a 2-photon microscope and is one of three techniques used to measure neural activity in the mouse brain. Photo from Margot Bennett

By Daniel Dunaief

Fidgeting, rocking and other movements may have some benefit for thinking. Yes, all those people who shouted to “sit still” may have been preventing some people from learning in their own way.

In a new experiment conducted on mice published in the journal Nature Neuroscience this week, Anne Churchland, an associate professor at Cold Spring Harbor Laboratory, linked idiosyncratic mouse movements to performance in a set of tasks that required making decisions with rewards.

“Moving when deep in thought is a natural thing to do,” Churchland said. “It deeply engages the brain in ways that were surprising to us.”

She suggested that many people believe thinking deeply requires stillness, like the statue of The Thinker created by Auguste Rodin. “Sometimes it does, but maybe not for all individuals,” adding that these movements, which don’t seem connected to the task at hand, likely provide some benefit for cognition.

“We don’t know yet for sure what purpose these movements are serving,” she said.

Margaret Churchland with the lab group at CSHL

Mammals tend to exhibit a process called “optimal motor control.” If a person is reaching out to grab a cup, she tends to move her arm in a way that is energy conserving. Indeed, extending this to her rodent study, Churchland suggests that somehow these ticks, leg kicks or other movements provide assistance to the brain.

In theory, she suggested that these movements may be a way for the brain to recruit movement-sensitive cells to participate in the process. These brain cells that react to movement may then participate in other thought processes that are unrelated or disconnected from the actions themselves.

Churchland offers an analogy to understanding the potential benefit of these extra movements in the sports world. Baseball players have a wide range of stereotyped movements when they step up to the plate to hit. They will touch their shirt, tug on their sleeves, readjust their batting gloves, lift up their helmet or any of a range of assorted physical activities that may have no specific connection to the task of hitting a baseball.

These actions likely have “nothing to do” with the objective of a baseball hitter, but they are a “fundamental part of what it means to go up to bat,” she said.

In her research, Churchland started with adult mice who were novices at the kinds of tasks she and her colleagues Simon Musall and Matt Kaufman, who are the lead authors on the paper, trained them to do. Over a period of months, the mice went from not understanding the objective of the experiment to becoming experts. The animals learned to grab a handle to start a trial or to make licking movements.

These CSHL researchers tracked the behavior and neural activity of the mice every day.

Churchland said a few other groups have measured neural activity during learning, but that none has studied the kind of learning her lab did, which is how animals learn the structure of an environment.

The extra movements that didn’t appear to have any connection to the learned behaviors transitioned from a disorganized set of motions to an organized pattern that “probably reflected, in the animal’s mind, a fundamental part of what it means to make a decision.”

Churchland suggested that some of these conclusions may have a link to human behavior. Each animal, however, has different behaviors, so “we always need to confirm that what we learn in one species is true for another,” she wrote in an email.

Parents, teachers, coaches and guest lecturers often look at the faces of young students who are shaking their legs, rocking in their chair, twiddling their thumbs or spinning their pens between their fingers. While these actions may be distracting to others, they may also play a role in learning and cognition.

The study “suggests that allowing certain kinds of movements during learning is probably very important,” Churchland said. “When we want people to learn something, we shouldn’t force them to sit still. We should allow them to make movements they need to make which will likely help” in the learning process.

Churchland believes teachers already know that some students need to move. These educators also likely realize the tension between allowing individual students to be physically active without creating a chaotic classroom. “Most teachers are working hard to find the right balance,” she explained in an email.

She also suggested that different students may need their own level of movement to stimulate their thinking.

Some adults may have already developed ways to enhance their own thinking about decisions or problems. Indeed, people often take walks that may “finally allow those circuits you need for a decision to kick in.”

Down the road, she hopes to collaborate with other scientists who are working with nonhuman primates, such as marmosets, which are new world monkeys that live in trees and have quick, jerky movements, and macaques, which are old world monkeys and may be familiar from their island perch in an exhibit in the Central Park Zoo.

Churchland said extensions of this research could also go in numerous directions and address other questions. She is hoping to learn more about attention deficit hyperactivity disorder and the brain.

“We don’t know when that strategy [of using movement to trigger or enhance thinking] interferes with the goal,” she said. “Maybe the movements are a symptom of the learner trying to engage, but not being able to do so.”

Ultimately, Churchland expects that different pathways may support different aspects of decision making, some of which can and likely are connected to movement.

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By Daniel Dunaief

Screws can’t be the best and only answer. That was the conclusion neurosurgeon Daniel Birk at the Stony Brook Neurosciences Institute came to when he was reconsidering the state-of-the-art treatment for spinal injuries. The screws, which hold the spine in place, create problems for patients in part because they aren’t as flexible as bone.

That’s where Stony Brook University’s College of Engineering and Applied Sciences, headed by Fotis Sotiropoulos, plans to pitch in. Working with Kenneth Kaushansky, dean of Stony Brook University’s Renaissance School of Medicine, the two Stony Brook leaders have been immersed in uniting their two disciplines to find ways engineers can improve medical care.

Fotis Sotiropoulos

The two departments have created the Institute for Engineering-Driven Medicine, which will address a wide range of medical challenges that might have engineering solutions. The institute will focus on developing organs for transplantation, neurobiological challenges and cancer diagnostics.

The institute, which already taps into the medical and engineering expertise of both departments, will move into a new $75 million building at the Research and Development Park, in 2023.

The original investment from New York State’s Economic Development Council was for an advanced computing center. The state, however, had given Buffalo the same funds for a similar facility, which meant that former Stony Brook President Sam Stanley, who recently became the president of Michigan State University, needed to develop another plan.

Sotiropoulos and Kaushansky had already created a white paper that coupled engineering and medicine. They developed a proposal that the state agreed to fund. In return for their investment, the state is looking for the development of economic activity, with spin-off companies, jobs, new industries and new ideas, Kaushansky said.

The two leaders are developing “a number of new faculty recruits to flesh out the programs that are going in the building,” Kaushansky added.

Sotiropoulos, who has conducted research in the past on blood flow dynamics in prosthetic heart valves, believes in the potential of this collaboration. “This convergence of engineering and medicine is already doing what it was intended to do,” he said. Clinicians can get “crazy sci-fi ideas, talk to engineers and figure out a way to make it happen.”

In addition to spinal cord support, researchers in engineering and medicine are working on developing algorithms to make decisions about surgical interventions, such as cesarean sections. 

A recent project from principal investigator Professor Petar Djurić, chair of SBU’s Department of Electrical and Computer Engineering, and Gerald Quirk, an obstetrician and gynecologist at Stony Brook Medicine, recently received $3.2 million from the National Institutes of Health. The goal of the project is to use computer science to assist with the decisions doctors face during childbirth. A potential reduction in C sections could lower medical costs. 

“This is a fantastic example of this type of convergence of engineering and medicine,” said Sotiropoulos.”

Dr. Kenneth Kaushansky. Photo from SBU

While the building will host scientists across a broad spectrum of backgrounds, researchers at Stony Brook will be able to remain in their current labs and coordinate with this initiative. Combining all these skills will allow researchers to apply for more grants and, Stony Brook hopes, secure greater funding.

“For a number of years now, the [National Institutes of Health have] really favored interdisciplinary approaches to important medical problems,” Kaushansky said. “Science is becoming a team sport. The broader range of skills on your team, the more likely you’ll be successful. That’s the underlying premise behind this.”

The notion of combining medicine and engineering, while growing as an initiative at Stony Brook, isn’t unique; more than a dozen institutions in the country have similar such collaborations in place.

“We’re relatively early in the game of taking this much more holistic approach,” said Kaushansky, who saw one of the earlier efforts of this convergence when he was at the University of California at San Diego, where he worked with the Founding Chair of the Department of Bioengineering Shu Chien. 

The Stony Brook institute has created partnerships with other organizations, including Albert Einstein College of Medicine and Montefiore Medical Center.

“The more clinical people we engage, the better it is for the institute,” Sotiropoulos said.

As for the bionic spine, Kaushansky has familial experience with spinal injuries. His mother suffered through several spinal surgeries. “There’s a need for much, much better mechanical weight-bearing device that will help people with back problems,” he said.

At this point, Stony Brook has gone two-thirds of the way through the National Science Foundation process to receive a $10 million grant for this spinal cord research. Sotiropoulos suggested that a bionic spine could be “a game changer.”

While the institute will seek ways to create viable medical devices, diagnostics and even organs, it will also meet the educational mandate of the school, helping to train the next generation of undergraduate and graduate students. The school already has a program called Vertically Integrated Projects, or VIPs, in place, which offers students experiential learning over the course of three or four years. The effort combines undergraduates with graduates and faculty members to work on innovative efforts.

“These projects are interdisciplinary and are all technology focused,” Sotiropoulos said. “We bring together students” from areas like engineering, computer science and medicine, which “go after big questions,” and that the VIP efforts are structured to unite engineers and doctors-in-training through the educational process.

Through the institute, Stony Brook also plans to collaborate with other Long Island research teams at Cold Spring Harbor Laboratory and Brookhaven National Laboratory, Sotiropoulos said, adding that the scientists are “not just interested in doing blue sky research. We are interested in developing services, algorithms, practices, whatever it is, that can improve patient care and costs.”

Indeed, given the translational element to the work, the institute is encouraging a connection with economic development efforts at Stony Brook, which will enable faculty to create spin-off companies and protect their ideas. The institute’s leadership would like to encourage the faculty to “create companies to market and take to market new products and developments,” said Sotiropoulos.

Photos from SBU

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Mircea Cotlet. Photo courtesy of BNL

By Daniel Dunaief

An innovative scientist in the world of nanostructures, Mircea Cotlet recently scored Inventor of the Year honors from Battelle.

A principal investigator and materials scientist in the Soft and Bio Nanomaterials Group at the Center for Functional Nanomaterials at Brookhaven National Laboratory, Cotlet has conducted a wide range of research over his dozen years on Long Island.

The distinction from Battelle, which manages BNL through Brookhaven Sciences Associates, honors researchers who have made significant scientific or engineering contributions that have societal or financial impacts.

“The award recognizes [Cotlet’s] ongoing contributions to materials science at BNL, specifically his work on low-dimensional semiconductors, 1-D nanowires, and tiny 0-D nanocrystals called quantum dots,” Katy Delaney, a Battelle spokesperson, explained in an email.

Researchers who have worked with Cotlet believe he deserves the honor.

Cotlet is an “extraordinary scientist” who “stands out” for his thorough work and creative approach” said Deep Jariwala, an assistant professor in the Department of Electrical and Systems Engineering at the University of Pennsylvania. Jariwala has known Cotlet for over two years and has collaborated with him over the last year.

Cotlet has “really laid the foundational ground in understanding the rules that govern charge and energy transfer across hybrid quantum confined materials systems that comprise quantum dots, organic molecules–two-dimensional materials as well as biologically photoactive materials,” Jariwala added.

The technologies will impact the science and technologies of sensing, displays and energy harvesting in the future, Jariwala predicted.

Eric Stach, a professor in the Department of Materials Science and Engineering at the University of Pennsylvania who had previously worked at the CFN, said Cotlet “tries to figure out ways of putting together disparate systems at the nanoscale.”

By combining these materials, Cotlet is able to “improve the overall performance” of systems, Stach continued. “He’s trying to tune the ability of a given material system to capture light and do something with it.”

Cotlet recently partnered self-assembled two-dimensional nanoparticles, such as the one-atom-thick graphene, with light-absorbing materials like organic compounds.

The result enhances their ability to detect light, which could be valuable in medical imaging, radiation detection and surveillance applications. The mini-partnership boosted the photoresponse of graphene by up to 600 percent by changing the structure of the polymer.

Indeed, a defense contractor has shown an interest in research they could use for low light level detection applications, Cotlet said.

Like other scientists at BNL, Cotlet not only conducts his own research, but he also helps other scientists who come to the Department of Energy facility to use the equipment at the CFN, to make basic and translational science discoveries.

Cotlet patented a self-assembly process before he published it.

He is continuing conversations with a big company that is exploring the benefits of this type of approach for one of its product, while he is also working with the technology transfer office at BNL to look at the development of photodetectors for low light applications.

“Having graphene and the conductor polymer would absorb light from ultraviolet to visible light,” Cotlet said.

The physics changes from bulk to nanoparticles to nanocrystals, Cotlet said, and he engineers the smaller materials for a given function.

“We basically like to play with the interface between different types of nanomaterials,” he said. “We like to control the light-simulated process.”

Working at an energy department site, he also has experience with solar panels and with light-emitting diodes.

Jariwala described the science as extending to interfaces that also occur in nature, such as in photosynthesis and bioluminescence. “By combining techniques and materials that we have developed and looked at, we hope to answer fundamental mechanistic questions and provide insights into long-standing questions about biological energy conversion processes,” he wrote.

As far as some of the current materials he uses, Cotlet works on graphene and the transition metal dichalcogenides and he explores their potential application as quantum materials. He tries to look for emerging properties coming out of nanomaterials for various applications, but most of his efforts are in basic science.

Jariwala explained that he and Cotlet are seeking to understand the efficient transduction of energy in quantum sized systems when they are brought close to one another in an orderly fashion.

After his upbringing in Romania, where he attended college, Cotlet appreciated the opportunity to learn from one of the pioneering groups in the world in single-molecule microscopy at the Katholieke Universiteit Leuven in Belgium, where he studied for his doctorate.

He also did a fellowship at Harvard, where he worked on unique microscopy, and then went on to conduct postdoctoral work at Los Alamos National Laboratory, where he worked on protein folding and on optimal imaging methods.

Cotlet arrived at the CFN just as the facility was going online.

“The CFN went beyond its original promise for cutting edge science,” he said. The center has been, and he continues to hope it will be, the best place he could dream of to conduct research.

The postdoctoral researchers who have come through his lab have all been successful, either leading their own projects or joining commercial teams.

Up until he was 18, Cotlet wasn’t focused on science, but, rather, anticipated becoming a fighter pilot. He discovered, however, that he had a vision defect.

“All my childhood, I was set up to become a fighter pilot,” but the discovery of a condition called chromatopsy changed his plans.

A resident of Rocky Point, Cotlet lives with his wife, Ana Popovici, who is an administrative assistant at BNL, and their middle school daughter.

As for his future work, he is interested in building on the research into quantum materials.

“I’m looking forward to trying to integrate my research” into this arena, he said.

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