Science & Technology

Stony Brook’s LCM facility will use $3 million of NIH funding for equipment and structural upgrades

The Laboratory for Comparative Medicine (LCM) at the Renaissance School of Medicine at Stony Brook University has received a $3 million grant from the National Institute of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health (NIH) for facility upgrades and new instrumentation to support advanced research on virulent and emerging pathogens.

David Thanassi, PhD, Scientific Director of the LCM. Photo from SBU

The grant was in response to a call for “Emergency Awards: Biocontainment Facility Improvements and Building System Upgrades to Support Pandemic Preparedness” from the NIAID. The one-time NIH funding allotment will help support research on the current COVID-19 pandemic and future investigations centering on antiviral programs, antimicrobial approaches, and therapeutic measures to prevent or mitigate infectious disease outbreaks or future pandemics.

The LCM is engaged in basic, translational, and preclinical research on SARS-CoV-2, the viral agent of COVID-19, as well as other infectious agents. During the past five years, researchers at Stony Brook University have conducted work investigating three different RNA virus families relevant under the American Pandemic Preparedness efforts. In addition, the LCM is being used for research on tick-borne pathogens, which are critical to our area, and for studies on tuberculosis, a global infection.

“This award enables us to make infrastructure improvements and acquire new scientific instrumentation to expand our capabilities to perform research on highly pathogenic agents,” says David Thanassi, PhD, Principal Investigator, Scientific Director of the LCM, and Chair of the Department of Microbiology and Immunology. “This is truly a key step toward pandemic-preparedness and provides enhanced resources to not only Stony Brook researchers from multiple school of medicine and other scientific departments, but also state and regional investigators working to combat current and future pandemic threats.”

Stony Brook has a long history of conducting microbial pathogenesis research on emerging pathogens and those that cause common and widespread infection globally. The LCM is a biocontainment facility working on a variety of microbial agents, including viruses and bacteria. Research in the LCM serves multiple academic investigators and groups, as well as biotechnology companies, both within and outside of Stony Brook University.

 

Nikita Nekrasov. Photo by Nina Mikhailyuk

AIP and the American Physical Society has announced that Nikita Nekrasov as the recipient of the 2023 Dannie Heineman Prize for Mathematical Physics “for the elegant application of powerful mathematical techniques to extract exact results for quantum field theories, as well as shedding light on integrable systems and non-commutative geometry.”

The annual award acknowledges significant contributions to the field of mathematical physics and will be presented at an upcoming APS meeting.

Nikita Nekrasov. Photo by Nina Mikhailyuk

“We are so pleased to recognize Nikita Nekrasov with this award,” said Michael Moloney, CEO of AIP. “His work has taken abstract principles in mathematics and proved them essential for theoretical physics, building upon our fundamental knowledge of how the universe works — the pondering on which has been an inspiration to generations of scientists.”

Nekrasov, a professor at Stony Brook University’s Simons Center for Geometry and Physics and Yang Institute for Theoretical Physics, used techniques from topology to solve important problems in theoretical physics, namely, exactly calculating the effects of the strong force holding together nuclei.

Complex problems in quantum physics are often broken into two pieces: an explicit solution of a simpler system, and the analysis of a “perturbation” that reflects the small difference of a realistic model from that simple system. As an example, in a simplified picture, freely propagating particles occasionally meet and interact with other particles along their way. Having many successive interactions is less likely, which makes the perturbation terms mathematically manageable. However, some natural phenomena, such as the strong force, do not follow this rule and require a different approach.

“One needs better understanding of how to account for the effects of strong force,” said Nekrasov. “I found a class of theories for which this can be done exactly, but you have to bring in a novel type of mathematics: topology and non-commutative geometry.”

The mathematics can also be used for exactly solvable models describing many-body interactions, be it planets in the solar system, cold atoms, or electrons in a quantum Hall effect. Nekrasov discovered that, under the assumption of supersymmetry, the mathematics of strong interactions is the same as the mathematics describing many particles living on a line and interacting with some repulsive force.

“Instead of trying to visualize the quarks and gluons inside an atomic nucleus, which we cannot see directly, you could set up a laboratory with quantum wires, do some measurements, and then try to translate that result to the world of elementary particles,” Nekrasov said. “That’s the amazing fact about physics and mathematics. There are unexpected connections between different fields.”

A French-Russian national, Nekrasov grew up in Russia, where he became hooked on string theory and mathematical physics after reading a Scientific American article by Prof. Michael Green (recipient of 2002 Dannie Heineman Prize for Mathematical Physics). He earned his Ph.D. at Princeton University and completed a postdoctoral fellowship at Harvard University as a Junior Fellow at the Harvard Society of Fellows. After briefly returning to Princeton University as a Dicke Fellow, he became professor at the Institut des Hautes Études Scientifiques in France. Since 2013 he has been a professor at the Simons Center for Geometry and Physics and Yang Institute for Theoretical Physics at Stony Brook University.

“It’s an honor to receive this award, and in some sense, it’s a way to shake hands with a lot of my heroes, the people who inspired me in my work,” said Nekrasov.

Nekrasov hopes to continue connecting abstract mathematics to theoretical physics and is currently interested in finding applications of quantum field theory to number theory.

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ABOUT THE HEINEMAN PRIZE

The Heineman Prize is named after Dannie N. Heineman, an engineer, business executive, and philanthropic sponsor of the sciences. The prize was established in 1959 by the Heineman Foundation for Research, Education, Charitable and Scientific Purposes, Inc. The prize will be presented by AIP and APS on behalf of the Heineman Foundation at a future APS meeting. A special ceremonial session will be held during the meeting, when Nekrasov will receive the $10,000 prize. http://www.aps.org/programs/honors/prizes/heineman.cfm

ABOUT AIP

The mission of AIP (American Institute of Physics) is to advance, promote, and serve the physical sciences for the benefit of humanity. AIP is a federation that advances the success of our 10 Member Societies and an institute that operates as a center of excellence supporting the physical sciences enterprise. In its role as an institute, AIP uses policy analysis, social science, and historical research to promote future progress in the physical sciences. AIP is a 501(c)(3) membership corporation of scientific societies.

ABOUT AMERICAN PHYSICAL SOCIETY

The American Physical Society is a nonprofit membership organization working to advance and diffuse the knowledge of physics through its outstanding research journals, scientific meetings, and education, outreach, advocacy, and international activities. APS represents more than 50,000 members, including physicists in academia, national laboratories, and industry in the United States and throughout the world. https://www.aps.org/

Electrons, shown as red dots above, collide with an ion. Such a collision will reveal the internal structure of the quarks and gluons that are the building blocks of the proton and neutron. Image from BNL

National labs, including Brookhaven National Laboratory, received considerable additional funds as a part of the federal Inflation Reduction Act.

BNL, which will get an additional $224 million over a five-year period, will collect the additional funding from the Department of Energy’s Office of Science to support several projects designed

In a statement, Secretary of Energy Jennifer Granholm called the additional funds for energy-related research and support, which total $1.5 billion, “one of the largest ever investments in national laboratory infrastructure” and suggested that the effort would “develop advanced energy and manufacturing technologies we need to advance the frontiers of science and tackle tomorrow’s challenges.”

At BNL, the Electron-Ion Collider, an enormous project that will start construction in 2024 and should start running experiments in the early part of the next decade, will receive $105 million.

BNL is building the EIC in partnership with the Thomas Jefferson National Accelerator Facility in Virginia, which will also receive $33 million for work towards the new facility.

As its name suggests, the EIC will collide electrons and protons or heavier atomic nuclei and hopes to make numerous discoveries, including providing an understanding of how the energy from quarks and gluons provides the mass of a proton.

Additionally, the EIC will provide advances in health and medicine, national security, nuclear energy, radioisotope production and industrial uses in particle beams. Research on the technologies that will become a part of the EIC will advance the development of magnets and other particle accelerator parts. These advances could lead to energy efficient accelerators, shrinking the size and costs of future accelerators, which could attack cancer cells, design solar cells and batteries and develop drugs and medical treatments.

While the additional funds will help advance the development of the EIC, the total cost is considerably higher, at an estimated $1.7 billion to $2.8 billion.

Beamlines

Additionally, the Office of Science will provide $18.5 million to speed the creation of three new beamlines at the National Synchrotron Light Source II.

The NSLS II already has a host of beamlines that enable researchers from around the world to study the structure of batteries as they are operating, catalysts that help tap into energy sources, and biologically active molecules that could play a role in understanding basic biochemistry or that could lead to the development of drugs.

The new beamlines, which, like others at the NSLS II, have three-letter abbreviations. The ARI will provide a complete picture of the electronic structure of a sample, particularly in connection with temperature, chemical, structural and atomic variation.

ARI will help understand and control the electronic structure of next generation quantum materials.

CDI, meanwhile, will explore the condensed matter macroscopic and microscopic physical properties of matter, including the solid and liquid phases that arise from electromagnetic forces between atoms. CDI is in its final stages of its design.

The SXN will provide element access from carbon to sulfur. The beamline will offer measurements of different signals, such as X-ray fluorescence and total electron yield absorption, which is important in catalysis, condensed matter physics and environmental science.

The DOE is also providing $20 million for five Nanoscale Science Research Centers. The Center for Functional Nanomaterials is leading the effort to revitalize the nanoscience infrastructure.

The funds will accelerate the acquisition, development and installation of five instruments, which will advance research in fuel cells, solar cells and other materials that are part of the country’s efforts to develop cleaner forms of energy.

A/C and Heating

BNL will receive $33 million to support an upgrade to the ATLAS detector at the Large Hadron Collider in Europe’s CERN laboratory. The upgrades will enable a high-energy particle detector to make use of increased particle collision rates.

The lab, which focuses on energy research, will also receive $14.5 million towards infrastructure improvements that will increase the efficiency in distributing electricity and heating and air conditioning in labs throughout the facility.

Finally, the lab will receive $1 million to develop instrumentation for a nuclear physics experiment that seeks to find neutrinoless double beta decay, which is led by the Lawrence Livermore National Laboratory.

BNL Lab Director Doon Gibbs described the funding as an investment in the nation’s innovation-based economy.

The funding will support “research with direct impact on the development of clean energy technologies as well as ground-breaking basic research in nuclear and high-energy physics — fields that could lay the foundation for future advances,” Gibbs said in a statement.

Arkarup Banerjee. Photo ciourtesy of CSHL

By Daniel Dunaief

Brain cells don’t always have easily discovered roles, the way various instruments do in an orchestra.

Sometimes, different cells share a function, making it possible to perform various tasks or to process information from the environment, while other times, different cells play their own part in making it possible for an organism to optimize its circuitry to act and react on the world.

So it is for the tufted and mitral cells of land based vertebrates, which are part of the olfactory system, sending signals to the brain about the odors and triggering thoughts about moving towards a desired food or away from the scent of a predator. In many studies, the names have been used interchangeably, as scientists were not sure how to separate them.

Florin Albeanu. Photo courtesy of CSHL

Researchers have spent considerable time studying mitral cells, which project into a region of the brain called the piriform cortex. These cells are nicely organized into one layer, which makes them easy to identify and are bigger in size compared to tufted cells.

Mitral cells, which have been the celebrated stars of the olfactory system, are easier to see and sort out than their nasal cousins, the tufted cells which, by contrast, are slightly smaller.

Recently, two scientists at Cold Spring Harbor Laboratory, Florin Albeanu, an Associate Professor, and Arkarup  Banerjee, an Assistant Professor, published a study that suggested there’s more than meets the eye, or, maybe, the nose, with these tufted cells.

Tufted cells, it turns out, are better at recognizing smells than mitral cells and are critical for one of two parallel neural circuit loops that help the brain process different odor features, according to a study the scientists published in the journal Neuron at the end of September.

“People had assumed mitral cells were very good at” differentiating odor, but “tufted cells are better,” Albeanu said. “How they interact with each other and what the mitral cells are computing in behaving animals remains to be seen.”

Albeanu and Arkarup, who had performed his PhD research in Albeanu’s lab before returning to CSHL in 2020, exposed mice to different odors, from fresh mint to bananas and at different concentrations. They chose these compounds because there are no known toxic effects. The scientists also screened for compounds that elicited strong responses on the dorsal surface of the olfactory bulb that they could access using optical imaging tools.

It is hard to distinguish mitral and tufted cells when doing recordings. Optical imaging, however, enabled them to see through layers and shapes, if they were recording activity in a particular type of cell.

So, Albeanu asked rhetorically, “why is this exciting?”

As it turns out, these two types of cells project to different regions of the brain. Mitral cells travel to the piriform cortex, while tufted cells travel to the anterior olfactory nucleus.

It appears at this point that tufted cells are more likely to share information with other tufted cells, while mitral cells communicate with other mitral cells, as if the olfactory system had two parallel networks. There may yet be cross interactions, Albeanu said.

Mitral cells may be part of a loop that helps enhance and predict smells that are important for an animal to learn. Tufted cells, however, appear superior to mitral cells in representing changes in odor identity and intensity. By flagging the tufted cells as sources of olfactory information, the researchers were able to suggest a different combination of cells through which animals detect smells.

“A large fraction of people in the field would expect that mitral cells and the piriform complex are representing odor identity more so than the tufted cells and the anterior olfactory nucleus, so this is the surprise,” Albeanu explained in an email. Thus far, the reaction in the research community has been positive, he added. 

Throughout the review process, the researchers encountered natural skepticism.

“It remains to be determined how the findings we put forward hold when mice are engaged in odor trigger behavior” as odors are associated with particular meaning such as a reward, an lead to specific actions,” Albeanu explained. “This is what we are currently doing.”

Albeanu added that a few different streams of information may be supported by tufted and mitral cells, depending on the needs of the moment.

Arkarup Banerjee. Photo ciourtesy of CSHL

The study that led to this work started when Banerjee was a PhD student in Albeanu’s lab. Albeanu said that a postdoctoral fellow in his lab, Honggoo Chae, provided complementary work to the efforts of Banerjee in terms of data acquisition and analysis, which is why they are both co-first authors on the study.

For Banerjee, the work with these olfactory cells was an “echo from the past,” Albeanu added. 

As for where the research goes from here, Albeanu said future questions and experiments could take numerous approaches.

Researchers are currently looking for markers or genes that are expressed specifically and differentially in mitral or tufted cells and they have found a few potential candidates. While some markers have been found, these do not sharply label all mitral only versus all tufted cells only.

One of the confounding elements to this search, however, is that these cells have subtypes, which means that not every mitral cell has the same genetic blueprint as other mitral cells.

Another option is to inject an agent like a virus into the piriform cortex and assess whether boosting or suppressing activity in that region in the midst of olfaction alters the behavioral response.

Additionally, researchers could use tools to alter the activity of neurons during behavior using optogenetic approaches, inducing or suppressing activity with cell type specificity and millisecond resolution.

Albeanu would like to test speculation about the roles of these cells in action, while a mice is sampling smells he presents.

By observing the reactions to these smells, he could determine an association between rewards and punishment and anything else he might want to include.

The upshot of this study, Albeanu said, is that an objective observer would have much less trouble extracting information about the identity and intensity of a smell from a tufted cell as compared with a mitral cell.

Tufted cells had been “slightly more mysterious” up until the current study.

Commemorating the start of construction for the Science and User Support Center from the U.S. Department of Energy and Brookhaven Lab are (from left) Joe Diehl, Caroline Polanish, Robert Gordon, Geri Richmond, Doon Gibbs, Chris Ogeka, Tom Daniels, Peggy Caradonna, Andrea Clemente, and Gary Olson. Photo from BNL

Construction is underway for the newest facility at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory. The Science and User Support Center (SUSC) is the first building for the planned Discovery Park, a development the Laboratory is pursuing near its entrance along William Floyd Parkway.

The three-story, 75,000-square-foot facility will serve as a welcome center for the 75-year-old Brookhaven Lab, which is home to seven Nobel Prize-winning discoveries and hosts thousands of guests annually. The SUSC will also offer conference and collaboration areas for scientists as well as office space for the Lab‘s support staff.

Officials from DOE and Brookhaven Lab commemorated the start of construction during a groundbreaking ceremony Wednesday, Oct. 26.

DOE’s Under Secretary of Science and Innovation Geri Richmond said, “This strategy—of welcoming the community to be part to our nationallaboratories and focusing on creative, innovative ways for public-private partnerships to strengthen the economy—is so important. This is a centerpiece, a catalyst for the campus and for the future.”

Manager of DOE’s local Brookhaven Site Office, Robert Gordon, said, “This is transformative for Brookhaven National Laboratory. We should be accessible. We’ve done that with our words and our actions. Now we’re doing it with concrete.”

Brookhaven Lab Director Doon Gibbs said, “This construction is a milestone in the Laboratory‘s long-term strategy to revitalize its physical plant. We look forward to welcoming visitors, users, students, and members of the community to connect with Brookhaven, the DOE, our science, and the impact it has.”

Plainview-based E.W. Howell is leading construction as the project’s general contractor. The Laboratory announced in February that it awarded E.W. Howell a $61.8 million contract to build the SUSC. DOE approved a total cost of $86.2 million for the project. E.W. Howell and BrookhavenLab are targeting 2024 for construction to be completed.

The SUSC is the first building planned for Discovery Park, a new vision for Brookhaven Lab‘s gateway with approximately 60 acres of previously used, publicly accessible land. The Laboratory is working with DOE on a process for developers, collaborators, and entrepreneurs to propose, build, and operate new facilities that could complement DOE and Brookhaven Lab‘s missions and leverage opportunities from close proximity to the Laboratory.

Empire State Development is supporting Brookhaven Lab‘s efforts for Discovery Park with a $1.8 million capital grant, recommended by the Long Island Regional Economic Development Council.

The future Science and User Support Center. Rendering courtesy of BNL

Increasing Efficiency for Discoveries, New Technology

Brookhaven Lab attracts scientists from across the country and around the world by offering expertise and access to large user facilities with unique capabilities.

Brookhaven hosted more than 4,400 in-person and virtual scientists from universities, private industry, and government agencies in fiscal year 2021. In the years before the COVID-19 pandemic, more than 5,000 guests and facility users visited each year. The Laboratory expects the number of guests researchers to increase in the coming years, particularly as capabilities expand at the National Synchrotron Light Source II—a DOE Office of Science User Facility—and with the design and construction of the future Electron-Ion Collider.

The SUSC, when complete, is where those guests will arrive. The SUSC will also help improve the guests’ experiences of visiting Brookhavenbecause the Laboratory will consolidate a number of guest services into a central, modern building close to the site entrance.

The SUSC will also feature reconfigurable conference space, designed in response to requests from facility user communities to create opportunities for scientists to collaborate.

In addition, the SUSC will help the Laboratory increase efficiencies by reducing its building footprint atop the 5,322-acre site. The Laboratory plans to relocate approximately 225 staff at the SUSC. They are currently spread across the Lab site, which contains 314 buildings—some that date back to the World War II era, when the Laboratory was the site of the Army’s former Camp Upton.

The SUSC project is funded by the DOE Office of Science.

Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit science.energy.gov.

Mercy Baez. Photo by Joseph Rubino/ BNL

By Daniel Dunaief

She is a greeter, a corporate concierge, a facilitator, a point of contact for people traveling thousands of miles, a Spanish translator, an important contact in case of emergencies, and whatever else visitors need.

While Mercy Baez, who was promoted to User Program Coordinator for the National Synchrotron Lightsource II and the Laboratory for BioMolecular Structure at Brookhaven National Laboratory early in October, wears many hats, one of the only ones she doesn’t wear is scientist, although that doesn’t keep her from appreciating and taking pride in the research conducted at the Department of Energy facility.

“We’re helping them and they are helping the world,” Baez said.

BNL has a steady stream of users who apply for time at the various research facilities at the national laboratories. 

Baez is specifically responsible for providing a wide range of support and services to the NSLS II and the LBMS. Users, which is how BNL describes potential visiting scientists who conduct research at the lab’s facilities, submit proposals to her office, which then distributes them to a proposal review panel.

When visiting scientists learn that their work, which includes monitoring batteries as they function and searching for fine structural sites in the molecular battle against pathogens, has earned a high enough score to receive coveted time on the lab’s instruments, they prepare for their visit by interacting with Baez and her current team of four by getting registered and approved for access.

Baez offers soup to nuts guidance that often also includes helping users literally find soup, nuts and numerous other items. Baez ensures that users take any necessary training courses, provides guidance regarding registering for on site access to BNL, provides information on the steps or items necessary when they arrive, helps find nearby hotels, coordinate travel to and from the lab and, if necessary, secures places to stay if they miss their planes, get snowed in or have other unforeseen changes in their schedules.

As of October 1st, visitors also have to have some type of active shooter training to access the lab’s facilities. Currently, users are required to take five training courses. Last week, the lab decided to incorporate active shooter training into one of these other training courses.

The lab has always had routine emergency training courses and drills for lab employees. With the changing times and current events, the lab is looking to equip users for such emergencies. The lab hopes never to have to use this training, but if such an event occurs, staff and users will know how to handle such a situation.

In addition to training to help users prepare to visit the facility, Baez provides visitors with a host of on site facilities, including adaptors in case they are using European electronics that don’t connect with the outlets, laptops in case the computer a scientist brought isn’t working, conference rooms for impromptu meetings, and dorm rooms for a respite while running time-intensive experiments.

BNL hosts employee resource groups including the African American Advancement Group, the Asian Pacific American Association, the Brookhaven Veterans Association, Brookhaven Women in Science, the Early Career Resource Group, the Pride Alliance and the Hispanic Heritage Group. Baez said the lab tries to involve users and visitors in as many cultural and social events as possible, which include outings to dinners, plays and cultural virtual cooking classes.

In September, Baez participated in the Port Jefferson Dragon Boat Race Festival which the Asian Pacific  American Association sponsored. 

Baez, whose mother is from Puerto Rico and whose father is from Ecuador, is a member of the Hispanic Heritage Group.

A people person

A member of the user offices since 2003, Baez had recently been responsible for coordinating conferences, workshops, and training courses, including financial and logistical aspects of the events for NSLS-II and the LBMS. She had been functioning as the user program coordinator since January, when Gretchen Cisco retired. Baez feels fortunate to have worked with Cisco since she joined NSLS in 2005.

A self-described “people person,” Baez said she loves the opportunity to interact with scientists from all over the world. She particularly appreciates the chance to get to know about other cultures and has added destinations to her travel itinerary from speaking with visitors. She is hoping to travel to Morocco and Peru next year and is hoping to travel to Japan and a few other countries in the near future.

Coming from a Latina family that tends to be loud and outspoken and whose family gatherings often includes more than 30 people, she has learned to speak in a softer voice, particularly with people from other cultures or backgrounds.

She also has a tendency to speak quickly and has learned to slow the pace down so visitors who haven’t interacted with her can understand what she’s saying.

A resident of Medford, which is a ten-minute drive from the lab, Baez has a son Xzavier and a granddaughter Francesca. She is excited for the upcoming arrival of her second granddaughter in November.

When she’s not at the lab, she uses her leisure time to go hiking, fishing and camping.

With her then teenage son in tow, she went to the jungle of Belize for a survival course, where they learned how to catch their own food, build shelters, and harpoon fish. She also learned which plants are safe to eat and which are poisonous.

While her work responsibilities can be hair-raising, particularly in emergencies, she “loves the feeling that I was able to help a scientist, whether to get him or her on site or in an emergency,” she said. Knowing that she’s a part of making all this science happen makes her day and job rewarding, she said.

Baez has had some requests from scientists who have wanted cultural foods, such as Turkish or vegan dishes, that might be harder to find, particularly during off hours.

Around Thanksgiving each year, some visitors have asked if they can hunt wild turkeys at BNL, which is located within the Pine Barrens and has turkeys and deer wandering on site. She has told those users that the lab does not allow hunting.

Hunting aside, Baez said she is “here to help [users] do what they need to do.”

From left, K. Barry Sharpless and John Moses. Photo from CSHL

By Daniel Dunaief

K. Barry Sharpless changed John Moses’s life. And that’s before Moses even started working as a postdoctoral researcher in Sharpless’s lab.

When Moses, who is the first chemist to work at Cold Spring Harbor Laboratory in its 132-year history, was earning his PhD in chemistry at Oxford, he read an article that Sharpless co-authored that rocked his world.

Nicknamed the “click manifesto” for introducing a new kind of chemistry, the article, which was published in Angewandte Chemie in 2001, was “one of the greatest I’ve ever read,” Moses said, and led him to alter the direction of his research.

Moses walked into the office of the late chemist Sir Jack Baldwin at Oxford, who was Moses’s PhD advisor, and announced that Sharpless, a colleague of Baldwin’s at the Massachusetts Institute of Technology, was the only chemist he wanted to work with in the next phase of his career.

Baldwin looked at Moses and said, in a “very old-fashioned gangster English, ‘That shows you’ve got some brains,’” recalled Moses.

Sharpless was important not only to Moses’s career, but also to the world.

Recently, Sharpless, who is the W.M. Kepp Professor of Chemistry at Scripps Research, became only the fifth two-time recipient of the Nobel Prize.

Sharpless will share the most recent award, which includes a $900,000 prize, with Carolyn R. Bertozzi, the Anne T. and Robert M. Bass Professor in the School of Humanities and Sciences at Stanford University, and Morten P. Meldal, professor at the University of Copenhagen, for the invention of a type of chemistry that has implications and applications from drug discovery and delivery, to making polymers, to developing anti cancer treatments.

The way click chemistry works is that chemists bring together catalysts and reagents, often attached to sulfur or carbon, that have a high level of specific attraction for each other. The click is like the sound a seat belt makes when secured, or the click a bike helmet lock makes when the two units are connected.

Scientists have often described the click reaction as being akin to LEGO blocks coming together, with an exact and durable chemical fit.

Natural product synthesis is generally challenging and often requires complex chemistries that are not always selective. This type of chemistry can produce side reactions that create unwanted byproducts and require purification.

Click reactions, by contrast, are selective and reliable and the products are generally easy to purify. Sometimes, purification is as simple as a water wash.

“It’s a democratization of synthetic chemistry,” Moses said.

Moses said biologists have performed click reactions. Chemists have developed click tablets that can be added to a reaction to create a plug and play system.

Moses described the reactions in click chemistry as “unstoppable” and suggested that they are part of a “domino rally” in which a latent build up of reactivity can create desired products with beneficial properties.

Moses, who arrived at CSHL in 2020, has collaborated with several researchers at the famed lab. He is submitting his first collaborative paper soon with Dr. Michael Lukey, who also started in 2020 and performed his PhD at Oxford, and Dr. Scott Lyons. He is also working on a New York State Biodefense funded project to create shape shifting antibiotics that can keep up with drug resistance pathogens. 

He has collaborated with Cancer Center Director David Tuveson to develop a new ligand to target a protein important in pancreatic cancer. Moses said they have a “very exciting” lead compound.

Early resistance

While the Nobel Prize committee recognized the important contribution of this approach, the concept met with some resistance when Sharpless introduced it.

“When [Sharpless] submitted this, the editor called colleagues and asked, ‘Has Barry gone crazy?’” Moses said.

Some others in the field urged the editor to publish the paper by Sharpless, who had already won a Nobel Prize for his work with chirally catalyzed oxidation reactions.

Still, despite his bona fides and a distinguished career, Sharpless encountered “significant resistance” from some researchers. “People were almost offended by it” with some calling it “old wine in new bottles,” Moses said.

In 2007, Moses attended a faculty interview at a “reasonably good” university in England,. where one of his hosts told him that click chemistry is “just bulls$#t!”

Moses recognized that he was taking a risk when he joined Sharpless’s lab. Some senior faculty advised him to continue to work with natural product synthesis.

In the ensuing years, as click chemistry produced more products, “everyone was using it and the risks diminished quickly,” Moses added.

Unique thought process

So, what is it about Sharpless that distinguishes him?

Moses said Sharpless’s wife Janet Dueser described her husband as someone who “thinks like a molecule,” Moses said.

For Moses, Sharpless developed his understanding of chemistry in a “way that I’ve never seen anyone else” do.

Moses credits Dueser, who he described as “super smart,” with coining the term “click chemistry” and suggested that their partnership has brought together his depth of knowledge with her ability to provide context.

Moses believes Sharpless “would admit that without [Dueser], his career would have been very different! In my opinion, [Dueser] contributed immeasurably to click chemistry in so many ways.”

Indeed, click chemistry won a team prize from the Royal Society of Chemistry last year in which Dueser was a co-recipient.

As for what he learned from working with a now two-time Nobel Prize winner, Moses said “relinquishing control is very powerful.”

Moses tells his research team that he will never say “no” to an innovative idea because, as with click chemistry, “you never know what’s around the corner.”

Moses said Sharpless is a fan of the book “Out of Control” by Kevin Kelly, the co-founder of Wired Magazine. The book is about the new biology of machines, social systems and the economic world. Sharpless calls Kelly “Saint Kevin.”

On a personal level, Sharpless is “humble and a nice person to talk to” and is someone he would “want to go to a pub with.”

Moses believes Sharpless isn’t done contributing to chemistry and the world and anticipates that Sharpless, who is currently 81 years old, could win another Nobel Prize in another 20 years.

An inspirational scientist, Sharpless ” is “that kind of person,” Moses said.

Peter Westcott, on right, in the lab with technicians Zakeria Aminzada, on left and Colin McLaughlin, center. Photo by Steven Lewis

By Daniel Dunaief

When Peter Westcott was growing up in Lewiston/Auburn, Maine, his father Johnathan Harris put the book “Human Genome” on his bed. That is where Westcott, who has a self-described “obsessive attention to detail,” first developed his interest in biology.

Westcott recently brought that attention to detail to Cold Spring Harbor Laboratory, where he is an assistant professor and Cancer Center member. He, his wife Kathleen Tai and their young children Myles and Raeya moved from Somerville, Massachusetts, where Westcott had been a postdoctoral fellow at the Koch Institute of Integrative Cancer Research at the Massachusetts Institute of Technology.

Westcott will take the passion and scientific hunger he developed and honed to the famed lab, where he plans to continue studies on colon cancer and the immune system.

“A lot of things attracted me to Cold Spring Harbor Laboratory,” said Westcott who had been to the lab during conferences, joining three Mechanisms and Models of Cancer meetings, and appreciated that the small size of the lab encourages collaboration and the sharing of ideas across disparate fields.

At this point, Westcott, who purchased a home in Dix Hills and started on campus on September 1st, has two technicians, Zakeria Aminzada and Colin McLaughlin working with him. He will be taking on a graduate rotation student from Stony Brook University soon and would also like to add a postdoctoral researcher within about six months. He plans to post ads for that position soon. 

Research directions

Westcott said his research has two major research directions.

The first, which is more translatable, involves looking at how T cells, which he described as the “major soldiers” of the immune system, become dysfunctional in cancer. These T cells balance between attacking unwanted and unwelcome cells relentlessly, disabling and destroying them, and ignoring cells that the body considers part of its own healthy system. When the T cells are too active, people develop autoimmunity. When they aren’t active enough, people can get cancer.

“Most cancers, particularly the aggressive and metastatic ones, have disabled the immune response in one way or another, and it is our focus to understand how so we can intervene and reawaken or reinvigorate it,” he explained.

During cancer development, T cells may recognize that something on a tumor is not healthy or normal, but they sometimes don’t attack. Depending on the type of genetic program within the T cells that makes them tolerant and dysfunctional, Westcott thinks he can reverse that.

A big push in the field right now is to understand what the genetic programs are that underlie different flavors of dysfunction and what cell surface receptors researchers can use as markers to define T cells that would allow them to identify them in patients to guide treatment.

Westcott is taking approaches to ablate or remove genes called nrf4a 1, 2 and 3. He is attacking these genes individually and collectively to determine what role they play in reducing the effectiveness of the body’s immune response to cancer.

“If we knock [some of these genes] out in T cells, we get a better response and tumors grow more poorly,” he said.

Westcott is exploring whether he can remove these genes in an existing T cell response to cause a regression of tumor development. He may also couple this effort with other immunotherapies, such as vaccines and agonistic anti-CD40 antibody treatment.

As a second research direction, Westcott is also looking more broadly at how tumors evolve through critical transitions. Taking an evolutionary biology perspective, he hopes to understand how the tumors start out as more benign adenoma, then become malignant adenocarcinoma and then develop into metastatic cancer. He is focusing in particular on the patterns of mutations and potential neoantigens they give rise to across the genome, while concentrating on the immune response against these neoantigens.

Each tumor cell is competing with tumor cells with other mutations, as well as with normal cells. “When they acquire new mutations that convey a selective advantage” those cells dominate and drive the growth of a tumor that can spread to the rest of the body, Westcott said.

Using a mouse model, he can study tumors with various mutations and track their T cell response.

T cells tend to be more effective in combating tumors with a high degree of mutations. These more mutated tumors are also more responsive to immunotherapy. Westcott plans to study events that select for specific clones and that might shift the prevalence, or architecture, of a tumor.

Some of the work Westcott has done has shown that it is not enough to have numerous mutations. It is also important to know what fraction of the cancer cells contain these mutations. For neoantigens that occur in only a small fraction of the total cells in the tumor, the T cell responses aren’t as effective and checkpoint blockade therapy doesn’t work.

He wants to understand how the T cell responses against these neoantigens change when they go from being subclonal “to being present in most or all of the tumor cells,” he explained. That can occur when a single or few tumor cells acquire a selective advantage. His hypothesis is that these selective events in tumor progression is inherently immunogenic. \

By exploring the fundamental architecture of a tumor, Westcott hopes to learn the mechanisms the tumor uses to evade the immune system.

Ocean breeze

As Westcott settles in at CSHL, he is excited by the overlap between what he sees around the lab and the Maine environment in which he was raised.

“Looking out the window to the harbor feels like New England and Maine,” he said. “It’s really nostalgic for me. Being near the ocean breeze is where I feel my heart is.”

Before his father shared the “Human Genome” book with him, Westcott was interested in rocks and frogs. In high school, his AP biology teacher helped drive his interest in the subject by encouraging discussions and participation without requiring her students to repeat memorized facts. The discussions “brought to life” the subject, he said.

As for his work, Westcott chose to study colon cancer because of its prevalence in the population. He also believes colon cancer could be a model disease to study all cancers. By understanding what differentiates the 12 percent of cases that are responses to immunotherapy from the remainder that don’t respond as well to such approaches, he hopes to apply these lessons to all cancer.

“There is a huge, unmet need,” he said.

Duckweed. Photo from BNL
Scientists drive oil accumulation in rapidly growing aquatic plants

Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory and collaborators at Cold Spring Harbor Laboratory (CSHL) have engineered duckweed to produce high yields of oil. The team added genes to one of nature’s fastest growing aquatic plants to “push” the synthesis of fatty acids, “pull” those fatty acids into oils, and “protect” the oil from degradation. As the scientists explain in a paper published in Plant Biotechnology Journal, such oil-rich duckweed could be easily harvested to produce biofuels or other bioproducts.

John Shanklin. Photo from BNL

The paper describes how the scientists engineered a strain of duckweed, Lemna japonica, to accumulate oil at close to 10 percent of its dry weight biomass. That’s a dramatic, 100-fold increase over such plants growing in the wild—with yields more than seven times higher than soybeans, today’s largest source of biodiesel.

“Duckweed grows fast,” said Brookhaven Lab biochemist John Shanklin [https://www.bnl.gov/staff/shanklin], who led the team. “It has only tiny stems and roots—so most of its biomass is in leaf-like fronds that grow on the surface of ponds worldwide. Our engineering creates high oil content in all that biomass.

“Growing and harvesting this engineered duckweed in batches and extracting its oil could be an efficient pathway to renewable and sustainable oil production,” he said.

Two added benefits: As an aquatic plant, oil-producing duckweed wouldn’t compete with food crops for prime agricultural land. It can even grow on runoff from pig and poultry farms.

“That means this engineered plant could potentially clean up agricultural waste streams as it produces oil,” Shanklin said.

Leveraging two Long Island research institutions

The current project has roots in Brookhaven Lab research on duckweeds from the 1970s, led by William S. Hillman in the Biology Department. Later, other members of the Biology Department worked with the Martienssen group at Cold Spring Harbor to develop a highly efficient method for expressing genes from other species in duckweeds, along with approaches to suppress expression of duckweeds’ own genes, as desired.

As Brookhaven researchers led by Shanklin and Jorg Schwender [https://www.bnl.gov/staff/schwend] over the past two decades identified the key biochemical factors that drive oil production and accumulation in plants, one goal was to leverage that knowledge and the genetic tools to try to modify plant oil production. The latest research, reported here, tested this approach by engineering duckweed with the genes that control these oil-production factors to study their combined effects.

“The current project brings together Brookhaven Lab’s expertise in the biochemistry and regulation of plant oil biosynthesis with Cold Spring Harbor’s cutting-edge genomics and genetics capabilities,” Shanklin said.

One of the oil-production genes identified by the Brookhaven researchers pushes the production of the basic building blocks of oil, known as fatty acids. Another pulls, or assembles, those fatty acids into molecules called triacylglycerols (TAG)—combinations of three fatty acids that link up to form the hydrocarbons we call oils. The third gene produces a protein that coats oil droplets in plant tissues, protecting them from degradation.

From preliminary work, the scientists found that increased fatty acid levels triggered by the “push” gene can have detrimental effects on plant growth. To avoid those effects, Brookhaven Lab postdoctoral researcher Yuanxue Liang paired that gene with a promoter that can be turned on by the addition of a tiny amount of a specific chemical inducer.

“Adding this promoter keeps the push gene turned off until we add the inducer, which allows the plants to grow normally before we turn on fatty acid/oil production,” Shanklin said.

Liang then created a series of gene combinations to express the improved push, pull, and protect factors singly, in pairs, and all together. In the paper these are abbreviated as W, D, and O for their biochemical/genetic names, where W=push, D=pull, and O=protect.

The key findings

Overexpression of each gene modification alone did not significantly increase fatty acid levels in Lemna japonica fronds. But plants engineered with all three modifications accumulated up to 16 percent of their dry weight as fatty acids and 8.7 percent as oil when results were averaged across several different transgenic lines. The best plants accumulated up to 10 percent TAG—more than 100 times the level of oil that accumulates in unmodified wild type plants.

Some combinations of two modifications (WD and DO) increased fatty acid content and TAG accumulation dramatically relative to their individual effects. These results are called synergistic, where the combined effect of two genes increased production more than the sum of the two separate modifications.

These results were also revealed in images of lipid droplets in the plants’ fronds, produced using a confocal microscope at the Center for Functional Nanomaterials [https://www.bnl.gov/cfn/] (CFN), a DOE Office of Science user facility at Brookhaven Lab. When the duckweed fronds were stained with a chemical that binds to oil, the images showed that plants with each two-gene combination (OD, OW, WD) had enhanced accumulation of lipid droplets relative to plants where these genes were expressed singly—and also when compared to control plants with no genetic modification. Plants from the OD and OWD lines both had large oil droplets, but the OWD line had more of them, producing the strongest signals.

“Future work will focus on testing push, pull, and protect factors from a variety of different sources, optimizing the levels of expression of the three oil-inducing genes, and refining the timing of their expression,” Shanklin said. “Beyond that we are working on how to scale up production from laboratory to industrial levels.”

That scale-up work has several main thrusts: 1) designing the types of large-scale culture vessels for growing the modified plants, 2) optimizing large-scale growth conditions, and 3) developing methods to efficiently extract oil at high levels.

This work was funded by the DOE Office of Science (BER). CFN is also supported by the Office of Science (BES).

Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit science.energy.gov. [https://www.energy.gov/science/]

Caroline Mota Fernandes Photo by Jonas Nascimento Conde

By Daniel Dunaief

Fungal infections represent a significant health risk for some patients, killing about 1.5 million people globally each year. Doctors struggle to provide medical help for some of these patients, especially those whose weakened immune systems offer insufficient protection against developing pathogens.

Invasive fungal infections, which people typically contract by inhaling them as spores, account for about half of all AIDS-related deaths.

Maurizio del Poeta, Distinguished Professor at the Renaissance School of Medicine at Stony Brook University, has been studying ways to boost the body’s defenses against these potentially deadly infections, even among people with weakened immunities.

Recently, Caroline Mota Fernandes, a postdoctoral researcher in del Poeta’s lab, published research in the journal mBIO, a publication of the American Society for Microbiology, that demonstrated that a heat-killed, mutated version of the fungus Aspergillus conveyed protection in an animal model of an immunocompromised individual.

“The biggest news is that we can simply use the ‘autoclaved’ mutated version,” explained del Poeta in an email. “This version cannot be more dead!”

An autoclave is like a scientific oven: it raises the temperature or pressure. In this case, it can kill the mutated fungus, leaving only the mutated signal that primes the immune system.

The mutated and heat-killed version of the fungus, however, still provided full protection in a condition in a model of a weakened immune system.

“That means this formulation is highly stable and resistant to heat degradation,” del Poeta added.

Del Poeta’s lab had conducted similar research with another fungus called Cryptococcus.

By demonstrating that this approach also works with Aspergillus, del Poeta said the result “validates the cryptococcal vaccine (after all, it uses a mutant of the homolog gene, Sg11 in Crypto and SglA in Aspergillus.”

It also shows that protection exists under an additional type of immunodepression that is different from the one used in the cryptococcal vaccine.

The encouraging results, while in the preliminary stages, are relevant not only for immunocompromised people in general, but also for those who have been battling Covid, as Aspergillus was the cause of death for many patients during the worst of the pandemic.

Homologous genes

Del Poeta’s lab has focused on genes that catalyze the breakdown of steryl glucosides, which scientists have also studied in the context of plants. Crops attacked by various fungi become less productive, which increases the need to understand and disrupt these pathways.

“Folks working with plants started observing that these molecules had some kind of immunomodulatory property,” said Fernandes. “That’s where the idea of this steryl glucosides, which also is medicating fungal virulence, came from.”

The mutation Fernandes studied removed the sterylglucosidase gene sglA. Without the enzyme that breaks up the steryl glucose, the fungus had less hypha, which are necessary for the growth of the fungus. The mutation also changed the cell wall polysaccharides. Mice vaccinated with this heat-killed mutation had a one hundred percent survival rate in response to exposure to the live fungus.

“What was a very great achievement of our work was getting 100 percent protection,” said Fernandes. For immunocompromised people for whom a live attenuated fungus might threaten their health, the effectiveness of the heat-killed mutation proved especially promising.

In the experiment, she administered the vaccine 30 days before exposure, while providing boosters as often as every 10 days.

Fernandes, who started her post doctoral research in del Poeta’s lab in 2018, said several questions remain. “After this study, we are going to try to characterize exactly how this strain induces the immunity and protection to a secondary challenge of Aspergillus,” she said. Dr. Veronica Brauer, another post doctoral researcher in del Poeta’s lab, is conducting this research.

At this point, it’s unclear how long protection against a fungal infection might last.

“For us to estimate the duration of the protection, we have to have a more specific understanding of which immune components are involved in the response,” said Fernandes.

As of now, the mice vaccinated with the mutated and heat-killed fungus had no off target effects for up to 75 days after vaccination.

Fernandes is also working to characterize the mechanism of action of a new class of antifungal drugs previously identified by the lab, called acylhydrazones. She hopes to identify a new virulence protein in Cryptococcus as well.

Collaboration origins

Fernandes, who was born and raised in Rio de Janeiro, Brazil, first worked in del Poeta’s lab in 2013, while she was conducting her PhD research at Federal University of Rio de Janeiro. She was studying antifungal peptides and explained to the Brazilian government why coming to Stony Brook would contribute to her research.

Fernandes started studying fungi when she was in her second year of college at Federal University of Rio de Janeiro.

The daughter of two chemists, Fernandes said she grew up in a house in which she had pH strips, which she used to test the acidity of shampoo, water and anything else she could test. She also entered numerous science fairs.

Fernandes met her husband Jonas Conde, who is a virologist at Stony Brook University and who has studied Covid-19, when they were in nearby labs during their PhD research.

Residents of Port Jefferson, Fernandes and Conde have a four-month-old son named Lucas.

Having a child “motivates me to be better in my work and to set an example for him to be committed in doing some good for other people,” Fernandes said.

Del Poeta described Fernandes as being “extremely effective” in managing her time and has “extraordinary motivation.” He appreciates her commitment to her work, which is evident in the extra papers she reads.

Fernandes appreciates being a part of del Poeta’s lab. She described him as an “amazing” researcher and supervisor and said being a part of his group is “an honor.”

Del Poeta said Fernandes will continue to make mutants for additional fungi, including Mucorales and Rhizopous, for which antifungal therapy is not particularly effective.

Del Poeta added that the urgency of this work remains high. With several other Stony Brook faculty, he has submitted grants to study Sgl1 as a vaccine and antifungal target.

“Imagine [making] a drug that not only can treat the primary infection, but, by doing so, can potentially prevent the recurrence of a secondary infection?” he asked rhetorically. “Exciting!”