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Krishna Veeramah. Photo by Dean Bobo

By Daniel Dunaief

People have left all kinds of signs about their lives from hundreds and even thousands of years ago. In addition to artifacts that provide raw material for archeologists, anthropologists and historians, they also left something modern science can explore: their genes.

Genetic information locked inside their bones can add to the dialogue by providing details about what regions people might have come from and when they arrived. A group that includes Krishna Veeramah, an assistant professor of primate genomics at Stony Brook University, is using genetic information, combined with archeological evidence, to gain a better understanding of the events in Europe immediately after the fall of the Roman Empire, between the fifth and sixth centuries.

“We want to test questions that integrate historical and biological information,” said Veeramah, who is working with a multinational team of scientists. “We want to integrate archeological information.”

This is a time period in which there is some disagreement among historians about what happened after the fall of the Roman Empire. Patrick Geary, the principal investigator on a project that traces early medieval population movements through genomic research, said that this period fundamentally changed not only the demographic makeup of the populations but also the social and political constellation of Europe. These scientists are hoping to contribute their analysis of the genetic material of 1,200 people from several cemeteries to a discussion of the history of the continent.

So, how does this work? Paleogenomic data offers information from hundreds of thousands to millions of positions along the genome, which are called markers or single-nucleotide polymorphisms. Looking at the markers in total, researchers can identify small but systematic genetic differences between groups. They hope to determine where an individual’s ancestors are from based on the bones they are studying. They can only come to these conclusions, Veeramah explained, once they have sampled large numbers of people from different geographic areas during that time period. The genetic differences he is seeing are extremely small. He uses enormous pools of data that can allow him to explore subtle patterns, which emerge at the group level.

While the notion of using the genetic code to contribute information to discussions about the movement of groups of people has its proponents and practitioners, Geary and Veeramah recognize the skepticism, alarm and misdirection that comes from exploring subtle genetic differences among various groups of people. “The application of genetics to the human past is dark,” Geary said, pointing to eugenics discussions. “That’s understandable. We are emphatically opposed to such previous misuses of genetic research.” Some scientists, Geary said, are also suggesting that genetic studies will replace manuscripts or other clues. “We need all types of information,” Geary said.

Indeed, in a cemetery in Hungary that contained about 45 graves, Veeramah is studying genetic differences between two graves that are oriented in another direction from the other adult-sized graves. These two graves don’t contain any grave goods and appear to have different construction. The initial genomic analysis of a subset of individuals suggest they have a genetic profile that is different from other members of the cemetery and may show more of a connection to modern people from southern Europe rather than northern and central Europe, like the rest of the samples. The way these two graves were arranged offers intriguing possibilities, Veeramah said. This may suggest that these individuals had a distinct biological identity, which could impact some aspects of their social identity. To reach any conclusions, he hopes to collect more data from more individuals.

Geary suggested the kind of work he and Veeramah are doing, along with partners in other countries, will offer insight into the different paths of men and women. When paleogenomics first arrived as a discipline, historians were slow to embrace it. At the 2008 American Historical Association’s annual meeting, Geary gave a talk at which about 10 people attended. In January, at the 2017 American Historical Association meeting in Denver, Veeramah will discuss how a study of the Lombards offers a framework for integrating history, archeology and genomics. The president of the American Historical Association invited Veeramah and has publicized the talk as a presidential panel.

“I do believe that paleogenomics has become an important aspect of archeological work, and that the newly developed procedures for sequencing and analyzing genetic material adds a whole new dimension to work on archeological sites,” Patrick Manning, the president of the AHA and a professor of world history at the University of Pittsburgh, wrote in an email. Veeramah’s “work on the Lombards addresses an important issue in the Germanic migrations throughout Europe, long debated and now with important new information.”

Veeramah arrived at Stony Brook University in 2014 and lives in Sound Beach. He grew up outside London in Dartford and attended the same secondary school as Mick Jagger. While he likes some of the Rolling Stones songs, he’s more of a Dizzee Rascal fan. Veeramah plans to have a lab installed by next summer, when he hopes to analyze bones from archeological sites shipped from Europe.

In the meantime, he will continue to analyze genetic information coming from partners in Europe. While Veeramah and others in the field have published papers in prestigious journals like the Proceedings of the National Academy of Sciences and Science, they have struggled to receive funding from American funding agencies at the same level as their European counterparts.

“It is somewhat surprising how far behind the U.S. has gotten in this area,” Veeramah said. European grants can be more adaptable and can put more value on multidisciplinary work. “This is a systematic issue for U.S. funding. I hope it will be addressed soon.”

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Raffaella Sordella. Photo from the laboratory of Raffaella Sordella

By Daniel Dunaief

Raffaella Sordella, whose lyrical name reflects her upbringing in Italy, takes the fight against cancer personally. That’s because she underwent surgery for a tumor in her pancreas a few years ago when she, her husband Manuel Barriola and their young daughters Victoria and Alicia were living in Boston.

“The past few years I have made friends with many people who share firsthand experience with cancer,” she recalled in an email. “I have witnessed their strength and courage and they have been an incredible source of inspiration for our work, especially at times when the glass looked half-empty.”

Indeed, while she fought cancer herself, Sordella and the lab she leads as an associate professor at Cold Spring Harbor Laboratory battle against the deadly disease every day. Recently, she made a discovery about a gene that has been among the most studied and carefully combed genetic regions of the human genome. A tumor suppressor gene, p53 protects against tumor growth. An increasing number of findings, however, point toward the possibility of p53 mutants that promote tumors.

In research published in eLife, Sordella found just such a mutant. Looking at a variation in which the gene is truncated, or cut short, a range of cancers can develop and can cause greater threats to a patient’s health. “Despite four decades and all these papers, this is completely new,” Sordella said.

As many as 10 to 15 percent of tumors of the pancreas, ovaries, melanoma, head and neck and small cell lung carcinoma have this truncated version of p53, according to Sordella. “If you have these mutations, your colon cancer tends to become more metastatic,” she said.

Sordella and her colleagues studied the signaling pathway that regulates the activity of this gene. They have found a path that may become a target for drugs. Her lab is in discussions with a pharmaceutical company to start clinical trials. Sordella suggested that this type of finding addresses the notion of individualized medicine, in which doctors and scientists search for the specific genetic regions that contribute to cancer, looking for ways to block them, turn them off or slow them down.

In this truncated version of p53, the genes are active in the mitochondria, or the powerhouse of the cell, where the energy molecule adenosine triphosphate, or ATP, is produced. Sordella is studying how this mutant p53 can affect metabolism.

“The result is exciting because it was so unexpected,” Scott Lowe, the chair of the Cancer Biology & Genetics Program at the Memorial Sloan Kettering Cancer Center, wrote in an email. “The current work shows that these mutations can act as an ‘accelerator’ of tumorigenesis as well.” Lowe was a co-author on the study, who described his lab’s contributions as providing human data on the prevalence of truncated mutations in p53 in human tumors.

Researchers have dedicated considerable effort to understanding the tumor microenvironment. They are seeking to understand what a cancer might need from its immediate surroundings. Scientists studying other diseases, such as fibrosis, tissue chronic injuries, Alzheimer’s and Parkinson’s are also dedicating considerable resources to understanding the microenvironment. The recent discovery has encouraged Sordella and her colleagues to explore the role of cancer cell metabolism, cancer cells and their interaction with the tumor microenvironment, while also exploring the druggability of downstream pathways. This form of the gene is interacting with cyclophilin D, which is an inner pore permeability regulatory. Cyclophilin D, as a result, could become the target for future drug treatments.

Lowe suggested that the “current study raises the possibility that cancers with truncating mutations in p53 would be susceptible to agents that block cyclophilin D,” but added that it “should be clear that this will require much further testing.” Still, he concluded that it “is exciting as the possibility of this approach was not previously appreciated.”

Sordella came upon the discovery of the role of this form of the gene by chance. The focus of her lab is to understand the mechanism of resistance in small cell lung cancers. She generated a model in which there was resistance to a particular inhibitor. When she conducted an expression profile, she found a shift in the molecular weight of p53. Cloning and sequencing the gene demonstrated an alternative splicing, or cutting, that nobody had described.

Sordella credits partners including Edward Kastenhuber, Marc Ladanyi and Lowe at Sloan Kettering with assisting in the analysis of the gene. Sordella appreciates the financial support of Swim Across America, an organization that raises money for cancer research and that has supported her research for several years. Swim Across America takes “great pride in each new finding as these are the building blocks for achieving the ultimate goal,” Daniel Cavallo III, the beneficiary chair of the Nassau-Suffolk Chapter of Swim Across America, wrote in an email. “All you need to do is speak with Dr. Sordella for a short time and it is so clearly evident just how passionate she is about her work,” Cavallo said. “Her hard work, dedication and commitment to the cause are extraordinary — this along with her achievements are part of why we continue to fund her research.”

As a child, Sordella said she had an interest in becoming a physicist. After witnessing the suffering and strain cancer inflicted on her family, including an uncle and grandfather who succumbed to the disease when she was 13, Sordella decided that battling this disease would be her mission. Her family, she said, instilled in her the sense of finding purpose beyond the accumulation of wealth and has established a foundation with the goal of caring for the elderly and promoting education. She hopes her work contributes to her family’s legacy. “Hopefully one day soon, I will be able to celebrate with them a new great victory in the fight against cancer,” she said.

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Athi Varuttamaseni. Photo couresty of BNL

By Daniel Dunaief

Athi Varuttamaseni is like an exterminator, studying ways pests can gain entry into a house, understanding the damage they can cause and then coming up with prevention and mitigation strategies. Except that, in Varuttamaseni’s case, the house he’s defending is slightly more important to most neighborhoods: They are nuclear power plants.

The pests he’s seeking to keep out or, if they enter, to expel and limit the damage, are cyberattackers, who might overcome the defenses of a plant’s digital operating system and cause a range of problems.

Varuttamaseni, an assistant scientist in the Nuclear Science & Technology Department at Brookhaven National Laboratory, started his career at BNL by modeling the failure of software used in nuclear power plant protection systems. Last year, he shifted toward cybersecurity. “We’re looking at what can go wrong with nuclear power plants” if they experience an attack on the control and protection systems, he said.

Varuttamaseni is part of a team that received a grant from the Department of Energy to look at the next generation of nuclear power plants, which are controlled and managed mostly by digital systems. A few existing plants are also looking to replace some of their analog systems with digital. “We asked what can go wrong if a hacker somehow managed to breach the outer perimeter and get in to control the system, or even if that is possible at all,” he said. By looking at potential vulnerabilities in the next generation of power plants, engineers can find a problem or potential problem ahead of time and can “go back to the drawing board to put in additional protection systems that could save the industry significant cost in the long run,” Varuttamaseni said.

Robert Bari, a physicist at BNL and a collaborator on the cybersecurity work, said Varuttamaseni, who is the lead investigator on the Department of Energy project, played “a major role” in putting together a recent presentation Bari gave at UC Berkeley that outlined some of the threats, impacts and technical and institutional challenges. The presentation included a summary and the next steps those running or designing nuclear power plants can take. Bari said it was a “delight” to collaborate with Varuttamaseni.

A colleague, Louis Chu, had recruited Varuttamaseni to work at BNL in another program, and Bari said he “recognized his abilities” and “we started to collaborate.” Varuttamaseni and Bari are going through a systematic analysis using logic trees and other approaches to explore vulnerabilities. The BNL team, which is collaborating with scientists at Idaho National Laboratory, shared the information and analysis they conducted with the Department of Energy and with an industrial collaborator.

In his second year of the work, Varuttamaseni said he is looking at the system level and is pointing out potential weaknesses in the design. He then shares that analysis with designers, who can shore up any potential problems. In the typical analysis of threats to nuclear power plants, the primary concern is of the release of radioactive material that could harm people who work at the plants or live in the communities around the facility.

Varuttamaseni, however, is exploring other implications, including economic damage or a loss of confidence in the industry. That includes the headline risk attached to an incident in which an attacker controlled systems other than a safety function and that are not critical to the operation of a plant. In addition to exploring vulnerabilities, Varuttamaseni is studying a plant’s response. Most of the critical systems are air-gapped, which means that the computer has no physical or wireless connection. While this provides a layer of protection against cyberattacks, it isn’t flawless or impenetrable. An upgrade of the hardware or patching of a hardware system might create just the kind of opening that would enable a hacker to pounce.

The Nuclear Regulatory Commission and the industry are “aware of those scenarios,” Varuttamaseni said. “There are procedures in place and mitigation steps that are taken to prevent those kinds of attacks.” Ideally, however, the power plant would catch any would-be attacker early in the process. Varuttamaseni is working on three grants that are related to systems at nuclear power plants. In addition to cyberattacks, he is also analyzing software failures in the protection system and, finally, he’s also doing statistical testing of protection systems.

Varuttamaseni, who was born in Thailand, lives in Middle Island. He appreciates that Long Island is less crowded than New York City and describes himself as an indoor person. He enjoys the chance to read novels, particularly science fiction and mysteries. He also likes the moderate weather on Long Island compared to Bangkok, although threats from hurricanes are new to him. Next June, Varuttamaseni will present a paper on cybersecurity at the American Nuclear Society’s Nuclear Plant Instrumentation, Control & Human-Machine Interface Technology Conference in San Francisco.

Varuttamaseni is “always on the lookout for insights into possible attack pathways that an attacker could come up with,” he said. “The mitigating factor of my work is that we’re looking at a longer-term problem. There’s still time to [work with] many of these potential vulnerabilities.”

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From left, Robert Catell, chairman of the board, Advanced Energy Research and Technology Center; Vyacheslov Solovyov; Sergey Gelman, a Stony Brook engineering student; and Yacov Shamash, vice president for economic development at Stony Brook University. Photo from Stony Brook University

By Daniel Dunaief

It’s lighter, cheaper and just as strong. In the age of manufacturing the latest and greatest high-technology parts, that is a compelling combination. Indeed, the Department of Energy recently awarded the Brookhaven Technology Group, a business incubator tenant of the Advanced Energy Research and Technology Center at Stony Brook University, $1.15 million to develop a high-temperature superconductor cable with a new architecture. The grant supports the research of Vyacheslav Solovyov, an adjunct professor in the Department of Electrical Engineering at SBU and the principal investigator at Brookhaven Technology Group.

“Very few projects are funded, so we’re very excited that ours was chosen,” said Paul Farrell, the president at BTG. The potential applications for Solovyov’s Exocable, as the new architecture is called, span a wide range of uses, including in high field magnets for a new breed of accelerator. The work entails creating a high-temperature superconducting cable that is an integral ingredient in creating the superconducting machinery. The BTG process produces a high-temperature superconducting cable after removing the substrate, which is a single-crystal-like material. Solovyov transfers the superconducting layer to a supporting tape that can be engineered for strength and not for crystallinity.

This work reduces the weight of the tape by as much as 70 percent per unit length for the same current capacity. The potential for this new cable is that it can contribute to the growing field of research at Stony Brook and Brookhaven National Laboratory on superconductivity, said Jim Smith, assistant vice president of economic development at Stony Brook. “Maybe this is the next industry that replaces the Grummans and the aerospaces that have left,” he said. Semiconductors are of particular interest to manufacturers because they transmit energy with no resistance. Right now, about 6.5 percent of energy transmitted around the United States is lost in distribution wires, Smith said. Maintaining the energy that’s lost in the wires would have “tremendous benefits.”

To be sure, while the research at BTG could contribute to lower cost and improved efficiency in high-temperature superconductivity, there are hurdles to making this process and the applications of it work. For starters, the company needs to produce kilometers of ExoCable. “The challenge is to demonstrate that the properties will be as uniform as they were before the substrate removal,” explained Solovyov, who has been working in superconductivity since 1986.

Recently, Smith said he, Farrell and Solovyov met to discuss the wiring for their facility. “A lot of power and wiring will be installed in the next four to five weeks,” Smith said. Scientists who worked with Solovyov expressed admiration for his work and optimism about his results. Solovyov’s “new activity will definitely advance the long-promised practical application of superconductivity electrical power transmission, as well as in the development of high-field magnets for both industrial and scientific application,” David Welch, a former collaborator and retired senior materials scientist at Brookhaven National Laboratory, wrote in an email. Welch explained that Solovyov focused on methods for making composites of superconducting material with normally conducting metals in the form of wires, tapes and cables necessary for their practical application. “Such a combination of talents is unusual,” Welch continued. Early on, it was clear “that [Solovyov] was going to become an important member of the scientific staff at BNL.”

Solovyov started working on this process with BTG about a year and a half ago. When he first started collaborating with BTG, the company was working on a superconducting project funded by the army. When that work ended, Solovyov and BTG worked together to submit new proposals to the DOE. According to Solovyov, Stony Brook has been “very helpful in terms of providing facilities and lab space.” Stony Brook’s goal, Smith said, is to help companies like BTG succeed and measures that success in the number of new jobs created in the energy field.

Solovyov, who grew up in the Ukraine, said he has had several breakthroughs in his career. He helped develop a patented technology that can speed up the processing of superconducting materials by a factor of 10. “That has been used in production and I’m very proud of it,” Solovyov said. The professor lives in Rocky Point with his wife Olena Rybak and their two children, Natasha, 19, who attends Suffolk County Community College, and Dennis, 14, who is in high school. Solovyov said he enjoys Long Island, where he can fish for striped bass and bluefish. He pan fries what he catches.

As for his work, Solovyov has four patents and applications for three more. He and Farrell said the company is looking for opportunities for expansion. He is exploring ways to work with large-scale generators and wind turbines. Farrell explained that BTG has ambitions to become a larger company. BTG would “like to become a major contributor in this field,” Farrell said. That could include adding staff and developing more products that can be sold and used worldwide. “If our product is successful, in the sense that it improves the capability of superconductors to be used commercially, we’ll be adding people.” This work will need more funding, which the company plans to get either from the Department of Energy, from private investors or both.

“If you can improve the usefulness of superconductors and reduce the cost of the wire, there’ll be wider use than there is right now,” Farrell said.

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Alfredo Fontanini in front of a poster of a neuron in his office. Photo from Alfredo Fontanini

By Daniel Dunaief

Pull into the parking lot of your favorite restaurant and you can almost taste the onion rings, the fresh baked bread or the steamed clams. The combination of the sign, the smell of the food piped out of the familiar building, and even the familiar voice of the restaurant owner welcoming you back is a hint of the experience of eating. Indeed, when these anticipatory stimuli are a part of the dining experience, they contribute to forming flavor.

Alfredo Fontanini, an associate professor in the Department of Neurobiology & Behavior at Stony Brook University, recently conducted research on rodents in which he explored how other senses — touch, taste, smell and sight — contributed to the part of the brain responsible for taste, the gustatory cortex.

In work published recently in the journal eLife, Fontanini demonstrated that rats who heard particular sounds, smelled odors, felt a puff of air against their whiskers, or saw the flash of an LED light before they ate showed increased activity in the gustatory cortex even before they started eating. If this experiment sounds familiar, it’s because Russian scientist Ivan Pavlov demonstrated the anticipation of food in conditioning experiments with dogs, showing that their digestive systems became active when they heard a tone before they ate, associating the sound with the presentation of food.

Dr. Alfredo Fontanini looks at slides of the gustatory cortex, the part of the brain that mediates the perception of taste. Photo from Stony Brook University
Dr. Alfredo Fontanini looks at slides of the gustatory cortex, the part of the brain that mediates the perception of taste. Photo from Stony Brook University

Fontanini took this research further, however, showing that the brain regions responsible for taste can, and did, show activity prior to eating. “As we paired the stimuli in a Pavlovian task, the animal would produce mouth movements and licks in response,” Fontanini said. These movements were not there right away, but developed after three to seven days of training, suggesting that the animal could infer taste. He recorded the responses of single neurons in the gustatory cortex. Before conditioning, the neuronal response in the gustatory cortex varied according to the sense stimulated. Prior to training, neurons in the gustatory cortex showed a 16 percent response, while that went up to 33 percent after learning. “This suggested that the stimulation was predictive of taste,” Fontanini said. “More neurons were integrating between all the stimuli.”

Donald Katz, a professor of psychology at Brandeis University who oversaw Fontanini’s graduate research for five years, suggested that his former student was one of a few neuroscientists studying how anticipation of an experience, knowing what’s coming, impacts how the brain handles that experience. This study, he explained in an email, “makes perfect sense — while few researchers study how different sensory systems work together, it is well-known that taste is linked to all of the other senses. It is of great evolutionary import that this be so,” because the animal that can recognize something good to eat at the greatest distance will be the one that eats.

Katz described Fontanini’s recent work as a “wonderful finding in that it provides a substantial, natural extension” to work completed in his lab, Katz’s lab and those of other scientists. In exploring which specific senses are most important to the gustatory reflex, Fontanini said olfaction and touch are considered more relevant for food-related decisions. “These are animals that use these senses to navigate their world and explore food,” he said.

In the bigger picture, Fontanini would like to understand how the brain integrates and fuses sensory perceptions with emotions. He explained that one of the tests in animal models of depression is to look at how much a test subject still likes something sweet. “Studying taste allows us to understand how the brain creates pleasure or creates aversion that negates emotions,” he said.

Fontanini plans to extend this study to additional research. He would like to know the neurological pathways that link the visual, auditory, somatosensory and olfaction senses that contribute to forming an expectation about taste. He is also eager to understand how the anticipatory activation influences the way taste is perceived. This, he explained, would be a way to explore how expectations shape perception.

Fontanini, who grew up in the town of Brescia, Italy, which is near Milan, arrived at this particular field of research because of his interest in understanding perception and emotion. He would like to explore how the brain creates emotions. Recognizing the multisensory element to taste and eating, Fontanini suggests that understanding how olfaction and taste can interact may lead to eating sweets where the smell enhances the flavor and taste, even of a lower-calorie dessert, like a piece of chocolate cake. “If you can leverage more of the odor and less” of the taste, “you can find a way of having that richness without the need for overwhelming sweetness.”

A resident of Setauket, Fontanini lives with his wife Arianna Maffei, who is an associate professor in the Department of Neurobiology & Behavior at Stony Brook and their 11-year-old son Carlo. Relying on vocabulary of the gustatory cortex, Fontanini suggested Long Island has a “soothing sweetness” that springs from the quaint and beautiful setting his family enjoys.

As for his work, Fontanini said studying taste in the brain is challenging. “What happens when you taste chocolate: are you activating chocolate neurons or are you activating a complex pattern of activity?” The answer, he said, describing taste while borrowing from another sense, is much more like a musical ensemble during a symphonic experience than like a solo. “Understanding how taste is represented in the cortex is incredibly complex,” he said.

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Front row, from left, Liliana Dávalos, Heather Lynch and Christine O’Connell; back row, from left, Robert Harrison, IACS director and STRIDE PI, Arie Kaufman, and Janet Nye. Photo from Stony Brook University

By Daniel Dunaief

If Stony Brook University has its way, the university will stand out not only for the quality of the research its graduate students produce but also for the way those budding scientists present, explain and interpret their results to the public and to policy makers.

Pulling together faculty from numerous departments across the campus, Robert Harrison, the director of the Institute for Advanced Computational Science, created a program that will teach graduate students how to use big data sets to inform difficult decisions.

The institute recently received a $3 million grant from the National Science Foundation Research Traineeship for this effort, called Science Training & Research to Inform DEcisions, or STRIDE. The grant will be used for students in the departments of Applied Mathematics and Statistics, Biomedical Informatics, Computer Science, Ecology and Evolution and the schools of Journalism and Marine and Atmospheric Sciences.

“This is unique,” said Arie Kaufman, a distinguished professor and chair of the Department Computer Science at Stony Brook. “It’s a new kind of approach to training and adding value to Ph.D. students.” Indeed, the students who complete the STRIDE training will earn their doctorates and will also receive a certificate for their participation in this program. Students in the participating departments will need to apply for one of the 10 positions available in the program next year. The partners involved in this program expect it to expand to 30 students within five years.

Kaufman said what enabled this collaboration was the range of skill sets across Stony Brook, including the Alan Alda Center for Communicating Science, which is a growing program that already offers the type of training more typical for an actor studying improvisation techniques than for a scientist studying neurotransmitters or DNA.

The Alda Center is “creating a new course,” said Christine O’Connell, an associate director at the center and assistant professor in the School of Journalism. She is currently working on developing the course description, which will include communicating to decision makers. O’Connell, who has a doctorate in marine and atmospheric sciences, sees her work with the Alda Center and with STRIDE as the “perfect combination in bringing the decision making piece to work with scientists to help them talk about their research.”

Scientists who take courses at the Alda Center with STRIDE learn how to understand their audience through various role-playing scenarios. They will also develop their abilities to present their goals or messages in a visual way and not just talk about their work.

Heather Lynch, an associate professor in the Department of Ecology and Evolution who is also a co-principal investigator on the STRIDE grant, will help design the program, mentor students and develop courses. She’s been involved with this proposal since its inception, over three years ago. “In many ways,” she explained in an email, “my interest stems from my own difficulties communicating effectively with policy makers, and finding tools and visualizations that are compelling to a non-scientist.” Lynch recounted her frustration with presenting science to help a policy making body, such as a committee, with the kind of analysis she believed they were seeking. After she did her best to answer the question, the committee sometimes dismissed her work as not being what they wanted. “That’s frustrating because that means I failed at the outset to define the science question and that’s what I hope we can teach students to do better,” Lynch explained.

Lynch said she wishes she had the training these students will be getting. For scientists, computers are an invaluable tool that can help delve into greater breadth and depth in analyzing, interpreting and collecting information. The STRIDE effort includes a greater awareness of the way computers can inform political or social science. Researchers generate “tremendous amounts of data that can be used to analyze trends or detect diseases,” Kaufman said. “The data science is tremendous in every discipline.”

The faculty who are a part of this program said they have already benefited from the interactions they’ve had with each other as they’ve developed the curriculum. “I know a few people in Ecology and Evolution and I know more people in Marine Sciences, but these particular individuals were new to me,” said Kaufman. “We have already been communicating about ideas for how to use the Reality Deck for other projects.”

Completed in late 2012, the Reality Deck is a $2 million rectangular room in the Center of Excellence in Information Technology building. The room has hundreds of monitors that cover the wall from floor to ceiling and provides a way for researchers to study images in exquisite detail.

Other scientists in the program include Liliano Dávalos, an associate professor in the Department of Ecology and Evolution, Janet Nye, an assistant professor in the School of Marine and Atmospheric Sciences, Joel Saltz, the founding chair of the Depatment of Biomedical Informatics, Erez Zadok, a professor in the Department of Computer Science and Mighua Zhang, a professor in the School of Marine and Atmospheric Sciences.

Lynch said the program will bring in people who are working on real-world problems, including those in government, industry and nongovernmental organizations who are “in a position to take science and use it for practical purposes.” As a part of the program, the scientists will monitor the progress of the STRIDE candidates, O’Connell said.

The evaluations will check to see if “they become better communicators and better at interpreting their data for different audiences,” O’Connell said. “The evaluation piece built in will help us assess the program.”

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From left, Lorne Golub, Joseph Scaduto, Francis Johnson, Ying Gu, Hsi-Ming Lee and Maria Ryan. Photo courtesy of Stony Brook Medicine

By Daniel Dunaief

You might not be able to teach an old dog new tricks for a variety of reasons, including that your old dog might be suffering from periodontal disease. An inflammatory condition of the mouth that affects about 80 percent of dogs by the age of three, periodontal disease often starts out as gingivitis, a swelling or reddening of the gums, and then proceeds to affect the soft and hard tissues that support teeth.

Scientists and dentists at Stony Brook have developed a new treatment for periodontal disease for dogs, and, they hope, eventually for humans. The National Institute of Dental and Craniofacial Research, a unit of the National Institutes of Health, recently awarded Stony Brook University’s School of Dental Medicine and Traverse Biosciences Inc., a Long Island research company, a $1.3 million award to continue to evaluate the preclinical safety and effectiveness of TRB-NO224 to treat periodontal disease.

“The grant was approved for funding because a panel of nationally prominent dental and medical scientists agreed that our grant proposal, and our qualifications and academic records were exemplary,” Lorne Golub, a distinguished professor in the Department of Oral Biology and Pathology explained in an email. Golub, who holds 55 patents and developed Periostat and Oracea, will lead the research, along with Ying Gu, an associate professor in the Department of General Dentistry at SBU.

While periodontal disease affects dogs, it is also widely prevalent among humans, with Golub calling it the “most common chronic inflammatory disease known to mankind.” Indeed, developing effective treatments is important not only for oral health, but it has implications for other conditions that are complicated or exacerbated by the collagenase enzyme prevalent in periodontal disease.

“Some studies indicate that chronic periodontitis can increase the risk for pancreatic cancer, head and neck cancer, cardiovascular disease and others,” Golub wrote in an email. “All of these diseases result in an increase in collagenase.”

A challenge in treating periodontitis is that the enzyme that is a part of the inflammatory response, collagenase, is present, and necessary, in normal metabolism. Ridding the body of the enzyme would cause harm. Golub worked with Francis Johnson, a professor of chemistry and pharmacological sciences at Stony Brook, to develop a new treatment using a modified form of curcumin, which is a bright yellow chemical that is a member of the ginger family. Naturally occurring curcumin does provide some benefit for periodontal diseases, Golub said, although the modified version Johnson helped create is more effective. “Very little” curcumin is absorbed from the gut into the blood stream after oral administration, Golub said.

The modification Johnson and Golub made was to make their variant triketonic. With the extra ketone, which has a negative charge, the attraction for zinc and calcium, which are a part of collagenase and have positive charges, is stronger, Golub said.

In dividing the work, Gu explained that Golub will supervise personnel, coordinate and oversee all experiments and provide technical oversight for the animal experiments and biochemical analysis. Gu will work with Hsi-Ming Lee, a research assistant professor in oral biology and pathology, to perform in vivo animal experiments and the biochemical analyses of pro-inflammatory mediator levels on blood, gingival fluid and gingival tissue samples. He and Golub will perform data analysis and prepare publications together. The scientific team involved in the study of TRB-NO224, which includes Maria Ryan, the chair of the Department of Oral Biology and Pathology, intends to develop this treatment for pets first. This, Golub suggested, was in part because the approval process for pet treatments is quicker to market.

The group hopes additional research, including safety and efficacy studies, will lead them to apply to the Food and Drug Administration for human uses. Ryan, who worked as a graduate student in Golub’s lab before she became the head of the department, is pleased with the process and the track record of a department Golub helped start in 1973.

“I am proud to say that this is Department of Oral Biology and Pathology’s fourth NIDCR grant for the development of new therapeutics for the management of periodontal diseases within the past four years,” Ryan wrote in an email. “The aim of this funding mechanism is to move these novel compounds further along in the FDA drug development process.” Ryan added that the benefits of TRB-NO224 extended to other medical arenas and has led to collaborations with additional scientists. TRB-NO224 not only impacts enzymes such as collagenase, but also affects pro-inflammatory mediators, she said.

“This new compound may be useful at preventing and/or treating numerous chronic conditions,” Ryan said. Studies are currently funded to investigate indications for osteoarthritis with the director of Orthopaedic Research, Daniel Grande, at the Feinstein Institute and for acute respiratory distress syndrome with Gary Nieman at SUNY Upstate Medical University in Syracuse. Golub has worked with international collaborators for decades. Some of them praised his legacy and the work he’s continuing to do.

Golub’s patents reflect his “everlasting translational mission from molecular and biotechnological medical/dental research to doctors’ daily and every-day practice,” wrote Timo Sorsa, the Chief Dental Officer in Periodontology at the University of Helsinki Central Hospital in Finland in an email. Golub received an honorary M.D. from the University of Helsinki in 2000.

A resident of Smithtown, Golub lives with his wife Bonny, who is a travel agent. They have two children, Marlo and Michael, and four grandchildren. Golub and his wife were among the first to see a showing at the New Community Cinema in Huntington, now the Cinema Arts Centre, in their own folding chairs. They watched one of Golub’s favorite films, “Henry V,” with Sir Laurence Olivier.

Golub is optimistic about the prospects and progress on TRB-NO224. “We are beginning to see evidence of efficacy in a variety of diseases,” he offered. He also believes the treatment may have rapid acceptance because natural curcumin has been used for decades in a number of populations and is “believed to be safe and effective.”

The content in this version has been updated from the original.

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Dave Jackson. Photo courtesy of CSHL

By Daniel Dunaief

If we get a text message that our son just gained admission to his first choice for college, we might throw our arms in the air, pick up the phone and call him, or stand on the top of our desk and shout our joy to the room. We might feel, in that instant, as if he can achieve anything and, as a result, so can we.

While plants don’t send and receive text messages, they process and react to a range of signals, some of which can determine how and when they grow, which can be key parts of determining how much food they produce.

Recently, David Jackson, a professor at Cold Spring Harbor Laboratory, explored a mutation that causes corn, or maize, to experience growth that is so out-of-control that the corn becomes a disorganized mess. Jackson wondered what caused this growth and disrupted the creation of succulent rows of juicy, yellow bits ready to explode off the cob.

Stem cells can grow to become any type of cell. In this pathway, which was disrupted in the mutant and caused the uncontrolled growth, Jackson showed that the signal came from the leaves, which is likely responding to its surroundings. He discovered that fine tuning that mutation — or weakening the “grow-out-of-control” signal — was enough to cause a regular ear of corn to include as much as 50 percent more food. “What was surprising about our work is that we found this new stem cell pathway that had not been discovered in Arabidopsis,” which is, as Jackson described, considered the equivalent of the well-studied fruit fly in the plant world. “We had gone on to show that it was also present in Arabidopsis.”

At this point, he’s hoping to introduce these mutations or alleles into breeding lines to try to generate a similar increase in yields that he’s seen in the lab. He’s collaborating with DuPont Pioneer on that testing. “As in all areas of science, we make a basic discovery and hope it’ll be applicable,” he said. “We can’t guarantee it’ll work until” it’s checked in the field. “People cure cancer in mice, but find it’s more complicated in people. We’re hoping cumulative knowledge will lead to breakthroughs,” he added.

Sarah Hake, the director of the USDA Plant Gene Expression Center at the University of California at Berkeley, described the work as “important.” In an email, she suggested that “translation to more corn yield can take time, but this information will be crucial for thinking about breeding.”

Jackson received the mutated maize from a breeder in Russia. He then altered a wild type, or normal plant, to cause a similar mutation that produced more food. Jackson is excited about the potential to use the gene-altering technique called CRISPR, in which researchers can edit a genome, changing one or multiple base pairs at a time.

Above left, normal corn and, right, corn with a weakened Fea3 mutation. The mutated corn has up to 50 percent more yield. Photo by Byoung Il Je
Above left, normal corn and, right, corn with a weakened Fea3 mutation. The mutated corn has up to 50 percent more yield. Photo by Byoung Il Je

Jackson is not adding new genes but, rather, is “tweaking” the ones that are already there. He said agricultural companies can use CRISPR instead of dumping in a foreign DNA. In past experiments, Jackson has worked to produce a greater number of seeds in his experimental plants. In that work, however, he increased the number of seeds, although the size of the seeds was smaller, so the overall yield didn’t increase. In this study, however, he and his postdoctoral student Byoung Il Je produced more seeds that generated greater yield. The gene involved in this signaling pathway is called Fea3. It is part of the signaling network that tells the plant to pump more into the ear of the corn to produce more yield. Jackson named the gene Fea because of the way the corn looked. Fea stands for fasciated ear. He and the members of his lab had already characterized another gene, called Fea2.

Jackson has been working on this gene for 20 years, although the intensive work occurred more in the last four or five years. He said he’s benefited from the ability to take a mutant and identify the gene. When he started out 25 years ago, a graduate student could take five years to characterize a mutation and find a gene. “It was like looking for a needle in a haystack,” he said. Now, genome sequencing and fast mapping enables researchers to find a gene in as little as a few months. When he first produced the weaker mutation, Jackson wasn’t anticipating a higher yield but, rather, was hoping to prove that this gene was the one responsible for this uncontrolled growth that created a pulpy mess of corn. Jackson said he is “excited about the stem cell pathway” his lab discovered. He hopes this finding can lead to a better understanding of the signals that determine how a plant uses its resources.

A resident of Brooklyn, Jackson lives with his wife Kiyomi Tanigawa, an interior designer, and their eight-year-old son Toma.

Jackson, whose lab has seven postdoctoral researchers and one lab manager, plans to start experiments on tomatoes and rice to see how this gene is involved in similar signals in other food crops. He is also working on similar mutations to other genes like Fea3, which also might affect a plant’s decision to produce more food.

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Ivan Bozovic. Photo courtesy of BNL

By Daniel Dunaief

How long and how much work does it take to defy conventional wisdom? Often, the prevailing belief about anything has backers who support the idea and aren’t eager to change or replace what they know with something new.

Recognizing this, Ivan Bozovic, the Oxide Molecular Beam Epitaxy (MBE) group leader at Brookhaven National Laboratory, checked and rechecked his work, spending close to a decade for parts of it, repeating his steps and checking the accuracy of his data points to make sure his case, which flew in the face of what so many others believed, was airtight.

Engineers, researchers and corporations have known about so-called high-temperature superconductivity for over a century. Using objects called cuprates, which are oxides of copper, researchers have created substances that can conduct electricity with close to no resistance at temperatures that are well above the requirements for most superconductivity.

While the name high-temperature superconductivity might suggest materials that allow the passage of energy through them in a sauna, the reality is far from it, with the temperatures coming in closer to negative 163 degrees Fahrenheit. While cold by everyday standards, that is still well above the record critical temperature before cuprates, which stood at – 418 degrees F.

Up until Bozovic’s study, which was recently published in Nature, scientists believed superconductivity in these cuprates occurred because of the strength of electron pairing. Carefully and in great detail, Bozovic demonstrated that the key factor in leading to this important property was the density of electron pairs, which are negatively charged particles.

Other scientists suggested Bozovic’s study was an important result that flew against the prevailing explanation for a phenomenon that holds promise for basic science and, perhaps one day, for the transmission of energy in the future.

Bozovic’s study “shows that [the] standard picture fails quite astonishingly in copper oxides that show high temperature superconductivity,” Davor Pavuna, a professor at the Swiss Federal Institute of Technology at Lausanne, explained in an email. “We are only begining to grasp how dramatic” this latest discovery is.

Pavuna described how he was recently at an event in Corsica, France and that his colleagues believed “this is a clear signal that we will have to develop much more advanced theoretical framework for cooperative phenomena, like superconductivity.”

Bozovic’s work and his latest result “show that our physics understanding and models require some new physics framework,” Pavuna said.

Bozovic and his colleagues studied over 2,150 samples. He explained that cuprates are complex for standards of condensed matter physics because some of them have 20 to 50 atoms in unit cells. That means that when engineers synthesize them, cuprates can have a mixture of unwanted secondary phases that could “spoil the experiment.”

Ivan Bozovic with his granddaughter Vivien at Vivien’s first birthday party last year in California. PhotoPhoto by Julie Hopkins, cameracreations.net
Ivan Bozovic with his granddaughter Vivien at Vivien’s first birthday party last year in California. Photo by Julie Hopkins, cameracreations.net

The number of samples necessary to demonstrate this property is a matter of personal standards, Bozovic suggested. He made sure he kept “checking and double checking and triple checking to be sure that what we had closed all the loopholes,” Bozovic said. He wanted “no possibility of an alternative explanation.”

The way Bozovic and his colleagues approached the problem was to start with a cuprate composition. They then replaced one atom at a time by another, which provided a series of samples that were almost identical, but slightly different in chemical composition. He was able to show how the critical temperature changes with electron density in small increments.

“What’s really impressive here is [Bozovic’s] ability to use a molecular beam epitaxy system — that he designed — to place single atomic layers on to a substrate, layer by layer,” James Misewich, the associate lab director for Energy & Photon Sciences at BNL explained in an email.

Bozovic’s work is “an exciting finding that could have wide-ranging impacts on how we identify, design, and build new superconducting materials,” continued Misewich.

As with other science, Bozovic said the answer to one question leads to a series of follow up questions, which include why do small pairs of electrons form in cuprates and not in anything else.

A resident of Mount Sinai, Bozovic lives with his wife Natasha, who is a mathematician. The couple has two daughters, Dolores, a professor of Physics and Astronomy at UCLA and Marijeta, an assistant professor of Slavic Languages and Literatures at Yale, where Bozovic is an adjunct professor of Applied Physics.

Born and raised in the former Yugoslavia, Bozovic is the son of two medical doctors. His father, Bosislav Bozovic, was twice nominated for the Nobel Prize for his work on the relation between cancer and the immune system. He was also a major general in the medical corp and the head of the Medical Division of the National Academy of Sciences.

His mother, Sasha Bozovic, wrote a best-selling memoir, devoted to a daughter she lost in World War II. His mother was also a colonel in the medical corps who worked in the army until she retired as the highest ranking woman in the army. “I had some big shoes to fill,” Bozovic acknowledges.

As a teenager, Bozovic played the lead guitar in a rock band. Nowadays, he strums nursery rhymes for his granddaughter Vivien using FaceTime.

A scientist who suggests a sense of humor is extremely important, especially in a field that can include disappointments and setbacks, Bozovic jokes that he speaks “zero” languages, a conclusion he reached after listening to an online description he gave of his recent work. In reality, he can read about four languages, although he has studied more.

As for his work, Bozovic is looking forward to discussing his recent results with theorists like Gabriel Kotliar, a Rutgers Professor of Physics and Astronomy who has a part time position at BNL. Kotliar is leading a new materials theory center at BNL.

“I hope that we’ve given them new pointers about where to look and what to calculate,” Bozovic said. “I’m pretty optimistic that there will be feedback from them.”

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Tony Zador. Photo courtesy of Cold Spring Harbor Laboratory

By Daniel Dunaief

For some people, the frontier lies deep in space, further than the eye can see. For others, the frontier resides at tremendous pressure beneath the surface of the ocean. For Tony Zador, the chair of neuroscience and professor of biology at Cold Spring Harbor Laboratory, the frontier is much closer to home, in the collection of signals in our brains that enable thought and direct our actions.

Recently, Zador and his research team helped explore that frontier, developing a technological innovation that allowed them to see where nervous system cells from one important region projected into other areas.

About six years ago, Zador came up with the idea to barcode the brain. Zador and his former graduate student Justus Kebschull explored the connections between the locus coeruleus (LC) and other parts of a rodent brain. The LC is responsible for reacting to stressful situations, allowing an animal to stimulate areas that might help save its life, including those responsible for visual or auditory processing.

Researchers believed that the intercom system that connected the LC to the rest of the brain could stimulate all areas at once, like a building-wide announcement coming over the public address system. What scientists didn’t know, however, was whether that communication system could send messages to individual areas.

“People knew before our work that neurons in the locus coeruleus broadcast their signals throughout the cortex,” Zador said. “What was not known was whether there was any specificity. It was always assumed.”

Zador found that individual neurons had precise connections to different parts of the brain. While this doesn’t prove that the LC can selectively activate one area, the way a superintendent might send a signal to one wing of a building, it demonstrates the specificity of the connections, which “raises the possibility” of selective signals.

Indeed, if each neuron diffusely spread out across the entire cortex, there would be no way to achieve localized control over cortical functions through the LC system. The visual cortex, for example, would be alerted at the same time as the auditory and frontal cortex.

Ultimately, Zador is interested in the brain’s neuronal network. The way nervous system cells communicate in our brains can help us understand how we process and interact with the world around us. Down the road, he is hoping to help create something called a connectome, which will provide a map of that network.

This information, at a basic level, could provide a better understanding of neurological conditions such as autism, schizophrenia, depression and addiction.

At this stage, however, Zador is building a network called the projectome, which provides a map of the specific regions neurons go in the brain. He collects this information by inserting a deactivated virus with a unique genetic code into the brain. These viruses act as a label, allowing Zador and his colleagues to trace the areas where individual neurons go. This technique, he said, doesn’t indicate whether neuron one is connected to neuron two, three or four, but, rather, it indicates whether neuron one is connected to a bunch of neurons in regions one and two but not in three and four.

Zador “had to develop a method of bar coding each neuron so that it is unique and a technique of detecting each bar code individually,” said Bruce Stillman, the president and chief executive officer of Cold Spring Harbor Laboratory. By collecting numerous samples of where these neurons go, Zador, his collaborators and other scientists can determine the natural range of variability for animal models of individuals with typical behaviors and reactions. Once they establish that range of typical wiring, they can compare that to animal models of neurological challenges, like autism. Zador wants to “create a baseline against which we can compare neuropsychiatric models of disease.”

Stillman explained that Zador’s focus at CSHL has been on cognition — how the brain makes decisions, retains memory and pays attention to tasks at hand. Zador, Stillman suggested, is “one of the pioneers in establishing the rodent cognition area.”

To understand cognition, however, Zador needed to see what regions of the brain are connected to other areas, providing a road map of the brain. Even though he didn’t have a background in molecular biology, Zador benefited from working with specialists at CSHL to create this bar coding, Stillman explained. Stillman described Zador as “bright” and “broad thinking.”

Zador said the next step in his work will be to relate the projections to the individual cells’ function in the brain. He would also like to see their neuron-to-neuron connectivity. He said he is pursuing both goals and hopes to submit a paper in the next month or two describing such a method for the first time.

“Although we can sequence the codes” from neighboring neurons, “we still have work to do to figure out connectivity,” Zador said. “That involves significant molecular tricks that we’re refining.”

Georgio Ascoli, a collaborator with Zador and the director of the Center for Neural Informatics at the Krasnow Institute of Advanced Study at George Mason University, described Zador as an “internationally renowned, highly respected scientist,” whose best known contributions relate to the challenge of understanding how the brain can seamlessly decide which stimuli in a varied environment like a cocktail party to listen to among numerous choices.

A resident of Laurel Hollow, Zador lives with his wife Kathy Shamoun, who practices Chinese medicine at CSHL and is a childbirth educator and doula. The couple has two sons, Ronin, 10, and Bowie, 6.

As for the benefits of this bar-coding approach, Ascoli explained that the technique is “potentially revolutionary because of its inherent scalability to full mammalian brain mapping, which is currently out of reach for alternative approaches.”

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