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From left, Jason Sheltzer, Nicole Sayles (who is a former lab technician and a co-author of an earlier MELK paper) and SBU undergraduates Chris Giuliano and Ann Lin. Photo by Constance Brukin

By Daniel Dunaief

If eating macaroni and cheese made Joe sick, he might conclude he was allergic to dairy. But he could just as easily have been allergic to the gluten in the macaroni, rendering the dairy-free diet unnecessary.

Scientists try to connect two events, linking the presence of a protein, the appearance of a mutation or the change in the metabolic activity of a cell with a disease. That research often leads to targeted efforts to block or prevent that protein. Sometimes, however, that protein may not play as prominent a role as originally suspected. That is what happened with a gene called MELK, which is present in many types of cancer cells. Researchers concluded that the high level of MELK contributed to cancer.

Jason Sheltzer, a fellow at Cold Spring Harbor Laboratory, and Ann Lin and Christopher Giuliano, undergraduates at Stony Brook University who work in Sheltzer’s lab, proved that wasn’t the case. By rendering MELK nonfunctional, Sheltzer and his team expected to block cancer. When they knocked out MELK, however, they didn’t change anything about the cancer, despite the damage to the gene. But, Sheltzer wondered, might there be some link between MELK and cancer that he was missing? After all, scientists had found a drug called OTS167 that was believed to block MELK function.

To test this drug’s importance for MELK and cancer, Sheltzer used this drug on cancer cells that didn’t have a functioning MELK gene or protein. Even without MELK, the drug “killed cancer cells,” regardless of the disappearance of a gene that researchers believed was important for cancer’s survival, he said.

“We showed for the first time that [the drug] was killing cells that didn’t express MELK,” Sheltzer said. The drug had to have another, unknown target.

Sheltzer suggested that this is the first time someone had used CRISPR, a gene-editing technique, to take a “deep dive” into what a drug is targeting. This drug, he said, has a different mechanism of action from the one most people believed.

Sheltzer, whose work was published in early February in eLife, expanded the research from a petri dish, where researchers grow and study cells, to mouse models, which are often more similar to the kinds of conditions in human cancers. In those experiments, he found no difference between the tumors that grew with a MELK gene and those that didn’t have the MELK protein, continuing to confirm the original conclusion. “The tumors that formed in cells that had MELK and the tumors that formed in cells that didn’t have MELK were the same size,” he said.

Originally, Sheltzer believed the MELK protein might be involved in chemotherapy resistance. His lab found, however, that no matter what they did to MELK in these cells, the cancer appeared indifferent. Other researchers suggested that Sheltzer’s work would be instructive in a broader way for scientists.

Sheltzer’s research on MELK “will motivate a new set of standards for target discovery and validation in the field going forward,” Christopher Vakoc, an associate professor at CSHL, explained in an email. Sheltzer “brings a rigorous approach to cancer research and an impressive courage to challenge prevailing paradigms.” Sheltzer’s work highlights the challenge of understanding the mechanism of action of new medicines, Vakoc added.

Sheltzer plans to explore several other genes in which a high concentration of a specific protein coded by that gene correlates with a poor prognosis.

Using CRISPR, Sheltzer believes his lab can get precise information about drug targets and their effect on cancer. He’s also tracing a number of other types of cancer drugs that he thinks might have compelling properties and will use CRISPR to study the action of these drugs. “We want to know not just that a drug kills cancer cells: We want to know how and why,” he said.

By figuring out what a drug targets, he might be able to identify the patients who are most likely to respond to a particular drug. So far, the finding that a drug doesn’t work by interfering with a specific gene, in this case MELK, has been easier than finding the gene that is the effective target, he explained.

One of Sheltzer’s goals is to search for a cancer cell that is resistant to the drug, so that he can compare the genes of the vulnerable one with those of the cell that’s harder to treat. Detecting the difference in the resistant cell can enable him to localize the region critical for a drug’s success.

Sheltzer said finding that MELK was not involved in a cancer’s effectiveness was initially “depressing” because researchers believed they had found a cancer target. “We hope that by publishing these techniques and walking through the experiments in the paper that other labs can learn from this and can use some of the approaches we used to improve their drug discovery pipelines,” he said.

Sheltzer is pleased that Lin and Giuliano made such important contributions to this paper. CRISPR has made it possible for these undergraduates to “make these really important discoveries,” he said. Lin, who has worked in Sheltzer’s lab for two and a half years, was pleased. “It is very exciting to share my knowledge of MELK in regards to its role in cancer biology,” she wrote in an email. “Authoring a paper requires a great deal of work and I am super thrilled” to see it published.

Sheltzer, who lives with his partner Joan Smith, who is a software engineer at Google, said he was interested in science during his formative years growing up in Wayne, Pennsylvania, which is just outside of Philadelphia, and appreciates the position he has at Cold Spring Harbor Laboratory. Soon after earning his doctorate at MIT, Sheltzer set up his own lab, rather than conducting research for several years as a postdoctoral researcher. “I was really fortunate to be given that opportunity,” he said.

As for his work with MELK, Sheltzer hopes he’s saved other labs from pursuing clinical dead ends.

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Adélie penguins jump off an iceberg of one of the Danger Islands. Photo by Rachel Herman from Stony Brook University/ Louisiana State University

By Daniel Dunaief

In October of 1957 when the Soviet Union launched the satellite Sputnik, people imagined that satellites hovering over their heads could see everything and anything down below. Indeed, in the early days, some Americans rushed to close their blinds, hoping the Kremlin couldn’t see what they might be eating for dinner or watching on TV.

Satellites today collect such a wealth of information about the world below that it’s often not easy to analyze and interpret it.

That’s the case with the Danger Islands in the Antarctic. Difficult for people to approach by boat because of treacherous rocks around the islands and sea ice that might trap a ship, these islands are home to a super colony of Adélie penguins that number 1.5 million.

Nesting Adelie penguins. Photo by Michael Polito from Louisiana State University

This discovery of birds that were photographed in a reconnaissance plane in 1957 but haven’t been studied or counted since “highlights the ultimate challenge of drinking from the firehose of satellite-based information,” said Heather Lynch, an associate professor of ecology and evolution at Stony Brook University and a co-author on a Scientific Reports publication announcing the discovery of these supernumerary waterfowl.

Adélie penguins are often linked to the narrative about climate change. Lynch said finding this large colony confirms what researchers knew about Adélie biology. In West Antarctic, it is warming and the population is declining. On the eastern side, it’s colder and icier, which are conditions more suited for Adélie survival. The Danger Islands are just over the edge of those distinct regions, on the eastern side, where it is still cold and icy.

A population discovery of this size has implications for management policies. At this point, different groups are designing management strategies for both sides of the peninsula. A German delegation is leading the work for a marine protected area on the east side. An Argentinian team is leading the western delegation.

Adelie penguins on sea ice next to Comb Island. Photo by Michael Polito, Louisiana State University

This discovery supports the MPA proposal, explained Mercedes Santos, a researcher from the Instituto Antártico Argentino and a co-convener of the Domain 1 MPA Expert Group. The MPA proposal was introduced in 2017 and is under discussion in the Commission for the Conservation of Antarctic Marine Living Resources, where the United States is one of 25 members.

Said Santos in a recent email, “This publication will help us to show the importance of the area for protection, considering that decisions should be made [with the] best available information.” The location of the Danger Islands protects it from the strongest effects of climate change, as the archipelago is in a buffer zone between areas that are experiencing warming and those where the climate remains consistent over longer periods of time.

Whales and other mammals that eat krill create an unknown factor in developing fisheries plans. While penguins spend considerable time above water and are easier to monitor and count, the population of whales remains more of a mystery.

Heather Lynch with a penguin. Photo from Heather Lynch

Lynch said the more she studies penguins, the more skeptical she is that they can “stand in” as ecosystem indicators. Their populations tend to be variable. While it would be simpler to count penguins as a way to measure ecosystem dynamics, researchers also need to track populations of other key species, such as whales, she suggested. Humpback whales are “in competition with penguins for prey resources,” Lynch said.

The penguin data is “one piece of information for one species,” but MPAs are concerned with the food web for the entire region, which also includes crabeater seals. For the penguin population study, Lynch recruited members of her lab to contribute to the process of counting the penguins manually. “I figured I should do my fair share,” she said, of work she describes as “painstaking.” Indeed, Lynch and her students counted over 280,000 penguins by hand. She and her team used the hand counting effort to confirm the numbers generated by the computer algorithm.

“The counting was done to make sure the computer was doing its job well,” she said. She also wanted to characterize the errors of this process as all census counts come with errors and suggested that the future of this type of work is with computer vision.

Lynch appreciated the work of numerous collaborators to count this super colony. Even before scientists trekked out to the field to count these black and white birds, she and Matthew Schwaller from NASA studied guano stains on the Danger Islands in 2015 using existing NASA images.

The scientific team at Heroina Island in Antarctica. Photo by Alex Borowicz, Stony Brook University

This penguin team included Tom Hart from Oxford University and Michael Polito from Louisiana State University, who have collaborated in the field for years, so it was “natural that we would work together to try and execute an expedition.” Stephanie Jenouvrier, a seabird ecologist at the Woods Hole Oceanographic Institute, has considerable expertise in the modeling side, especially with the climate; and Hanumant Singh, a professor of mechanical and industrial engineering at Northeastern University has experience using drones in remote areas, Lynch said.

The penguins on the Danger Islands react to the presence of humans in a similar way to the ones elsewhere throughout the Antarctic. The birds generally don’t like creatures that are taller than they are, in part because they fear skuas, which are larger predatory birds that work together to steal an egg off a nest. Counting the penguins requires the researchers to stand, but when the scientists sit on the ground, the penguins “will approach you. You have to make sure you’re short enough.”

Lynch would like to understand the dynamics of penguin nest choices that play out over generations. She’s hoping to use a snapshot of the layout of the nests to determine how a population is changing. Ideally, she’d like to “look at a penguin colony to see whether it’s healthy and declining.” She believes she is getting close.

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From left, Karen Chen-Wiegart, Silvia Centeno from the Metropolitan Museum of Art and BNL’s Juergen Thieme and Garth Williams in front of a computer image of Jan Van Eyck’s ‘Crucifixion,’ which they used to study the effects of soap formation in oil paintings. Photo from BNL

By Daniel Dunaief

Paintings can be so evocative that they bring images and scenes to life, filling a room with the iridescent flowers from an impressionist or inspiring awe with a detailed scene of human triumph or conflict. While the paints themselves remain inanimate objects, some of them can change over time, as reactions triggered by anything from light to humidity to heat can alter the colors or generate a form of soap on the canvas.

Recently, a team led by Silvia Centeno, a research scientist of the Department of Scientific Research at the Metropolitan Museum of Art in New York City, explored the process that caused lead-tin yellow type I to form an unwanted soap. Soap formation “may alter the appearance of paintings in different ways, by increasing the transparency of the paints, by forming protrusions that may eventually break through the painting surface, or by forming disfiguring surface crusts,” Centeno explained in an email.

Karen Chen-Wiegart with her husband Lutz Wiegart at Paumanok Vineyards in Aquebogue in November of 2017. Photo by Jen You

A team that included Karen Chen-Wiegart, who is an assistant professor at Stony Brook  University and has a joint appointment at Brookhaven National Laboratory, looked specifically at what caused a pigment common in numerous paintings to form these soaps. The research proved that the main component in lead-tin yellow pigment reacts, Centeno said. The causes may be environmental conditions and others that they are trying to discover. Lead-tin yellow changes its color from yellow to a transparent white. The pigment was widely used in oil paintings.

The pigment hasn’t shown the same deterioration in every painting that has the reactive ingredients, which are heavy-metal-containing pigments and oil. This suggests that specific environmental conditions may contribute to the pace at which these changes occur. Most of the time, the changes that occur in the paintings are below the surface, where it may take hundreds of years for these soaps to form.

The scientists are hoping this kind of research helps provide insights that allow researchers to protect works of art from deterioration. Ideally, they would like a prognostic marker that would allow them to use noninvasive techniques to see intermediate stages of soap formation. That would allow researchers to follow and document change through time. The scientists analyzed a microscopic sample from the frame of a painting from Jan Van Eyck called “Crucifixion,” which was painted in 1426.

Samples from works of art are small, around several microns, and are usually removed from areas where there is a loss, which prevents any further damage. Samples are kept in archives where researchers can do further analysis. In this case, a microscopic sample was taken from the frame of the painting, from an area where there was already a loss.

Centeno worked with a group led by Cecil Dybowski, a professor in the Department of Chemistry and Biochemistry at the University of Delaware, who has used solid-state nuclear magnetic resonance spectroscopy available at the university to study soap formation since 2011.

She also partnered with Chen-Wiegart to work at BNL’s National Synchrotron Light Source II, a powerful tool with numerous beamlines that can see specific changes on an incredibly fine scale. Centeno said she was very pleased to add Chen-Wiegart’s expertise, adding that she is “an excellent collaborator.”

When they started working together, Chen-Wiegart worked at BNL as an assistant physicist, and then became an associate physicist. As a beamline scientist, she worked at a beamline led by Juergen Thieme, who is a collaborator on this project as well. The researchers see this as an initial step to understand the mechanism that leads to the deterioration of the pigment.

The team recently applied for some additional beamline time at the NSLS-II, where they hope to explore how porosity, pore size distribution and pore connectivity affect the movements of species in the soap formation reactions. The humidity may have more impact in the soap formation. The researchers would like to quantify the pores and their effects on the degradation, Chen-Wiegart said.

In addition, Centeno plans to prepare model samples in which she accelerates the aging process, to understand, at a molecular level, what might cause deterioration. She is going to “try to grow the soaps in the labs, to see and study them with sophisticated techniques.”

Chen-Wiegart will also study the morphology at microscopic and macroscopic levels from tens of nanometers to microns. Both Centeno and Chen-Wiegart are inspired by the opportunity to work with older paintings. “I feel fortunate to have the opportunity to enjoy works of art as part of my daily work,” Centeno said.

Chen-Wiegart was eager to work with art that was created over 500 years ago. “The weight of history and excitement of this connection was something enlightening,” she said. “Thinking about it and processing it was a unique experience.”

A resident of Rocky Point, Chen-Wiegart lives with her husband Lutz Wiegart, who is a beamline scientist working at the Coherent Hard X-ray Scattering beamline at BNL. People assume the couple met at BNL, but their relationship began at a European synchrotron called ESRF in France, which is in Grenoble.

The couple volunteers at the North Shore Christian Church in Riverhead in its Kids Klub. For five days over the last five summers, they did science experiments with children who are from 4 to 11 years old.

The scientific couple enjoys the natural beauty on Long Island, while traveling to the city for cultural events. They kayak in the summer and visit wineries.

As for her work, Chen-Wiegart is excited about continuing her collaboration with Centeno.“The intersection between science, art and culture is inspiring for me.”

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Anil Yazici, center, with Eren Ozguven, right, and Ayberk Kocatepe, left, who worked in Ozguven’s lab as a doctoral student, at a conference in Florida last year.Photo from Anil Yazici

By Daniel Dunaief

Anil Yazici wants to help the elderly population with transportation, public safety and emergency services and housing.

An assistant professor in civil engineering at Stony Brook University, Yazici is organizing a series of meetings to address the needs of the elderly. He is recruiting a host of speakers from around the world and is inviting the public to listen and participate in roundtable discussions for a two-day event at the Hilton Garden Inn at Stony Brook as a part of a Research Coordination Network.

The workshop schedule with a list of speakers will be available around mid-March. Those interested in attending can visit the website https://you.stonybrook/edu/agingpopulationrcn/events/rcn-workshops/.

Yazici received a $499,999 four-year grant from the National Science Foundation last fall to develop a way to study the connection between smart and connected communities and areas with varying resources and population densities. The group will host workshops at the University of Michigan and at Florida State University.

Anil Yazici, right, with Harold Walker, left, a professor and chair in the Department of Civil Engineering and Laura Coronel, center, a member of the class of 2017.Photo by Erin Giuliano

The goal is to maintain mobility and access to services for the aging population. “Our focus is to involve aging populations within smart and connected communities … which generally employ technology to address mobility and access,” he explained in an email.

Yazici would like to get the government, communities and researchers to work together to address these issues. Groups involved in the effort will produce white papers, which can provide a proposal to help governments and community organizations plan various services.

Jacqueline Mondros, the dean of SBU’s School of Social Welfare and assistant vice president for Social Determinants of Health, described housing and transportation as “two of the most problematic issues of older adults, particularly in suburbia and rural areas.”

Mondros, who will be giving one of the talks in April, hopes the tech sector and engineering dedicate more attention to this area. She believes this effort will provide a greater understanding of the kind of connectedness that will help seniors and their caregivers. She also hopes the initiative helps people learn “about the intersection between connectivity and technology and social intervention.”

The funding for this effort is designed to create networks and develop ideas. Further work to develop projects, however, would require additional financial support.

Developing a broad plan in an area such as transportation will require flexible and location-specific solutions. Indeed, Long Island reflects such varying dynamics. Areas in or closer to the city have higher population density and a deeper transportation infrastructure, with subways, buses and trains offering transportation throughout the area. Further out east, however, the population density drops considerably, limiting such options.

“Once you don’t drive” when you’re in suburbia “it’s almost impossible to get around and go where you need to go,” Mondros said. People end up in “social isolation [which] clearly creates poor health outcomes and depression.”

Presenters will include people with expertise from Europe and Australia who can bring the solutions they have developed through smart and connected communities. Some locations have developed a system to help the aging population with routine transportation.

Anil Yazici after he went spearfishing for Mediterranean parrotfish in Turkey.Photo by Meliha Yazici

In one community, Yazici learned about a personal network in which people call each other to provide rides for regular travel, like weekly doctor or hospital visits. The network, which was organized through a church, involved calls to find rides through church members.

Eren Ozguven, who met Yazici in high school in Turkey and is a collaborator on the project, plans to do a presentation at Stony Brook on the challenges the aging population faces during hurricanes.

That includes a look at “how the technology usage is shaping this and how [to] provide better accessibility and safety during evacuations and sheltering,” Ozguven, who is an assistant professor in the Department of Civil and Environmental Engineering at FAMU-FSU College of Engineering in Tallahasse, Florida, explained in an email. “We are hoping to have very fruitful brainstorming sessions with practitioners, researchers, students and the public.”

More broadly, Yazici’s work is focused on the resilience of various civil engineering systems, such as transportation.

Organizational networks require contact among all the various infrastructure agencies, he said. They need to keep in contact and make decisions through context. He is working on a way to measure resiliency, so that when storms break communication links and disrupt power grids, the agencies in charge of those systems can restore them to previous levels.

He would like to see how to make an agency’s response to a disruption more efficient. Resilience can be improved through developing sound models for a physical infrastructure response.

A resident of Harlem where he lived during his postdoctoral training, Yazici has had to create his own system to ensure a successful commute. He leaves early, before much of the reverse commuting traffic builds, and returns home late. Yazici, who has been at Stony Brook since the fall of 2014, said he appreciates the opportunity to contribute to a new and growing department.

Yazici moved eight times when he was younger, as the family followed his father Mesut, who was also a civil engineer, from projects including water treatment plants to industrial waste processing. His father tried to dissuade him from following in his footsteps. His academic position, however, doesn’t require Yazici to follow projects from one place to another.

Starting in his first year in college, Yazici played bass in a band. He performed mostly ’70s Turkish progressive rock. He enjoys making music and plans to start an ensemble with his students to have a live music event after graduation.

As for his work, Yazici appreciates the opportunity to study areas that cross disciplines and that help people. “What drives me and most of the academics I know is to make a difference in people’s lives,” he explained in an email. “This could be through teaching and seeing students evolve personally and professionally or researching a topic to solve a problem and improve someone’s life.”

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Above, R.C. Murphy Junior High students Gregory Garra and Gianna Raftery with Catherine Markham in Dawn Nachtigall’s seventh-grade science class last year. Photo from Three Village school district

By Daniel Dunaief

A recent study of 57 species around the world, published in the journal Science, showed that mammals moved distances two to three times shorter in human-modified landscapes.

Catherine Markham, an assistant professor in the Department of Anthropology at Stony Brook University, contributed to this research, adding information about the ranges for baboons in the Amboseli Baboon Research Project in Kenya.

Marlee Tucker, an ecologist at the Senckenberg Nature Research Society based in Frankfurt, Germany, led the effort, which involved working with 114 other scientists who are studying mammals around the world. Tucker “brought together all these research groups on a scale and scope that had not been undertaken before,” Markham said. “She evaluated in an unprecedented way what the implications of human expansion and development are for wildlife movement.”

According to Tucker, a reduction in animal movement could have ecological implications. “It is likely that ecosystem functions such as nutrients and seed dispersal will be altered,” she explained in an email. “However, whether these impacts are negative, positive or neutral requires further research.”

Tucker suggested that it is “important to maintain landscape connectivity so that animals can move freely,” which could include the creation of corridors that link natural landscapes.

While the study made it clear in a comprehensive way that mammals tend to move less when humans interact with them, it didn’t offer specific indications about the causes of that reduction. Some of that, scientists say, could come from fear, as mammals may avoid humans. Alternatively, some mammals might find a new and concentrated food source at garbage dumps and elsewhere that would reduce the need to travel.

Susan Alberts, a professor of biology at Duke University and a collaborator with Markham on baboon research, said that the “take home message” is that “this is a pervasive phenomenon and occurs on a large scale in the mammalian world.”

Markham has been studying baboons in Kenya at the Amboseli site since 2004. When Tucker reached out to her to see if she could contribute to this work, Markham saw an opportunity to collaborate using information she was already gathering.

Above, baboons with a radio collar in the Amboseli National Park in Kenya. Photo by Catherine Markham

As it turns out, baboons in the research project in Kenya live in what Markham describes as a “relatively pristine area” so they did not see “over the time period an increase in the human footprint index.”

Markham shared information about 22 baboons for about 900 days as a part of this research. Tucker’s overarching conclusion included areas where people weren’t encroaching on a mammal’s range. “When she compared the movement of animals living in relatively pristine environments — like the baboons in Amboseli — to the movement of animals living in areas of higher human encroachment, that lead to exciting conclusions,” Markham said. Tucker indicated that future research should focus on exploring the underlying mechanism of the reduction in movement.

In the meantime, Markham is continuing her studies on baboons, exploring the energetic consequences of group size. Larger groups tend to beat out smaller groups when they are competing for food and water in a particular habitat. At the same time, however, those larger groups have stress levels caused by group competition, as one baboon might find the constant proximity and rivalry with another baboon stressful. Baboon group sizes range from a low of around 20 to a high of about 100. Markham is exploring the tension within and between groups.

Over the past few years, Markham, who has been studying this competitive dynamic extensively, has used noninvasive techniques, such as gathering fecal samples, to look for levels of thyroid hormones, which can indicate an animal’s energetic condition.

Alberts explained that Markham was an important contributor to the work at Amboseli, adding that Markham “asks questions at the group level that the rest of us don’t.”

Within the community, Markham has been involved in recent efforts to inspire middle school students at R.C. Murphy Junior High school in Stony Brook to enjoy and appreciate science, working closely with science teacher Dawn Nachtigall, who has been at Murphy for 20 years.

In her second year at Murphy, Markham visits seventh-grade classes several times, discussing her work and explaining how to analyze images from camera traps set up in Kenya and at Sweetbriar Nature Center in Smithtown.

The students receive about 30 photos per pair, Nachtigall explained. Based on the pictures, the students have had to generate questions, which have included whether young deer spend more time with male or female parents, or whether hyenas come out more on full or new moons.

According to Nachtigall, Markham “has such a friendly veneer and an approachable affect” that she readily engages with the students. “She has this wonderful demeanor. She’s soft-spoken, but strong.”

Students in her class appreciate the opportunity to interact with a Stony Brook researcher. “By the end of the period, they are glad to have met her,” Nachtigall added. “Some of them want to become her.”

At the same time, Nachtigall and the other science teachers appreciate the opportunity to hear more from local scientists.

“We live vicariously through her,” Nachtigall said. “It really ignites our own passion for science. Seeing the real-world science for science teachers is just as exciting as it is for students.” Markham is working to post materials online so that teachers and parents can access the information.

A native of Rockville, Maryland, Markham, who joined Stony Brook in 2014, resides in St. James. When she was young, Markham enjoyed the opportunity to join class events in kayaks along the Potomac River. She occasionally saw beaver and bald eagles. Indeed, along the way toward working with baboons, she has also conducted research on bald eagles, monitoring their nests with remote cameras.

As for her work on the Science article, Markham said she is pleased that this kind of collaborative research can provide broad ranging insight to address questions that extend beyond the realm of any one lab or species.

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Matthew Lerner, far right, with his lab group at Stony Brook University. Photo from Matthew Lerner

By Daniel Dunaief

An actor draws in members of an audience, encouraging them to understand, appreciate and perhaps even become sympathetic to a world created on a stage. The process of creating scenes for the actor, however, can also change his or her world off the stage.

A team of scientists from Vanderbilt University, University of Alabama at Tuscaloosa and Stony Brook University recently received $3 million in funding from the National Institutes of Mental Health for four years to study how participation in a theater production can help people with autism spectrum disorders.

Matthew Lerner. Photo by Graham Chedd from the Alan Alda Center for Communicating Science

“Theater is a venue for learning and gaining skills,” said Matthew Lerner, an assistant professor of psychology, psychiatry and pediatrics at the Department of Psychology at SBU who is leading the Long Island part of a study that will involve about 240 participants from age 10 through 16. “The process of putting on a play with others and being able to successfully produce and perform that has key benefits to learn and practice.”

Called SENSE Theatre (for Social Emotional NeuroScience Endocrinology), the shows were created by the project leader, Blythe Corbett, an associate professor of psychiatry and behavioral sciences and psychology and investigator at Vanderbilt Kennedy Center, who herself performed in stage plays before pursuing her scientific career.

Corbett writes the plays, which have themes she believes are important not only for autism but also for the general public. The topics include acceptance, belonging and diversity and offer a current of core ideas that are “part of having a condition that is unique,” she said. The plays, which typically have about 20 characters, include music and last about 45 minutes.

Tiffany Adams and Jane Goodwin participate in the SENSE Theatre program. Photo by Steve Green, Vanderbilt University

Corbett explained that the experience uses theater as a platform for teaching fundamental areas that could help people with autism spectrum disorders, including reciprocal social communication, flexible thinking and behavior and imagination.

“It also gives [the participants] an opportunity to be exposed to social situations and to engage with others in a safe and supportive environment,” she said. “They can be John today and Henry tomorrow, which allows them to expand their repertoire in a playful, fun way” which, she hopes, might help them assimilate lessons when the program ends.

Corbett has been developing SENSE Theatre for nine years. This specific multisite project will allow her to see how transportable this program is to other locations, where other investigators who have not been involved with this before can employ it with other participants.

The investigators, which include Corbett, Lerner and Susan White at the University of Alabama, will monitor the participants through psychological testing, social interaction and research EEG, or electroencephalography. This is a noninvasive way of monitoring electrical activity in the brain that involves placing electrodes on or below the scalp. The EEG testing takes about 45 minutes.

Participation is free, although members, who go through a screening process, need to contribute to the research program by completing the evaluations.

The theater program has a control study, calling Tackling Teenage Training, in which participants will “address some of the challenges of being a teen,” which include dating and puberty, knowing how to know if somebody likes or doesn’t like you and how to express desires or interests appropriately, Lerner said.

Savannah Bradley participates in the SENSE Theatre program. Photo from Steve Green , Vanderbilt University

Corbett chose to work with Lerner because of considerable overlap in their interests in using performance to provide clinical help for people with autism spectrum disorders. Lerner “has a very strong interest in theater and is able to understand the core approach” to the training and shows as a form of intervention. He is an “engaging, charismatic individual who is extremely hard-working” and is a “really good choice in terms of harnessing his energy and intelligence.”

Indeed, Lerner and Karen Levine, a licensed psychologist and the co-author of “Treatment Planning for Children with Autism Spectrum Disorders,” developed a model in 2004 for youths with disabilities to work on social skills called Spotlight, which utilized techniques of theater games and dramatic training. Spotlight is a program of Northeast Arc, a human services organization founded in 1954 and based in Massachusetts.

The Spotlight efforts started with nine students and has expanded to include hundreds of families each year.

In early high school, Lerner met someone who would change his life. He was having dinner with the family of a friend of his younger sister’s when he noticed a boy, Ben, playing on his own in another room. Lerner asked if he could play with Ben, who was 2 at the time and was running a car back and forth across the top of a toy playhouse.

Lerner mirrored what Ben did. “He looked at me curiously and kept doing what he was doing,” Lerner recalled. “I followed him around for over two hours.”

A scene from a performance by SENSE Theatre. Photo by Steve Green, Vanderbilt University

Up to that point in his life, Lerner thought the experience with Ben was “the most fascinating two hours of my life.” He had made a connection in which he “loved the joy and challenge of trying to meet him where he was, rather than behave in a way that was consistent with what the world expected.”

Lerner studied philosophy and music at Wesleyan University. After earning his doctorate at the University of Virginia, where his dissertation explored why youths with autism experience social problems, Lerner worked at the University of Chicago and then moved to SBU in 2013.

A native of Swampscott, Massachusetts, Lerner lives in Port Jefferson with his wife Chelsea Finn, a pediatric nurse practitioner in the Stony Brook Hospital Emergency Room and a nurse practitioner at SV Pediatrics in Patchogue. The couple has a 4-year-old son Everett and a 6-month-old son Sawyer.

Lerner is looking for people who would like to participate in the study. They can reach out to him by phone at 631-632-7857 or by email at [email protected]. The first set of students will begin working in the SENSE Theatre program this spring and summer.

Corbett said the participants aren’t the only ones who benefit from the program.

“The overwhelming sentiment from those who come to see the performance is that it changes their perception of what it means to have autism,” Corbett said. After the show, some of the audience members “ask who are the children with autism.”

Parents of the actors are pleasantly surprised by the things their children are able to do, which exceed their expectations. “In one of our previous studies, parents reported that their stress went down” during the program, she said, “which appeared to be in response to the child participating in intervention.”

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From left, Deyu Lu (sitting), Anatoly Frenkel (standing), Yuwei Lin and Janis Timoshenko. Photo from BNL

By Daniel Dunaief

What changes and how it changes from moment to moment can be the focus of curiosity — or survival. A zebra in Africa needs to detect subtle shifts in the environment, forcing it to focus on the possibility of a nearby predator like a lion.

Similarly, scientists are eager to understand, on an incredibly small scale, the way important participants in chemical processes change as they create products, remove pollutants from the air or engines or participate in reactions that make electronic equipment better or more efficient.

Throughout a process, a catalyst can alter its shape, sometimes leading to a desired product and other times resulting in an unwanted dead end. Understanding the structural forks in the road during these interactions can enable researchers to create conditions that favor specific structural configurations that facilitate particular products.

First, however, scientists need to see how catalysts involved in these reactions change.

That’s where Anatoly Frenkel, a professor at Stony Brook University’s Department of Materials Science and Chemical Engineering with a joint appointment in Brookhaven National Laboratory’s Chemistry Division, and Janis Timosheko, a postdoctoral researcher in Frenkel’s lab, come in.

Working with Deyu Lu at the Center for Functional Nanomaterials and Yuwei Lin and Shinjae Yoo, both from BNL”s Computational Science Initiative, Timoshenko leads a novel effort to use machine learning to observe subtle structural clues about catalysts.

“It will be possible in the future to monitor in real time the evolution of the catalyst in reaction conditions,” Frenkel said. “We hope to implement this concept of reaction on demand.”

According to Frenkel, beamline scientist Klaus Attenkofer at BNL and Lu are planning a project to monitor the evolution of catalysts in reaction conditions using this method.

By recognizing the specific structural changes that favor desirable reactions, Frenkel said researchers could direct the evolution of a process on demand.

“I am particularly intrigued by a new opportunity to control the selectivity (or stability) of the existing catalyst by tuning its structure or shape up to enhance formation of a desired product,” he explained in an email.

The neural network the team has created links the structure and the spectrum that characterizes the structure. On their own, researchers couldn’t find a structure through the spectrum without the help of highly trained computers.

Through machine learning, X-rays with relatively lower energies can provide information about the structure of nanoparticles under greater heat and pressure, which would typically cause distortions for X-rays that use higher energy, Timoshenko said.

The contribution and experience of Lin, Yoo and Lu was “crucial” for the development of the overall idea of the method and fine tuning its details, Timoshenko said. The teaching part was a collective effort that involved Timoshenko and Frenkel.

Frenkel credits Timoshenko for uniting the diverse fields of machine learning and nanomaterials science to make this tool a reality. For several months, when the groups got together for bi-weekly meetings, they “couldn’t find common ground.” At some point, however, Frenkel said Timoshenko “got it, implemented it and it worked.”

The scientists used hundreds of structure models. For these, they calculated hundreds of thousands of X-ray absorption spectra, as each atom had its own spectrum, which could combine in different ways, Timoshenko suggested.

They back-checked this approach by testing nanoparticles where the structure was already known through conventional analysis of X-ray absorption spectra and from electron microscopy studies, Timoshenko said.

The ultimate goal, he said, is to understand the relationship between the structure of a material and its useful properties. The new method, combined with other approaches, can provide an understanding of the structure.

Timoshenko said additional data, including information about the catalytic activity of particles with different structures and the results of theoretical modeling of chemical processes, would be necessary to take the next steps. “It is quite possible that some other machine learning methods can help us to make sense of these new pieces of information as well,” he said.

According to Frenkel, Timoshenko, who transferred from Yeshiva University to Stony Brook University in 2016 with Frenkel, has had a remarkably productive three years as a postdoctoral researcher. His time at SBU will end by the summer, when he seeks another position.

A native of Latvia, Timoshenko is married to Edite Paule, who works in a child care center. The scientist is exploring various options after his time at Stony Brook concludes, which could include a move to Europe.

A resident of Rocky Point during his postdoctoral research, Timoshenko described Long Island as “extremely beautiful” with a green landscape and the nearby ocean. He also appreciated the opportunity to travel to New York City to see Broadway shows. His favorite, which he saw last year, is “Miss Saigon.”

Timoshenko has dedicated his career to using data analysis approaches to understanding real life problems. Machine learning is “yet another approach” and he would like to see if this work “will be useful” for someone conducting additional experiments, he said.

At some point, Timoshenko would also like to delve into developing novel materials that might have an application in industry. The paper he published with Frenkel and others focused only on the studies of relatively simple monometallic particles. He is working on the development of that method to analyze more complex systems.

This work, he suggested, is one of the first applications of machine learning methods for the interpretation of experimental data, not just in the field of X-ray absorption spectroscopy. “Machine learning, data science and artificial intelligence are very hot and rapidly developing fields, whose potential in experimental research we have just started to explore.”

 

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Gray mouse lemur

By Elof Axel Carlson

Elof Axel Carlson

In 2016 a 54.5-million-year-old set of some 25 bones were unearthed in Gujarat, India. They belonged to the closest ancestor of all primates that lived about 56 million years ago. One branch of that ancestor produced the lemurs, lorises and an extinct group of adapoids. A longer branch produced the tarsiers and an extinct group of omomyids. Even more recently from that tarsier branch came the New World monkeys, followed by the Old World monkeys and most recently the apes and humans. The Gujarat primate has bones that are like a mixture of the lemurlike and monkeylike lineages.

The primates arose from an earlier line of dermopterans, and they in turn came from a line of tree shrews. The dermopterans are represented by a nearly extinct line of flying mammals that superficially look like bats but that differ in their mode of flight. They have a flap of skin that serves as a gliding organ, and they can glide about 200 feet from tree to tree in a forest. They are not good climbers, lack opposable thumbs and are nocturnal. Their diet consists of fruits, leaves and sap. 

One species lives in the Philippines. They are called by their popular name, colugos. Colugos are unusual in the trade-offs they have made in adapting to the rain forests in which they live. They gave up the marsupial pouch as they shifted to the placental pregnancies of mammals, but like marsupials, the colugo babies are born immature and are shielded by their mothers for about six months in the skin flaps that serve as both gliders and a pseudopouch.

We humans (Homo sapiens) can decide which of our ancestors to call human. The Neanderthals and Denisovans are our closest ancestors, and we acknowledge that they shaped tools, lived in communities and even bred with us, leaving behind as much as 3 percent of their genes in our genomes in many parts of the world.

The 54.5 million-year-old animal would have most closely resembled the gray mouse lemur.

Less human in appearance are Homo erectus and Homo habilis. All of these walked upright, unlike apes. Their skeletons are more humanlike than apelike. The very fact that they could reach reproductive age and survive tells us they knew how to shape the environments in which they lived or extract from them the protection, food and materials needed for their survival. 

Humans are remarkable in their plasticity of opportunities. They can migrate to frigid arctic or antarctic climates or live in deserts, in high altitude or sea level, in four seasons or one.   

As a geneticist I am aware that the contribution of any one of my Homo sapiens ancestor’s genes some 200,000 years ago had a low probability of remaining in contact with its neighboring genes, and in all likelihood those genes in me are from virtually all of the individuals alive then. 

When we do genealogy, assuming four generations per century, it only takes 2,000 years for any one of those ancestors in our family history to have less than 1 percent of our genes. If we are lucky (like royalty) to have records of our ancestors going back to the Middle Ages, we would likely find ourselves related to everyone in an ancestral region (a person like me whose father was from Sweden would be related to virtually every Swede in the age of the Vikings a little over 1,000 years ago).

In many ways our past genetic heritage is like the history of my Montblanc fountain pen, which was given to me by my students at UCLA in 1968. In the 40 years I wrote with it, I sent it to be repaired dozens of times either because I dropped it or a part wore out. Each time my pen came back looking new. I still think of it as the 1968 gift, but I doubt if there is any part that is still of the original pen given to me then.

This makes it unlikely that there is a genetic basis for behavior traits in a family that can go through more than 10 generations. The processes of shuffling genes every time we make eggs or sperm breaks up whatever cluster of genes we wish to assign to a human behavior. This is good because the genes of conquerors were spread widely while they held power, but having one of Ivan the Terrible’s genes or Genghis Khan’s genes would not make us a predatory monster in our relations with others. We inherit genes, not essences. If there is a mark of Cain, it is not engraved in our genes.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

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From left, Brenna Henn and Meng Lin at a conference last year in New Orleans. Photo from Meng Lin

By Daniel Dunaief

The story of the genetics of skin pigmentation in humans may have even more layers than the skin itself, depending on how close people live to the equator. The conventional wisdom for skin pigmentation is that it is a relatively simple trait, with a small number of genes accounting for almost half of the variety of skin tones.

That, however, isn’t always the case. Pigmentation genetics likely becomes more complex in populations near the equator or with greater variation in pigmentation, like with the Khoisan living in southern Africa.

Above, Brenna Henn, right, with an elder in the Khomani San community who gave her a book on the language formerly spoken in the southern Kalahari Desert. Photo from Brenna Henn

“As you move further toward the equator, the distributions are wide,” Brenna Henn, an assistant professor in the Department of Ecology and Evolution at Stony Brook University, said about the results she, along with collaborators from her lab and from Stanford University, recently published in the journal Cell.

Exploring the genetic determination of skin can serve as a model to understand the broad implications for various genetic variations for different populations as they confront a range of health challenges.

Henn has also worked with tuberculosis studies in South Africa. About one in three people in the world has a latent tuberculosis infection. Researchers have conducted studies to see which genes might be responsible for the different reactions to this disease. Tuberculosis susceptibility studies indicate that different genes may be responsible for infection in different populations, in areas including Russia, West Africa and South Africa.

According to Henn, scientists need to study and understand the disease in different populations to identify, through gene interactions, who will benefit from specific treatments in a vaccination campaign.

When Henn, who is a native of California, started the pigmentation study seven years ago when she was a graduate student at Stanford University, she had considerably different expectations. “When I was a post doc at Stanford, I expected the project to be quick because the genetics of pigmentation in Europeans was relatively well understood,” she explained in an email. When she started analyzing the results, she found that her hypothesis “was not true at all. There are so many different things involved.”

Calling this analysis the “tip of the iceberg,” Henn said she discovered many new genes beyond the ones scientists already knew contributed to skin pigmentation. She estimates that there are 50 if not more genetic sequences involved in skin pigmentation near the equator.

The range of skin pigmentation in South African populations reflected this increased genetic blueprint, with people in these areas demonstrating about twice the variation as people might encounter in a western European population.

These studies require the analysis of considerable data, through a field called bioinformatics, in which researchers analyze and process information through programs that search for patterns. “There’s a huge computational component” to this work, Henn said. “We don’t know where the genes are. We have to sample the entire genome” for as many as 500 people. “This blows up into a computational problem.”

Above, from left, Meng Lin and Brenna Henn at Lin’s graduation ceremony where she earned her PhD. Photo from Brenna Henn

Meng Lin, who worked in Henn’s lab for four and a half years and recently earned her doctorate, performs just such analyses. “We were hoping we’d be able to find some signals that had never been found before, to demonstrate the difference” in the genetic architecture, said Lin, who is now applying for postdoctoral research positions. “Given the prior studies on skin pigmentation traits, the complexity of the genetic architecture we found out was unexpected.”

People near the equator would likely need to have pigmentation that balanced between producing vitamin D from sunlight with protecting their skin from too much exposure to ultraviolet light. In areas such as in Africa, the ultraviolet light can be so strong that “the primary selection factor would be to avoid the photo damage from the strong UV, which favors melanin enriched dark skin pigmentation for photo protection,” Lin explained in an email.

Generally, people further from the equator, such as Scandinavian populations, have lighter skin because they need to process the limited vitamin D they can get, particularly during the darker months. That, however, isn’t the case for the Inuit people, who have darker skin in an area that gets limited sunlight. “Anyone who lives there should be under pressure for light skin,” Lin said. The Inuit, however, are darker skinned, which might be because their diet includes fish and fish oil, which is a rich source of vitamin D. “That would relax the selection force on lighter skin color,” she said.

With people able to travel and live in a wide range of regions across the Earth, selection pressures might be harder to decipher in the modern world. “Travel across continents is a recent” phenomenon, Lin said. The history of such travel freedom is “way too short for changing the genetic components.” Selection pressure occurs over tens of thousands of years, she added.

Diversity and the intake of vitamin D interact closely with each other. They can have impacts on the balance point. Using vitamin supplements could relax the selection on lighter skin, so the balance might shift to a darker population, Lin explained. Other modern lifestyles, such as wearing clothes, staying indoors and consuming vitamin D could complicate this and relax the strength of selection in the future, she added.

A native of China, Lin lives in Port Jefferson Station and enjoys applying math and computer skills to biology. “It’s great fun to solve the questions we have by developing and applying computational methods to existing data,” she said.

After five years at Stony Brook, Henn is transitioning to a position at the University of California at Davis, where she hopes to continue this ongoing work. “We want to follow up on how quickly these selective events occur,” Henn said. She’d like to discover how long it takes for the genetic average of the population to shift.

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Furie, above sailing on her 26-foot boat that is moored at Manhasset Bay, is navigating the American Journal of Pathology toward new waters. Photo by Richard Furie

By Daniel Dunaief

Martha Furie has a job no other woman has held in the 122-year history of a highly regarded scientific periodical. A professor of pathology and molecular genetics and microbiology at Stony Brook University, Furie is the new editor-in-chief of the American Journal of Pathology, taking over the top editorial job at a journal where she has been a contributor since 1993.

Martha Furie. Photo by SBU

“As a woman, it is certainly gratifying to see an accomplished and capable woman such as Martha being chosen to lead the way,” said Kari Nejak-Bowen, an assistant professor in the Department of Pathology at the University of Pittsburgh, School of Medicine, in an email. “Seeing women such as [Furie] in positions of power and visibility will empower other female scientists to dream that they can accomplish similar goals.”

Richard Mitchell, a senior associate editor at the journal and a professor of pathology and health sciences and technology and vice chair for education at Brigham and Women’s Hospital also applauded the choice. Furie “was probably the very best person we could recruit for the job and is someone who has the energy and vision for leading us into the challenging future,” Mitchell said.

From 1986 through 2014 Furie ran a lab that focused on the study of the body’s immune response to infections from Lyme disease and tularemia, which is cause by a bacterium that is classified as a potential agent of bioterrorism. In 2014, she became the director of the Graduate Program in Genetics at Stony Brook.

Kenneth Shroyer, the chair of the Department of Pathology at SBU, described the periodical Furie starts leading in 2018 as the “top pathology journal.”

As she takes the helm of the journal, Furie plans to navigate the periodical toward more translational research. “The Journal has been very focused on understanding the basic mechanisms of disease,” she said. “Research in all areas is getting much more translational: The bench-to-bedside thinking is where funding agencies are focusing their efforts,” and it’s also where the periodical she now leads is heading.

The tagline for the journal, which Nejak-Bowen said helped pioneer the current understanding of cell death, used to be Cellular and Molecular Biology of Disease. Furie changed that to Discoveries in Basic and Translational Pathobiology.

Shroyer believes the new direction should help the journal compete and redefine its niche for a wider range of readers. While Furie is excited about the opportunity, she acknowledges the increasingly challenging nature of the business. “Scientific publishing is a tough area right now,” she said. “There are fewer people in research because funding has diminished,” while, at the same time, more journals are competing to highlight research discoveries.

She will try to raise the journal’s profile for research scientists. Furie plans on expanding the journal’s social media presence and will do more marketing, while working with expert associate editors and getting them more involved in soliciting submissions. She also plans to make collections of highly cited papers in targeted areas and intends to use these to market the journal to attendees at specialized conferences.

Furie will spend this month contacting each of the associate editors and will solicit suggestions for people who might like to join the publication. She will also seek ideas for the journal. Mitchell suggested that Furie would likely benefit from these interactions. She is a “very good listener and is thoughtful in the questions she asks,” he said. “She is very discerning in assimilating the answers she gets back.” Shroyer expressed confidence in Furie’s leadership, citing a string of accolades and accomplishments in an SBU career that began in 1986.

Above, Furie welcomes students and faculty to the graduate program’s retreat in 2016. Photo by Constance Brukin

Furie was the president of the American Society for Investigative Pathology from the middle of 2011 through the middle of 2012. She was also the recipient of the Robbins Distinguished Educator Award in 2017, which recognizes people whose contributions to education in pathology had an important impact at a regional, national or international level.

Furie and Nejak-Bowen co-organized and co-chaired the ASIP Scientific Sleuthing of Human Disease for High School Teachers and Students in April 2017. With this effort, Furie has already had some success in changing the direction and target audience of an ongoing program. The session, which provides high school teachers with concepts of human disease that they can incorporate into their classroom, now includes high school students.

“This has really revitalized the program, as the students are inquisitive and very engaged with the material,” Nejak-Bowen explained. Furie was “instrumental in encouraging this change in focus, and is passionate about building an improving this session every year.”

The opportunity Furie has as editor-in-chief of the Journal of Pathology “continues her role as a national leader that she’s established,” Shroyer said.

Furie said she benefited from a diverse staff at Stony Brook, that included women like current Professor Emeritus Gail Habicht, when she first arrived. One of the best pieces of advice she received from Habicht was to understand that you can have a family and a successful career.

“You might not be able to do it to the same standard of perfection you did before you had children, but you can have a meaningful career and raise successful children and be happy doing both,” recalled Furie, who has two sons, Jon and Dan, and a 10-month-old grandson Tyler, who lives in Bedford, New York. She is married to Richard Furie, the chief of the Division of Rheumatology at Northwell Health, whom she met in a physics class at Cornell over 45 years ago.

Nejak-Bowen said Furie “leads by example when it comes to work/life balance.” Nejak-Bowen urges women scientists to find a mentor who can offer advice through all stages of a career. She has long considered Furie “a friend, mentor and inspiration.”

Based on Furie’s track record, Shroyer is confident in her continued success and anticipates that the journal will “thrive under her direction.”

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