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Daniel Dunaief

Minghua Zhang

By Daniel Dunaief

Minghua Zhang spent a sabbatical year in China trying to improve climate models, which included analyzing errors of current models.

A professor at the School of Marine and Atmospheric Sciences at Stony Brook University, Zhang focused on the Southern Great Plains of the United States. He explored how the current models did not accurately simulate convection, which created a warm and dry bias.

In convection, heat and moisture get carried upward. The models account for summer rainfall but do not calculate the organizational structure of the convective systems, which led them to simulate insufficient precipitation.

By adding in the new information, Zhang predicts in recent research published in the scientific journal, Nature Communications, that the projected warming in the region would be 20 percent less than previously thought. Precipitation, meanwhile, would be about the same as it is today, instead of the drying that was previously anticipated.

“The resolution of the models is not high enough to predict the change of the convection with a high degree of precision,” Zhang explained in an email.

He suggested that using 10 times the specificity of model calculations, he expects a clearer picture of the likely climate by the end of the 21st century. This is like looking through binoculars at a nondescript moving shape in the distance. By adding focal power to the lens, the image can become sharper and clearer.

The climate is a big picture view of trends over the course of many years. That is distinct from weather, which involves day-to-day variations and which meteorologists describe each morning and evening with colorful images of cold and warm fronts on local maps.

“You have many things you can’t see and now you have better binoculars,” he suggested. “This tiny thing in the binoculars can make a bigger impact. What we see is that these [variables] actually matter.”

Zhang suggested that a climate model that better accounts for summer rainfall still includes higher temperatures in this sensitive region. “The warming is going to be there and will be significant,” he said. If carbon dioxide emissions continue at their current rate, the warming will still be about five degrees by the end of the century, he suggested. That, he predicted, will still have a significant impact on agriculture.

Edmund Chang, a professor at the School of Marine and Atmospheric Sciences at Stony Brook who was not involved in this study, said this research addresses “a specific bias of the model that needs to be taken care of.” He added that researchers know that the “models are not perfect” and suggested that the “scientific and climate modeling community is trying to refine and improve” these tools.

Chang agreed that the refinement “doesn’t change the fact that we still project a large increase in the temperatures over the central United States.”

The Southern Great Plains region has some unique elements that make climate predictions challenging. It has considerable organized convection, which increases the occurrence of tornadoes. There’s also a large coupling between the soil moisture and the clouds, which means that whatever happens on the land has feedback for the atmosphere.

Zhang said his research focus is on climate simulation modeling. He knew the models had problems simulating convective events, which is why he started exploring this specific region. “The way the models are constructed, the granules are not small enough,” he said.

Chang expected that this work would “spur more research on trying to understand this mechanism. Model developers will need to try to find out how to improve the physical model.”

Zhang has been working for the last two years with scientists from Tsinghua University in China, which included his time on sabbatical. “When you are on sabbatical, you have more time to really think about problems,” he said.

Chang added that sabbaticals can provide some time to focus on specific scientific questions. During a typical semester that includes administrative responsibilities and teaching, professors “are very busy,” He said. “We really don’t have an extended period of time to focus on one project. The sabbatical gives us a chance to focus.”

Zhang hopes this study “motivates people to think about how to improve their models in describing” other climate systems.

One of the many challenges scientists like Zhang face in developing these climate models is that their computers are still not powerful enough to resolve elements like clouds, which not only dot the landscape and provide shade during the summer but also send the sun’s energy back into space.

The system he’s studying is “chaotic by nature,” which makes accounting for elements that change regularly challenging. He suggested that these studies were akin to the butterfly effect. Scientists have suggested that someone who went back in time and committed a seemingly trivial act, like killing a single butterfly, might return to his familiar time and surroundings to discover profound changes.

While that’s an exaggeration, that’s still the kind of system he said researchers are confronting as they try to account for, and weigh, climate defining factors. That’s why he’s looking for statistical, or probabilistic, predictions that are averaged over time periods.

The United States, China and the European Union are all pursuing more powerful computers for these kinds of applications, Zhang said.

Zhang, who is the editor-in-chief of the Journal of Geophysical Research: Atmospheres, has been involved in an advisory capacity with the United States Department of Energy in developing these models. A

s for this specific effort, Zhang said he was pleased that the paper pointed out a research direction to refine models for climate in this area. “What we see is that these things [including convection] actually matter,” he said. “That’s the main contribution of this paper.”

From left, BNL Staff Scientist Lihua Zhang, former postdoctoral researcher Vitor Manfrinato and BNL Senior Scientist Aaron Stein. Photo courtesy of BNL

By Daniel Dunaief

It took a village to build this particular village or, more precisely, a pattern so small it could fit thousands of times over on the head of a pin.

Working at Brookhaven National Laboratory’s Center for Functional Nanomaterials, a team of researchers wanted to exceed the boundaries of creating small patterns with finely honed features. The group included Aaron Stein, a senior scientist at CFN, Charles Black, the head of CFN, Vitor Manfrinato, a former postdoctoral researcher at BNL and several other key members of the BNL team. The team added a pattern generator that allowed them to control a microscope to create a pattern that set a record for drawing at the 1-nanometer scale.

Just for reference, the width of a human hair is about 80,000 to 100,000 nanometers. The size of the pattern is a breakthrough as standard tools and processes generally produce patterns on a scale of 10 nanometers. “We were able to push that by a factor of five or 10 below,” Stein said. “When you get to those small size scales, that’s pretty significant.”

In this case, the novelty that enabled this resolution originated with the idea of employing the scanning transmission electron microscope, which isn’t typically used for patterning to create these images. The scanning transmission electron microscope has an extraordinarily high resolution, while the pattern generator allowed them to control the patterns they drew and other aspects of the exposure.

Researchers at CFN are focusing on this spectacularly small world to manipulate properties such as chemical reactivity, electrical conductivity and light interactions. “This new development is exciting because it will allow other researchers to create nanomaterials at previously impossible size scales,” Kevin Yager, a group leader at CFN explained in an email. “There are numerous predictions about how materials should behave differently at a size scale at 1 to 3 nanometers. With this patterning capability, we can finally test some of those hypotheses,” he said.

Stein and the research team were able to create this pattern on a simple polymer, polymethyl methacrylate, or PMMA for short. “It’s surprising to us that you don’t need fancy materials to create these kinds of features,” said Stein. “PMMA is a common polymer. It’s Plexiglas. It’s kind of exciting to do something that is beyond what people have done” up until now.

One of the many possible next steps, now that the researchers have developed this proof of principle, is to apply this technique to a substance that might have commercial use. Taking the same approach with silicon, for example, could lead to innovations in electronics. “We can make them with a high clarity of patterns and sharp corners, which we can’t do with other techniques,” Stein said.

The BNL research team would “like to apply this to real world research,” which could include electronics and transistors, as well as photonics and plasmonics, he added. This project arose out of a doctoral thesis that Manfrinato was conducting. He is one of the many scientists who came to BNL, which isa Department of Energy funded user facility that provides tools to conduct research for scientists from around the world.

Manfrinato was a doctoral student in Professor Karl Berggren’s group at the Massachusetts Institute of Technology. In an email, Manfrinato explained that he was interested in pushing the resolution limits of e-beam lithography. “BNL has state of the art facilities and expert staff, so our collaboration was a great fit, starting in 2011,” he explained.

Other scientists thought it was worthwhile to continue to pursue this effort, encouraging him to “come here and work on this. It’s a home grown project,” Stein said. Manfrinato worked on his doctorate from 2011 to 2015, at which point he became a postdoctoral researcher at BNL. His efforts involved several groups, all within the Center for Functional Nanomaterials at BNL. Stein, Manfrinato and Black worked on the lithography part of the project, while Lihua Zhang and Eric Stach developed the microscopy. Yager helped the team to understand the processes by which they could pattern PMMA at such small scale lengths.

“No one or two of us could have made this happen,” Stein said. “That’s really the joy of working in a place like this: There are [so many] permutations for collaborating.” Indeed, the other scientists involved in this study were Yager; Zhang, a staff scientist in electron microscopy; Stach, the electron microscopy group leader at CFN; and Chang-Yong Nam, who assisted with the pattern transfer.

Manfrinato, who is now a research and development engineer at a startup company in the San Francisco Bay area, explained that this lithographic technique has numerous possible applications. Other researchers could create prototypes of their devices at a level below the 10-nanometer scale at CFN. Manfrinato interacts with the BNL team a few times a month and he has “exciting results to be further analyzed, explored and published,” he wrote in an email.

Stein said BNL would like to offer this patterning device for other users who come to BNL. Ultimately, researchers use materials at this scale to find properties that may vary when the materials are larger. Sometimes, the properties such as color, chemical reactivity, electrical conductivity and light interactions change enough to create opportunities for new products, innovations or more efficient designs.

A resident of Huntington, Stein and his wife Sasha Abraham, who works in the planning department for the Town of Huntington, have a 15-year-old daughter Lily and a 13-year-old son Henry.

As for his work, Stein said he’s interested in continuing to push the limits of understanding various properties of nanomaterials. “My career has been using the e-beam lithography to make all sorts of structures,” he said. “We’re in a regime where people have not been there before. Finding the bottom is very interesting. Figuring out the limits of this technique is, in and of itself” an incredible opportunity.

The greater bamboo lemur will struggle to survive amid a shorter rainy season. Photo by Jukka Jernvall

By Daniel Dunaief

An elusive primate is living on a shrinking island within an island. The greater bamboo lemur, which is one of the world’s most endangered primates, now inhabits a small section of Madagascar, where it can find the type of food it needs to survive.

The greater bamboo lemur, which was one of numerous lemurs featured in the 2014 iMax movie, “Island of Lemurs: Madagascar,” is finding that the time when it can eat the most nutritious types of bamboo is narrowing each year amid a longer dry season.

Patricia Wright has dedicated her life to helping lemurs in Madagascar. File photo from SBU

In a publication last week in the journal Current Biology, Patricia Wright, the founder of Centro ValBio research campus, driving force behind the creation of Ranofamana National Park and a distinguished professor of anthropology at Stony Brook University, along with several other researchers, including Jukka Jernvall from the University of Helsinki and Alistair Evans from Monash University, showed that the population of lemurs is threatened by a changing climate. The bamboo that sustains the greater bamboo lemurs depends on water to produce shoots that are higher in nutrition.

Indeed, when the rains come, the new bamboo shoots are “filled with protein,” said Wright. Jernvall, however, predicted that the driest season will get longer by a day each year. By 2070, rains necessary for bamboo growth and greater bamboo lemur survival will be delayed by as much as two months.

This is problematic not only for the current generation of greater bamboo lemurs but also for the more vulnerable younger generations, who need their lactating mothers to eat more nutritious bamboo to help them grow. Bamboo shoots typically come up from the ground about two weeks after the rains begin, in the middle of November. Bamboo lemurs, whose annual clocks are set to the rhythm of an island off the southeast coast of Africa that is the size of California, are born around the time of these bamboo-shoot-producing rains.

“Any village elder will tell you that the rains used to come at about Nov. 15 and continue until March 15,” Wright said. “That’s the way the world was, even in the 1980s and 1990s and probably many years before that. Suddenly, we started to get some evidence of climate changes and periods of a longer dry season.”

Above, a mother greater bamboo lemur holds her infant, which weighs about half a pound at birth. Photo by Jukka Jernvall

Wright is currently in Madagascar, where she says there is a drought right now. “No water for our research station means no electricity since we are near a hydroelectric power plant,” she explained by email. In fact, in some years, the rains start as late as January, which reduces the food offerings for the mother lemur, who weighs about 6.5 pounds, and her offspring, who need considerable nutrition to grow from birth weights Wright estimates are less than half a pound. The lemur mother “has to have nutritious shoots to feed her baby milk,” Wright said. “She can survive on leaves and trashy stuff in the culm, but she can’t raise her babies” on it.

Wright and Jernvall worked together in 2005 on a study of climate and another type of lemur called sifakas, whose name comes from the alarm sound it makes. In their earlier work, Wright and Jernvall found that aging sifakas with worn teeth could still produce offspring, but that their infants typically died if the weather was dry during the lactation season, Jernvall explained in an email.

“This alerted us about the potential impact of climate change,” he continued. “The bamboo lemur were an obvious concern because they are critically endangered and because they eat the very tough bamboo.”

Jernvall said the work on bamboo lemurs combines Wright’s efforts in Madagascar with climate modeling he performed with Jussi Eronen at the University of Helsinki and an analysis of dental features conducted by Evans and Sarah Zohdy, who is currently at Auburn University. Stacey Tecot, who is on sabbatical from the University of Arizona, also contributed to the research.

Wright believes some efforts can help bring these bamboo lemurs, who survive despite consuming large amounts of cyanide in their bamboo diet, back from the brink. Creating a bamboo corridor might improve the outlook.

Growing bamboo would not only benefit the lemurs, who depend on it for their survival, but would also provide raw materials for the Malagasy people, who use it to construct their homes, to build fences and to cover their waterways.

Bamboo corridors could be a “win-win situation,” where scientists and local communities grew and then harvested these hearty grasses, Wright continued. She has started a bamboo pilot study near one of the small populations of lemurs and hopes the lemurs can expand their range.

The greater bamboo lemur will struggle to survive amid a shorter rainy season. Photo by Jukka Jernvall

Like other animals with unusual lifestyles, the greater bamboo lemurs offer a potential window into an unusual adaptation. Through their typical diet, lemurs consume a high concentration of cyanide, which is stored in the bamboo. Understanding the bamboo lemur could provide evidence of how one species manages to remain unaffected by a toxin often associated with spies and murder mysteries.

As a part of her efforts to improve the chances of survival for this lemur, Wright is considering moving some lemurs to a protected area. She needs permission from Madagascar officials before taking any such actions and recently met with Madagascar National Park official to discuss such remediation efforts.

In Madagascar, Wright said observing the bamboo lemur is challenging because it is such a “cryptic animal.” She has sat beneath a tree where a lemur is hiding for seven hours waiting for it to emerge, watching as a lemur brought in its legs and curled up its body to hide from the scientist’s inquisitive eyes. “I’d get really hungry, so they would win and I would leave,” Wright recalled.

She suggests that the data in the Current Biology article demonstrates the urgency to take action to protect these primates. “We are trying our best to help the bamboo lemur not go extinct,” she said. “Bamboo corridors should help, but we may have to irrigate the bamboo during November to January.”

Pavel Osten. Photo by Joelle Wiggins

By Daniel Dunaief

Male mice, as it turns out, might also be from Mars, while female mice might be from Venus. Looking at specific cells in the brain of rodents, Cold Spring Harbor Laboratory Associate Professor Pavel Osten has found some noteworthy differences in their brain cells.

In the scientific journal Cell, Osten presented data that showed that in 10 out of 11 subcortical regions of the mouse brain, female mice showed greater flexibility and even more cells. These regions of the brain are responsible for reproduction, and social and parenting behaviors. “There were more cells [in these regions] in the female brain, even though the brains tended to be bigger in the males,” Osten said.

These results are part of a multiyear collaboration called the National Institutes of Health’s Brain Initiative Cell Census Network.

In the recent Cell article, Osten indicated that his analysis offered a surprising result in the number of cells of specific types in various regions of the cortex. “Those areas that have higher cognitive functions have different compositions,” he said. The ratios of cell types “vary according to the level of cognitive function.” In retrospect, Osten indicated that he saw the logic in such a cellular organization. “It makes sense that different cortical areas would have different cell type composition tuned to the specific cortical functions,” he explained.

In an email, Hongkui Zeng, the executive director of structured science at the Allen Institute for Brain Science, in Seattle, Washington, suggested that “people never looked at this issue carefully before. She added that the “sexual dimorphism was somewhat expected, but it is still interesting to see the real data.”

Pavel Osten sailing in St. Barts and St. Martin last summer. Photo from Pavel Osten

Osten used a system called qBrain to see and count inhibitory neurons in the mouse brain. Over the next five years, he and his collaborators will build an online resource database for other researchers that will have distribution maps for numerous cell types throughout the mouse brain.

Osten estimates that there could be hundreds or even a thousand cell types within the brain that are largely uncharacterized in their specialized functions. A cell type is defined by its function in terms of its morphology, including dendritic and axonal branches. These cells are also defined by their physiology, which includes spiking properties, and connectivity, which indicates which cell is talking to other cells.

The anatomy and physiology of the cells will validate these transcriptome single-cell RNAseq studies, which probe for the variability between cells based on their gene expression, which includes differences due to day-to-day variability and differences from distinct cell types.

By analyzing the location and modulatory functions of these cell types, Osten would like to determine ways human brains differ from other animal brains. “In the human, we can mainly analyze the location and distribution which includes the ratios of specific cell types and our hypothesis is that fine-tuning the ratios of neuronal cell types may be a powerful evolutionary mechanism for building more efficient circuits and possibly even for distinguishing between human and other animals,” Osten explained in an email.

Humans, he continued, don’t have the largest brains or the most neurons. At one point, spindle neurons were considered unique to humans, but other researchers have shown that great apes, elephants and cetaceans, which is a group that includes whales and dolphins, also have them.

Osten’s hypothesis is that one of the differences is that the ratios of cells of different types built a computational circuit that’s more powerful than the ones in other species.

When he studies mouse brains, Osten collects information across the entire brain. With humans, he explores one cubic centimeter. The human work is just starting in his lab and represents a collaboration with Zsófia Maglóczky from the Hungarian Academy of Sciences at the Institute of Experimental Medicine in Budapest.

Each mouse brain dataset is between 200 gigabytes and 10 terabytes, depending on the resolution Osten uses to image the brain. He can process 10 terabytes of data in about a week.

Osten uses machine learning algorithms that develop with guidance from human experts. This comes from a long-standing collaboration with Sebastian Seung, a professor of computer science at Princeton University.

He suggested that the research has a translational element as well, offering a way to study cellular and wiring elements characteristic of diseases. “We are looking at several of the models that are well established for autism.” He is also planning to write grants to find funds that supports the analysis of brains from people with schizophrenia and Alzheimer’s disease.

The analysis is a promising avenue of research, other scientists said. “It will be extremely interesting to compare the ratio of different cell types in various diseased brains with normal healthy brains, to see if the diseases may preferentially affect certain cell types and why and how,” Zeng explained in an email. “This could be very helpful for us to devise therapeutic means” to treat diseases.

Zeng has known Osten for about seven years. Last year, she began a collaboration using qBrain to quantify cell types.

A current resident of Williamsburg, where his reverse commute is now about 40 minutes, Osten works with a company he and Seung started called Certerra, which provides a rapid analysis of brain activity at different times. The company, located in Farmingdale, has a growing customer base and has a staff of about five people.

As for the recent work, researchers suggested it would help continue to unlock mysteries of the brain. This research is “a basic but important step toward understanding how the brain works,” Zeng added. “This paper provides a new and efficient approach that will be powerful when combined with genetic tools that can label different cell types.”

Heather Lynch at Spigot Peak in the Antarctic. Photo by Catherine Foley

By Daniel Dunaief

Counting penguins is like riding the highs and lows of Yankees rookie Aaron Judge’s home run streaks, followed by his series of strike outs. He’s not as bad as his strike outs suggest, although he’s also not a sure thing at the plate either.

Similarly, in local populations, the Adélie penguin, which waddles to and fro squawking on land and gliding gracefully through the water, isn’t as clear a barometer of changes in the environment. Also, like Judge, when populations rise and fall, people are eager to offer their explanations for exactly what’s happening, even if the sensational explanations — he’s not that good, no, wait, he’s the greatest ever — may overstate the reality.

Heather Lynch visits Cape Lookout in Antarctica during recent trip that included an NBC TV crew that produced a feature for ‘Sunday Night with Megan Kelly.’ Photo by Jeff Topham

“We have to be careful not to be overreactive,” said Heather Lynch, an associate professor of ecology and evolution at Stony Brook University. “The concern is that, when we see increases or decreases, the implication is that there’s a miraculous recovery or a catastrophic crash.”

That, however, is inconsistent with Lynch’s recent results, which were published in the journal Nature Communications. Examining penguin data from 1982 to 2015, Lynch, Christian Che-Castaldo, who is a postdoctoral researcher in Lynch’s lab, and nine other researchers looked to see if there’s a way to connect the size of the population to changes in the environment. The study involved two teams of researchers, one supported by NASA and the other backed by the National Science Foundation.

“It’s a noisy system,” Lynch concluded. Managers of the populations of krill, small crustaceans that are the mainstay of the Adélie diet, try to use time series of key indicator species to understand what’s going on in the marine realm. In this article, Lynch said, local Adélie penguin populations may not be a clear signal of the health of the krill stocks because penguin abundance fluctuates for reasons she and her team couldn’t pinpoint.

These penguins, which Lynch has counted during her field work in the Antarctic, exhibit changes in population that can run contrary to the health, or stressed condition, of the environment.

“You can’t have your finger on the pulse” with the available data, Lynch said. “Part of our inability to model year-to-year changes is because we can’t measure the right things in the environment.”

The drivers of abundance fluctuations likely involve other animals or aspects of the krill fisheries they couldn’t model, she suggested.

“There’s a lot we don’t know about what penguins do under water, where they spend a large portion of their time and where they feed,” Grant Humphries, who was in Lynch’s lab for a year and now runs his own data science company in Scotland called Black Bawks Data Science Ltd, explained in an email. “The signals that drive year to year changes might actually lie there.”

Tom Hart, a researcher of the Department of Zoology at the University of Oxford who was not involved in this study, explores local scale variation in penguin populations. Locally, Hart said in an interview by Skype, “Things are incredibly noisy. When you aggregate, you get good signals, but with some error.” He suggested that this research drives him on further, showing that “local influences are important” because there’s so much variance left to explain. Lynch’s research is “a really good study and shows very well what’s happening on the regional scale, but leaves open what happens below that,” he said.

Indeed, Lynch suggested that by putting sites together, researchers can look at larger areas, which provide a clearer picture on shorter time scales.

Michael Polito, an assistant professor in the Department of Oceanography and Coastal Sciences at Louisiana State University who was not involved in the study, suggests that this extensive analysis indicates that “you can still look at the relationship between the abundance of penguins and the environment in a robust way. Even though any individual time series may not be the best way to understand these relationships, in the aggregate you can use them.”

Managers who set fishery policies in Antarctic waterways are often concerned about harvesting too much krill, leaving the penguins without enough food to survive and feed their chicks.

The challenge with this result, Lynch acknowledges, is that it makes setting krill boundaries more difficult.

A strategy that involves resetting conservation targets based on annual monitoring appears unrealistic given these results, Lynch said. “From a practical standpoint, we threw in everything we could and could explain only a tiny fraction of the variation,” she said.

Hart added that this is “not an argument to fish away,” he said. “We need to understand what’s going on at a local scale and we’re not there yet.”

To get people involved, Lynch and her team created a science competition, called Random Walk of the Penguins, to see who could predict the overall penguin populations for Adélie, gentoo and chinstrap penguins from the 2014 to 2017 seasons.

The competition, which was a collaborative effort with Oceanites, Black Bawks Data Science and Driven Data included $16,000 in prize money, which was donated by NASA. Entrants could use data from the 1982 through the 2013 seasons. The contest drew competitors from six continents. Of the five winners, all were from different countries.

Humphries, who was the lead on the data science computation, said the results were “somewhat humbling” because competitors were able to make “decent predictions” using only the time series. “With long-term predictions and for determining the tipping points, there is still a lot of work to be done.”

Lynch is relieved that her co-authors supported the direction the article took. “I’m a skeptic by nature and more than happy to throw orthodoxy (or even my own previous work) under the bus,” she wrote in an email. “I do hope that others will use our model as a starting point and we’ll never go back to the old days where everyone looked only at ‘their sites.’”

Adam Gonzalez. Photo from SBU

By Daniel Dunaief

More than four days after lift off, pioneering astronauts Neil Armstrong and Buzz Aldrin had landed in the Sea of Tranquility on the surface of the moon. The NASA schedule, which included preparing the vehicle for an emergency abort of the mission in the event of a problem, called for a nap of four hours. Once they were there, however, Armstrong and Aldrin couldn’t imagine taking a four-hour respite.

“Both Armstrong and Aldrin were, understandably, excited about where they were and decided to forgo the sleeping and changed history,” Thomas Williams, element scientist in Human Factors and Behavioral Performance at NASA, described in an email.

A future trip to Mars, however, would involve considerably longer delayed gratification, with the round trip estimated to take over 400 days. The stresses and strains, the anxiety about an uncertain future and the increasing distance from family and friends, not to mention the smell of cut grass and the appearance of holiday decorations, could weigh on even the most eager of astronauts.

Determined to prepare for contingencies, NASA is funding research to understand ways to combat the mental health strains that might affect future astronauts who dare to go further than anyone has ever gone.

‘Being in long-duration space missions with other people, we expect the mental health risk will be much more elevated’. — Adam Gonzalez

Gonzalez, an assistant professor of psychiatry at Stony Brook University, received over $1 million in funding from NASA to explore ways to help these future astronauts who might be anxious or depressed when they’re on the way to the red planet.

In a highly competitive process, Gonzalez received the financial support to provide guidance on what NASA considers a low-probability, high-consequence mental health event, according to Williams.

Gonzalez “was funded because of the soundness of his research proposal and the clinical and technological expertise of the research team he assembled to help NASA address this research gap,” Williams explained.

Gonzalez started providing three different types of psychological assistance to 135 people in the middle of September. He is testing ways to provide mental health assistance with a delay that could require over 40 minutes to travel back and forth.

One group of test subjects will use a system called myCompass, which is a mental health self-help program. Another group will use myCompass coupled with a delayed text messaging response from a therapist, and a third will have a myCompass system along with delayed video messaging from a therapist.

“Being in long-duration space missions with other people — in this case, months and potentially years — stuck in extremely close quarters with others, we expect the mental health risk will be much more elevated relative to what they are going to have on the International Space Station,” Gonzalez said.

Williams said astronauts to date have not had any diagnosable disorders, but NASA has seen fluctuations in their mood, which appears linked to workload demands and the phase of the mission, Williams said. For astronauts, NASA does not want a continuing negative trend that, over a longer term, could turn into a problem.

“Part of what we hope to achieve with [Gonzalez’s] research is a validated approach to address any of these concerns,” Williams said, adding that astronauts typically understand that their contributions involve work in “high-demand, extreme environments,” Williams said.

Still, like explorers in earlier centuries, astronauts on a trip to Mars will journey farther and for a longer period of time than anyone up to that point. MyCompass is a “good, efficacious program” that takes a “trans-diagnostic cognitive behavioral therapy approach,” Gonzalez said. He suggested that the program is broad enough to help individuals manage their emotions more generally, as opposed to targeting specific types of health disorders.

Gonzalez emphasized that the choice of using myCompass as a part of this experiment was his and might not be NASA’s. The purpose of this study is to investigate different methods for communicating for mental health purposes when real-time communication isn’t possible.

William suggested that Gonzalez’s work, among others, could lead to individualized procedures for each astronaut. In addition to his work with NASA, Gonzalez also assists people at the front lines after man-made or natural disasters. He has worked with Benjamin Luft, the director of Stony Brook University’s WTC Wellness Program, on a program that offers assistance to first responders after the 9/11 attacks.

Gonzalez’s father, Peter, was a police officer who worked on the World Trade Center cleanup and recovery efforts. The elder Gonzalez has since had 9/11-related health conditions.

Gonzalez and associate professor Anka Vujanovic, the co-director of the Trauma and Anxiety Clinic at the University of Houston, are putting together a research project for the Houston area. Vujanovic did a mental health survey on Houston area firefighters earlier this year. They are inviting these firefighters to complete an online survey and telephone assessment to determine their mental health after Hurricane Harvey.

They are also conducting a three- to four-hour resilience training workshop for Houston area firefighters engaged in Harvey disaster relief efforts. “This resilience program, developed by [Gonzalez] and his colleagues, has shown promising results in reducing various mental health symptoms when tested among first responders in the aftermath of Hurricane Sandy,” Vujanovic explained in an email.

Vujanovic has known Gonzalez for over 10 years and suggested his questions were focused on “how can we better serve others, how can we improve existing interventions and how can we develop culturally sensitive approaches for vulnerable, understudied populations.” Gonzalez, who grew up in Bensonhurst, Brooklyn, and came to Stony Brook in 2012, said he was always interested in helping others.

Williams suggested that this kind of research can help people outside the space program. “We openly share and encourage the sharing of any of our relevant research findings to help address societal needs,” he added. Gonzalez’s research is “a great example of how a NASA focus on delivering personalized interventions in support of long-duration spaceflight could potentially be generalized to more rural settings where mental health providers may be scarce.”

From left, Zachary Lippman and Dave Jackson, professors at CSHL who are working on ways to alter promoter regions of genes to control traits in tomato and corn. Photo by Ullas Pedmale

By Daniel Dunaief

He works with tomatoes, but what he’s discovered could have applications to food and fuel crops, including corn, rice and wheat.

Using the latest gene editing technique called CRISPR, Zachary Lippman, a professor at Cold Spring Harbor Laboratory, developed ways to fine-tune traits for fruit size, branching architecture and plant shape. Called quantitative variation, these genetic changes act as a dimmer switch, potentially increasing or decreasing specific traits. This could help meet specific agricultural needs. Looking at the so-called promoter region of genes, Lippman was able to “use those genes as proof of principal” for a technique that may enable the fine-tuning of several traits.

For decades, plant breeders have been looking for naturally occurring mutations that allow them to breed those desirable traits, such as a larger fruit on a tomato or more branches on a plant. In some cases, genetic mutations have occurred naturally, altering the cell’s directions. At other times, breeders have sought ways to encourage mutations by treating their seeds with a specific mutagenic agent, like a chemical.

In an article in the journal Cell, Lippman said the results reflect a road map that other researchers or agricultural companies can use to create desirable traits. This article provides a way to “create a new, raw material for breeders to have access to tools they never had before,” he said. Lippman has taken a chunk of the DNA in the promoter region, typically on the order of 2,000 to 4,000 base pairs, and let the CRISPR scissors alter this part of the genetic code. Then, he and his scientific team chose which cuts from the scissors and subsequent repairs by the cell’s machinery gave the desired modifications to the traits they were studying.

Invented only five years ago, CRISPR is a genetic editing technique that uses tools bacteria have developed to fight off viral infections. Once a bacteria is attacked by a virus, it inserts a small piece of the viral gene into its own sequence. If a similar virus attacks again, the bacteria immediately recognizes the invader and cuts the sequence away.

Scientists sometimes use these molecular scissors to trim specific gene sequences in a process called a deletion. They are also working toward ways to take another genetic code and insert a replacement. “Replacement technology is only now starting to become efficient,” Lippman said. Clinical researchers are especially excited about the potential for this technique in treating genetic conditions, potentially removing and replacing an ineffective sequence.

In Lippman’s case, he used the scissors to cut in several places in the promoter regions of the tomato plant. Rather than targeting specific genes, he directed those scissors to change the genome at several places. When he planted the new seeds, he explored their phenotype, or the physical manifestation of their genetic instructions. These phenotypes varied along a continuum, depending on the changes in their genes.

By going backward and then comparing the genes of the altered plants to the original, he could then hone in on the precise changes in the genetic code that enabled that variation. This technique allows for a finer manipulation than turning on or off specific genes in which an organism, in this case a plant, would either follow specific instructions or would go on a transcriptional break, halting production until it was turned on again.

At this point, Lippman has worked with each trait individually but hasn’t done quantitative variation for more than one at a time. “The next question,” he said, “is to do this multitargeting.” He will also use the tool to study how genes are instructed to turn on and off during growth, including exploring the levels and location of expression.

Lippman is talking with agricultural and scientific collaborators and hopes to go beyond the tomato to exploring the application of this approach to other crops. He is working with Dave Jackson, who is also a professor at Cold Spring Harbor Laboratory, on applying this model to corn.

The scientific duo has known each other for 20 years. Jackson taught his collaborator when Lippman was a graduate student at Cold Spring Harbor Laboratory and Jackson was chair of his thesis committee.

They have worked together on and off since Lippman became a faculty member about nine years ago. Last year, the two received a National Science Foundation genome grant to work on using CRISPR to study the effect of changes in promoter regions in their respective plant specialties.

“Unfortunately for us, tomato has a faster life cycle than corn, but we hope to have some results in corn this fall,” Jackson explained in an email. Lippman hopes to continue on the path toward understanding how regulatory DNA is controlling complex traits. “We can use this tool to dissect critical regulatory regions,” he said. “When we create this variation, we can look at how that translates to a phenotypic variation.”

Lippman said he is especially excited about the fundamental biological questions related to plant growth and development. When other scientists or agricultural companies attempt to use this approach, they may run into some challenges, he said. Some plants are “not transformable [genetically] easily.” These plants can be recalcitrant to plant transformation, a step sometimes needed for CRISPR gene editing. Still, it is “likely that CRISPR will work in all organisms,” he said.

Lippman hopes others discuss this technique and see the potential for a system that could help to customize plants. “My hope and my anticipation is that people all over the world will look at this paper and say, ‘Let’s start to try this out in our own systems.’ Hopefully, there will be a grass roots effort to import this tool.”

Anne Churchland. Photo from CSHL

By Daniel Dunaief

Someone is hungry and is walking through a familiar town. She smells pizza coming from the hot brick oven on her left, she watches someone leaving her favorite Chinese restaurant with the familiar takeout boxes, and she thinks about the fish restaurant with special catches of the day that she usually enjoys around this time of year. How does she make her decision?

While this scenario is a simplified one, it’s a window into the decision-making process people go through when their neurons work together. A team of 21 neuroscientists in Europe and the United States recently created a new collaboration called the International Brain Laboratory to explore how networks of brain cells support learning and decision-making.

“We understand the simple motor reflex,” such as when a doctor taps a knee and a foot kicks out, said Anne Churchland, an associate professor at Cold Spring Harbor Laboratory and the American spokesperson for this new effort. Scientists, however, have only a limited understanding of the cognitive processes that weigh sensory details and a recollection of the outcomes from various courses of action that lead to decision-making, Churchland said.

Scientists likened the structure of the new multilaboratory effort to the circuitry involved in the brain itself. The brain is “massively parallel,” said Alexandre Pouget, a professor at the University of Geneva and the spokesperson for the IBL. “We know it’s working on consensus building across areas so, in that respect, the IBL is similar.”

A greater awareness of the decision-making process could provide a step into understanding the brain network problems involved in mental health disorders.

Churchland’s lab is one of three facilities that will house a new behavioral apparatus to study decision-making in mice. The other sites will be in the United Kingdom and in Portugal. Eventually, other labs will use this same technique and house the same apparatus.

An ongoing challenge in this field of research, Churchland said, is that scientists sometimes create their own models to test the neurological basis of behavior. While these approaches may work in their own labs, they have created a reproducibility problem, making it difficult for others who don’t have expertise in their methods to duplicate the results.

Creating this behavioral apparatus will help ensure that the collaborators are approaching the research with a reliable model that they can repeat, with similar results, in other facilities.

While the scientists will all be exploring the brain, they will each be responsible for studying the activity of circuits in different parts. The researchers will collect a wealth of information and will share it through a developing computer system that allows them to maneuver through the mountains of data.

To address this challenge, the IBL is creating a data architecture working group. Kenneth Harris, a professor of quantitative neuroscience at the University College London, is the chair of the effort. He is currently looking to hire additional outside staff to help develop this process.

Harris suggested that the process of sharing data in neurophysiology has been challenging because of the complex and diverse data these scientists share. “In neuroscience, we have lots of different types of measurements, made simultaneously with lots of different experimental methods, that all have to be integrated together,” he explained in an email.

The IBL collaboration will make his job slightly easier than the generic problem of neurophysiology data sharing because “all the labs will be studying how the brain solves the same decision-making task,” he continued.

Harris is looking to hire a data coordinator, a senior scientific programmer and a scientific MATLAB programmer. He has a data management system already running with his lab that he plans to extend to the IBL.

Pouget said there are two milestones built into the funding from the Wellcome Trust and the Simons Foundation for this new collaboration. After two years, the researchers have to have a data sharing platform in place, which will allow them to share data live as they collect it.

Second, they plan to develop standardized behaviors in all 11 of the experimental labs, where the behavior has to be as indistinguishable from one lab to another as possible.

In addition to the experimentalists involved in this initiative, several theoretical neurobiologists will also contribute and will be critical to unraveling the enormous amounts of data, Pouget suggested. “If you’re going to tackle really hard computational problems, you better have people trained in that area,” he said, adding that he estimates that only about 5 percent of neuroscientists are involved in the theoretical side, which is considerably lower than the percent in an area like physics.

Researchers involved in this project will have the opportunity to move from one lab to another, conducting experiments and gaining expertise and insights. The principal investigators are also in the process of hiring 21 postdoctoral students.

Churchland said each scientist will continue to conduct his or her own research while also contributing to this effort. The IBL is consuming between a quarter and a third of her time.

Pouget suggested that Churchland was “instrumental in representing the International Brain Laboratory to the Simons Foundation,” where she is the principal investigator on that grant. “Her role has been critical to the organization,” he said.

Churchland said the effort is progressing rapidly. “It’s moving way faster” than expected. “This is the right moment, with an incredible team of people, to be working together. Everyone is dedicated to the science.”

Harris indicated that he believes this effort could be transformative for the field. “Neuroscience has lagged behind many other scientific domains” in creating large-scale collaborations, he explained. “If we can show it works, we will change the entire field for good.”

From left, Lisa Miller with her research team Andrew McGregor, Alvin Acerbo, Tiffany Victor, Randy Smith, Ruth Pietri, Ryan Tappero, Nadia Hameed, Tunisia Solomon, Paul Panica and Adam Lowery. Photo by Roger Stoutenburgh, BNL

By Daniel Dunaief

Most of the people at the building that cost near a billion dollars are pulled in different directions, often, seemingly, at the same time. They help others who, like them, have numerous questions about the world far smaller than the eye can see. They also have their own questions, partnering up with other researchers to divide the work.

Lisa Miller, a senior biophysical chemist at Brookhaven National Laboratory, lives just such a multidirectional and multidimensional life. The manager for user services, communications, education and outreach at the National Synchrotron Light Source II, Miller recently joined forces with other scientists to explore the potential impact of copper on a neurodegenerative disease called cerebral amyloid angiopathy (CAA).

Miller is collaborating with Steve Smith, the director of structural biology in the Department of Biochemistry and Cell Biology at Stony Brook University and William Van Nostrand, a professor in the Department of Neurosurgery at SBU who will be moving to the University of Rhode Island. The trio is in the second year of a five-year grant from the National Institutes of Health.

Miller’s role is to image the content, distribution and oxidation state of copper in the mouse brain and vessels. Van Nostrand, whom Smith described as the “glue” that holds the group together, does the cognitive studies and Smith explores the amyloid structure.

In an email, Smith explained that Van Nostrand’s primary area of research is in CAA, while he and Miller were originally focused elsewhere.

Potentially toxic on its own, copper is transported in the body attached to a protein. When copper is in a particular ionic state — when it has two extra protons and is looking for electrons with which to reduce its positive charge — it reacts with water and oxygen, producing hydrogen peroxide, which is toxic.

Miller and her colleagues are working on a technique that will enable them to freeze the tissue and image it. Seeing the oxidation state of the metal requires that it be hydrated, or wet. The X-rays, however, react with water, causing radiation damage to the tissue.

To minimize this damage, the researchers freeze the tissue. At NSLS-II, a team of scientists are working to develop X-ray-compatible cryostages that will allow them to freeze and image the tissue.

Miller is trying to figure out where and why the copper is binding to an amyloid beta protein. This is the same protein that’s involved in plaques prevalent in the brains of people with Alzheimer’s disease.

In Alzheimer’s patients, the plaques are found in the parenchyma, or the extracellular space around the brain cells. In CAA, the deposits are attached to the surface of the blood vessels on the brain side.

Lisa Miller and her dog Dora on a recent 100-mile trek from Hiawassee, Georgia, to Fontana Dam in North Carolina Photo from Lisa Miller

The current hypothesis about how copper becomes reactive in the brain originates from work Van Nostrand and Smith published recently. They suggested that the amyloid fibrils in CAA adopt an anti-parallel orientation and the fibrils in the plaques in Alzheimer’s are in a parallel orientation. The anti-parallel structure predicts that there is a binding site for copper that, if occupied, would stabilize the structure.

“We are currently working to establish if this idea is correct,” Smith explained in an email, suggesting that the NSLS-II provides a “unique resource for addressing the role of copper in CAA. The data [Miller] is collecting are essential, key components of the puzzle.”

The NSLS-II will provide the kind of spatial resolution that allows Miller to measure how much copper is in the deposits. Ideally, she’d like to see the oxidation state of the copper to see if a reaction that’s producing hydrogen peroxide is occurring.

A challenge with peroxide is that it’s hard to find in a living tissue. It is highly reactive, which means it does its damage and then reverts to water and oxygen.

As someone with considerable responsibilities outside her own scientific pursuits, Miller said she spends about a quarter of her time on her own research. One of Miller’s jobs during the summer is to host the open house for NSLS-II, which allows members of the community to visit the facility. This year, at the end of July, she “was thrilled” to host about 1,600 members of the community.

“Most of them wanted to go on the floor and meet the scientists and walk” around the three quarters of a mile circle, she said. While they are interested in the research, the surprising mode of transportation strikes their fancy when they trek around the site.

“The thing that fascinates them when they walk in the door is the tricycles,” she said. The NSLS-II can’t take credit for being the first facility to use these adult-sized tricycles, which number over 100 at the facility. “It’s a synchrotron thing.”

The previous NSLS at BNL was too compact and had too many turns, which made the three-wheeled vehicles, which, like a truck, need a wider turning radius to maneuver on a road, impractical.

Miller, who is a part of the trike-share program, is an avid hiker. This summer, she completed a 100-mile trek from Hiawassee, Georgia, to Fontana Dam in North Carolina. This section was located in the area of totality for the solar eclipse and Miller was able to witness the astronomical phenomenon at Siler Bald in North Carolina.

A resident of Wading River, Miller, who grew up in the similarly flat terrain of Cleveland, spends considerable time walking and running with her rescue mutt Dora, who accompanied her on her recent hike.

While Miller finds the research she does with copper rewarding, she said she also appreciates the opportunities NSLS-II affords her. “Every day is different and we never know what project will show up next,” she said.

Laurie Shroyer, center, with Gerald McDonald, left, who was chief of surgery survive at the VA Central Office and is now retired, and Fred Grover, right, a professor of cardiothoracic surgery in the Department of Surgery at the University of Colorado. Photo from Laurie Shroyer

By Daniel Dunaief

To use the pump or not to use the pump? That is the question heart surgeons face when they’re preparing to perform a surgery that occurs about 145,000 times a year in the United States.

Laurie Shroyer. Photo from SBU

Called coronary artery bypass graft, surgeons perform this procedure to improve blood flow to a heart that is often obstructed by plaque. Patients with severe coronary heart disease benefit from a technique in which an artery or vein from another part of the body is inserted into the heart, bypassing the blockage.

Doctors can perform the surgery with a heart-lung machine, which is called on pump, or without it, which is called off pump.

Recently, a team of researchers led by Laurie Shroyer, who is a professor of surgery and the vice chair for research at the Stony Brook University School of Medicine, published a study in the New England Journal of Medicine that compared the survival and health of 2,203 veterans five years after surgery, with or without the pump.

Contradicting some earlier research that showed no difference in the health and outcomes after the surgery, the study revealed that using the pump increased the survival rate and reduced the rate of other health problems.

Along with the other research articles in this area, this study “should help in deciding the relative value and risks of each technique,” Frederick Grover, a professor of cardiothoracic surgery in the Department of Surgery at the University of Colorado, explained in an email.

The study Shroyer led, which is known as the Rooby trial, showed that on-pump patients had a five-year mortality of 11.9 percent, compared with 15.2 percent for the off-pump patients, Shroyer explained.

The five-year rate of medical complications, including death, nonfatal heart attacks and revascularization procedures was also lower for the on-pump group than the off-pump group, at 27.1 percent compared to 31 percent, respectively.

Consistent with these findings, the overall use of off-pump procedures has declined, from a peak of 23 percent in 2002 to 17 percent in 2012, down to 13.1 percent in 2016, according to data from the Society of Thoracic Surgeons Adult Cardiac Surgery Database Committee.

At one point, surgeons had considered an off-pump approach to be safer, but when other trials didn’t show a benefit and when the current Rooby trial demonstrated on pump had better outcomes, it “likely influenced many surgeons to use the off pump less often for specific reasons, considering it is a somewhat more difficult technique except in the most experienced hands,” Grover wrote.

The explanation for the difference five years after surgery are “not clear,” Shroyer explained in an email. The article suggests that the off-pump patients had less complete revascularization, which is known to decrease long-term survival.

Grover explained that the outcomes may have been better for the on-pump procedures in the Rooby trial for several reasons, including that the surgeons in the different trials had different levels of experience.

Leaders of the study suggested that patients and their surgeons needed to consider how to use the information to inform their medical decisions. Participants in the study were men who were veterans of the armed services.

“The data can likely be extrapolated to the general population since it is not an extremely high-risk population, but it is all male so would primarily extrapolate to males,” Grover suggested. Additionally, patients with specific conditions might still have better outcomes without the use of a pump.

“Our manuscript identifies an example for ‘patients with an extensively calcified aorta, in whom the off-pump technique may result in less manipulation of the aorta, potentially decreasing the risk of aortic emboli or stroke,’” Shroyer wrote in an email. Grover also suggested people with severe liver failure also might want to avoid the pump to prevent additional harm to the liver.

Shroyer and her team have already submitted a proposal to the VA Central Office Cooperative Studies Program. “Pending approval and funding, 10-year follow-ups will be coordinated appropriately,” Shroyer said.

Grover described Shroyer as a “spectacular investigator with a very high level of knowledge of clinical research” and, he added, a “perfectionist.” When he met Shroyer, Grover said he was “blown away by her intelligence, experience, background and energy.” He interviewed her many years ago to direct a major VA Cooperative Study. After the interview and before the next meeting, he called another interviewer and asked if he, too, agreed to hire her on the spot.

Grover recalled a trip back from Washington to Denver 15 years ago after they had been in a 10-hour meeting with no scheduled breaks. She took out her laptop on the airplane and asked him to write up results for a new grant.

“I was beat and finally said if she didn’t let up, I was going to jump out of the airplane just to get away from her,” he recalled. She shut her computer, ordered drinks and they enjoyed a peaceful flight back.

A resident of Setauket, Shroyer lives with her husband Ken, who is the chair of the Department of Pathology at Stony Brook School of Medicine. The professor said she loves the Staller Center, which she considers one of the greatest kept local secrets. She appreciates the opportunity to hear classical music performances by the Emerson String Quartet and by cellist Colin Carr.

When she entered biomedical research in 1992, it was unusual for women to rise to the level of full professor at an academic medical center. She strives to be an outstanding mentor to her trainees, including women and under-represented minorities, so that they can achieve their potential, too. As for her work, Shroyer’s hope is that the Rooby research “will provide useful information to guide future changes in clinical care practices” and, in the longer term “to improve the quality and outcomes for cardiac surgical care.”

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