Authors Posts by Daniel Dunaief

Daniel Dunaief


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Associate professor and his team look at stages of frog reproduction: egg to tadpole to frog

An attacking snake causes the eggs of most red-eyed tree frogs to hatch immediately, sending young tadpoles that were developing on leaves in the air to plunge into the water below to escape the slithering predator.

This is just one of many life-history strategies frogs have developed over the more than 200 million years since they started snatching insects and hopping and lunging around waterways.

While just over half the frogs in a survey of 720 species of frogs around the world follow the same life history they employ on Long Island — namely, laying eggs in water, hatching as tadpoles and developing into frogs — the others go through a range of reproductive cycles, including laying eggs out of the water (like the red-eyed tree frog) or even developing directly (i.e., hatching as frogs).

Those frogs that develop directly are found primarily in moist, warm regions in the tropics.

Stony Brook Associate Professor John Wiens, in collaboration with Ivan Gomez-Mestre from the Donana Biological Station in Seville, Spain and Alexander Pyron from George Washington University, wanted to know how these different reproductive strategies evolved and why so many frogs continued to employ the aquatic approaches.

“It seems like laying eggs terrestrially is great because the eggs are out of the water and are protected from aquatic predators, but at the same time, that comes with a cost,” Wiens suggested.

Indeed, the frogs that lay eggs out of the water typically produce fewer offspring. There’s a mechanical explanation for this: the eggs are larger but the momma frogs are the same size. The eggs of direct developers also need to contain all the resources necessary to become a frog.

Frogs that lay eggs in the water, on the other hand, can lay more and smaller eggs, because the tadpoles can feed themselves. The squiggly swimmers can eat algae that they scrape off rocks, bacteria at the bottom of ponds or invertebrates like freshwater shrimp. Some tadpoles, Wiens pointed out, eat other tadpoles and, in some species, the mothers feed the tadpoles with unfertilized eggs.

But, as with the red-eyed tree frog, some of these amphibians have stayed with what might be considered an evolutionarily intermediate stage: instead of choosing direct development or aquatic development, they place their eggs outside water, until they hatch into tadpoles.

In South America, for example, glass frogs have been laying their eggs outside of water for over 50 million years. Once they hatch, tadpoles breathe and eat in the water until they become frogs. For glass frogs, this isn’t a true intermediate stage, because they never evolved into direct development.

For some frogs that make the evolutionary hop from aquatic to direct development, however, the intermediate steps may not be necessary.

“In about half the cases in which direct development evolves, it seems to evolve directly from the primitive mode,” Wiens offered. While it is possible that intermediate stages occurred in these frogs, the results “suggest it would have had to do so relatively rapidly.”

Frog reproductive cycles can provide insight into medical questions or problems.
There is an extinct frog that was a gastric brooder in Australia. That frog kept its eggs and young in its stomach. Somehow, during its reproductive cycle, the frog turned off its gastric juices, allowing its young to grow and develop in the relative safety of its mother’s stomach. Scientists have been hoping this frog’s life cycle might provide additional tools to treat ulcers.

In addition to frogs, Wiens studies salamanders, lizards, snakes and turtles.

He studies the interface between evolution and ecology.

“Using the reconstructed or evolutional history of reptiles and amphibians and other groups, we try to understand how biodiversity originates,” he suggested. He looks at questions such as why there are more species in the tropics.

Wiens lives in Stony Brook with his wife, Ramona Walls, a postdoctoral research associate at the New York Botanical Garden. The scientific couple, who have a daughter in college, enjoy visiting beaches on the island and hiking.

As for frogs, the recent study contradicts some of what scientist had believed for years.

“In many cases, rather than going from having eggs laid in water to eggs laid on land to direct development, frogs jumped the queue, going straight from eggs laid in the water to direct development,” he offered.

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In October, a trip to Hawaii aboard the Spirit should add data to the ongoing study

Ernie Lewis likes to play the cloud game, looking for familiar shapes in our puffy white neighbors overhead. While he’s contemplating whether that one resembles a dog and this one looks like a lizard, he wonders how he might capture the clouds mathematically or model them in a climate system.

A researcher at Brookhaven National Laboratory, Lewis can appreciate the aesthetic wonder of the clouds even as he would like to understand them much better than modern science currently does. Clouds are one of the most confounding variables in predicting and understanding climate.

“The ability to accurately represent clouds and cloud properties in climate models is lacking and is one of the largest gaps in our understanding,” explained Lewis.

The BNL researcher is at the beginning of coordinating an effort to understand how clouds transition from the predominantly stratocumulus versions in Los Angeles to the mostly cumulus types in Hawaii. A stratocumulus cloud is white, grey or a mixture of the two and often looks thick and dark and appears in waves or sheets. Cumulus clouds, by contrast, look harmless and often have more defined boundaries and look like puffy balls of cotton.

Starting in October, a team of scientists under his direction will travel the 2,548 miles back and forth from California to Hawaii aboard the Horizon cargo ship Spirit. They will bring with them their own container of sophisticated equipment and will launch weather balloons four times a day. The balloons, which contain equipment housed in a small container Lewis said looks like a Chinese food take-out package, will send back information about the temperature, pressure and relative humidity, as well as wind speed and direction.

The scientists will use the information to figure out how clouds change along the route through the Pacific.

Scientists aboard the Spirit will coordinate their data with NASA, which is collecting information from its satellites. The team aboard the cargo ship will compare their photos of the clouds from below with what NASA satellites see from above. This will help validate NASA’s satellite retrieval.

Clouds absorb outgoing infrared radiation from the Earth’s surface, which warms the planet. At the same time, clouds scatter incoming infrared, visible and ultraviolet radiation from the sun, which cools it.

“As nearly all of Earth’s energy comes from the sun, understanding the behavior of this incoming radiation and how it is transferred is important to understanding climate,” Lewis wrote in an online update of his research. You can follow his efforts through the link:

Lewis plans to take the two-week trek aboard the Spirit in October. He will also go back and forth in December or January. Others from the project will ride in September to set up the equipment.

On a test voyage, Lewis said the accommodations are quite comfortable, and include such amenities as a weight room and a lounge with movies.

“We are grateful for Horizon Lines and to the captains and crew of the Horizon Spirit,” Lewis offered.

Lewis, who did oceanographic research through Woods Hole in Massachusetts, is especially appreciative of the size and sturdiness of the ship. When he was aboard smaller vessels in the North Atlantic, he’d get seasick, especially during Nor’easters.
Lewis put his oceanographic background to good use when he wrote a book called “Sea Salt Aerosol Production.” Steve Schwartz and Lewis described how the bubbles comprising whitecaps send seawater drops into the air. The drops evaporate and climb into the atmosphere, where some form the seeds of cloud drops.

“It’s a summary of knowledge of how these are produced,” he explained. “It’s a consolidation of the work that has been done” on these white caps.

Lewis, who lives in Calverton, looks to the skies for one of his other passions, birds. An avid birder, Lewis enjoys going to Fire Island in the fall to watch migrating raptors (i.e., predatory birds, like hawks). He also enjoys watching birds at the lab.

Lewis is married to Northeastern University Professor Laura Henderson Lewis. They commute back and forth from Boston to Long Island.

“I hope my research will lead to a better understanding of clouds and their effect on climate,” he explained.

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BNL’s Chang-Jun Liu works experiments with plants to more easily make biofuel

Plants build a biological fortress around one of their most important jewels: sugars. They fortify a wall with a substance called lignin, whose name in Latin means wood.
When scientists want to turn plants into biofuel, their first step is to delignify the plant, or, as Ronald Reagan might say, to “tear down that wall” to free up the sugars. The process is expensive and reduces the energy efficiency of using plants for biofuel.

Brookhaven National Laboratory biologist Chang-Jun Liu has been working for over four years to figure out how to get plants to produce less lignin, i.e., to produce walls that would be weaker, making it easier to get at those precious sugars.

Liu, Kewei Zhang, Mohammed-Wadud Bhuiya and Yuchen Miao, along with a team from the University of Wisconsin, needed to figure out how to reduce the amount of lignin in the walls without destroying a plant’s ability to grow. Lignin, after all, is necessary to help a plant maintain its structure and climb toward the light.

Liu and the team of scientists looked for ways to send a signal to the plant that the work of putting lignin together was done before the walls of the lignin fortress became too strong. The process of building a complex polymer like lignin involves putting many steps together. What Liu created was a premature “good to go” signal so that the plant produced walls with less lignin.

The scientists tested over a thousand different classes of enzymes that might interfere with the process of forming lignin. By 2009, they had found that an enzyme that naturally occurs in plants but has a different function might do the trick. If they mutated (or genetically altered) two key amino acids in the enzyme, it would change the lignin in such a way that would prevent the molecules from coupling to form a tight bond.
While the amino acid changes worked outside the plant in lab experiments, they didn’t work when used in a live plant. Using BNL’s National Synchrotron Light Source to determine the enzyme’s crystal structure, they discovered more amino acid mutations that worked.

The new enzyme reduced lignin by 24 percent, leading to a 21 percent increase in the release of cell wall sugars.

At the same time, though, the reduced lignin didn’t affect the plant’s ability to develop and grow, a key consideration in the development of biofuel.

“You can’t see any difference in the plant,” Liu explained.

Liu remained aware of the delicate balance between weakening the lignin to gain easier access to the cellulose sugars in the cell wall and the need to leave enough for the plant to survive.

Lignin is involved in water transportation, allowing the leaves at the top of the plant to receive water delivered from the soil. Lignin also provides a physical barrier to prevent a plant from becoming too susceptible to damage from changes to the environment or from insect attacks.

“Within a certain range, the plant can still survive well,” Liu offered. “We think our method compared with others is an advantage.”

Liu has inserted his enzyme into poplar trees to reduce lignin. He is seeking collaborators to test whether the lignin reduction will help in promoting the conversion of wood into bioethanol with laboratory scale fermentation. He is discussing this with scientists at SUNY Syracuse.

Liu recognizes the benefit of contributing to improving the nature of biofuel production.

“Biofuel is one of the solutions to reduce our dependence on fossil fuels,” he explained. “Currently, our ability to convert to biofuel is low.”

Natives of China, Liu and his wife Yang Chen, who works as a special education aid at Rocky Point Middle School, moved to Oklahoma in 1999. That’s where their children, who now attend the middle school and elementary school in Rocky Point, were born.

After a brief stopover in California, Liu joined BNL in 2005. He enjoys hiking and walking in the state park with his family.

As far as his research, Liu hopes it will benefit his children’s generation.

“We have to find a way to secure our energy future,” he explained. “We have to find alternative sources of energy to meet our needs.”

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SBU assistant professor Heather Lynch uses high tech tracking to study avian populations

While Heather Lynch has seen close-up some of the incredible tales of survival, loyalty and determination that documentaries like “March of the Penguins” highlight, she also has firsthand experience with some other penguin realities. For one thing, these birds are incredibly loud, with noise levels that would easily top the decibels reached by a town pool packed with screaming children.

They also stink something fierce.

“You can smell them a mile out to sea,” laughs the assistant professor of ecology and evolution at Stony Brook University. After spending six weeks living among the penguins in the Antarctic, researchers themselves develop such a foul odor that those who bring them back from their stations “step back in horror. The clothes we wear can’t be worn in public. They can only be worn again in Antarctica.”

Lynch, however, said the scientists don’t notice the smell after a while. Instead, they focus on some of the more incredible and inspiring moments from birds that are as awkward on the land as they are graceful in the water. She has seen some of them fall 20 feet off a cliff onto their heads and bounce up like nothing happens.

And while she enjoys taking a step back to appreciate these flocks of water fowl, she journeys to their homes primarily to count their shifting populations. A Princeton-trained physicist, with a PhD from Harvard, Lynch uses her background with numbers to understand bigger picture ecological questions.

For over five years, Lynch has studied the populations of three species of penguins to document how they have been changing and to pinpoint what might be causing those changes.

Global warming, she concluded, is the biggest reason two out of three penguin species populations have declined. The chinstrap and adelies penguins have had a harder time finding food amid warming in the region. The chinstrap has declined at the rate of 1.1 percent per year, while the adelie has lost 3.4 percent of its numbers each year.

The gentoo, however, has come out ahead.

It “can take advantage of environmental conditions to breed at the right time,” Lynch observed. “They also have a more varied diet and are more flexible about where they nest. Its whole life history strategy is focused on flexibility.”
Unlike the other two species, the gentoo does not migrate long distances away from the colony in non-breeding months. Indeed, the gentoo population has risen 2.4 percent per year.

Lynch has been counting penguins not only from her annual visits to their southern home, but also from the comfort of her home and her one-year old laboratory at SBU, where she can track and monitor these birds through satellite images that allow her to see birds with a resolution of 50 centimeters.

Satellites are a “complete game changer,” she declared.

When scientists are in the Antarctic, they often spend considerable time observing and tracking individual penguin populations.

“There are so many populations of penguins that we can’t get to because of the logistical difficulty,” she noted. With satellite images, she can observe and track more groups in the region.

Through her research, Lynch has also concluded that tourists, who numbered over 33,000 from 2010 to 2011, have not had an effect on the birds they so eagerly travel to see.

“We now have strong evidence that tourism is not driving these changes,” Lynch stated.

She has found that reproductive success does not decline in heavily visited colonies and there is no relationship between visitation and populations.

In addition to her population research, Lynch and Ron Naveen, the president of Oceanites, lead a team of about a dozen biologists who conduct fieldwork in the Antarctic. She helped coordinate other scientific studies, including studying moss and lichen biodiversity on the Antarctic Peninsula, and genetic sampling to look at patterns of genetic diversity.

The mother of a daughter who will soon turn three, Lynch, who is a resident of Port Jefferson, has found penguin parenting and dedication inspiring. Lynch met her husband, Brookhaven National Laboratory scientist Matthew Eisaman, in a quantum mechanics class at Princeton.

A proud fifth-generation Red Sox fan, Lynch made a sign on Petermann Island that declared the site the “southernmost point of Red Sox nation.”

Despite the smells and the noise from visiting the Antarctic, Lynch plans to stick with penguins for the long haul.

The Antarctic Peninsula is “one of the most rapidly warming places on our entire planet, so I think it can teach us a lot about how ecosystems respond to climate change,” she said.

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As part of a research group, he studies a wide variety of potential treatments to help patients heal

Burns present an especially challenging problem for doctors and medical researchers. While lacerations and abrasions harm skin directly affected by the injury, a burn can cause damage to skin nearby.

Adam Singer, the director of research for Stony Brook Medical School’s emergency medicine program, has worked with a team of physicians, students and researchers to understand how to limit the damage from a burn.

In the lab, they have tested a range of therapies, from using age-old remedies derived from spices and other natural substances to creating new products.

“Our main efforts are focused on understanding how burns progress,” Singer explained. “Unlike a mechanical injury, where the maximum extent of the injury takes place at the time of wounding, burns tend to extend in depth and size. Burns are more challenging because the injury tends to get worse before it gets better.”

Singer and a team at Stony Brook that includes Dr. Richard Clark in the dermatology department and Mary Frame in the bioengineering department, have studied synthetic products and natural herbs to understand burns.

The researchers examined blood flow in preclinical burn models treated with curcumin. Found in the spice turmeric, curcumin has been used for years in a range of herbal remedies. In testing, curcumin increases the dilation of blood, which might help nearby skin.

Singer explained that curcumin has been used in India before nuptials to add color
to the cheeks of those getting married.

“It was used for centuries in weddings,” explained Singer. “We found out it causes vasodilation. That’s probably how it caused that flushing.”

Singer explained that the medical school has tested other ways of minimizing damage and scarring, including stem cells.

There is no Food and Drug Administration approved treatment that prevents the progression of a burn injury. Treatment using topical solutions or antibiotics promotes healing without infection, but doesn’t address the surrounding skin, he explained.

The research in the emergency department at Stony Brook draws from several places. In addition to a group that could include doctors and Ph.D.s from around the campus, the effort may include postdoctoral students, graduate students, medical students, international fellows and even interested high school students.

“We’ve created one of the first academic associate programs for undergraduate students,” explained Singer. “They spend time in the emergency department, screening and enrolling patients in clinical students. In return, they get credit from
the university.”

He estimated that there are between 20 and 30 undergraduates per semester who rotate through the emergency department.

“There are a wide spectrum of studies, from cell to human patients at all levels of basic research,” said Singer.

Another challenge with burns lies in predicting which ones will be deep and require surgery and which ones will heal on their own.

Doctors currently use laser Doppler to look at the blood flow in a wound. While the Doppler is helpful, it may not be reliable until the third day after a burn or injury. During that time, patients wait in a hospital, where they are exposed to the risk of infection.
The Stony Brook team is looking at novel technologies to try to predict which burns will progress to the point where they’ll require surgery.

One approach is based on infrared light emissions and the other is based on a fluorescent marker. Fluorescein measures flow, whereas infrared light measures temperature, which is dependent on underlying blood flow. The less flow, the colder the skin.

“We’re looking at state of the art technology to diagnose burn depth early to improve the care of patients,” explained Singer, who divides his time equally between treating patients and conducting or directing research.

Singer and his wife Ayellet, who designs jewelry, have three children, Daniel, who is starting medical school, Lee, who is premed, and Karen, who is attending a SUNY School and wants to study biomedical engineering.

Singer, who grew up in Westchester and spent 20 years in Israel, has connections to Long Island that predate his move here. His grandfather, Seymour Singer, was active in the Chamber of Commerce in Smithtown, which named Singer Lane after him. His father grew up in Lake Ronkonkoma.

As for Stony Brook’s research department, Singer explained that it has been involved in trials of products that emergency room physicians use regularly, including glue to seal lacerations and incisions.

Stony Brook was the “largest site in the country” for clinical trials of a glue that has now been used millions of times per year.

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The world’s largest digital camera will help scientists ‘see’ dark matter, asteroids and much more

Paul O’Connor at Brookhaven National Laboratory is part of a team building a combination telescope and camera whose “wow” factor is off the charts. When the Large Synoptic Survey Telescope (LSST) is up and running in 2021, it will allow us to look deep into billions of galaxies, keep a close eye on nearby asteroids and even help us see so-called dark matter, which does not emit, reflect or absorb light.

The LSST will be the largest digital camera in the world, will survey a volume of the universe in its first week of operation larger than all previous telescopes combined, will take three-gigapixel photographs, and will survey the entire sky every three nights.
And, from its perch at 8,800 feet in Cerro Pachon in Chile, the LSST will monitor asteroids near the planet.

The telescope will make an “orbit determination for asteroids that may pose a threat from colliding with our planet,” O’Connor explained.

It will also be able to see dark matter, which comprises 25 percent of the universe, or 5 times more than things we can see, like puppies, the Olympic games and fireworks.

Here’s how it works: the telescope looks at light that comes from incredibly far away that was sent into space billions of years earlier. If there weren’t any dark matter, the light would take a direct route. Dark matter, however, causes the light to bend, as if it were going through a lens. How the light bends reveals the “clumpiness” of the dark matter. (If you’re wondering about the remaining 70 percent of the universe, that’s comprised of dark energy, a force that played a role in cosmic evolution and works against gravity, allowing the universe to expand.)

O’Connor is helping with the “film” part of the camera. The LSST will need over 200 charge-coupled devices, which process even the faintest of signals.

The charge-coupled devices will be arranged in a mosaic inside the telescope and have to be almost perfectly flat when lined up, with no more than a 10-micron tilt in any direction. The thickness of a human hair, by comparison, is 100 microns.

The LSST team has asked private companies to build these charge-coupled devices. When those are completed, the read out time on them will be 10 times faster than the state of the art in astronomy. One of O’Connor’s jobs is to test their work, to make sure they meet the requirements for the telescope.

“We give them our suggested design approach and then we let the companies provide a manufacturing method,” he offered. “When the prototypes come back, we have to verify that they’ve met the requirements. It involves a rigorous test protocol.”

O’Connor, who is the associate division head of the instrumentation unit at BNL, does considerable coordinating between scientists and the manufacturers. He can spend seven hours or more on teleconference calls, speaking with collaborators.

“It’s the nature of big science projects,” he explained. It’s required to keep “coherent, large collaborations functioning and communicating well.”

Assembling and testing the small parts necessary for this three-ton telescope requires clean rooms, where scientists have to wear full-body suits, masks and gloves.

Brookhaven has a clean room and is in the process of building another, which will be finished later this year. Its initial occupant will be the LSST project.

“Human beings are the worst actors in producing particles,” explained O’Connor. “We have to take precautions.”

O’Connor lives in Bellport with his wife Leslie, who is an elected trustee of the village.

The O’Connors have one daughter at Massachusetts Institute of Technology and another who is entering her final year at Bellport High.

When he’s not checking parts for the LSST, O’Connor enjoys kayaking and sailing in the Great South Bay.

As for his work, O’Connor explains that he is “charged to provide the next generation technology in the support of a science mission.” He enjoys the opportunity to work in a multidisciplinary effort. He has also worked on projects closer to home, including developing a process for screening for breast cancer that combines the best of positron emission tomography and magnetic resonance imaging.

“It’s very exciting and satisfying to be able to work in all those fields of cutting edge science,” he explained.

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Some have suggested that the link is so tight that they are manifestations of the same disease

The answer is A, not B. The appointment was at 11 am on Tuesday, not 1 pm. The Magna Carta was signed in 1215, not 1512. You’re wrong, you’re wrong, you’re wrong!

Those are innocent enough mistakes. It turns out, though, that the neurological reaction to those mistakes is different for some children, especially those with anxiety disorders.
Stony Brook assistant psychology professor Greg Hajcak (pronounced “high-chuck”) has found that the brains of different children react to mistakes differently. An anxious child will likely have a larger neurological response than the brain of someone who shows no signs of anxiety.

Hajcak treats patients at the Anxiety Disorders Clinic while he also does research to look for ways the brains of people with different disorders react under various conditions.

In a doctor’s office, many children present symptoms that are nearly identical in cases of anxiety or depression.

“The link in anxiety and depression is so tight that some have suggested these aren’t really separate diseases, but are manifestations of the same disease,” Hajcak offered.

That’s not the case, however, when the brain responds to mistakes. Putting caps that look like Olympic swimwear (except for the noninvasive electrodes inside them) on the heads of his young subjects, Hajcak conducted electroencephalograms (EEGs) as his young charges performed tasks in his lab. The children with anxiety disorder showed stronger electrical reactions after errors even than those with depression.

This kind of information could be helpful for parents and doctors, especially if it provides early evidence of the development of emotional challenges.

Hajcak’s research provides the “notion that we could have unique markers for these difficult-to-distinguish disorders,” he suggested. “We might be able to say what the earliest place where we could differentiate the trajectories of risk.”

That could be useful for the 10 to 20 percent of the population that will likely have an anxiety disorder before they’re 18, explained Hajcak.

To be sure, Hajcak and other researchers are years from being able to connect brainwave activity in response to a test or set of tests to the likelihood of a disorder.
Nonetheless, these types of studies are important first steps in looking for signs of anxiety or depression that could become useful for children, parents, and mental health professionals.

Hajcak recognizes that these markers could suggest to parents what kind of programs might help their children if they see signs of anxiety.
Like any biological marker, a potential sign for anxiety disorder could become one part of the total medical picture.

“If we know that child A vs. child B is at risk, it’s just a risk factor,” he explained.
The son of a retired clinical psychologist, Hajcak described himself as a “more worried kid” when he was younger. “Lots of people in clinical psychology would say that people tend to study things that are more relevant to them. Those personality features drew me to the anxiety world.”

A resident of Manhattan who commutes to Stony Brook to do his clinical and research work, Hajcak said he had a unique opportunity when he attended graduate school at the University of Delaware to study with Edna Foa, who works at the University of Pennsylvania. Foa, whom Hajcak described as “one of the foremost experts on anxiety disorders,” was named one of Time Magazine’s 100 most influential people in the world in 2010.

Hajcak worked with Foa for four years, during which time he learned “everything I know about anxiety disorders and their treatment,” including cognitive therapy, an especially effective solution for anxiety.

“Treating anxiety disorders is so fulfilling,” he offered. “It works so well: 75 percent or more of people will see at least a 50 percent reduction in symptoms. That’s pretty much as good as it gets in the mental health world.”

Hajcak got engaged earlier this month to Christine Proudfit, an obstetrician/ gynecologist who works with high-risk pregnancies at New York University. The couple, who work out together at the gym, also have plans to marry their professional pursuits. They have talked about examining how anxiety among low and high-risk populations relates to obstetrical and neonatal outcomes.

In the world of pregnancy, labor and childbirth, where new mothers face daunting challenges, anxiety can go hand-in-hand with picking out names and shopping for baby clothing.

“Unknowns and uncertainty,” explained Hajcak “are the wind in the sails of anxiety.”

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The physicist turned biologist working to map the entire brain’s circuitry

Partha Mitra sees a landscape dotted with isolated settlements. The researchers in each region focus on their area, but few have taken a step back to tackle the total terrain. A professor in neuroscience and theoretical biology at Cold Spring Harbor Labs, Mitra’s landscape is the brain. The Calcutta-born scientist wants to change that by mapping the entire brain circuitry.

“Parts of the brain get neglected,” he asserted. “I want to get coverage of the whole brain.”

There is considerable scientific research into the regions of the brain responsible for vision and smell, for example, but the core circuitry where emotions reside — apart from the “fear” and “reward” circuitry, has received considerably less attention.
Looking at the interaction of the entire mouse brain should provide a database that researchers exploring a wide range of topics — from evolution to psychiatric disorders — may employ.

Up until the last decade, a significant problem has been the cost of looking at the whole brain. In 1990, the expense for examining a mouse brain at a resolution of one micron was in the millions of dollars. Just for a sense of scale, a human hair is about 100 microns thick. Now, scientists can gather and store that information, which uses as much as 1 terabyte, or 1,000 gigabytes of computer storage, for closer to hundreds of dollars.

Mitra has taken what he calls a meso-level approach to the brain.

“We’re using classical neuroanalytical methods,” Mitra offered. “We inject a tracer into a part of the brain and let neurons transport that, either from synapse to cell body or from cell bodies to synapses.”

The big picture map of the brain is similar to what genetic scientists did when they mapped the human genome. By recognizing how the genome comes together, researchers can look for changes to understand diseases.

A more complete overview of the brain’s circuits could also help provide evidence in evolutionary debates.

“There are big controversies” relating to the brains of different animals, Mitra explained. “There is no empirical evidence to settle the controversy.”

Scientists used to believe brains evolved like onions – with a reptilian core, a “bird brain” intermediate shell and a mammalian cortical outer layer. While this theory has been discredited and scientists have suggested there are portions of the bird brain that are similar to the cortex, the controversy continues.

“Having the circuit diagram for the mouse brain and a comparative diagram for the bird brain of an appropriate species will help settle this,” he explained.

Mitra believes the publication process could use modification and improvement. Within minutes of something major happening in Egypt, people around the world can learn about it. A major advance in a scientific lab, however, can sometimes take years before people see it.

To that end, Mitra releases data as it comes off his experimental pipeline before publishing a manuscript on the subject. While this model is more common in physics, it hasn’t gained the same kind of traction in the biology community.

“The style now accepted in the physics community seems to be a better solution as it speeds up the communication of results,” he suggested.

Mitra believes an author-driven, freely published preprint, followed by a more traditional journal publication, strikes a balance between the conventional publication model and the potential for sharing results in real time.

When he’s not at the lab or at home in Manhattan, Mitra enjoys the chance to practice yoga. He attends three to six classes a week. A certified instructor, he hasn’t taught yoga since last fall.

He has been at Cold Spring Harbor since 2003. He earned a PhD in physics from Harvard and then went to Bell Labs, where he registered for about 10 patents, including improving wireless transmission capacity and holographic data storage.
Mitra also did research for about a decade examining song learning in the Zebra Finch. He believes nature plays a more important role in learning songs than had previously been thought.

The physicist turned biologist — who has also recorded a CD of himself singing Indian music — acknowledged he doesn’t fit into the usual mold of a biomedical researcher.

“I keep a broad scope,” he concluded.

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SBU professor Miriam Rafailovich and team of scientists study potential hazards of energy efficient bulbs

Miriam Rafailovich was concerned when she walked into her neighbor’s house. Her friends were putting together a jigsaw puzzle and had brought over a collection of compact fluorescent lamps (CFL) to make it easier to see the small pieces.

The Stony Brook professor of materials science and engineering urged them to use their ceiling chandelier or to look for incandescent lamps. While the energy-efficient CFL lights were helping them see, they were also likely bathing their skin in damaging ultraviolet light.

Rafailovich, who is the director of the Garcia Center for Polymers at Engineered Interfaces, learned this from her recent research. Using a broad range of CFL bulbs that junior high school students in Plainview, Syosset, Uniondale, Woodmere and Commack purchased from around Long Island, she tested the bulbs to see whether UV radiation — some of the same type emitted by the sun — was leaking out of them.

In almost every case, the protective cover around the fluorescent light had small cracks or leaks that released radiation. This confirmed what a recent European study had shown. Teaming up with Marcia Simon, the director of the Living Skin Bank at Stony Brook, Tatsiana Mironava, an adjunct faculty member and Michael Hadjiargyrou, a professor in the biomedical engineering department, Rafailovich took the European results a step further, testing the effect of this radiation on live skin cells that were grown and nurtured in a lab within a foot of the lamps to test the effect of this radiation. The light damaged the skin cells.

“We saw skin cells dying and we saw irritation,” she said. “It’s what you’d expect for cells exposed to that amount of UV rays.”

The ultraviolet exposure within a foot of CFL bulbs reached the threshold limit value (TLV — a measure of maximum dose to a specific wavelength in an eight-hour period) within 20 minutes. That means in eight hours, a person could get 17 times the maximum exposure.

“It is also important not to look into these bulbs, since UV penetrates the eye even easier than the skin,” Rafailovich contends.

Exposure to radiation at a close distance may not cause an immediate reaction because skin has an ability to adapt to UV light, the same way it would if you went to the beach every day.

“After a long time, though, you could see the effects of this exposure,” she suggested.

Based on her research, the Romanian-born Rafailovich suggests consumers should make sure CFL desk lamps have glass covers or are more than two feet away.

To be sure, the energy-efficient CFL lamps that don’t have additional glass covers are safe to use on ceilings and at greater distances. The UV radiation decreases at a rate that is the inverse square of the distance from the source. That means the further you get from the bulb, the lower the level of radiation.

Rafailovich said she has a CFL bulb in her house in Plainview and has no intention of removing it because it is far enough away that she doesn’t have to worry about radiation.

The Stony Brook professor also found that titanium dioxide, a nanoparticle (incredibly small) found in products ranging from toothpaste and tooth whiteners to some skin care products, can increase the absorption of ultraviolet radiation.

While the titanium dioxide wouldn’t necessarily be a problem for healthy skin, it could allow more absorption of the UV rays if a person had a wound.

Rafailovich’s research mission at Stony Brook includes looking at how nanoparticles more broadly affect skin cells.

When gold, which is used for imaging, is turned into a nanoparticle, it can damage cells by changing the metabolism (or burning up) of fat and will cause stem cells to differentiate differently. When it is used as a nanoparticle, titanium dioxide is even more damaging and can break the cell membrane and cause cell death.

At the same time, Rafailovich is working on ways to engineer nanoparticles for thin film coatings and biomaterials and tissue engineering.

“It’s important to have an interdisciplinary approach,” she offered.

Rafailovich has been at Stony Brook since 1994. When she was conducting her Ph.D. work, she met her husband, Jonathan Sokolov, who works in the same department. The professors have four children and five grandchildren.

Rafailovich said she enjoys Long Island for its proximity to the ocean and to New York City.

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Horizontal gene transfer has the Rafflesia potentially using the host’s information against it

They’re a member of a group that includes some of the world’s best thieves. They’re so good at stealing that they don’t make or produce food for themselves.

And, to top it off, like the high school students who rule the school because they are the tallest, most attractive or most athletic, they are physically stunning. Known in the scientific community as Rafflesia cantleyi, they have some of the world’s largest flowers, spanning as much as two feet across.

Found in Malaysia and named after a 19th century curator of the Singapore Botanic Gardens, the Rafflesia doesn’t have chlorophyll, the critical green molecule that allows plants to turn light, carbon dioxide and water into food. Instead, it lives deep inside the host vine, Tetrastigma rafflesia, a member of the grape family.

But that, it turns out, is not the only thing the parasitic plant pilfers. Recent research from Stony Brook assistant professor Joshua Rest, in collaboration with Harvard Professor Charles Davis, suggests Rafflesia has somehow taken something surprising: 49 genes from the Tetrastigma.

While bacteria and viruses take genes wherever they find them and attach them to their own set of life blueprints, it is much more unusual for plants to take genetic material, much less a region this large, from another plant. That means the Rafflesia is not only invading the space and food of the Tetrastigma plant, but it is also grabbing some of the plant’s hard-earned genetic identity.

When he first examined the genetic sequence of the Rafflesia, Rest was so stunned, he wondered whether he might have “just contaminated something,” by mixing the genes of the two plants.

Careful analysis, however, confirmed it was not the researchers who mixed the genes, but rather the plant that had gone through a process called horizontal gene transfer. Unlike vertical gene transfer, where individuals get their genes from their parents, in horizontal gene transfer, an individual can acquire its code from something outside its genetic tree.

“It definitely turns the way we think about things a bit on its head,” acknowledged Rest.

This discovery is new enough that scientists like Rest and Davis can only begin to guess at what advantage the Rafflesia gets from copying the genes of its host. One plausible explanation is that the parasite weakens the grape plant’s ability to defend itself against its unwelcome guest. The copied genes might send a signal to the host plant that disguises the parasite, allowing it to live like a disguised but sated wolf among sheep.
Rest cautioned that scientists don’t understand how the gene transfer affects the ongoing battle.

“We don’t know that there’s any cost” to the grape plant, Rest offered. “To whatever extent the transfer makes the parasites better at what they do, it could make the [grape] vines worse off.”

While the copied genes may protect the parasite against an immune response, they are also a part of other activities, including metabolism and respiration.

“They are involved in different cellular functions,” he explained. “We were expecting maybe we would find genes that were just involved in the immune response.”

To be sure, the notion of combining different genes to form a new organism isn’t unique, even in the world of eukaryotes. In fact, because the DNA from mitochondria and chloroplasts are different, scientists believe that, at one point, these organelles existed separate from each other, and proto-eukaryotic cells enveloped them. The parasitic gene copying is “on a much smaller scale,” Rest assured.

Given the range of parasites, it’s likely that others besides the Rafflesia have taken more than just food, sunlight or structural support at the expense of their hosts.

“Nature is a big place, so it’s unlikely that this mechanism is unique,” Rest suggested.

When he’s not looking closely at the genes of plant parasites, Rest, a native of the Chicago area, enjoys the chance to explore nature on Long Island, where he likes to run and hike in parks along the North and South Shore.

Rest lives in Bellmore with his husband Scott Stuart, a music therapist who works in a nursing home.

As for his work, Rest is fascinated by the implications of the range of what Rafflesia takes from its grape vine.

“The parasite,” he explained, “is potentially using the host information against it.”