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.”

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.

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.

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.

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.”

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.