Authors Posts by Daniel Dunaief

Daniel Dunaief


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Work leads to understanding how viruses infect cells; has potential for correcting genetic disorders

With their miniature parallel tracks twisting and turning and their connections in the middle, the structure looks like a winding ride. As it turns out, it is, although not for humans.

Using an 11-amino acid sled, viruses shuttle proteases along the double helical structure of DNA, enabling them to infect other cells.

Leading an international team of researchers, Walter Mangel, a biophysicist at Brookhaven National Laboratories, recently found the sled that slides along the phosphate spine of DNA. It carries a protease important in the activation of a virus to its destination.

When the protease and another protein collide on DNA, it begins a reaction that leads to the removal of clumps of proteins that support the construction of viral DNA.
Mangel likens the proteins that are cut away to the scaffolding builders use when they put together a cathedral. With the scaffolding in place, the viral DNA can’t become an effective invading genetic force.

“We took a model virus, one that was not dangerous to work with, and we wanted to understand how this protein functions,” Mangel said. “If we do, we can inhibit that protein.”

The researchers chose the adenovirus, which causes common colds, pink eye, blindness, weight gain and diarrhea.

The molecular sled moves by thermal (i.e. heat) energy and doesn’t use miniature wheels to move along the track, but rather has electrical charges that keep it stuck to the DNA. The sled has four positive charges that interact with the negatively charged phosphates in the major groove of the DNA.

“The sled enables the molecule to collide with another molecule on DNA,” he explained.

Once the protease removes the scaffolding, the virus can infect other cells. Mangel said the concept of a molecular sled came together in his mind when he was visiting a museum in Vermont that had farm equipment. He saw a large sled and realized this was likely how these proteins were navigating through the nucleus to their destination.

“Once we saw the 11-amino acid peptide slide by itself, we thought it might be a sled,” he said. This molecular sled not only could transport molecules to the right destination in the DNA, but could also ensure that they collided in a way that ensured a reaction would take place.

In a solution, molecules typically only bind to each other when they collide at a specific speed at particular sites on their surfaces. In most collisions, even those molecules with complementary functions recoil. If both molecules are stuck to DNA and one or both slide on the sled, the speed of the collisions is set by the speed of the sled.

“This could give rise to chemistry that is far more efficient, in which almost all collisions by sliding lead to binding,” Mangel said.

While researchers will try to disable or deactivate the sled — perhaps by attaching other blocker molecules to keep the protease from navigating down to its spot on the viral DNA — they may also find ways to use the sled.

“The sled is capable of carrying anything attached to it,” Mangel said. That means it could be used in transgenic therapy, where doctors and scientists may want to replace one genetic sequence for another, potentially correcting a genetic disorder.

Mangel explained that the experiments with the molecular sled took considerable collaborative coaxing. He wrote to 10 labs that had equipment that would allow him to do single molecule experiments. When he spoke to Sunney Xie at Harvard, a partnership began.

The first set of experiments in Massachusetts failed.

He had planned to return to Long Island the next day, but wanted to try one last experiment, in which he increased the acidity of the solution. Immediately, he saw considerable sliding.

Mangel lives in Shoreham with his wife Anne. They enjoy running together and visiting the beaches and parks in the area, especially along the east end.

Mangel is a fan of opera and classical music and has conducted his work while listening to classical music from a BBC station. He also is an avid artist and has sketched his colleagues in the lab.

The direction of his work and his artistic interested collided when he discovered the use of this molecular sled.

“What comes out of the work is rather simple,” he said, alluding to the sled. “The experiments are sophisticated to support that theory.”

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Strokes, cancer and other diseases can be more accurately studied and treated with new technology

Yingtian Pan works at the cutting edge of biological imaging, looking with increasing breadth and depth into cells ranging from bladder cancer to diabetes. Congwu Du, meanwhile, who has also done imaging, has studied the effects of cocaine on the brain.

One night, Du suggested the two Stony Brook scientists, who met when they were undergraduates studying biology in their native China, work together to get a better view of how blood flow changes in the brain after cocaine use.

Strokes, in which brain cells die because they don’t have enough oxygen, are one of the most serious medical risks of cocaine abuse. Getting a closer look at blood flow in the brain might suggest how these strokes develop.

Pan didn’t take too long with his decision. After all, he said he was eager to collaborate with Du, who isn’t just his professional colleague, but is also his wife and the mother of their two children.

Using animal models, Pan and Du employed 3D optical Doppler imaging tomography to look closely at the effect of cocaine on cerebral blood flow. Sure enough, even a single dose of the drug causes the flow to decrease. The scientists observed a disruption in some terminal arterioles and the connecting capillaries.

“When cocaine is administered, it causes constriction,” Pan explained. “The local brain oxygen is reduced.”

Cerebral blood flow decreased by as much as 70 percent within two to three minutes after a dose of cocaine. While the blood flow often returns to normal within three minutes, some flows were shut down and did not come back for at least 45 minutes. The delayed recovery was a new observation, Pan explained.

Another dose of cocaine soon thereafter causes the area with restricted blood to grow like a cloud.

“We see more of this shutting down” of blood flow, Pan commented. “That’s very unhealthy. There’s a long period of time with very low oxygen supply.”

The next step in this research is to look at the effects of longer-term cocaine abuse.
Pan, who has been at Stony Brook since 2002, has applied his imaging skills to a wide range of projects.

He worked on bladder cancer, which, if detected early, can have a good prognosis but becomes much more problematic if it progresses without intervention.

Using optical coherence tomography, which is similar to the Doppler technology he used for the cocaine study, Pan was able to increase the reliability of determining cancer screenings from 75 percent to 94 percent for sensitivity.

While some scientists have called this type of screening optical biopsies (i.e. looking closely at suspected cancers without removing any living tissue and screening it in at pathology lab), Pan is cautious in his use of that term.

“The issue with any new technology is that before it’s been clinically approved and without histological (or cellular) proof, we haven’t reached that stage yet,” he explained.

With these images, however, doctors can be more specific and targeted in their approach to bladder tumors. The next step is to provide computer-aided diagnosis to physicians for more accurate diagnosis in the operating room and for outpatient facilities.

Pan has also worked with wound healing for people with diabetes. By using imaging technology, doctors can monitor every lesion and can understand the exact benefit, or lack thereof, of any potential drug.

At this point, that work was limited to an animal model to track the growth of skin under different bioactive implants.

He has also worked on interstitial cystitis (also called IC, a condition in which people can feel intense pain in their bladder when they urinate) and geriatric incontinence.
Pan said he has found collaborators by building up a network of fellow researchers, many of whom approach him with imaging questions and opportunities.

“We hope we can provide a device to physicians,” he said. “We need to give them some understanding of the technology so they can get a good idea of how to interpret the images.”

Eventually, Pan expects that this technology, which is already widely used in eye clinics, will become similar to ultrasound in its medical usage. While it has high resolution, its image depth is limited depending on the type of tissue.

Right now, the field is very competitive, with scientists around the world looking for better, clearer, and more specific images of biological systems.

“We like competition,” he offered. “It means we have to work hard.”

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Engineering hardier plants could feed a growing population or provide biofuel

The sports adage, “it’s not the size of the athlete in the fight, but the size of the fight in the athlete,” might apply to Ben Babst’s research.

Instead of studying athletes, the Brookhaven National Laboratory researcher is looking at something that fights numerous unseen battles — plants.

A postdoctoral fellow at BNL since 2010, Babst uses positron emission topography scans to track how labeled elements move and change as they go through plants. This is the same technology doctors use to test for breast or lung cancer.

Babst is examining corn, sorghum, grasses and some of their relatives to understand how they grow and respond to their environment. He is also looking at what makes some grow bigger than others, while others tolerate drought or low-soil nutrients.

“We need to understand the underlying mechanism for fast growth, for stress tolerance, for pest resistance,” he offered. “We are not only measuring how big they are or how they look, but what they are doing inside. [We are looking at] what is happening with their metabolism and with signaling.”

The benefits of understanding plant growth apply to the conversion of plants to biofuels and the expansion of previously unused or undeveloped land for agriculture. Down the road, this could enhance our ability to generate plants to feed the increasing global population and to provide alternative, sustainable energy.

“One of our major goals is to come up with new strategies to find or engineer plants that can grow vigorously on lands not useful for food production,” he explained. “Another goal is to find new strategies to develop plants that have a biochemical composition favorable for conversion to fuel, for example high sugar or starch content.”

The challenge is to combine all the desirable traits into one crop.
Through agriculture, farmers have gone through a selection process that might not benefit the plants, or us, in the long run.

By watering, fertilizing and using pesticides to get rid of insects, bacteria and fungi, we have produced plants with an unintentional loss of hardiness. By cultivating plants under these conditions, we may have diminished the resistance plants might have to some of these challenges.

Babst and his colleagues are studying plant hormones, called phytohormones, to see how they protect plants. The plant hormones might tell a tree in a drought to close the pores on its leaves to prevent water loss.

“A recent new direction for the group is that we’re using carbon 11 [a radioactive carbon that’s easy to see with the advanced technology] to label specific phytohormones and biomolecules,” he explained. “We are looking to see how the phytohormones are made and if, under different treatments, they are made at different rates.”

He is also looking at movement of the phytohormones because the rate of that movement might determine their effect.

Babst started working with PET when he did his Ph.D. research at Tufts University. While he was there, he simulated an insect infestation with plants to determine their reaction. To his surprise, the plants in his experiment hid some of their precious resources in their roots, farther away from what they perceived as a threat from insects that might steal their sugars.

“I had a different project goal in mind,” he recalled. “When I saw that plants were bunkering their resources down in the roots after a herbivore attack, I was pretty excited. It changed the course of my research.”

In addition to seeking basic information about plant growth and metabolism, Babst also hopes to contribute to an understanding of how to harness plants for biofuel and how to help find plants that might grow in areas of the world people had once thought couldn’t sustain plant growth.

“Energy is central to our economy and has an impact on everybody’s everyday life,” he said. “I’ve noticed [in recent years ] that every time the economy seems to get moving, gas prices and energy prices go up and that muzzles economic progress.”

A married father, Babst lives in Manorville with his wife Clare Norcio, an adjunct professor of history, and two primary-school children.

He recently took his children to the pumpkin festival at Suffolk County Farm. He enjoys hiking along some of the trails on Long Island.

“When I see plants, I see one that looks stressed, or one that has caterpillars that have mauled it. Sometimes, I see it for its beauty. I’ll see an understory plant that looks so tiny but is probably decades old.”

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Shinnecock Bay gets help from Christopher Gobler, Ellen Pikitch and their team

Christopher Gobler is tired of being the bearer of bad news for Shinnecock Bay. Every time someone wants to talk about ecological problems in the bay, they reach out to the Stony Brook scientist for information.

Gobler finally has some good news to share. He and a team of scientists at Stony Brook received a $3 million grant from the Simons Foundation and a private donor to turn the tide in Shinnecock Bay. Through a five-year plan, Gobler and fellow scientist Ellen Pikitch are leading an effort to restore the water quality and improve conditions at Shinnecock Bay. They hope their efforts will allow the bay to sustain larger populations of shellfish and finfish.

“We’re trying to do something to improve and reverse the things that have happened in the bay,” Gobler offered.

The effort was funded by a philanthropic gift from the Laurie Landeau Foundation, matched by similar funds from the Simons Foundation.

The eastern-most lagoon along the South Shore estuary system, Shinnecock contains 9,000 acres of open water, salt marshes and intertidal flats.

The bay, which was once home to a thriving range of shellfish, has had a decline in water quality because of the run off of nutrients like nitrogen and phosphorous, especially from septic tanks. Researchers believe nitrogen loading and the absence of shellfish are the biggest contributors to toxic red and brown tides, Gobler said.

“Part of the problem is that there’s stuff going into the bay” that leads to algal blooms, he offered.

Shinnecock is a tale of two bays. On the eastern side, it’s still closer to the best of times, as ocean water flushes through every day. The west side, however, is suffering through closer to the worst of times, as nutrients introduced by human actions remain in the bay for over a week because of less active ocean cleansing.

Researchers at Stony Brook’s School of Atmospheric and Marine Sciences plan to turn that around. The first step involves restocking shellfish, which will filter the water, and replanting eelgrass beds. This will create habitats for juvenile fish, which can hide from predators.

Scientists will also bring seaweed into the bay, which will act as a sponge, taking out the nutrients that lead to these red and brown tides. The scientists will remove the seaweed once it has absorbed enough nutrients, and will bring in a fresh batch.
Researchers like Pikitch and Gobler will monitor the bay regularly.

“This will be a continual effort we will build on,” suggested Gobler, a graduate of Ward Melville High School who now lives in East Quogue with his wife Dianna Berry and their three primary school-aged children. “We’re starting out with hard clams and oysters.”

Pikitch has already started surveying fish throughout the bay and has found, as she expected, that there is a greater range of fish living in the eastern part of the bay, where the water quality is considerably better.

Pikitch expects improvements in water quality and an expansion of a healthy habitat throughout the bay to foster growth of a broad range of fish.

“As water quality improves and as eelgrass beds flourish, fish will be able to reproduce, hide from predators, and grow,” she suggested.

Stony Brook University President Samuel Stanley hopes the restoration effort will “serve as a template for similar projects worldwide,” he said in a statement.

Those interested in learning more about the restoration program can visit the website

Pikitch, who lives in East Quogue, said one of her favorite activities is to take her grandchildren to the ocean, where she hopes they fall in love with it at an early age, the way she did.

“I worry about what kind of world my grandchildren will grow up in,” she offered. “I worry about harmful algal blooms. I wonder: What if we didn’t do anything and things got worse.”

If, she added, “the bays aren’t healthy, we won’t be healthy.”

She said she feels a sense of urgency about her work. After all, humans caused the problem and we should be able to turn it around, she offered.

“We’re going to make a big dent,” she predicted. “This is a problem that can be solved.”

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Learning how cells cross the blood-brain barrier may help with neurological diseases and injuries

Brains have a security system that is similar to that of a plane’s cockpit. Everyday cells can’t enter the control center unless they clear a careful screening process. Blood has to cross through a blood-brain barrier — the body’s equivalent of a metal detector.

Doctors and researchers believed this process kept larger cells from the immune system, which are too big and pack the kind of weapons the blood-brain barrier would filter out, from getting into the central nervous system.

The central nervous system has cells called microglia which are on active patrol, in much the same way as macrophages in the rest of the body. They are looking for potential problems that require immediate correction or attention.

In some neurological diseases, these microglia are especially prevalent and may exacerbate a problem. In other cases, however, a different type of microglia may help stabilize neurological function and signaling.

Stella Tsirka, a professor in the pharmacology department at Stony Brook University, has been studying these special cells to determine what roles they play in disease and in signaling between the immune system and the central nervous system.

Tsirka explained that her lab has divided their research into two areas. The first looks at the pathology of neuro-immune interactions. They are studying a model of stroke, multiple sclerosis and models of spinal cord injuries.

After an injury, “immune cells play an important role in maintaining or modifying the environment around the area of trauma,” she said.

The microglia are thought to be the first line of defense against injury. Later, additional peripheral immune cells infiltrate the central nervous system (when the normally secure blood-brain barrier is compromised) and modify or preserve the injured central nervous system.

At the same time, their more recent work studies the role of microglia to see how they function in the normal central nervous system (CNS).

“We’re trying to find out how neurons behave when there are microglia or not microglia present,” she offered.

Microglia may be something of a neurological stabilizer, she added, although it’s “not established yet.”

During development, microglia are thought to help in the maturation of the CNS by removing unwanted cells from neuronal terminals.

In the normal process of aging, microglia numbers increase, Tsirka observed. Exactly how they are involved in aging and potential neurological regulation with time isn’t clear yet.

Complicating matters further is that there are two different types of microglia: M1 and M2. They have opposite functions. M1 promote inflammation and cell death. M2 are anti-inflammatory and enhance cell repair and regeneration.

Treating microglia with a small beta peptide called Tuftsin has, during neuronal injury, fostered M2 properties. Using this in a model of multiple sclerosis resulted in a reduction in behavioral symptoms associated with multiple sclerosis.

So, if these microglia are relatively large and function like immune cells in the central nervous system, how did they pass through the security system that has such strict restrictions?

The key, Tsirka offered, is that they were in the pre-brain before the body constructed the security system. Indeed, a paper, which has not been verified yet, suggested that microglia migrated into the central nervous system from the human embryo’s yolk sac.
A resident of Setauket, Tsirka has worked at Stony Brook since 1992, when she came to do her postdoctoral research. She is married to Michael Frohman, the chairman of the pharmacology department. She does not report to her husband: she reports to the Dean of Research in the School of Medicine.

Their 18-year-old son Evan recently started college at Northwestern University, where he plans to blaze his own trail by studying mathematical models in social science. Their daughter Dafni, 15, entered Ward Melville in September.

Born and raised in Greece, Tsirka is the local president of the New York chapter of the American Foundation for Greek Language and Culture. Tsirka has supported the university’s efforts to build a Hellenic Studies minor and, eventually, a major.

Tsirka, who met her husband — who does not share her Greek heritage — when they lived in San Francisco, said she can relate to several elements of the movie “My Big Fat Greek Wedding.”

Despite the distance to her parents in Greece, they play an important role in her life. Every morning, she talks to them via Skype.

“If I’m not on by 7 am, my mom is worried something is wrong,” she laughed.
While her family tradition doesn’t include spraying Windex on everything (like the movie), she said family celebrations include food (although not lamb).

She also has been known around her lab for finding the Greek root of words and for sharing Greek expressions. One of her favorites: “It is not the sign of a wise man to commit the same sin twice.”

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Developing an inexpensive device to measure inflammation in the lungs

It’s an all-too-familiar fear. A parent hears a child struggling to breath in the next room, jumps out of bed and wonders whether to grab the child and race to the hospital or call 911.

Researchers from Stony Brook are working to let children (and their parents) breathe a little easier, at least in terms of knowing the severity of an asthma or breathing attack.

Led by Perena Gouma, a professor in the Department of Materials Science and Engineering, along with Milutin Stanacevic, an associate professor in the Department of Electrical and Computer Engineering, and Sanford Simon, a professor in biochemistry and cell biology and pathology, the scientists are developing a nanosensor-based system (i.e., extremely small) that captures, quantifies and displays an accurate measure of the nitric oxide concentration in one exhaled breath.

Nitric oxide is a known marker for measuring airway inflammation.
The scientific trio received a three-year award for $599,763 from the National Science Foundation to develop the monitor.

Creating an affordable, personalized device like this — Gouma estimates the finished product could cost between $20 and $50 — is “urgent” for people who struggle with asthma, she explained. “It’s a matter of working hard and getting this out as soon as possible.”

The group that might use something like this includes young children, the elderly and incapacitated patients.

Hospitals currently employ devices that monitor nitric oxide, but they use gas chromatography, which cost upwards of $10,000 and require considerably more air. They also use chemiluminescence detectors, which cost $30,000.

Through nanotechnology, Gouma and her team hope to screen for nitric oxide in a single breath and at a cost that’s affordable in a home.

“We can measure hundreds of molecules of nitric oxide in billions of molecules of air,” Gouma explained. “We would like to take that sensitivity down one or two orders of magnitude, so that we can measure a few molecules in billions of molecules of air.”

Gouma said the monitor not only could diagnose the severity of an asthma attack, but might also help prevent one.

Users can “exhale once a day and record the concentration of nitric oxide,” she offered.

“If you see that nitric oxide is elevated” you might prevent an imminent attack.
Different concentrations of the signal gas might also lead to different treatments, she suggested. By developing such a diagnostic tool, Gouma and her colleagues believe some patients may be able to take medication only when their body signals they need it.

The concept for the nitric oxide detector is similar to what police use when they administer breathalyzer tests to people as an noninvasive way of determining how much alcohol they’ve consumed. The technology, however, is different.

The breathalyzer uses resistive sensors that are nonselective and respond to all hydrocarbons, while the nanotechnology, which uses crystal nanowires, has a selectivity for one particular gas.

Gouma, who leads the project with her material science background, has teamed up with Stanacevic and Simon on other projects and believes the combination of their skill sets will make a prototype possible in the next year or so.

Stanacevic will work on the microelectronics, while Simon will carry out the trials in the early stages, once the trio has produced a new monitor.

“This is an interdisciplinary approach,” explained Gouma.

A resident of Port Jefferson, Gouma, who is originally from Greece, has been on Long Island for 12 years. She is married to Antonios Michailidis. They have a son in kindergarten.

A world traveler who has spent time in England, Italy, Switzerland, Japan, Australia and Brazil, Gouma calls Long Island the “best place to be.” On the board of the Maritime Museum in Port Jefferson, she praised the region’s smaller museums, including the Whaling Museum in Cold Spring Harbor.

“We really enjoy the lifestyle on Long Island,” she said. “It is so serene, peaceful and safe. At the same time, you get the feeling you are in a metropolitan area.”

She believes Long Island could become the equivalent of Silicon Valley for the rapidly expanding world of bionanotechnology.

“If we were to set up a lot of activity in developing, manufacturing, testing and selling” various nanomedical devices, Long Island could easily become a business hub that would attract investment and industry, she urged.

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Improving on genome sequencing, team studied parrot genome to understand human language development

Humans are constantly at war with our environment. No, not in a cut-down-the-trees-to-build-the-latest-condo way, but in a battle with small pathogens and microbes that would like to set up shop — at our expense — in our bodies.

Our immune system remains on 24-hour patrol, looking for familiar invaders or even for disguised armies that might attack before we can mount a strong enough defense.
While our bodies and medical research have helped weaken and control some predators, scientists like Michael Schatz at Cold Spring Harbor Laboratory believe we can mount another type of defense.

Tapping into the latest technology, Schatz believes researchers can create what David Lipman of the National Center for Biotechnology Information has described as a “digital immune system.” Like a good Terminator, sensors distributed at hospitals, schools, offices, airports and even farms and food processing plants would scan microbial genomes, searching for those that would harm us.

The technology, Schatz suggests, is “right around the corner.” Oxford Nanopore Technologies (a company founded in 2005 on the science of Professor Hagan Bayley of the University of Oxford) announced they would mass produce this type of scanner later this year or early next year. A tougher part of making this a reality, however, is organizing the amount of data that would come in to separate microbial friend from foe.
Schatz doesn’t know when this new surveillance system will be available, but he’s certain medicine will take advantage of the immunological edge computers give us.

“It will take time to develop on a global scale, but everything is pointed in that direction,” Schatz said. It would work like the global weather system that monitors storms, except that instead of watching for hurricanes, it would be on the lookout for emerging disease outbreaks, he suggested.

With a Ph.D. in computer science from the University of Maryland, Schatz said he applies his computational background to areas like sequencing (or putting together the list of DNA base pairs).

He has worked on human genetics to study areas ranging from autism and cancer to plant biology.

“DNA is very much like a computer program, except that instead of ones and zeroes, the digital code is the nucleotide,” he offered. “The sequence is so long that you can’t study it by hand. It’s packed with really important information.”

Indeed, Schatz and his colleagues at the National Biodefense Analysis and Countermeasures Center and the University of Maryland published a paper this summer in which they described ways to improve on third-generation genome sequencing. The biggest problem is that it misreads every fifth or sixth DNA letter about 15 percent of the time.

Each type of sequencing created puzzle pieces or “contigs,” which are connected strands of DNA. “Contigs” are short for contiguous sequences. The second-generation technology created smaller contigs, which made it highly accurate. However, the pieces in the second generation became too small to reassemble.

With third-generation sequencing, the contigs were bigger — making it easier to put the pieces back together. Like a speed reader flipping through a book, however, the third generation technology wasn’t accurate enough. Schatz and his colleagues married the accuracy of the second-generation technology with the speed and size of the third generation. The median size of the contigs in this hybrid model was about twice that of the second generation. It cut the errors down from 15 percent in third-generation sequencing to less than 1/10th of 1 percent.

Using their advanced system, Schatz and his collaborators published the parrot genome, which is more than a third the size of the human genome.

The parrot, he said, is a particularly appealing model for understanding how language develops.

Schatz is a late-night owl, sometimes sending emails as late as 3 am.

“During the day, there’s nonstop interactions,” he explained. “It’s hard to get a long block of time when you can focus. Late at night, that cools off and you can focus.”

Schatz lives in Huntington Village with his wife, art therapist Emery Mikel. They have been on Long Island for two years.

Schatz is thrilled to work at the nexus between computer science and applied biology.

He appreciates the dual advances in biotechnology and computer science, enabling him to participate in and contribute to studies of everything from harnessing biofuels from plants to understanding the genetics of autism.

“I’m trained as a computer scientist and I’m able to apply those skills” in a “really meaningful” way, he offered.

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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.”