Authors Posts by Daniel Dunaief

Daniel Dunaief


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Hollywood came to Leemor Joshua-Tor’s lab. When actress Rachel Weisz was preparing for her role as a scientist in “The Bourne Legacy,” she and director Tony Gilroy visited Joshua-Tor’s lab at Cold Spring Harbor Laboratory.

Like Weisz’s aunt, Olga Kennard, Joshua-Tor explores the unknown structure of complex molecules. While she may not have a Hollywood pedigree, Joshua-Tor has had a hit of her own, thanks to her research on a protein linked to an important function in biology.

A professor at Cold Spring Harbor Laboratory and an investigator at Howard Hughes Medical Institute, Joshua-Tor was one of many scientists seeking to understand how a gene-regulating mechanism worked. Through a process called RNA interference, a small RNA molecule either enters the cell or is produced from long RNAs in the cell and is cut to pieces. That small piece sticks to an RNA that is normally part of the process of converting DNA to proteins. Once that RNA gets cut, the genetic machinery comes to a stop.

While researchers knew there was a collection of proteins in the silencing signal, they weren’t sure which one was helping to hit the stop button or how that protein might work. A structural biologist, Joshua-Tor took a different approach. She figured she might be able to find the important protein by looking at molecular architecture. What she found was that the small RNA sticks to the Argonaute protein and then “seeks” the larger RNA.

Steve Harrison, a professor at Harvard Medical School and an investigator with the Howard Hughes Medical Institute, called Joshua-Tor’s 2004 discovery of Argonaute’s role an “important contribution. It is a key step for understanding the biochemistry of small RNA-guided gene regulation.”

Joshua-Tor explained that being able to see the molecules provides a better understanding of what is happening and, perhaps, how.

“All RNA interference processes included the Argonaute protein, but no one knew what it did,” she recalled. The protein is “at the heart of the execution phase” of interference.

RNA interference can protect cells against viruses, while it can also help monitor and regulate gene expression.

While the Argonaute protein carries out many processes, it works through other proteins as well, Joshua-Tor said. It plays a role as a tumor suppressor in prostate cancer.

In addition to the work her nine-person lab does on Argonaute, Joshua-Tor’s team is also looking at proteins that are involved in papilloma viruses. These viruses, which can cause benign or malignant tumors in areas like the cervix, use an initiator protein, called E1. Together with a former postdoctoral student, Eric Enermark, who now works at St. Jude Children’s Research Hospital and in collaboration with CSHL’s Arne Stenlund, they discovered how E1 recognizes and binds the start site. Enermark and Joshua-Tor later figured out how the protein uses the energy of adenosine triphosphate to travel on the DNA.

While structural biology involves numerous steps to go from targeting a molecule to seeing how all the parts fit together, the effort can create “an amazing feeling. You put up with a lot of grief in order to relive that rush when you see a structure for the first time. It’s just unbelievable,” Joshua-Tor said.

A resident of Huntington, Joshua-Tor lives with her five-year-old daughter Avery. The mother-daughter team enjoy going to beaches and visiting the Long Island Aquarium and Exhibition Center in Riverhead. Avery also “loves playing with the kids on our block,” which includes an annual fall block party, which has a deejay, races, water-balloon competition and scarecrow making.

Joshua-Tor, who spent part of her childhood in Israel and attended high school in Great Neck during her junior year, also enjoys the wineries and the “amazing” fresh corn of the east end.

Joshua-Tor said she loves the history of science and finds herself thinking about earlier discoveries that used the same technique, X-ray crystallography, that she employs in some of her research.

“Molecular biology is riddled with discoveries in structural biology,” she said, including by researchers like Dorothy Hodgkin, who confirmed the structure of penicillin and of vitamin B12, which helped her win the Nobel Prize in Chemistry in 1964. “We stand on the shoulders of our predecessors.”

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Mice rely on their sense of smell for their survival, sniffing out food, finding mates, or scampering away from the butcher’s wife or, more likely, a hungry fox.

Dinu Florin Albeanu wants to understand how the scents in the air translate into signals in a mouse’s brain that cause the animal to understand its environment and react accordingly.

An assistant professor at Cold Spring Harbor Laboratory, Albeanu studies the neurological circuits in mouse brains, trying to figure out how information translates into behavior.He is attempting to understand how the mouse decides what aspects are important and what are not important.Albeanu is excited to ask these kinds of scientific questions at a time when the technology to monitor individual neurons on a real-time basis has taken such enormous strides in recent years.

He is able, for example, to take a thirsty mouse that has smells coming from its right and left. If the mouse licks a port on the left in response to a specific signal, it gets water. While the mouse is considering the smells around it, Albeanu and his colleagues can monitor the specific activity in the brain to see how it is changing.

To check to see how important any neurons are in perception, the CSHL research team can suppress activity in those circuits and see if the mouse reacts to the smell in a different way. The scientists turn off different subsets of neurons, so they can ask “at what point is smell A perceived as something different,” Albeanu said.

Going further than this, Albeanu looks at how altering specific features of activity, such as the timing of when neurons spike or the number of spikes, can alter the circuit and, eventually, the behavior of the animal.

The animals have a neurological feedback loop, where the cortex sends signals back to the olfactory, or smell, area. In one experiment, Albeanu’s crew is monitoring the information from those signals. By doing so, he can determine whether the feedback ensures that there is not an error signal, where the initial reaction to a scent requires reinforcement with additional odor gathering before reacting. He performs similar experiments with the feedback loop, suppressing some of the returning neurological information to determine its role in generating behavior.

In his broad range of research, Albeanu is also interested in how mice process olfactory stimuli with visual information or other types of sensory cues. Would a mouse sooner trust what it sees, if there’s an image of a predator nearby, or what it smells, if that image includes the scent of food or a mate?

“The brain extracts and processes information about the environment combining multiple senses,” he explained. “We’re probing how and where in the brain visual and olfactory cues are compared and integrated, and indeed pursuing a range of experiments along these lines.”

Vivek Jayaraman, a group leader at Janelia Farm Research Campus of the Howard Hughes Medical Institute, called Albeanu “technically gifted and resourceful.” He suggested that the CSHL scientist, whom he’s known for a decade, uses “a powerful combination of techniques to record and stimulate neural activity and, importantly, they’re also busy adding interesting animal behavior tasks to the mix. This makes for a pretty potent cocktail.”

Albeanu, who said he himself has probably an average sense of smell, explained that he is “fascinated by how little is known about how you go from the smells to complex perceptions.”

A resident of Huntington, Albeanu has been at CSHL since 2008. He also rents an apartment in the city. While he’s on the Island, he enjoys running, biking and swimming.

Albeanu spends about a month each year in his native Romania to co-organize a summer course called Transylvanian Experimental Neuroscience Summer School. This past June, the second summer for the course, organizers received applicants from 37 countries.

The course focuses on experimental and theoretical methods to study how the brain operates at the level of neuronal circuits.Albeanu describes his work as basic research, in which he asks questions and seeks answers to understand the way systems like olfaction can generate behavior. He can imagine an extension of this work, in which future research could get at how the human brain operates.

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They ask far-reaching questions, from looking at exactly how fleeting flame is to exploring supernova to studying chemistry and materials for clean energy production to examining the interaction of clouds with aerosols. The eight researchers who conduct a broad range of experiments using computers and a large numbers of data points are part of a growing one-year old group called the Institute for Advanced Computational Science.

A combined effort of Stony Brook University and Brookhaven National Laboratory, the IACS was created to use computers and their applications to solve problems in the physical sciences, life sciences, medicine, sociology, industry and finance.

The analysis of wide-ranging data is “incredibly broad and has a high payoff,” said Robert Harrison, director of the IACS, who moved to Long Island from Tennessee last year.

Funded with a $10 million donation from an anonymous contributor combined with a matching donation from the Simons Foundation, the IACS plans to hire an additional eight researchers over the next few years. Stony Brook is in the process of building a facility in what used to be the north half of the Life Sciences Library.

Harrison described computational sciences as a “very competitive” area for recruiting, which requires state-of-the-art facilities to build the best faculty and student team. The group has already purchased a $550,000 system from IBM.

Harrison, who is also the head of BNL’s Computational Sciences Center, said IACS faculty can contribute to the National Synchrotron Light Source II.

The new facility, which will open in 2015, will produce X-rays that are 10,000 times stronger than the current light source and will allow scientists to look at the molecular structure of anything from batteries as they wear down to the development of marine shells to superconductors.

Once experiments begin at the NSLS-II, the ability to process information will become especially important. The new light source “will create a lot of data at high rates,” said Reinhold Mann, the associate laboratory director for Environmental, Biological and Computational Sciences Directorate. “We need to manage the data and archive and analyze it. That needs to happen on the fly, as the data comes in. It’s a unique challenge [that requires] applied math, networking and connectivity.”

Mann, who is Harrison’s supervisor, has known him for over 10 years. Harrison leads by example and has an engaging vision, Mann said. He has a “good combination of skills on the technical and communication and people side.”

Harrison expects the computational science group to become a part of a team that enables researchers with different expertise to collaborate. “If you want to design a new fuel cell for clean energy production, by turning methanol into energy,” Harrison offered as a possible example, then “you [will work in] chemistry, material sciences and engineering. In order to understand the device, you might need to look inside it by using X-rays from the new light source.”

When he first visited Long Island in February of 2011, Harrison was surprised at how cold, raw and beautiful the area was. He said he marvels at the world around him. People are “surrounded by this miracle” he said. “Pick up a leaf and look under it at the insects or the pores in the leaf. There is all this wondrous stuff.”

Harrison and his three sisters (including a twin sister) are the first generation in their family to attend college. Harrison said he recalls sitting with his father, a World War II veteran who served in the British Army in India and who left school at the age of 14, when he was 17.

“My father didn’t understand what stars in the night sky were,” he said. Harrison suggested that understanding the “world around us” might give people “more confidence that things are okay.”

A resident of Port Jefferson, Harrison said he writes snippets of programs every day. He marvels at the rate of advancement in computers. His $700 cell phone is 10 times faster than the $20 million supercomputer he used for his Ph.D. thesis. He believes he is like many other scientists when it comes to facing an unfamiliar situation. He sees a problem as an opportunity to build knowledge.

“You work your way out of the maze,” he said, “and at each step, you learn. Even the dead ends” can provide information.

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As the director of the Research in Interventional Cardiology unit at Stony Brook Medical School, Luis Gruberg does more than 400 procedures a year in which he rebuilds the collapsing or blocked walls that provide blood to the heart.

The professor in the Department of Medicine is screening for as many as 40 candidates who might benefit from a new stent, a device made by a unit of Abbott Laboratories that will open artery walls and, after two years, will dissolve.

“This is a unique new type of stent that is made out of a type of sugar that will be reabsorbed into the body,” Gruberg said. “It will serve as a scaffold” for the heart and will prevent the arteries from “renarrowing or closing.”

The stent, called Absorb, is made of polylactide, which includes corn starch or sugar cane and is commonly used in dissolvable sutures, screws and pins.

Currently, patients who need a stent typically receive one that is made out of metal, Gruberg said. While those stents are durable and are considered safe and reliable, they remain in the body, which may not enable a restoration of the blood vessel function. During the trial, Gruberg will monitor vasomotion, a measure of how much natural motion returns to the blood vessel.

“If the clinical trial proves to show this is as good as or better than the metal stent used today, this will be a significant step forward,” he said. This new stent has a drug coating that prevents an immediate renarrowing of the artery by scar tissue. Stents are often used to treat coronary artery disease, which is the most common type of heart disease. Gruberg, who has been at Stony Brook for seven years, said he has been involved in numerous studies of other novel therapies or approaches to medical care. He participated in the Plato study that led to the approval of ticagrelor. He also contributed to the Champion studies with cangrelor that is being considered at the Food and Drug Administration for approval. These drugs are used in patients that undergo coronary artery interventions.

“When you use these medications or devices, you don’t know” exactly how well they’ll work, he said. “Patients trust you. [The studies] try to improve our medical knowledge. We don’t know until the study comes out.”

William Lawson, the acting chairman of the division of cardiovascular medicine and Gruberg’s supervisor, said it “benefits the university, cardiology and the heart institute to have someone so engaged and productive.”

Lawson described Gruberg’s research as cutting edge and suggested it would “advance what we do clinically in the next couple of years.” Lawson was especially impressed with Gruberg’s ability to engage high school students, medical students and residents, which he said would help develop the next generation of people going into medicine. A native of Bolivia, Gruberg has worked at institutions with strong research programs, including Washington Hospital Center and Rambaum Medical Center in Haifa, Israel.

Gruberg started the Research in Interventional Cardiology unit at Stony Brook when he arrived in August, 2006. He is pleased with the progress of a group that currently has 10 active trials. Stony Brook has been “very successful in establishing a research program,” he said. “We have nothing to envy to those major institutions. We’ve established ourselves in the field.”

Lawson, who has known Gruberg for over five years, said Gruberg’s work has helped accomplish what he set out to do when he arrived, by participating in so many clinical trials and advancing cardiac technology.

Indeed, Gruberg said Stony Brook has conducted more than 70 studies in interventional cardiology. “Since I came here, I’ve been a part of these amazing studies,” he said. “That’s just the proof that Stony Brook is out there, doing great research and trying to help patients.”

Gruberg and his wife Rakefet, whom he met in Israel, live in Setauket. Their older son, Barr, graduated from Ward Melville and is attending Geneseo, while Jonathan is in ninth grade at Gelinas Junior High School.

In his personal decisions, Gruberg said he tries to promote what he tells his patients. “I exercise and try to eat healthy and don’t smoke,” he said. “I try to lead by example.”


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In Taiwan and Balkan countries, Arthur Grollman has seen first hand how Aristolochia, a popular ingredient in herbal remedies, can be anything but helpful.

The plant, which includes over 800 species, was a part of herbal medicine in ancient Greece and Rome, where it was used to expel the placenta. It has also been a remedy for gout, arthritis, stomach pain and female disorders. Called birthwort in herbal remedies, Aristolochia grows in temperate climates throughout the world.

“This is the most potent human carcinogen ever reported,” said Grollman, distinguished professor in pharmacological sciences at Stony Brook and the Evelyn Glick Professor of Experimental Medicine. Aristolochia causes chronic kidney disease and, over time, also causes urothelial cancers of the upper urinary tract. Symptoms of cancers of the urothelium, which lines the renal pelvis and the upper ureter, often include bleeding.

“If [a patient] comes in with bleeding, doctors can do the appropriate X-ray and see a tumor and remove the single kidney,” he said. The carcinogenic properties of the plant, however, are unlikely confined to one kidney. “What usually happens,” he said, “is anywhere from one to five years later, the other kidney develops it.”

The United States, most European countries and many Asian countries have banned importation of any Aristolochia herb. Consumer Reports put it at the top of their list of dangerous herbs sold as dietary supplements.

Grollman has been “involved in integrating much of this” research, said Francis Johnson, a professor in pharmacological sciences at Stony Brook, who has known Grollman since 1965. Grollman is a researcher who “can take a bird’s-eye view.”

In 2004, Grollman went to the Balkans with his wife Annette, where he spoke with farmers in a dialysis clinic through an interpreter about whether they took herbal remedies. The farmers insisted they hadn’t consumed them. Still, while he was there, he went to a library, where he found an article in German that indicated that horses in the area that had ingested Aristolochia weeds also had kidney problems.

Grollman traveled with one of the farmers to his farm, where he noticed Aristolochia growing in the wheat fields.

Grollman deduced later on that seeds from Aristolochia contaminated the wheat. A staple of the diet of many farmers in these villages, bread contains wheat which, in this case, also had toxic seeds. Over time, “only a few seeds was enough” to damage their kidneys since the toxin/carcinogen binds to DNA in renal and urothelial tissue and remains there for many years.

He held his first symposium on the subject in 2007. Most of the scientists believed the data, but the public had heard before about possible causes of the disease, called Balkan endemic nephropathy, that didn’t work out and remained skeptical.

One of the biggest challenges in sharing his lab’s conclusion about BEN was that the country had just gone through a civil war, which minimized cooperation among Bosnians, Serbians and Croatians. He arranged a scientific conference in each capital city, showing results of studies from their own country.

Grollman has been “very much involved in the epidemiology, the biochemistry and biology of this situation,” said Johnson. In Asia, herbal remedies that include Aristolochia have been a part of Chinese herbal medicines for 2,000 years.

Except for a few scientists, the Asian communities were “very skeptical” of the dangers of Aristolochia at first. Based on the frequency of use of this plant as a part of herbal remedies, there could be as many as 100 million people in China suffering from kidney problems, Grollman estimates.

In his own lab, Grollman discovered a genetic fingerprint in a tumor suppressor gene that shows exposure to Aristolochia. The next step, he said, is to develop a cost-effective test that will show not only who has taken it but who is at risk of developing health problems as a result.

A resident of Setauket, Grollman, who is traveling in Taiwan this week as one of the main outside speakers in a symposium on cancer in Taiwan, said he has a keen appreciation for Long Island each time he travels.

“Wherever I go in the world, when I come back, I know I’m living in a great place,” he said. That’s helped over the years because it’s “awfully easy to recruit faculty to Stony Brook.”

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Some objects are like closed boxes. They have some observable properties but scientists don’t know exactly what is happening inside or why.

That’s where experimental physicists like Mark Dean and his colleagues at Brookhaven National Laboratory enter the picture. Dean fires X-rays with a specific energy level at copper oxide-containing materials (compounds that have copper and oxygen). To determine what’s going on inside, he sees how the X-rays change in energy and direction.

“We try to understand materials at a fairly fundamental level,” Dean said. “We think of that as a recipe that can be used for future technology.”

Copper oxide materials have magnetic properties and act as superconductors. Typical conductors have resistance, which reduces the amount of electricity received.

Superconductors, however, don’t have any resistance, which makes them potentially more efficient materials to send electricity. The catch, however, is that most superconductors require temperatures at near absolute zero — the universe’s coldest possible temperature — which makes them less practical. The energy required to cool the superconductors can be higher than the cost savings from avoiding the resistance of typical conductors.

Dean is focused on understanding the relationship between magnetism and superconductivity in these copper oxide substances.

The X-rays he fires into a material kick an electron out of the core of an atom, sending it up into a higher energy state where that electron can interact magnetically. That makes the X-rays sensitive to the magnetic properties of the material, he explained.

When a new electron replaces the one that was kicked out, it emits an X-ray photon. Dean measures the direction and energy loss of the photon in a process called resonant inelastic X-ray scattering.

Dean studies flat planes of compounds with copper and oxygen that are stacked on top of each other. These objects have superconducting properties at a relatively high temperature — about 90 Celsius degrees above absolute zero. That is still incredibly cold by human standards: about 300 degrees below zero on the Fahrenheit scale.

In the world of superconductors, that is considered “very warm,” or about a factor of 10 higher temperature than most normal superconductors, he said.

In terms of the energy trade-off between benefiting from the properties of a superconducting material and keeping that object cold enough to function, it is “becoming closer and closer to break-even,” Dean said. In five to 10 years, “we might hope to see some more areas where it’s economic” to use superconductors instead of conventional wiring.

Researchers discovered objects with copper and oxygen that had superconducting properties about 25 years ago and have been studying them extensively. To this point, they have “yet to find a satisfactory explanation of this phenomenon,” Dean said.

Dean is eager to refine the experiments when the National Synchrotron Light Source II comes online in 2015. At the NSLS-II, researchers will produce X-rays that are 10,000 times brighter than the current NSLS, enabling researchers to analyze the structure of new materials.

Chris Howard, a lecturer in the Department of Physics and Astronomy at University College in London, U.K., has confidence that Dean, with whom he has collaborated since 2007, will build on his success.

Dean is “currently proving his ability with a string of important and far-reaching publications in superconductivity and materials physics,” Howard offered. He called Dean a “real doer” and observed that he “is rapidly gaining the respect of the community he works in.” Howard appreciates the combination of Dean’s technical expertise, scientific discipline, writing skills, analytical skills and experimentation abilities.

Growing up in Broadstairs, Kent, a coastal town in southeast England, Dean developed an interest in science when he was young, where nature, through insects and wildlife documentaries and trips to zoos, appealed to him.

“As I grew older, the elegance of physics is what caught me,” he said. “The idea to conceptualize something and write down a formula: it’s such a beautifully efficient way of explaining something. You can convey a spectacular amount of information if you know how to write down the formula to describe it.”

A resident of Rocky Point, Dean came to the United States immediately after earning his doctorate. He enjoys mountain biking.

As for his work, Dean said the first semiconductor transistor was made at Bell Labs without any thought for its possible connection to the computer. It was made by scientists who were working to understand the properties of semiconductors. They didn’t realize this would lead to a semiconductor-based computer.

In a similar way, he said, by studying materials with novel properties, scientists will create “opportunities to make interesting new devices.”

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That self-described slow jogger who makes his way back and forth along Old Field Road five days a week — when he’s not in high-level meetings in Austria or Japan — just might be making everyone safer. That’s especially true for those people who live or work near nuclear power plants.

A condensed-matter physicist at Brookhaven National Laboratory, Robert Bari specializes in the kinds of “what if” scenarios scientists, policymakers and government officials need to consider when building, maintaining, and running the country’s nuclear power plants.

Bari is one of 22 people on a committee studying the lessons learned from the Fukushima power plant meltdown, which occurred two years ago in March following an earthquake that triggered a deadly tsunami. The committee, created by the National Academy of Sciences, will present its findings to Congress next spring.

“I visited Fukushima last November and talked with officials from the plant, from government and with the public,” Bari said. “We had open and closed meetings as appropriate.”

A physicist at Brookhaven since 1971 (with a year at Stony Brook as a visiting professor), Bari brings his expertise in nuclear power reactor safety, security and proliferation resistance to the committee.

Recently elected as a fellow of the prestigious American Physical Society, Bari has developed a career around probabilistic risk assessment and methods for analyzing proliferation resistance. He does severe accident analysis, mainly for nuclear power plants, but also for other nuclear fuel cycle facilities. He has also performed analyses of ship safety for the Navy and electrical grid performance for the Department of Energy.

In the immediate aftermath of Fukushima, he spoke with officials at the DOE at least weekly. He contributed as a part of a briefing for the Secretary of Energy and the president’s science adviser, who attended at least two presentations.

Robert Budnitz, a physicist at the Lawrence Berkeley National Laboratory at the University of California, said Bari’s role on the NAS committee is well-deserved and earned.

Bari is “an analyst who is more likely than most to come up with an imaginative answer,” Budnitz added. Bari can consider a design problem and, more effectively than most, figure it out, Budnitz said.

Bari gained experience in March of 1979, after the Three Mile Island accident. He built a risk-assessment capability for other plants. He eventually led a division of 60 people who specialized in “what can go wrong in a U.S.-type facility; what are the consequences, physical parameters and human factors involved in those types of activities,” he said.

Through his career, he said he’s been involved in studying nuclear safety and nuclear reactors through a range of responsibilities, from managing large teams to serving as associate lab director and department chair.

Budnitz said nuclear power plants are safer today than they were when many of them were built in the 1970s. The reason is that there a few dozen people worldwide who have worked to improve their design. “[Bari’s] in the middle” of that group and is “one of the most respected” contributors, Budnitz said.

A decade ago, the U.S. and 12 other countries got together to discuss the design of the next set of nuclear facilities, called Generation IV reactors. The Generation IV members discussed design plans for the commercial introduction of new nuclear plants from 2015 to 2030 and beyond.

As the co-chairman of the proliferation-resistance and physical protection group, Bari is responsible for increasing the assurance that the reactors are unattractive and the least desirable route for diversion or theft of weapons-usable materials, and to provide increased physical protection against acts of terrorism.

The Generation IV discussions started before 9/11, but took on a different urgency and design component when potential terrorism became a concern.

Bari lives in Setauket with his wife, Angela Bari, who is an instructor at the Osher Lifelong Learning Institute at Stony Brook, where she teaches courses in physics and on the history and holdings of the Metropolitan Museum. The couple have two children, Robin Sanchez, who works in a media company, and Robert Bari, who is an agent for Aflac Insurance.

As for his work, Bari recognizes that his scientific approach isn’t the typical “publish or perish” paradigm. “I like to think at the end of the day that we’re doing something that is for the public good and also creating new knowledge. I always ask myself ‘Have I created new knowledge?’”

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By Daniel Dunaief

While plants don’t generally reach for a glass of milk, crouch down to stalk their prey or seek higher ground in a storm, they do respond to changes around them. They compete for sunlight, water and territory. They also have ways of turning on or off their own genes in response to stressful conditions.

Qiong Alison Liu, a principal investigator and research assistant professor at Stony Brook University, recently revealed how microRNA, which is involved in gene expression, changes in response to elevated carbon dioxide levels and higher temperatures.

These conditions are likely to continue to increase as a result of global warming.

In a research paper published in the journal Nature Communications, Liu is the “first to show greenhouse gas can function quite similarly as other stressors,” she said. “This opens up many questions.” Other greenhouse gases, like ozone, methane and nitrous oxide, could possibly have a similar impact on small RNA expression, she said.

She explored how a change of 3 to 5 degrees Celsius alters miRNA, Liu said.

While scientists have known that higher temperatures and carbon dioxide have opposite effects on plant growth, Liu showed that they have competing characteristics in miRNA.

The next step, Liu suggested, is to understand which influence is dominant.

If higher temperatures prevail, leading to photorespiration, plants may produce less biomass and become less productive. Scientists can potentially lend a hand, Liu suggested, through genetic engineering.

These altered plants can be “made to mask miRNAs effects by simply introducing mutations in miRNA target genes to block” their activity, she said.

The Stony Brook researcher cautioned, however, that such engineering, especially with economically important plant species, would need to await a better understanding of how “all the factors work together.” The information in model plants, like the Arabidopsis in Liu’s studies, could be used as a guide to study higher and more complex plants.

Liu explained that the study of miRNA is relatively new. Scientists recognized their role as biological regulators with conserved functions in the early 2000s.

The reason she took this approach relates to her indirect path to plants. From 1985 to 1987, she was enrolled in the first environmental program at Beijing University, where she studied environmental law and environmental biology and ecology.

When she worked at Cold Spring Harbor Laboratory in Michael Hengartner’s lab, she conducted her research in the shadow of Barbara McClintock, a Nobel Prize winner who had occupied the same lab space at CSHL. Indeed, she saw a portrait of McClintock holding a magnifying glass observing corn on the wall next to the entrance to the lab.

“My idea that elevated carbon dioxide and elevated temperature will lead to epigenetic changes in 2007 was inspired by [McClintock’s] ‘dynamic genome’ theory,” Liu explained. McClintock’s theory gave Liu the initial confidence that there would be epigenetic responses, although there weren’t any previous reports suggesting that.

“The climate changes slowly,” said Vitaly Citovsky, a professor of biochemistry and cell biology at Stony Brook. “We want to know the effect on all different organisms, including plants. This is an important step in understanding that effect.”

Citovsky, who has known Liu for three years and provides space in his lab for her research, described her as “very dedicated” and “committed to her career.”

On Long Island, Liu feels like a part of an international community. That group includes her husband, BNL scientist Andrew Gifford, who is originally from England. The couple live in Brookhaven with their 11-year-old daughter Helena.

While Liu feels at home on Long Island, she said she “satisfies myself by eating what I like to eat,” at home with her parents in China. She is especially fond of a cold rice noodle dish.

When she’s out bicycling or walking on the beach, Liu feels as if she can see through the surface of nature.

“I can imagine, when I see the forests, trees and flowers, something on a molecular level happening to them,” she said. “I can see the secret behind” their response to changes in the environment.

She has already received several requests for her manuscript and is excited about the potential future direction of these studies.

“People are interested in looking at the [effects of] climate change,” she said. This work on microRNA “adds something new” to the research direction.

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Archaeopteryx, a dinosaur the size of a turkey, has often been viewed as the Kitty Hawk of bird flight. Around 150 million years ago, this early bird changed the way dinosaurs moved around in the world, from running, climbing, slithering, leaping or swimming to soaring through the air.

This celebrated species glided above the spike-backed Stegosaurus and the long-necked Brachiosaurus of the Jurassic period.

Feathers, hollow bones and a brain capable of processing information to make flight possible all came together, distinguishing Archaeopteryx from its land-limited cousins.

And yet, recent research suggests that while this creature may have been among the first to fly, it was likely not the first to have the brain power to make flight possible.

Led by Stony Brook University research instructor Amy Balanoff, a team of scientists used CT scanners to examine the brains of older dinosaurs that are considered the distant cousins of Archaeopteryx, modern birds and Archaeopteryx itself.

While the researchers weren’t able to look at the brains themselves, they were able to study the relative size of different areas by looking at the skulls. It is like examining the outline of a hard suitcase stuffed to capacity. By looking at different compartments, scientists could see what was there and how much space it filled. In the scientists’ case, they used CT scanners to determine the volume of different brain regions.

Archaeopteryx, it seems, wasn’t alone among its contemporaries and even, in some cases, its predecessors in having a bird-like brain capable of flight.

“This feature that we thought was more restricted in its nature now needs to be expanded to include more groups,” said Balanoff, who is also a research associate in paleontology at the American Museum of Natural History.

Creatures that have an enlarged or hyperinflated forebrain, which is important in providing superior vision and the coordination necessary for flight, include oviraptorosaurs and troodontids.

This study “establishes that the evolutionary origin of the relatively large brain of Archaeopteryx was not the result of nature selecting for flight capability,” explained Gabriel Bever, an assistant professor of anatomy at the New York Institute of Technology, a co-author on the study and Balanoff’s husband. “Large brains evolved prior to flight and were simply inherited by Archaeopteryx and other early birds.”

This, Bever, continued, is an important example of evolution taking existing structures and assembling them in a way that moves the group along its evolutionary trajectory.

The forebrain is what really expanded along bird lineage, Balanoff added. That part of the brain is larger among species with stronger cognition.

“A lot of characteristics that we’ve associated with flying birds are not unique to flying birds,” she said. “They show up much earlier with nonavian dinosaurs.”

Balanoff described the finding as further evidence of a random process, rather than being directional.

She said the result wasn’t surprising, given that other bird-like features, like feathers and hollow bones, were present before Archaeopteryx. One of the first-known dinosaurs capable of powered flight, Archaeopteryx was discovered only two years after Darwin predicted in “The Origin of Species” that there should be “transitional fossils,” Balanoff said.

The latest findings were published in the journal Nature in July of this year.

Balanoff joined SBU this summer and will be one of several teachers in a gross anatomy class for medical students this fall. “Paleontologists in general are often found in anatomy departments, teaching human gross anatomy,” she said.

Balanoff and Bever met when they were at the University of Texas, when Balanoff was working on her master’s degree and Bever was conducting research for his doctorate.

Balanoff didn’t grow up in Texas with a burning desire to uncover more information about dinosaurs or dinosaur brains.

“My father [Howard Balanoff, a professor at Texas State] is a political scientist. I was thinking more along the lines of politics,” she said.

As a freshman in college at the University of Texas, however, she took a course with Timothy Rowe — a collaborator on the Nature article — and switched her major to geology.

Going forward, Balanoff plans to focus on an area of the modern bird brain called the wulst, which may have a similarity to a structure in the brain in the Archaeopteryx.

“The scientific importance of the wulst to our understanding of neurological evolution,” predicted Bever, “will eventually far outweigh its importance as a systematic character supporting Archaeopteryx as an early bird.”

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The brain is like an enormous orchestra, as neurological signals from different regions work together to create a symphony of thought, emotion and behavior. When some of those signals are out of tune or come at the wrong time, the melody, and indeed the thought process, can become difficult to follow.

Pavel Osten, an associate professor at Cold Spring Harbor Laboratory, has helped develop ways to compare the signals from mouse brains that are functioning within the range of normal with those that have wiring or signaling problems because of mouse models of disorders like schizophrenia or autism.

“There are disorders linked to brain development that are, in a way, subtle,” he said. “There is nothing dramatically wrong with the brains of patients” on a larger scale. Autism and schizophrenia are likely caused by different wirings of brain connections, without dramatic changes, such as the cell loss in neurodegenerative disorders like Parkinson’s and Alzheimer’s, Osten explained.

To understand what happens in the brains of people with schizophrenia and autism, Osten worked with TissueVision, a Cambridge, Mass., company, to develop an imaging system called serial two-photon tomography. In the past, scientists would take one to two months to image the entire brain at the same resolution that this technique can now do in a day.

It works by integrating automated images of thin parts of the brain, starting with the top. By looking at which regions of a brain are active, scientists can see how the communication among circuits may be disrupted in disease and can look at what drugs might correct these problems.

“When we got to that point, we realized that we have a really good drug-screening method,” he said. This process can map out how drugs affect different regions of the brain.

Indeed, Osten and MIT professor Sebastian Seung started a company called Certerra, which provides a rapid analysis of brain activity at different times. Based at Cold Spring Harbor, the company employs three people. Osten hopes to increase that to 10 to 15 staff members in the next few years.

Osten works one day a week at that company, named for the “territory of the brain,” while he spends the rest of a work week that often exceeds five days in his lab. Osten said tomography can reveal unexpected benefits of drugs by suggesting ways medicines affect the brain.

Many drugs used for depression were “prescribed for something else,” he said. When patients took them, however, they got better. By seeing the effect of a wide range of remedies, researchers can depend “less on serendipity. They can see the clinical effect.”

The CSHL scientist said that seeing which regions of the brain are active doesn’t necessarily reveal every cellular and molecular detail linked to a specific disorder.

“We focus on the large picture,” he explained.

Peter Seeburg, a professor in the Department of Molecular Neurobiology at the Max Planck Institute for Medical Research in Germany, who has known Osten since 1999, described serial two-photon tomography as a “promising way to determine the brain circuitry. Whether it will allow [researchers] to see differences in schizophrenia or autism is at this point unclear.” He explained that the key to its effectiveness lies in the ability to see how the circuitry determined by tomography differed from “normal” individuals which, he contended, was still a “huge amount of work.”

Seeburg described Osten as a driven scientist with an excellent reputation and an international renown, adding, “He has a passion for medically relevant science and a nose for excellent projects.”

A scientist at CSHL for five years, Osten lives in Huntington with his wife, Julia Kuhl, a fine and graphic artist who works part-time at Cold Spring Harbor. The gallery Frosch & Portmann in New York has exhibited her work, which is available at the website This year, she had a solo exhibit at the gallery.

The couple, who also have a residence on the lower East Side, enjoy viewing the countryside on Long Island and in the area from their 1967 butternut-yellow Camaro Convertible.

Osten, who grew up in Czechoslovakia, is pleased with his decision to join Cold Spring Harbor Laboratory, where he feels the collaborations with colleagues in the neuroscience department make it a “pretty spectacular place to work.”