Some Chinese herbal remedies have had it right for many years, even if no one could point to a specific reason. Now, however, researchers at Stony Brook have figured out why some remedies taken as a tea for arthritis and pain work.

A chemical in the brain, and elsewhere, can send a signal that relieves pain, inflammation and stress. The reason pain sometimes continues, causing ongoing aches and discomfort, is that the body also has a system for breaking down or putting away its own pain-easing solution.

The Chinese remedy has an active chemical in the herb that is a truxillic acid compound. This is similar to a chemical Stony Brook scientists found that allows a pain relieving neurotransmitter, called endocannabinoid anandamide (or AEA) to remain active.

The body has a “natural marijuana system,” explained Dale Deutsch, a professor of Biochemistry and Cell Biology at Stony Brook. Deutsch has locked onto one of the key players in the breakdown of that system.

Deutsch recently received a $3.8 million, five-year grant from the National Institute on Drug Abuse to develop new drugs for pain, inflammation, and drug addiction. The research involves scientists from the Biochemistry and Cell Biology departments, Chemistry, Applied Mathematics and Anesthesiology. The research also involves the Institute for Chemical Biology and Drug Discovery, and the Laufer Center for Physical Biology.

Deutsch and his team are looking to block a protein called fatty acid binding protein. The scientists are trying to figure out if preventing these FABPs from becoming active allows AEA to continue to provide pain relief.

In drug addiction, interfering with these FABPs might reduce the pain and perhaps cravings associated with removing drugs, Deutsch said.

“In theory, if you can increase the AEA when people are coming off drugs, you may be able to help them with withdrawal, and diminish drug-seeking behavior,” Deutsch said.

The drug addiction component to this system is still at the early stages, cautioned Deutsch.

Martin Kaczocha, who identified the FABP’s role with AEA as a graduate student in Deutsch’s lab and is now an assistant professor in the Anesthesiology Department, is studying how the neurotransmitter reduces pain.

The potential upside to finding inhibitors that block the breakdown of AEA is that they work off the body’s own systems and may not have the same negative side effects as the drugs currently on the market, like NSAIDs, which, while effective can also cause stomach problems.

Tapping into this natural pain-relieving system may enable patients to feel the kind of physical relief from neuropathic pain that they might get from marijuana, without having the same psychotropic effects of the drug, he explained.

Deutsch has been studying AEA for over 20 years. In fact, towards the beginning of his work with the neurotransmitter, he discovered an enzyme that is involved in breaking down AEA. Some companies are working on drugs even now that are moving into Phase 2 trials that inhibit that enzyme, Deutsch said.

What excites Deutsch about this new FABP target, however, is that it is organ specific. That means that the transporters in the brain are different from those in the liver or other areas of the body.

The studies with the enzyme, while effective, may wind up inhibiting AEA breakdown throughout the body.

With this grant, Deutsch and colleagues, including Iwao Ojima, distinguished professor of Chemistry, Kaczocha and Robert Rizzo, associate professor in the Department of Applied Mathematics and Statistics and a member of the Laufer Center, can screen for additional compounds that might work on FABPs. So far, they’ve looked through a million possible options and expect to screen for an additional four to five million compounds within the next few years to get more potent inhibitors of the FABPs.

Deutsch credited the work of undergraduate student Brian Ralph, graduate students Bill Berger and Trent Balius and research assistant Liqun Wang as providing instrumental contributions.

Within the next few years, Deutsch and his team hope to partner with pharmaceutical companies that may develop drugs with them.

A resident of Stony Brook, Deutsch lives with his wife Lou Charnon Deutsch, an author and professor of Hispanic languages and literature at Stony Brook. Deutsch has been sailing for 20 years and especially enjoys heading to the Great South Bay.

Deutsch became fascinated with science when he received a chemistry set from his mother when he was 12.

As for his most recent efforts with FABP inhibitors, Deutsch said it “works in animals,” so he “knows we’re on the right track.”

Worms are fine. Mice and rats? Sure. Dogs and monkeys also have their value, especially to basic research. But what really interests Gholson Lyon are people. “I study humans because that’s what I’m interested in,” said Lyon, a child, adolescent and adult psychiatrist and researcher at Cold Spring Harbor Laboratory. “Humans are an incredibly complex species.”

An assistant professor at CSHL since March 2012, Lyon is establishing connections with Stony Brook as he builds a research and clinical team that benefits from an understanding of human genetics. “Part of the reason to partner with Stony Brook is that it’d be nice to work with clinicians who have done a lot of work with families,” he said.

Indeed, Lyon worked closely with a close-knit family in Utah in which some of their sons were born with unusual symptoms and died at young ages. Starting in 1979, five boys that were born in that family over a three-decade period got some aspect of the disease.

Looking closely at the family’s genes, Lyon found a mutation that, as he put it, has a “high expression.” He named the disorder Ogden Syndrome, after the town where the first family lives. While it would be hard to develop a treatment for Ogden Syndrome, “It’s about knowledge,” Lyon said. “Giving the family knowledge that it has this mutation helps to bring awareness.”

Indeed, knowing that a child is born with this genetic change can help alert parents to find ways to avoid various symptoms for their children.

In Ogden Syndrome, boys sometimes have trouble when food goes down the wrong tube, causing lung infections. In the future, with the family more aware of this problem, parents can work with doctors to prevent sending food to the lungs with the type of food choices or with earlier placement of a feeding tube, he said.

Lyon’s medical mission is to provide and encourage other doctors to offer individualized care. “There are lots of people who want to develop drugs,” he said. “I firmly believe that identifying illness before it begins and then working to prevent or decrease the severity of the illness is far easier than trying to fix a full-blown illness with drugs after the fact.”

He said he understood actress Angelina Jolie’s informed decision to have a double mastectomy based on her genetic predisposition to breast cancer.

“Every individual has their own risk-benefit analysis,” Lyon said. Lyon derives considerable satisfaction from working with the family with Ogden Syndrome. He found it similarly rewarding to work with someone who had such a severe obsessive compulsive disorder that he struggled to function.

For many months, Lyon treated this patient with Prozac, without any effect. After doing a full genetic analysis of his patient, he realized his patient had a gene that affects the metabolism of fluoxetine, the ingredient in Prozac. If he had known that upfront, he would have chosen a different drug.

Lyon used deep brain stimulation with this patient. The effort completely changed his life, enabling him to function at a higher level and even to date. His patient got married this past summer.

Deep brain stimulation is not the current standard of care, has potential side effects and is a more expensive treatment, costing tens of thousands of dollars. Lyon, however, believes the technique — in which a machine sends regular, controlled electrical signals into the brain — will prove useful for other patients.

It shows promise not only for treating severe obsessive compulsive disorder, but also for helping with other illnesses like Tourette Syndrome.

“Now is the time to be putting a lot of effort into advancing deep brain and precision medicine,” Lyon said.

The Cold Spring Harbor researcher said he has had patients for whom even individualized approaches haven’t improved the quality of life. “Medical doctors try their best to provide individualized care to each person,” he explained. “I have certainly had many times in which I could not help certain people due to the severity of their illness and the limited resource at hand.”

Eric Topol, the director of the Scripps Translational Science Institute and the chief academic officer at Scripps Health, called Lyon a “rising star” who is not afraid to “tell it like it is.” He said Lyon, whom he asked to give a talk on the future of genomic medicine last year, is making “major contributions to get the field moving forward.”

Many expectant parents live their lives somewhere between hope and prayer. The big question, and fear, often isn’t whether the child will be a boy or girl, but whether he or she will develop in a healthy way.

The agony and ecstasy of the process was exponentially more dramatic for Gerald Thomsen and his wife Julia Todorov-Thomsen during three pregnancies that produced healthy children. Scientists who met at Stony Brook, the couple knew each phase of development for the skin, muscles, heart, brain, and everything in between.

“I tried to push out of my mind all the scenarios where things could go wrong,” Thomsen said. “There are so many complicated circuits and events.”

Indeed, Thomsen has considerably more than textbook knowledge about development, albeit with other organisms. The Stony Brook professor in the Department of Biochemistry and Cell Biology has dedicated much of the last 20 years to understanding some of the signals and processes that help animals, in his case, mostly frogs, develop.

The big picture question he explores in his lab is, “How does an embryo put itself together? How do cells with different specialties — nerve cells, skin cells — emerge from a single egg cell?”

Thomsen is interested in exploring this question at the whole animal, cellular and molecular level. In his lab, he is studying a process called induction, in which cells respond to signals from neighboring cells.

When a signal, often in the form of a protein or polypeptide, binds to a cell, it often sends a signal from the cell membrane to the nucleus, where it might start or stop a genetic process.

He’s currently working on how an understudied gene, which seems to regulate cell differentiation, might affect growth. When this gene is taken away, the frog embryo doesn’t develop tissues and organs critical for its survival.

Thomsen said many scientists in the world of developmental biology look specifically at what is new about a cell as it moves from one state to another. They want to know what genes are turning on or off. To explore that, the researchers often block them or make those genes more active, to see how that influences what a cell does.

In the late 1990s, Thomsen and a student of his, Haitao Zhu, observed a protein that interacts with a set of signals that go from the cell membrane to the nucleus, where the frog’s genetic machinery resides. When Thomsen and Zhu put the gene for that protein into the frog embryo, it generated another backbone and nervous system.

“It was really dramatic,” Thomsen recalled. The gene turned out to be a key regulator in a signaling pathway, called TGF beta.

Thomsen’s work in this arena is “a major contribution to our understanding of how embryos develop,” said Amy Sater, a professor at the University of Houston in the Biology and Biochemistry Department. “It’s had applicability across all vertebrate systems.”

Sater and Thomsen have taught the Cell and Developmental Biology of Xenopus course at Cold Spring Harbor Laboratory for the last three years. Sater has appreciated Thomsen’s sense of humor and said, “The community has a lot of confidence in [his] work.”

Thomsen has a grant right now from the Stony Brook Medical School to look at a protein to see whether it might be operating in breast or other cancers. His lab, which includes eight people, is also focused on understanding the signals that lead to regeneration. In this arena, he is studying frog and sea anemone embryos.

Adult anemones can regenerate a complex body part from a stump of tissue, he said, the same way starfish can. Frogs have a limited ability to regenerate, so he could potentially test the lab’s findings with sea anemones in frogs.

A resident of Port Jefferson, Thomsen brings special guests to his children’s classes, introducing them to adult frogs, embryos and tadpoles. His children are Liam, 7, Isabella, 5, and Luca, who is almost 3.

Initially interested in oceanography, a specialty his wife pursued, Thomsen was fascinated by biochemistry and gene regulation in the context of differentiating cells. His particular field “always has something new.”

As he felt when his children were developing, Thomsen said the process is “amazing. Even though we know a lot of detail, we also appreciate that we know these details in a spotty way.”

Katherine Bachner speaks Russian, regularly spends a week in Kazakhstan and understands Russian culture. That is why she recently decided it was time someone worked on a project that would help her colleagues connect with their Russian counterparts without committing any cultural faux pas.

Back when she was starting to work with a Russian program, she went on a trip with an American team who attended an enormous banquet arranged by their hosts. The head of the American group didn’t give a toast.

“If you’re the leader of a delegation, it’s incredibly rude” not to give a toast, even if it’s through an interpreter, she said. “That’s Russia 101 and they weren’t doing it. I thought that was very strange.”

At Brookhaven National Laboratory, where she has worked since 2011, Bachner is a part of the Nonproliferation and National Security Department. That means she works with people in numerous countries to provide safeguards for their nuclear power plants and to help detect undeclared nuclear activities and procurement networks.

In Kazakhstan, for example, she’s been helping a nuclear facility upgrade its measurement procedures to improve the accuracy of data that the International Atomic Energy Agency collects when they conduct inspections. The BNL team works with executives at the plant, with the IAEA and with a national company in Kazakhstan.

It’s a multilateral effort to “assist a partner country to improve their safeguards,” she explained.

A cornerstone of her work is “helping the U.S. government develop policies that will make the Nonproliferation Treaty more effective and viable in the long term,” she said. Much of her work is with the IAEA, which “helps implement nuclear safeguards and creates a better regime of safeguards in [other] countries.”

A self-described idealist, Bachner got into the world of nuclear safeguards because she said she hopes some day that the world can be free of nuclear weapons. “I have a passion for trying to make the world a better place,” she said. “I think the field is doing that slowly and sometimes invisibly. We need more young people working on it. It needs to be demystified.”

Indeed, other experts in the nonproliferation world believe Bachner is among a key group of professionals who will ensure a world of nuclear accountability and safety. Bachner “is part of the next generation of nonproliferation experts,” said Susan Burk, a former special representative of the president for nuclear nonproliferation and currently a consultant who has worked with Bachner at BNL. Bachner can be “an important role model for other young people who can look at her and her accomplishments and appreciate how gratifying working on these issues can be.” Burk said she is confident Bachner is an “excellent U.S. representative who is sensitive to the unique cultures of those countries.”

Bachner, who has a master’s degree in cultural anthropology from Columbia as well as a master’s degree in international policy studies from Monterey Institute of International Studies, said the results of her work on enhancing an understanding for scientists and regulators of cultural differences is unlikely to be a simple checklist for each country.

“If you’re working in Russia, the first thing the person would need to do is take a class or course in basic concepts that there are these international differences,” she said. “You need to try to learn some specific things about the culture you’ll be a part of.”

She is hoping to produce a paper that will explain the need for intercultural empathy and training, even for people with expertise in traveling and foreign languages. “If you improve your relationships with your counterparts, you improve the likelihood that the project will be effective,” she said.

Bachner, who grew up in Washington, D.C., and upstate New York, said she loves being near the water. She and her husband Eric live in East Moriches, where she swims, kayaks and bikes. She’s working on a “hilarious, fantastical book” that is in its first draft. An animal lover, Bachner has experience on two continents milking goats. She worked in Hawaii and in Mongolia, where she was performing anthropological field work.

“Central Asian goat milking is really different,” she said. “Our goats give more milk and are better fed. They don’t have to range as far. It’s kind of shocking when I came back from Mongolia to notice how plentiful our lives are.”

As for her work on nuclear safety, Bachner said she is working toward disarmament in part because “there is little that could threaten so much of the world at once.”

Doreen Ware brings her work home with her. Then again, her work is everywhere. An adjunct associate professor at Cold Spring Harbor Laboratory, Ware studies large sections of plant genes and the way those genes affect what a plant becomes.

With the world’s population continuing to increase and the type of land for farming crops that will provide food under various conditions of stress, the urgency to find and harness the best combination of plant genes is building. “In the U.S. right now,” she said, “more than 50% of the agricultural land has been under drought conditions.”

Ware, a computational biologist in the Department of Agriculture, is involved in her own experiments with plants and helps create tools to understand the wealth of information coming from other people’s basic genetic research.

Her group is focused on understanding regulatory networks, or the genes that control the level of expression of other genes. Specifically, she studies microRNAs and transcription factors, which are protein-coding genes that bind to DNA to promote or repress gene expression. She described part of her work as “setting up resources that other people can use to do their own work. I’m a firm believer that supporting many people will bring out more product than my group can do.”

Ware is a co-principal investigator on iPlant, which is as an entity that is by, for and of the community, according to its website. She is also the administrative lead for the Cold Spring Harbor effort on iPlant.

Part of the original iPlant Collaborative grant that started in 2008, Ware and her lab members “provide scientific support for several of our collaborations in genome-wide studies,” said Steve Goff, the project director and principal investigator for iPlant.Ware said comparing genes across different plants helps scientists understand which code is responsible for a plant’s responses to changes in its environment.

Ware likened the process of understanding how to optimize different genes in her work to designing a bicycle. Bikes all use the same underlying parts, although some work better in mountains while others, like tricycles, are designed for stability.

“My group is focused on understanding which sets of parts might be important in developmental outcomes, which parts are important to environmental outcomes and which contribute to both,” she said. The conditions she examines range from less potable water to limited supplies of nitrogen and phosphorus. Unlike mammals, plants make their parts as they go through their lifestyle, in response to sunlight or other cues, signaling cells to flower or to go into dormancy or die.

In her lab, Ware has seen some results that surprised her. She was looking at two maize plants that looked identical. The regions in between the genes didn’t look similar when she looked at their exact location. “The DNA between the genes in many cases are different,” she explained. “This DNA may be regulatory” and will introduce “flexibility” differences in how and when the genes will be expressed. “When you see that they are this different, it’s pretty amazing,” she said.

Her colleagues have offered a similar adjective to describe Ware herself. “Understanding both computational analysis and plant biology is a rare combination that [Ware] and her team bring to the iPlant Collaborative,” Goff explained. “Many people in the agricultural research fields, both applied and academic, seek to benefit from [her] knowledge and reputation.”

Ware and her husband, Joseph Lanzone, a software quality engineer, live in Melville. She has a 21-year-old son, William, and an 8-year-old son, Marc. Long Island appeals to her because she likes “all water activity,” which includes sailing and heading to beaches.

At home, she has trees and flowers that bloom all year-round, giving her “something beautiful to look at” during each season. Ware also regularly attends services at her church, St. Elizabeth of Hungary.

As for her work, she turns to an old saying: You can give people a fish and feed them for a day or you can teach people to catch fish and feed them for a lifetime.

“From my perspective, I want to teach them to farm the fish,” she said.

John Tranquada, the great grandson of a Portuguese stowaway on a ship to Honolulu, was in junior high school in California when the Beatles’ “Abbey Road” came out. The iconic cover image, with John Lennon, Ringo Starr, Paul McCartney and George Harrison, walking over a crosswalk stayed with him over four decades later.

In recent months, when a group of scientists at Brookhaven National Laboratory were preparing to announce the results of their latest finding, Tranquada suggested that the image of the four Beatles walking across that striped crosswalk all those years ago and thousands of miles from the original location might be worth copying. Their recent experiments, after all, detected through an indirect method the fluctuating stripes in a model compound designed to study superconducting materials.

They readily agreed and the stage was set to borrow an iconic musical image to illustrate their research.

Superconductivity holds promise for future technology and innovation because superconductors allow the transfer of energy without any resistance. The cost of manufacturing superconducting cable has been prohibitive.

Tranquada has been studying the magnetic stripes in superconductors for over 18 years.

The electrons, or negatively charged particles, tend to spread out uniformly in space in a superconductor. An analogy, Tranquada offered, is water in a flat bottomed pan. It will spread out to uniform depth. If the water formed a ripple pattern that stayed in the same place, “We would be shocked,” he said. This, however, is just the sort of thing that happens to the electrons in certain superconducting materials.

While copper-oxides are superconductors, the scientists replaced the copper with nickel to create a model compound that could be easier to study. Tranquada knew from previous work that stripes form in nickel-oxide when cooled.

In recent research, he warmed up a nickel-oxide compound, causing the ordered stripes to disappear. The measurements of the team, however, indicated that the stripes still had to be present. Since they knew the stripes weren’t present in a static fashion, they inferred the stripes had to be fluctuating dynamically — or moving.

“This model system teaches us what diffraction-scattering signature to look for in copper-based semiconductors to see if these fluctuations exist,” Emil Bozin, a co-author on the study and member of the X-Ray Scattering Group at BNL, said in a statement.

That search, the researchers suggested, should lead to a better understanding of the role of stripes in superconductivity and, down the road, to new approaches to create superconductors in the energy arena.

Tranquada said his role in the band of scientists was to provide a history and understanding of the materials. “I’ve been studying these nickel oxides for 20 years,” he said.

Tranquada’s colleagues at BNL praised his contribution to the department. He is “a great colleague to have around,” said Peter Johnson, the chair of BNL’s Condensed Matter Physics & Materials Science Department. “He has a really deep and wide-ranging understanding of the field of superconductivity. He’s the guy I go to when I want to get insight into newly published results.”

Tranquada’s discoveries have “provided inspiration to the larger community for more than two decades,” Johnson said. Tranquada said scientists are looking for a convincing explanation for what makes materials superconducting.

Tranquada is excited to be a part of a team that is providing evidence that these stripes can coexist with superconductors. The experiments on superconductors “often reveal behavior that theorists have not anticipated, so it’s like exploring an unknown world,” he said.

Tranquada lives in Stony Brook with his wife Lisa, who is retired after a career that included working at the Pacific Science Center in Seattle and doing administrative work at BNL for 20 years. Their daughter Jessica, 23, graduated from Cornell last year and is revitalizing a riding stable as a “one-person design and construction team,” Tranquada said.

Their son Matthew, 27, is in Washington, D.C., where he has cleared the first few hurdles in the process of applying for a job in the State Department.

Tranquada enjoys jogging in the area and sea kayaking. His family bought a couple of kayaks last summer.

As for the picture of the stripes from Abbey Road, Tranquada said he proposed the idea initially almost as a joke, but his collaborators, which include lead author and BNL X-Ray Scattering Group member Milinda Abeykoon, liked it. They even asked the facilities and operations staff to park a red cart where the Volkswagen car was in the original album.

In the 1970s, Tranquada said he knew he wanted to be a scientist and, for about “two seconds” thought about becoming an astronaut, but realized that probably wouldn’t fly because he gets “sick on the tea cup ride in Disneyland.”

John Tranquada, the great grandson of a Portuguese stowaway on a ship to Honolulu, was in junior high school in California when the Beatles’ “Abbey Road” came out. The iconic cover image, with John Lennon, Ringo Starr, Paul McCartney and George Harrison, walking over a crosswalk stayed with him over four decades later.

In recent months, when a group of scientists at Brookhaven National Laboratory were preparing to announce the results of their latest finding, Tranquada suggested that the image of the four Beatles walking across that striped crosswalk all those years ago and thousands of miles from the original location might be worth copying. Their recent experiments, after all, detected through an indirect method the fluctuating stripes in a model compound designed to study superconducting materials.

They readily agreed and the stage was set to borrow an iconic musical image to illustrate their research.

Superconductivity holds promise for future technology and innovation because superconductors allow the transfer of energy without any resistance. The cost of manufacturing superconducting cable has been prohibitive.

Tranquada has been studying the magnetic stripes in superconductors for over 18 years.

The electrons, or negatively charged particles, tend to spread out uniformly in space in a superconductor. An analogy, Tranquada offered, is water in a flat bottomed pan. It will spread out to uniform depth. If the water formed a ripple pattern that stayed in the same place, “We would be shocked,” he said. This, however, is just the sort of thing that happens to the electrons in certain superconducting materials.

While copper-oxides are superconductors, the scientists replaced the copper with nickel to create a model compound that could be easier to study. Tranquada knew from previous work that stripes form in nickel-oxide when cooled.

In recent research, he warmed up a nickel-oxide compound, causing the ordered stripes to disappear. The measurements of the team, however, indicated that the stripes still had to be present. Since they knew the stripes weren’t present in a static fashion, they inferred the stripes had to be fluctuating dynamically — or moving.

“This model system teaches us what diffraction-scattering signature to look for in copper-based semiconductors to see if these fluctuations exist,” Emil Bozin, a co-author on the study and member of the X-Ray Scattering Group at BNL, said in a statement.

That search, the researchers suggested, should lead to a better understanding of the role of stripes in superconductivity and, down the road, to new approaches to create superconductors in the energy arena.

Tranquada said his role in the band of scientists was to provide a history and understanding of the materials. “I’ve been studying these nickel oxides for 20 years,” he said.

Tranquada’s colleagues at BNL praised his contribution to the department. He is “a great colleague to have around,” said Peter Johnson, the chair of BNL’s Condensed Matter Physics & Materials Science Department. “He has a really deep and wide-ranging understanding of the field of superconductivity. He’s the guy I go to when I want to get insight into newly published results.”

Tranquada’s discoveries have “provided inspiration to the larger community for more than two decades,” Johnson said. Tranquada said scientists are looking for a convincing explanation for what makes materials superconducting.

Tranquada is excited to be a part of a team that is providing evidence that these stripes can coexist with superconductors. The experiments on superconductors “often reveal behavior that theorists have not anticipated, so it’s like exploring an unknown world,” he said.

Tranquada lives in Stony Brook with his wife Lisa, who is retired after a career that included working at the Pacific Science Center in Seattle and doing administrative work at BNL for 20 years. Their daughter Jessica, 23, graduated from Cornell last year and is revitalizing a riding stable as a “one-person design and construction team,” Tranquada said.

Their son Matthew, 27, is in Washington, D.C., where he has cleared the first few hurdles in the process of applying for a job in the State Department.

Tranquada enjoys jogging in the area and sea kayaking. His family bought a couple of kayaks last summer.

As for the picture of the stripes from Abbey Road, Tranquada said he proposed the idea initially almost as a joke, but his collaborators, which include lead author and BNL X-Ray Scattering Group member Milinda Abeykoon, liked it. They even asked the facilities and operations staff to park a red cart where the Volkswagen car was in the original album.

In the 1970s, Tranquada said he knew he wanted to be a scientist and, for about “two seconds” thought about becoming an astronaut, but realized that probably wouldn’t fly because he gets “sick on the tea cup ride in Disneyland.”

They don’t line up like Legos or brick blocks in a house that the big bad wolf can’t knock down. In fact, many proteins, which are at the heart of pathways that tell other parts of cells what to do, fold over on themselves.

In a healthy person, those folds follow certain patterns, helping to conduct a signal or start or end a process. In people who have diseases like Parkinson’s, Alzheimer’s, or Huntington’s disease, the proteins don’t fold properly, causing a range of problems.

As the director of the Laufer Center for Physical and Quantitative Biology, Ken Dill, who is also in the Chemistry Department at Stony Brook, is interested in developing tools and principals of protein folding, some of which may help provide a better understanding of health and disease and may lead to more effective approaches to drug delivery.

“What happens in Alzheimer’s and Parkinson’s is that the proteins all glom together,” Dill said. “When and how they form is of interest to us.”

The typical drug delivery process targets a particular site on a protein and plugs it up “like a cork in a wine bottle,” he said. With Parkinson’s, however, the proteins are all bound together, which leaves no particular place to find a tight binding site.

Dill works with biotechnology companies including Amgen and Genentech. These companies make proteins as drugs, as opposed to pharmaceutical companies, which often make chemicals as drugs.

“It’s complicated to make a protein as a drug,” he said. “When you take a biotechnology drug, if you want to inject a solution of proteins, you want to concentrate the proteins as much as possible.” Putting them together in such a large group, however, causes them to stick together, which limits the ability to make them effective once they’re inside the body.

His lab, which includes 13 people, explores questions of how to keep proteins from tangling up, which is a goal of biotechnology companies designing drug therapies.

Companies design drugs that kill most of the bacteria in a population, but there are some that survive. Those last cells multiply and continue to develop, sometimes without any known remedy.

Scientists and bacteria are locked in a struggle Dill said was like the phenomenon from the Red Queen in “Alice in Wonderland,” where each participant has to keep running just to stay in place. Jim Wang, a chemistry professor at Stony Brook and an affiliate at the Laufer Center, is directly engaged in studying this dynamic.

Stony Brook faculty members have appreciated Dill’s leadership. Dill is “transforming research in physical and quantitative biology at Stony Brook,” said Joshua Rest, an assistant professor in the Department of Ecology and Evolution who is affiliated with the Laufer Center. “Before [Dill] arrived, scientists from different departments working on quantitative approaches to biology weren’t always talking to each other and taking advantage of each other’s expertise in a systematic way.”

Rest credits Dill with developing a community of researchers from diverse fields. He said Dill led an effort to understand the fundamental factors that affect cellular growth rates. Rest called Dill a “science superstar.”

Dill became interested in protein folding over a quarter of a century ago. He was fascinated by the intellectual challenge of understanding such a fundamental problem in nature.

Dill said he feels privileged to work at a place like the Laufer Center, where he doesn’t have to focus as much on short-term payoffs, but can think about and go after longer-term, harder problems.

In addition to about a dozen affiliated faculty members, the Laufer Center includes Dill and Associate Director Carlos Simmerling, who is also in the chemistry department, and Sasha Levy, who arrived from Stanford at the beginning of November. The group will also add Gabor Balazsi, who is currently a professor at the University of Texas M.D. Anderson Cancer Center, in June.

Dill and his wife Jolanda Schreurs live in Port Jefferson. Their older son Tyler is in graduate school at the University of California at San Diego and is studying nanoengineering, while Ryan is at UCLA and is majoring in chemistry.

Prior to working at Stony Brook three years ago, Dill lived in the San Francisco area. He said he appreciates Long Island and the variety of seasons, including the fall foliage.

As for his work, Dill said he remains “at least as excited as ever before” about the opportunities, where he feels as if the Laufer Center enables him to “take his own little moon shots.”

Alistair Rogers left his home in Rocky Point and traveled to Barrow, Alaska, which is above the Arctic Circle and is the northernmost community in the United States, for five weeks this summer. Rogers foregoes the cycling group he enjoys on Long Island and a home with a comfortable bed to live in a dormitory-style room, complete with bunk beds.

Where Rogers works, the mosquitoes can be so aggressive that he wears a full bodysuit, complete with hood and gloves. Any piece of exposed skin becomes a target for bloodthirsty bugs.

For Rogers, a plant physiologist in the Environmental Sciences Department at Brookhaven National Laboratory, Barrow is an ideal location to study how tundra plants, many of which are grasses and small shrubs, take up carbon dioxide. His research will contribute to improving models other scientists have created for the climate in 2050 and beyond. Rogers is a part of a multidisciplinary study called Next-Generation Ecosystems Experiments in the Arctic. The 120 scientists in the study come from Oak Ridge, Lawrence Berkeley and Los Alamos National Laboratories, the University of Alaska, Fairbanks and several other institutions.

The group measures the changes in the physical, chemical and biological response of land-based ecosystems in Alaska. One of the biggest unknowns is how much carbon dioxide some of these plants can take up as a part of photosynthesis.

Rogers’ data, he said, shows that the models’ assumptions were wrong: the models underestimate the capacity for carbon dioxide uptake by three to five times. Armed with a Licor 6400 photosynthesis instrument, Rogers puts a leaf in the chamber and controls carbon dioxide concentration, light intensity, humidity and temperature. The instrument measures the amount of carbon dioxide and water released.

The Arctic is an especially important region to study because the permafrost is beginning to thaw and degrade. Once that happens, dead plants trapped in the ice release their stored carbon dioxide, which has the potential to increase the rate of global climate change, he said.

“The greatest uncertainty surrounds the fate of frozen organic matter that only now is becoming accessible to microbial degradation as permafrost thaws and degrades,” he explained. The thaw also creates opportunities for plants because of the availability of nutrients. The question, he explained is whether the greening of the Arctic will counter the release of old carbon.

Other researchers have appreciated how Rogers has contributed to the group’s understanding of the tundra. “While many scientists classically trained in biochemistry stay in the laboratory and wear a white lab coat, Alistair has taken the sophistication of a modern-day laboratory to the frozen tundra,” said Stan Wullschleger, the projector director for NGEE Arctic from Oak Ridge National Laboratory.

“We have Alistair and a few others to thank for making measurements that show how much more there is to know about the sensitive and poorly understood ecosystems.”

Wullschleger said the soil and plants in the arctic are “critical to our understanding of how our planet works.” The mosquitoes and the separation from Long Island notwithstanding, Rogers described the experience of traveling to Barrow as “a real privilege. Not many people get to go up to the top of the world.”

He said the local Inupiat still hunt whale. He has eaten something called mikiaq, which is raw whale blubber that is fermented in whale blood for a number of weeks. “I bolted it down as quickly as possible,” he said. “Heavy salting improved the flavor” but it most definitely did not “taste like chicken.”

A native of England, Rogers said he enjoys the Long Island weather. He appreciates the proximity to parks and beaches.

Rogers initially started his scientific career with a focus on animals. He transitioned, however, to plants when he “realized as an undergrad that plants determine the rate of global change.”

Rogers has contributed to the development of the next generation of scientists on Long Island. Three times, the Department of Energy has named the BNL scientist an outstanding mentor for undergraduate research programs: in 2009, 2004, and 2002.

“I really enjoy” mentoring, he said. The questions from curious students can “keep you on your toes and that’s a good thing.”

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.”