Mount Sinai Ocean Sciences Bowl team co-advisers David Chase and Glynis Nau-Ritter with members, Ariele Mule, Ben May, Claire Dana and Jonathan Yu. Photo from Glynis Nau-Ritter
Mount Sinai High School’s Ocean Sciences Bowl team is going national.
The group recently went head-to-head at Stony Brook University against 16 other teams throughout the state, and won first place at the regional Bay Scallop Bowl, an academic competition testing the students’ knowledge of marine sciences, including biology, chemistry, physics and geology. Mount Sinai’s 28-27 win against Great Neck South High School clinched its spot in the National Ocean Sciences Bowl, where they’ll join 25 teams from across the country in Corvallis, Oregon from April 20 to 23.
“Going in, we were skeptical, but once we started going through the day, our confidence really built up and everybody got to shine.”
—Ben May
On Feb. 18, the school’s four-student “A” team — senior Ben May, junior Jonathan Yu, sophomore Claire Dana, and freshman Ariele Mule — was one of two left standing after competing in a series of 10 fast-paced, undefeated buzzer, with the next determining the winner. With three seconds left on the clock, Great Neck South ran out of time on a bonus question that would’ve made it the winner, and Mount Sinai came out victorious. The high school has now placed first in 10 of the 16 annual Bay Scallop Bowls.
“It was probably the most exciting competition we’ve had in the Ocean Bowl,” said team co-advisor Glynis Nau-Ritter, a science teacher at the high school. “We work them hard and it pays off.”
Co-advisor David Chase echoed Nau-Ritter’s excitement.
“The students here have not only won the competition, but they’ve expanded their knowledge,” he said. “I’m very proud to be able to contribute to their success, and it’s great to be working with the best of the best.”
May, the team’s captain, said he and his teammates experienced “the ultimate coming-from-behind story” after going through a reconstruction year. May was the only returning member of the “A” team from last year, as the others had all graduated.
“It was thrilling to win and have the experience with so many people who share my love of the ocean.”
—Claire Dana
“Going in, we were skeptical, but once we started going through the day, our confidence really built up and everybody got to shine,” May said. “It was the closest competition I’ve ever been part of. We had no control over it. The other team captain and I were very friendly and it was a bonding experience. The stress of it really pulled us together.”
Calling nationals “a nerd’s dream,” May expressed pride for each of his teammates and said to prepare for the nationals, they met to study over winter break and will be meeting several days a week leading up to the nationwide competition.
“It was thrilling to win and have the experience with so many people who share my love of the ocean,” Dana said. “It was a great surprise, and I thought we all found pride in each other. We were all super ecstatic.”
In addition to competing in the nationals and receiving an all-expenses paid trip to Oregon, each of the four Mount Sinai students received a check for $400 for their victory.
The highest the Mount Sinai team has placed is fourth at nationals. If the students place in the top three or four teams, there are other monetary awards, as well as a trophy and possible student accessories like a netbook. The team could also potentially win a field trip to various research stations, like the Caribbean or West Coast.
Benjamin Martin in his lab at Stony Brook University. Photo courtesy of SBU
By Daniel Dunaief
Last week, the Times Beacon Record Newspapers profiled the work of David Matus, an assistant professor in the Department of Biochemistry and Cell Biology. Matus and Benjamin Martin, who has the same title in the same department, are working together on a new cancer study.
While neither Matus nor Martin are cancer biologists, these researchers have experience in developmental biology with different organisms that could contribute to insights in cancer. Specifically, they are exploring the processes that lead to cell division or invasion. Matus is working with the transparent roundworm, while Martin is focusing on the zebrafish.
The duo recently won the 2017 Damon Runyon–Rachleff Innovation Award, which includes a grant of $300,000. Martin got involved in the research “based on learning more about [Matus’] work and the general hypothesis” about division and invasion, Martin said. The overall perspective is that the cell doesn’t “invade through tissues and divide at the same time.”
Martin has done innovative work with a neuromesodermal progenitor in the zebrafish. These cells are highly plastic and can give rise to numerous other cell types. Martin is focused on trying to understand the basic biology of these cells.
From left, David Matus and Benjamin Martin in the lab where they investigate metastatic cancer. Photo courtesy of SBU
Martin is known for the “very original discovery that a signaling protein called Wnt can regulate the decision between these progenitor cells becoming muscle or neurons,” explained David Kimelman, a professor of Biochemistry at the University of Washington who oversaw Martin’s research when he was a postdoctoral student.
“What is very nice is that [Martin’s] discovery in zebrafish has since been replicated in other organisms such as the mouse and even in human stem cells, showing that this is a fundamental property of vertebrates,” Kimelman explained in an email.
Similar to Matus’ work with the worm, Martin has been working with cells that go through invasive behavior and don’t engage in cell proliferative activities. “We already knew that notochord progenitors are not proliferating when they undergo convergence and extension” from other published works, explained Martin in an email. “Since notochord progenitors exist in the tailbud and we were already studying them, it was a natural jumping off point to address the same question.”
Martin is testing a transcription factor, called brachyury, which drives metasasis-like behavior in human cancer cells. He has studied this transcription factor in the context of early zebrafish development and will see if it helps drive metastasis through inhibition of the cell cycle. At this point, Martin said, there is some “evidence that it does arrest the cell cycle” using human cells in another lab.
So far, the work he has done with brachyury and the cell cycle/invasion in zebrafish is preliminary. Their hypothesis is that halting the cell cycle is a prerequisite for invasive behavior. Like the roundworm, the embryonic zebrafish is transparent, which makes it easier to observe cellular changes.
One of the goals of the project is “to observe the cell cycle of human cancer as it invades through tissues in the fish embryo,” Martin said. In the long term, he hopes to see whether the overexpression of a transcription factor Matus has found in the worm is sufficient to drive metastasis in the zebrafish.
Martin described winning the Damon Runyon–Rachleff Award as “exciting,” and suggested that it “pushes back a little bit of the worry phase” of finding funding for compelling scientific projects. Kimelman said Martin is an “exceptional scientist” and one of the “best I have had the privilege to train.”
Kimelman believes the work Martin and Matus are doing has the potential to provide “important insight into the basic changes that occur during cancer as cells become metastatic,” he explained in an email. “While it doesn’t immediately lead to a therapeutic, understanding the basic biology of cancer is the first step to defining new ways of affecting it.”
Kimelman particularly appreciated the way Matus and Martin combined two different model systems, which offers the potential to provide insight into the basic changes that occur during cancer as cells become metastatic.
Martin learned about science and research during his formative years. His father Presley Martin was a graduate student at Johns Hopkins in Baltimore when the younger Martin was born. Presley Martin recently retired from Hamline University in St. Paul, Minnesota, where he studied the genetics of the fruit fly Drosophila. “At a young age, I was exposed to a lot of the lab and experiments and it was certainly appealing to me,” said Martin.
Benjamin Martin with his son Calvin. Photo by Richard Row
Martin is married to Jin Bae, whom he met at the University of California at Berkeley, where he was studying the molecular control of how muscle precursor cells move to distant parts of the embryo in frogs and fish. Bae is a registered nurse at Stony Brook Hospital. The couple’s son Calvin, who enjoys visiting the lab, will be four in April.
Matus and Martin are collaborating with Scott Powers, a professor in the Department of Pathology at Stony Brook, and Eric Brouzes, an assistant professor in the Department of Biomedical Engineering at Stony Brook.
Powers said the work Martin and Matus are doing is a “basic discovery but an important one,” he explained in an email. “Conceivably, further research could lead to translation but as of right now, any thoughts along those lines are speculative.”
Martin appreciates the opportunity to work on these cells that are so important in development and that might lead to insights about cancer. “It seems like in the past few years” these discoveries have “opened up a subfield of developmental biology,” he said. “It’s exciting to see.”
David Matus in his lab at Stony Brook University. Photo courtesy of SBU
By Daniel Dunaief
At first look, the connection between a roundworm, a zebrafish and cancer appears distant. After all, what can a transparent worm or a tropical fish native to India and the surrounding areas reveal about a disease that ravages its victims and devastates their families each year?
Plenty, when talking to David Matus and Benjamin Martin, assistant professors in the Department of Biochemistry and Cell Biology at Stony Brook University whose labs are next door to each other. The scientific tandem recently received the 2017 Damon Runyon–Rachleff Innovation Award, which includes a two-year grant of $300,000, followed by another renewable grant of $300,000 to continue this work.
In the first of a two-part series, Times Beacon Record Newspapers will profile the work of Matus this week. Next week the Power of Three will feature Martin’s research on zebrafish.
Long ago a scientist studying dolphin cognition in Hawaii, Matus has since delved into the world of genetic development, studying the roundworm, or, as its known by its scientific name, Caenorhabditis elegans. An adult of this worm, which lives in temperate soil environments, measures about 1 millimeter, which means it would take about 70 of them lined up end to end to equal the length of an average earthworm.
From left, David Matus and Benjamin Martin. Photo courtesy of SBU
Matus specifically is interested in exploring how a cell called the anchor cell in a roundworm invades through the basement membrane, initiating a uterine-vulval connection that allows adult roundworms to pass eggs to the outside environment. He is searching for the signals and genetic changes that give the anchor cell its invasive properties.
Indeed, it was through a serendipitous discovery that he observed that the loss of a single gene results in anchor cells that divide but don’t invade. These dividing cells are still anchor cells, but they have lost the capacity to breach the basement membrane. That, Matus said, has led the team to explore the ways cancer has to decide whether to become metastatic and invade other cells or proliferate, producing more copies of itself. In some cancers, their hypothesis suggests, the cells either divide or invade and can’t do both at the same time. It could be a cancer multitasking bottleneck.
Mark Martindale, the director of the Whitney Laboratory at the University of Florida in Gainesville who was Matus’ doctoral advisor, said a cell’s decision about when to attach to other cells and when to let go involves cell polarity, the energetics of motility and a host of other factors that are impossible to study in a mammal.
The roundworm presents a system “in which it is possible to manipulate gene expression, and their clear optical properties make them ideal for imaging living cell behavior,” Martindale explained in an email. Seeing these developmental steps allows one to “understand a variety of biomedical issues.”
Last year, Matus and Martin were finalists for the Runyon–Rachleff prize. In between almost getting the award and this year, the team conducted imaging experiments in collaboration with Eric Betzig, a group leader at the Janelia Research Campus of the Howard Hughes Medical Institute in Ashburn, Virginia. Betzig not only brings expertise in optical imaging technologies but also has won a Nobel Prize.
“We really appreciate the opportunity to work with [Betzig] and his lab members on this project,” said Matus, who also published a review paper in Trends in Cell Biology that explored the link between cell cycle regulation and invasion. He and his graduate student Abraham Kohrman explored the literature to find cases that showed the same switching that he has been exploring with the roundworm.
Yusuf Hannun, the director of the Stony Brook Cancer Center, said the work is highly relevant to cancer as it explores fundamental issues about how cells behave when they invade, which is a key property of cancer cells. Hannun said the tandem’s hypothesis about division and invasion is “consistent with previous understandings but I believe this is the first time it is proposed formally,” he suggested in an email.
Their work could apply to invasive epithelial cancers, suggested Scott Powers, a professor in the Department of Pathology at Stony Brook and the director of Clinical Cancer Genomics at the Cancer Center. That could include breast, colon, prostate, lung and pancreatic cancers, noted Powers, who is a recent collaborator with Matus and Martin.
The additional funding allows Matus and Martin to focus more of their time on their research and less on applying for other grants, Matus said.
Back row from left, David Matus and his father in law Doug Killebrew; front row from left, Maile 9, Bria, 7, and Matus’ wife Deirdre Killebrew. Photo by Richard Row
Matus lives in East Setauket with his wife Deirdre Killebrew, who works for Applied DNA Sciences. The couple met when they were working with dolphins in Hawaii. Matus’ first paper was on dolphin cognition, although he switched to evolutionary and developmental biology when he worked in Martindale’s lab at the University of Hawaii.
Martindale described Matus as prolific during his time in his lab, publishing numerous papers that were “profoundly important in our continued understanding of the relationship between genotype and phenotype and the evolution of biological complexity,” Martindale wrote in an email.
Following in Martindale’s footsteps, Matus replaced his middle name, Samuel, in publications with a Q. Martindale said several of his colleagues adopted the phony Q to pay homage to the attitude that drove them to pursue careers in science. Matus has now passed that Q on to Korhman, who is his first graduate student.
Matus and Killibrew have two daughters, Bria and Maille, who are 7 and 9 years old. Their children have a last name that combines each of their surnames, Matubrew. Matus said he feels “fortunate when I got here three years ago that they had me set up my lab next to [Martin]. That gave us an instantaneous atmosphere for collaboration.”
Adrian Krainer with Emma Larson earlier this year. Photo from Dianne Larson
The prognosis hit Dianne Larson of Middle Island hard. Within three weeks, anxiety attacks, a lack of sleep and fear caused her weight to plummet from 135 to 120 pounds. She found out her daughter Emma, who was 17 months old at the time, had a potentially fatal genetic condition called spinal muscular atrophy in which the motor nerve cells of the spinal cord progressively weaken. Normally, the SMN1 gene produces the survival of motor neuron protein, which, as its name suggests, helps maintain motor neurons. People with SMA, which has four types and severity, produce a lower amount of the functional protein.
“My mind went to the darkest of dark places,” said Larson, whose daughter couldn’t crawl or sit up to eat. “There was no hope. There was nothing I could do.”
At the time of Emma’s diagnosis, there was no treatment for a disease that is the leading genetic cause of death among infants and affects about 1 in 10,000 newborns. Thanks to the work of Adrian Krainer, a professor and program chair of cancer and molecular biology at Cold Spring Harbor Laboratory, that changed early enough to alter the expectations for Emma and children around the world battling a genetic condition that causes progressive weakness and can make moving and even breathing difficult.
Turning to a back up gene called SMN2, Krainer hoped to fix a problem with the way that gene is spliced. On SMN2, exon 7 is normally skipped and the resulting protein has a different sequence at the end. Krainer developed an antisense olignocleotide that binds to a sequence in the intro following exon 7, blocking the splicing receptor. The treatment, which is called Spinraza, helps guide the splicing machinery, which carries out one of the steps in gene expression that is necessary to build a functional protein.
The Larson family of Middle Island, from left, Dianne, Emma and Matthew. Photo from Dianne Larson
Larson had heard of Krainer’s work and was eager to see if his success with animal models of the disease would translate for humans. As soon as Emma reached her second birthday, Larson enrolled her daughter in a clinical trial for Spinraza. After her daughter had a few shots, Larson was stunned by the change. “I was in the master bedroom and she was in the den and I heard a voice getting closer,” Larson recalls. “Next thing I know, she was in my bedroom. I couldn’t believe she crawled from the den to the bedroom. I put her in the den and told her to do it again,” which she did.
The SMA community and Krainer received an early holiday present in late December when the Food and Drug Administration not only approved the treatment, but it also gave doctors the green light to prescribe it for all types of SMA and for patients of all ages. While the SMA community, doctors and Krainer have been delighted with the FDA approval, the excitement has been tempered by concerns about the price tag Biogen, which manufactures and commercializes Spinraza and funded the drug’s development, has placed on the treatment.
For the first full year of injections, the drug costs $750,000. Every year after that will cost $375,000, which Biogen has said publicly is consistent with the pricing for other drugs for so-called orphan diseases, which affect a much smaller percentage of the population.
Knowledge Ecology International, a nonprofit advocate for affordable medicines, sent a letter to the Office of the Inspector General at the Department of Health and Human Services, seeking an investigation. The letter claims that the inventor and maker of Spinraza failed to disclose that the treatment received federal funding. KEI urges the government to use that alleged disclosure failure to end the patent and authorize a generic manufacture of the treatment.
Biogen didn’t return a call and email for comment. Patients and their families, meanwhile, are looking for immediate access to a life-altering treatment. “To be honest, I really don’t know what we’re going to do,” said Larson, whose daughter has four injections left as part of the extension trial soon. “I’m hoping insurance will cover it.”
Insurer Anthem announced late in January that the treatment was only medically necessary for patients with Type 1 SMA, which include people diagnosed with the disease within six months of birth. Anthem created a pay for performance model, which will require patients or their families to prove that the treatment is improving the lives of the recipients.
Larson said she has been in touch with a personal liaison at Biogen, which has been “helpful and supportive,” she said. “They have been going out of their way to reach out to the community to make sure everyone gets access.”
Larson, who is a financial advisor, said she understands the need for the company to generate a profit. “A lot of money goes into” research and development Larson said. “If they’re not gong to make money, they’re not going to” support the efforts to create a treatment.
Emma Larson will be turning 4 this month. Photo from Dianne Larson
Joe Slay, who is the chairman of FightSMA, a group he and his wife Martha founded in 1991 after they learned their son Andrew had Type 2 SMA, sounded hopeful that people who need this treatment will receive it. “I understand there’s constructive, good conversations between insurance companies and Biogen,” Slay said. “We’re monitoring that.”
While Andrew, who is now 30, considers the potential benefits of Spinraza, Slay is pleased the treatment is an option for people and is proud of Krainer’s work.Krainer is “by any definition of the word a hero,” Slay said. “He’s taken his natural gifts, his brilliance in science, his discipline year in and year out approach to his work and has applied himself 100 percent.”
Slay and FightSMA, which has raised over $8 million since its founding, helped provide seed money to Krainer more than 15 years ago, attracting a promising scientist to what was then an intractable medical challenge.
Tom Maniatis, who is the chairman of the Department of Biochemistry and Molecular Biophysics at Columbia University, said Krainer, who did his doctoral work in Maniatis’s lab, showed considerable scientific promise early in his career. Krainer “clearly had the intelligence, drive and experimental skills to make important contributions,” Maniatis said. His work is “a perfect example of how deep basic science studies can lead to profound understanding of a disease mechanism and that, in turn to the development of a treatment,” explained Maniatis in an email.
Within Krainer’s own family, there is a connection to patient care. Krainer’s daughter Emily, who is a pediatric neurology resident at Rochester, may one day prescribe a treatment her father developed. “It will be quite something for me if she eventually prescribes Spinraza to one of her patients,” Krainer said. Even as other scientists and companies like AveXis continue to search for ways to treat SMA, Krainer enhances and refines his research.
“We continue to work on understanding aspects of SMA pathophysiology, the role of SMN levels outside the central nervous system and the potential for prenatal therapy,” he explained in an email. “We are also working on antisense therapies for other genetic diseases and cancer.”
Larson, who is overjoyed with her daughter’s progress, calls Krainer her “superhero” who “saved my daughter’s life.” “It’s such a different feeling when you know you can do something,” she said. When she found out that the FDA approved the treatment, it was “the best day.”
There are millions of species of living things. Until the 1860s biologists divided them into two kingdoms, animals and plants.
Louis Pasteur revealed a third group of microscopic bacteria that caused disease, fermented foods (like cheeses), rotted food and decomposed dead organisms. In the mid-20th century this third group, known as prokaryotes, was shown to consist of eubacteria and archaea, differing mostly in how they used energy to carry out their living activities.
Bacteria mostly use oxygen, sunlight and carbon dioxide as fuels and an energy source. Some bacteria are like green plants and use chlorophyll to convert carbon molecules to food and release oxygen. Most of Earth’s atmosphere arose from that early growth of photosynthetic bacteria. Archaea mostly use sulfur, superheated water and more extreme environmental conditions (like deep sea vents) for their energy.
Biologists today identify cellular life as having three domains — archaea, bacteria and eukaryotes. We belong to the eukaryotes whose cells have nuclei with chromosomes. The eukaryotes include multicellular animals, multicellular plants, unicellular protozoa (protists), unicellular algae and fungi.
The two prokaryotic domains and the five eukaryotic groups are designated as kingdoms. A rough time table of early life on Earth would put prokaryotic life about 3.5 to 3.8 billion years ago, the first free oxygen in our atmosphere about 3.5 billion years ago, the first eukaryotic cells about 2.5 billion years ago and the first multicellular organisms about 1.5 billion years ago.
The branches of the tree of life biologists construct have an earliest ancestor called LUCA (for the last universal common ancestor of a particular branch). There may have been a biochemical evolution preceding the formation of the first cellular LUCA with RNA and protein associations, RNA and DNA associations and virus-like sequences of nucleic acids.
The three domains have produced six million different genes. Molecular biologists have identified 355 genes that all cellular organisms share in common. This is possibly the genome of the LUCA of all living cellular organisms. Whether such a synthetic DNA chromosome could be inserted into a bacterial or archaeal cell or even a eukaryotic cell whose own DNA has been removed has not yet been attempted. It may not work because we know little about the non-DNA components of bacterial or archaeal cells.
Biologists have known for some time that a nucleus of a distant species (e.g., a frog) placed in a mouse egg whose nucleus has been removed will not divide or produce a living organism. But two closely related species (like algae of the genus Acetabularia) can develop after swapping nuclei. In such cases the growing organism with the donated nucleus resembles the features of the nuclear donor.
There is a LUCA for the first primate branch with the genus Homo. We are described as Homo sapiens. Anthropologists and paleontologists studying fossil human remains have worked out the twigs of the branch we identify as the genus Homo. Neanderthals and Denisovans (about 500,000 years ago) are the two most recent branches that preceded the origins of H. sapiens (about 160,000 years ago). Most humans have a small percentage of Neanderthal or Denisovan genes. Fossils of Homo erectus (about 1.8 million years ago) or Homo habilis (about 2.8 million years ago) are much older than the recent three species of Homo. Those fossils do not have DNA that can be extracted from teeth.
A second objective of studying LUCA’s 355 genes will be the identification of each gene’s function. That will tell biologists what it is that makes these genes essential in all cellular organisms.
I can think of a third important consequence of studying LUCA. There are millions of different viruses on Earth, especially in the oceans. If cellularity arose from clusters of viruses, the genes of the mother of all LUCAs may be scattered among some of those viruses and give biologists insights into the step-by-step formation of that first LUCA cell.
In Gilbert and Sullivan’s operetta, “The Mikado,” one character boasts of tracing his ancestors to a primordial bit of protoplasm. The genome of LUCA might become an unexpected example where science imitates art.
Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.
First responders, soldiers or those exposed to any kind of chemical weapons attack need a way to remove the gas from the air. While masks with activated carbon have been effective, the latest technological breakthrough involving a metal organic framework may not only remove the gas, but it could also disarm and decompose it.
That’s the recent finding from research led by Anatoly Frenkel in a study on a substance that simulates the action of sarin nerve gas.
Frenkel, who is a senior chemist at Brookhaven National Laboratory and a professor in the Department of Materials Science and Chemical Engineering at Stony Brook University, worked with metal organic frameworks, which contain zirconium cluster nodes that are connected through a lattice of organic linkages.
Anatoly Frenkel with his son, Yoni, at Lake Hopatcong in New Jersey. Photo by Mikhail Loutsenko.
These structures would “do the job even without any catalytic activity,” Frenkel said, because they are porous and capture gases as they pass through them. “It’s like a sponge that can take in moisture. Its high porosity was already an asset.”
Frenkel and his colleagues, which include John Morris and Diego Troya from Virginia Tech, Wesley Gordon from Edgewood Chemical Biological Center and Craig Hill from Emory University, among other contributors, suspected that these frameworks might also decompose the gas.
Theoretically, researchers had predicted this might be the case, although they had no proof. Frenkel and his team used a differential method to see what was left in the structure after the gas passed through. Their studies demonstrated a high density of electrons near the zirconium atoms. “These were like bread crumbs congregated around a place where the zirconium nodes with the connecting linkers were,” Frenkel said.
While this work, which the scientists published in the Journal of the American Chemical Society, has implications for protecting soldiers or civilians in the event of a chemical weapons attack, Frenkel and his colleagues, who received funding from the Defense Threat Reduction Agency, can share their results with the public and scientific community because they are not working on classified materials and they used a substance that’s similar to a nerve gas and not sarin or any other potentially lethal gas.
“This knowledge can be transferred to classified research,” Frenkel said. “This is a stepping stone.” Indeed, Frenkel can envision the creation of a mask that includes a metal organic framework that removes deadly nerve gases from the air and, at the same time, disarms the gas, providing a defense for first responders or the military after a chemical weapons attack. Even though he doesn’t work in this arena, Frenkel also described how manufacturers might use these frameworks in treating the fabric that is used to make clothing that can prevent gases that can be harmful to the skin from making contact.
A physicist by training, Frenkel’s work, which includes collaborations on five other grants, has a common theme: He explores the relationship between structure and function, particularly in the world of nanomaterials, where smaller materials with large surface areas have applications in a range of industries, from storing and transmitting energy to delivering drugs or pharmaceuticals to a targeted site.
Eric Stach, a group leader in electron microscopy at BNL, has collaborated with Frenkel and suggested that his colleague has helped “develop all these approaches for characterizing these materials.” Stach said that Frenkel has “an outstanding reputation internationally” as an expert in X-ray absorption spectroscopy, and, in particular, a subarea that allows scientists to learn about extremely subtle changes in the distance between atoms when they are subjected to reactive environments.
Frenkel said some of the next steps in the work with metal organic frameworks include understanding how these materials might become saturated with decomposed gas after they perform their catalytic function. “It’s not clear what can affect saturation,” he said, and that is something that “needs to be systematically investigated.” After the catalyst reaches saturation, it would also be helpful to know whether it’s possible to remove the remaining compound and reuse the catalyst.
“The next question is whether to discard” the framework after it’s trapped and deactivated the chemicals or regenerate it, Frenkel said. He is also exploring how temperature ranges might affect the performance of the framework. Ideally, it would function as well in an arctic environment as it would in a desert under extreme heat. A commercial application might require the synthesis of a material with different physical characteristics for a range of temperature conditions.
Frenkel has been working on this project for about one and a half years. A colleague approached him to become a part of this new collaboration. “My role was to bring this work to a national lab setting,” where the scientists could use the advanced tools at BNL to study the material as it was working, he said.
A resident of Great Neck, Frenkel, who grew up in St. Petersburg, Russia, lives with his wife Hope Chafiian, a teacher at the Spence School in Manhattan for almost 30 years. He has three children: Yoni lives in Manhattan and works at JP Morgan Chase, Ariela is a student at Binghampton and Sophie is in middle school in Great Neck.
Frenkel appreciates the opportunity to explore the broader world of nanomaterials, which, he said, are not constrained by crystal structures and can be synthesized by design. “They show a lot of mysteries that are not understood fully,” he said. Indeed, Frenkel explained that there are numerous commercial processes that might benefit from design studies conducted by scientists. As for his work with metal organic frameworks, he said “there’s no way to overestimate how important [it is] to do work that has a practical application that improves technology, saves costs, protects the environment” and/or has the potential to save lives.
From left, outgoing Secretary of the Department of Energy Ernest Moniz with BNL Laboratory Director Doon Gibbs taken at the opening of the National Synchrotron Light Source II at BNL. Photo courtesy of BNL
By Daniel Dunaief
Before Ernest Moniz ends his tenure as Secretary of the Department of Energy, he and his department released the first annual report on the state of the 17 national laboratories, which include Brookhaven National Laboratory.
On a recent conference call with reporters, Moniz described the labs as a “vital set of scientific organizations” that are “critical” for the department and the country’s missions. Experts from the labs have served as a resource for oil spills, gas leaks and nuclear reactor problems, including the meltdown at Fukushima in 2011 that was triggered by a deadly tsunami. “They are a resource on call,” Moniz said.
In addition to providing an overview of the benefit and contribution of the labs as a whole, the annual report also offered a look at each of the labs, while highlighting a research finding and a translational technology that has or will reach the market. In its outline of BNL, the report heralded an “exciting new chapter of discovery” triggered by the completion of the National Synchrotron Light Source II, a facility that allows researchers at BNL and those around the world who visit the user facility to explore a material’s properties and functions with an incredibly fine resolution and sensitivity.
Indeed, scientists are already exploring minute inner workings of a battery as it is operating, while they are also exploring the structure of materials that could become a part of new technology. The DOE chose to shine a spotlight on the work Ralf Seidl, a physicist from the RIKEN-BNL Research Center, has done with several collaborators to study a question best suited for answers at the Relativistic Heavy Ion Collider.
Seidl and his colleagues are exploring what gives protons their spin, which can affect its optical, electrical and magnetic characteristics. The source of that spin, which researchers describe not in terms of a top spinning on a table but rather as an intrinsic and measurable form of angular momentum, was a mystery.
Up until the 1980s, researchers believed three subatomic particles inside the proton created its spin. These quarks, however, only account for a third of the spin. Using RHIC, however, scientists were able to collide protons that were all spinning in a certain direction when they smash into each other. They compared the results to protons colliding when their spins are in opposite directions.
More recently, Seidl and his colleagues, using higher energy collisions, have been able to see the role the gluons, which are smaller and hold quarks together, play in a proton’s spin. The gluons hadn’t received much attention until the last 20 years, after experiments at CERN, in Geneva, demonstrated a lower contribution from quarks. “We have some strong evidence that gluons play a role,” Seidl said from Japan, where he’s working as a part of an international collaboration dedicated to understanding spin.
Smaller and more abundant than quarks, gluons are like termites in the Serengeti desert in Africa: They are hard to see but, collectively, play an important role. In the same report, the DOE also celebrated BNL’s work with fuel cell catalysts. A senior chemist at BNL, Radoslav Adzic developed a cheaper, more effective nanocatalyst for fuel cell vehicles. Catalysts for fuel cells use platinum, which is expensive and fragile. Over the last decade, Adzic and his collaborators have developed a one-atom-thick platinum coating over cheaper metals like palladium. Working with BNL staff scientists Jia Wang, Miomir Vukmirovic and Kotaro Sasaki, he developed the synthesis for this catalyst and worked to understand its potential use.
N.E. Chemcat Corporation has licensed the design and manufacturing process of a catalyst that can be used to make fuel cells as a part of a zero-emission car. This catalyst has the ultra low platinum content of about two to five grams per car, Adzic said. Working at BNL enabled partnerships that facilitated these efforts, he said. “There is expertise in various areas and aspects of the behavior of catalysts that is available at the same place,” Adzic observed. “The efficiency of research is much more convenient.”
Adzic, who has been at BNL for 24 years, said he has been able to make basic and applied research discoveries through his work at the national lab. He has 16 patents for these various catalysts, and he hopes some of them will get licensed. Adzic hopes this report, and the spotlight on his and other research efforts, will inspire politicians and decision makers to understand the possibility of direct energy conversion. “There are great advances in fuel cell development,” Adzic said. “It’s at the point in time where we have to do some finishing work to get a huge benefit for the environment.”
At the same time, the efficiency of fuel-cell-powered vehicles increases their economic benefit for consumers. The efficiency of an internal combustion engine is about 15 percent, whereas a fuel cell has about 60 percent efficiency, Adzic said.
BNL’s Laboratory Director Doon Gibbs welcomed the DOE publication. “This report highlights the remarkable achievements over the past decade of our national lab system — one that is unparalleled in the world,” he said. Gibbs suggested that the advanced details in the report, including the recognition for the NSLS II, span the breadth of BNL’s work. “They’re just a snapshot of what we do every day to make the world a better place,” Gibbs said.
While the annual report is one of Moniz’s final acts as the secretary of the agency, he hopes to communicate the vitality and importance of these labs and their work to the next administration.“I will be talking more with secretary nominee [Richard] Perry about the labs again as a critical jewel and resource,” Moniz said. “There’s a lot of support in Congress.” Moniz said the DOE has had five or six lab days, where labs share various displays with members of the legislative body. Those showcases have been “well-received” and he “fully expects the labs to be vital to the department.”
Esther Takeuchi with photo in the background of her with President Obama, when she won the 2009 National Medal of Technology and Innovation. Photo courtesy of Brookhaven National Laboratory
By Daniel Dunaief
Pop them in the back of a cell phone and they work, most of the time. Sometimes, they only do their job a short time, discharge or generate so much heat that they become a hazard, much to the disappointment of the manufacturers and the consumers who bought electronic device.
Esther Takeuchi, a SUNY distinguished professor in the Departments of Chemistry and Materials Science and Engineering and the chief scientist in the Energy Sciences Directorate at Brookhaven National Laboratory leads a team of scientists who are exploring what makes one battery work while another falters or fails. She is investigating how to improve the efficiency of batteries so they can deliver more energy as electricity.
Esther Takeuchi with a device that allows her to test batteries under various conditions to see how they function. Photo courtesy of Brookhaven National Laboratory
The process of manufacturing batteries and storing energy is driven largely by commercial efforts in which companies put the ingredients together in ways that have, up until now, worked to produce energy. Scientists like Takeuchi, however, want to know what’s under the battery casing, as ions and electrons move beneath the surface to create a charge.
Recently, Takeuchi and a team that includes her husband Kenneth Takeuchi and Amy Marschilok, along with 18 postdoctoral and graduate students, made some progress in tackling energy storage activity in iron oxides.
These compounds have a mixed track record among energy scientists. That, Takeuchi said, is what attracted her and the team to them. Studying the literature on iron oxides, her graduate students discovered “everything from, ‘it looks terrible’ to, ‘it looks incredibly good,’” she said. “It is a challenging system to study, but is important to understand.”
This offered promise, not only in finding out what might make one set of iron oxides more effective in holding a charge without generating heat — the energy-robbing by-product of these reactions — but also in providing a greater awareness of the variables that can affect a battery’s performance.
In addition to determining how iron oxides function, Takeuchi would like to “determine whether these [iron oxides] can be useful and workable.” Scientists working with iron oxides didn’t know what factors to control in manufacturing their prospective batteries.
Takeuchi said her group is focusing on the linkage between small-scale and mesoscale particles and how that influences battery performance. “The benefit of iron oxides is that they are fairly inexpensive, are available, and are nontoxic,” she said, and they offer the potential of high energy content. They are related to rust in a broad sense. They could, theoretically, contain 2.5 times more energy than today’s batteries. “By understanding the fundamental mechanisms, we can move forward to understand their limitations,” she said, which, ultimately, could result in making these a viable energy storage material. T
akeuchi is also looking at a manganese oxide material in which the metal center and the oxygen connect, creating a tube-like structure, which allows ions to move along a track. When she started working with this material, she imagined that any ion that got stuck would cause reactions to stop, much as a stalled car in the Lincoln Tunnel leads to long traffic delays because the cars behind the blockage have nowhere to go.
Takeuchi said the ions don’t have the same problems as cars in a tunnel. She and her team believe the tunnel walls are porous, which would explain why something that looks like it should only produce a result that’s 5 percent different instead involves a process that’s 80 percent different. “These escape points are an interesting discovery, which means the materials have characteristics that weren’t anticipated,” Takeuchi said. The next step, she said, is to see if the researchers can control the technique to tune the material and make it into the constructs that take advantage of this more efficient flow of ions.
Through a career that included stops in Buffalo and North Carolina and West Virginia, Takeuchi, who has over 150 patents to her name, has collected numerous awards and received considerable recognition. She won the 2009 National Medal of Technology and Innovation, a presidential award given at a ceremony in the West Wing of the White House. Takeuchi developed compact lithium batteries for implantable cardiac defibrillators.
Takeuchi is currently a member of the National Medal of Technology and Innovation Nomination Evaluation Committee, which makes recommendations for the medal to the president. Scientists who have known Takeuchi for years applaud the work she and her team are doing on Long Island. “Dr. Takeuchi and her research group are making great advances in battery research that are very clearly promoted by the strong relationship between Stony Brook and BNL,” said Steven Suib, the director of the Institute for Materials Science at the University of Connecticut.
Indeed, at BNL, Takeuchi has used the National Synchrotron Light Source II, which became operational last year. The light source uses extremely powerful X-rays to create incredibly detailed images. She has worked with three beamlines on her research. At the same time, Takeuchi collaborates with researchers at the Center for Functional Nanomaterials at BNL.
Although she works with real-world experiments, Takeuchi partners with scientists at Stony Brook, BNL and Columbia University who focus on theoretical possibilities, offering her an insight into what might be happening or be possible. There are times when she and her team have observed some interaction with batteries, and she’s asked the theorists to help rationalize her finding. Other times, theorists have suggested what experimentalists should search for in the lab.
A resident of South Setauket, Takeuchi and her husband enjoy Long Island beaches. Even during the colder weather, they bundle up and enjoy the coastline. “There’s nothing more mentally soothing and energizing” than going for a long walk on the beach, she said.
In her research, Takeuchi and her team are focused on understanding the limitations of battery materials. Other battery experts believe her efforts are paying dividends. Suib said the recent work could be “very important in the development of new, inexpensive battery materials.”
Alan Alda received the Double Helix Award from Cold Spring Harbor Laboratory this month. Photo by Constance Brukin, Cold Spring Harbor Laboratory
By Daniel Dunaief
In a world of tirades and terrifying tweets, the Alan Alda Center for Communicating Science at Stony Brook University is encouraging its professors and students to do something the center’s namesake urges: Listen.
Tough as it is to hear what people mean behind an explosive expression that fuses reason and emotion, the scientists in training, established researchers and others who attend some of the lectures or workshops at the center go through an exercise called “rant” in which each person listens for two minutes to something that drives their partner crazy. Afterward, the scientist has to introduce their partner to the group in a positive way.
Alan Alda. Photo by Constance Brukin, Cold Spring Harbor Laboratory
The staff at the Alan Alda Center finds inspiration, a role model and a humble but willing listener in Alda, the highly decorated actor of “MASH” who has spent the last several decades drawing scientists out of dense shells constructed of impenetrable jargon and technical phrases.
For his dedication to forging connections for scientists, Times Beacon Record News Media is pleased to name Alan Alda a 2016 Person of the Year.
“He’s doing a wonderful job,” said Jim Simons, the former chairman of the Stony Brook Mathematics Department and hedge fund founder who shared the stage with Alda this summer as a part of a Mind Brain Lecture at Stony Brook. “I can’t think of anyone better to be an honoree.”
Simons described a moment with Alda, who is not a scientist nor does he play one on TV, when he was sharing some abstruse mathematics. Alda’s eyes “glazed over when I was first talking to him. He’s teaching scientists not to get a glaze over their audience’s eyes.”
Alda works tirelessly to share a method that blends scientific communication with the kind of improvisational acting he studied early in his career.
“Improv is not about being funny,” said Laura Lindenfeld, the director at the center. “It’s about being connected.”
Last June, Alda was a part of a team that traveled to California to share an approach that is in demand at universities and research institutions around the world. The day of the workshop, three people who were supposed to help lead the session were delayed.
Alda suggested that he run the event, which would normally involve several instructors and break-out groups. Learning about the art of connecting with an audience from someone who reached people over decades through TV, movies and Broadway performances, the attendees were enchanted by their discussion.
“He’s the master,” said Lindenfeld, who was at the campus when the team received news about the delay for the other instructors.
As soon as the session ended, Alda headed for Los Angeles to conduct a radio interview.
“I handed him a granola bar,” recalled Lindenfeld, who joined the center last year. “I was afraid he hadn’t eaten.”
Alda celebrated his 80th birthday earlier this year and shows no signs of slowing down, encouraging the spread of training techniques that will help scientists share their information and discoveries.
“He’s teaching scientists not to get a glaze over their audience’s eyes.”
— Jim Simons
The Alda Center is planning a trip to Scotland next year and has been invited to go to Norway, Germany and countries in South America, Lindenfeld said.
When the University of Dundee received a grant from the Leverhulme Trust to create the Leverhulme Research Centre for Forensic Science, officials in Scotland, one of whom knew Lindenfeld personally, researched the Alan Alda Center’s mission and decided to forge a connection. Lindenfeld helped coordinate a congratulatory video Alda sent that the Scottish centre played at its opening ceremony.
“Everyone present from the highest Law Lord in Scotland, through to the principal of the university and the Leverhulme trustees did not know it was going to happen, and so it was a huge surprise that stunned the room into complete silence,” recalled Sue Black, the director of the centre in an email. “Brilliant theatre of which Mr. Alda would have been proud.”
Established and internationally known scientists have expressed their appreciation and admiration for Alda’s dedication to their field.
The training sessions “drag out of people their inhibitions and get them to think about interacting with the public in ways that they might not have felt comfortable doing before,” said Bruce Stillman, the president and CEO of Cold Spring Harbor Laboratory. This month, Cold Spring Harbor Laboratory gave Alda the Double Helix Medal at a ceremony at the American Museum of Natural History in New York City.
Stillman described the public understanding and perception of science as “poor.” To bridge that gap, Alda’s programs “induce scientists to feel comfortable about talking to the public about their ideas and progress.”
Nobel Prize winner Eric Kandel suggested that Alda’s accomplishments exceed his own.
“There ain’t many Alan Aldas, but there are a lot of Nobel Prizes out there,” Kandel said. While Kandel is “extremely indebted to having won the Nobel Prize,” he said the totality of Alda’s accomplishments are “enormous.”
The Alda Center is working with Columbia University, where Kandel is the director of the Kavli Institute for Brain Science and a professor, to develop an ongoing program to foster scientific communication.
Alan Alda, left, at a ceremony at the American Museum of Natural History. Photo by Constance Brukin, Cold Spring Harbor Laboratory
Kandel, who considers Alda a friend, appreciates his support. Kandel said Jeff Lieberman, the chairman of the Department of Psychiatry at Columbia, asked Alda and Kandel to give a talk on issues related to neuroscience. Lieberman “was my boss,” Kandel said, “I had to be there, but [Alda] didn’t have to be there. He goes out of his way for people.”
In 2017, the center will not only share its communication techniques around the world, but it will also create conferences for timely scientific topics, including climate change and women in science.
The glass ceiling is a “real issue for women in science,” said Valerie Lantz Gefroh, the improvisation program leader at the center. “We’re hoping to give [women] better communication tools so they can move forward in their careers.”
The center is also adding new courses. Next fall, Christine O’Connell, who is a part of a new effort at Stony Brook called the Science Training & Research to Inform Decision and is the associate director at the center, will teach a course on communicating with policy and decision makers.
That will include encouraging scientists to invite state senators to see their field work, going to Congress, meeting with a senator or writing position papers. In political discussions, scientists often feel like “fish out of water,” O’Connell said. The course will give scientists the “tools to effectively engage” in political discussions.
Scientists don’t have to be “advocates for or against an issue,” O’Connell said, but they do have to “be advocates for science and what the science is telling us.”
Given an opportunity to express her appreciation directly to Alda, Black at the University of Dundee wrote, “Thanks for having the faith to collaborate with our centre so far away in Scotland, where we are trying to influence the global understanding of forensic science in our courtrooms — where science communication can make the difference between a guilty or an innocent verdict and in some places, the difference between life and a death sentence.”
To borrow from words Alda has shared, and that the staff at the center believe, “Real listening is a willingness to let the other person change you.” Even if, as those who have gone through some of the sessions, the speaker is ranting.
Huloin Xin. Photo courtesy of Brookhaven National Laboratory
By Daniel Dunaief
The unexpected appearance of Swiss cheese may be preferable to the predicted presence of a balloon. When it comes to the creation of catalysts for fuel-cell-powered vehicles, the formation of a structure that has miniature holes in it may reduce costs and improve energy efficiency.
Using a state-of-the-art facility where he also supports the work of other scientists around the world, Huolin Xin, an associate materials scientist at the Center for Functional Nanomaterials at Brookhaven National Laboratory, recently made the discovery about the structure of a cheaper catalyst. Xin and his collaborators published their work in Nature Communications.
Huloin Xin. Photo courtesy of Brookhaven National Laboratory
The finding “goes against conventional wisdom,” Xin said. “If you have a precursor that’s nanometers in size that’s a metal and you heat it up in oxygen, normally, it would grow into a hollow structure, like a balloon.” Instead, Xin and his colleagues discovered that mixing nickel and cobalt produces a structure that has porosity but is more like spherical Swiss cheese than a balloon. The new architecture has more material crammed into a smaller region than the hollow balloon. It is also stronger, creating a broader range of potential applications.
Scientists at Brookhaven and at other institutions around the world are seeking ways to take advantage of the growing field of nanotechnology, in which physical, electrical or other types of interactions differ from the macromolecular world of hammers, nails and airplane wings. These nanomaterials take advantage of the high surface area to volume ratio, which offers promise for future technologies. What that means is that these materials contain numerous surfaces without taking up much space, like an intricate piece of origami, or, in Xin’s case, a sphere with higher packing density.
The potential new catalyst could be used as a part of an oxygen reduction reaction in an alkaline environment. In a car that uses hydrogen, the reaction would produce water with zero emissions, Xin said. To see the structure of this catalyst, Xin used environmental transmission electron microscopy and electron tomography. The TEM uses computed axial tomography. This is similar to the CAT scan in a hospital, except that the sample Xin studied was much smaller, about 100 nanometers in size, which is 100 times thinner than the width of a human hair.
In addition to determining and defining the structure of the final product, scientists are trying to understand the process that led to that configuration. They can use the environmental transmission electron microscope, which allows gas flowing to study the formation of the catalyst.
Charles Black, the director at the Center for Functional Nanomaterials, said Xin is “off the charts talented” and is a “world leader” in figuring out ways to get more information from the electron microscope. Xin, Black said, has helped create a three-dimensional picture by tilting a two-dimensional sample at different angles in the microscope. “He had already made great strides in improving the speed with which this could be done,” Black said. “He’s also improved the process to the point where you don’t have to be a super expert to do it anymore.”
By slowing the reaction in the nickel-cobalt catalyst down and studying how it forms, Xin uncovered that the shell is not solid: It has pinholes. Once those small holes form, the oxygen infiltrates the pores. The process repeats itself, as shells form, then break up, then oxygen forms another shell, which breaks up, until the process leads to a spherically stacked collection of Swiss cheese structures. The process is ready for industrial-scale applications, Xin said, because the whole synthesis involves putting the elements into a furnace and baking it. While this could have applications in fuel cells, the catalyst still awaits a breakthrough technology with alkaline fuel cells.
The technological breakthrough Xin awaits is an alkaline membrane that can conduct a hydroxyl group. “We are definitely doing research for the future,” he said. “We’re still awaiting the essential element, which is the ionic conductive membrane, to become a technologically mature product.” Xin isn’t focused on creating that membrane, which is a task for organic chemists. Instead, his main focus is on inorganic materials.
As a member of the BNL staff at the Center for Functional Nanomaterials, which is a facility that provides technical support to other scientists, Xin spends half of his time with other researchers on the TEM and half of his time on his own research. “We really have been fortunate to have found someone like [Xin] who wants to excel in both sides of his mission,” Black said “Someone as talented as [Xin], who is very smart with big ideas and increasingly ambitious in terms of what he wants to accomplish for himself … checks his ego at the door and he helps others accomplish their goals.” To improve his ability as a colleague, Xin reads about what the users of the TEM are doing and talks with them about their work.
Xin has been working at BNL for over three years. When he’s not in the lab, Xin enjoys traveling to snorkel in the U.S. Virgin Islands, including his favorite destination, St. John. A skier, Xin’s favorite winter recreational mountain is Lake Placid. Xin grew up in Beijing, where his father is a professor in a business school and his mother is an engineer. He appreciates the opportunity to engage in a broad universe of fields through the work he does at BNL and appreciates the scientific partnerships he’s formed. “My primary focus is on creating novel microscope techniques that can advance the electron microscopy field,” he explained. “I apply them to a variety of materials projects.” Xin estimates that half of his materials application projects come from collaborators.
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