They aren’t quite wonder twins, but some day the dedicated work of husband and wife scientists Christopher Vakoc and Camila dos Santos may help people batting against a range of cancers, from leukemia to breast cancer.

An assistant professor at Cold Spring Harbor Laboratory, dos Santos recently won the prestigious and highly coveted Pershing Square Sohn prize. Dos Santos, who studies breast cancer, will receive $200,000 in funds per year for the next three years. She won the same prize her husband, an associate professor at Cold Spring Harbor Laboratory, collected two years earlier for his work using the gene-editing technique CRISPR to study the molecular pathways involved in leukemia.

Dos Santos and Vakoc are the first family of prize winners in the Pershing Square Foundation’s five years of supporting research in the New York area.“The board was very much taken by how original her approach is and how thoughtful she is about it,” said Olivia Tournay Flatto, president of the foundation. “There was a lot of early stage data that would say that the observations she’s making are interesting to pursue, but that the National Institutes of Health would not fund. We felt this was something we wanted to be a part of.”

Dos Santos is studying so-called epigenetic changes that protect women from breast cancer if they become pregnant before they are 25. Women who have pregnancies before that cut-off age have a 30 to 40 percent decrease in breast cancer, even decades after their pregnancy.

Dos Santos has been digging into this process, looking at why some women who are pregnant before this age still develop breast cancer later in life.

The Cold Spring Harbor scientist is exploring how infections block the protective effects of pregnancy. She hasn’t defined the panel of infections that could influence cancer risk before or after pregnancy. The hypothesis in her work is that “the whole process that is fighting inflammation could change the breast cells,” which could “take away the advantage that pregnancy brings.”

If she proves her theory — that changes to inflammation could take away benefits of an early pregnancy — she could define changes to proteins and genes as biomarkers to predict the risk of breast cancer, even in the event of an early pregnancy. One of the challenges in the three-step application process for this prize was to explain to a group of experts how what she’s doing was different from what others are pursuing. Her approach is to look at cells before and during the process of turning into cancer cells. That strategy led to the current hypothesis, which was the basis for her application for this prize.

To study breast cancer, dos Santos recently developed a mouse model in her lab, to see how pregnancy changes pre-malignant lesions. When the mice they are studying have a gene that would turn into cancer, some of them don’t develop cancer if they’ve already been pregnant. Those mice that haven’t been pregnant develop cancer. She uses this mouse model to ask questions about how pregnancy changes a cell such that oncogenes cannot operate to change a cell into a cancer.

“We are not only investigating how prevention works, but we are also learning what signals break that prevention,” dos Santos said.

Dos Santos has used the mouse model experiments to test an unusual element to human breast cancer resistance. Women who reach their second trimester before 25, but don’t give birth to a child, have the same resistance, decades later, to breast cancer. Mice whose pregnancies last through the equivalent of the second trimester also experience similar epigenetic benefits.

She has tested mice who have a pseudo-pregnancy —who have higher pregnancy hormone levels without being pregnant — to see if a similar pregnancy environment would convey the same resistance. “Even in those cases, with no fetus, no embryo, no birth and no nursing, we see that the epigenetics changes,” dos Santos said. The scientist plans to use the funds from this award to perform high-tech experiments, such as single-cell, multiple mouse models and human tissue analysis that she wouldn’t have been able to tackle without the funding.

Dos Santos is grateful for the funding, which she said she wouldn’t have been able to secure through other means based on “the stage we are right now,” she said. The work is “risky” and “provocative,” but it’s also “outside of the box ideas and experiments and approaches.”

When she puts all the variants together, the risky outcome could be beneficial, leading to a better understanding of how to copy or, perhaps, understand nature to try to cure or prevent cancer.

Dos Santos said she learned about the award when she was on a train on the way to Jamaica, where she was catching a flight to Washington, D.C. She said she turned into a “texting machine,” sharing the good news with everyone, including her husband Vakoc, who called her as soon as he saw the news. “He was super happy,” she recalled.

She said Vakoc was particularly helpful in discussing the work and in watching their sons Lucas and Marcus who are 8 and 5, respectively. She also received some unexpected help from him before an extensive seven- to eight-minute finalist screening process.

She asked him about the interview, and he remembered that there were five people in the audience and that he didn’t get that many questions. When she appeared for her interview, she saw about 25 people in the audience and received numerous questions. In a way, she said, his memory of his experience may have helped her, because she didn’t have time to worry about the size of the audience or the number of questions.

Dos Santos said their sons are proud of their parents for winning awards for their work on cancer.

When her sons are upset with dos Santos, they sometimes warn, reflecting their parents’ threat to take away TV, that they’re going to “take your epigenetics away.”

Dos Santos said the couple maintains a healthy work-life balance. She is grateful for her husband’s support, as well as for the environment and expertise at Cold Spring Harbor Laboratory.

“Here at the lab, we not only have the technology to move this forward, but we also have a pretty outstanding body of scientists that are very collaborative,” she said.

Power of 3: SBU, BNL’s Takeuchi wins coveted innovation award

by Daniel Dunaief - July 5, 2018

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By Daniel Dunaief

Replacing batteries in a flashlight or an alarm clock requires simple effort and generally doesn’t carry any risk for the device. The same, however, can’t be said for battery-operated systems that go in human bodies and save lives, such as the implantable cardiac defibrillator, or ICD.

Earlier versions of these life-saving devices that restore a normal heart rhythm were large and clunky and required a change of battery every 12 to 18 months, which meant additional surgeries to get to the device.

Esther Takeuchi with Michaëlle Jean, the secretary general of the Organisation Internationale de la Francophonie, and moderator Fernando Tiberini at the award ceremony in Paris on June 7. Photo courtesy of European Patent Office

That’s where Esther Takeuchi, who is now Stony Brook University’s William and Jane Knapp Endowed Chair in Energy and the Environment and the chief scientist of the Energy Sciences Directorate at Brookhaven National Laboratory, has made her mark. In the 1980s, working at a company called Greatbatch, Takeuchi designed a battery that was much smaller and that lasted as long as five years. The battery she designed was a million times higher power than a pacemaker battery.

For her breakthrough work on this battery, Takeuchi has received numerous awards. Recently, the European Patent Office honored her with the 2018 innovation prize at a ceremony in Paris. Numerous high-level scientists and public officials attended the award presentation, including former French Minister of the Economy Thierry Breton, who is currently the CEO of Atos, and the Secretary General of the International Organisation of Francophony Michaëlle Jean.

Takeuchi was the only American to win this innovation award this year.

Takeuchi’s work is “the epitome of innovation, as demonstrated in this breakthrough translational research for which she was recognized,” Dr. Samuel L. Stanley Jr., the president of Stony Brook and board chair of Brookhaven Science Associates, which manages Brookhaven National Laboratory. “Her star keeps getting brighter, and I’m proud that she is part of the Stony Brook University family.”

As a winner of this award, Takeuchi joins the ranks of other celebrated scientists, including Shuji Nakamura, who won the European Inventor Award in 2007 and went on to win the Nobel Prize in physics, and Stefan Hell from Germany, whose European Inventor Award predated a Nobel Prize in chemistry.

Among the over 170 innovators who have won the award, some have worked on gluten substitutes from corn, some have developed drugs against multi-drug-resistant tuberculosis, and some have developed soft close furniture hinges.

“The previous recipients have had substantial impact on the world and how we live,” Takeuchi explained in an email. “It is incredible to be considered among that group.” Nominated for the award by a patent examiner from the European Patent Office, she described the award as an “honor” for the global recognition.

The inventor award is a symbolic prize in which the recipients receive attention for their work, explained Rainer Osterwalder, the director of media relations at the European Patent Office.

Takeuchi was one of four women to receive the award this year — the largest such class of women innovators.

“It was very meaningful to see so many accomplished women be recognized for their contributions,” she explained. “I was delighted to meet them and make some additional contacts with female innovators as well.”

About half the researchers in her lab, which currently includes three postdoctoral researchers and usually has about 12 to 16 graduate students, are women. Takeuchi has said that she likes being a role model for women and that she hopes they can see how it is possible to succeed as a scientist.

Implantable cardiac defibrillators are so common in the United States that an estimated 10,000 people receive them each month.

Indeed, while she was at the reception for an awards ceremony attended by over 600 people, Takeuchi said she met someone who had an ICD.

“It is very rewarding to know that they are alive due to technology and my contributions to the technology,” she explained.

Takeuchi said that many people contributed to the battery project for the ICD over the years who were employed at Greatbach. These collaborators were involved in engineering, manufacturing, quality and customer interactions, with each aspect contributing to the final product.

The battery innovation stacks alternating layers of anodes and cathodes and uses lithium silver vanadium oxide. The silver is used for high current, while the vanadium provides long life and high voltage.

Takeuchi, who earned her bachelor’s degree from the University of Pennsylvania and her doctorate from Ohio State University, has received over 150 patents. The daughter of Latvian emigrants, she received the presidential level National Medal of Technology and Innovation from Barack Obama and has been inducted into the National Inventors Hall of Fame.

Takeuchi continues to push the envelope in her energy research. “We are now involved in thinking about larger scale batteries for cars and ultimately for the grid,” she wrote in an email. “Further, we have demonstrated methods that allow battery components to be regenerated to extend their use. This could potentially minimize batteries going into land fills in the future.”

Takeuchi is one of a growing field of scientists who are using the high-tech capabilities of the National Synchrotron Light Source II at BNL, which allows her to see inside batteries as they are working.

“We recently published a paper where we were able to detect the onset of parasitic reactions,” she suggested, which is “an important question for battery lifetime.”

In the big picture, the scientist said she is balancing between power and energy content in her battery research.

“Usually, when cells need to deliver high power, the energy content goes down,” she said. “The goal is to have high energy and high power simultaneously.”

Life Lines: Model organisms and their contributions to science

by Elof Carlson - June 26, 2018

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canstockphoto19462720 — Silkworms are popular among Japanese geneticists because of the silk industry.

By Elof Axel Carlson

I got my doctorate working with a model organism, the fruit fly, Drosophila melanogaster. It was introduced to science about 1905 at Harvard where William Castle and his students studied the wing veins of these flies for subtle changes that Darwin’s theory of natural selection proposed. Castle suggested to Thomas Morgan at Columbia that he could use fruit flies for a study of mutations that Morgan hoped to launch.

Morgan was luckier than Castle because his use of fruit flies led to the discovery of sex-linked inheritance and a process of shifting genes between matched chromosomes. It led to the chromosome theory of heredity and the theory of the gene as a unit of inheritance present in chromosomes.

Botanists found corn or maize (Zea mays) an ideal organism and classical genetics had inputs from both fruit flies and maize. The most famous contributor to maize genetics was Barbara McClintock who worked out a field of cytogenetics by isolating structural components and consequences for broken chromosomes that experienced rearrangements.

The bacteriophage viruses and bacteria like Escherichia coli were major contributors to molecular biology. Bacteria are cells but viruses are not. Viruses do have a life cycle, living as destructive parasites or beneficial insertions into bacterial chromosomes. Bacteriophage studies confirmed many of the predictions of DNA as the chemical basis of heredity. They also confirmed that a virus’ proteins are not needed to produce the proteins of its progeny.

The flow of information goes from the genes as DNA to molecules of RNA carrying the genetic messages to cellular units that translate them into proteins. Bacteria were also used to work out how genes are switched on and off, an important process that regulates how cells work. Most of these early studies in molecular genetics were initiated by Max Delbrück for bacteriophage viruses and by Joshua Lederberg for bacteria.

For higher organisms a life cycle involves fertilization of an egg by a sperm and the formation of an embryo, which forms different organs with the resulting baby turning into an infant or child and eventually a mature adult and lastly an aged or senescent individual who dies. Sydney Brenner in 1963 suggested using a nematode, the roundworm found in the soil, Caenorhabditis elegans, to work out how this life cycle can be studied at a molecular level. They are similar to the roundworms called vinegar eels seen in flasks of organic apple cider vinegar.

Genetics is a composite of the work with many different organisms in plant, animal, and microbial worlds of life. The designation model organism for research biologists distinguishes the usage of research organisms. Applied genetics is often used with specific purposes in mind that benefit the economy. Silkworms are popular among Japanese geneticists because of the silk industry. Tomato geneticists are interested in color, flavor, texture, size and shelf life as they are for most vegetable crops, applying genetics to improve varieties.

Model organisms were chosen to explore the biology, especially the genetics, reproduction, embryology, metabolism, neurobiology or other fundamental ways living organisms have adapted to their environments and evolved. Biologists working with model organisms often find that once the basic biology is worked out it can be applied to benefit health and the economy. It may take decades before that happens.

When Calvin Bridges in Morgan’s laboratory found extra or missing chromosomes associated with fruit flies, he did not know that some 40 years later extra chromosomes would be associated with birth defects or disorders in humans such as Down syndrome (trisomy 21) or Klinefelter syndrome (XXY males).

In some ways humans serve as a model organism. Linus Pauling was interested in how red blood cells carry oxygen from the air and discharge carbon dioxide into it. His curiosity led to a working out of the structure of the hemoglobin molecule and its mutational difference when healthy individuals have their hemoglobin analyzed and compared to that of persons with sickle cell anemia. Pauling called sickle cell anemia a molecular disease. Note that Pauling’s motivation was not that of a physician seeking a cure for a disease but that of a chemist seeking the molecular basis of how we breathe and why oxygen and carbon dioxide ended up exchanging places in red blood cells.

Humans are also model organisms for the field of neurobiology, especially for processes like memory, learning, association, pattern recognition and speech, most of which would be difficult to infer from the study of a roundworm’s much limited nervous system. This human study is more likely to be at the physiological and anatomical level rather than the molecular level because there are numerous brain injuries and genetic disorders of the nervous system that can be used to identify where to look for these functions.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

CSHL’s Tiriac a ‘rising star’ in pancreatic cancer

by Daniel Dunaief - June 23, 2018

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cshltiriac — Hervé Tiriac during a recent visit to the University of Nebraska Cancer Center. Photo by Dannielle Engel

By Daniel Dunaief

What if doctors could copy human cancers, test drugs on the copies to find the most effective treatment, and then decide on a therapy based on that work?

Hervé Tiriac, a research investigator at Cold Spring Harbor Laboratory, moved an important step closer to that possibility with pancreatic cancer recently.

Tiriac, who works in the Cancer Center Director Dave Tuveson’s lab, used so-called organoids from 66 patients with pancreatic ductal adenocarcinoma tumors. These organoids reacted to chemotherapy in the same way that patients had.

“This is a huge step forward,” Tiriac said, because of the potential to use organoids to identify the best treatments for patients.

Tuveson’s lab has been developing an expertise in growing these organoids from a biopsy of human tumors. The hope throughout the process has been that these models would become an effective tool in understanding the fourth most common type of cancer death in men and women. The survival rate five years after diagnosis is 8 percent, according to the American Cancer Society.

The study, which was published in the journal Cancer Discovery, “shows real promise that the organoids can be used to identify therapies that are active for pancreatic cancer patients,” Tuveson explained in an email. “This may be a meaningful advance for our field and likely will have effects on other cancer types.”

Kerri Kaplan, the president and CEO of the Lustgarten Foundation, which has provided $150 million in financial support to research including in Tuveson’s lab, is pleased with the progress in the field.

“There’s so much momentum,” Kaplan said. “The work is translational and it’s going to make a difference in patients’ lives. We couldn’t ask for a better return on investment.”

Tiriac cautions that, while the work he and his collaborators performed on these organoids provides an important and encouraging sign, the work was not a clinical trial. Instead, the researchers retrospectively analyzed the drug screening data from the organoids and compared them to patient outcomes.

“We were able to show there were parallels,” he said. “That was satisfying and good for the field” as organoids recapitulated outcomes from chemotherapy.

Additionally, Tiriac’s research showed a molecular signature that represents a sensitivity to chemotherapy. A combination of RNA sequences showed patterns that reflected the sensitivity for the two dominant chemotherapeutic treatments. “It was part of the intended goal to try to identify a biomarker,” which would show treatment sensitivity, he said.

While these are promising results and encourage further study, researchers remain cautious about their use in the short term because several technical hurdles remain.

For starters, the cells in the organoids take time to grow. At best right now, researchers can grow them in two to four weeks. Drug testing would take another few weeks.

That is too slow to identify the best first-line treatment for patients with advanced pancreatic cancer, Tiriac explained. “We have to try to see if the organoids could identify these biomarkers that could be used on a much shorter time frame,” he added.

Tuveson’s lab is working on parallel studies to accelerate the growth and miniature the assays. These efforts may reduce the time frame to allow patients to make informed clinical decisions about their specific type of cancer.

As for the RNA signatures, Tiriac believes this is a first step in searching for a biomarker. They could be used in clinical trials as is, but ideally would be refined to the minimal core gene signatures to provide a quick and robust assay. It is faster to screen for a few genes than for hundreds of them. He is studying some of these genes in the lab.

Researchers in Tuveson’s lab will also continue to explore biochemistry and metabolism of the organoids, hoping to gain a better insight into the mechanisms involved in pancreatic cancer.

Going forward, Tiriac suggested that his main goal is to take the gene signatures he published and refine them to the point where they are usable in clinical trials. “I would like to see if we can use the same approach to identify biomarkers for clinical trial agents or targets that may have a greater chance of impact on the patients,” he said.

The research investigator has been working at Tuveson’s lab in Cold Spring Harbor since the summer of 2012.

Tuveson applauded Tiriac’s commitment to the work. Without Tiriac’s dedication, “there would be no Organoid Profiling project,” Tuveson said. “He deserves full credit for this accomplishment.”

Tiriac lives in Huntington Station with his wife Dannielle Engle, who is a postdoctoral researcher in the same lab. He “really enjoyed his time on Long Island,” and suggested that “Cold Spring Harbor has been a fantastic place to work. It’s probably the best institution I’ve worked at so far.”

He appreciates the chance to share the excitement of his work with Engle. “You share a professional passion with your loved one that is beyond the relationship. We’re able to communicate on a scientific level that is very stimulating intellectually.”

Born in Romania, Tiriac moved to France when his family fled communism. He eventually wound up studying in California, where he met Engle.

Tuveson is appreciative of the contributions the tandem has made to his lab and to pancreatic cancer research.

“Although I could not have imagined their meritorious accomplishments when I interviewed them, [Tiriac and Engle] are rising stars in the cancer research field,” he said. “They will go far in their next chapter, and humanity will benefit.”

Kaplan suggested that this kind of research has enormous potential. “I feel like it’s a new time,” she said. “I feel very different coming into work than I did five years ago.”

SBU’s Benjamin Martin scores first Sohn Research prize

by Daniel Dunaief - June 15, 2018

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sbmartinawarddinner — From left, Evan Sohn, co-founder of the Sohn Conference Foundation; Benjamin Martin, associate professor at Stony Brook University; and Bill Ackman, co-founder of the Pershing Square Foundation and CEO of Pershing Square Capital Management at an awards dinner. Photo by Melanie Einzig/PSSCRA

By Daniel Dunaief

Up and coming scientists are often stuck in the same position as promising professionals in other fields. To get the funding for research they’d like to do, they need to show results, but to get results, they need funding. Joseph Heller, author of “Catch 22,” would certainly relate.

A New York-based philanthropy called the Pershing Square Sohn Cancer Research Alliance is seeking to fill that gap, providing seven New York scientists with $600,000 each over the course of three years.

In the fifth annual competition, Benjamin Martin, an associate professor in the Department of Biochemistry & Cell Biology at Stony Brook University, won an award for his study of zebrafish models of metastatic cancer. Martin is the first Stony Brook researcher to win the prize.

Working with Assistant Professor David Matus, whose lab is across the hall and whose research team conducts weekly group meetings with Martin’s lab, Martin is able to see in real time the way grafted human tumor cells spread through blood vessels to other organs in the transparent zebrafish.

“It’s been very challenging to understand what process cancer cells are using to metastasize and leave the blood vessels,” said Olivia Tournay Flatto, the president of the Pershing Square Foundation. “With this technology, he can see what’s happening. It’s a really powerful tool.”

The work Martin presented was “really appealing to the whole board, and everybody felt this kind of project” had the potential to bring data and insights about a process researchers hope one day to slow down or stop, said Flatto.

This year, about 60 early-stage investigators applied for an award given specifically to researchers in the New York City area. When he learned that he won, Martin said, “There was some dancing going on in the living room.” He suggested that the award is a “validation” of his research work.

The process of a cancer cell leaving a blood vessel is “basically a black box” in terms of the mechanism, Martin said. It’s one of the least understood aspects of metastasis, he added.

Indeed, a developmental biologist by training, Martin is hoping to discover basics about this cancer-spreading process, such as an understanding of how long it takes for cancer cells to leave blood vessels. The process can take hours, although it’s unclear whether what he’s seen is typical or abnormal.

Martin would like to identify how the cancer cells adhere to the blood vessel walls and how and why they leave once they’ve reached their target.

Metastatic cancer is likely using the same mechanism the immune system uses to travel to the sites of infection, although researchers still need to confirm several aspects of this model.

Moving in involves interactions with white blood cells, including macrophages. With white blood cells, an area of infection or inflammation becomes activated, which triggers a reaction of adhesion molecules called selectins.

By watching a similar transport process in cancer, Martin and Matus can “see things people haven’t seen before” and can explore way to inhibit the process, Martin suggested.

He is hoping to find ways to stop this process, forcing cancer cells to remain in the blood vessels. While he doesn’t know the outcome of a cancer cell’s prolonged stay in the vessel, he predicts it might end up dying after a while. This approach could be combined with other therapies to force the cancer cells to die, while preventing them from spreading.

Through this grant, Martin will also study how drugs or mutations in selectins generate a loss of function in these proteins, which affects the ability of cancers to leave the blood vessel.

Martin plans to use the funds he will receive to hire more postdoctoral researchers and graduate students. He will also purchase additional imaging equipment to enhance the ability to gather information.

Martin appreciates that this kind of research, while promising, doesn’t often receive funding through traditional federal agencies. This type of work is often done on a mouse, which is, like humans, a mammal. The enormous advantage to the zebrafish, however, is that it allows researchers to observe the movement of these cancer cells, which they couldn’t do in the hair-covered rodent, which has opaque tissues.

“There’s a risk that these experiments may not work out as we planned,” Martin said. He is hopeful that the experiments will succeed, but even if they don’t, the researchers will “learn a great deal just from seeing behaviors that have not been observed before.”

Indeed, this is exactly the kind of project the Pershing Square Sohn Cancer Research Alliance seeks to fund. They want scientists to “put forward the riskiest projects,” Flatto said. “We are ready to take a chance” on them.

One of the benefits of securing the funding is that the alliance offers researchers a chance to connect with venture capitalists and commercial efforts. These projects could take 20 years or more to go from the initial concept to a product doctors or scientists could use with human patients.

“We are not necessarily focused on them starting a company,” Flatto said. “We think some of those projects will be able to be translated into something for the patient,” which could be through a diagnosis, prevention or treatment. “This platform is helpful for young investigators to be well positioned to find the right partners,” he added.

Aaron Neiman, the chairman of the Department of Biochemistry & Cell Biology at SBU, suggested that this award was beneficial to his department and the university.

“It definitely helps with the visibility of the department,” Neiman said. The approach Matus and Martin are taking is a “paradigm shift” because it involves tackling cells that aren’t dividing, while many other cancer fighting research focuses on halting cancer cells that are dividing.

Neiman praised the work Martin and Matus are doing, suggesting that “they can see things that they couldn’t see before, and that’s going to create new questions and new ideas,” and that their work creates the opportunity to “find something no one knew about before.”

BNL team uses distant cues to see shrubs, trees

by Daniel Dunaief - June 12, 2018

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bnlserbinzhaomengfire — From left, Shawn Serbin, University of Maryland collaborator Feng Zhao and Ran Meng. Photo by Roger R. Stoutenburgh

By Daniel Dunaief

Not all greenery is the same. From above the Earth, forests recovering after a fire often look the same, depending on the sensing system. An area with bushes and shrubs can appear to have the same characteristics as one with a canopy.

From left, Shawn Serbin, University of Maryland collaborator Feng Zhao and Ran Meng. Photo by Roger R. Stoutenburgh

Working in associate ecologist Shawn Serbin’s laboratory at Brookhaven National Laboratory, Ran Meng, a postdoctoral researcher, recently figured out a way to improve the level of information gained from these remote images, enabling them to distinguish among the different types of growth after a forest fire.

Examining the growth in a pine forest on Long Island after a fire near BNL in 2012, Meng used various spectral properties to get a more accurate idea of how the forest was recovering. Meng and Serbin recently published their results in the journal Remote Sensing of Environment.

“Using our remote sensing analysis, we were able to link detailed ground measurements from [BNL’s Kathy Schwager and Tim Green] and others to better understand how different burn severities can change the recovery patterns of oak and pine species,” Serbin explained in an email. The information Meng and Serbin collected and analyzed can map canopy moisture content and health as well as fuels below the canopy to identify wildfire risk.

The imagery can be used to map the water content or moisture stored in the leaves and vegetation canopies, Serbin explained. LiDAR data can see through the canopy and measure the downed trees and other fuels on the forest floor. This type of analysis can help differentiate the type of growth after a fire without requiring extensive surveys from the ground. “One of the issues on the ground is that it’s time consuming and expensive,” Serbin said. Remote sensing can “cover a much larger area.”

Assisted by Meng’s background in machine learning, these researchers were able to see a higher resolution signal that provides a more detailed and accurate picture of the vegetation down below. One of the purposes of this work is to help inform forest managers’ decision-making, Serbin added. A forest with a canopy will likely capture and retain more water than one dominated by bushes and shrubs. A canopied forest acts “more like a sponge” in response to precipitation.

A canopied forest can “hold water,” Meng said. If the canopy disappears and changes to shrubs or grass, the forest’s capacity to store water will be damaged. Altering the trees in a forest after a fire can start a “reaction chain.” Without a nearby canopied forest, the water cycle can change, causing more erosion, which could add more sediment to streams.

Serbin recently met with the Central Pine Barrens Commission, the Department of Environmental Conservation and SUNY College of Environmental Science and Forestry, which is based in Syracuse.

Serbin had planned to meet with these groups several years ago to try to build a better relationship between the information the lab was collecting and the pine barrens and ESF to “use the lab as a field research site.”

They discussed ways to use the science to inform management to keep the pine barrens healthy. The timing of the meeting, so soon after the publication of the recent results related to fire damage surveys, was fortuitous.

“It just happens that this work with [Meng] comes out and is highly relevant,” Serbin said. “This is a happy coincidence.” He said he hopes these groups can use this information to feed into a larger model of research collaboration. This work not only provides a clearer picture of how a forest recovers, but also might suggest areas where a controlled burn might benefit the area, minimizing the effect of a more intense fire later on.

“These forests used to burn more often but with less intensity due to the lower fuel loads from more frequent fire,” Serbin explained. Fire suppression efforts, however, have meant that when fires do burn, they occur with higher intensities. “It could be harder to maintain the pine barrens because the fires burn more strongly, which can reduce or destroy the soil seed stock or alter the recovery trajectory in other ways,” he said.

The remote sensing analysis of trees uses shapes, sizes, leaf color and chemistry to explore the fingerprints of specific trees. This could offer researchers and conservationists an opportunity to monitor endangered species or protected habitats.

“We can do even better using platforms like NASA G-LiHT because we can use both the spectral fingerprint as well as unique structural characteristics of different plants” to keep track of protected areas, Serbin explained.

As for what’s next, Serbin said he would like to scale this study up to study larger areas in other fire-prone systems, such as boreal forests in Alaska and Canada. He plans to apply these approaches to develop new forest recovery products that can be used in conjunction with other remote sensing data and field studies to understand forest disturbances, recovery and carbon cycling.

Meng plans to move on in August to work directly with the NASA G-LiHT team. He said he believes this kind of work can also track infestations from beetles or other pests that attack trees or damage forests, adding, “There are some slight changes in spectral patterns following beetle outbreaks.”

A final goal of this project, which admittedly requires considerably more work according to Meng, is to monitor those changes early to enable forest managers to intervene, potentially creating the equivalent of an insect break if they can act soon enough.

Serbin appreciated the work his postdoc contributed to this project, describing Meng as a “dedicated researcher” who had to “sort out what approaches and computational techniques to use in order to effectively characterize” the images.

“[He] persevered and was able to figure out how to analyze these very detailed remote sensing data sets to come up with a new and novel pattern that hadn’t really been seen before,” said Serbin.

Eastern Long Island Mini Maker Faire returns to the Village of Port Jefferson

by Kyle Barr - June 6, 2018

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Mini Maker Faire 1 — Costume maker Tom DePetrillo will return this year as the Marvel Comics Giant Hulkbuster. Photo from Angeline Judex

By Kyle Barr

Creativity, innovation, experimentation and a whole lot of fun are all on the menu as the Village of Port Jefferson gears up for the third annual Eastern Long Island Mini Maker Faire to be held on June 9 from 10 a.m. to 5 p.m.

Hosted by the nonprofit Long Island Explorium (formerly the Maritime Explorium) and the Greater Port Jefferson-Northern Brookhaven Arts Council, the event will take place at the Explorium, all three floors of the Port Jefferson Village Center and spill out onto the adjacent Jeanne Garant Harborfront Park as makers from all over Long Island and beyond will come bringing robots, music, woodworking, metal sculptures and practically anything handmade to celebrate the exciting worlds of science, technology, engineering, music, art and math.

Last year the event drew more than 2,000 visitors who were able to experience everything from 3-D printing to flame belching metal sculptures.

Ray Rumore with his robot ‘Volt’ at last year’s Mini Maker Faire. Photo from Chris Rumore

Angeline Judex, executive director of the Explorium in Port Jefferson, said she expects close to 60 “Makers” will be there for this year’s event. “At this event, people are able to explore new concepts and technologies, take [this knowledge] home with them and then dive into their own exploration and engagement to create their own maker experience,” Judex said in an email. “It transforms theory into reality. It excites, inspires and motivates the next generation to embrace STEM as a resource for innovative problem solving.”

New this year will be the Long Island Vegetable Orchestra featuring students from the Waldorf School in Garden City using carrots, squash and gourds as musical instruments and a visit from the Suffolk County Chapter of the Society for Creative Anachronism, which will demonstrate how trades such as blacksmithing, inks and paints and naval shipbuilding technology have evolved over time.

Returning this year will be costume maker Tom DePetrillo from Rhode Island-based Extreme Costumes who dazzled participants in last year’s Makers Faire with his burly Transformers Bumblebee costume. This year he will be bringing a to-scale HulkBuster Iron Man suit seen in the movies “Avengers: Age of Ultron” and “Avengers: Infinity War.”

“People really enjoy the giant costumes,” said DePetrillo.

The Hulkbuster costume took 10 months and approximately 1,600 man hours to complete. DePetrillo tours all over the world with his giant designs as a full-time job. It enables him to keep making and creating. “It allows me to have an outlet for my creative energy,” he said. “I do this because I love doing it.”

Father and son team Chris and Ray Rumore have been attending the Mini Maker Faire every year since its inception. Ray Rumore got involved with 3-D printing, crafting and robotics, and created a robot named “Volt,” a companion robot who can follow him around and live stream events with his on-board camera.

“Ray enjoys three main things about Maker Faires — they allow him the opportunity to encourage others to join the fun and become a Maker, the opportunity to meet other Makers and learning about their creations and the food,” the elder Rumore said in an email.

The event is sponsored in part by Stony Brook University, BASF Chemical Company, Capital One, Riverhead Building Supplies and Suffolk County Community College.

The Eastern Long Island Mini Maker Faire will be held on June 9 from 10 a.m. to 5 p.m., rain or shine, at the Maritime Explorium, 101 East Broadway, Port Jefferson. Tickets, which are $10 per person, are available online at www.easternlongislandmakerfaire.com and at the door. Parking will be available around the Village of Port Jefferson, Off Street Parking, Brookhaven Town Lot as well as Spring Street. The Port Jeff Jitney will be running during the day. For further information, please call 631-331-3277.

SBU’s Caston finds damage from dust on the moon

by Daniel Dunaief - June 5, 2018

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sbcastonlab — Rachel Caston looks at lunar soil simulant JSC1A. Photo by Upasna Thapar

By Daniel Dunaief

It’s the ultimate road trip into the unknown. Space travel holds out the possibility of exploring strange new worlds, boldly going where no one has gone before (to borrow from a popular TV show).

While the excitement of such long-distance journeys inspires people, the National Aeronautics and Space Administration, among other agencies, is funding scientific efforts to ensure that anyone donning a spacesuit and jetting away from the blue planet is prepared for all the challenges to mind and body that await.

Rachel Caston, recently completed her doctorate, which included work at Stony Brook University in the laboratory of Bruce Demple for a project that explored the genetic damage lunar soil simulants have on human lung cells and on mouse brain cells.

Geologist Harrison Schmitt, who was the Apollo 17 lunar module pilot, shared symptoms he described as “lunar hay fever,” which included the types of annoyances people with allergies have to deal with during the spring: sore throat, sneezing and watery eyes.

Using simulated lunar soil because actual soil from the moon is too scarce, Caston found that several different types of soil killed the cell or damaged the cell’s genes, or DNA for both human lung and mouse brain cells.

While there has been considerable research that explores the inflammation response to soil, “there wasn’t any research previously done that I know of [that connected] lunar soil and DNA damage,” said Caston, who was the lead author on research published recently in the American Geophysical Union’s journal GeoHealth.

The moon’s soil becomes electrostatic due to radiation from the sun. Astronauts who walked on the moon, or did various explorations including digging into its surface, brought back some of that dust when it stuck to their space suits.

Caston sought to understand what causes damage to the DNA.

Going into the study, Demple, a professor of pharmacological sciences at SBU, suggested that they expected that the materials most capable of generating free radicals would also be the ones that exerted the greatest damage to the cells and their DNA. While free radicals may play a role, the action of dust simulants is more complex than that created by a single driving force.

Caston looked at the effect of five different types of simulants, which each represented a different aspect of lunar soil. One of the samples came from soil developed to test the ability of rovers to maneuver. Another one came from a lava flow in Colorado.

Demple said that the materials they used lacked space weather, which he suggested was an important feature of lunar soil. The surface of the moon is exposed constantly to solar wind, ultraviolet light and micrometeorites. The researchers mimicked the effect of micrometeorites by crushing the samples to smaller particle sizes, which increased their toxicity.

Farm to table: Caston eats ice cream and pets the cow that provided the milk for her frozen dessert at Cook’s Farm Dairy in Ortonville, Michigan. Photo by Carolyn Walls

In future experiments, the researchers plan to work with colleagues at the Department of Geosciences at SBU, including co-author Joel Hurowitz and other researchers at Brookhaven National Laboratory to mimic solar wind by exposing dust samples to high-energy atoms, which are the main component of solar wind. The scientists expect the treatment would cause the simulants to become more reactive, which they hope to test through experiments.

Caston credits Hurowitz , an assistant professor in the Department of Geosciences, with providing specific samples.

The samples are commonly used simulants for lunar rocks that mimic the chemical and mineral properties of the lunar highlands and the dark mare, Hurowitz explained.

“This has been a really fruitful collaboration between geology and medical science, and we’ll continue working together,” Hurowitz wrote in an email. They plan to look at similar simulants from asteroids and Mars in the future.

NASA has considered engineering solutions to minimize or eliminate astronaut’s exposure to dust. It might be difficult to eliminate all exposure for workers and explorers living some day on the moon for an extended period of time.

“The adherence of the dust to the space suits was a real problem, I think,” suggested Demple, adding that the next steps in this research will involve checking the role of the inflammatory response in the cytotoxicity, testing the effects of space weathering on toxicity and applying to NASA for actual samples of lunar regolith brought back by Apollo astronauts.

It took about two years of preliminary work to develop the methods to get consistency in their results, Demple said, and then another year of conducting research.

In addition to her work on lunar soil, Caston has studied DNA repair pathways in mitochondria. She used her expertise in that area for the DNA damage results they recently reported.

Caston, who is working as a postdoctoral researcher in Demple’s lab, is looking for a longer-term research opportunity either on Long Island or in Michigan, the two places where she’s lived for much of her life.

Caston lives in Smithtown with her husband Robert Caston, a software developer for Northrop Grumman. She earned her bachelor’s degree as well as her doctorate from Stony Brook University.

Her interest in science in general and genetics in particular took root at an early age, when she went with her father Kenneth Salatka, who worked at Parke Davis, a company Pfizer eventually bought.

On April 23, 1997, she convinced her friend and her identical twin sister to attend a “fun with genetics” event.

Two of the people at her father’s company were using centrifuges to isolate DNA out of blood. “That was the coolest thing I ever saw,” she said. “I wanted to be a geneticist from that point on.”

Her sister Madeline, who now sells insurance for Allstate, and her friend weren’t similarly impressed.

As for the work she did on lunar soil, Caston said she enjoys discussing the work with other people. “I like that I’m doing a project for NASA,” she said. “I’ve learned quite a bit about space travel.”

SBU’s Ya Wang wins funds for brain, energy studies

by Daniel Dunaief - May 29, 2018

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sbwangwithstudents — From left, Libo Wu, Zhangjie Chen (both are doctoral students on the ARPA-E project), Ya Wang, Xing Zhang (graduated), Muzhaozi Yuan and Jingfan Chen (both are doctoral students on the NSF project). Photo courtesy of Stony Brook University

By Daniel Dunaief

Picture a chalkboard filled with information. It could include everything from the basics — our names and phone numbers, to memories of a hike along the Appalachian Trail, to what we thought the first time we saw our spouse.

Diseases like Alzheimer’s act like erasers, slowly moving around the chalkboard, sometimes leaving traces of the original memories, while other times removing them almost completely. What if the images, lines and words from the chalk could somehow be restored?

Ya Wang with former student Wei Deng at Stony Brook’s Advanced Energy Research and Technology Center. Photo courtesy of SBU

Ya Wang, a mechanical engineering assistant professor at Stony Brook University, is working on a process that can regenerate neurons, which could help with a range of degenerative diseases. She is hoping to develop therapies that might restore neurons by using incredibly small magnetic nanoparticles.

Wang recently received the National Science Foundation Career Award, which is a prestigious prize given to faculty in the early stages of their careers. The award lasts for five years and includes a $500,000 grant.

Wang would like to understand the way small particles can stimulate the brain to rebuild neurons. The award is based on “years of effort,” she said. “I’m happy but not surprised” with the investment in work she believes can help people with Alzheimer’s and Parkinson’s diseases.

“All neuron degeneration diseases will benefit from this study,” Wang said. “We have a large population in New York alone with patients with neuron degeneration diseases.” She hopes the grant will help trigger advancements in medicine and tissue engineering.

Wang’s “work on modeling the dynamic behavior of magnetic nanoparticles within the brain microenvironment would lay the foundation for quantifying the neuron regeneration process,” Jeff Ge, the chairman and professor of mechanical engineering, said in a statement.

Wang said she understands the way neurodegenerative diseases affect people. She has watched her father, who lives in China, manage through Parkinson’s disease for 15 years.

Ge suggested that this approach has real therapeutic potential. “This opens up the exciting new possibility for the development of a new microchip for brain research,” he said.

At this point, Wang has been able to demonstrate the feasibility of neuron regeneration with individual nerve cells. The next step after that would be to work on animal models and, eventually, in a human clinical trial.

That last step is a “long way” off, Wang suggested, as she and others will need to make significant advancements to take this potential therapeutic breakthrough from the cell stage to the clinic.

She is working with a form of coated iron oxide that is small enough to pass through the incredibly fine protective area of the blood/brain barrier. Without a coating, the iron oxide can be toxic, but with that protective surface, it is “more biofriendly,” she said.

The size of the particles are about 20 nanometers. By contrast, a human hair is 80,000 nanometers thick. These particles use mechanical forces that act on neurons to promote the growth or elongation of axons.

As a part of the NSF award, Wang will have the opportunity to apply some of the funds toward education. She has enjoyed being a mentor to high school students, some of whom have been Siemens Foundation semifinalists. Indeed, her former students have gone on to attend college at Stanford, Harvard and Cal Tech. “I was very happy advising them,” she said. “High school kids are extremely interested in the topic.”

A few months before she scored her NSF award, Wang also won an Advanced Research Projects Agency–Energy award for $1 million from the Department of Energy. In this area, Wang also plans to build on earlier work, developing a smart heating and cooling system that enables a system to direct climate control efforts directly at the occupant or occupants in the room.

Extending on that work, Wang, who will collaborate in this effort with Jon Longtin in the Department of Mechanical Engineering at SBU and Tom Butcher and Rebecca Trojanowski at Brookhaven National Laboratory, is addressing the problem in which the system no longer registers the presence of a person in the room.

Wang has “developed an innovation modification to a simple, inexpensive time-honored position sensor, but that suffers from requiring that something be moving in order to detect motion,” Longtin explained in an email. The sensors can’t detect a person that is not moving. The challenge, Longtin continued, is in fooling the sensor into thinking something is there in motion to keep it active.

Wang described a situation in which a hotel had connected an occupant-detecting system to its HVAC system. When a person fell asleep in the room, however, the air conditioning turned off automatically. On a hot summer night, the person was frustrated. She put colored paper and a fan in front of the sensor, which kept the cool air from turning off.

Instead of using a fan and colored paper, the new system Wang is developing cuts the flow of heat to the sensor, which enhances its ability to recognize stationary or moving people.

Wang and her colleagues will use low-power liquid crystal technology with no moving parts. “The sensor detects you because you are a human with heat,” she said. “Even though you are not moving, the amount of heat is changing.”

The sensor will be different in various locations. People in Houston will have different temperature conditions than those in Wisconsin. Using a machine-learning algorithm, Wang said she can pre-train the system to respond to different people and different conditions.

She has developed a smart phone app so that the house can react to the different temperature preferences of a husband and wife. People can also choose night or day modes.

Wang also plans to work on a system that is akin to the way cars have different temperature zones, allowing one side of the car to be hotter than the other. She intends to develop a similar design for each room.

SBU, BNL team seeks to build a better engine

by Daniel Dunaief - May 18, 2018

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sbmamalishighres — From left, Jon Longtin, Sotirios Mamalis and Benjamin Lawler. Photo courtesy of Stony Brook University

By Daniel Dunaief

It’s not exactly Coke and Pepsi designing a better soda. It’s not Nike and Reebok creating a more efficient sneaker. And, it’s not McDonald’s and Burger King uniting the crown and the golden arches. At Stony Brook University, it is, however, a combination of energy systems that haven’t historically worked together.

“Fuel cells and engines have been seen as competing technologies,” said Sotirios Mamalis, an assistant professor of mechanical engineering at SBU. “The truth of the matter is that these two technologies are very complementary because of their operating principals.”

Indeed, Mamalis is the principal investigator on a multi-year project to create a hybrid fuel cell-engine system that recently won a $2.3 million award from the Department of Energy’s Advanced Research Projects Agency-Energy.

Working with Benjamin Lawler and Jon Longtin at Stony Brook and Tom Butcher, leader of the Energy Conversion Group at Brookhaven National Laboratory, Mamalis plans to build a system that uses solid oxide fuel cells partnered with a split-cylinder, internal combustion engine. The engine system will use the tail gas from the fuel cell to provide additional power, turning the inefficiency of the fuel cell into a source of additional energy.

“These ARPA-E awards are extremely competitive,” said Longtin, adding “If you land one of these, especially a decent-sized one like this, it can move the needle in a lot of ways in a department and at the university level.” The group expects that this design could create a system that generates 70 percent fuel to electricity efficiency. That is well above the 34 percent nationwide average.

Reaching that level of energy efficiency would be a milestone, said Longtin, a Professor in the Department of Mechanical Engineering at Stony Brook. The core of the idea, he suggested, is to take the exhaust from fuel cells, which has residual energy, and run that through a highly tuned, efficient internal combustion engine to extract more power. The second part of the innovation is to repurpose the cylinders in the engine to become air compressors. The fuel cell efficiency increases with higher pressure.

A fuel cell is a “highly efficient device at taking fuel and reacting it to produce DC electricity,” Lawler said. One of its down sides, aside from cost, is that it can’t respond to immediate needs. An engine is the opposite and is generally good at handling what Lawler described as transient needs, in which the demand for energy spikes.

The idea itself is ambitious, the scientists suggested. “These projects are high-risk, high-reward,” said Mamalis. The risks come from the cost and the technical side of things.

The goal is to create a system that has a disruptive role in the power generation market. To succeed, Mamalis said, they need to bring something to market quickly. Their work involves engineering, analysis and design prior to building a system. The project could involve more tasks to reduce technical risk but “we’re skipping a couple of steps so we can demonstrate a prototype system sooner than usual,” Mamalis said.

They will start by modeling and simulating conditions, using mathematical tools they have developed over the years. Once they have modeling results, they will use those to guide specific experimental testing. They will take data from the engine simulation and will subject the engine to conditions to test it in a lab.

“The biggest challenges will be in changing the operation of each of these two technologies to be perhaps less than optimal for each by itself and then to achieve an integrated system that ends up far better,” Butcher explained in an email. “The target fuel-to-electricity efficiency will break barriers and be far greater than is achieved by conventional power plants today.”

Butcher, whose role will be to provide support on system integration concepts and testing, suggested that this could be a part of distribution power generation, where power is produced locally in addition to central power plants. People have looked into hybrid fuel cell-gas turbine systems in the past and a few have been installed and operational, Mamalis explained. The problem is with the cost and reliability.

Mamalis and his colleagues decided they can tap into the inefficiency of fuel cells, which leaves energy behind that a conventional engine can use. The reason this works is that the fuel cell is just inefficient enough, at about 55 percent, to provide the raw materials that a conventional engine could use. A fuel cell that was more efficient, at 75 or 80 percent, would produce less unused fuel in its exhaust, limiting the ability of the system to generate more energy.

The team needs to hit a number of milestones along the way, which are associated with fuel cell development and engine and hybrid system development.

The first phase of the work, for which the team received $2.3 million, will take two years. After the group completes Phase I, it will submit an application to ARPA-E for phase II, which would be for an additional $5 million.

Lawler suggested that fundamental research made this kind of applied project with such commercial potential possible. “The people who did fundamental work and [were involved in] the incremental steps led us to this point,” he said. “Incremental work leads to ground-breaking ideas. You can’t predict when groundbreaking work will happen.”

The other researchers involved in this project credit Mamalis for taking the lead on an effort that requires considerable reporting and updating with the funding agency.

Every three months, Mamalis has to submit a detailed report. He also participates in person and on conference calls to provide an update. He expects to spend about 90 percent of his time on a project for which the team has high hopes.

“It’s an exciting time to be a part of this,” Longtin said. “These folks are pivotal and we have developed into a very capable team, and we have been setting our sights on larger, more significant opportunities.”