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Daniel Dunaief

Elizabeth Boon, back row, center, with graduate students from her lab at Stony Brook University. Photo from Elizabeth Boon

By Daniel Dunaief

It was in the back of Elizabeth Boon’s mind for the last decade. How, she wondered, could the switch that is so critical to life not be there and yet still allow for normal functioning? She suspected that there had to be another switch, so the associate professor in the Department of Chemistry at Stony Brook University, spent the last five years looking for it.

Sure enough, she and graduate students including Sajjad Hossain, found it.

Bacteria, like so many other living creatures, need to have a way of detecting nitric oxide gas. At a high enough concentration, this gas can kill them and, indeed, can kill other living creatures as well, including humans.

Nitric oxide is “toxic to any organism at a high enough concentration,” Boon said. “Most organisms have ways of detecting high concentrations … to avoid toxic consequences.” Other research had found a way other bacteria detect this toxic gas through a system called H-NOX, for heme nitric oxide/ oxygen binding protein.

When bacteria live together in colonies called biofilms, many of them typically rely on a signal about the presence of nitric oxide from the H-NOX protein. And yet, some bacteria survived without this seemingly critical protein. “We and others have shown that H-NOX detection of nitric oxide allows bacteria to regulate biofilm formation,” Boon explained.

Elizabeth Boon with her family, from left, Sheridan, 3, Cannon, 7, Beckett, 1, with her husband Isaac Carrico, who is also an Associate Professor in the Chemistry Department at Stony Brook University. Photo by Alfreda James

Named the nitric oxide sensing protein, or NosP, Boon and her team discovered this alternative signaling system that has some of the same functional group as the original mechanism. When activated in one bacteria, the Pseudomonas aeruginosa, this signaling mechanism causes biofilm bacteria to react in the same way as they would when an H-NOX system was alerted, by breaking up the colony into individuals. Using a flagella, an individual bacteria can move to try to escape from an environment containing the toxic gas.

Nicole Sampson, a professor of chemistry at Stony Brook University, suggested that this work was groundbreaking. While some biofilms are benign or even beneficial to humans, including a biofilm in the human gut, many of them, including those involved in hospital-borne infections, can cause illness or exacerbate diseases, particularly for people who are immunocompromised. Bacteria in biofilm are difficult to eradicate through drugs or antibiotics. When they are separated into individuals, however, they don’t have the same rigid defenses.

“They are resistant to most forms of treatment” when they are in biofilms, Boon said. “If we could get the bacteria to disperse, it’d be much easier to kill them. One of the hopes is that we could develop some sort of molecule that might loosen up the film and then we could come in with an antibiotic and kill the bacteria.”

Boon and her team published their results on the cover of the magazine ACS Infectious Disease, where they presented evidence of what they describe as a novel nitric oxide response pathway that regulates biofilm in the bacteria P. aeruginosa, which lack the H-NOX gene. The day the lab discovered this other protein, they celebrated with a trip for frozen yogurt at Sweet Frog.

In an email, Sampson said that finding the mechanism through which bacteria responds to nitric oxide “is important for developing therapies that target biofilms.”

While Boon is pleased that her lab found an alternative nitric oxide signaling system that answered a long-standing question about how some bacteria could respond to an environmental signal that suggested a threat to the biofilm, she said the answer to the question, as so many others do in the world of science, has led to numerous other questions.

For starters, the lab doesn’t yet know the structure of the NosP. “Not all proteins are immediately willing to crystallize,” Boon said. “We’re hopeful we’ll have a structure soon.” She knows it has a heme group, which includes an iron ion in the middle of an organic compound. That’s where the nitric oxide binds.

“We’d like to have the structure to piece together how that signal is relayed out to the end of the protein and how that gets transferred to other proteins that cause changes in behavior,” she said. The NosP is longer than the H-NOX protein, although they appear to have the same function.

Boon has also found that some bacteria have both the H-NOX and the NosP, which raises questions about why there might be an apparent redundancy. In organisms that have both proteins, it’s tempting to conclude that these bacteria live in a broader range of environments, which might suggest that the two systems react to the gas under different conditions. At this point, however, it’s too early to conclude that the additional sensing system developed to enable the bacteria to respond in a wider range of conditions.

Boon believes the nitric oxide system could be a master regulator of bacterial biofilms. “Detecting nitric oxide might be one of the first things that happen” to protect a bacteria, she said. The reason for that is that bacteria, like humans, use iron proteins in respiration. If those proteins are blocked by nitric oxide, any organism could suffocate.

Boon believes a multistep therapeutic approach might work down the road. She believes breaking up the biofilm would be an important first step in making the bacteria vulnerable to attack by antibiotics. She and her graduate students work with bacteria in the lab that generally only cause human disease in people who are already immunocompromised. Even so, her staff takes safety precautions, including working in a hood and wearing protective equipment.

Boon and her husband Isaac Carrico, who is an associate professor in the Department of Chemistry at Stony Brook University, have a 7-year-old son Cannon, a 3-year-old daughter Sheridan and a 1-year-old son Beckett. Boon said she and her husband are equal partners in raising their three children.

In her work, Boon is excited by the possibility of addressing new questions in this nitric oxide mechanism. “We’re trying to cover as much ground as fast as possible,” she said.

Standing near one of the X-ray scattering instruments, Kevin Yager holds a collection of samples, including a self-assembling polymer film. Photo courtesy of BNL

By Daniel Dunaief

Throw a batch of LEGOs in a closed container and shake it up. When the lid is opened, the LEGOs will likely be spread out randomly across the container, with pieces facing different directions. Chances are few, if any, of the pieces will stick together. Attaching strong magnets to those pieces could change the result, with some of the LEGOs binding together. On a much smaller scale and with pieces made from other parts, this is what researchers who study the world of self-assembled materials do.

Scientists at the Center for Functional Nanomaterials and at the National Synchrotron Light Source II at Brookhaven National Laboratory experiment with small parts that will come together in particular ways based on their energy landscapes through a process called self-assembly.

Every so often, however, a combination of steps will alter the pathway through the energy landscape, causing molecules to end up in a different final configuration. For many scientists, these so-called nonequilibrium states are a nuisance.

Above, Kevin Yager listens to sonified data. When data is sonified, it is translated into sound. Photo by Margaret Schedel

For Kevin Yager, they are an opportunity. A group leader at the CFN who works closely with the NSLS-II, the McGill University-educated Yager wants to understand how the order of these steps can change the final self-assembled product. “In the energy landscape, you have these peaks and valleys and you can take advantage of that to move into a particular state you want,” Yager said. “The high level goal is that, if we understand the fundamentals well enough, we can have a set of design rules for any structure we can dream up.”

At the CFN, Yager manages a nanofabrication facility that uses electron-beam lithography and other techniques to make nanostructures. He would like to fabricate model batteries to show the power of nanomaterials. He is also determined to understand the rules of the road in the self-assembly process, creating the equivalent of an instruction manual for miniature parts.

In future years, this awareness of nonequilibrium self-assembly may lead to revolutionary innovations, enabling the manufacture of parts for electronics, drugs to treat disease and deliver medicine to specific locations in a cell and monitors for the detection of traces of radioactivity or toxins in the environment, among many other possibilities.

Yager’s colleagues saw considerable opportunities for advancement from his work. Nonequilibrium self-assembly has “significant potential for a broad range of nanodevices and materials due to its ability to create complex structures with ease,” Oleg Gang, a group leader in Soft and Bio Nanomaterials at the CFN, explained in an email. Yager is an “excellent scientist” who produces “outstanding results.”

One of the things Yager hopes his research can develop is a way to “trick self-assembly into making structures they don’t natively want to make” by using the order of steps to control the final result.

As an example, Yager said he developed a sequence of steps in which nanoscale cylinders pack hexagonal lattices into a plane. These lattices tend to point in random directions as the cylinders form. By following several steps, including sheer aligning a plane and then thermal processing, the cylinders flip from horizontal to vertical as they inherit the alignment of the sheered surface. Flipping these cylinders, in turn, causes the hexagons all to point in the same direction. When Yager conducted these steps in a different order, he produced a different structure.

Broadly speaking, Yager is working on stacking self-assembling layers. In his case, however, the layers aren’t like turkey and swiss cheese on a sandwich, in which the order is irrelevant to the desired final product. Each layer has a hand in directing the way the subsequent layers stack themselves. Choosing the sequence in which he stacks the materials controls their structure.

Yager is working with Esther Takeuchi and Amy Marschilok at Stony Brook University to develop an understanding of the nanostructure of batteries. Gang suggested that Yager’s expertise is “invaluable for many scientists who are coming to the CFN to characterize nanomaterials using synchtrotron methods. In many cases, it would probably be impossible to achieve such quantitative understanding without [Yager’s] input.”

Yager and his wife Margaret Schedel, an associate professor in the Department of Music at Stony Brook University who is a cellist and a composer, live in East Setauket. The couple combined their talents when they sought ways to turn the data produced by the CFN, the NSLS and the NSLS-II into sound.

Scientists typically convert their information into visual images, but there’s “no reason we can’t do that with sound,” Yager said. “When you listen to data, you sometimes pick up features you wouldn’t have seen.”

One of the benefits of turning the data into sound is that researchers can work on something else and listen to the collection of data in the background, he said. If anything unexpected happens, or there is a problem with a sample or piece of equipment, they might hear it and take measures more rapidly to correct the process. “This started as a fun collaboration,” Yager said, “but it is useful.”

Schedel is working on sonifying penguin data as well. She also sonified wave data on Long Island. “By listening to the tides quickly, larger patterns emerge,” she said, adding that Yager thought the idea was theoretically interesting until he listened to misaligned data and then he recognized its benefit.

Schedel’s goal is to see this sonification effort spread from one beamline to all of them and then to the Fermilab near Chicago and elsewhere. She wants sonification to become “an ear worm in the science community.”

While Schedel introduced Yager to the world of sound in his research, he introduced her to sailing, an activity he enjoyed while growing up in the suburbs of Montreal. When she sails with him, they are “half in and half out of the boat,” Schedel said. It’s like two people “flying a kite, but you are the kite. You have to learn how to counterbalance” the boat. They hike out so they can take turns faster without tipping over, she said.

HXN team members, from left, Evgeny Nazaretski, Ken Lauer, Sebastian Kalbfleisch, Xiaojing Huang, Yong Chu, Nathalie Bouet and Hanfei Yan. Photo courtesy of BNL

By Daniel Dunaief

There’s precision in measurements and then there’s the world of Yong Chu. The head of a beamline that’s housed off to the side in a separate, concrete structure from similar efforts at Brookhaven National Laboratory, Chu led the design, construction and commissioning of a sophisticated beamline with a resolution of as low as 3 nanometers, which he hopes will get down to 1 nanometer within a year.

Just as a measure of contrast, a human hair is about 80,000 nanometers wide. Why so fine a resolution? For starters, seeing objects or processes at that high level can offer insights into how they function, how to improve their manufacture or how to counteract the effects of harmful processes.

With a battery, for example, the Hard X-ray Nanoprobe, or HXN beamline, could help reveal structural weaknesses in the nanostructure that could cause safety issues. In biology, numerous functions involve sub-cellular organelles that respond to proteins. Proteins are typically smaller than the HXN beamline can image, although researchers can tag the proteins with metals, which allows Chu, his colleagues and visiting scientists to see an aggregate of these proteins.

The HXN beamline can also help explore environmental problems, such as how plants transport harmful nanoparticles to their fruits or how artificial compounds absorb nuclear waste. Imaging beamlines that use micro-focused beams typically offer spatial resolution of 10 microns, 1 micron or even 100 nanometers, according to Ryan Tappero, the head scientist at the X-ray Fluorescence Microprobe at BNL, who has used the HXN for his research. Using the NSLS II source properties and a new x-ray optics development routinely offers resolution of 10 nanometers, which pushes the spatial resolution down by another factor of 10, which makes the HXN, according to Tappero, a “game changer.”

Tappero described Chu as a “rock star” and suggested he was an “exceptional beamline scientist” who is “very knowledgeable about X-ray optics.”

BNL houses 19 beamlines at the National Synchrotron Light Source II, a state-of-the-art facility large enough that scientists ride adult tricycles inside it to travel from one beamline to another and to transport supplies around the facility. BNL is building another nine beamlines that it hopes to have operational within the next 18 months. Each of these beamlines offers a different way to explore the world of matter. Some beamlines do not use a focused beam, while others produce beams with high angular or high energy resolution. Imaging beamlines such as the HXN produce a small beam size.

The HXN beamline has the highest spatial resolution of any beamline at the NSLS-II. Scientists building the HXN grew a nanofocusing lens with a dedicated deposition system that was constructed at the NSLS-II Research and Development lab. The system grew a nanofocusing lens a layer at a time, alternating materials and controlling the thickness at better than 1 nanometer, Chu explained.

The beamline where Chu works has padded walls, a door separating it from the rest of the light source and a monitor that records the temperature to the thousandths of a degree. “We are constantly monitoring the temperature around the X-ray microscope and inside of the X-ray microscope chamber,” he said. Around the microscope, he can keep the temperature stable within 0.03 degree Celsius. In the chamber, the scientists maintain the temperature at better than 0.003 degree Celsius.

So, now that Chu and his colleagues built their beamline, have the scientists come? Indeed, the interest in using the HXN has been well above the available time slots. For the three cycles each year, BNL receives about four requests for each available time. This reflects the unique qualities of the instrument, Chu said, adding that he doesn’t expect the rate to drop considerably, even as the HXN continues to operate, because of the ongoing demand.

Researchers have to go through a peer review process, where their ideas are graded for the likelihood of success and for the opportunity to learn from the experiments. All beam time proposals are reviewed by external expert panels, which examine the scientific merit, appropriateness of use of the facility, capability of proposers and quality of prior performance and the research plan and technical feasibility.

Chu fields about 10 calls per month from scientists who want to speak with him about the feasibility of their ideas. He may suggest another station at the NSLS-II or at the Advanced Photon Source at Argonne National Laboratory in Chicago, where he was a beamline scientist starting in 1999.

“I know many of the beamlines” at the Advanced Photon Source, he said. “I recommend some of the potential users to perform experiments at the APS first before coming to the HXN.” By the time scientists arrive at his beamline, Chu said he’s gotten to know them through numerous discussions. He considers them “as a guest” at the HXN hotel. “We try to make sure the experimental needs for the users are met as much as possible,” he said.

The HXN beamline has three staff scientists and two postdoctoral fellows who remain in contact with scientists who use the facility. “For most of the users, at least one of us is working throughout the weekends and late evenings,” said Chu.

Not just a staff scientist, Chu is also a user of the HXN, with currently one active general user proposal through a peer review process in which he is collaborating with Stony Brook University and BNL scientist Esther Takeuchi to explore the nanostructure of metal atoms during phase separation in batteries.

Chu and his wife Youngkyu Park, who works at Cold Spring Harbor Laboratory as a research investigator in basic and preclinical cancer research, live in Northport. The couple’s 22-year-old son Luke is attending Nassau Community College and is planning to transfer to Stony Brook this fall to study engineering. Their daughter Joyce is 18 and is enrolled in the Parsons School of Design in New York.

Chu grew up in Seoul, South Korea, and came to the United States when he was 18. He attended Caltech. While Chu’s parents wanted him to become a doctor, he was more inspired by a cartoon called Astro Boy, in which a scientist, Dr. Tenma, is a hero solving problems. As for the work of the scientists who visit his beamline, Chu said the “success of individual users is the success of the beamline.”

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By Daniel Dunaief

Hurry, hurry, hurry! You’ve got five minutes to get to the high school before your daughter’s graduation. It usually takes six. You might have to go faster than the speed limit, but you’ve done it before.

Your daughter looks great and she’s so calm. You push on the accelerator on the straight road ahead. Your daughter takes a deep breath.

OK, just a little faster and you’ll make it. Oh, no, no, no, a small car pulls in front of you. It’s being driven at 25 mph in a 35 mph zone. Why do cars pull in front of you and then go slowly? “Come on!” you implore, flicking your fingers forward as if you were trying to scratch a chalkboard from the bottom up.

“Dad, it’s OK,” your daughter insists. “I don’t want you to be late,” you say.

You drive carefully around a curve and head for another straight part of the road. You reach a stop sign, where a BMW misses an opening to go. It was a small one, but you’ve got to make your own openings in this town. That’s what you’d tell everyone today if you were giving the speech your daughter won the right to deliver.

Your daughter did better in school than you did. That makes you proud, but you don’t have time to be proud. All these people are slowing you down. You just have a few more turns.

A Girl Scout troop crosses the road in front of you. Your daughter was in Girl Scouts years ago, but you don’t like them now. They’re making you late for such an important day for the family.

Then the Girl Scouts, whose uniforms make you think of those mint cookies, cross the street. You’re a block from the school and a sedan takes forever to park.

You grind your teeth and lift your hand to touch the horn. Your daughter puts her hand firmly on yours and shakes her head slowly.

The woman with streaks of gray in her hair and a green suit looks vaguely familiar as she gets out of a car.

Finally, you park, get in the school and, shockingly, your daughter’s friends have reserved you great seats.

You pick up your phone to start recording your daughter’s speech. The camera’s out of memory. You grind your teeth as you try to delete enough old pictures to record this magic moment.

“Good morning,” your daughter’s voice offers the room. Your wife tells you to stop fiddling with your phone and look up. After your daughter shares memories of high school, she wants to offer advice to her class.

“I want you to remember to leave some margin for error,” she urges. Right, you smile. Your daughter, who made so many fewer errors than you did, is talking to the other people about their mistakes. You nod to the other people.

“If we need to do something, to be somewhere or to accomplish anything, we need to accept that the route might include detours or unexpected obstacles,” she offers, sharing that crooked smile she developed in middle school. “It’s not anyone else’s fault. If it’s important, don’t blame the obstacles. Be prepared for them. Planning means understanding them and giving yourself some extra time to reach your goals.”

You take a deep breath, the way she did so many times while she waited for you at the entrance to the house. You look around the room to see if anyone else knows she’s talking to you. You now recognize the woman on stage with streaks of gray in her hair and a green suit; she’s the superintendent of schools.

You realize how much smarter your daughter is than you.

SBU graduate student and grand niece of world renowned anthropologist Richard Leakey, Acacia Leakey, draws a sketch of huts in the village of Ambodiaviavy, Madagascar as the children look on. Photo from Mickie Nagel

By Daniel Dunaief


Mickie Nagel recently returned from the island nation of Madagascar, and she’s filled with ideas, inspiration, observations and opportunities. One of the three founders of a new nongovernmental organization called BeLocal, the Laurel Hollow resident spent several weeks with Stony Brook University graduate students Leila Esmailzada and Acacia Leakey taking videos and gathering information about life in Madagascar.

The goal of the new organization is to share this footage and insight with undergraduate engineers at SBU, who might come up with innovations that could enhance the quality of life for the Malagasy people.

In one village, a man showed her a three-inch lump on his shoulder, which he got by dragging a long stick with bunches of bananas that weigh over 100 pounds along a clay footpath out of the forest. People also carry rice that weighs over 150 pounds on their heads, while many others haul buckets of water from rivers and streams to their homes while walking barefoot.

In addition to transportation, Nagel also found that villagers around Centre ValBio, a Stony Brook research station, had basic food and water needs. Over 17 years ago, another group had installed four water pumps in a village to provide access to water. Only one pump now works.

SBU graduate student Leila Esmailzada helps villagers in Ambodiaviavy, Madagascar, clean rice. The job is usually delegated to the children who pound the rice for 30 minutes. Photo by Mickie Nagel

As for food, some villagers in Madagascar spend hours preparing rice, including beating off the husks and drying the rice. They store this hard-earned food in huts that are often infiltrated with rats, who consume their rice and leave their feces, which spreads disease.

Traveling with Esmailzada and Leakey, Nagel not only helped document life in these villages but also searched for information about available resources to drive engineering innovations, while Leakey gathered information about an invasive species of guava.

“Ideally, if any projects require wood, then they should incorporate guava sticks into their design, as opposed to planks from forest trees,” explained Leakey in an email sent from Madagascar. The graduate student, who recently earned her bachelor’s degree at Stony Brook, will be recording the average thickness of the stems, the average length of a straight piece and the load capacity of the branches. Leakey plans to return from the African continent in the beginning of August.

Leakey also visited metalworkers to explore the local capacity. The raw materials come from scrap metal dealers, who often get them from old car parts.

Nagel started BeLocal with her husband Jeff Nagel and a classmate of his from their days as undergraduates at Carnegie Mellon University, Eric Bergerson. Indeed, BeLocal fulfills a long-standing goal of Jeff Nagel’s. Before freshman year in college, Nagel told Bergerson that he wanted to do something that had a positive impact on the world.

While the founders have contributed through their work, their jobs and their families, they found that partnering with Stony Brook University and Distinguished Professor Patricia Wright in Madagascar presented a chance to have a meaningful impact on life on the island nation.

Nagel, whose background is in marketing, visited Madagascar over two years ago, where she traveled for over a hundred hours on a bus through the country. “You just see people living below the poverty line and you see how that plays out in normal day-to-day activities,” she said. “You see a young mom carrying a child on her back and one on her front, with heavy produce on her head and you just think, ‘Wow, there has to be an easier way for some of this.’”

Mickie Nagel, far right, on an earlier trip to Central ValBio with her daughters Gabrielle, far left, and Lauren, center. when they first visited Centre ValBio. Photo by Heidi Hutner

When Nagel returned from her initial trip to Madagascar with her daughters Gabrielle, 18, and Lauren, 17, she and her husband thought people around the world would likely want to help but that not everyone could afford to travel that far.

Nagel recalls Bergerson, who is the director of research at the social data intelligence company Tickertags, telling her that they “don’t have to travel there. You can videotape the daily challenges and crowd source” innovations.

That’s exactly what Leakey and Esmailzada did for the last few weeks. Leakey said she is looking forward to working with senior design students as they go through their projects at Stony Brook and is eager to see how they understand the situation “through the footage and pictures we collect.”

The BeLocal approach isn’t limited to Madagascar, the BeLocal founders suggested. Indeed, given the distance to an island famous for its lemurs, animated movies and an Imax film that features primates with personality, BeLocal could have started in a Central American country like Belize.

Mickie Nagel, however, urged them to start at a location where they would immediately have the trust of local residents. That, she suggested, came from the over quarter of a century of work from Wright, an award-winning scientist who has not only helped preserve Ranomafana [National Park in Madagascar] but has also helped bring health care and education to the villages around the CVB research station. Wright and the Malagasy people have a “mutual respect for each other,” Nagel said.

“People have been exceptionally warm and welcoming,” Leakey said. Getting people accustomed to the presence of cameras hasn’t been straightforward, as people sometimes stop what they are doing, but the guides have helped make the villagers more comfortable.

Jeff Nagel, who works at a private equity firm in New York City, explained that Madagascar is the first step for BeLocal. This effort “can be expanded to other countries or other areas,” Nagel said. “It doesn’t have to be engineers and universities,” but can be instituted by creative people everywhere.

At this point, BeLocal is not looking for any additional funding but might consider expanding the effort at this time next year. Nagel said this fall, they will look for professional engineers to advise on projects. “We would like people who are interested in participating or just keeping up with developments to come and register on our website, www.BeLocalgrp.com,” she suggested.

The site, which the group is upgrading, is up and running. Bergerson explained that they have a “lot of infrastructure to build on” to create the crowd sourcing platform.

Jeff Nagel suggested that this effort is designed to use technology constructively. “Technology’s job, first and foremost, is to help humanity,” he said. “This is a chance to use it in a way that matters to people.”

Gal Gadot tackles the role of Wonder Woman in Warner Brothers new superhero flick. Image courtesy of Warner Bros.

By Daniel Dunaief

Remember those Mad Libs games? You’d insert an adjective, a noun, a verb, adverb, a command, perhaps, into a premade sentence and then you’d read it back, laughing or pondering the combination of words thrown into the structure of a familiar narrative?

Superhero movies, particularly those about the origin of a character we all know, are like a game of Mad Libs. Few superheroes start out life with a cape, a star or a penchant for helping society and standing up against supervillains. Superheroes start out not knowing their fate, or some secret about themselves, and then have to learn the truth along the way.

“Wonder Woman,” the film version from Warner Brothers Studios based on the DC Comics, provides an enjoyable Mad Libs experience, sticking, for the most part, to a familiar structure. The movie, which has been flying high at the box office despite the lack of an invisible plane, executes on its premise well, while offering a few moments of levity scattered through its mix of high-action battle scenes.

Played by the easy-on-the-eyes Gal Gadot, to whom the movie’s other characters react with the kind of awe and attraction the audience might have if they met her, Wonder Woman tells the tale of Diana, the Amazonian princess of Themyscira. We meet her as a young girl, on a picturesque island full of woman who are forever training to fight a battle against man, who may discover their island some day despite remaining hidden from view.

Diana’s mother Hippolyta, played by Connie Nielsen, doesn’t want her daughter to be a warrior, which, of course, means that Diana’s primary focus is on developing her battle skills.

Enter Steve Trevor, an American spy played by Chris Pine, whose plane penetrates the fog that renders the island invisible. Now grown up, Diana races to save Trevor, who crash lands off shore. Trevor, unfortunately, brings an armada of Germans to the beach, where the first of many battles occurs. Diana is determined to end the War to End All Wars by returning to the outside world and fighting an enemy Trevor doesn’t see. While Pine’s Trevor doesn’t understand much about Diana and the island, Diana, in turn, finds the American warrior confounding and slightly amusing.

The interactions between Diana and Trevor throughout the film are amusing, filled with a blend of Trevor’s humorous awe and Diana’s unrelenting sincerity in her quest to end the war.

Complete with the Mad Libs collection of damaged heart-of-gold band of merry men, which fits conveniently into the superhero plot, Diana, Trevor and company seek out the evil General Ludendorff, played by Danny Huston, who seems bent on using a toxin Dr. Maru, Elena Analya, is creating.

The best parts of the film are when Diana, who is unaware of the broader conflict around her, drives the action. She races out of the trenches to try to save a town held by the Germans, followed by the reluctant heroes-despite-themselves band, including Trevor. Movie aficionados have focused on the glass ceiling shattered by director Patty Jenkins, who set a box office record for a movie directed by a woman. Jenkins has blended character development, high energy and an enjoyable script to create a worthwhile comic book movie. Her direction, with battle scenes alternating with the ongoing quest to end the war, kept the pace of the movie. The interaction among the main characters — friend and villain alike — made this Mad Libs origin story a success.

Now playing at local theaters, “Wonder Woman” is rated PG-13 for sequences of violence and action.

Priya Sridevi with her golden doodle Henry. Photo by Ullas Pedmale

By Daniel Dunaief

Priya Sridevi started out working with plants but has since branched out to study human cancer. Indeed, the research investigator in Cold Spring Harbor Laboratory Cancer Center Director David Tuveson’s lab recently became the project manager for an ambitious effort coordinating cancer research among labs in three countries.

The National Cancer Institute is funding the creation of a Cancer Model Development Center, which supports the establishment of cancer models for pancreatic, breast, colorectal, lung, liver and other upper-gastrointestinal cancers. The models will be available to other interested researchers. Tuveson is leading the collaboration and CSHL Research Director David Spector is a co-principal investigator.

The team plans to create a biobank of organoids, which are three-dimensional models derived from human cancers and which mirror the genetic and cellular characteristics of tumors. Over the next 18 months, labs in Italy, the Netherlands and the United States, at Cold Spring Harbor Laboratory, expect to produce up to 150 organoid models.

The project officially started in January and the labs have been setting up the process through June. Sridevi is working with Hans Clevers of the Hubrecht Institute, who pioneered the development of organoids, and with Vincenzo Corbo and Aldo Scarpa at the University and Hospital Trust of Verona.

Sridevi’s former doctoral advisor Stephen Alexander, a professor of biological sciences at the University of Missouri, said Sridevi has had responsibilities beyond her own research. She was in charge of day-to-day operations in his lab, like ordering and regulatory reporting on radioactive material storage and usage, while he and his wife Hannah Alexander, who was Sridevi’s co-advisor, were on sabbatical. “She is hard working and determined,” said Alexander. “She knows how to get things done.”

In total, the project will likely include 25 people in the three centers. CSHL will hire an additional two or three scientists, including a postdoctoral researcher and a technician, while the Italian and Netherlands groups will also likely add another few scientists to each of their groups.

Each lab will be responsible for specific organoids. Tuveson’s lab, which has done considerable work in creating pancreatic cancer organoids, will create colorectal tumors and a few pancreatic cancer models, while Spector’s lab will create breast cancer organoids.

Clevers’ lab, meanwhile, will be responsible for creating breast and colorectal organoids, and the Italian team will create pancreatic cancer organoids. In addition, each of the teams will try to create organoids for other model systems, in areas like lung, cholangiocarcinomas, stomach cancer, neuroendocrine tumors and other cancers of the gastrointestinal tract.

For those additional cancers, there are no standard operating procedures, so technicians will need to develop new procedures to generate these models, Sridevi said. “We’ll be learning so much more” through those processes, Sridevi added. They might also learn about the dependencies of these cancers during the process of culturing them.

Sridevi was particularly grateful to the patients who donated their cells to these efforts. These patients are making significant contributions to medical research even though they, themselves, likely won’t benefit from these efforts, she said. In the United States, the patient samples will come from Northwell Health and the Tissue Donation Program of Northwell’s Feinstein Institute of Medical Research. “It’s remarkable that so many people are willing to do this,” Sridevi said. “Without them, there is no cancer model.”

Sridevi also appreciates the support of the philanthropists and foundations that provide funds to back these projects. Sridevi came to Tuveson’s lab last year, when she was seeking opportunities to contribute to translational efforts to help patients. She was involved in making drought and salinity resistant rice and transgenic tomato plants in her native India before earning her doctorate at the University of Missouri in Columbia.

Alexander recalled how Sridevi, who was recruited to join another department at the University of Missouri, showed up in his office unannounced and said she wanted to work in his lab. He said his lab was full and that she would have to be a teaching assistant to earn a stipend. He also suggested this wasn’t the optimal way to conduct research for a doctorate in molecular biology, which is a labor-intensive effort. “She was intelligent and determined,” Alexander marveled, adding that she was a teaching assistant seven times and obtained a wealth of knowledge about cell biology.

Sridevi, who lives on campus at CSHL with her husband Ullas Pedmale, an assistant professor at CSHL who studies the mechanisms involved in the response of plants to the environment, said the transition to Long Island was initially difficult after living for six years in San Diego.

“The weather spoiled us,” she said, although they and their goldendoodle Henry have become accustomed to life on Long Island. She appreciates the “wonderful colleagues” she works with who have made the couple feel welcome.

Sridevi believes the efforts she is involved with will play a role in understanding the biology of cancer and therapeutic opportunities researchers can pursue, which is one of the reasons she shifted her attention from plants. In Tuveson’s lab, she said she “feels more closely connected to patients” and is more “directly impacting their therapy.” She said the lab members don’t get to know the patients, but they hope to be involved in designing personalized therapy for them. In the Cancer Model Development Center, the scientists won a subcontract from Leidos Biomedical Research. If the study progresses as the scientists believe it should, it can be extended for another 18 months.

As for her work, Sridevi doesn’t look back on her decision to shift from plants to people. While she enjoyed her initial studies, she said she is “glad she made this transition” to modeling and understanding cancer.

Leemor Joshua-Tor. Photo from CSHL

By Daniel Dunaief

Like many of the other talented and driven professionals at Cold Spring Harbor Laboratory, Leemor Joshua-Tor often works far from the kind of spotlight that follows well-known actors or authors.

That changed in April and early May. First, the American Academy of Arts and Sciences elected her a member on April 11. Other members joining the academy this year include Carol Burnett, New York Times columnist Nicholas Kristof, actor Ian McKellen, who played Gandalf in the Hobbit films and Magneto in the X-Men movies, and Israeli writer David Grossman.

Then, on May 2, the National Science Foundation elected the Cold Spring Harbor Laboratory professor and Howard Hughes medical investigator to join its ranks. “I got a huge amount of congratulatory emails from many friends, some of which I haven’t been in touch with for a while,” Joshua-Tor said. “It’s humbling.”

Joshua-Tor’s research covers a range of areas in structural and molecular biology. She works with RNA interference, where she focuses on how small molecules regulate gene expression or translation. She has also worked with Cold Spring Harbor Laboratory President Bruce Stillman on the early stages of DNA replication.

Early this year, Joshua-Tor and Stillman published a paper in eLife Sciences in which they offered more details about the human origin recognition complex. Stillman suggested that Joshua-Tor was the “main driver” for the research, studying the structure of a protein he had isolated years ago. “I am not a structural biologist, but she is an outstanding one and together, we came up with a very satisfying result.”

The origin recognition complex begins the process of replication, recruiting a helicase, which unwinds DNA. It also brings in regulatory factors that ensure smooth timing and then other factors such as polymerase and a clamp that keeps the process flowing and ensures accurate copying of the genetic code. “We don’t know how ORC’s motor activity is used,” Joshua-Tor explained. “We don’t really know what it is on the DNA that the ORC likes to bind to.”

In the recent work, the scientists explored the ORC’s structure and tinkered with it biochemically to understand it. The ORC binds and hydrolyzes the energy molecule adenosine triphosphate, or ATP, in the same way a motor would, although it probably isn’t continuous. “It might use ATP hydrolysis to perform one sort of movement, perhaps a detachment,” Joshua-Tor suggested.

In the early stages of replication, ATP is necessary for the integrity of the ORC complex, as well as the helicase that gets recruited. “We knew from biochemistry that ORC bounds multiple ATP molecules, but we did not know precisely how,” Stillman explained in an email. “The structure told us. ORC does not open the DNA by itself, but loads a protein complex onto the DNA that, when activated, can open the DNA.” Stillman is working on that process now. The next step for the CSHL collaborators is to get a structure of human ORC bound to DNA.

In their recent work, the researchers characterized how mutations involved in ATP hydrolysis affect a condition called Meier-Gorlin syndrome. Of the mutations they characterized, one affects the ability to hydrolyze ATP. Patients with this syndrome have one copy of the gene with typical function and the other that doesn’t. This likely leaves the patient with half of the molecules to do the required job.

The misregulation of replication is often associated with cancer and is something Joshua-Tor and others consider when they conduct these studies.

ATP, meanwhile, is associated with all kinds of activities, including cell adhesion and taking down misfolded proteins. Many processes in the cell connect to these types of molecular machines.

In her research with RNA interference, she is studying how a microRNA called Let7 is produced. Let7 is involved in development. Before cells differentiate when they are stem cells, they make Let7 continuously and then destroy it. She is studying the pathway for this process. Let7 is absent from stem cells and in some cancers.

Interested in science and theater when she was young, Joshua-Tor grew up in Israel, where she participated in activities at the Weizmann Institute of Science. The institute has biology, biochemistry, chemistry, math, computer science and physics, as well as an archeology unit that didn’t exist when she was there. Later, when she was a graduate student, Joshua-Tor returned to the institute and became an instructor.

An important moment in her scientific development occurred when she was in seventh grade. She was learning about elements and she put each one on a card. She brought these cards to class to study them. Her mother gave her a container that had housed her perfumes, which created a positive association for chemistry every time she studied the elements.

Joshua-Tor was also interested in theater, where she was initially in shows and then became an assistant director. The researcher lives with her daughter Avery, who is 8 and attends the Jack Abrams Magnet School. The tandem have a Schnauzer named Charles Darwin. Her daughter is proud of her mother and tells “anyone that would listen” about the awards her mother recently won, Joshua-Tor said.

Joshua-Tor, whose lab now has 11 people, said she is excited for the opportunity to meet some of her fellow honorees this fall.

Stillman expressed pride in “all our scientists and especially when they make major discoveries and they receive such peer recognition,” he wrote in an email. Joshua-Tor is “one of our best, but we have many scientists who will go on to gain substantial peer recognition. This is her turn, at least for these two awards!”

Fan Ye. Photo from SBU

By Daniel Dunaief

Fan Ye has a vision for the future filled with high service and efficiency that doesn’t involve butlers or personal attendants. The assistant professor of electrical and computer engineering in the College of Engineering and Applied Sciences at Stony Brook University is focused on creating smart environments in which window blinds open as people pull into their driveways, lights turn off in unoccupied rooms and the building guides a new student turn by turn through complex floors and hallways from entrance to the registrar’s office.

“The physical environment would be like a caring mother,” said Ye. It would sense and figure out people’s needs and “take care of the occupants inside the building.”

In Ye’s vision, which he estimates is about one year to decades away from a reality, objects that rely on people to turn them on or off, reposition them or alter their settings would have chips embedded in them, working together to create an environment that anticipates and learns in response to the need around it.

“With sensors, [a smart environment] can sense both physical conditions and human activities and adjust the environment in manners that create/improve comfort, safety, convenience” and the productivity of the occupant, he explained in an email.

Ye recently received a $450,000 award over the next five years from the National Science Foundation for early-career faculty for his study of smart environments. The prestigious award is the highest honor given by the government to scientists and engineers beginning their independent careers.

Initially, Ye is developing and testing a security system with the Stony Brook University Police Department and the Center of Excellence in Wireless and Information Technology that grants specific access to buildings or facilities depending on the specifications of an administrator.

Many of the buildings on campus have electric locks, which someone can open with a badge where there’s a badge reader. A badge, however “isn’t that flexible,” Ye said. If an administrator would like to grant someone one-time access to open a door that doesn’t provide ongoing access, that is difficult to do with a badge system.

“What’s lacking in this closed proprietary system is flexible access control, which can determine who has what access based on context factors,” he said. Ye, his team, the police department and the CEWIT are building a system that can enable greater flexibility that allows someone to open an office door for five minutes during a specific hour. “If any of these context factors is not satisfied, they don’t have access,” he said.

Ultimately, he would like to construct a system using modern mobile technology, like smartphones, instead of physical badges. The system would include embedded security that employs modern cryptography so a hacker or attacker can’t trick the system.

By using software and hardware security, Ye is hoping to develop a system that prevents the most common attacks at a reasonable cost, which he hopes would prevent someone from gaining access.

Ye is building real systems and testing them. The cost-benefit of these systems depends on the object. A motor to open and close a window would cost money to manufacture, install and operate. As with any technological innovation, he said, “the question comes down to, How do you invest versus how much do you get in return?”

Looking at the historical trend for computation resources, Ye said computing and storage costs are falling at an exponential rate, while the price for radio and sensing is also falling rapidly, although not at the same pace.

“I believe this trend will continue, especially for a lot of these objects that need small embedded systems” that can be manufactured at a scale with low cost, he continued. The process of turning the environment into an efficient, high-service system isn’t an all-or-nothing proposition. Consumers might decide to focus on the air-conditioning or heat use in their homes.

Other researchers are developing ways to harness the vibrational energy of movement or sound, which, conceivably, could power some of these electronics without requiring the delivery and consumption of more energy.

Ye recognizes that these parts can and will break down and require repair, just as dishwashers sometimes stop working and iPhones can lose a list of contacts. So many small electronic parts in a smart environment could seem like an invitation to malfunctions.

He likens the repair process to cloud computing, which allows small to medium-sized companies to rent computing resources from larger companies. “A smart environment, especially for public buildings like a university or office, could potentially run in a similar model,” he said. Individuals might rely on IT support from dedicated personnel who, like a superintendent in a building, could be responsible for a host of smart products.

A native of Hubei Province in China, Ye, who now lives in Setauket, loves to hike in national parks. His favorite is Canyonlands in Utah. Ye had worked at IBM for about 10 years before joining Stony Brook almost three years ago. While he was there, Ye worked on numerous projects, including distributed stream processing, cloud-based queueing and wide-area dependable messaging. “I learned tremendously at IBM,” he said.

Ye is “”well known and respected in the mobile and wireless computing research community,” Hui Lei, an IBM distinguished engineer, wrote in an email. “He conducted pioneering work on scalable message delivery, robust coverage and security in wireless sensor networks, which are well received and highly cited and closely related to the smart environment work he is doing now.”

Lei suggested that Ye’s experience and accomplishments provide him with a solid track record and he is “confident that [Ye] will be able to come up with innovative solutions in this area.”

From left, Christopher Gobler with his research team Andrew Griffith, Theresa Hattenrath-Lehmann and Yoonja Kang. Photo from SBU

By Daniel Dunaief

Christopher Gobler searches the waters around Long Island for signs of trouble, which can appear starting in April. This year, he found it, in Shinnecock Bay. Monitoring for a toxin carried by algae called Alexandrium, Gobler recently discovered levels that were three times the allowable limit from the Food and Drug Administration. His finding, along with measurements from the New York State Department of Environmental Conservation of toxins in shellfish in the bay, have caused the recent closure of shellfishing in the bay for the fourth time in seven years.

While Gobler, a marine science professor at the School of Marine and Atmospheric Sciences at Stony Brook University, watches carefully for the appearance of red tides from these algae locally, he recently completed a much broader study on the spread of these toxins.

Gobler led a team that explored the effect of ocean warming on two types of algae, Alexandrium and Dinophysis. Since 1982, as the oceans have heated up, these algae have become increasingly common, particularly in the northern Atlantic and Pacific oceans, according to a study Gobler and his colleagues recently published in the Proceedings of the National Academy of Sciences. When they become concentrated in shellfish, these algae can lead to diarrhea, paralysis and even death if people consume enough of them.

Over the course of the study, algae have begun to form “denser populations that are making shellfish toxic,” Gobler said. Temperature is one of many factors that can affect the survival, growth and range of organisms like the algae that can accumulate toxins and create human illness. “As temperatures get higher, they are becoming closer to the ideal for some species and out of the ideal for other species,” Gobler said.

The strongest effect of changing temperatures are at higher latitudes, which were, up until recently, prohibitively cold for these types of algae. The biggest changes over the course of the study came in the Bay of Fundy in Canada, in Scotland, Ireland, Scandinavia, Iceland, Greenland and Alaska. The toxic algal blooms increased in frequency between 40 and 60 degrees north latitude, according to the study. These are places where toxic algae lived but weren’t as prevalent, but the warming trend has created a more hospitable environment, Gobler said.

Raphael Kudela, a professor of ocean sciences at the University of California, Santa Cruz who wasn’t involved in this research, explained that other papers have suggested a similar link between temperature and the movement of these algae. “We’ve seen the expansion of ciguatera fish poisoning, as the temperature range has moved poleward for those algae,” Kudela wrote in an email. NOAA biological oceanographer Stephanie Moore has documented an expanded window of opportunity for paralytic shellfish poisoning linked to changes in temperature, Kudela said. “While we can point to specific events, and it makes intuitive sense, the Gobler paper actually documented these trends using a long time series, which hasn’t been done before,” Kudela continued.

R. Wayne Litaker, a supervisory ecologist at NOAA’s National Ocean Service, collaborated with Gobler on the project. He said small differences in temperature are significant for the growth rate of these toxic algae. Extending this to other organisms, Litaker explained that fish are also extending their ranges amid a rise in global temperatures. “There’s been a general movement of temperate species toward the poles,” Litaker said. He’s seen tropical fish, such as butterfly fish, off the docks of North Carolina that he hadn’t seen that far north before.

Gobler and his colleagues estimate that the need to close shellfish beds, the increase in fish kills, and the health care damage to people has exceeded a billion dollars since 1982. The largest problem for people in areas like Alaska is their lack of experience with red tides.

“Communities are being exposed to these blooms where they had not been in the past,” Gobler said. “[The blooms] can be most dangerous when they take a community by surprise.” Gobler said this happened in Alaska during the study. In the last decade, shellfish toxins that are 1,000 times more potent than cyanide caused illnesses and were suspected in two deaths in Haines, Alaska.

Litaker said he gave a talk several years ago at a conference. Gobler approached him and asked if they could work together. “One of the wonderful things about these meetings is that you see things that trigger possibilities and whole new projects are born,” Litaker said.

Litaker described Gobler as a “major player in the field” who has done “fantastic work over the years.” Litaker said he was “quite impressed with what he’s done.” Litaker explained that the climate is changing and urged fisheries and shellfish experts to prepare to respond throughout the country. “As we get warmer and more run off of nutrients, toxic cyanobacteria [algal blooms] are causing problems in all 50 states,” Litaker said.

Kudela suggested that the “new records every year for the last several years … will undoubtedly continue to impact the range, duration and toxicity of blooms.”

Locally, Gobler continues to monitor dozens of sites on Long Island, where he suggested that Alexandrium could become less prevalent with warming, while Dinophysis could become more common. Temperature and other factors favorable for algae growth have led to red tides in the past.

In oceans across the world, Kudela said the next logical step would be to explore the interaction of temperature and nutrients. “We know both are changing, and they are likely to have additive or synergistic effects, but we haven’t done the same careful study as the Gobler paper looking at how the trends are interacting,” he explained.