Science & Technology

Algae built up on a lake where birds and other marina life inhabit. File photo

By Rebecca Anzel

Long Island’s economic prosperity and quality of life are at risk from an unlikely source, but both the Suffolk County and Town of Brookhaven governments are taking steps to combat the issue.

Bodies of water in the county face nitrogen pollution, which leads to harmful algae blooms and a decrease in shellfish population, among other environmental defects. Critically, nitrogen seeps into the Island’s groundwater, which is the region’s only source of drinking water.

Fishing, tourism and boating are billion-dollar industries in Suffolk County — approximately 60 percent of the Island’s economy is reliant on clean water. County property values are also tied to water clarity, according to a Stony Brook University report.

Nitrogen enters ground and surface water from various sources of runoff, such as landscaping, agriculture and pet waste. But the largest contributor of nitrogen pollution is failing septic systems, which County Executive Steve Bellone (D) designated as “public water enemy No. 1.”

Elected officials and environmental advocates gathered at the home of Jim and Donna Minei, recipients of a Innovative and Alternative Onsite Wastewater Treatment Systems through the Suffolk County Septic Demonstration Pilot Program. Photo from Steve Bellone's office
Elected officials and environmental advocates gathered at the home of Jim and Donna Minei, recipients of a Innovative and Alternative Onsite Wastewater Treatment Systems through the Suffolk County Septic Demonstration Pilot Program. Photo from Steve Bellone’s office

Which is why Bellone signed into law last month a resolution that amended Suffolk County’s sanitary code to help protect the county’s aquifer and surface water by improving wastewater treatment technologies to combat nitrogen pollution as part of the county’s Reclaim Our Water initiative.

“It doesn’t help our tourism industry, our quality of life or our ecosystems,” county Legislator Kara Hahn (D-Setauket) said of issues with the Island’s water. “Tackling the nitrogen problem, while not a sexy issue, is a very important one.” Hahn is chairwoman of the county’s Environment, Planning & Agriculture Committee.

Town and county officials are tackling the problem by utilizing what Hahn called a “multipronged approach.” Brookhaven is working to track any issues with outfalls, where drains and sewers empty into local waters, and Suffolk County is employing alternative septic systems.

Municipalities like Brookhaven are required by New York State to inspect each point where waste systems empty into a body of water and create a map of their location. It is part of a Municipal Separate Storm Sewer System (MS4) permit because, according to the state Department of Environmental Conservation, storm sewers collect pollutants like bacteria, motor oil, fertilizer, heavy metals and litter, and deposit them directly into bodies of water.

In addition to conducting the inspections of outfalls necessary to comply with the MS4 permit, the Town of Brookhaven conducts a DNA analysis of any outfall that has indications of impacting water quality. Since 2007, Brookhaven has spent more than $880,000 on this state requirement, Veronica King, the town’s stormwater manager, said.

“You want to put your resources where it makes the most sense,” she said. “Instead of dumping millions of dollars into structural retrofits that don’t address the true problem, the DNA analysis helps us to prioritize and make educated and cost-effective decisions.”

Town Councilwoman Jane Bonner (C-Rocky Point) said Brookhaven contracts with Cornell Cooperative Extension because it maintains a DNA “library” of Long Island wildlife, which it uses to identify the source of any pathogens in collected stormwater. For instance, if the DNA tests conclude they came from pets, Brookhaven might conduct an educational campaign to remind residents to clean up after their furry friends. If the pathogens come from a human source, there might be an issue with a septic system.

“This type of analysis could prove of great importance because any patterns identified as a result of this study can help determine what next steps can be taken to improve water quality where necessary,” Councilwoman Valerie Cartright (D-Port Jefferson Station) said.

Brookhaven has applied for a state grant to help pay for these DNA tests and outfall inspections for the first time this year, because, King said, this is the first time New York State has offered a grant to cover the work.

The DNA tests are important, Brookhaven Supervisor Ed Romaine (R) said, because they help to identify ways to decrease the amount of nitrogen seeping into groundwater.

“The amount of nitrogen in the Magothy aquifer layer has increased over 200 percent in 13 years,” he said of one of the sub-layers that is most commonly tapped into in Suffolk, although not the deepest in the aquifer. “Cleaning up our waterways is not going to be done overnight — this is going to take a long time — but the waterways did not become polluted overnight.”

Suffolk County launched its Septic Demonstration Program to install cesspool alternative systems in 2014, called Innovative and Alternative Onsite Wastewater Treatment Systems (known as I/A OWTS), on the property of participants. Manufacturers of the technology donated the systems and installed them at no cost to the homeowner.

The county’s goal in testing these alternative systems is to lower the levels of nitrogen seeping into groundwater. According to a June 2016 Stony Brook University report, “the approximately 360,000 septic tank/leaching systems and cesspools that serve 74 percent of homes across Suffolk County have caused the concentrations of nitrogen in groundwater to rise by 50 percent since 1985.”

More than 10,000 of the nitrogen-reducing systems are installed in New Jersey, Maryland, Massachusetts and Rhode Island — all areas with similar environmental concerns to Suffolk County — according to the county executive’s office. County employees met with officials from these states to help shape its program.

“Tackling the nitrogen problem, while not a sexy issue, is a very important one.”

—Kara Hahn

The I/A OWTS installations worked out so well during a demonstration program that on July 26, the county passed a resolution to allow the Department of Health Services to regulate their use.

Typical cesspools are estimated to cost between $5,000 and $7,000 to install. The low nitrogen systems cost between $12,000 and $20,000, Hahn said. She added that as more areas facing similar environmental concerns require lower nitrogen standards and, as the technology improves, the cost of cesspool alternatives will go down.

Until then, Hahn said county officials have been discussing the possibility of subsidizing the cost of installing the I/A OWTS. It might begin requiring new homes to install low-nitrogen systems instead of traditional cesspools. Or, upon an old system’s failure, it might require an I/A OWTS be installed.

“We hope to eventually be able to help in some way,” she said.

County Legislator Sarah Anker (D-Mount Sinai) said she hopes local businesses begin producing the alternative systems that the county determines best work for the area since it would “keep the economic dollar here” and provide jobs.

In January, Brookhaven will be the first town, Romaine said, that will begin mandating new constructions within 500 feet of any waterway to install an alternative wastewater treatment system.

“I think alternative systems work,” he said. “In many ways, even though we’re a local government, we are on the cutting edge of clean water technologies.”

Both the initiatives by Brookhaven and Suffolk County “go hand and glove,” George Hoffman, of the Setauket Harbor Task Force, said. Many of Suffolk’s harbors and bays are struggling due to stormwater and nitrogen pollution, including Great South Bay, Lake Ronkonkoma, Northport Harbor, Forge River, Port Jefferson Harbor, Mount Sinai Harbor and Peconic River/Peconic Bay.

“Living on an island on top of our water supply and with thousands of homes along the shores of our harbors and bays, it never made sense to allow cesspools to proliferate,” he said.

The success of the initiatives, though, depends on residents.

“The public needs to be always recognizing that whatever we do on land here on Long Island and in Suffolk County affects not only the drinking water beneath us but the quality of our bays and waterways, streams and rivers all around us,” Hahn said. “It’s critically important that folks have that understanding. Everything we do on land affects our water here on the Island.”

From left, Paul Dodorico and Fred Drewes stand by ‘the sun' at Heritage Park. Photo from Fred Drewes

Volunteers at the Heritage Park in Mount Sinai, known affectionally as The Wedge, recently added a unique feature to the park. “The Solar System has landed at the Wedge,” said volunteer Fred Drewes. Along with fellow volunteer Paul Dodorico, Drewes installed signs modeled after The 1000 Yard Peppercorn Model of the Solar System throughout the park.

Heritage Park sunTom and Nick Nagle of Letter Perfect Graphics formatted and printed the signs on metal sign plates, funds for the posts and screws were donated and Yvonne Francis of Port Jeff Bowl donated the bowling ball sun. Visit the Wedge and tour the Solar System by starting at the south end of the park. Look for the planet signs along the fence line and find out where Neptune and the dwarf planet Pluto would be in this model of the solar system.

Heritage Park, located at 633 Mount Sinai-Coram Road in Mount Sinai is open daily from dawn to dusk. For more information, please call 631-509-0882.

Stony Brook’s Center for Planetary Exploration opens

Renee Schofield explains the testbed for the PIXL she built. Photo by Kevin Redding

By Kevin Redding

Although some might not think of Suffolk County as an obvious hotbed of planetary exploration, it doesn’t take long to discover just how impactful the research and work conducted on Long Island has been on the growth of space science.

Going back to the Apollo program in the early 1960s, the Grumman corporation was vital in landing astronauts on the moon by designing, assembling and testing the lunar module at its facility in Bethpage.

Even closer to home, the founder of Stony Brook University’s Department of Earth and Space Sciences, Dr. Oliver Schaeffer, became the first person to date celestial objects. He confirmed that the moon rocks brought back by Apollo astronauts were more than four billion years old.

Donald Hendrix leads a research team to help future astronauts prevent long-term illnesses. Photo by Kevin Redding
Donald Hendrix leads a research team to help future astronauts prevent long-term illnesses. Photo by Kevin Redding

Now half a century later, Stony Brook University has once again cemented Long Island’s place in innovative planetary research.

In 2014, Timothy Glotch, a professor in the department of geosciences, received a $5.5 million grant from NASA through their Solar System Exploration Research Virtual Institute program to support his research. The department eventually obtained a 6,500-square-foot, world-class facility consisting of three different labs.

On Aug. 26, the public was invited to the official opening of Stony Brook’s Center for Planetary Exploration, where faculty members and students in the department gave a tour of their labs and showcased the inspiring work that has taken place so far.

At the core of CPEX is the Stony Brook-led multi-institutional Remote, In Situ, and Synchrotron Studies for Science and Exploration Institute, one of the nine nodes of the NASA program.

“We’re trying to pave the way for future human exploration of the solar system,” Glotch said. “Right now we are doing basic science; we are doing exploration activities that are going to get humans to Mars, back to the moon, and to the moons of Mars. That work is going on right here. We’re kind of leading the way in space exploration and we’re very proud of that. ”

He stressed the importance of the overall goal: to train the next generation of solar system explorers and scientists. The students are going to be running missions in the next decade or two, he said.

“Just as Schaeffer put together a young and talented group of researchers, we now have an extraordinarily talented group of young researchers working in planetary science,” current Chair of the Department Dan Davis said.

“We’re trying to pave the way for future human exploration of the solar system.”

—Timothy Glotch

As for the three different labs, professor Joel Hurowitz runs the geochemistry lab, which includes a student-built test bed for the Planetary Instrument for X-ray Lithochemistry, which will fly on the Mars 2020 rover.

The PIXL is an X-ray microscope that looks at rock samples and builds maps of the elemental distribution in those samples to make it easier to analyze.

“From there, we can start to dig in and try to understand whether the environment that those rocks were deposited in were habitable,” Hurowitz said. “PIXL can detect things that are chemical biosignatures. It can detect biosignature in a rock on the surface of Mars. So we’re trying to place some constraints on whether or not there was ever life on Mars.”

The lab is also conducting a series of experiments to determine the damaging effects of lunar dust inhalation by future astronauts.

“What I do is I try to find minerals here on Earth that are similar to what’s found on the moon,” Donald Hendrix, a graduate student leading the research, said. “I grind them up into powders and determine what chemicals are made when they are exposed to fluid, because whenever you breathe in a mineral powder, they can produce chemicals inside your lungs that can potentially cause a lot of damage and turn into lung cancer.

Since humans are going to go back to the moon in the next 20 or 30 years, for really long periods of time, I want to know what hazards astronauts might face while they’re up there.”

Through the research he’s conducting with his team, he’s trying to figure out where astronauts could go that won’t be quite as dangerous.

Professors Joel Hurowitz, Deanne Rogers and Timothy Glotch guide their students in planetary research. Photo by Kevin Redding
Professors Joel Hurowitz, Deanne Rogers and Timothy Glotch guide their students in planetary research. Photo by Kevin Redding

Deanne Rogers runs the remote sensing facility, where faculty, students and postdoctoral researchers analyze various images and infrared data that come from Mars and the moon. From there, they incorporate observation skills and geological training to learn about the planet or moon’s environmental and climatic history.

Glotch’s spectroscopy lab is where students acquire infrared spectra of minerals and rocks for comparison to data collected by Mars and Moon orbiters. Within this lab is the Planetary and Asteroid Regolith Spectroscopy Environmental Chamber, used to re-create the conditions on the lunar surface for accurate measurements.

“I can make the moon on Earth, basically, and that’s pretty exciting,” graduate student Katherine Shirley said. “This machine is special because we can make different environments in this. Eventually we’re going to get some attachments so we can simulate the Martian surface or asteroid surface.”

The lab includes a small piece from Mars, which visitors were encouraged to hold.

Assemblyman Steve Englebright (D-Setauket), who was once a student and employee at SBU, spoke about how much the department means to him.

“I’m practically retired, but my heart is still here,” he said. “I served in this department and am proud to have been among such extraordinary researchers and wonderful human beings for 43 years. It’s a privilege now to help send resources in the direction of these extraordinary individuals who are literally writing the next chapter of our understanding of the universe and solar system. I look forward to continuing to work with you as you go forward. They say I’m technically retired, but don’t believe it. I’m just one phone call away.”

Legislator Kara Hahn (D-Setauket) presented the faculty with a proclamation from the county legislature to celebrate what this research means for the community, the university and the overall future of science.

Wei Zhu with a photo of her mother, Shenzhen Du. Photo by Joyce Ruan

By Daniel Dunaief

Wei Zhu’s long personal and professional journey began in China. Devoted to her mother, Shenzhen Du, Zhu watched her hero fight through a long illness with chronic kidney disease. Shortly before she died, her mother woke from a coma and suggested that her daughter become a doctor, like the people who were helping her in the hospital.

Driven to fulfill her mother’s request, Zhu attended college where, despite aspirations to become a writer like Charles Dickens or Charlotte Bronte, she studied math. She found the subject challenging but stuck with it. “Math was absolutely hard work,” she recalled. “We had to devote longer time to our study than many other majors. It all paid off in my case.”

Indeed, after she completed a one-year graduate program in math, she and her husband, Yeming Ma, came to the United States, where she used her experience in math to explore ways to understand how statistics can provide a perspective on everything from drug dosage to global warming to the causes of cancer.

“You can use math to improve people’s health,” said Zhu, who is now the deputy chair and professor in the Department of Applied Mathematics & Statistics at Stony Brook University.

Wei Zhu with her daughter, Merry Ma. Photo  by Merry Ma
Wei Zhu with her daughter, Merry Ma. Photo by Merry Ma

At the beginning of the year, Yusuf Hannun, the director of the Stony Brook Cancer Center, emailed Zhu to ask her to pitch in to help understand a major question about cancer. In the prestigious journal Science, several researchers had concluded that the “bad luck” hypothesis suggested cancer was something that was written in a person’s genes. This scientific conclusion was akin to suggesting that a character’s fate in a play may have been written in the stars.

Hannun, Song Wu, an assistant professor in her department, Scott Powers, a professor in the Department of Pathology and Zhu came to a different conclusion, which they published in the equally prestigious magazine Nature.

Putting the data and the theory together, the group suggested that lifestyle choices and environmental exposure were also instrumental in this disease. The argument is the equivalent of nature versus nurture for a deadly disease.

“We were able to quantify what we observed,” Zhu said. For most cancers, the group concluded, the majority of the risk was due to lifestyle and environmental factors other than pure intrinsic genetic mutations. The disease debate, scientists recognize, doesn’t end there.

“The entire cancer research community still has a long way to go in order to perfectly understand the causes, prevention and treatments for each cancer, for each individual,” Zhu explained.

Hannun suggested that the direction cancer research is going requires advanced expertise in several areas of applied mathematics, physics and related disciplines. These are now needed for working with large data sets, for modeling pathways and events and for generating new hypotheses and organizing principles, Hannun wrote in a recent email. Hannun described Zhu as “terrific, highly dedicated and very collaborative” and suggested that the work has been “rewarding.”

Zhu is hoping that the recent Nature publication will trigger additional funding to support more research with this team of Stony Brook University scientists.

Wu, who was the first author on the Nature article, described Zhu as “well respected in the scientific community. She has done a lot of work on the analyses of brain image and proteomics data,” he wrote in an email.

Throughout her career, Zhu has sought to use statistics, bioinfomatics and other modern tools to enhance a scientific understanding of complex questions. She recently worked with Ellen Li, a professor of medicine and chief of the Division of Gastroenterology and Hepatology at Stony Brook University School of Medicine, who wanted to understand the development of digestive diseases such as inflammatory bowel disease and colon cancer. Putting the numbers together could provide the kind of information that offers an understanding of how lifestyle and food choices contribute to some diseases over time, Zhu said.

“We have published several papers together over the years,” Zhu said. “We are still in the data collecting stage for the diet analysis.” In her career, which spans 24 years, Zhu has worked on a wide range of topics. She has helped analyze data on the regions of the brain that are active in addiction and helped refine and enhance global climate models. In her early work, she also help pharmaceutical companies come up with optimal drug dosage. Numbers have been a part of Zhu’s life wherever she goes. “You do see numbers in the air,” she said. “When it’s getting hot,” she asks, “what does it have to do with my climate model? Does it fit the data?”

In more recent years, Zhu has struggled with the tension between contributing to larger projects and budgetary constraints. She worries that the “funding situation has changed the dynamics of the job market for the young generation of statisticians,” she said. “Now the majority of my doctoral students hope to focus their research on financial models, instead of biological models.”

Zhu and her husband Ma, who is a financial manager for GE, live in Setauket. Their son Victor, 24, recently earned his graduate degree in finance, while their daughter Merry, 11, attends Mount Elementary School. Zhu appreciates living on Long Island, where she can be close to the ocean.

As she looks back on the developments in her life that brought her to this point in her career, Zhu recognizes that the decision to learn more about math and statistics provided her with the kind of background that allowed her to fulfill her mother’s wish. “I can always honestly tell young students that it is a good idea to choose mathematics or statistics as their undergraduate majors,” she said. It will pave the way for them to have “a solid foundation for a variety of future graduate studies.”

A photo of the sun taken with the new telescope by Alan Friedman

Visitors to the Suffolk County Vanderbilt Museum’s Reichert Planetarium can now view the sun through a new solar telescope. The planetarium has just installed a Lunt Solar Systems hydrogen-alpha solar telescope in the observatory — for daytime observation of the sun.

Dave Bush keeps an eye on the sun with the new Vanderbilt solar telescope. Photo courtesy of the Vanderbilt Museum
Dave Bush keeps an eye on the sun with the new Vanderbilt solar telescope. Photo courtesy of the Vanderbilt Museum

Dave Bush, the planetarium’s technical and production coordinator, and an astronomy educator, said the solar telescope is mounted “piggy back” onto the 16-inch Meade reflecting telescope in order to track the sun across the sky.

“The refractor-style telescope with its 80-milimeter optical aperture gives us sharp detail and contrast of features on the surface and the limb, or edge, of the sun,” he said. “This telescope allows us to see prominences, flares, super granulation, filaments and active regions.”

Bush explained that hydrogen-alpha light is emitted by the hydrogen atoms that make up the majority of the sun’s composition. When electrons within the hydrogen atoms absorb energy and rise to a higher energy level and then fall back to their original orbits, light is emitted at a particular wavelength that can be seen with the specialized telescope.

“Typically, telescopic views of objects in outer space rarely change before our eyes in real time,” Bush said. “However, on a day when the sun is particularly active we can watch features on the sun evolve before our eyes while looking through an H-alpha telescope! The sun is dynamic and alive. It changes daily, and rotates,” he said.

A photo of the sun taken with the new telescope by Alan Friedman
A photo of the sun taken with the new telescope by Alan Friedman

In explaining the solar features in the picture of the sun, right, shot by photographer Alan Friedman, Bush said:

◆ The wisps of white curling off the upper left curve of the sun are prominences or arcs of gas that erupt from the surface. Sometimes the loops extend thousands of miles into space.

◆ The lighter spots and streaks are called plages, the French word for beaches, and are, appropriately, hot spots or bright emissions caused by emerging flux regions associated with the magnetic field of the sun.

◆ The tiny hair-like lines that extend from the surface are spicules. These are jets of hot gas that can rise up to 6,000 miles high. Most last only 15 minutes before morphing into new spicules.

◆ The dark spots are sun spots, which are cooler areas of the surface caused by the suppression of convection cells due to the sun’s strong magnetic field.

◆ The sun is 93 million miles from Earth and its size is almost beyond human comprehension — 1.3 million Earths could fit inside the sun.

The solar telescope is available for viewing on a limited schedule, on clear days. (The sun is not observable on cloudy or rainy days.)

The Suffolk County Vanderbilt Planetarium is located at 180 Little Neck Road in Centerport. For more information, call 631-854-5579 or visit www.vanderbiltmuseum.org.

Dr. Kenneth Kaushansky, senior vice president for Health Sciences at Stony Brook University; said Stony Brook University President Samuel L. Stanley Jr.; and Dennis S. Charney, dean of the Icahn School of Medicine at Mount Sinai Hospital in New York City shake hands during the signing of the agreement for the two hospitals to partner. Photo from Stony Brook University School of Medicine

By Talia Amorosano

Two major medical institutions have agreed to team up, and the partnership could lead to big scientific breakthroughs.

In order to create more academic research opportunities and streamline and expand clinical care initiatives, Stony Brook Medicine and Mount Sinai Health System, in New York City, have entered into a comprehensive affiliation agreement. The change will promote inter-institution collaboration encompassing all five of Stony Brook’s Health Science schools, Stony Brook University Hospital, all 25 academic departments of the Stony Brook University School of Medicine, Mount Sinai Health System facilities and Medical School, and the Icahn School of Medicine at Mount Sinai inclusive of seven hospitals and an expanding ambulatory network.

Facilitators of the partnership believe that the expansion of clinical trials and research opportunities for both institutions will prompt research and studies that could lead to major discoveries, especially in the treatment and understanding of disease.

Dr. Kenneth Kaushansky, senior vice president for Health Sciences at Stony Brook University, noted that the alliance will make use of the strengths of each individual institution.

“What we both get out of the affiliation is enhanced possibilities for science and education,” he said. “Multiple groups of investigators [with members from each institution] work together and look at things in slightly different ways.”

In a press release, he noted Mount Sinai’s Icahn School of Medicine for its strong biomedical, clinical research and health policy expertise and Stony Brook University for its advanced mathematics, high-performance computing, and physical and chemical science departments to illustrate the point that these institutions can accomplish collaboratively more than each can do alone.

“In the long term were gonna roll out more and more in the way of clinical interactions,” said Kaushansky, who mentioned Stony Brook’s recent recruitment of two new cardiac surgeons from Mount Sinai. “We don’t do heart transplants, but Mount Sinai does.”

He emphasized the new potential for patients to easily seek services from either hospital. In fact, joint research programs ranging from fields of biomedical engineering and computer science to medicinal chemistry science, neurology, psychiatry, therapeutics and more are currently in the works.

“Stony Brook Medicine and the Icahn School of Medicine at Mount Sinai are two powerhouses of research that when partnered will definitely yield more than just the sum of their parts.”

—Lina Obeid

In terms of education, University students will now be afforded the unique opportunity to take classes offered on either or both campuses, and participate in a variety of summer programs geared toward students of all ages. The two schools plan to facilitate joint graduate and medical educational programs in a wider range of subjects than ever before, and have agreed to invest a collaborative $500,000 for the development of academically challenging pilot programs to be supervised by a joint committee.

“The joint pilots in research have immense promise to advance health at the most exciting time in the biomedical sciences, including advanced computational, bioinformatic and engineering approaches,” said Lina Obeid, MD, dean for research and vice dean for scientific affairs at Stony Brook University School of Medicine. “Stony Brook Medicine and the Icahn School of Medicine at Mount Sinai are two powerhouses of research that when partnered will definitely yield more than just the sum of their parts.”

Other leaders of each institution have already expressed similar enthusiasm about the affiliation, which was effective immediately upon signing, and many have verbalized hopes that groundbreaking research will take place as a result of this strategic partnership.

Dr. Kenneth L. Davis, president and chief executive officer of the Mount Sinai Health System, said, “Together [Mount Sinai and Stony Brook] will use our outstanding resources to create changes in medicine.”

“Each institution has so much to offer,” said Stony Brook University President Samuel L. Stanley Jr., “this is an opportunity that will prove to be beneficial to all — now and in the future — as we explore and grow this incredible collaboration.”

Looking toward the future, Kaushansky said that Stony Brook has more affiliation agreements in the works, contingent upon state approval.

“We are working very hard with our friends in the state of New York to get approval for affiliation with Southampton Hospital and Eastern Long Island Hospital in Greenport,” he said.

Also pending is a potential partnership with John T. Mather Memorial Hospital in Port Jefferson. “In April, Mather Hospital asked a number of healthcare systems — us included — whether they were interested in affiliating with Mather Hospital, and we said yes,” Kaushansky said. “We made a proposal to the Mather hospital board … and they were supposed to decide [with whom they wish to affiliate] back in June.”

About a year ago, Kaushansky said he wondered aloud how it is that the insistution could make a bigger impact on clinical medicine, education and research. He now expresses confidence that Stony Brook’s affiliation with large city medical center, Mount Sinai, and future mutually-beneficial partnerships with Long Island hospitals and medical centers, is the most surefire way to achieve such an impact.

Most market tomatoes are recent varieties created in university and commercial farms since 1940. Stock photo

By Elof Axel Carlson

The tomato is botanically a fruit or more specifically a berry. We think of it as a vegetable because of its use in pasta sauces, soups and stews. The Supreme Court in 1893 ruled that for taxing and tariff purposes, it is a vegetable because of its usage in cooking.

The tomato belongs to the species Solanum lycopersicum. Thus, it belongs to a family of some 3,000 species worldwide. But tomatoes arose and were cultivated in the Andes and made their way to Mexico where they were domesticated. From there they were imported to Europe in the 15th century.

Because they are classified as members of the Solonaceae family, which includes the deadly nightshade, they were sometimes regarded as poisonous. But the domesticated tomato varieties began appearing in Spain, Italy and England and soon spread as far as China, which is now the world’s largest consumer and producer of tomatoes.

The tomato gets its name from the Aztec word “tomatl.” Until 1940 the domesticated tomatoes throughout the world came from the Mexican varieties the Spanish brought back in the late 1400s and early 1500s.

The tomato plant cell has a total of 24 chromosomes, and its pollen or ovules have a chromosome number of 12. Their genome was not worked out until 2009, and a comparative study of 360 varieties and species of tomatoes was published in 2014. The pre-1940 tomato varieties for food had very few of the mutant gene varieties found in the wild species in South America (less than 10 percent).

Thus, most market tomatoes are recent varieties created in university and commercial farms since 1940.

The farmers buy hybrid seed, and tomato seed companies make sure that their seeds are hybrid to keep farmers from planting crops from the tomatoes that are harvested. This was a policy first started by agribusiness for hybrid corn beginning in 1908.

The genomic analysis of tomatoes and their related species give an evolutionary history of tobacco, then peppers, then eggplants, then potatoes and finally tomatoes as the sequence of species emergence. The molecular insights into plant genomes, by sequencing their genes, have led to a controversial field of genetically modified foods.

One of the first was short lived. I remember buying “Flavr Savr” tomatoes in a supermarket in Setauket. The manufacturer had inserted a gene for delayed ripening and thus longer shelf life in stores. I could not tell any difference in taste or texture from those manufactured by inserting genes from other varieties of tomato plants.

Just as people in the 1500s feared tomatoes when first introduced into Europe as likely to be poisonous (they weren’t), the fear of genetically modified foods led to their quick demise in the market. Today it is almost impossible to buy foods (grains, vegetables, fruits, fish, fowl, or livestock) that are guaranteed to be free of genetic modification.

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

A boy looks through the Relativistic Heavy Ion Collider at Brookhaven National Lab during an event meant to examine the birth of the universe July 31. Photo from BNL

By Colm Ashe

Hundreds of North Shore residents gathered at Brookhaven National Laboratory in Upton July 31 for the last Summer Sunday of the season, a program which offers the public a chance to immerse themselves in the wide range of scientific endeavors that take place at the lab.

The final Summer Sunday’s events focused on a Relativistic Heavy Ion Collider. The RHIC is the modern culmination of an age-old inquiry into the origins of the universe and the only operating particle collider in the United States.

The day’s events gave the public a chance to witness the enormity of the project, a size measured not only in square mileage, but also in international collaborators. Thousands of scientists from all over the world, even those on opposite sides of warring nations, have been brought together by this quest to unlock the secrets of matter.

The RHIC re-creates an explosion similar to the one that created the universe. Photo from BNL
The RHIC re-creates an explosion similar to the one that created the universe. Photo from BNL

From the main control room, scientists at BNL send ions spinning around a 2.5-mile circular track and smash them together at a velocity close to the speed of light. When the ions collide, they create a small explosion that lasts for an extremely brief time span—one billionth of one billionth of one one millionth of a second.

During the explosion, scientists get a finite window into the birth of the universe, measuring one billionth of one millionth of a meter across. In order to study this small speck of short-lived matter, the remnants of these collisions are recorded in two detectors, STAR and PHENIX. This data is then examined by some of world’s top minds.

According to Physicist Paul Sorensen, this collision re-creates “the conditions of the early universe” so scientists can “study the force that holds together that matter as well as all of the matter that exists in the visible universe today.”

What is this force that binds the universe together? At the event, renowned physicist and deputy chair of BNL’s physics department Howard Gordon addressed this puzzling question. His lecture provided the audience some background on the history of this quest, as well as an update on the discovery of the elusive particle that started it all—the Higgs boson.

Though theories regarding the Higgs field — a field of energy presumed to give particles their mass — have been around since the 1960s, it took five decades to finally find the Higgs boson. As reported by TBR’s very own Daniel Dunaief, this “God particle” was finally discovered in 2012 at Geneva’s Large Hadron Collider, the world’s first ever particle accelerator.

This was the puzzle piece scientists worldwide had been counting on to validate their theory about the origins of matter. According to Gordon, “atoms, therefore life, would not form without the Higgs boson.”

Since this discovery, a vast global network of scientists and centers, including BNL, has been created to sift through the enormous amount of data generated by the Large Hadron Collider. The LHC produces enough data “to fill more than 1,000 one-terabyte hard drives — more than the information in all the world’s libraries,” according to theoretical physicist Lawrence M. Krauss.

After Gordon’s lecture, some of the most promising physicists in the U.S. led guests on a tour of the facilities which process this data, along with an up-close introduction to RHIC, STAR and PHENIX, all of which are undergoing maintenance this summer.

Gaofeng Fan
Gaofeng Fan at Cold Spring Harbor Laboratory. Photo by Siwei Zhang

The terror in the opening of the horror movie “When a Stranger Calls” comes when the police tell an anxious babysitter that threatening calls are “coming from inside the house.”

With the killer disease cancer, researchers spend considerable energy and time focusing on signals that might be coming from outside the cell. Many of those signals bind to a receptor in the membrane that corrupt a cell’s normal pathways, leading the cell to uncontrolled growth, the production of tumors or other unhealthy consequences.

Working in the laboratory of Nicholas Tonks, a professor at Cold Spring Harbor Laboratory, postdoctoral researcher Gaofeng Fan has spent over four and a half years studying a particular signal that comes from inside the cell. I

n a recent study published in Genes & Development, Fan demonstrated that a protein called FER, which adds a phosphate group to the inside part of a receptor called MET, plays a role in the ability of ovarian cancer to spread or metastasize. Already the target of drug development, MET is overexpressed in 60 percent of ovarian tumors. Thus far, developing drugs that block MET alone has not been particularly effective. Indeed, a humanized antibody that prevents human growth factor from binding to this receptor has shown “weak anti-tumor effect” in clinical trials, Fan suggested. In his research in cells, cultures and animal models, Fan demonstrated that ovarian cancer doesn’t spread and may have a different prognosis without FER.

“We found that the ligand [the human growth factor] is not necessary for the activation of the MET,” Fan said. “In the presence of FER, without the ligand, MET can be activated.” Understanding the role of FER in ovarian cancer may offer some clues about why only preventing signals from the outside aren’t enough to protect the cell. While Fan worked with ovarian cancer, he explained other scientists have shown that FER activation has been reported in lung, hepatic, prostate, breast and ovarian cancer. FER plays a part in cell motility and invasion, drug resistance and programmed cell death.

Fan’s work with FER started with a genetic experiment. Taking FER out of a cell, through a process called a loss-of-function assay, Fan found that the cell motility, or its ability to move, decreases. Once he took out FER, he also looked closely at MET activation. If the receptor required only human growth factor, which he included in his experiment, the removal of FER shouldn’t have any effect on its activity. “We found the opposite result,” Fan said.

Gaofeng Fan with his son Ruihan at Tall Ships America in Greenport in 2015. Photo by Xan Xu
Gaofeng Fan with his son Ruihan at Tall Ships America in Greenport in 2015. Photo by Xan Xu

A set of experiments with mice provided stronger evidence to support his belief that FER played a role in the spread of ovarian cancer. One of the mice had normal FER expression, while the other was missing the FER protein. When he compared the ability of cancer to metastasize, he found that cancer spread in a more limited way in the mice without the protein. “This confirmed the in vitro data and all the cell-based assays,” he said.

After six and a half years as a postdoctoral researcher, Fan is now looking for opportunities to teach and, perhaps, start his own lab in his native China. Fan hopes to continue to work on this system and would like to be a part of the discovery process that might find a small molecule inhibitor for FER. Once he and others find a FER inhibitor, they might be able to use it in combination with other drugs, including small molecules that inhibit human growth factor’s effect on the MET receptor.

Fewer than one in four women with Stage 3 ovarian cancer, which is typically the stage at which doctors find the disease, survive for five years.

Fan said he feels driven to help find a way to slow down the progression of this disease. “There’s an urgency to find a good, effective treatment.” To be sure, Fan cautioned that these studies, while encouraging and an important step in learning about ovarian cancer metastasis, require considerable work to become a part of any new treatment.

In his work, Fan was grateful for the support of Peter A. Greer, a principal investigator at the Cancer Research Institute at Queen’s University at Kingston in Ontario, Canada. Greer “is the leading scientist in research of FER proteins and he opened up all his toolbooks to me,” Fan said.

In an email, Greer described Fan as a “very gifted scientist with an outstanding training experience.” He hopes to “continue our collaboration in the area of ovarian cancer after [Fan] establishes his independent research program” in China. Greer, who spoke with Fan regularly through the process, said he is hopeful that the publication of the study in Genes & Development, in addition to other studies he and other labs have published, will “encourage drug development aimed at FER inhibitors suitable for clinical use.”

Fan also appreciated the guidance and flexibility of his CSHL mentor Nicholas Tonks, famous for his work on tyrosine phosphatase in which he studies the effect of removing phosphate groups. Fan’s research, however, involved understanding adding a phosphate group, through a kinase. “I got humongous support” from Tonks. “Without his help, I couldn’t come this far.”

A resident of Port Jefferson, Fan lives with his wife Yan Xu, who is earning her Ph.D. in materials science at Stony Brook. The couple has a six-year old son, Ruihan, who has enjoyed the Summer Sunday opportunities at Brookhaven National Laboratory, where Ruihan spent hours viewing and constructing the structure of DNA. As for his work, Fan sees opportunities to help people battling this disease.“If we can collect more evidence from this story, we can propose” a way to boost the outcome of treatment, he said.

Joanna Kiryluk during her trip to the South Pole in 2009. Photo from Joanna Kiryluk

By Daniel Dunaief

She traveled to a place she felt might have been as unfamiliar as visiting the moon or Mars. The project that is such a large part of her life is looking for signals sent from well beyond those relative celestial neighbors.

Joanna Kiryluk, an assistant professor of physics at Stony Brook University, didn’t travel off the planet, although she visited a remote location that was considerably different, less populated and at a higher altitude than the sandy beaches of Long Island. In 2009, Kiryluk traveled to the South Pole as a part of the aptly named IceCube project, which was completed in 2010. Kiryluk and hundreds of other physicists around the world are studying the information gathered from detectors drilled deep into the ice below the surface.

Kiryluk is studying tau and electron neutrinos, which are created as products of cosmic ray interactions and carry very high energies. Scientists do not know which sources in the universe are capable of creating such high energies. Unraveling this is one of her research goals. The neutrinos produced by collapsing stars, or supernova, typically have energies that are about a million times smaller than the high-energy neutrinos discovered by IceCube.

Neutrinos have very small masses and travel at speeds close to the speed of light, Kiryluk explained. Since they interact with matter weakly, they pass through most objects without any interactions. On rare occasions, however, these neutrinos collide with a neutron or a proton, causing a characteristic reaction that provides a clue about where they are, what energy they had when they collided, and, perhaps where they originated.

For her research, Kiryluk recently received the prestigious National Science Foundation Career Award, which provides almost $900,000 to support her work over the next five years. “It’s a great honor,” said Kiryluk. “The chances of success for such proposals are small and, in this sense, it was also a pleasant surprise.” Kiryluk said the funding will enable her to employ two graduate students per year. Part of the money will also be used for educational purposes and outreach. Kiryluk has reached out to high schools including Brentwood and Riverhead High School to involve students and teachers in research. Kiryluk is also a proponent of a Women in Science and Engineering program, or WISE, that encourages the “involvement of under-represented groups” in science, including women.

Kiryluk credits her Ph.D. advisor, Barbara Badelek, a professor at the University of Warsaw in the Department of Physics and a professor at Uppsala University, for believing in her and in her ability. She suggested that such support was critical to her success and her focus. Badelek met Kiryluk in 1994 and supervised her undergraduate and Ph.D. work. Kiryluk was “immediately recognized as a remarkably good student: hard working, trying to achieve a deep understanding of problems and very enthusiastic,” Badelek explained in an email. Badelek added that she is “very pleased to see her maturity and growing scientific prestige.”

In the IceCube project, Kiryluk is a part of an experiment that involves over 300 scientists from 48 institutions from around the world. IceCube, which took seven years to build, was manufactured as a discovery experiment to find high-energy neutrinos, which originate from astrophysical sources. People who have known Kiryluk for decades suggest that she has the right temperament for such an ambitious joint effort.

Kiryluk is “quiet and calm, but works hard and never leaves things because she finds some difficulties,” explained Ewa Rondio, the deputy director for scientific matters at the National Centre for Nuclear Research in Poland, who met Kiryluk when she was an undergraduate. Kiryluk’s goal is to measure the energy spectrum of these neutrinos. “We are interested in fluxes,” she said. These fluxes and energy spectra of high-energy neutrinos will provide insights in the sources and mechanisms of the most powerful accelerators in the universe.

A cubic kilometer of ice, IceCube, which has enough water to fill one million swimming pools, is large enough to capture more of these rare neutrino events. The key to unraveling what these signals indicate is to understand their energy and direction. The detectors don’t collect information from the neutrinos directly, but, rather from the interaction with particles in the ice. The neutrino interactions in ice produce a flash of light in the South Pole ice that the scientists measure with sensors. They study the pattern, the arrival times and the amplitude of this light at the sensors. This information can help determine the neutrino energy and direction.

Kiryluk is looking for high-energy events that are “most likely coming from outside of our galaxy,” she said. These particles are distributed all over the sky. While IceCube is capable of collecting data from the highest energy particles, it hasn’t yet gathered enough of these events to provide conclusive information at this range.

Kiryluk visited the South Pole for two weeks in 2009 before IceCube was finished. She was involved in the commissioning of the newly deployed detectors for the data acquisition system. The detectors are between 1,500 and 2,600 meters deep, which helps them “suppress any background events,” such as cosmic rays that are produced in the atmosphere. The facility is 3,000 meters high and has low humidity, which means it’s “easy to get dehydrated,” Kiryluk said. She described the working and living conditions at the South Pole as “modern.”

A native of eastern Poland, Kiryluk arrived on Long Island in 2001, when she worked at Brookhaven National Laboratory. She lives in Rocky Point. Kiryluk said the physics department is “growing.” Since her hire, nine assistant professors have joined the Department of Physics and Astronomy at Stony Brook University. As for her work, Kiryluk is inspired to understand how IceCube can be used as a “probe to study astronomy,” which enables her to be a part of the process of discovering “what is out there.”