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Experts share tips to enjoy the solar eclipse

by TBR Staff - August 18, 2017

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Solar-eclipse-glasses_nh-billingalls-4w — A boy wears protective glasses during a partial solar eclipse in 2014. Photo from nasa.gov

By Jill Webb

It won’t be an average Monday, Aug. 21, this year as the moon will completely block the sun for two-and-a-half minutes.

The day marks the first total solar eclipse to happen in North America since 1979, and it’s the first one to stretch from coast to coast in 99 years. In a total solar eclipse the disk of the moon seems to entirely cover the disk of the sun. This will happen Monday on a path about 70 miles wide.

Unfortunately, Long Island isn’t on the eclipse’s path of totality, but you still will be able to see a partial eclipse. New York will have about 71 percent of the sun covered during the eclipse. At 1:24 p.m. the eclipse begins on Long Island, and will last till 4:01 p.m. The peak eclipse time is 2:46 p.m.

“I think it’s wonderful for families to experience this with their children,” NASA expert Laurie Cantillo said. “It could be an experience like this that will get a child to stop looking at a phone or tablet and look up to the sky and perhaps motivate them to want to learn more.”

Fredrick Walters, an astronomy professor at Stony Brook University, has put together a list of ways to maximize your viewing experience of the eclipse. Walters said to focus on looking at the stars emerging during the daytime, the shadow bands that will appear across the land and the changing colors as the light fades.

Most importantly, you need to have the proper viewing tool: eclipse glasses. Regular sunglasses won’t cut it, and it’s very dangerous to directly expose your eyes to the sun.

“We’ve all been taught ever since we were kids don’t ever look directly at the sun and that advice applies,” Cantillo said. “The only time it’s safe to remove eclipse glasses is if you’re in the path of totality, during those couple minutes of totality.”

Unprotected viewing may not cause immediate pain, but Walters said he has heard of cases of people waking up the next morning with blurry vision or blindness. Some people can recover in months to years, but it’s not worth the risk.

North Shore solar eclipse events

Middle Country Public Library

2017 Solar Eclipse: Celestial Event of the Century

At its Centereach building, the library will be hosting a solar eclipse viewing between 1:15 and 3:45 p.m. Along with the viewing, activities and eclipse glasses will be provided for all ages. Register for the event by calling 631-585-9393.

Huntington Public Library

Astronomy Crafts

From noon to 2:00 p.m. Huntington Public Library will be offering an astronomy craft session at its main building as well as the Huntington Station branch. One of the space-themed crafts is an eclipse on a stick. There will also be a viewing event in the afternoon at both buildings where you will receive a free pair of eclipse glasses; no registration is required. For more information, visit www.thehuntingtonlibrary.org.

Long Island Science Center

Solar Eclipse Event

From 1 to 4 p.m. the Long Island Science Center will be hosting solar activities, live streaming and more. Planetarium presentations will happen at 1, 2 and 3 p.m. Admission is $10 and free for children 2 and under. For more information, visit www.lisciencecenter.org.

North Shore Public Library

Catch the Eclipse!

At 1:30 p.m. Tom Madigan of Suffolk County Community College, who is a part of Astronomy for Change, will give a brief presentation on solar eclipses before leading the event outside to view the solar eclipse. Eclipse glasses will be provided. Register for the event by calling 631-929-4488.

South Huntington Public Library

See the Solar Eclipse

Bring some snacks and a blanket to lay out on the lawn behind the library from 1:30 to 3:30 p.m. to witness the eclipse. The library will provide glasses (four per family) while supplies last. Inside, the eclipse will be live streamed from NASA in the library’s theater. Visit www.shpl.info for more information.

Maritime Explorium

Totality 2017 Solar Eclipse

Become a citizen scientist at the Maritime Explorium in Port Jefferson by attending a viewing from 1:30 to 3:30 p.m. and helping to crowd source data for researchers at NASA and EclipseMob. Eclipse glasses will be available while supplies last; no registration required. For more information, visit www.maritimeexplorium.org.

The professor said that these special glasses are basically pieces of Mylar foil shielding your eyes. The glasses should be from proper sources that are certified by testing organizations.

“If you have a pair of eclipse glasses and want to test them, put them on and look —not at the sun — but just look at bright lights and things.” Walters said. “If you can see anything, throw them away. You shouldn’t be able to see [anything] except the sun.”

If you can’t get a pair of eclipse glasses in time, you can DIY them by putting a small round hole in an index card and project the image of the sun onto a flat surface.

“One thing you will notice if you don’t look at the sun through your glasses is if you look at the shadows on the ground, you’ll see the shadows are crescent-shaped,” Walters said.

Leaves in the trees could act as projection tools too, casting multiple tiny crescent-shaped shadows on the ground.

During the partial phase, according to Walters, you won’t notice anything besides the sun getting dimmer.

“Unless, you look at the sun through your eclipse glasses, and you can see the sun is no longer circular — there’s a chunk taken out of it,” Walters said. “But, nothing much changes until you have the total phase of the eclipse because the sun just fades.”

Viewers along the path of totality will have a different viewing experience than Long Islanders.

“Inside the path of totality is completely different, it will be night for two and a half minutes.,” Walters said. “The sun gets completely blocked out, the corona of the sun is about as bright as the full moon, that will provide illumination.”

Walters also pointed out that in the path of totality, regular colors might appear different. Where sunrises and sunsets usually appear to have reddish tints, during the eclipse the tone will have a blue tinge. Another thing to notice is temperature; during the peak eclipse things will get colder.

Eclipses have provided researchers with data to uncover scientific discoveries. This time, the scientists are letting the public partake in their findings.

“One of the things that is being planned for next Monday is the National Solar Observatory and the National Science Foundation have handed out a number of telescopes [and] cameras to people along the eclipse line,” Walters said. “The idea is to have them take pictures and movies and stitch it all together to a 90-minute-long movie of how the sun’s corona is changing. This has never been done.”

If you miss this eclipse, don’t fret because another one is coming April 8, 2024, that will run from Texas through Maine — and upstate New York will be in the path of totality.

“It’s almost a mystical experience — you really have to experience this,” Walters said. “It’s good scientifically, but it’s really a great thing to observe on a human level.”

News 12 meteorologist Rich Hoffman said in an email that the weather forecast for Aug. 21 is good, even though things could change between press time and the eclipse. Hoffman said mostly sunny skies are expected for the day with temperature highs near 84.

Life Lines: Causality, coincidence and the unprovable coexist in our lives

by Elof Carlson - August 17, 2017

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By Elof Axel Carlson

We tend to generalize in making judgments about ourselves and others. Some claim they are self-made and promote their work ethic as the reason for their success. Some claim they are victims of circumstances over which they had limited control. Examples exist of people who have moved from rags to riches, and no one would blame victims of racial prejudice or the Holocaust for the misery they or their family members experienced.

In my own life I can think of many such events that have either made my life possible or significantly influenced it. My father told my brother and me that when his father was on a business trip from Stockholm, Sweden, to Hamburg, Germany, he was walking down a street when a German officer was walking directly toward him.

It was the custom there to step in the gutter to let a military officer have the right of way. My grandfather felt no such sense of obligation and felt his side of the road was appropriate for continuing his walk. The officer pulled out his sword and slapped my father’s face with it. The insult made him a pacifist, and that outlook was passed on to my father and to me. It also made him shorten his trip, and he went to Normandy to visit friends and relatives who had a summer house near the Baltic Sea.

There he met the young woman he eventually married, my grandmother, Amanda, who lived near Göteborg. I can say that I owe my existence to a slap in the face. My parents, too, met in a strange circumstance.

My mother was selling key rings on Broadway in Manhattan on a cold winter day. She entered a hotel entrance on 75th street to warm up, and the doorman told her to go downstairs to warm up in the employee’s room. There she met a Swedish elevator operator who was changing out of his uniform to go home. He took her to dinner and that began the courtship of my parents. I could say I owe my existence to a sympathetic doorman who felt compassion on a woman down on her luck.

When I was a graduate student at Indiana University, I met my wife Nedra, also by a curious circumstance. I had written letters to my parents and friends and lacked 3-cent stamps to mail them. I asked around and was told there was a girl who may have stamps who was usually working in a laboratory the floor above me. I knocked on the door and met a nervous undergraduate who did have stamps and I invited her to tea. When she did not come, I brought the tea to her. That was our first day of courtship. I could say that I owe my marriage to Nedra to a 3-cent stamp.

I do not doubt that such chance events play major roles in our lives. But most of our lives are under our control and shaped by habits and circumstances. We do not choose our partners randomly. Assortative mating is influenced by religion, race, ethnicity, social class, education, looks, personality and many other features that steer us toward or away from possible partners. Before the 20th century most marriages were arranged or required parental approval.

But it is not just social factors that determine how we come into this world. Each act of intercourse involves tens of millions of sperm. The odds of the one that made you on a particular day were not predictable when that sperm was in a testis or when it made its initial way to the cervix of the uterus and eventually to the oviduct where it would meet the egg that formed you.

That is quite a contrast to the injection of single sperm into an egg during a form of in vitro fertilization (IVF) used by infertile couples where the sperm has problems wiggling its tail or having the right surface proteins to recognize it is encountering an egg. In that case we get the paradoxical conclusion that the child born by the IVF procedure owes its existence to the father being sterile!

Life is filled with rare events, the overwhelming number of them not even being recognized as significant in our lives. At the same time society is so organized that much of what we do is planned and anticipated and goes essentially as we hoped it would.

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

Nikola Tesla exhibit in Stony Brook Village is electrifying

by TBR Staff - August 8, 2017

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Exhibit showcases the brilliance of the Serbian American inventor

By Kevin Redding

Asked in 1927 about not getting the proper recognition for inventing radio among other uncredited scientific achievements, Nikola Tesla said, “Let the future tell the truth and evaluate each one according to his work and accomplishments … the present is theirs; the future, for which I really worked, is mine.”

Ninety years later, not only is the truth out about the greatness of the Serbian American inventor — whose long list of contributions to modern science includes the alternating current motor, the electric motor, wireless communication, X-rays, the remote control, and, yes, radio — his work is utilized everywhere we go.

And now it is celebrated every day in Stony Brook Village for the rest of the summer. Residents far and wide are invited to explore the radical genius of Tesla in a new exhibit at Ward Melville Heritage Organization’s Educational & Cultural Center titled Nikola Tesla: Past, Present, Future. Visitors can immerse themselves in the life and inventions of the man who electrified history, powered the present and continues to shape the future.

On view through Sept. 4, the exhibit was designed by board members within the nonprofit Tesla Science Center at Wardenclyffe in Shoreham, where Tesla’s last remaining laboratory stands and features a litany of displays such as an operating replica of the famous Tesla coil, augmented reality technology and a signed Tesla Roadster off the Tesla Motors assembly line.

Buzzing sounds of electricity, dramatic music and compelling narration of Tesla’s life pervade throughout the large room, where kids, teens, adults and seniors have enjoyed since July 8 interactive kiosks, screens showing in-depth documentaries, biographical banners, models and more.

“There’s a real desire on the public’s part to learn more about him because he’s an unsung American and international scientific hero,” said David Madigan, the Tesla Science Center board member who was tasked with bringing the exhibit to life. “He’s also the name that most people don’t know, and yet he’s one of the most influential scientists of the 20th century. It’s very important that the public supports it.”

Back in March, Ward Melville Heritage Organization President Gloria Rocchio approached Madigan and other members of the Tesla board and asked them to take up the exhibit space for the summer as a way to give the nonprofit visibility and promote their cause. (The Tesla Science Center is in the process of raising funds to open its doors to the public next year.)

Board Director Marc Alessi and Madigan took on the challenge, seeing the exhibit as a mini version of what will ultimately be their expansive Visitor’s Center, which will serve as the site’s main focus until the museum is in operation — the group needs a minimum amount of $20 million to open it.

“We made a decision as an organization that this would force us to put together an exhibit and start collecting the necessary materials; we’re going to need to put items into our building when we open next year so why not get started now?” Alessi said during a recent tour. “I think people are getting a bit of a taste of what this will be and this is just one pillar of what the Tesla Science Center will eventually be.”

But filling the exhibit room was no easy feat, as the two would learn. “It was a huge and heavy lift for us because I wasn’t aware of what we might have on hand in storage,” Alessi said. “I knew we had some donations, but did we really have enough material for an exhibit this size? At the time, we didn’t.”

Madigan quickly got on the horn with everyone he knew would want to contribute to a Tesla-centric space, which, luckily for him, ended up being a lot of impassioned people. In two months, the exhibit bursted with life.

Banners were brought in from the Tesla Science Foundation in Philadelphia and Belgrade, Serbia, and a Rocky Point artisan named Rob Arnold built a replica of Tesla’s teleautomaton — the first ever remote-controlled boat that Tesla premiered at Madison Square Garden’s Electrical Exhibition in 1898. Local filmmaker Joseph Sikorski, who made the documentaries “Fragments from Olympus: The Vision of Nikola Tesla” and “Tower to the People” about the history and preservation of Wardenclyffe, set up the exhibit’s kiosks and even donated his model of Tesla’s laboratory used in many of his films.

Nan Guzzetta of Antique Costumes & Prop Rental in Port Jefferson submitted Tesla-period wardrobe to be displayed; neon sculptor Clayton Orehek created a spectacular portrait of Tesla as well as a coil-inspired design of the inventor’s signature; and Richard Matthias of Hot Springs, Arkansas, built and donated a Jacob’s ladder display and the replica of the Tesla coil — which visitors are able to charge with the help of neon glass tubes.

Next to the Tesla Roadster in the corner of the room sits a 3D hands-on exhibit brought in by the National Museum of Mathematics in New York City that allows people to manipulate the magnetic field on which the Tesla induction motor is based.

“We found it all very inspiring,” Madigan said of the support. “Everywhere we go with this, it’s not us, it’s Nikola Tesla that is fascinating to people. We wanted to put together an illustrative exhibit that would help educate the public as to exactly who this man was and how he contributed to society, and continues to. You can’t talk about Tesla in the past without talking about the future.”

Madigan demonstrated in the exhibit what’s called the Nikola Tesla augmented reality app, designed by Brian Yetzer of Philadelphia, that superimposes a 3D animation of a Tesla-related image over something in the room with a quick scan of a phone. Upon scanning over a banner, a film of Tesla played on the phone screen.

Bill Pagels and Sue Ann Wilkinson of Salt Lake City, Utah, made sure to go to the exhibit during a recent vacation to the area. Both of them waved neon glass tubes and watched in amazement as the Tesla coil erupted with electricity. “We know [Tesla’s] a towering giant,” Pagels said. “But we didn’t know the extent to which his inventions resulted in something we would be carrying around in our pockets, or the range of technology he invented. It’s fascinating to understand the depth of his impact on humanity and, frankly, that he was such a humanitarian. It’s really quite amazing.”

Looking around the active room, Alessi said, “For us, it’s remarkable that this was pulled together the way it was over the course of a few months and we’re grateful Ward Melville gave us this opportunity. Having them help us with this first exhibit is remarkable and we’re seeing the benefit, we’re seeing local profile raised as a result.”

Gene editing conference a big draw at CSHL

by Daniel Dunaief - August 8, 2017

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cshlcrisprorganizers — Organizers of the 3rd annual Genome Engineering: The CRISPR-Cas Revolution event, from left, Maria Jasin, Jonathan Weissman, Jennifer Doudna and Stanley Qi. Photo courtesy of CSHL

By Daniel Dunaief

One day, the tool 375 people from 29 countries came to discuss in late July at Cold Spring Harbor Laboratory may help eradicate malaria, develop treatments for cancer and help understand the role various proteins play in turning on and off genes.

Eager to interact with colleagues about the technical advances and challenges, medical applications and model organisms, the participants in Cold Spring Harbor Laboratory’s third meeting on the CRISPR-Cas9 gene editing system filled the seats at Grace Auditorium.

“It’s amazing all the ways that people are pushing the envelope with CRISPR-Cas9 technology,” said Jason Sheltzer, an independent fellow from Cold Spring Harbor Laboratory who presented his research on a breast cancer treatment.

The technology comes from a close study of the battle between bacteria and viruses. Constantly under assault from viruses bent on commandeering their genetic machinery, bacteria figured out a way of developing a memory of viruses, sending out enzymes that recognize and destroy familiar invaders.

By tapping into this evolutionary machinery, scientists have found that this system not only recognizes genes but can also be used to slice out and replace an errant code.

“This is a rapidly evolving field and we continue to see new research such as how Cas1 and Cas2 recognize their target, which opens the door for modification of the proteins themselves, and the recent discovery of anti-CRISPR proteins that decrease off-target effects by as much as a factor of four,” explained Jennifer Doudna, professor of chemistry and molecular and cell biology at the University of California at Berkeley and a meeting organizer for the last three years, in an email.

Austin Burt, a professor of evolutionary genetics at the Imperial College in London, has been working on ways to alter the genes of malaria-carrying mosquitoes, which cause over 430,000 deaths each year, primarily in Africa.

“To wipe out malaria would be a huge deal,” Bruce Conklin, a professor and senior investigator at the Gladstone Institute of Cardiovascular Disease at the University of California in San Francisco and a presenter at the conference, said in an interview. “It’s killed millions of people.”

Carolyn Brokowski. Photo by Eugene Brokowski

This approach is a part of an international effort called Target Malaria, which received support from the Bill and Melinda Gates Foundation.

To be sure, this effort needs considerable testing before scientists bring it to the field. “It is a promising approach but we must be mindful of the unintended consequences of altering species and impacting ecosystems,” Doudna cautioned.

In an email, Burt suggested that deploying CRISPR in mosquitoes across a country was “at least 10 years” away.

CSHL’s Sheltzer, meanwhile, used CRISPR to show that a drug treatment for breast cancer isn’t working as scientists had thought. Researchers believed a drug that inhibited the function of a protein called maternal embryonic leucine zipper kinase, or MELK, was halting the spread of cancer. When Sheltzer knocked out the gene for MELK, however, he discovered that breast cancer continued to grow or divide. While this doesn’t invalidate a drug that may be effective in halting cancer, it suggests that the mechanism researchers believed was involved was inaccurate.

Researchers recognize an array of unanswered questions. “It’s premature to tell just how predictable genome modification might be at certain levels in development and in certain kinds of diseases,” said Carolyn Brokowski, a bioethicist who will begin a position as research associate in the Emergency Medicine Department at the Yale School of Medicine next week. “In many cases, there is considerable uncertainty about the causal relationship between gene expression and modification.”

Brokowski suggested that policy makers need to appreciate the “serious reasons to consider limitations on nontherapeutic uses for CRISPR.”

Like so many other technologies, CRISPR presents opportunities to benefit mankind and to cause destruction. “We can’t be blind to the conditions in which we live,” said Brokowski.

Indeed, Doudna recently was one of seven recipients of a $65 million Defense Advanced Research Projects Agency award to improve the safety and accuracy of gene editing.

The funding, which is for $65 million over four years, supports a greater understanding of how gene editing technologies work and monitors health and security concerns for their intentional or accidental misuse. Doudna, who is credited with co-creating the CRISPR-Cas9 system with Emmanuelle Charpentier a scientific member and director of the Max Planck Institute for Infection Biology in Berlin, will explore safe gene editing tools to use in animal models and will specifically target Zika and Ebola viruses.

“Like most misunderstood disruptive technologies, CRISPR outpaced the necessary policy and regulatory discussions,” Doudna explained. The scientific community, however, “continued to advance the technology in a transparent manner, helping to build public awareness, trust and dialogue. As a result, CRISPR is becoming a mainstream topic and the public understanding that it can be a beneficial tool to help solve some of our most important challenges continues to grow.”

Visitors enjoyed a wine and cheese party on the Airslie lawn during the event. Photo from CSHL

Cold Spring Harbor Laboratory plans to host its fourth CRISPR meeting next August, when many of the same scientists hope to return. “It’s great that you can see how the field and scientific community as a whole is evolving,” Sheltzer said.

Doudna appreciates the history of Cold Spring Harbor Laboratory, including her own experiences. As a graduate student in 1987, Doudna came across an unassuming woman walking the campus in a tee-shirt: Nobel Prize winner Barbara McClintock. “I thought, ‘Oh my gosh, this is someone I revere,” Doudna recalled. “That’s what life is like” at the lab.

Brokowski also plans to attend the conference next year. “I’m very interested in learning about all the promises CRISPR will offer,” she said. She is curious to see “whether there might be more discussion about ethical and regulatory aspects of this technology.”

Brookhaven boasts new green initiatives

by TBR Staff - August 7, 2017

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Romaine-Panico-compostw — Brookhaven Town Supervisor Ed Romaine and Councilman Dan Panico, on left, with the new food scrap composters. Photo from Town of Brookhaven

As far as the Town of Brookhaven is concerned, going green is not just a casual practice — it’s a moral obligation to ensure Long Island’s future.

In the last few months, Supervisor Ed Romaine (R) and members of the town board have launched a series of environmentally friendly initiatives and continued ongoing efforts that encourage local residents to
reduce their carbon footprints and preserve the serenity of their surroundings.

“Whenever there are ways to benefit the environment, I’m 100 percent involved [and] I’m blessed by an extremely supportive town board,” Romaine said, highlighting an especially strong partnership with Councilwoman Jane Bonner (C-Rocky Point). “I don’t want to say Jane is my environmental soulmate, but she and I are on the exact same page. She is one of my cheerleaders in every manner, shape or form.”

Other environmental actions taken by Brookhaven:

– A 127-acre solar farm called Shoreham Solar Commons will be constructed on the recently closed Tallgrass Golf Course.

– The extension of the Pine Barrens to include 800 acres of national property around the former Shoreham nuclear plant will go forward upon Gov. Andrew Cuomo’s (D) signed authorization.

– A multiyear project to convert all 40,000 of Brookhaven’s streetlights to LED bulbs has begun with 5,000 already converted.

– Through a partnership with U.S Rep. Lee Zeldin (R-Shirley) and the Federal Emergency Management Agency, the town has secured funding to fix stormwater infrastructures along the North Shore, from Miller Place to Shoreham.

– A center at Ceder Beach in Mount Sinai has been established to grow millions of oysters and sea clams that filter and clean the water.

In May, Bonner held her fifth bi-annual Go Green event at the Rose Caracappa Senior Center in Mount Sinai. It’s the town’s biggest recycling event where residents can dispose of unwanted medication and prescriptions and recycle old TVs and computers, as well as paper. The e-waste drive gathered 15,000 pounds of electronic waste and shredded 13,580 pounds of paper products and 26 boxes of unwanted pharmaceutical drugs, according to the town.

The councilwoman also hosted a Homeowner’s Guide to Energy Efficiency forum at the center later in the month, educating residents on how to get a free energy audit, affordable home energy improvements and save $1,000 a year on home energy bills. Through this effort, less fossil fuels are used to heat and light homes.

“We take it very seriously,” Bonner said of the town’s green initiatives. “We have a moral obligation to be good stewards of the Earth and this transcends party lines. Regardless of party affiliation, we all know we can do a better job of taking care of the planet.”

Aside from providing free compost and mulch to residents at Brookhaven Town Hall, officials also recently utilized a $5,000 grant to rip up the back lawn of the property to plant and restore native Long Island grasses, from which seeds can be collected and used.

In June, the town officially authorized the nonprofit Art & Nature Group Inc. to transform Brookhaven’s historic Washington Lodge property into a community nature center that offers environmental education programs.

Romaine and Councilman Dan Panico (R-Manorville) organized Brookhaven’s Food Scrap Composting pilot program at town hall last month, with hopes to expand it as a townwide initiative.

Through the program, town employees can deposit food waste, such as banana peels and coffee grinds, into organic material collection containers placed throughout the buildings, which are then collected and composted to be used for garden beds around town buildings.

“We must provide alternative waste management solutions like these if we are going to provide a cleaner, greener earth for future generations,” Panico said in a statement.

CSHL’s Alexander Krasnitz part of early cancer detection team

by Daniel Dunaief - July 25, 2017

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krasnitzcshlheadshot — Alexander Krasnitz. Photo from CSHL

By Daniel Dunaief

If homeowners could find insects in their home, confirm that they were termites and locate nests before the termites damaged a house, they’d save themselves numerous problems. The same holds true for cancer.

Using the latest molecular biology techniques, researchers at Cold Spring Harbor Laboratory including Associate Professor Alexander Krasnitz and Professor Michael Wigler have explored ways to detect cancer earlier.

Unlike other scientists, who have created tests that reveal the genetic probability of developing cancer, Krasnitz and Wigler developed a blood test to reveal the presence of a tumor that might be hard to spot. Such a test could be particularly valuable for cancers such as ovarian and pancreatic cancer, which can be inoperable by the time they present clinical symptoms.

Urging what Wigler described as a “call to arms,” Krasnitz said they created a blood test, called copy number variation, that they hope will be economically feasible. In copy number variation, sections of genes are repeated. While healthy cells have copy number variation, cancer cells use them like a Jack Nicholson mantra in “The Shining,” where the repetition of “all work and no play makes Jack a dull boy” becomes a calling card for a killing spree.

In cancer, chromosomes or chromosome arms are duplicated or deleted. Sometimes, a narrow region of the genome undergoes amplification, creating multiple copies of the region. Other times, a region of the genome may be lost. Genome-wide copy number variation is a hallmark of cancer. Copy number variation occurs often amid the disruption of DNA repair mechanisms and the breakdown in the way DNA separates into daughter cells during division.

In a recent article in Trends in Molecular Medicine, Krasnitz, Jude Kendall, Joan Alexander, Dan Levy and Wigler — all scientists at CSHL — suggest the potential for single-cell genomic analysis that searches for the presence of copy number variations could raise the alert level for cancer, signaling the need to search more closely for developing tumors.

In most massive cancers in the population, including breast, ovarian and prostate cancer, copy number variation is “ubiquitous,” Krasnitz said. Screening for these changes could provide “evidence for the presence of something abnormal,” which can be validated through other tests, Krasnitz said.

Copy number variation, on its own, is not sufficient to detect cancer, Krasnitz said. Researchers need evidence of similar abnormal copy number profiles in multiple cells. For this test to have clinical relevance, it would need to minimize false positives, which could create alarm and lead to future tests that might not be warranted, while also avoiding false negatives, which would miss the presence of cancer.

The main sources of false positives could come from copy number variation that’s already in cells in the blood that randomly look like a tumor. Cells with partially degraded DNA can have high copy number variation, which the researchers have observed. These profiles, however, arise from random processes and typically look different from each other. Cells from a cancer clone, however, have similar copy number profile.

Cancers with low copy number variation were a minority among the 11 cancers the scientists studied and include a type of colorectal cancer called microsatellite-unstable. If these CSHL researchers developed a preclinical test, they would look for additional ways to detect such cancers.

While numerous technological innovations required for the test exist, including copy number profiling of single cells and methods to enrich specimens from blood for suspected tumors, Krasnitz explained that considerable work remains before its clinical use, including establishing tumor cell counts in the blood of early patients, making single-cell profiling cheaper and finding optimal ways to identify the tissue of origin.

They are planning to study newly diagnosed patients to observe the presence of circulating cells from tumors. Once the scientists prove that the test has some predictive value, they need to ensure that it is economical and that they can follow up with patients to find tumors.

At this point, it’s unclear what the presence of copy number variation might reveal about the type of tumor, which could be a slowly growing or an aggressive type. Additionally, an abnormal indication from this type of analysis wouldn’t reveal anything about the type of cancer. Further tests, including on RNA, would help direct doctors to a specific organ or system.

Apart from his work with Wigler, Krasnitz also has numerous collaborations, including one with CSHL Cancer Center Director David Tuveson.

In his work with Tuveson, Krasnitz is ensuring that the organoid models Tuveson’s lab creates, which are living replicas of tumors taken from patients, faithfully reflect the genetic make up of the tumors. That, Tuveson said, is a significant undertaking because it can validate the organoid model for exploring the biology of tumors.

“This is a deliverable that many people are waiting for,” Tuveson said. The researchers want to make sure “what we grew is what the patient had in the first place.” So far, Tuveson said, the data looks good and the scientists don’t have any examples of the genetics of the organoids differing from that of the tumor.

Krasnitz also attempts to predict an organoid’s response to drugs that haven’t been tested yet based on the organoid’s reaction to other drugs. Tuveson reached out to Krasnitz to work with his group. He said Krasnitz is “a major player” and is “very skilled” in the type of analysis of big data his group generates through the genome, the transcriptome and drug screens. “He’s able to look at those three types of information and make sense of it,” Tuveson said.

Krasnitz is grateful for the support of the Simons Foundation, the National Institutes of Health and the Breast Cancer Research Foundation for his work with Wigler. The most recent article with Wigler is an “invitation for the [research] community to join in the effort,” Krasnitz said. “We want collaborators and more competition in this area.”

Vanderbilt Planetarium opens two new shows

by Heidi Sutton - July 14, 2017

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The Suffolk County Vanderbilt Reichert Planetarium, 180 Little Neck Road, Centerport has premiered two intriguing new shows for the summer and brought back a popular show.

New on the playbill is Sunstruck! during which visitors can travel back in time to experience the birth of our sun and solar system. Discover how the sun came to support life, how it threatens life as we know it and how its energy will one day fade away. Show runs Tuesdays through Sundays at 3 p.m. through Sept. 3.

Also new this summer is Laser U2. Enjoy the classics and modern hits of the band U2, one of the greatest bands of the last three decades. This concert is set against a backdrop of the latest laser art. Your eyes and ears will be your guides into an immersive journey through this British band’s rise and success. Show runs on Friday and Saturday nights at 10 p.m. through Sept. 3.

Finally, back by popular demand is Pink Floyd: The Wall. Based on the 1979 album of the same name, this is the tale of the rock star named Pink Floyd and his downward spiral into madness. This gripping and spellbinding musical journey is beautiful, haunting, powerful and thought provoking. Show runs on Saturday nights at 9 p.m. through Sept. 3.

Tickets for the daytime shows are $13 adults, $12 seniors and students, $9 children. (This price includes required general admission fee.) Tickets for the evening shows are $10 adults, $9 seniors and students, $8 children ages 12 and under. For further information, please call 631-854-5579 or visit www.vanderbiltmuseum.org.

SBU’s Boon finds alternative signal to break up bacteria party

by Daniel Dunaief - July 14, 2017

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boonSBlaboutside — 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.

Super-charged celebration honors Nikola Tesla

by TBR Staff - July 11, 2017

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Electric Dream Expo at Tesla Science Center in Shoreham brings hundreds

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It’s no shock that the legacy of Nikola Tesla, the man responsible for alternating current electricity, resonates so profoundly in Shoreham, given it’s where the Serbian-American inventor’s last remaining laboratory sits.

So in honor of his 161st birthday, more than 600 residents of all ages and from all over the map journeyed to the historic Shoreham site, the Tesla Science Center at Wardenclyffe, for a supercharged celebration of the prolific pioneer.

Under sunny skies Saturday, July 8, the center kicked off its Electric Dream Expo, an all-afternoon event for all things Tesla-inspired.

From interactive exhibits of 3-D printers, high school robotics and old ham radios to demonstrations of the Tesla coil and Tesla-oriented augmented reality, to science-based activities for kids, the event carried a theme of technological innovation of the past, present and future.

“We’re just so thrilled to see so many people are interested and incredibly humbled knowing what Tesla represents to people.”

— Jane Alcorn

Vibrant Tesla cars were also on display throughout the grounds with raffles for 24-hour test drives available to the public. A Tesla impersonator, in full Victorian-era garb, walked around the premises and was photographed with attendees.

The grand event was even broadcast live to more than 50,000 people on Facebook with the help of a hovering drone.

While the center has held birthday celebrations for Tesla in the past, this one was the biggest yet and was also in acknowledgement of the 100th anniversary of the dismantling of his legendary and ahead-of-its-time wireless transmitting tower, which sat on the Shoreham property before being torn down July 4, 1917.

“It seemed important that we do something with a little more bang,” Jane Alcorn, Tesla Science Center board president said of this year’s event, the funds from which would go toward the development of the long-awaited Tesla museum and science center in the laboratory. “It’s exhilarating and humbling. We’re just so thrilled to see so many people are interested, and incredibly humbled knowing what Tesla represents to people.”

Dozens of vendors, including Brookhaven National Lab, North Shore Public Library, Museum of Interesting Things, Custer Institute & Observatory and Long Island Radio & TV Historical Society, set up at tables as people wearing Tesla shirts and pins browsed and bonded over their shared interest in the man who paved the way for several modern gadgets like cellphones. TVs and radios.

“He’s the father of just about everything we use … the hero of modern science,” Manorville resident and longtime Tesla researcher Axel Wicks said.

“He’s the father of just about everything we use … the hero of modern science.”

— Axel Wicks

Rachel Zyats, of Rocky Point, said she was excited that Tesla was finally getting the credit he deserved, as somebody who was greatly overshadowed by rival Thomas Edison

“Tesla was the real inventor,” Zyats said. “I think it’s great that more people are starting to learn about [him].”

Lynbrook mother Leeanne Chiulli and her 11-year-old daughter Kate, wearing a T-shirt with the slogan, “Never underestimate a woman who loves Nikola Tesla,” said the creator is their idol. James Angell, a retired engineer from Commack, pointed to Tesla as a hero in the field of science.

“Tesla is one of the greatest geniuses in the last 100 years in engineering and electrical theory,” Angell said, noting his early development of quantum mechanics. “One hundred years before anyone started talking about it today, Tesla was talking about it. [He] had a concept years and years before anyone thought of it. [So] it’s very encouraging to see so many people who now have an interest in Tesla and his inventions.”

Standing at one of the booths was Joseph Sikorski, a Babylon-based filmmaker who made a documentary entitled “Tower to the People” about the history of Wardenclyffe and Tesla’s accomplishments there.

“Tesla is a great unifier and it’s awesome to see him opening a lot of doors for people of all types,” he said.

Several speakers took to the podium in front of the historic brick building where Tesla built his laboratory in 1901 with the help of renowned architect Stanford White.

“[He] had a concept years and years before anyone thought of it. [So] it’s very encouraging to see so many people who now have an interest in Tesla and his inventions.”

— James Angell

William Terbo, Tesla’s grandnephew, was also in attendance, recounting memories of his great-uncle.

With Suffolk County Legislator Sarah Anker (D-Mount Sinai) alongside, Brookhaven Town Supervisor Ed Romaine (R) presented Alcorn and Marc Alessi, executive director, with a proclamation for their work in keeping Tesla’s legacy alive. “Long live Tesla, long live ideas, long live science,” Romaine said.

At the end of the ceremony, young Kyle Driebeek, of Connecticut, performed “America the Beautiful” and “Happy Birthday” on the theremin, a Russian electronic instrument played without physical contact. Tesla-decorated birthday cake was also served.

Rock Brynner, professor, author and son of famous actor Yul, read Tesla-related excerpts from his book about the New York Power Authority’s origins and expressed his joy in seeing so many people in attendance.

“I expected to see maybe three kids and a sullen nanny, and instead there’s this enormously enthusiastic crowd … it’s wonderful,” Brynner said. “In the 1930s, a journalist asked Albert Einstein what it was like to be the most brilliant genius in the world and Einstein replied, ‘I don’t know, you’ll have to ask Nikola Tesla.’ I urge all of you to learn more about Tesla. His story is enthralling and tragic, beautiful and terribly moving.”

BNL’s Yager turns nuisances into opportunities

by Daniel Dunaief - July 7, 2017

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bnlyagerlab-2 — 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.

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Page 58 of 71

Experts share tips to enjoy the solar eclipse

Life Lines: Causality, coincidence and the unprovable coexist in our lives

Nikola Tesla exhibit in Stony Brook Village is electrifying

Exhibit showcases the brilliance of the Serbian American inventor

Gene editing conference a big draw at CSHL

Brookhaven boasts new green initiatives

CSHL’s Alexander Krasnitz part of early cancer detection team

Vanderbilt Planetarium opens two new shows

SBU’s Boon finds alternative signal to break up bacteria party

Super-charged celebration honors Nikola Tesla

BNL’s Yager turns nuisances into opportunities

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