Reliving the year in scientific discoveries

From finding prehistoric groundhog-like creatures to fostering mutations that help tomato plants produce more fruit to doubling the understanding of what causes a proton to spin, scientists on Long Island, working with teams from around the world, had a busy, productive and, in some cases, lucky year in 2014.

Experts from all three local institutions made waves well beyond their scientific peers, as their papers in Science, Nature to the Proceedings of the National Academy of Sciences generated headlines around the world.

While the researchers at Stony Brook University, Brookhaven National Laboratory and Cold Spring Harbor Laboratory answered important questions in their fields, they consider the achievements of the past year a starting point for the next set of questions, experiments and opportunities.

Times Beacon Record Newspapers will take a look back at the remarkable achievements, findings researchers working in our communities enjoyed in 2014.

Stony Brook
A long time ago on an island far, far away, a 20-pound mammal walked with dinosaurs, including the carnivorous 2,400-pound Majungasaurus. This mammal, which is much larger than the mammals that were mostly the size of shrews and rats at that time, was hidden in a 150-pound slab of sandstone for over 66 million years in Madagascar. That is, until David Krause, a distinguished service professor in the Department of Anatomical Sciences, and his graduate students brought back the creature.
Krause was fishing through the block for, well, fossil fish, but instead stared into the face of an unknown chapter in ancient history. Removing one grain of sand at a time, Krause and his colleagues spent six months extricating the extraordinary find. They named the mammal Vintana sertichi. Vintana comes from the Malagasy word for “luck,” because they had no idea what awaited them in the heavy rock. “It’s good to have strong graduate students,” Krause said.
On the same island nation of Madagascar, Patricia Wright had a year that would make the lemurs she studies and considers her extended family howl. Only two years after opening a state-of-the-art, five-story research facility called Namanabe Hall on the boundary of Ranomafana National Park, Wright and her research were featured in an Imax movie called “Island of Lemurs: Madagascar.” As if that weren’t enough, Wright became the first female scientist to win the top award in conservation: the Indianapolis Prize, which included a $250,000 cash gift.
Meanwhile, ecologist Heather Lynch used satellite images to study penguin poop in Antarctica. Lynch and Michelle LaRue from the University of Minnesota estimated that the population of Adelie penguins was considerably larger than expected. While some conservationists suggested such a result might run counter to concerns raised by global warming, Lynch said the story was more complicated than the overall number, with groups declining in some areas and increasing in others.
Studying temperatures that would make those in the Antarctic seem balmy by comparison, researchers in the Department of Physics and Astronomy sought to understand properties of metallic materials as they approached absolute zero. Liusuo Wu, a doctoral student, Moosung Kim and Keeseong Park worked with Professor Meigan Aronson to explore the start of ferromagnetism, which is the same property in electrical motors or refrigerator magnets, in a specially made iron compound near this extremely cold temperature.
Exploring the quantum phase transition allows researchers to predict and possibly boost the performance of new materials in practical ways that had previously been theoretical, explained Brookhaven Lab physicist Alexei Tsvelik, a co-author on the study.
Looking at how life copies itself on the genetic scale, Huilin Li, a professor of biochemistry and cell biology at Stony Brook and a biologist at BNL, teamed up with researchers from BNL and Cold Spring Harbor Laboratory. The group found structural details of an enzyme that unzips and splits the double helical DNA into two halves. This, Li explained, may help researchers explore how that process can go wrong and may one day lead to new treatments that stall or break runaway genetic machinery. The findings came from a close collaboration with lead author Jingchuan Sun at BNL, Bruce Stillman at CSHL and Christian Speck at Imperial College, London.

Cold Spring Harbor Laboratory
At CSHL, scientists made strides in gathering information about human diseases, like schizophrenia, Alzheimer’s and cancer. They also developed a new genetic toolkit for growing more productive tomato plants.
Looking at de novo mutations in a broader range of diagnoses, including schizophrenia, autism and intellectual disabilities, W. Richard McCombie and Shane McCarthy found overlapping genes. Some of these genes are involved in reading, writing and editing chemical marks on DNA and proteins that help control when specific genes are switched on or off. It is possible, a group that includes professor Aiden Corvin of Trinity College speculates, that the genes that affect the same biological function in some disorders are examples of those that contribute to normal brain development.
Associate Professor Bo Li, meanwhile, helped identify neurons that actively participate in fear conditioning. By studying a group of long-range neurons that extend from the central amygdala to an area of the brainstem called the midbrain periaqueductal gray in an animal model, he discovered a neural circuit that connects the site of fear memory with a part of the brainstem that controls behavior. His work could have applications to models of post-traumatic stress disorder.
Also studying the brain, Associate Professor Adam Kepecs asked rats how confident they were in their decisions. Designing experiments that required rodents to wait for a reward, Kepecs was able to show that a part of the brain called the orbitofrontal cortex plays a role in confidence and decision making. Animals with a blocked orbitofrontal cortex made decisions just as effectively, but their confidence, even with incorrect choices, remained high even when they didn’t get their desired reward.
Using a mouse model for prostate cancer, Associate Professor Lloyd Trotman studied the genetics of a disease that afflicts one in six men. In these mice, the typical driver of prostate cancer, PI 3-kinase, was absent in metastasized tumors. Instead, he and colleagues from Weill Cornell Medical College, Mt. Sinai School of Medicine and Dana-Farber Cancer Institute discovered that a cancer gene called Myc had become active. By lowering the amount of Myc in cells, they shrunk the metastases. Trotman hopes the model provides a fast and faithful way to test new approaches to find a cure for what is up to now an incurable disease.
Finally, associate professor and tomato expert Zachary Lippman, working with colleagues in Israel, discovered a genetic toolkit that allows researchers to double fruit production. The team found a collection of new gene mutations that allow scientists, and potentially farmers, to fine-tune the balance between the hormones florigen and anti-florigen. This has the potential to maximize fruit production without compromising the energy leaves need to support the fruit.
In the bigger picture, scientists at all three institutions showed considerable excitement for discoveries in the year, and years, ahead. Tribble pointed to the opening of the National Synchrotron Light Source II, the next-generation light source that cost about $900 million to build and that will provide images that are 10,000 times brighter than the original NSLS.
“NSLS II is poised to have some phenomenal information coming out,” Tribble said. “We can set a big battery in the beam and watch what’s happening” inside the battery without taking it apart.
At Stony Brook, the past year was “notable for the huge potential related to imaging,” said Lina Obeid, the dean for research at the Stony Brook Medical School. She said the university, with the construction of the new Medical and Research Translation building is “poised to have lots of great ideas and strong data.”
Cold Spring Harbor Laboratory is celebrating its 125th anniversary next year. Bruce Stillman, the president and CEO, said he hopes 2015 “will be a big year for expanding opportunities to apply our basic research to the medical clinic and other areas like food production and biofuels.”

Brookhaven National Laboratory
Scientists at BNL explored everything from the origins of the universe to nanoscale — i.e., very small — reactions in electric car batteries, to processes even more rare than the recently discovered Higgs boson, to increasing the production of oil in plants.
“It’s an enormously exciting time at BNL right now,” said Bob Tribble, the deputy director for science and technology, who joined the research center in February. A nuclear physicist, Tribble highlighted several studies that have broader implications.
Over the last decade, researchers could only account for a third of what gives a proton — that positively charged particle in the nucleus — its spin. As recently as six years ago, researchers believed subatomic particles called gluons had only a small effect. Now, “it’s clearer that the gluon field is playing a significant role in developing that spin,” Tribble said. Indeed, Elke Aschenauer, a leader in the spin program at the Relativistic Heavy Ion Collider, in collaboration with researchers at Star and Phenix, benefited from accelerator advances and added running time to collide polarized protons. The knowledge of gluon’s larger role in a proton’s spin, which no one had measured conclusively until now, could not only provide a better awareness of the internal structure of particles but could also affect optical, magnetic and electrical properties.
Scientists at the RHIC also learned about the phase transition of matter. Say what? Yes, that’s the equivalent of ice turning into water, although at a subatomic level. Zhangbu Xu, a spokesperson for RHIC’s Star collaboration, said RHIC provides the ability to explore what happens over a wide range of collisions. As Tribble put it, “now that we’ve been able to probe in some different regimes of the phase diagram, we’re seeing evidence that the first-order phase transition occurs in certain parts of the phase diagram. That’s new.”
Meanwhile, physicists at the ATLAS experiment at the Large Hadron Collider continue to test the Standard Model of particle physics. To do that, they are looking for incredibly rare events, where two same-charged particles called W bosons scatter off one another. Physicist Marc-Andre Pleier studied 34 such events that confirm that the Higgs boson particle does what physicists predicted.
In the world of superconductivity, senior physicist and director of the DOE’s Center for Emergent Superconductivity at BNL J.C. Seamus Davis helped lead a team that showed how electrons in a pseudogap are less free to move than they are in their superconductive state. By understanding these gaps, the team may be able to conduct the kind of science that leads to the speeding up of efficient power generators and transmission and computers at levels more than thousands of times faster than the machines currently in use.
John Shanklin, Jilian Fan and Changcheng Xu didn’t build a better mousetrap, but they did figure out how to encourage the development of a better plant, at least in the world of biofuel. The researchers found the detailed biochemical steps in the breakdown of oils. They disabled an enzyme that breaks down oil droplets to release fatty acids. The result was a 150-fold increase in oil content compared to the leaves of the naturally occurring counterpart. This could enhance production of biofuels.