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Authors Posts by Daniel Dunaief

Daniel Dunaief

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We have spent the better part of the last two weeks glued to the television watching extraordinary people perform incredible acts under unimaginable pressure. Maybe we should come up with an Olympic Games for the ordinary person. To enter these games, contestants will have to go through a speed round of sports clichés, to see who can come up with the most trite phrases for any circumstance.

“Yes, I just lost, but I learned a great deal and was proud to be here. I’m going to refocus and redouble my efforts, and come back that much stronger.”

“We just take it one game at a time.”

“I know I’m only 8, but this is what I wanted my whole entire life.”

We can add a contest for would-be reporters. Ordinary people can sit down with athletes and see who can ask either the most inane questions or share superlatives.

“You just won your 18th Olympic gold medal. What’s next? Oh, right, your 19th?”

“That was sensational, spectacular and unbelievable. I’m just wondering what it must be like to be you.”

How about a remote-control Olympics? Let’s see who can change from channel to channel — without switching to movie stations — the longest without hitting a commercial. I pride myself on my ability to watch three shows without seeing too many advertisements, but every so often I flip from one station that’s cut to a commercial to another that’s still in commercial. That’s a remote control error.

How about if we put teenagers in a room and push their endurance? We can have their parents talking to them while they are sending texts, updating their Instagram accounts and using Snapchat. In fact, not only will their parents be talking to them, but they also will have to answer questions about their days. The first one-word answer — “good” for example — disqualifies the contestant.

Teenagers might want to turn that contest around, requiring instead that they only answer in one syllable. The problem with that, though, is that the game might not end until they hit their 20s.

We could also bring in couples who have been together for more than 40 years. We can ask a question and see how long it takes before they finish each other’s sentences. Or, perhaps, we can ask them to tell a story about something that happened early in their relationship and see how long it takes before they argue about the details.

“No, I wasn’t wearing the blue dress. I was wearing the green dress and we weren’t in Philadelphia, we were in Boston; and we weren’t at a park, we were at a movie theater.”

We can invite a group of people who have made an art form out of noticing absolutely everything wrong with others around them. A person can stroll by and the contestants can try to one-up each other’s observations.

“Oh, seriously? She didn’t make eye contact with anyone.”

“Did you notice how she breathed with her mouth open?”

“She wore those shoes? What is she trying to sell, know what I’m saying?”

We could also set up a movie competition, where people quote the most lines from sports movies.

Borrowing from one of my favorite films, “Bull Durham”:

“You lollygag the ball around the infield. You lollygag your way down to first. You lollygag in and out of the dugout. You know what that makes you? Larry!”

“Lollygaggers!”

This 19th-century word has various meanings, including fooling around, wasting time, dawdling or dallying.

Yes, there’s exceptional speed and there are talented people pushing themselves to extreme levels to defy gravity, each other and the clock. And then there are the rest of  us and maybe, just maybe, there’s the

Lollygagger Olympics.

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Abraham Lincoln did it. So did Jon Stewart, Dave Letterman, Walter Cronkite and Lou Gehrig.

On July 4, 1939, as he announced that he considered himself “the luckiest man on the face of the earth,” the Yankees’ Gehrig, known as the Iron Horse, reached up to the bridge of his nose and wiped away tears.

The list of those who cry in public includes influential men with impressive pedigrees. Yet it is the exception rather than the rule for men to cry.

Recently, I attended a wedding where not only the groom cried as he read his vows, but the father of the bride also shed tears when he gave a speech during the reception. The groom was barely a few words into his vows when his voice cracked.

The audience waited, willing him to go on and all of them, except my son who was at his first wedding and was studying his image in the mirrored ceiling, appreciated the struggle to speak.

The man on the threshold of becoming a husband stopped several times, as he made fun of the tears and the mess he’d become, giving the audience a chance to laugh with him.

I have experienced larger moments, both positive and negative, when I felt such a strong flood of emotions that filled my eyes with tears and made it difficult to speak. Clearly, however, it’s not a regular occurrence because my son asked me when, or if, I cried. Part of that, I suppose, comes from my reflexive need to turn off the tears in public.

I grew up at a time when boys and men had to experience something extraordinary — either positively or negatively — to shed public tears. We had examples like the actor Alan Alda, who shed gut-wrenching tears in the final episode of “M*A*S*H.”

I recall being unable to say more than a few words to my mother when I called her from a pay phone to tell her that she had a granddaughter. Facing the corner of a phone booth, I shed tears of joy, especially when I said my daughter’s name for the first time. My mother must have heard my unsteady voice and asked, in the silence that followed, if I’d like her to come visit us in the hospital. Wiping away tears and nodding, I grunted something like “uh-huh.”

Men cry and, for the same physiological and psychological reasons as women, we benefit from that release, giving us an outlet for the literal flood of emotions.

At that recent wedding, the father of the bride knew when I spoke to him at the cocktail hour that he’d struggle to get through his speech. When the time came, he thanked everyone for coming and described the connection he felt with his daughter. He could barely finish a sentence before his lips turned down and the tears fell beneath his glasses.

He and his new son-in-law clearly started off this marital connection with something in common: tears at the wedding.

I was sure when his first daughter was born that he felt the same way at the beginning of her life, as he contemplated the excitement and terror at the responsibility that came from becoming a father.

As he considered the start of her married life he seemed, like Steve Martin in “Father of the Bride,” to have an awareness of these new steps which, some day, may include her coming to terms with a little life wrapped in her arms.

His voice broke at the end of his speech when he said his daughter would “always be my girl.”

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Dima Kozakov. Photo courtesy of Stony Brook University

A high five becomes a natural celebration after a home run because the hitter and the celebratory teammate are standing on their feet and are looking directly at each other. What if gravity didn’t keep our feet on the ground and our heads in the air? We might slap a hand into a foot or a foot into an elbow, sharing a nonverbal exchange with a different meaning.

Proteins inside our bodies don’t have the same gravitational and physical limits. They can and do come together in a soup of cytoplasm, blood, plasma and other mediums. Some of the time, those exchanges, like the high fives, communicate a message in the ordinary course of life. In other circumstances, however, those protein-protein interactions can lead to diseases like cancer.

Researchers around the world have studied these interactions using a variety of tools, trying to combat signals that contribute to damaging and life-threatening conditions.

Dima Kozakov, assistant professor in the Department of Applied Mathematics and Statistics and faculty member of the Laufer Center for Physical and Quantitative Biology at Stony Brook University, has spent several years creating a general way to model the mechanical details of how two proteins interact. This tool could become useful for researchers who are studying problematic interactions.

Leading an international team of scientists, Kozakov, who is also a faculty member at the Institute for Advanced Computational Science at SBU, created a new algorithm to model protein interactions. This algorithm accelerated how to model particular protein-protein interactions to identify harmful couplings. Kozakov and his colleagues recently published their findings in the prestigious journal, Proceedings of the National Academy of Sciences.

Applications of this technology include helping to design therapeutic proteins and speeding up vaccine design. If, for example, the interaction of a pair of proteins contributes to disease, scientists may want to design some other protein that is safe for the patient that will interact with one of the proteins. This additional coupling can avoid the more harmful protein connection.

Scientists also sometimes know that two proteins interact, but they don’t know how. Proteins often have large surfaces with many potential connections. Researchers might need to know “how two bodies come together,” Kozakov said. Proteins are flexible three-dimensional objects that consist of molecules. In modeling the interactions, Kozakov can find the three-dimensional way these proteins come together.

Computational modeling is less expensive than running experiments. At this point, the computer system needs as its starting point the three-dimensional structure of the proteins. That, Kozakov said, is much easier than determining the structure of a protein complex.

The next step is to work on methods where scientists don’t need the structure but only the chemical formula, which they can find through the amino acid sequence. Kozakov and his collaborators will use the information on the structure of similar proteins to build the models. “We’re developing a methodology that will work with the models,” Kozakov said. He described his approach as “physics based,” in which he solves a statistical mechanistic problem by using an energy function that can account for different environments.

“In principal, we can modify our energy function to account for different environments,” like changes in pH, temperature or other variables that might affect how two proteins come together. Given the way Kozakov and his colleagues designed the model, it can account for all possible configurations of two almost rigid proteins coming together.

Kozakov is also in discussions with Brookhaven National Laboratory to explore the results of small-angle X-ray scattering. The benefit of this approach is that he doesn’t need proteins in a crystalline structure, which is a requirement of crystallography. While small-angle X-ray scattering provides less information than crystallography, Kozakov said he and his colleagues can develop it in combination with other techniques where it would be equivalent.

Kozakov has been developing models since 2007 or 2008 to understand these interactions. The project in his recent paper took three years to finish. The program takes 10 to 15 minutes to run on a personal computer. Before, this kind of effort required a supercomputer.

Kozakov believes there could be other applications of this technology, where scientists could model candidate protein drugs in real time to see how the drug interacts with the protein of interest. The first version of the program came out about a year and a half ago and it took the intervening time to perfect it, he said.

Born in Eastern Europe in a region that used to be part of the Soviet Union but is now on the western border of the Ukraine, Kozakov lives in Stony Brook with his wife Olga Kozakova. The couple has a six-year old son, Platon. Kozakov’s grandparents were scientists: his grandfather, Mikhail, was a university professor and his grandmother, Nina, worked at the university. He grew up surrounded by books on physics. He “had fun, digging into antiquities books” and thought the science presented an “inspiring environment.”

As for his work, Kozakov has a big picture view of his efforts. “I want to make something useful to the community and to the world,” he said. “I want to do what I can to help.”

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The media coverage of Hillary Clinton and Donald Trump misses the point. While the race for president is about each person, the process, the scandals, the outrage and the stories that have a life of their own are not about the people — they are about the “brand.”

The most passionate advocates for each candidate have defended and supported them, recognizing their shortcomings but urging us to believe each candidate will be better because they just are better — the way any brand with a loyal following just is.

Newspapers and advocates of each side shout at the top of their lungs about this historic election, offering evidence of Clinton’s inappropriate handling of emails and Trump’s personal attacks.

In the latest battle, Trump has taken to the airways to respond to Khizr Khan, the parents of a Muslim-American war hero.

The question isn’t whether this reveals something new about Trump, the person. It doesn’t. Surely anyone who has watched Trump over the last year or so realizes that his personal style, and the brand under which he is running for the highest office in the land, emanate from a scripted character. He doesn’t let anyone question him or his brand without counterattacking. He has become a talking head in touch with his irascible side.

That may be what attracts people to him. There is no political correctness, a term he utters with such disdain that he says it as if he is standing at a podium filled with soiled diapers. The Trump brand and playbook mandate that a best defense is a good offense.

If he’s offensive in the process, who cares? He doesn’t — and on the whole it appears many of his supporters don’t, either. He may have been right that he could shoot somebody in Times Square and not lose votes because outrageous words and actions are a part of his brand.

While I don’t agree with the slash-and-burn approach to the personal and political battles he fights, I recognize he’s probably not fighting for the little guy, the medium-sized guy or the big guy so much as he’s fighting for his brand. In a country where products and marketing are so inextricably intertwined, he is the best advocate for Brand Trump. Does being Trump prohibit him from saying “I’m sorry” or “I’m wrong”?

Those who hated him before have more ammunition in their battle with him. But what does he care? If they weren’t loyal to the brand and they weren’t his customers, he hasn’t lost anything.

What will cause voters loyal to Brand Trump — or, put another way, those who are angry, fearful or resentful of the Clinton brand — to change their minds? How far can he go before some of those who identify with him decide he shouldn’t become president?

Does this pitched battle with the Khans — parents of a slain and decorated war hero — do for the Trump brand what the attack on the U.S. Army did for Sen. Joseph McCarthy? His pursuit of communists damaged and destroyed lives and careers in the early 1950s until Joseph Welch, the chief counsel for the Army, asked McCarthy in 1954 if he had “no sense of decency.”

For Brand Trump, decency doesn’t seem to have been a priority up until now. The question, however, is whether those buying the product will care enough about what he says or thinks to force a change in the brand before they, themselves, choose the other brand.

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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.

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A man walks into a doctor’s office and can only say two things: teepee and wigwam.

The doctor considers the curious case and decides he’s “too tents.”

While you may have heard the homophone joke, you may also know that the New York Yankees are in a similar position: dealing with two tenses.

They are stuck between trying to do what they can to win now and making trades and decisions that may help them for the future. While this is a baseball-specific problem for the Yankees, it’s an eminently relatable problem.

Should we go for it in the present, hoping to win, win, win now, or should we allow ourselves the opportunity to rebuild and move toward a better future by adding some education, by moving to a new house, getting a new job, or starting or ending a relationship?

We generally live in the present, because that’s what is wanted by our ids — the impulse-driven parts of our psyches. We’re hungry, we want food. We’re tired, we want sleep. We’re sick of hearing politicians who starred in reality shows turning the process into a reality show, we change the channel.

These Yankees, with their high-priced talent, glitz and glamor, and the endless celebration of their own history, have mastered the art of staring in the mirror and liking what they see. The team could easily change its name to “The Narcissi.”

Anyway, can, should, will the Yankees pull the trigger on a host of deals that may replenish a farm system, sacrificing the all-important present for a future that may not produce a better team than the mediocrity they’ve demonstrated?

I don’t have a crystal ball and I don’t rely on the position of the stars, the moon or the tides to make decisions for my favorite team or for my life. Early this week the flamethrowing rent-a-closer on a one-year deal with the Yankees, Aroldis Chapman, was traded to the Chicago Cubs for a four-player package headed by stud shortstop prospect, Gleyber Torres.

How much further they can, or should, go in swapping assets, repositioning the team or realigning their strategy is a favorite game of the endless sports pontificators in the New York area, who always seem to know so much better than everyone else until a player or a team proves them wrong.

From my perspective, the Yankees aren’t a contending team. They are, as the old saying goes, exactly what their record indicates. Early this week, they were a .500 team, which means they win as many games as they lose. In the incredibly competitive American League East, where talented teams like the Red Sox overcome their own pitching flaws with sensational hitting, a win-one, lose-one Yankees team isn’t inspiring confidence.

Of course, the fun of life — and all these games — are the many unpredictable parts. Would anyone have expected the Mets to become a World Series team last year? There are no guarantees, which is what makes any present sacrifice a leap of faith.

We, the fans and the team, might not get something better by making a change.

From my armchair, however, I would plant a “for sale” sign in front of this team with a declining A-Rod, a shadow-of-himself Mark Teixeira and a smoke-and-mirrors starting pitching staff. No one is going to buy Teixeira or A-Rod, but the scales seem to be leaning toward an investment in the future. Now, if the never-give-up Yankees can change course on a faltering season, maybe we can consider moves that might help us win in the future.

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Erik Muller. Photo by Yizhi Meng

By Daniel Dunaief

Diamonds may not only be a girl’s best friend, they may also be important for doctors, particularly those using radiation to treat cancer patients.

Erik Muller, a principal investigator and adjunct professor in the Department of Materials Science and Chemical Engineering at Stony Brook University, recently demonstrated that a particular type of synthetic diamond can measure the flux, position and timing of radiation beams used in cancer therapies. His research seeks to adapt diamond detectors for use with an emerging type of therapy using high-energy protons and carbon ions. “There currently does not exist a technology which can precisely measure the flux, position and timing of these proton and carbon ion beams used in radiotherapy,” Muller explained.

The diamonds Muller and his team use are more pure than any natural diamond. They contain fewer than five parts per billion of nitrogen and less boron or other impurities. They are clear with no color. Nitrogen gives diamonds a yellow or brown color and acts as a charge trap, making natural diamond unsuitable for radiation detectors.

As an SBU postdoctoral researcher, Muller joined an effort at Brookhaven National Laboratory to investigate the use of diamond as an electron source. During that study, researchers found that diamond was a valuable X-ray detector. The success of that work led to the Department of Energy funding work to develop sensors for radiotherapy.

Diamonds can provide information that enable scientists to measure in real time the development of the beam.

Once diamond growers send the product to his lab, Muller and his team screen for a defect that can lead to unwanted hot spots in the detector response to X-rays. When Muller’s lab receives the diamonds, they look like small square pieces of glass. These diamonds are bread sliced into two to three pieces that are about half the thickness of a human hair.

Partners at the Center for Functional Nanomaterials at BNL prepare, characterize, etch and pattern the diamonds in the cleanroom. The Instrumentation Division at BNL provided custom electronics, circuit design, wire bonding and assembly. “The development of the detectors, particularly the pixellated diamond X-ray detector, would not be possible without the talent and expertise” in the Instrumentation Division, Muller explained.

Muller also lauded the contribution of the Stony Brook University students who worked on the diamond effort, including Mengjia Gaowei, Tianyi Zhou, Mengnan Zou and Wenxiang Ding. In preparing a proposal for the Department of Energy to improve beam diagnostics for particle therapy, Muller met Samuel Ryu, chair of the Department of Radiation Oncology and deputy director for clinical affairs at Stony Brook University’s Cancer Center. Ryu “expressed a strong interest in using these detectors for X-ray beam therapy and we have been pursuing that as well,” Muller said.

Ryu said the existing conventional detector, which measures radiation dosage, is “limited in some sense.” He likened the radiation detector to a thermometer. If a thermometer indicates that it’s 90 degrees, it may be 91 degrees, but the thermometer may not read the temperature with enough precision to indicate the exact temperature. Similarly, the diamond detector “will improve” the precision of the radiation dose measurement. The gap in the detection of the radiation dose has been like that for more than 100 years, Ryu said.

Ryu said the addition of the diamond to the detector should be commercialized and that he and Muller are “really trying to find out how we can use these detectors in the clinic.” Ryu said he doesn’t know the time frame for when this might become available in a radiation delivery system, but he would “like to see it as soon as possible.” Ryu and his staff meet regularly with Muller and his team to analyze the data and discuss how to proceed. He described Muller as “very open-minded” and indicated that it is a “very good collaboration.”

One of the challenges in taking this diamond discovery to the next step is to ensure that the software is robust and that it has enough redundancies to turn the beam off amid any contradictory readings. Before diamonds can become a part of these carbon or ion beam treatments, researchers need to demonstrate that the radiation itself won’t damage the diamond. While Muller doesn’t expect this to happen, he said he has to prove its viability.

In the bigger picture, Muller said he and the members of his lab spend considerable time understanding the physics of radiation sensing devices in high-radiation environments. “Diamond is a very promising material in this field for continued development and is our current focus,” he suggested. “In general, I am interested in any technique and material where we can understand how the structure affects the device function.”

Residents of South Setauket, Muller lives with his wife Yizhi Meng, an assistant professor in the Department of Materials Science and Chemical Engineering at Stony Brook, and their daughter, who is in primary school. Meng, who is a graduate of Ward Melville High School, develops drug delivery materials for breast cancer and osteosarcoma, a type of bone cancer. The couple met when they were graduate students at Cornell University. They shared an interest in photography. Meng uses Nikon cameras, while Muller prefers Canon. “There’s a funny rivalry between us,” Meng said.

As for his work, Muller is optimistic that it will have an application in radiation delivery. He believes he can address the engineering challenges and is “planning to continue the commercialization of these devices.” Meng is excited by the progress Muller has been making. Muller is “working with some really great people,” she said. “It’s really exciting.”

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The news is in my blood. If you don’t believe me, check the name of the person who writes the column on the same page and who started this business 40 years ago — go Mom!

And yet there’s far too much blood in the news these days. It’s not enough that storms and natural disasters kill: People are murdering each other in stomach-churning numbers.

It’s heart-wrenching to read about the losses in our country and around the world. Far too often, headlines about senseless violence fill the news.

News organizations shouldn’t ignore these horrific acts, because we want to know what’s going on in the world, what we need to do to stay safe and what other people are doing and thinking.

It seems to me that there are things we can do. We can give blood. Why? We might save someone’s life, we might give someone a vital supply of something we can’t grow in a field, pull from a river or manufacture in a laboratory.

Recently, I met a woman who had been donating blood to her father for two years. He was sick and he needed blood on a regular basis. After he died, she continued to give blood. She said her father received blood from other people besides her during his illness, and she wanted to give back to a system that improved and extended his life.

Do we read about her? No, generally, we don’t, because it’s a small act of kindness and social awareness that doesn’t get politicians angry and doesn’t cause people to write messages to each other over the Internet. It’s not an opportunity to resort to name calling: It’s just a chance to save lives.

We can also volunteer to make our communities better places. We can be a big brother or big sister, or we can find a charitable organization that provides caring and support for families that have children with special needs. My Aunt Maxine had Down syndrome and gave so much more than she ever took.

Sure, she dominated the airwaves with her husky voice and, yes, she sometimes said and did things that made us roll our eyes, but, more often than not, she displayed the kind of unreserved love and affection that jaded and vulnerable adults find difficult to display. When Maxine laughed or did something extraordinarily funny, like sharing a malapropism, she laughed so hard that she cried. Nowadays, after she died, we find ourselves sharing tears of joy when we think of how much she contributed to our lives and to the room.

When the big things seem to be going in the wrong direction, we the people can commit random acts of kindness. Yes, we can and should pray for each other. It certainly can’t hurt, regardless of whether we’re Christian, Jewish, Muslim or any other religion.

We can also take the kind of actions that define who we are and that show our character. We are living in a world after the Brexit vote and after the failed coup attempt in Turkey. We may not know what to make of all that, but we can decide who we want to be.

We can’t stand on a platform, the way all the former Miss America contestants of bygone days used to, and wish for “world peace,” because that seems naive. And, yet, we can hope that small acts, committed in the name of counterbalancing all the negative news, echoed and amplified across the nation, can turn the tone.

We are fortunate enough to live in a place where we can shape the world in a way we’d like it to be, one community and one random act of kindness at a time.

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From left, postdoctoral associate Yuanheng Cai, biological research associate Xuebin Zhang and plant biochemist Chang-Jun Liu in the BNL greenhouse. Photofrom Brookhaven National Laboratory

By Daniel Dunaief

It provides structural support, allowing gravity-defying growth toward the sky. While it offers necessary strength, it also makes it more difficult to get inside to convert plant biomass into fuel.

Lignin is the major component that makes cell walls harder. Plants can tolerate the loss of lignin, but dramatically reducing it or altering its structure could severely affect its growth, which makes any effort to modify lignin challenging.

Seeking to balance between the plant’s structural needs and the desire to gain access to biofuel, Chang-Jun Liu, a plant biochemist at Brookhaven National Laboratory, added a step in the synthesis of lignin. “Most studies in this field rely on knocking down or knocking out one or two biosynthetic pathway genes,” said Liu. “We added one more reaction” that competes for the precursors of lignin formation. Liu said he and his collaborators figured that adding that last step in the production of lignin, which is a natural part of plant cell walls, would have the least effect on plant growth while it can effectively reduce lignin content or change its structure.

Liu said he redirected the metabolic precursor by using a modified enzyme he created over the course of several years. The enzyme diverts biosynthetic precursors away from making lignin. Plants typically have three types of lignin, called S, G and H lignin. In a wild-type aspen tree, the ratio of S to G is two to one. This change, however, altered that, turning the ratio to one to two. The general perception is that increasing G lignin would make the cell wall structure stronger and harder, making it harder to release simple sugars. The surprising finding, however, was that reducing S and maintaining G greatly enhanced the release of sugar with digestive enzymes from aspen cell walls.

Scientific partners including John Ralph at the University of Wisconsin and the Great Lakes Bioenergy Research Center confirmed the alteration of lignin structure. Liu tested his enzyme in his earlier work on the flowering plant Arabidopsis. When it worked, he moved on to aspen trees, which grow rapidly and can thrive in environments where typical farm crops struggle to grow. The aspen experiments proved more fruitful in part because these trees contained more S lignin, and the enzyme he developed preferentially blocked the S lignin. The aspen trees with the modified enzyme can yield up to 49 percent more ethanol during fermentation, compared to controls.

Using infrared light at the National Synchrotron Light Source, Liu and his collaborators were able to see an increase in the production of cellulose fibers, which are a primary source of sugars in the cell wall. This may contribute to the release of simple sugars. Liu will continue to explore other possibilities. Other lignin researchers applauded these results.

Liu’s “approach will definitely have a great impact on the cost reduction of cellulosic biofuels,” Dominique Loque, the director of Cell Wall Engineering at the Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, explained in an email. “With no impact on biomass yield and a reduction in recalcitrance, it will reduce the conversion costs of biomass to fermentable sugars.”

While this research, which was recently published in Nature Communications, shows potential commercial promise, Liu and his team are working to answer basic questions. He is interested in further testing his approach in grasses and different trees to determine the effects on lignin content, structure, cell wall digestibility and plant growth. The trees in this experiment were grown in a greenhouse, where scientists could control light and temperature and mimic the natural environment without natural stressors, like insects or fungus. Loque suggested that Liu’s approach can be “easily and quickly optimized to alleviate potential issues such as susceptibility to pathogens” if they exist.

Liu has planted 150 of these altered trees in the field. So far, he said, the biomass yield is not compromised with these experimental plants. “Field tests will allow evaluating the impact of engineering on predators, pathogens and other stresses,” Loque said. Liu was able to create this enzyme after developing an understanding of enzyme structures using x-rays at the NSLS. In that research, Liu was able to gain a better knowledge of how the enzymes that occur naturally worked. Once he knew the structure and method of operation of the enzymes in the lignin pathway, he could make changes that would alter the balance of the different types of lignin.

Liu lives with his wife Yang Chen, a teacher’s assistant in Rocky Point Middle School and their two children, 16-year-old Allen and 14-year-old Bryant. For the last few years, Liu and his family have added hiking, table tennis and tennis to their recreational repertoire.

Liu is encouraged by these findings and is extending and expanding his studies and collaborations. He will work with a Department of Energy sponsored Energy Frontier Research Center. He will also pursue more applied studies to explore the more efficient use of cell wall biomass to produce biomaterials or bio-based products. He is forming a collaboration with Stony Brook’s material science team and with the NSLS-II. “Plant cell wall represents the most abundant biomass on Earth,” Liu said. “Understanding its synthesis, structural property and efficient way in its utilization are critical for our future bio-based economy.”

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0 2017
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.”

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