Stony Brook University

Stony Brook’s iGem team pose with Randy Rettberg, president of the iGem Foundation, at the event. Photo from SBU

Stony Brook’s University’s 2018 team for the International Genetically Engineered Machine (iGEM) competition took home the university’s first gold medal during the four-day iGEM Giant Jamboree held at Hynes Convention Center in Boston in October. 

Since 2014, Stony Brook’s iGEM teams have competed at this annual event, previously receiving bronze and silver medals for their student-designed synthetic biology projects. This year’s competition involved 343 teams from around the world, including 60 from different colleges and universities in the U.S. Stony Brook was one of only seven collegiate teams from the U.S. to earn a gold medal.

Stony Brook’s iGem team pose with Randy Rettberg, president of the iGem Foundation, at the event. Photo from SBU

Led by sophomores Priya Aggarwal and Matthew Mullin, the 14-member team’s project, The Sucrose Factory, focused on the use of cyanobacteria to economically sink carbon dioxide by simultaneously producing sucrose that can be used to produce biofuels and bioplastics. Their project proposal was the only one to win all three open competitions offered by the iGEM sponsors Genscript, Opentrons and Promega. 

The iGEM competition promotes the advancement of synthetic biology through education and a competition aimed at developing an open and collaborative community of young scientists. Synthetic biology projects developed by previous SBU iGEM teams have ranged from a search for innovative treatments for diabetes and pancreatic cancer to lowering the cost of vaccine preservation. At Stony Brook, new teams are recruited each year, and members are mentored by students from previous teams and advised by Peter Gergen, director of undergraduate biology and a professor in the Department of Biochemistry and Cell Biology. 

“The Jamboree was a great experience for the 14 students on the team, and I think there may actually be some long-term potential in the ideas behind their project,” said Gergen, who said he is very proud of this interdisciplinary and talented group of students. 

In addition to Aggarwal, a human evolutionary biology major, and Mullin, a mechanical engineering major, members of Stony Brook’s 2018 iGEM team are Stephanie Budhan ’21, chemistry; Woody Chiang ’19, biochemistry and psychology double major; Dominika Kwasniak ’20, biochemistry; Karthik Ledalla ’21, biomedical engineering; Matthew Lee ’21, biology; Natalie Lo ’21, biology; Lin Yu Pan ’20, health science; Jennifer Rakhimov ’21, biology; Robert Ruzic ’19, biomedical engineering; Manvi Shah ’21, psychology; Lukas Velikov ’21, computer science; and Sarah Vincent ’19, biology.

More details on the team’s project are available at https://2018.igem.org/Team:Stony_Brook/Team.

Stony Brook University Hospital. File photo

Most people only think about Lyme disease when taking a hike in a park, but for many doctors, the condition weighs heavily on their minds every day.

Dr. Benjamin Luft, director and principal investigator of Stony Brook WTC Wellness Program, is one of those doctors. He is currently working on two clinical studies examining the disease. One involves those who continue to present symptoms after being treated, and the other study involves Latinos on Long Island who work in the landscaping and agricultural fields.

In a recent phone interview, Luft said the clinical study involving Latinos is a straightforward one, where the aim is to help a population that has been underserved and understudied due to their work schedules. The other study is more involved.

After being bitten by a tick infected with a bacterium called Borrelia burgdorferi, many people with a bull’s eye rash or flulike symptoms may receive treatment and feel better; but there are those who will continue to suffer for a prolonged period, even years, with a variety of complaints like aches, pains and brain fogginess. Luft said at times there may be no clear signs of the disease in the body, but doctors may find evidence of it after thorough neuropsychological exams that can detect subtle abnormalities.

Dr. Benjamin Luft is one of the doctors at Stony Brook Medicine looking for answers when it comes to those who continue to suffer from Lyme disease after treatment. Photo from Stony Brook Medicine

“This study is really geared toward diagnosing and to find ways to be able to monitor the disease,” Luft said, adding in the future his hope is to conduct studies testing new ways to treat Lyme disease.

The doctor said it’s essential to receive a diagnosis because if Lyme disease is left untreated, it can lead to joint swelling, arthritis, neuropathies, meningitis or cardiac problems.

When Stony Brook University recently began making a more significant investment in its imagining facilities, Luft said he saw a chance to find an answer for those with chronic symptoms.

“I thought this is the opportunity to see what is going on in the brain of these patients with using X-ray techniques and radiological techniques which may give us some insight,” he said.

He said with cutting-edge neuroimaging studies researchers can look for evidence of inflammation in the brain which may be a reaction to the infection.

“That would be an important thing to do because it may give us another target for therapy,” Luft said. “A lot of the therapy that we now use is really just geared toward the organism itself, but it’s not really geared toward the body’s reaction to the organism which may also have to be treated in order to alleviate some of these symptoms.”

The doctor has studied Lyme disease for more than 30 years. When he arrived at SBU from Stanford University Hospital, he was involved in work with AIDs and age-related diseases, but he said at the university’s clinic in the 1980s many people complained of Lyme disease problems and there were no effective therapies at the time. Many of the first therapies and treatments used today were developed at SBU, he said, but there have always been people who haven’t responded well to those treatments.

“So that’s been something that’s been bothering me for many years as to why that is,” Luft said.

He said he will present initial data, which is promising, from the clinical imagining study at a conference in Barcelona, Spain, later this month and hopes to get more patients for the clinical study. Those who are interested can call 631-601-5615. Subjects must meet stringent criteria including not having any other disease, having serological evidence of Lyme disease and a clear history that they had the rash.

In addition to Luft’s studies, Dr. Christy Beneri, assistant professor of pediatrics at SBU, and her team are working on a pilot study to look at newer diagnostic tools to establish a better way to diagnose early Lyme disease.

“We also will be doing work on understanding tick epidemiology in our area and working with the local health department to understand potential new tick-borne pathogens,” Beneri said.

Stony Brook Lyme Disease Laboratory has been performing Lyme disease testing on clinical specimens since 1984. Both inpatients and outpatients can have a Lyme ELISA screening test and Western blots confirmatory test at Stony Brook Medicine. Almost 10,000 screenings were done in 2017 at the hospital, which has been actively working with state senators for funding for Lyme disease outreach and research, according to Beneri.

Stony Brook University professor Patrice Nganang has been detained in Cameroon. Photo from Stony Brook University's website

By Rita J. Egan

A Stony Brook University professor discovered firsthand the difference between freedom of speech in the United States and in the country of Cameroon in Central Africa.

On Dec. 6, Cameroon police detained writer, poet and professor Patrice Nganang as he was leaving the country for Zimbabwe at Douala International Airport, according to a press release from PEN America, an advocacy group that fights for writers’ rights to freedom of expression. The detainment came after the Cameroonian-native and U.S. citizen published an article on the website Jeune Afrique. In the piece in question, the professor was critical of Cameroon President Paul Biya’s administration’s approach to the ongoing instability in Anglophone regions of Cameroon.

Stony Brook University administration officials were notified of the detainment immediately, according to the university.

“Stony Brook University is aware of the situation, and we are working around the clock with the appropriate authorities and elected U.S. representatives to help facilitate the safe return of Professor Nganang,” university president Dr. Samuel L. Stanley Jr. said in a statement.

Nganang is one of a number of writers who recently have been questioned, detained or imprisoned by police in Cameroon after commenting unfavorably on political or human rights issues, according to PEN America.

“Detaining an important independent voice like Patrice Nganang, who has used his writing to investigate the consequences of violence, is indicative of a movement by the government to silence all political criticism and dismantle the right to free expression,” said Karin Deutsch Karlekar, PEN America director of Free Expression at Risk Programs. “We condemn Nganang’s detention and call on the Cameroonian authorities to release him unharmed immediately.”

According to writer Dibussi Tande, one of the administrators of the Facebook page, Free Patrice Nganang, on Dec. 11 a prosecutor postponed the decision to determine if there was enough evidence to proceed to trial until Dec. 13. On the same day, Nganang’s lawyer Emmanuel Simh was notified that the charge of contempt for the president was dropped. Tande said as of Dec. 11 the three remaining charges are for making a death threat against the president; forgery and use of forgery due to the professor having a Cameroonian passport despite being a U.S. citizen as the country does not recognize dual citizenship; and illegal immigration due to not having the proper papers as a U.S. citizen.

Tande said Nganang has been in isolation in the offices of the judicial police in Cameroon’s capital Yaoundé. A representative of the U.S. Embassy visited Nganang Dec. 11.

“This is essentially a political witch hunt by folks in government who want to punish him for his decade-long activism on behalf of democracy and the downtrodden in Cameroon,” Tande said. “However, with negative international attention that his arrest has brought on Cameroon, some elements in government think it would be better to simply expel him from Cameroon on grounds that he entered Cameroon illegally.”

Robert Harvey, a distinguished professor at SBU, said it was a relief when the contempt charge was dropped, and he remains hopeful. The embassy representative contacted him with a message from Nganang. He wanted his former students to know that he hasn’t forgotten about their letters of recommendation. Harvey said Nganang was on a leave of absence this semester to attend to family business in Zimbabwe.

“He’s a popular teacher,” Harvey said. “He’s impassioned; he’s effective.”

On his SBU profile page, the professor wrote that his intellectual work covers scholarly activities, writing and essayistic interventions.

“I investigate the diverse ramifications of violence, and I am particularly interested in what is commonly referred to as the ‘colonial archive’ (pictures, books, instruments),” Nganang’s profile said. “I have published and lectured extensively on this topic. I have also published on numerous topics related to postcolonial African literature, theaters and cultures.”

This article was updated Dec. 12 to include quotes from Free Patrice Nganang Facebook administrator Dibussi Tande and Dec. 13 to included quotes from SBU distinguished professor Robert Harvey.

 

Youthire.org provides an easy way for Stony Brook University students to find odd jobs in the surrounding areas. Photo from Thomas Cerna

An established job resource website will now enable young adults in the Three Villages to make some extra cash, proving the adage “There’s an app for that” to be eminently true.

More than three years ago, Thomas Cerna created Youthire America to provide more opportunities for young people between 16 and 26 years old to earn cash while gaining work experience. The entrepreneur set up the website www.youthire.org where Sea Cliff, Glen Head, Glenwood Landing and Glen Cove students could connect with homeowners and business owners. Now the nonprofit organization is extending the same opportunities to Stony Brook University students and residents in the surrounding areas.

“It’s a really great way to connect kids with adults in the neighborhood, and they’re making money doing odd jobs,” Cerna said.

Although a mobile app doesn’t yet exist, the website serves as a hub offering work opportunities in four separate categories — internships, volunteer projects, traditional employment and odd jobs.

Cerna said he got the idea to partner with the university when he noticed a homeowner from Setauket posted a request. He reached out to the poster and discovered they were informed about the site by Joanna Durso, senior career counselor with the university’s career center, who lives near Cerna and was familiar with Youthire.

Brian and Travis Danoski clean out a shed after finding the odd job on www.youthire.org. Photo from Thomas Cerna

Durso said the site makes it easier for the career center to help residents who need help, especially since the school is unable to promote jobs that need to be done inside private homes on its website.

“In addition to offering SBU students another source of job listings, Youthire is helpful for us when we hear from local residents who want to hire students for household work, baby-sitting, and so on,” Durso said.

Students set up profiles on the site and are notified by email when jobs within five miles are posted. If a student is interested in a task, the homeowner receives an email and can check the student’s profile page, which includes a photograph, narrative and past work history, before contacting them.
Everyone using the site goes through a background check and screening for misdemeanors and felonies.

Cerna said he decided to start the nonprofit after
remembering the odd jobs he worked while growing up in Mamaroneck. His high school had a career services center where students could sign up for odd jobs.

The founder said he believes working at a young age
creates personal responsibility and a good work ethic, and in a society where drug use has skyrocketed, he said he feels it can keep kids out of trouble.

“It’s something that could steer a kid in the right direction for a kid going in the wrong direction,” Cerna said.

Kevin McDonagh, of Glen Head, said he used Youthire to clean out his shed. He said with his own children in college, he needed help with the big job and remembered making signs for Cerna at the sign shop where he works.

“It was a really satisfying experience,” McDonagh said. “They came in, they did the job. Not only did the job, but they were proactive in the work. I didn’t have to direct them every step of the way.”

One of the students who worked on his shed was Brian Danoski. The senior at Stony Brook University, who is studying to be an entrepreneur, said he discovered the site on his own a few years ago.

“It’s building my experience and desire for learning new things,” Danoski said.

The college student said he likes that the site easily connects him with those who need help and allows flexibility, especially with the demands of his class schedule. He said the site is also perfect for high schoolers.

“[Cerna’s] really passionate about it,” Danoski said. “That’s why it’s going to succeed because he wants the youth to get out there and do more and learn about the world.”

For more information, visit www.youthire.org.

Dr. R. Trevor Marshall, right, consults with a New York Presbyterian Hospital nurse while assisting patients at a coliseum in Manati. Photo by Alejandro Granadillo

Many in Puerto Rico still reeling from the devastation of Hurricane Maria recently received much-needed medical care from a local Long Island hospital.

There were 23 staff members from Stony Brook Medicine stationed on the island from Oct. 24 to Nov. 8 as part of a 78-member relief team consisting of professionals from New York metropolitan hospitals. Three physicians, two nurse practitioners, nine nurses, four paramedics, four nursing assistants and one pharmacist from Stony Brook put their skills to use to help those with physical aliments and relieve overloaded hospitals in Puerto Rico.

The Coliseo Juan Aubin Cruz  Abreu “Bincito” in Manati, Puerto Rico, was the temporary workplace of 19 from Stony Brook, while four others assisted at Hospital HIMA San Pablo-Fajardo for a week, followed by another seven days on the U.S. Navy hospital ship USNS Comfort, which is docked in Old San Juan.

Dr. R. Trevor Marshall, emergency physician and director of Emergency Medical Services at Stony Brook, said he and 18 others worked with the Disaster Medical Assistance Teams — part of the National Disaster Medical System — Veterans Affairs and the U.S. Army at the coliseum in Manati.

“It was a nice way to be able to provide additional resources down there to help the local community,” he said.

The grateful husband of a patient wears a Stony Brook Medicine hat while serenading the medical staff. Photo by Alejandro Granadillo

The physician said the staff members treated patients with diarrhea, conjunctivitis, abscesses, severe cuts and broken bones. Marshall said the patients were appreciative, and the staff was grateful for local high school and college students who volunteered their time to translate. The South Setauket resident said it was his first medical relief trip, and he’s open to volunteering for another one in the future due to his positive experience in Puerto Rico.

“This was an outstanding opportunity,” Marshall said.

Dr. Richard Scriven, associate professor of surgery and pediatrics at Stony Brook University, was one of the doctors working alongside Marshall at the coliseum. While driving from the airport to the arena he said he could see half of the homes were covered with the tarps that the Federal Emergency Management Agency provided to protect the houses that lost roofs during the Category 5 hurricane.

He said the staff would alternate working 12-hour shifts, slept on cots in the mezzanine section and bathed in outdoor showers. Scriven said food was provided from the local veterans agency, nearby residents and appreciative patients who bought them pizzas.

The physicians said DMAT tents were set up outside the arena, where many patients were treated for minor ailments. Inside were 50 to 70 inpatients who were frail and on ventilators and mostly relocated from nursing homes.

Scriven, who lives in Stony Brook, said he and others would walk to the nearest Walgreens, and while Manati didn’t have as much damage as other areas, many were still without power and he didn’t witness any utility crews working on restoring it.

“Yet the people were so nice, so appreciative and really amazing,” Scriven said.

Many areas in Puerto Rico still have downed power lines after Hurricane Maria. Photo by Ralph Rodriguez

Emergency Medical Specialist Dr. Rolando Valenzuela, a St. James resident, was one of the team members who spent time in Fajardo and on the USNS Comfort. He said the hospital in Fajardo needed help with its emergency room, and the New York medical professionals assisted with ambulatory patients and mostly dealt with benign medical complaints. He said a number of people were in distress because they were unable to get treatment for diabetes or use medical equipment such as nebulizers and oxygen concentrators without electricity. Others were experiencing health problems as a result of a lack of water or medications.

Valenzuela said many hospitals on the island are low on supplies and are operating on generators. Any kind of extensive imaging or lab work wasn’t available on site; however, the staff had basic medications, antibiotics, IV fluids and EKG machines on hand.

“The medical infrastructure is ground down to a halt,” Valenzuela said.

Patients with more serious problems in Fajardo were transported to San Juan or to the USNS Comfort. The ship was staffed by Navy personnel and DMAT tents were set up outside for ambulatory patients. Valenzuela said medical professionals from around the country working in the tents saw 500 to 600 patients a day. Patients with serious conditions were transferred to the Comfort.

“I can’t say enough about how amazing the Navy personnel was,” Valenzuela said. “These guys had been on board for over a month before they were allowed off the ship. They were getting a few hours of sleep here and there but their main focus was on treating patients.”

Valenzuela visited Puerto Rico in the past and remembered how friendly the people were, and said despite the devastation on the island, the residents were in good spirits.

“The people were extremely enthusiastic to have us there,” he said. “They were so grateful for any kind of assistance. They just wanted to make sure that they weren’t being forgotten, and we did our best to provide them with the standard of care that would be acceptable on Long Island. I think we were successful.”

Stony Brook University professor Christopher Gobler discusses the quality of local bodies of water at a press conference Sept. 12. Photo by Kyle Barr

By Kyle Barr

There’s still something in the water — and it’s not a good kind of something.

Scientists from the Stony Brook University School of Marine and Atmospheric Sciences released an annual report highlighting the concern over the prolonged existence of toxic algae blooms, and a deficiency of oxygen in Long Island waters caused high levels of nitrogen.

Stony Brook Professor Christopher Gobler and several members of the advocacy collective Long Island Clean Water Partnership, a conglomerate of several Long Island environmental groups, revealed the findings of a study done from May to August.

The Roth Pond, a Stony Brook University body of water that plays host to the annual Roth Regatta, is affected by blue-green algae. File photo from Stony Brook University

“In order to make Long Island sustainable and livable, clean water needs to be established,” said Adrienne Esposito, the executive director of Citizens Campaign for the Environment. “The challenge has been very great over the last decade … though the problem, unfortunately, is getting a bit worse. Algae blooms and the degradation of water quality across Long Island are serious threats to Long Island’s health.”

On the North Shore, there are several severe cases of hypoxia, or a depletion of dissolved oxygen in water, which is necessary for sea life to survive. Cases were found in Stony Brook Harbor, Northport Bay, Oyster Bay and Hempstead Bay. Measured on a milligram per liter of water scale,any case of hypoxia below two milligrams per liter can be harmful to fish, and almost anything else living on the bottom of the bays.

There were also periodic outbreaks of blue-green algae in Lake Ronkonkoma and Stony Brook University’s Roth Pond. This algae releases a poison harmful to humans and animals, but Gobler said students at the university shouldn’t worry, because he and other scientists at Stony Brook are constantly monitoring the water, especially before the annual Roth Regatta.

“[If nothing is done] the areas could expand — it could get more intense,” Gobler said. “We use a cutoff of three milligrams per liter, which is bad, but of course you can go to zero. An area like Hempstead Harbor went to zero, [Northport and Oyster Bays] went to zero at some points in time. There’s a usual day-night cycle, so it’s at night that the levels get very, very low.”

“We have the problem growing worse, and it is going to get worse before it gets better.”

—Dick Amper

As a result of the possibility of hypoxia expanding, Gobler said he and other scientists have also been monitoring Port Jefferson Harbor and Setauket Harbor.

Though Setauket Harbor is not currently experiencing any problems with hypoxia or algae, the harbor has experienced periods of pathogens, like E. coli, some of which were born from runoff into the harbor, but others might have come from leakage of antiquated cesspools in the area, according to George Hoffman, a trustee of the Setauket Harbor Task Force, which is also a member of the Clean Water Partnership.

Next May the task force hopes to start monitoring directly inside Setauket Harbor. Runoff from lawn fertilizers can also increase the nitrogen levels in the harbor.

“If our problem isn’t hypoxia, we have a problem with pathogens,” Hoffman said in a phone interview. “Prevention is really [Dr. Gobbler’s] goal — to know what is happening and to start taking steps. I think people’s information levels [on the topic] are high in the surface waters that they live by.”

In addition to hypoxia and blue-green algae, some of the water quality problems found in the assessment were brown tides on the South Shore, rust tide in the Peconic bays and paralytic shellfish poisoning on the East End — all of which are also nitrogen level issues that can be  traced back to cesspool sewage and fertilizers.

Port Jefferson Harbor is being monitored due to the speading of hypoxia across local bodies of water. File photo by Alex Petroski

“Make no mistake about it, this is so big that even … still, we have the problem growing worse, and it is going to get worse before it gets better,” said Dick Amper, the director of The Long Island Pine Barrens Society. “What’s the solution to this problem? We have to do more.”

There have been several efforts to help curb water degradation on Long Island. New York Gov. Andrew Cuomo (D) signed legislation in April that put $2.5 billion toward clean water protection, improving water infrastructure and building new sewer systems in Smithtown and Kings Park, and adding a rebate program for those upgrading outdated septic systems.

Despite doing more, the repairs will take some time.

“This is going to be a long, long marathon,” said Kevin McDonald, the conservation project director at The Nature Conservancy said.

There is also worry that the U.S. Army Corps of Engineers — announcing the dumping of dredged materials into Long Island Sound — could compound the problem.

“We have more political funding and will try to implement solutions,” Esposito said. “The problems are getting worse, but the solutions are becoming clearer.”

Dr. Samuel L. Stanley Jr., Stony Brook University president, helps a student move into a residence hall Aug. 25. Photo from Stony Brook University

By Rita J. Egan

Stony Brook University has been doing its part to make campus life feel more like home for most students, by offering gender-inclusive housing.

For a decade, the option has allowed students to share a room with friends or siblings no matter what their gender, or choose housing based on the gender they identify with. The only requirements are that students have to be 18 or older and sign a contract stating they will respect everyone in their residence hall.

On Aug. 25, move-in day for freshmen and transfer students, resident assistant Derrick Wegner, who is transgender, was on hand to greet newcomers. The senior psychology major said he was happy to have the option when he came to Stony Brook. Wegner, who lives in Wurtsboro,  said college is a great opportunity for a fresh start, especially for young people looking to transition. 

Derrick Wegner stands in the gender-inclusive room he shares with his best friend Sydney. Photo by Rita J. Egan

Wegner said the gender-inclusive housing option at Stony Brook creates a happy and safe environment, and he feels being happy and healthy plays a big part in being a successful student.

“You’re of value, and you belong here,” he said.

This year the senior is thrilled to be sharing a dorm with his best friend Sydney Monroe Gaglio, who he met early on in college through mutual friends.

“She’s my best friend, and I’m her best friend,” he said. “Just having somebody that I know I can go home to, and [say] this happened, and she’s like ‘I’m sorry.’ She just gets it.”

Ian Rose, who majors in engineering chemistry and applied mathematics and statistics, was thrilled when he heard of the gender-inclusive option. The junior said last year he made friends with Daniel Mahoney, Brandon O’Rourke, Bianca Mugone and Brittany Voboril, and they all became great friends. They lived in the same residence hall — the males in one room on one floor and the girls in their own room on another floor. Many nights last year they would find themselves in each other’s rooms studying or talking and decided to live together.

“We’re friends just hanging out,” Rose said.

This academic year the five are living in a suite with three bedrooms and one bathroom. Rose said at first his only concern was how things would work out in the bathroom, but so far things are going smoothly.

“I just want this to show everyone that guys and girls living together isn’t weird or uncomfortable,” Rose said. “You’re living with your friends; friends are friends. It doesn’t matter if you’re a boy or girl or different skin tone. It doesn’t matter; we’re all the same.”

Ian Rose, right, and friends settle in their three-bedroom suite after a long day. Photo from Ian Rose

Catherine-Mary Rivera, director of residential programs at SBU, said the program began as a small pilot initiative at the university 10 years ago, and grew slowly through the years. In 2016, approximately 40 students took advantage of the housing option, while this year more than 200 students — out of 10,683 living on campus — chose gender-inclusive residences across the campus.

She said the university wants to ensure that all students feel safe and welcome because it’s their home, and they have received plenty of positive feedback regarding the housing.

“The fact that it has grown from 42 to 200 has shown us students feel that they have a place here, and that they don’t have to either feel not comfortable being themselves or feel that Stony Brook doesn’t have a place for them, or they have to remain quiet about who they are or how they express themselves,” Rivera said. “That freedom has come through very clearly that this is a place they can thrive and be their true selves and live with their friends.”

The housing option also allows couples to live together; however, the university does recommend romantic partners think twice before making that decision.

“We want you to branch out and build a stronger community and have healthy relationships, and it may not be best to live with your significant other at this point,” Rivera said.

In addition to gender-inclusive housing, she said SBU offers all-gender, multi-stall bathrooms throughout campus and on the main floors of residence halls, in addition to all-men and all-women restrooms. Software updates have also been made to the school’s system allowing students and faculty members to choose their preferred names and pronoun if they would prefer to be addressed by something other than their legal name. The change means that identification cards and email addresses now show the name a person uses on a regular basis instead of their legal name.

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.

File photo

By Lu-Ann Kozlowski

Lu-Ann Kozlowski

As one of the premier research institutions in New York, Stony Brook University conducts clinical studies to advance our understanding of the prevention, diagnosis and possible roads to cures of all types of diseases. Every day, researchers at Stony Brook are going far beyond in their efforts to find answers to questions that face not only our own community but those around the globe.

At Stony Brook, major discoveries have been made that change the landscape of medicine thanks to the dedication of researchers willing to embark on new endeavors for the betterment of humankind. However, progress cannot be accomplished by a study team alone. Our research needs volunteers to help us answer the questions that advance medicine.

One of the leading reasons for the failure of a study is the lack of volunteer participation. There simply is no substitute for people willing to step up and get involved as research participants. Stony Brook understands this and has made great strides in reaching out and educating our community about this very important issue.

To educate the community about opportunities available in research and the importance of getting involved, we post on social media, attend health and wellness fairs and head a weekly informational kiosk in the lobby of our University Hospital. Stony Brook also maintains a website that assists individuals who would like to take the next step and volunteer and lists studies that are currently available.

Further, the university has hired a research subject advocate, an expert in research volunteer rights who is able to facilitate communication between patients and researchers, discuss questions or concerns with a volunteer and assist researchers in understanding and complying with the rules that ensure safe and ethical research.

In addition, Stony Brook has aligned with ResearchMatch, a national volunteer registry that connects people who want to participate in clinical studies with researchers who are seeking volunteers. This free Web-based service has one mission: to help to ensure the success of clinical research today, so that we can make a difference in the health of the future.

Deciding to participate in research is an important and personal decision. If you would like to learn more about participating or want to sign up for the ResearchMatch Registry, visit Stony Brook’s Volunteering in Research website at www.research.stonybrook.edu/volunteer or contact our research subject advocate at 631-632-9036. Medical breakthroughs cannot happen without you. Together, discovery is possible.

Lu-Ann Kozlowski is a Human Research Protection Program administrator and research participant advocate at Stony Brook University.

Demonstrators, above, at the May 10 March for Humanities at Stony Brook University protested potential cuts to humanities programs. Photo by Caroline Parker

Despite protests from students and faculty members, which included a March for Humanities rally May 10, the administration of Stony Brook University has decided to move ahead with the consolidation of departments in the College of Arts and Sciences.

In a June 22 email from Sacha Kopp, dean of the College of Arts and Sciences, the announcement was made the school will create a new Department of Comparative World Literature by combining the current departments of European Languages; Literatures & Cultures; Cultural Studies & Comparative Literature and Hispanic Languages & Literature.

“This newly combined department will draw upon faculty strengths in literature, culture and language across the college and reinforce Stony Brook’s position as a global institution,” he said in the email.

Kopp said undergraduate majors and minors in Spanish, French, Italian and German as well as a minor in Russian and master’s degree programs in language teaching would all be contained within the new department. The university will also continue to offer the graduate degree program in Hispanic languages and literature.

Other changes include the suspension of admissions into the undergraduate degree programs in theatre arts; comparative literature; cinema and cultural studies and into the graduate degree programs in cultural studies and comparative literature.

“While suspending admissions into programs is an extremely difficult decision, it is important to recognize that if constrained resources were spread over a growing number of programs, all of our programs would be weakened,” Kopp said. “That said we are building resources in key departments that have demonstrated academic and scholarly excellence.”

Port Jefferson resident Naomi Solo, whose husband Richard was part of the university faculty for five decades, said she was disappointed in the news, especially when it came to the suspension of admissions to the theatre arts program as she remembers the political theater of the 1960s and 70s.

“[The theatre arts program] is something that’s not a big money maker but makes a fuller university,” Solo said.

Kopp said that the university has planned no course changes for the 2017-18 academic year and students enrolled as of May 1 in the upcoming suspended programs will be able to complete their studies.

“For the fewer than 100 students who are currently enrolled in the degree programs into which new admissions are being suspended, every one of these students will have the opportunity to complete their programs, and we will honor existing commitments to graduate students for teaching assistantships,” he said.

According to a Frequently Asked Questions section created by the university on their website regarding the changes, the institution is making every effort to limit the impact to faculty and staff. The university is planning to reassign most; however, “some term appointments may not be renewed.” Administrators are also exploring other elements as part of a process to address the university’s “overarching budgetary challenges. According to the FAQ, “when put into practice we anticipate savings in excess of $1 million.”

Kopp said the changes occurred after discussions with faculty leadership, members of the university administration, the provost, the graduate school and the university senate.

Jordan Helin, a Ph.D. candidate in history and a department mobilizer in the history department for the Graduate Student Employees Union, participated in the May rally that the GSEU organized. Helin in an email said he wasn’t surprised by the announcement, and he sees no reason for the GSEU to give up on opposing the plan.

“A decision made is a decision that can be unmade,” he said. “Up until now, the administration has gotten by on waving off criticism because they are just floating ideas and nothing has been decided. Now that they have decided, they can be attacked with more specificity.”

Caroline Parker, who just completed her sophomore year and participated in the May rally, said in an email the combining of departments “flies in the face of the ‘commitment to diversity’ Stony Brook likes to uphold.”

“It’s true that these programs are small in numbers, but the critical thinking skills, cross-cultural exploration, creative expression and research taught therein are immeasurable for their far-reaching implications beyond borders and disciplines,” she said.

Parker said she is concerned about the future of the college.

“A true university cannot exist without humanities,” she said. “While people will be able to finish their degrees in the suspended programs, I fear the loss is a slippery slope and shows Stony Brook has lost sight of its mission, which will certainly affect future prospective students and the richness of our campus now.”