Following the people and events that make up the research community at Duke

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Duke Scientists Studying the Shape of COVID Things to Come

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The novel coronavirus pandemic has now resulted in more than 3 million confirmed cases globally and is pushing scientists to share ideas quickly and figure out the best ways to collaborate and contribute to solutions.

SARS-CoV-2 surface proteins illustrated by We Are Covert, via Wikimedia Commons

Recently, Duke researchers across the School of Medicine came together for an online symposium consisting of several short presentations to summarize the latest of what is known about the novel coronavirus, SARS-CoV-2.

This daylong event was organized by faculty in the Department of Molecular Genetics and Microbiology and researchers from different fields to share what they know about the virus and immunity to guide vaccine design. This conference highlighted the myriad new research pathways that Duke researchers are launching to better understand this pandemic virus.

One neat area of research is understanding viral processes within cells to identify steps at which antivirals may block the virus. Stacy Horner’s Laboratory studies how RNA viruses replicate inside human cells. By figuring out how viruses and cells interact at the molecular level, Horner can inform development of antivirals and strategies to block viral replication. Antivirals stop infections by preventing the virus from generating more of copies of itself and spreading to other cells. This controls damage to our cells and allows the immune system to catch up and clear the infection.

At the symposium, Horner explained how the SARS-CoV viral genome consists of 29,891 ribonucleotides, which are the building blocks of the RNA strand. The viral genome contains 14 areas where the RNA code can be transcribed into shorter RNA sequences for viral protein production. Though each RNA transcript generally contains the code for a single protein, this virus is intriguing in that it uses RNA tricks to code for up to 27 proteins. Horner highlighted two interesting ways that SARS-CoV packs in additional proteins to produce all the necessary components for its replication and assembly into new viral progeny.

The first way is through slippery sequences on the RNA genome of the virus. A ribosome is a machine inside the cell that runs along a string of RNA to translate its code into proteins that have various functions. Each set of 3 ribonucleotides forms one amino acid, a building block of proteins. In turn, a string of amino acids assembles into a distinct structure that gives rise to a functional protein.

One way that SARS-CoV-2 packs in additional proteins is with regions of its RNA genome that make the ribosome machinery slip back by one ribonucleotide. Once the ribosome gets offset it reads a new grouping of 3 ribonucleotides and creates a different amino acid for the same RNA sequence. In this way, SARS-CoV-2 makes multiple proteins from the same piece of RNA and maximizes space on its genome for additional viral proteins.

An example of an RNA ‘hairpin’ structure, which might fool a ribosome to jump across the sequence rather than reading around the little cul de sac. (Ben Moore, via Wikimedia Commons)

Secondly, the RNA genome of SARS-CoV-2 has regions where the single strand of RNA twists over itself and connects with another segment of RNA farther along the code to form a new protein. These folds create structures that look like diverse trees made of repetitive hairpin-like shapes. If the ribosome runs into a fold, it can hop from one spot in the RNA to another disjoint piece and attach a new string of amino acids instead of the ones directly ahead of it on the linear RNA sequence. This is another way the SARS-CoV-2 packs in extra proteins with the same piece of RNA.

Horner said a step-by-step understanding of what the virus needs to survive at each step of its replication cycle will allow us to design molecules that are able to block these crucial steps.

Indeed, shapes of molecules can determine their function inside the cell. Three Duke teams are pursuing detailed investigation of SARS-CoV-2 protein structures that might guide development of complementarily shaped molecules that can serve as drugs by interfering with viral processes inside cells.

Some Duke faculty who participated in the virtual viral conference. (L-R from, top) Stacy Horner, Nick Heaton, Micah Luftig, Sallie Permar, Ed Miao and Georgia Tomaras. (image: Tulika Singh)

For example the laboratory of Hashim Al-Hashimi, develops computational models to predict the diversity of structures produced by these tree-like RNA folds to identify possible targets for new therapeutics. Currently, the Laboratories of Nicholas Heaton and Claire Smith are teaming up to identify novel restriction factors inside cells that can stop SARS-CoV-2.

However, it is not just the structures of viral components expressed inside the cells that matter, but also those on the outside of a virus particle. In Latin, corona means a crown or garland, and coronaviruses have been named for their distinctive crown-like spikes that envelop each virus particle. The viral protein that forms this corona is aptly named the “Spike” protein.

This Spike protein on the viral surface connects with a human cell surface protein (Angiotensin-converting enzyme 2, abbreviated as ACE2) to allow the virus to enter our cells and cause an infection. Heaton proposed that molecules designed to block this contact, by blocking either the human cell surface protein or the viral Spike protein, should also be tested as possible therapies.

One promising type of molecule to block this interaction is an antibody. Antibodies are “Y” shaped molecules that are developed as part of the immune response in the body by the second week of coronavirus infection. These molecules can detect viral proteins, bind with them, and prevent viruses from entering cells. Unlike several other components on our immune defense, antibodies are shaped to specifically latch on to one type of virus. Teams of scientists at Duke led by Dr. Sallie Permar, Dr. Georgia Tomaras, and Dr. Genevieve Fouda are working to characterize this antibody response to SARS-CoV-2 infection and identify the types of antibodies that confer protection.

Infectious disease specialist Dr. Chris Woods is leading an effort to test whether plasma with antibodies from people who have recovered can prevent severe coronavirus disease in acutely infected patients.

Indeed, there are several intriguing research questions to resolve in the months ahead. Duke scientists are forging new plans for research and actively launching new projects to unravel the mysteries of SARS-CoV-2. With Duke laboratory scientists rolling up their sleeves and gowning up to conduct research on the novel coronavirus, there will be soon be many more vaccine and therapeutic interventions to test.

Guest post by Tulika Singh, MPH, PhD Candidate in the Department of Molecular Genetics and Microbiology (T: @Singh_Tulika)

Duke’s Fundamental Research Can Turn Viruses Into Marvels

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The COVID-19 epidemic has impacted the Duke research enterprise in profound ways. Nearly all laboratory-based research has been temporarily halted, except for research directly connected to the fight against COVID-19. It will take much time to return to normal, and that process of renewal will be gradual and will be implemented carefully.

Trying to put this situation into a broader perspective, I thought of the 1939 essay by Abraham Flexner published in Harper’s magazine, entitled “The Usefulness of Useless Knowledge.” Flexner was the founding Director of the Institute for Advanced Study at Princeton, and in that essay, he ruminated on much of the type of knowledge acquired at research universities —  knowledge motivated by no objective other than the basic human desire to understand. As Flexner said, the pursuit of this type of knowledge sometimes leads to surprises that transform the way we see that which was previously taken for granted, or for which we had previously given up hope. Such knowledge is sometimes very useful, in highly unintended ways.

Gregory Gray, MD MPH
Gregory Gray, MD MPH

The 1918 influenza pandemic led to 500 million confirmed cases, and 50 million deaths. In the Century since, consider how far we have come in our understanding of epidemics, and how that knowledge has impacted our ability to respond. People like Greg Gray, a professor of medicine and member of the Duke Global Health Institute (DGHI), have been quietly studying viruses for many years, including how viruses at domestic animal farms and food markets can leap from animals to humans. Many believe the COVID-19 virus started from a bat and was transferred to a human. Dr. Gray has been a global leader in studying this mechanism of a potential viral pandemic, doing much of his work in Asia, and that experience makes him uniquely positioned to provide understanding of our current predicament.

From the health-policy perspective, Mark McClellan, Director of the Duke Margolis Center for Health Policy, has been a leading voice in understanding viruses and the best policy responses to an epidemic. As a former FDA director, he has experience bringing policy to life, and his voice carries weight in the halls of Washington. Drawing on faculty from across Duke and its extensive applied policy research capacity, the Margolis Center has been at the forefront in guiding policymakers in responding to COVID-19.

Through knowledge accrued by academic leaders like Drs. Gray and McClellan, one notes with awe the difference in how the world has responded to a viral threat today, relative to 100 years ago. While there has been significant turmoil in many people’s lives today, as well as significant hardship, the number of global deaths caused by COVID-19 has been reduced substantially relative to 1918.

One of the seemingly unusual aspects of COVID-19 is that a substantial fraction of the population infected by the virus has no symptoms. However, those asymptomatic individuals shed the virus and infect others. While most people have no or mild symptoms, other people have very adverse effects to COVID-19, some dying quickly.

This heterogeneous response to COVID-19 is a characteristic of viruses studied by Chris Woods, a professor medicine in infectious diseases. Dr. Woods, and his colleagues in the Schools of Medicine and Engineering, have investigated this phenomenon for years, long before the current crisis, focusing their studies on the genomic response of the human host to a virus. This knowledge of viruses has made Dr. Woods and his colleagues leading voices in understanding COVID-19, and guiding the clinical response.

A team led by Greg Sempowski, a professor of pathology in the Human Vaccine Institute is working to isolate protective antibodies from SARS-CoV-2-infected individuals to see if they may be used as drugs to prevent or treat COVID-19. They’re seeking antibodies that can neutralize or kill the virus, which are called neutralizing antibodies.

Barton Haynes,MD
Barton Haynes, MD

Many believe that only a vaccine for COVID-19 can truly return life to normal. Human Vaccine Institute Director Barton Haynes, and his colleagues are at the forefront of developing that vaccine to provide human resistance to COVID-19. Dr. Haynes has been focusing on vaccine research for numerous years, and now that work is at the forefront in the fight against COVID-19.

Engineering and materials science have also advanced significantly since 1918. Ken Gall, a professor of mechanical engineering and materials science has led Duke’s novel application of 3D printing to develop methods for creatively designing personal protective equipment (PPE). These PPE are being used in the Duke hospital, and throughout the world to protect healthcare providers in the fight against COVID-19.

Much of the work discussed above, in addition to being motivated by the desire to understand and adapt to viruses, is motivated from the perspective that viruses must be fought to extend human life.

In contrast, several years ago Jennifer Doudna and Emmanuelle Charpentier, academics at Berkeley and the Max Planck Institute, respectively, asked a seemingly useless question. They wanted to understand how bacteria defended themselves against a virus. What may have made this work seem even more useless is that the specific class of viruses (called phage) that infect bacteria do not cause human disease. Useless stuff! The kind of work that can only take place at a university. That basic research led to the discovery of clustered regularly interspaced short palindromic repeats (CRISPR), a bacterial defense system against viruses, as a tool for manipulating genome sequences. Unexpectedly, CRISPR manifested an almost unbelievable ability to edit the genome, with the potential to cure previously incurable genetic diseases.

Charles Gersbach, a professor of Biomedical Engineering, and his colleagues at Duke are at the forefront of CRISPR research for gene and cell therapy. In fact, he is working with Duke surgery professor and gene therapy expert Aravind Asokan to engineer another class of viruses, recently approved by the FDA for other gene therapies, to deliver CRISPR to diseased tissues. Far from a killer, the modified virus is essential to getting CRISPR to the right tissues to perform gene editing in a manner that was previously thought impossible. There is hope that CRISPR technology can lead to cures for sickle cell and other genetic blood disorders. It is also being used to fight cancer and muscular dystrophy, among many other diseases and it is being used at Duke by Dr. Gersbach in the fight against COVID-19. 

David Ashley, Ph.D.
David Ashley, Ph.D.

In another seemingly bizarre use of a virus, a modified form of the polio virus is being used at Duke to fight glioblastoma, a brain tumor. That work is being pursued within the Preston Robert Tisch Brain Tumor Center, for which David Ashley is the Director. The use of modified polio virus excites the innate human immune system to fight glioblastoma, and extends life in ways that were previously unimaginable. But there are still many basic-science questions that must be overcome. The remarkable extension of life with polio-based immunotherapy occurs for only 20% of glioblastoma patients. Why? Recall from the work of Dr. Woods discussed above, and from our own observation of COVID-19, not all people respond to viruses in the same way. Could this explain the mixed effectiveness of immunotherapy for glioblastoma? It is not known at this time, although Dr. Ashley feels it is likely to be a key factor. Much research is required, to better understand the diversity in the host response to viruses, and to further improve immunotherapy.

The COVID-19 pandemic is a challenge that is disrupting all aspects of life. Through fundamental research being done at Duke, our understanding of such a pandemic has advanced markedly, speeding and improving our capacity to respond. By innovative partnerships between Duke engineers and clinicians, novel methods are being developed to protect frontline medical professionals. Further, via innovative technologies like CRISPR and immunotherapy — that could only seem like science fiction in 1918 (and as recently as 2010!) — viruses are being used to save lives for previously intractable diseases.

Viruses can be killers, but they are also scientific marvels. This is the promise of fundamental research; this is the impact of Duke research.

“We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time.”

T.S. Eliot, Four Quartets

Post by Lawrence Carin, Vice President for Research

Contaminated Drinking Water in Our Backyard

About 70% of the human body is made up of water. Water is something we consume on a daily basis. Therefore, when a community’s water source is threatened or contaminated it can be extremely detrimental. 

In 2017, it became apparent that there was water contamination in eastern North Carolina. Specifically, PFAS or per- and polyfluoroalkyl Alkyl chemicals were found in the water supply. As a result, several legislative mandates were issued in 2018 establishing a PFAS Testing Network to investigate the contamination.

Lee Ferguson, an Associate Professor of Civil and Environmental Engineering at Duke and Kathleen Gray, a professor at UNC’s Institute for the Environment, are testing PFAS water contamination and communicating any risks to the public. 

Gray is part of the network’s risk communication team. She explained that PFASs are hard to address because the health effects are unknown and they have yet to determine a standard or guideline for these substances. However, because this water contamination affects the lives of everyone connected to the water supply it is extremely important to communicate risk to the affected community but without eliciting panic. 

Gray explained that people often ask, “Are my family and I safe?” “What can I do to protect myself and my family?” “Why did this happen?” and “Why wasn’t it prevented?”

In the last year Ferguson and his research team have tested 409 sites in North Carolina for PFAS compounds.

He explained that PFAS substances are particularly dangerous because they are non-degradable, potentially toxic and constantly changing. Long-chain PFASs are being replaced by fluorinated alternatives.

Ferguson described this phenomenon as “playing environmental ‘whack-a-mole’ with different substances.”

Ferguson and his testing team have found two contaminated water supply sites in North Carolina. Dangerous contamination is based on the EPA health advisory level of 70ng/Liter. The exceedances were found in Maysville and Orange Water and Sewer Authority. Maysville was able to switch to the Jones County water source once the problem was identified.

New data that came in within the last couple weeks found high month-to-month variability in PFAS in the Haw River near Pittsboro. Ferguson and his team predict that it is coming downstream from a waste treatment plant. 

Brunswick County is shown having the worst PFAS concentrations. However, Dr. Ferguson and his team have recently found that the contamination in Haw River is even worse.

While all of this information may seem very alarming, Gray and Ferguson both reiterated that it is not necessary to panic. Instead, people should make sure they are drinking filtered water or invest in a water filter. 

Ferguson added, “The best choice is reverse osmosis.”

Gray and Ferguson presented their work at a SciComm Lunch-and-Learn, a monthly event sponsored by Duke Science & Society Initiative that explores interesting and innovative aspects of science communication. The event is free and open to anyone in the Duke community.

By Anna Gotskind

Curating a New Portrait of Black America

It’s been over three years since the National Museum of African American History & Culture (NMAAHC) opened in D.C. in September 2016, but the excitement around it doesn’t seem to have dimmed much. Chances are, you’re going to have to get your tickets three months in advance if you want to visit. Infants need their own timed pass, too.

The National Museum of African American History and Culture.
Photo courtesy of Prabal Tiwari

On Friday, January 17, Duke’s From Slavery to Freedom Lab hosted a panel in conjunction with the Franklin Humanities Institute on the topic of contemporary Black arts and icons. The panel, “New Black Aesthetics,” featured speakers Rhea L. Combs, curator at the National Museum of African American & Culture, and Richard J. Powell, John Spencer Bassett Professor of Art & Art History at Duke, and was one half of a two-panel conference titled “Black Images, Black Histories.”

According to Combs and Powell, the reason for the unprecedented popularity of works like the NMAAHC by contemporary Black artists is likely because they do something that other pieces and people rarely do: allow African Americans to tell the African American story.

As a museum curator, Combs doesn’t simply curate cohesive mixed-media exhibitions that shed light on the Black experience. In order to create those exhibitions, she must also dig through and analyze a wide range of old archival materials.

20180925-Rhea Resized.jpg
Rhea L. Combs, Curator at the NMAAHC.
Photo courtesy of the Smithsonian

However, these archival materials at the NMAAHC aren’t necessarily just historical artifacts and records associated with figures like Rosa Parks or the Obamas; the Museum wants people to shuffle through their own attics to find things to donate. It demystifies the question of who belongs in a museum, according to Combs. “We create agency in terms of who gets to tell everyday stories,” she said.

She’s especially interested in the role of photography and film in African American studies. “We use cameras to culturally agitate the ways in which African Americans are understood,” she explained; the camera is a pathway into self-representation.

Captured in the Museum’s photos and moving images are stories of duplicity, or “celebrations that happened in the midst of tragedies.” Combs often finds themes of faith and activism as well as education and uplift, but she says that there’s plenty of variety within those overarching ideas. A photo of boys playing basketball on unicycles, for example.

“Art creates social understanding of who we are,” Combs said. Like hip-hop remixes and re-envisions things that are already understood in one way, so too does the NMAAHC.

On a similar vein, Powell’s presentation focused on the famous Obama portraits, and I’m guessing you might already know which ones I’m referring to. A fully-suited Barack Obama, seated in a wooden chair against a lush green background of flora and fauna; Michelle Obama in a flowing black-and-white colorblock dress, her chin resting on the back of her hand.

Powell examines how these portraits, simply titled “President Barack Obama” and “First Lady Michelle Obama,” manage to blend visual elements with socio-historical allusions and contexts to become world-famous 21st-century icons.

Richard J. Powell, Professor of Art and Art History at Duke.

While the portraits are visually exceptional, Powell said their context is what envelops. These images of the first Black U.S. president and first lady do allude to the old, white traditions of portraiture, “but they dismantle the genre’s conventional outcomes” for something new, he explained.

The portrait of Barack Obama is, visually, extremely similar to those of Abraham Lincoln and Franklin Delano Roosevelt. Likewise, Michelle Obama’s portrait quite closely resembles that of Madame Moitessier, for example. But unlike these representations of pre-21st-century white men and women, the Obama portraits finally depict people of color. According to Powell, portraits elevate status, and it isn’t very often that you see Black individuals portrayed.

And yet there’s also a sad irony involved, Powell explained. Especially for other similar contemporary works of portraiture that depict Black people, there’s a decorative, incongruous grandeur that highlights the tension between social realities and the manner of portrayal. For instance, “saintly” portraits exist of Black men wearing urban clothing, but despite whatever “saintliness” might be visually depicted, the realities of Blackness in the inner cities of America is often far from positive.

One of the most striking features of the Barack Obama portrait is the blooming greenery behind the former president. It’s a metaphor of sorts, Powell said: social and historical context isn’t absent from art. Or, in other words, “The world can never be left out of the garden.”

By Irene Park

Inventing New Ways to Do Brain Surgery

This is the sixth and final 2019 post written by students at the North Carolina School of Science and Math as part of an elective about science communication with Dean Amy Sheck.

Dr. Patrick Codd is the Director of the Duke Brain Tool Laboratory and an Assistant Professor of Neurosurgery at Duke. Working as a neurosurgeon and helping with the research and development of various neurosurgical devices is “a delicate balance,” he said.

Patrick Codd

Codd currently runs a minimally invasive neurosurgery group. However, at Massachusetts General Hospital, he used to run the trauma section. When asked about which role was more stressful, he stated “they were both pretty stressful” but for different reasons. At Mass General, he was on call for most hours of the day and had to pull long shifts in the operating room. At Duke, he has to juggle surgery, teaching, and research and the development of new technology.

“I didn’t know I was going to be a neurosurgeon until I was in college,” Codd said. Despite all of the interesting specialties he learned about in medical school, he said “it was always neurosurgery that brought me back.”

Currently, he is exclusively conducting cranial surgery.

 Neurosurgeon U.S. Air Force Maj Jonathan Forbes,looks through loupes as he performs brain surgery at the Bagram Air Field in Afghanistan, Oct. 10, 2014. 

Though Dr. Codd has earned many leadership positions in his career, he said he was never focused on advancement. He simply enjoys working on topics which he loves, such as improving minimally invasive surgical techniques. But being in leadership lets him unite other people who are interested in working towards a common goal in research and development. He has been able to skillfully bring people together from various specialties and help guide them. However, it is difficult to meet everyone’s needs all of the time. What is important for him is to be a leader when he needs to be.

Dr. Codd said there are typically five to eight research papers necessary in to lay the groundwork for every device that is developed. However, some technologies are based on the development of a single paper. He has worked on devices that make surgery more efficient and less minimally invasive and those that help the surgical team work together better. When developing technologies, he tries to keep the original purpose of the devices the same. However, many revisions are made to the initial design plans as requirements from the FDA and other institutions must be met. Ironically, Dr. Codd can’t use the devices he develops in his own operating room because it would be a conflict of interest. Typically other neurosurgeons from across the country will use them instead.

Post by Andrew Bahhouth, NCSSM 2020

Infants, Immunity, Infections and Immunization

This is the fourth of several posts written by students at the North Carolina School of Science and Math as part of an elective about science communication with Dean Amy Sheck.

Dr. Giny Fouda’s research focuses on infant immune responses to infection and vaccination.

Her curiosity about immunology arose during her fourth year of medical school in Cameroon, when she randomly picked up a book on cancer immunotherapy and was captivated. Until then, she conducted research on malaria and connected it to her interest in pediatrics by studying the effects of the parasitic disease on the placentas of mothers.

Genevieve Giny Fouda M.D., Ph.D.

As a postdoctoral fellow at Duke, she then linked pediatrics and immunology to begin examining mother to child transmission of disease and immunity.

Today she is an M.D. and a Ph.D. and a member of the Duke Human Vaccine Institute. She’s an assistant professor in pediatrics and an assistant research professor in the Department of Molecular Genetics and Microbiology at Duke University School of Medicine.

Based on the recent finding that children of HIV-positive mothers are more susceptible to inheriting the disease, Fouda believes that it is important to understand how to intervene in passive immunity transmissions in order to limit them. Children and adults recover from diseases differently and uncovering these differences is important for vaccine development.

This area of research is personally important to her, because she learned from her service in health campaigns in Central Africa that it is much easier to prevent disease than to treat.

Babies!

However, she believes that it is important to recognize that research is a collaborative experience with a team of scientists. Each discovery is not that of an individual, but can be accredited to everyone’s contribution, especially those whose roles may seem small but are vital to the everyday operations of the lab.

At the Duke Human Vaccine Institute, Fouda enjoys collaborating as a team and contributing her time as a mentor and trainer of young scientists in the next generation.

Outside of the lab, Fouda likes to spend time reading books with her daughter, traveling, decorating and gardening. If there was one factor that improve how science in immunology is conducted, she would stress that preventing disease is significantly cheaper than treating those that become infected by it.

Dr. Fouda has made some remarkable progress in the field of disease treatment with her hard working and optimistic personality, and I know that she will continue to excel in her objectives for years to come.

Post by Vandanaa Jayaprakash NCSSM 2020

Games, Art, and New Frontiers

This is the third of several posts written by students at the North Carolina School of Science and Math as part of an elective about science communication with Dean Amy Sheck.

Beneath Duke University’s Perkins library, an unassuming, yet fiercely original approach to video games research is underway. Tied less to computer science and engineering than you might expect, the students and faculty are studying games for their effects on players.

I was introduced to a graduate researcher who has turned a game into an experiment. His work exists between the humanities, psychology, and computer science. Some games, particularly modern ones, feature complex economies that require players to collaborate as often as they compete. These researchers have adapted that property to create an economics game in which participants anonymously affect the opportunities – and setbacks – of other players. Wealth inequality is built in. The players’ behavior, they hope, will inform them about ‘real-world’ economic decisions.

Shai Ginsburg playing

At the intersection of this interdisciplinary effort with games, I met  Shai Ginsburg, an associate professor in the department of Asian and Middle Eastern studies who studies video games and board games the way other humanities professors might study Beowulf.

For example, he is able to divide human history into eras of games rather than of geopolitics.

“Until recently, games were not all that interactive,” he says. “Video games are, obviously, interactive, but board games have evolved, too, over the same period of time.” This shift is compelling because it offers us new freedoms in the way we express human experience.

A new gaming suite at Lawrence Tech University in Southfield, Mich. (LTU/Matt Roush)

“The fusion of storytelling and interactivity in games is very compelling,” Ginsburg says. “We haven’t seen that many games that handle issues like mental illness,” until more recently, he points out. The degree of interactivity in a video game grants a player a closeness to the narrative in the areas where writing, music, and visual art alone would be restricted. This closeness gives game designers – as artists – the freedom to explore themes where those artistic restrictions also hinder communication.

However, Dr. Ginsburg is not a game historian; the time that a game feature evolved is far less relevant to him than how its parent game affects players. “We tend to focus on the texts that interest us in a literature class,” he says, by way of example. He studies the games that interest him for the play opportunities they provide.

One advantage of using games as a medium to study their effects on people is that, “the distinction between highbrow and lowbrow is not yet there,” Ginsburg says. In painting, writing, and plenty of other mediums, a clear distinction between “good” and “bad” is decided simultaneously by communities of critics and consumers. Not so, in the case of games.

“I look at communities as a measure of the effectivity of the game less than for itself,” Ginsburg notes. “I think the question is ‘how was I reacting?’ and ‘why was I reacting in such a way?’” he says. Ginsburg’s effort seeks to reveal the mechanisms that give games their societal impact, though those impacts can be elusive. How to learn more? “Play lots of games. Play different kinds of games. Play more games.”

Guest Post by Jackson Meade, NCSSM 2020

Sharing is Caring, But How Does it Start?

This is the second of several posts written by students at the North Carolina School of Science and Math as part of an elective about science communication with Dean Amy Sheck.

As an occasional volunteer at a local children’s museum, I can tell you that children take many different approaches to sharing. Some will happily lend others their favorite toys, while others will burst into tears at the suggestion of giving others a turn in an exhibit.

For Rita Svetlova Ph.D. at the Duke Empathy Development Lab, these behaviors aren’t just passing observations, they are her primary scientific focus. In November, I sat down with Dr. Svetlova to discuss her current research, past investigations, and future plans.

Margarita Lvovna Svetlova

Originally from Russia, Svetlova obtained an M.A. from Lomonosov Moscow State University in Moscow before earning her Ph.D in developmental psychology from the University of Pittsburgh. She later worked as a post-doctoral researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Now at Duke University as an assistant research professor of psychology and neuroscience and the principal investigator in the Empathy Development Lab, Svetlova looks at the development of ‘prosocial’ behavior in children — behaviors such as sharing, empathy, and teamwork.

Svetlova credits her mentor at the University of Pittsburgh, Dr. Celia Brownell, for inspiring her to pursue child psychology and development. “I’ve always been interested in prosociality, but when I was in Russia I actually studied linguistics,” she says. “When I moved to the U.S., I changed paths partly because I’ve always wanted to know more about human psychology. The reason I started studying children is partly because I was interested in it and partly because I met Dr. Brownell. I branched out a little bit, but I generally found it interesting.”

An unsuccessful sharing experience. (From Awkward Family Photos)

Although her passion for childhood development research began in Pittsburgh,  Svetlova has embraced her role as a Duke researcher, most recently tackling a scenario that most academically-inclined readers are familiar with — a partner’s failure to perform in a joint-commitment — in a co-authored May 2017 paper titled “Three-Year-Olds’ Reactions to a Partner’s Failure to Perform Her Role in a Joint Commitment.”

In the study, 144 three-year-olds were presented with a common joint commitment scenario: playing a game. For one third of the children, the game ended when their partner defected, while another third of the test group had a partner who didn’t know how to play.  The final third of the group saw the game apparatus break. Svetlova looked at how the children’s reactions varied by scenario: protesting defectors, teaching the ignorant partner, and blaming the broken apparatus. The results seem to suggest that three-year-olds have the ability to evaluate intentions in a joint commitment.

Another paper Svetlova co-authored, titled “Three- and 5-Year-Old Childrens’ Understanding of How to Dissolve a Joint Commitment,” compared the reactions of three- and five-year-olds when a puppet left a collaborative game with either permission, prior notification, or suddenly without prior notification. If the puppet left without warning, three-year-old subjects protested more and waited longer for the puppet’s return, but both age groups seemed to understand the agreement implicit in a joint commitment.

These joint commitments are only a small fraction of the questions that Svetlova hopes to address.

“A longitudinal study of prosociality would be amazing,” she says. “What I’m interested in now is the intersection of fairness understanding and in-group/out-group bias. What I am trying to look into is how children understand their in-group members vs. out-group members and whether there’s something we can do to make them more accepting of their out-group members.”

“Another one I am interested in is the neural basis of empathy and prosocial behavior. I haven’t started yet, but I’m planning a couple of studies on looking into the brain mechanisms of empathy in particular,” Svetolova says. “We plan to scan children and adults while experiencing an emotion themselves and compare that brain activation to the brain activation while witnessing someone experiencing an emotion, the question being ‘do we really feel others’ emotions as our own?’”

Svetlova also expressed her interest in the roles that gender, culture, and upbringing play in a child’s development of prosociality.

I had to ask her why teenagers seemed to “regress” in prosociality, seemingly becoming more selfish when compared to their childhood selves.

“I would distinguish between self-centered and selfish,” she assured me. “You are not necessarily selfish, it’s just that during teenagehood you are looking for your place in the world, in the ‘pack.’ That’s why these things become very important, other’s opinions about you and your reputation in this little group, people become very anxious about it, it doesn’t mean that they become selfish all of a sudden or stop being prosocial.” She added, “I believe in the good in people, including teenagers.”

Guest Post by Sellers Hill, NCSSM 2020

How Do You Engineer a Microbial Community?

This is the first of several posts written by students at the North Carolina School of Science and Math as part of an elective about science communication with Dean Amy Sheck.

Claudia Gunsch, the Theodore Kennedy distinguished associate professor in the department of civil and environmental engineering, wants to know how to engineer a microbial community. An environmental engineer with a fascination for the world at the micro level, Gunsch takes a unique approach to solving the problem of environmental pollution: She looks to what’s already been done by nature.

Claudia Gunsch, Ph.D.

Gunsch and her team seek to harness the power of microbes to create living communities capable of degrading contamination in the environment.

“How can you engineer that microbial community so the organisms that degrade the pollutant become enriched?” she asks. “Or — if you’re thinking about dangerous pathogenic organisms — how do you engineer the microbial community so that those organisms become depressed in that particular environment?”

The first step, Gunsch says, is to figure out who’s there. What microbes make up a community? How do these organisms function? Who is doing what? Which organisms are interchangeable? Which prefer to live with one another, and which prefer not living with one another?

“Once we can really start building that kind of framework,” she says, “we can start engineering it for our particular purposes.”

Yet identifying the members of a microbial community is far more difficult than it may seem. Shallow databases coupled with vast variations in microbial communities leave Gunsch and her team with quite a challenge. Gunsch, however, remains optimistic.

Map of U.S. Superfund Sites (2013)

“The exciting part is that we have all these technologies where we can sequence all these samples,” she says. “As we become more sophisticated and more people do this type of research, we keep feeding all of this data into these databases. Then we will have more information and one day, we’ll be able to go out and take that sample and know exactly who’s there.”

“Right now, it’s in its infancy,” she says with a smile. “But in the long-term, I have no doubt we will get there.”

Gunsch is currently working on Duke’s Superfund Research Center designing bioremediation technologies for the degradation of polycyclic aromatic hydrocarbon (PAH) contamination. These pollutants are extremely difficult to break down due to their tendency to stick strongly onto soil and sediments. Gunsch and her team are searching for the right microbial community to break these compounds down — all by taking advantage of the innate capabilities of these microorganisms.

A photo montage from Dr. Gunsch’s lab page.

Step one, Gunsch says, has already been completed. She and her team have identified several different organisms capable of degrading PAHs. The next step, she explains, is assembling the microbial communities — taking these organisms and getting them to work together, sometimes even across kingdoms of life. Teamwork at the micro level.

The subsequent challenge, then, is figuring out how these organisms will survive and thrive in the environment they’re placed in, and which microbial seeds will best degrade the contamination when placed in the environment. This technique is known as “precision bioremediation” — similar to precision medicine, it involves finding the right solution in the right amounts to be the most effective in a certain scenario.

“In this particular case, we’re trying to figure out what the right cocktail of microbes we can add to an environment that will lead to the end result that is desired — in this case, PAH degradation,” Gunsch says.

Ultimately, the aim is to reduce pollution and restore ecological health to contaminated environments. A lofty goal, but one within sight. Yet Gunsch sees applications beyond work in the environment — all work dealing with microbes, she says, has the potential to be impacted by this research.

“If we understand how these organisms work together,” she says, “then we can advance our understanding of human health microbiomes as well.”

Post by Emily Yang, NCSSM 2021

Scientists Made a ‘T-Ray’ Laser That Runs on Laughing Gas

‘T-Ray’ laser finally arrives in practical, tunable form. Duke physicist Henry Everitt worked on it over two decades. Courtesy of Chad Scales, US Army Futures Command

It was a Frankenstein moment for Duke alumnus and adjunct physics professor Henry Everitt.

After years of working out the basic principles behind his new laser, last Halloween he was finally ready to put it to the test. He turned some knobs and toggled some switches, and presto, the first bright beam came shooting out.

“It was like, ‘It’s alive!’” Everitt said.

This was no laser for presenting Powerpoint slides or entertaining cats. Everitt and colleagues have invented a new type of laser that emits beams of light in the ‘terahertz gap,’ the no-man’s-land of the electromagnetic spectrum between microwaves and infrared light.

Terahertz radiation, or ‘T-rays,’ can see through clothing and packaging, but without the health hazards of harmful radiation, so they could be used in security scanners to spot concealed weapons without subjecting people to the dangers of X-rays.

It’s also possible to identify substances by the characteristic frequencies they absorb when T-rays hit them, which makes terahertz waves ideal for detecting toxins in the air or gases between the stars. And because such frequencies are higher than those of radio waves and microwaves, they can carry more bandwidth, so terahertz signals could transmit data many times faster than today’s cellular or Wi-Fi networks.

“Imagine a wireless hotspot where you could download a movie to your phone in a fraction of a second,” Everitt said.

Yet despite the potential payoffs, T-rays aren’t widely used because there isn’t a portable, cheap or easy way to make them.

Now Everitt and colleagues at Harvard University and MIT have invented a small, tunable T-ray laser that might help scientists tap into the terahertz band’s potential.

While most terahertz molecular lasers take up an area the size of a ping pong table, the new device could fit in a shoebox. And while previous sources emit light at just one or a few select frequencies, their laser could be tuned to emit over the entire terahertz spectrum, from 0.1 to 10 THz.

The laser’s tunability gives it another practical advantage, researchers say: the ability to adjust how far the T-ray beam travels. Terahertz signals don’t go very far because water vapor in the air absorbs them. But because some terahertz frequencies are more strongly absorbed by the atmosphere than others, the tuning capability of the new laser makes it possible to control how far the waves travel simply by changing the frequency. This might be ideal for applications like keeping car radar sensors from interfering with each other, or restricting wireless signals to short distances so potential eavesdroppers can’t intercept them and listen in.

Everitt and a team co-led by Federico Capasso of Harvard and Steven Johnson of MIT describe their approach this week in the journal Science. The device works by harnessing discrete shifts in the energy levels of spinning gas molecules when they’re hit by another laser emitting infrared light.

Their T-ray laser consists of a pencil-sized copper tube filled with gas, and a 1-millimeter pinhole at one end. A zap from the infrared laser excites the gas molecules within, and when the molecules in this higher energy state outnumber the ones in a lower one, they emit T-rays.

The team dubbed their gizmo the “laughing gas laser” because it uses nitrous oxide, though almost any gas could work, they say.

Duke professor Henry Everitt and MIT graduate student Fan Wang and colleagues have invented a new laser that emits beams of light in the ‘terahertz gap,’ the no-man’s-land of the electromagnetic spectrum.

Everitt started working on terahertz laser designs 35 years ago as a Duke undergraduate in the mid-1980s, when a physics professor named Frank De Lucia offered him a summer job.

De Lucia was interested in improving special lasers called “OPFIR lasers,” which were the most powerful sources of T-rays at the time. They were too bulky for widespread use, and they relied on an equally unwieldy infrared laser called a CO2 laser to excite the gas inside.

Everitt was tasked with trying to generate T-rays with smaller gas laser designs. A summer gig soon grew into an undergraduate honors thesis, and eventually a Ph.D. from Duke, during which he and De Lucia managed to shrink the footprint of their OPFIR lasers from the size of an axe handle to the size of a toothpick.

But the CO2 lasers they were partnered with were still quite cumbersome and dangerous, and each time researchers wanted to produce a different frequency they needed to use a different gas. When more compact and tunable sources of T-rays came to be, OPFIR lasers were largely abandoned.

Everitt would shelf the idea for another decade before a better alternative to the CO2 laser came along, a compact infrared laser invented by Harvard’s Capasso that could be tuned to any frequency over a swath of the infrared spectrum.

By replacing the CO2 laser with Capasso’s laser, Everitt realized they wouldn’t need to change the laser gas anymore to change the frequency. He thought the OPFIR laser approach could make a comeback. So he partnered with Johnson’s team at MIT to work out the theory, then with Capasso’s group to give it a shot.

The team has moved to patent their design, but there is still a long way before it finds its way onto store shelves or into consumers’ hands. Nonetheless, the researchers — who couldn’t resist a laser joke — say the outlook for the technique is “very bright.”

This research was supported by the U.S. Army Research Office (W911NF-19-2-0168, W911NF-13-D-0001) and by the National Science Foundation (ECCS-1614631) and its Materials Research Science and Engineering Center Program (DMR-1419807).

CITATION: “Widely Tunable Compact Terahertz Gas Lasers,” Paul Chevalier, Arman Armizhan, Fan Wang, Marco Piccardo, Steven G. Johnson, Federico Capasso, Henry Everitt. Science, Nov. 15, 2019. DOI: 10.1126/science.aay8683.

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