Joining the Team: Anika Ayyar

By Anika Ayyar

Hi! My name is Anika Ayyar and I am currently a Duke freshman. I grew up in warm, lovely Saratoga, California, where I picked up my love for long distance running, organic farming, and the ocean. When I was 14, I moved to across the country to Exeter, New Hampshire to attend a boarding high school, and here I developed a deep interest in biology and medicine. Exeter’s frost and snow were far from the Cali weather I was used to, but my fascinating classes, caring teachers, and wonderful friends more than made up for the cold.

My sophomore semester abroad program at The Island School, on an island called Eleuthera in the Bahamas, certainly provided a welcome change to East coast weather as well. At the Island School I studied marine biology and environmental conservation, earned my SCUBA certification, and spent time with the local middle schoolers refurbishing a library and stocking it with books. I was also part of a research team that studied species richness and diversity on patch reefs off the coast of the island.

Dissecting fruit fly larvae under the microscope at the Seung Kim Lab at Stanford.

Dissecting fruit fly larvae under the microscope at the Seung Kim Lab at Stanford.

My marine research stint in the Bahamas drove me to join a molecular biology lab the summer after I returned; a decision that transformed my passion for science. At the Seung Kim Lab for Pancreas Development at Stanford University, I worked on a project that used binary systems to study the expression of specific genes related to insulin production and diabetes in fruit flies. I soon grew so immersed in my work that I wanted to share the project with others in the scientific community at Exeter, and my research mentors, biology professors, and I worked to create a novel course where other students could take part in the project as well. This unique research collaboration, called the “StanEx” project, proved to be a huge success, allowing other students to experience the trials and joys of real-world research while also generating Drosophila fly strains that were useful to the larger scientific community. If you are interested in reading more, check out my website about the StanEx project!

While my current interests lie more at the intersection of technology and medicine, I hope to be involved in equally compelling and fulfilling research here at Duke. Hearing about the various projects my professors are working on, and reading about the discoveries made in labs on campus, I have no doubt that this will be the case.

Outside of classes and research, I enjoy being part of the Duke Debate team, and Lady Blue, one of Duke’s all-female a cappella groups. You can often find me on the trails on a long run, or trying out a new dessert recipe I found on Pinterest. I am beyond excited to be a part of the research blogging team, and can’t wait to start attending talks and interviewing research personalities whose stories I can share with our readers!

Origami-Inspired Chemistry Textbook Brings Molecules To Life

by Anika Radiya-Dixit

Your college textbook pages probably look something like the picture below – traffic jams of black boats on a prosaic white sea.

blackAndWhiteText

Textbook without illustrations.

But instead of reading purely from static texts, what if your chemistry class had 3D touch-screens that allowed you to manipulate the colors and positions of atoms to give you visual sense of how crystal and organic structures align with respect to each other? Or what if you could fold pieces of paper into different shapes to represent various combinations of protein structures? This is the future of science: visualization.

Duke students and staff gathered in the Levine Science Research Center last week to learn more about visualizing chemical compounds while munching on their chili and salad. Robert Hanson, Professor in the Department of Chemistry at St. Olaf College, was enthusiastic to present his research on new ways to visualize and understand experimental data.

Exhibition poster of “Body Worlds”

 

Hanson opened his talk with various applications of visualization in research. He expressed a huge respect for medical visualization and the people who are able to illustrate medical procedures, because “these artists are drawing what no one can see.” Take “Body Worlds,” for example, he said. One of the most renowned exhibitions displaying the artistic beauty of the human body, it elicited a myriad of reactions from the audience members, from mildly nauseated to animatedly pumped.

Hanson also spoke about the significance of having an effective visualization design. Very simple changes in visualization, such as a table of numbers versus a labeled graph, can make a “big difference in terms of ease of the audience catching on to what the data means.” For example, consider the excerpt of a textbook by J. Willard Gibbs below. One of the earliest chemists to study the relationship between pressure and temperature, Gibbs wrote “incredibly legible, detailed, verbatim notes,” Hanson said. Then he asked the audience: Honestly, would one read the text fervently, and if so, how easy would it be to understand these relationships?

Gibbs'Text

Excerpt of J. Gibbs’ text.

Not very, according to James C. Maxwell, a distinguished mathematician and physicist, who attempted to design a simpler mechanism with his inverted 3D plaster model.

Maxwell'sPlaster

Maxwell’s plaster model of Gibbs’ surface

Subsequent scientists created the graph shown below to represent the relationships. Compared to the text, the diagram gives several different pieces of information about entropy and temperature and pressure that allow the reader to “simply observe and trace the graph to find various points of equilibrium that they couldn’t immediately understand” from a block of black and white text.

Graph

Graphical view of Gibbs’ theory on the relation between temperature and pressure.

Hanson went further in his passion to bring chemistry to the physical realm in his book titled “Molecular Origami.” The reader photocopies or tears out a page from the book, and then folds up the piece of paper according to dotted guidelines in order to form origami molecular “ornaments.” The structures are marked with important pieces of information that allow students to observe and appreciate the symmetry and shapes of the various parts of the molecule.

origami

3D origami model of marcasite (scale: 200 million : 1)

 

One of his best moments with his work, Hanson recounted, was when he received a telephone call from some students in a high school asking him for directions on how to put together a 3D model of bone. After two hours of guiding the students, he asked the students what the model finally looked like – since he had knowledge of only the chemical components – and was amused to hear a cheeky “He doesn’t know.” Later that year, Hanson was rewarded to see the beautiful physical model displayed in a museum, and was overjoyed when he learned that his book was the inspiration for the students’ project.

More recently, Hanson has worked on developing virtual software to view compounds in 3D complete with perspective scrolling. One of his computer visualizations is located in the “Take a Nanooze Break” exhibition in Disneyland, and allows the user to manipulate the color and location of atoms to explore various possible compounds.

TouchAMolecule

“Touch-A-Molecule” is located in the Epcot Center in Disneyland.

By creating images and interactive software for chemical compounds, Hanson believes that good visualization can empower educators to gain new insights and make new discoveries at the atomic level. By experimenting with new techniques for dynamic imagery, Hanson pushes not only the “boundaries of visualization,” but more importantly, the “boundaries of science” itself.

Hanson

Professor Hanson explains how to visualize points of interaction on a molecule.

 

Contact Professor Hanson at hansonr@stolaf.edu

Read more about the event details here.

View Hanson’s book on “Molecular Origami” or buy a copy from Amazon.

Curiosity, Music and Mentors Led Nowicki to Science

By Duncan Dodson

“The only reason I got into the program I wanted to was because I was a pretty good low brass player—I’m actually sure of it!”

Stephen Nowicki, Dean and Vice Provost of Undergraduate Education, chuckles as he recounts his journey from early scientific beginnings to his most recent research. As part of Duke BioCoRE program, prominent Duke Scientists are asked to answer the question, “Why am I a scientist?”

Nowicki talk picture

Nowicki explains his most recent research with swamp sparrows and phonemes, the smallest derivative of vocal communication, at Love Auditorium January 23, 2015.

Nowicki started his answer to that question on January 23 with a picture of a dissected—well more like massacred—frog, commenting that he never thought he liked science because of his high school science courses that were not well-taught.

“All I remember from that course was dissecting a frog, and not knowing what I was supposed to get out of it.” This led him to pursue a music major at Tufts University. It was Tufts’ equivalent of Duke’s Trinity requirements in a natural science field that led to an ironic turn of events—quickly picking up a biology double major.

“I had some friends that said ‘Oh you should take this biology course,’ and I did and it changed my life, because it was really well taught,” he said. From there, his mentor at Tufts reached out to a colleague, the head of a competitive graduate neurobiology program at Cornell, Tom Eisner. Eisner mentioned to Nowicki that he was looking to start an amateur orchestra at Cornell;  Nowicki responded that he could play lower brass, sparking Eisner’s interest, and ultimately, according to Nowicki, his acceptance into the program.

Flash forward about 30 years. Nowicki has an impressive career in the field of neurobiology. His most recent publication challenges the neurological methods in which swamp sparrows process the subtle differences of phonemes, the smallest derivatives of vocal communication, in other birds’ songs.

Steve Nowicki

Nowicki’s tweet (@SteveNowickiDU) January 13, 2015. “Back where I belong at last!” Nowicki is a regular in the Cameron pep band who has always combined his passion for music with a curiosity for science.

Nowicki spent a majority of his talk relating entertaining anecdotes about his work with “Robobird,” a titanium swamp sparrow used to test these theories.

He repeatedly stressed the importance of curiosity, which led him to discover subjects he was passionate about. He discussed the process of instilling the same kind of curiosity in three undergraduate engineers through the two-and-a-half year research project. “[The first year engineers] didn’t have a clue, but they were not deterred. When they started to understand the problem they just kept digging in and digging in.”

When asked why he is a scientist, Nowicki responded, “I was lucky to run into mentors who revealed me to aspects of science that interested me, and I wasn’t afraid to fail.”

Behind the Scenes at Duke’s Student-Run Science Journal

By Nonie Arora

What do tuberculosis vaccines, water quality, and protein trafficking share in common? All may be featured in articles for the upcoming issue of Duke Science Review. I spoke with Matthew Draelos, co-editor-in-chief, and other publication team members.

Duke Science Review Publication. Credit: Nonie Arora

Duke Science Review Publication. Credit: Nonie Arora

Draelos explained that the Duke Science Review deals with broad topics with an emphasis on review articles and draws from the undergraduate, graduate, and professional school communities.

Draelos’s motivations for leading the Duke Science Review stem from his previous research experiences. Draelos worked in an undergraduate lab for four years at NC State University. There, he felt integrated into the publication process in the laboratory of Dr. Gavin Williams. At Duke, he is excited to have the opportunity to get involved in a student-run science journal and take on a leadership role.

His interest in science is focused on pharmaceutical development, particularly antibiotics. He has worked previously with enzymes called polyketide synthases, which are nature’s machinery for making antibiotics. He hopes to someday develop novel chemical solutions to unsolved medical problems.

Students learn about the publication process. Credit: Nonie Arora.

Students learn about the publication process. Credit: Nonie Arora.

“I think it’s important for students to publish their research primarily because in the current funding environment it’s publish or perish. This is increasingly true for young scientists. We must be able to write well, and the Duke Science Review establishes a risk-free forum for students to practice scientific writing,” Draelos commented.

A second reason he mentioned for enabling students to publish their work is that people spend considerable time and energy writing papers for courses, and a lot of that effort is wasted if only the professor is able to read their work. This journal is a way for people to spread their work to a larger audience and perhaps gain some additional recognition.

Lefko Charalambous, an editor for the journal, added that it is important to improve scientific communication and literacy in budding scientists. “It’s a way for us to appreciate what goes into producing a journal article and the reward from having it published at our age,” he said.

“We hope to enrich the scientific discourse, especially for freshmen and sophomores who are looking into scientific research and don’t know where to start,” Draelos said.

To submit an abstract for a potential report or article, check out their website.

Touring Duke’s Biggest Laboratory

Sari Palmroth

Sari Palmroth and the 130-foot research tower in the Blackwood Division of Duke Forest.

By Karl Leif Bates

You may think of Duke Forest as a nice place to run or walk your dog, but it’s actually the largest research laboratory on campus, and probably the oldest too.

Last week, Duke Forest director Sara Childs and operations manager Jenna Schreiber took about a dozen interested stakeholders on a whirlwind tour to see three active research installations tucked away in areas of Duke Forest the public often doesn’t see.

 

We had to hunt a little to find UNC Biology grad student Jes Coyle in the Korstian division off Whitfield Road, but at least she wasn’t 30 feet up in an oak tree like she usually is. Jes showed the group some of her cool climbing gear while explaining her work on figuring out which part of a lichen, the fungus or the algae, is more responsible for the lichen’s adaptation to microclimates.

She does this by climbing way the heck up into trees to affix little data loggers that track temperature and sunlight at various places on the trunk.

Coyle is looking at 67 lichen species in 54 sampling locations, which is a lot of climbing and a lot of little $50 loggers.

The whole time Jes was talking, we were eyeing her six-foot-tall slingshot and waiting for it to come into play.

Jes Coyle

UNC grad student Jes Coyle shows off her climbing gear.

Indeed it did, as she let three participants, including Sara Childs, have a go at shooting a ball on a fine string over a likely-looking branch to start a climbing rope. (None succeeded.)

 

Abundant data was the theme at our second stop too, where Sari Palmroth, an associate research professor in the Nicholas School of the Environment, explained how she measures how much water goes into and out of a tree.  Her installation is in the Blackwood Division off Eubanks Road, tucked behind the old FACE experiment.

Standing next to an imposing 130-foot scaffolding tower studded with active and abandoned instruments of all sorts, Palmroth said a square meter of Duke Forest exhales about 700 mm of rainfall a year, which is about half of what falls on it. “How do I know these numbers? Because it’s my job.”

In addition to being a lovely place to get away from the world and sway with the treetops, the tower measures CO2 levels at different heights throughout the canopy.

Sari Palmroth

Palmroth reveals where probes go into a tree trunk.

The tower also hosts a big white box stuffed with wires that capture data streaming in from sensors embedded in the tree trunks all around the tower.

Palmroth and her colleagues are seeing the trees breathe. During the day, when the tiny pores on the underside of their leaves – called stomata — are open and exhaling water and oxygen, roots in the top 40 centimeters of soil are pulling in more water. When the sun sets and the stomata close, then the tree’s deeper roots pull water up to the top level for tomorrow’s drinking.  Unless it doesn’t get cool at night and the stomata don’t completely close, which is the prediction for some climate change scenarios. What then?

 

Aaron Berdanier

Back in the vans and even deeper into the Blackwood division, we come upon an intrepid young man in a flannel shirt sitting in a sunny spot by the side of the two-track. He’s Aaron Berdanier, a doctoral candidate at Duke who is also looking at water use by taking  automated measurements of 75 trees every minute for four straight years.

His work is part of a larger research project established by Nicholas School professor Jim Clark 15 years ago. Every one of the 14,000 trees in this sloping 20-acre stand of the forest — from spindly saplings to giants —  is labeled and has its data regularly collected by a platoon of undergrads armed with computer tablets.

Other data flows automatically on webs of wiring leading to data loggers situated every few yards. Some of the trees wear a stainless steel collar with a spring that measures their circumference constantly and precisely. They change noticeably both seasonally and by the year, Berdanier says.

The forest is alive and its trees are breathing and pulsing. Berdanier likens his detailed measurement of water consumption to taking a human patient’s pulse. “We’re trying to determine winners and losers under future climate conditions.”

Duke Forest Q&A

Aaron handled a wide-ranging Q&A with the curious visitors as the sun set and the temperature fell.

RISK: The Adolescent Mind

By Anika Radiya-Dixit

Have you ever been labeled an out-of-control teenager? A risky driver? An impulsive troublemaker? Here’s the bad news: That’s partially correct. The good news? It’s not your fault: blame the brain.

On November 18, the department of Psychology and Neuroscience introduced students to “The Origins of Heightened Risk Behavior in Adolescence.” The presenter, Dustin Albert, is a PhD research scientist at the Center for Child and Family Policy here at Duke University, who is interested in cognitive neuroscience, problem behaviors, and peer influence.

Researchers have identified the stage of adolescence as the peak time of health and performance, but at the same time, they noticed a jump in morbidity and mortality as children approached teen years, as seen in the graphs below. Specifically, adolescents show increased rates of risky behavior, alcohol use, homicide, suicide, and sexually transmitted diseases. However, as Allen tells the audience, “These are only the consequences.” In other words, what teenagers are stereotypically ridiculed for is actually the result of something else. If that’s the case, then what are the causes?

Professor Albert

Professor Albert explaining the spike in risky behavior during teenage years.

Psychologically speaking, researchers believed that these behaviors are caused by a lack of rational decision, perhaps because adolescents “are unable to see their own vulnerability” to the outcomes, meaning that teens are apparently inept at identifying consequences to their actions. However, the studies they took demonstrated that adolescents are not only able to see their own vulnerability, but are also able to intelligently evaluate costs and effects to a certain decision. If teenagers are so smart, then what is actually causing this “risky behavior”?

One important reason Professor Albert discussed is brain activity and maturation before, during, and after adolescence. As a child ages from early to middle adolescence, fast maturation of incentive processing circuitry drives sensation seeking – in other words, the willingness to take risks in order to gain a reward increases as the child approaches teen years. In the brain, this occurs due to increased dopamine availability in reward paths as well as heightened sensitivity to monetary and social reward cues. In one interesting study, adolescents were instructed to press a button only when they saw an angry face. However, the researchers noticed that when the teens saw a happy face, they had a “particularly difficult time restraining themselves” to not press the button. Essentially, the happy-angry face study demonstrates that adolescents have more struggle in restraining themselves against impulsive actions, which often translates into responses during driving, alcohol use, and the other aforementioned risky behaviors.

Later in their life, there is a slower maturation of cognitive control circuitry that leaves a window of imbalance in the teen’s life. In the brain, this period is noted by thinning of gray matter and increasingly efficient cortical activation during inhibition tasks. In other words, older people “use smaller parts of [their] cortex to stop inappropriate responses.” Essentially, due to the way the physical and hormonal brain matures, adolescents are more prone to impulsive behavior. The take away: it’s not your fault.

Another influence on teens’ risky behavior is called the peer presence effect, commonly known as “peer pressure.” Based on arrest records, “adolescents, but not adults, [are] riskier in the presence of peers,” pointing out that the percentage of co-offenders arrested for the top eight crimes decreased with age after teenage years (Gardner & Steinberg, 2005). Perhaps the need to “establish their status,” Albert speculated, decreases with age as they gain more experience about living in the real world.

The test to evaluate the result of peer presence simulates the effect of teens taking a driving exam when in the car alone as compared to when with peers. In terms of peer influence, the study shows that adolescents ran more intersections when sitting with a peer than when sitting alone. In terms of risky behavior compared with adults, adolescents when watched by peers showed over 20% increase in risky behavior of running through intersections, as opposed to the 5-10% increase seen for adults in peer presence. Albert partially attributed this effect to the fact that “teens driving the first time could assess the probability of crashing less than adults do,” but he doesn’t have specific evidence for this claim.

While Albert claimed that the study was valid because the adolescents participating were made aware of the outcome of driving recklessly – damage to the car, injury, time it would take to get a new car, insurance problems – I believe that the study should have taken into account the fact that the teens may have subconsciously known the simulated driving test wasn’t real – viewing it as a mere video game – and so may have succumbed more into peer pressure as the true fear of dying in a crash would not have been present.

Albert ended his talk by giving one last piece of advice to people working with teens: It’s “not enough to [simply] increase their knowledge,” but rather to “understand and work towards developing impulse control and reward sensitivity.”

Below are some of the thought-provoking questions raised by audience members during the Q&A session:

Q: What would be the result of peer presence effect for same-sex peers as compared to peers of the opposite sex?

A: While Albert admitted that this particular situation has not been tested yet, he believes it may be based on personal perceptions of what the peer thinks, and what the opposite person likes.

Q: What would be the result of risky behavior for the simulated driving test if the participant’s parent(s) and peer(s) were both present in the car?

A: On one hand, the participant might drive more carefully due to the presence of an authoritative figure. However, if the participant opinionates the peer as a stronger influence, he / she would effectively neutralize the effect the parent has and drive more recklessly. Other audience members claimed that they would drive more cautiously irrespective of who was sitting with them in the car because they are aware there is another life at stake for every decision they made behind the wheel. “It would be interesting to see the [results of the study] based on this internal conflict,” the audience member who posed this question said. Overall, Albert said the results would be primarily influenced by the type of person participating – whether they would “take the small amount of money or be willing to wait for the big amount” in front of peers – that would determine whether the parent or peer becomes a stronger influence in risky behavior.

Q: How could someone going into education help keep high school students away from risky behaviors?

A: Albert noted that these behaviors are more the result of personal experience rather than something that can be quickly taught. In a school setting, teachers could introduce the practice of challenging situations to help the kids acting ‘in-the-moment’ recognize and understand “changes in their own thought patterns for decision making,” but simply giving them a “lesson in health class is not necessarily going to translate into the Friday night situation.”

If you are interested in these type of topics, Professor Albert is teaching PUBPOL 241: METHODS SOCIAL POLICY RESEARCH  this Spring (2015).

More details about the presenter can be read at: http://fds.duke.edu/db/Sanford/ccfp/william.albert