Duke Research Blog

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

Category: Students Page 1 of 26

An Indirect Path to Some Extreme Science

Dr. Cynthia Darnell’s path to becoming a postdoctoral researcher in the Amy Schmid Labat Duke University was, in her words, “not straightforward.”

Dr. Cynthia Darnell is a Postdoc at Duke, studying ‘extremophiles.’

At the start of her post-high school career, Darnell had no clue what she wanted to do, so she went to community college for the first two years while she decided. She had anticipated that she was going to go to college as an art major, but had always enjoyed biology.

While at community college she took a couple biology courses. She transferred to another college where she took a course in genetics and according to her, “it blew my mind.” While at the college she took a variety of different biology courses. Her genetics professor’s wife was looking for a lab technician in the microbiology lab she ran. After Darnell worked there for two years, she decided to go to graduate school and had a whole list of places/universities she could attend.

However, after going to a conference in Chicago and meeting her future graduate advisor, Darnell made the decision to go to Iowa for six years of Graduate school. She ended up in the Schmid Lab at Duke University for her “postdoc” after her boss had recommended the lab to her.

Previously, Darnell had done research on the connectedness of genetic pathways in halophilic extremophiles — bacteria that lived in extremely salty conditions. She developed projects to understand the how their genetic network sends and receives signals.

Darnell is continuing that research at Duke while also looking at the effects of different environmental factors on growth and the genetic network using mutant halophilic extremophiles.

Darnell with some plated archaebacteria in her Duke lab

There are generally three different paths Darnell’s day in the lab can take. The first path is a bench day. During a bench day, she will be doing experiments looking at growth curves, microscopes or RNA extracts. The second path is a computational day in which she will do sequencing to look at gene expression. The third option is a writing day in which she spends a majority of her time writing up grants, papers, and applications.

Dr. Darnell wishes to open up her own lab in the future and serve underprivileged students in underserved areas. She wishes to do more research in the area of archaebacteria because of how under researched and underrepresented it is in the scientific community. Dr. Darnell hopes to study more about the signaling networks in archaebacteria in her own lab someday.

She especially wishes to be able to open her lab up to underprivileged students, exposing them to the possibilities of research and graduate programs.

Guest Post by Tejaswi Siripurapu, NCSSM 2019

New Blogger Jeremy Jacobs: What’s in a Name?

Surviving my first snow day at Duke

Let’s start with my name: Jeremy Abraham Jacobs. It’s a surprisingly Biblical one,
a name that draws more from the Judeo-Christian tradition than my
Indian roots. Jeremy, derived from the prophet Jeremiah and the depths of my mother’s imagination. Abraham, both the name of my father’s father and the patriarch of Judaism. And Jacobs, the latest Americanization of my family name Yakob, Chacko, then Jacob.

At the heart of my name is language, the offspring of a million-year synthesis of firing neurons, geography, and culture. I too grew up a child of intersection, living a blend of the Indian tradition my parents brought over with them and the rich culture of the Deep South that’s flavored ever moment of my life.

I’m a freshman here at Duke, with all the uncertainties—and possibilities—of an undeclared major. But my passion lies in the crossroads that has defined my life. I want to understand the inseparable intertwining of linguistics and neuroscience. And communication enthralls me, from the individual cells that make up the tongue to the Spanish pluperfect subjunctive.

Who knows if, after four years, organic chemistry will have knocked me off the pre-med track, or if English will still hold my interest as tightly as it does today? But for now, at least, mysteries like the power of a name still keep me invested in the intricate interplay of science and language.

Move-in day featuring an injured arm!

What cascading forces of nature and nurture brought my mother to a small hospital in Tupelo, Mississippi, where I came into the world kickin’ and screaming’ one hot July morning? Was there some memory burned into her hippocampus that caused her to choose the name “Jeremy” in a sea of Chad’s, Luke’s, or Matt’s? And how different would my life have been if my name were not Jeremy Abraham Jacobs but rather Aakash Bola, or Harley Covington Pike III?

It took generations of missteps, chance encounters, and biological improbabilities for this name to fall to me, for this name to be mine. Perhaps one day I’ll understand every aspect of my unlikely existence, every factor that led to the genetically unique organism currently typing up this article. More likely, though, is that I’ll spend my life exploring the unknown, learning more about my own place in the mechanisms of the world.

But I know, at least, that intersection follows me, even here at the Duke Research Blog. I’m thrilled to infuse my own mix of science, writing, and culture into each article I produce, so I can ignite the passions of others students of science who seek their own common ground.

Post by Jeremy Jacobs

Math on the Basketball Court

Boston Celtics data analyst David Sparks, Ph.D, really knew his audience Thursday, November 8, when he gave a presentation centered around the two most important themes at Duke: basketball and academics. He gave the crowd hope that you don’t have to be a Marvin Bagley III to make a career out of basketball — in fact, you don’t have to be an athlete at all; you can be a mathematician.

David Sparks (photo from Duke Political Science)

Sparks loves basketball, and he spends every day watching games and practices for his job. What career fits this description, you might ask? After graduating from Duke in 2012 with a Ph.D. in Political Science, Sparks went to work for the Boston Celtics, as the Director of Basketball Analytics. His job entails analyzing basketball data and building statistical models to ensure that the team will win.

The most important statistic when looking at basketball data is offensive / defensive efficiency, Sparks told the audience gathered for the “Data Dialogue” series hosted by the Information Initiative at Duke. Offensive efficiency translates to the number of points per possession while defensive efficiency measures how poorly the team forced the other offense to perform. These are measured with four factors: effective field goal percentage (shots made/ shots taken), turnover rate, successful rebound percentage, and foul rate. By looking at these four factors for both offensive and defensive efficiency, Sparks can figure out which of these areas are lacking, and share with the coach where there is room for improvement. “We all agree that we want to win, and the way you win is through efficiency,” Sparks said.

Since there is not a lot of room for improvement in the short windows between games during the regular season, a large component of Sparks’ job involves informing the draft and how the team should run practices during preseason.

David Sparks wins over his audience by showing Duke basketball clips to illustrate a point. Sparks spoke as part of the “Data Dialogue” series hosted by the Information Initiative at Duke.

Data collection these days is done by computer software. Synergy Sports Technology, the dominant data provider in professional basketball, has installed cameras in all 29 NBA arenas. These cameras are constantly watching and coding plays during games, tracking the locations of each player and the movements of the ball. They can analyze the amount of times the ball was touched and determine how long it was possessed each time, or recognize screens and calculate the height at which rebounds are grabbed. This software has revolutionized basketball analytics, because the implication of computer coding is that data scientists like Sparks can go back and look for new things later.

The room leaned in eagerly as Sparks finished his presentation, intrigued by the profession that is interdisciplinary at its core — an unlikely combination of sports and applied math. If math explains basketball, maybe we can all find a way to connect our random passions in the professional sphere.

Meet New Blogger Anne Littlewood – Working on Biology and Puppies

My name is Anne Littlewood and I am a sophomore here at Duke. I grew up in San Francisco, spent a brief moment living on the island of Kauai, and finished high school in Pebble Beach, California. I am studying the intersection of biology and psychology here at Duke, in an effort to understand how biological mechanisms inform our interactions with the environment.

Snuggles in Puppy Kindergarten!

Outside the classroom, I can be found frequenting Duke’s beloved Puppy Kindergarten, where I work as a volunteer. Recently, I’ve become an Associate Editor for Duke’s literary magazine, The Archive. I love writing creatively, and it’s been so great to find a community of my literature- loving peers. I’m also participating in a Bass Connections project this year, and working on a team to evaluate the outcomes of different conservation interventions through the synthesis of an evidence gap map for World Wildlife fund.

Me and Cricket on Carmel Beach

Most of all I love to spend time outdoors, whether it’s exploring the mountains of North Carolina on a backpacking trip, lying in my hammock at Eno Quarry, or walking through the gardens each day on my way to class. I’m a huge animal lover, and I’m way too obsessed with my dog, a 12-pound cavalier King Charles spaniel named Cricket.

I’ve always been into science, but I think I really fell in love with Biology my freshman year of high school, when my all time favorite teacher, Mr. Cinti helped me extract my DNA one afternoon, just for fun. Writing is my passion, and I’m excited to explore my skills in a variety of genres this year. This blog is my first ever attempt at journalism/ science writing, and I’m excited to give it a try!

Coding: A Piece of Cake

Image result for cake

Imagine a cake, your favorite cake. Has your interest been piqued?

“Start with Cake” has proved an effective teaching strategy for Mine Cetinkaya-Rundel in her introduction-level statistics classes. In her talk “Teaching Computing via Visualization,” she lays out her classroom approaches to helping students maintain an interest in coding despite its difficulty. Just like a cooking class, a taste of the final product can motivate students to master the process. Cetinkaya-Rundel, therefore, believes that instead of having students begin with the flour and sugar and milk, they should dive right into the sweet frosting. While bringing cake to the first day of class has a great success rate for increasing a class’s attention span (they’ll sugar crash in their next classes, no worries), what this statistics professor actually refers to is showing the final visualizations. By giving students large amounts of pre-written code and only one or two steps to complete during the first few class periods, they can immediately recognize coding’s potential. The possibilities become exciting and capture their attention so that fewer students attempt to vanish with the magic of drop/add period. For the student unsure about coding, immediately writing their own code can seem overwhelming and steal the joy of creating.

Example of a visualization Cetinkaya-Rundel uses in her classes

To accommodate students with less background in coding, Cetinkaya-Rundel believes that skipping the baby steps proves a better approach than slowing the pace. By jumping straight into larger projects, students can spend more time wrestling their code and discovering the best strategies rather than memorizing the definition of a histogram. The idea is to give the students everything on day one, and then slowly remove the pre-written coding until they are writing on their own. The traditional classroom approach involves teaching students line-by-line until they have enough to create the desired visualizations. While Cetinkaya-Rundel admits that her style may not suit every individual and creating the assignments does require more time, she stands by her eat-dessert-first perspective on teaching. Another way she helps students maintain their original curiosity is by cherishing day one through pre-installed packages which allow students to start playing with visualizations and altering code right away.

Not only does Cetinkaya-Rundel give mouth-watering cakes as the end results for her students but she also sometimes shows them burnt and crumbling desserts. “People like to critique,” she explains as she lays out how to motivate students to begin writing original code. When she gives her students a sloppy graph and tells them to fix it, they are more likely to find creative solutions and explore how to make the graph most appealing to them. As the scaffolding falls away and students begin diverging from the style guides, Cetinkaya-Rundel has found that they have a greater understanding of and passion for coding. A spoonful of sugar really does help the medicine go down.  

    Post by Lydia Goff

Creating a Gender Inclusive Campus: Reflecting on “Becoming Johanna”

Following Duke’s Oct. 4 screening of the 2016 documentary, “Becoming Johanna,” students, faculty, staff and community members in the audience were eager to ask questions of the panel, which included the film’s director/producer, Jonathan Skurnik, and even the film’s transgender subject, Johanna Clearwater herself.

Johanna Clearwater pictured with the film’s director/producer Jonathan Skurnik

The film showcases the heart-wrenching and empowering story of a latina transgender teenager growing up in Los Angeles. After beginning her transition at age 16, Johanna faced the rejection of her mother and intense opposition from school authorities. Soon after, she was abandoned by her family and entered the foster care system, where she was lucky to find a much more supportive family environment. After changing schools, she connected on a personal level with her school principal, Deb, who helped Johanna find a community where she felt understood and supported. This success story of self-advocacy and resilience in the face of abandonment and exclusion highlights the daily struggles of many transgender teenagers. For these individuals, becoming comfortable in their own skin is the end of a long and demanding journey, often made even more difficult by the ignorance and cruelty of society. Finding and following the path to authentic expression takes a huge amount of courage, as this route is often layered with adversity.

Before the screening, Duke clinical social worker Kristin Russel put the film in context for the audience, inviting our reflection with her words: “A well told story… is really what can help us bridge the unfortunate distance that can remain uncrossed and misunderstood if such stories are silenced.” Chief Diversity Officer for the School of Medicine Judy Seidenstein then introduced the film and facilitated the panel discussion.

After the film, the audience was invited to join the conversation. Questions came from every demographic of the crowd, and provided a nice sampling of opinions. Many audience members pointed out how important these conversations are, especially in a conservative state like North Carolina that has so recently struggled with the protection of LGBTQ rights with last year’s ‘Bathroom Bill.’ Specifically, the questions and comments from hospital staff and faculty from the School of Medicine gave a nice insight into the direction of support on campus for sexual and gender diversity.

Audience members reflect on the film with those nearby

Cheryl Brewer, the Associate Vice President of Nursing, told the room about the inclusion work that she is leading in the School of Nursing. They have developed a new core curriculum to promote acceptance and support of gender and sexual diversity through situational trainings. She noted that there have been some people that struggle with implicit biases more than others, but that the program has been a success overall.

Russell spoke briefly about her work with transgender and gender diverse youth in the clinical setting and emphasized the importance of having family support. Legally and psychologically, maintaining family involvement and support of patients is essential for treatment.

Events like this one reflect ongoing efforts to support sexual and gender diversity within and beyond Duke, by promoting conversation and increasing empathy through storytelling. Duke is well on the way to becoming a much more inclusive community, where everyone can feel a sense of belonging.

Guest post by Anne Littlewood

Meet New Blogger Brian Du

Brian survives his week in the desert.

Hi! My name is Brian Du, and I’m a sophomore from Texas. I’m a pre-med majoring in computer science. I like vacations, hiking, and hiking on vacation. Besides these hobbies, I also love learning about science and hearing a good story. These latter two are exactly why I’m excited to be writing for the Duke Research Blog.

My first exposure to science happened in third grade because my goldfish kept getting sick and dying. This made me sad and I became invested in making them well again. I would measure pH levels regularly with my dad and keep notes on the fishes’ health. Eventually the process turned into a science fair project. I remember I loved presenting because I got to point out to the judges the ‘after’ pictures of my fish, which showed them alive, healthy, and happy (I think? it’s hard to tell with fish).

One happy fish!
Source: Reddit

My fish and I go way back.

After that third-grade experiment, I kept doing science projects — almost year after year actually — since I love the research process. From framing the right questions and setting up the experiment, to running the trials and writing up and sharing my work, my enthusiasm grew with each step. Come competition day, I noticed that in interviews that went well, my excitement was contagious, so that judges grew more eager too as they listened. And so I understood: a huge part to science is communication. Science, like food or a good story, is meant to be shared with others. The scientist is a storyteller, adjusting his presentation to captivate different audiences. With judges, I spoke jargon, but during public exhibition, where I chatted with anyone who came up to me, I got creative when asked about my research. Analogies helped me link strange concepts to everyday objects and experiences. An important protein channel became a pipe, and its inhibitor molecule a rock which would clog the pipe to make it unusable.

protein channel “pipe”
edited from CThompson02

Now that I’m at Duke, there’s so many stories to tell of the rich variety of research being done right on campus! I’ve written a few articles for the Chronicle covering some of the new medicine or proteins Duke professors have been involved in developing. As I keep an ear out for more stories, I hope to share a few of them in my upcoming posts, because I know they’ll be exciting!

New Blogger Rebecca Williamson: The Moon and Some Stars

Hello! My name is Rebecca Williamson, and I am a freshman here at Duke University. Coming into college, I plan to major in economics, but that could very well change. As for my interests outside of the classroom, I enjoy singing and theater and am a member of Out of the Blue, one of the all-female a cappella groups here at Duke!

Rebecca Williamson, Duke 2022

Rebecca Williamson, Duke 2022

I fell in love with Duke the second I stepped on campus. I am excited to see what Duke has to offer me, but more importantly, what I can offer to Duke.

My interest in science, specifically astronomy, was piqued at a very young age. By age six, I had not one, but three,  Moon in my Room light up toys (remote controlled models of the Moon that scrolled through the waxing and waning phases of the Moon at the touch of a button) mounted in my bedroom. By nine, I had the entire planetary system (yes, including Pluto) hanging from my ceiling. Though I cannot say that my interests remain with astronomy, it is what first got me invested in science. I have since gained interest in the natural sciences and animal sciences, though every so often I do press some of the buttons on my Moon in my Room remote.

Some random boy imagines he's as cool as six-year-old Rebecca.

Some random boy imagines he’s as cool as six-year-old Rebecca.

My love of writing, however, was spawned by my love of theater. As an active member of my high school’s theater community, I was roped into being a part of, and eventually became the president, of my school’s Cappies Critics team. As a Cappie, I was expected to watch local high school plays and musicals and write critical, holistic reviews of them. This program jump-started my love for writing and helped me to develop my own unique journalistic voice.

solar system mobile. www.luxrysale.comI hope to combine my interest in the natural and animal sciences with my love for writing and chronicle some of the amazing research going on in these fields both on campus and around Durham! I also hope to incorporate my interests in music and theater into my inquiries and document scientific research surrounding music and the arts in the Duke community.

Duke University Research Blog, look out, because here I come!

Post by Rebecca Williamson

New Blogger: Victoria Priester Loves Animals and Books

Hi! My name is Victoria Priester, and I’m a sophomore at Duke and one of this year’s new Duke Research bloggers.

Victoria meeting a very intelligent mammal.

I’m pre-vet, but I’ve always been a bookworm and have a love for expressing myself through writing that has given me a strained relationship with word counts. I’ll try to keep this intro post brief!

I’m majoring in English in addition to taking pre-veterinary classes, so my time in the library so far this year has been spent alternating between drawing resonance structures for organic chemistry and reading Jane Eyre in the Gothic Reading Room, which is my favorite study spot on campus.

Effective puppy medicine includes hugging and kissing.

I grew up in the suburbs of Washington, D.C. and now I work in the veterinary department at Duke Lemur Center. I’m also an editor and opinion columnist for The Chronicle. My favorite part of the academic scene at Duke is that pursuing such different interests at the same time is encouraged.

This year, I’m a part of the Bass Connections team that is studying how using expressive writing for resilience can help cancer patients process their experiences during treatment. I love finding new ways to connect my passion for writing with my interest in science, conservation and zoology.

One of the reasons I want to be a veterinarian is because I think veterinarians can and do play a crucial role in species conservation in zoos and animal sanctuaries. However, there is still a lot left to be learned about the animal species they care for.

For example, there is a species of lemur that consistently develops dental problems in captivity that lead to tooth loss, so there must be something about its diet in captivity compared to its diet in Madagascar that affects the health of its teeth. I care a lot about research concerning animals, conservation and pets, in addition to the health benefits of cathartic writing.

Victoria REALLY likes books.

I follow National Geographic on Twitter and read their articles as often as I can, but I usually end up just telling all of the cool facts I just learned to my parents, close friends or anyone else who is close enough to me to feel a slight obligation to listen and feign interest.

Through blogging, I hope to find a platform to synthesize new scientific findings surrounding animals, marine life or cathartic writing and post them to a place where people who care about and want to read about these topics can find them.

Post by Victoria Priester

Medicine, Research and HIV

Duke senior Jesse Mangold has had an interest in the intersection of medicine and research since high school. While he took electives in a program called “Science, Medicine, and Research,” it wasn’t until the summer after his first year at Duke that he got to participate in research.

As a member of the inaugural class of Huang fellows, Mangold worked in the lab of Duke assistant professor Christina Meade on the compounding effect of HIV and marijuana use on cognitive abilities like memory and learning.

The following summer, Mangold traveled to Honduras with a group of students to help with collecting data and also meeting the overwhelming need for eye care. Mangold and the other students traveled to schools, administered visual exams, and provided free glasses to the children who needed them. Additionally, the students contributed to a growing research project, and for their part, put together an award-winning poster.

Mangold’s (top right) work in Honduras helped provide countless children with the eye care they so sorely needed.

Returning to school as a junior, Mangold wanted to focus on his greatest research interest: the molecular mechanisms of human immunodeficiency virus (HIV). Mangold found a home in the Permar lab, which investigates mechanisms of mother-to-child transmission of viruses including HIV, Zika, and Cytomegalovirus (CMV).

From co-authoring a book chapter to learning laboratory techniques, he was given “the opportunity to fail, but that was important, because I would learn and come back the next week and fail a little bit less,” Mangold said.

In the absence of any treatment, mothers who are HIV positive transmit the virus to their infants only 30 to 40 percent of the time, suggesting a component of the maternal immune system that provides at least partial protection against transmission.

The immune system functions through the activity of antibodies, or proteins that bind to specific receptors on a microbe and neutralize the threat they pose. The key to an effective HIV vaccine is identifying the most common receptors on the envelope of the virus and engineering a vaccine that can interact with any one of these receptors.

This human T cell (blue) is under attack by HIV (yellow), the virus that causes AIDS. Credit: Seth Pincus, Elizabeth Fischer and Austin Athman, National Institute of Allergy and Infectious Diseases, National Institutes of Health

This human T cell (blue) is under attack by HIV (yellow), the virus that causes AIDS. Credit: Seth Pincus, Elizabeth Fischer and Austin Athman, National Institute of Allergy and Infectious Diseases, National Institutes of Health

Mangold is working with Duke postdoctoral associate Ashley Nelson, Ph.D., to understand the immune response conferred on the infants of HIV positive mothers. To do this, they are using a rhesus macaque model. In order to most closely resemble the disease path as it would progress in humans, they are using a virus called SHIV, which is engineered to have the internal structure of simian immunodeficiency virus (SIV) and the viral envelope of HIV; SHIV can thus serve to naturally infect the macaques but provide insight into antibody response that can be generalized to humans.

The study involves infecting 12 female monkeys with the virus, waiting 12 weeks for the infection to proceed, and treating the monkeys with antiretroviral therapy (ART), which is currently the most effective treatment for HIV. Following the treatment, the level of virus in the blood, or viral load, will drop to undetectable levels. After an additional 12 weeks of treatment and three doses of either a candidate HIV vaccine or a placebo, treatment will be stopped. This design is meant to mirror the gold-standard of treatment for women who are HIV-positive and pregnant.

At this point, because the treatment and vaccine are imperfect, some virus will have survived and will “rebound,” or replicate fast and repopulate the blood. The key to this research is to sequence the virus at this stage, to identify the characteristics of the surviving virus that withstood the best available treatment. This surviving virus is also what is passed from mothers on antiretroviral therapy to their infants, so understanding its properties is vital for preventing mother-to-child transmission.

As a Huang fellow, Mangold had the opportunity to present his research on the compounding effect of HIV and marijuana on cognitive function.

Mangold’s role is looking into the difference in viral diversity before treatment commences and after rebound. This research will prove fundamental in engineering better and more effective treatments.

In addition to working with HIV, Mangold will be working on a project looking into a virus that doesn’t receive the same level of attention as HIV: Cytomegalovirus. CMV is the leading congenital cause of hearing loss, and mother-to-child transmission plays an important role in the transmission of this devastating virus.

Mangold and his mentor, pediatric resident Tiziana Coppola, M.D., are authoring a paper that reviews existing literature on CMV to look for a link between the prevalence of CMV in women of child-bearing age and whether this prevalence is predictive of the number of children suffer CMV-related hearing loss. With this study, Mangold and Coppola are hoping to identify if there is a component of the maternal immune system that confers some immunity to the child, which can then be targeted for vaccine development.

After graduation, Mangold will continue his research in the Permar lab during a gap year while applying to MD/PhD programs. He hopes to continue studying at the intersection of medicine and research in the HIV vaccine field.

Post by undergraduate blogger Sarah Haurin

Post by undergraduate blogger Sarah Haurin

 

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