Category Archives: BSURF 2018

Blogs for the Biological Sciences Undergraduate Research Fellowship 2018

Reflecting on a talk by Dr. Chantell Evans

This summer, through BSURF, I’ve had the opportunity to hear talks from a vast array of Duke professors, allowing me to gain a better understanding of the many possible paths through academia.

Dr. Chantell Evans’ talk stood out to me–not only because of her fascinating research, but also because of her approach to thriving in academia. As someone especially interested in the cellular mechanisms of neurodegenerative diseases, I was drawn to her research, which focuses on how neuronal homeostasis is maintained through mitochondrial quality control pathways. As she discussed her career path, particularly her recent journey starting the Evans lab, I learned for the first time the intricacies of running and maintaining a lab. 

A common theme throughout the BSURF talks this summer, especially those in the last few weeks, was that running a lab was much like running a small business. Before these talks, I had never taken time to think about the process of becoming a PI and setting up a lab. Dr. Chantell Evans humanized this process, telling a light-hearted story about working with a new undergrad to unbox lab equipment, label cabinets, and generally set up the lab space–tasks I’d never realized to be a part of being a PI.

Dr. Evans approached her talk with humor and lightheartedness, while effectively communicating the intricacies of her research. She presented her career choices logically, laying out the pros and cons for each, and humanizing an often intimidating path.

When I think about the type of researcher I’d like to be, and the type of lab environment I’d like to foster, I hope I can reflect the joy for research I saw in Dr. Evans’ work.

Categorical Perception with Dr. Steve Nowicki

This summer, I’m really grateful to have had the opportunity to learn from so many amazing scientists through our faculty seminars. Our first talk was given by Dr. Steve Nowicki, and it set the tone for all the interesting talks we heard this summer.

I appreciated that Dr. Nowicki told us both about his journey and his research. Most of his presentation focused on categorical perception, an interesting phenomenon that I’d never heard of—which is strange considering that it shapes how I perceive the world. Categorical perception occurs when things that occur along a spectrum, such as colors or vocal onset times, are grouped into distinct categories. For example, humans see the spectrum of wavelengths that make up a rainbow as distinct, mostly solid bands, even though the wavelengths differ within the bands as well. Another example is the difference between the sounds /pa/ and /ba/. They’re the same sound, but they differ in the amount of time between when the lips start moving to when the sound is made: the vocal onset time. Vocal onset times vary, but people mostly perceive them into two different categories without much confusion. Dr. Nowicki explained that categorical perception is cognitively less work than perceiving the whole spectrum. 

Dr. Nowicki walked us through a few experiments that he had conducted on categorical perception, which I found really interesting. At the beginning of the summer, most of us hadn’t had the opportunity to understand how experiments were developed, their conclusions, and their implications, so Dr. Nowicki’s talk gave us a great introduction. He mostly focused on his work with birds, and how they differentiate between two very similar notes. He played us recordings that emphasized just how difficult it is to tell these notes apart!

Overall, I’m really happy I got to hear Dr. Nowicki’s fascinating talk about his research and journey through science!


The prevalence of neurodevelopmental disorders (NDDs) has increased rapidly in recent decades. Genetic mechanisms of these disorders have been studied extensively; however, environmental factors contributing to NDD development remain less understood. Current evidence suggests that alterations in synaptogenesis and pruning underlie NDD pathology. Sleep is essential to this synaptic remodeling process. Disturbed sleep is a highly conserved trait affecting nearly 86% of NDD patients. Additionally, sleep appears to be particularly sensitive to environmental perturbations, as negative sleep outcomes have been strongly linked to exposure to air pollutants. The Diesel Exhaust Particle and Maternal Stress (DEP/MS) paradigm was used to co-expose pregnant mice to DEP and a maternal stressor, modeling epidemiological data suggesting that combined prenatal exposure to DEP is strongly linked to socioeconomic stressors. Previous studies have revealed that DEP/MS offspring show male-specific social and behavioral traits consistent with NDD pathology. Based on preliminary data demonstrating sleep deficits in DEP/MS adult offspring, this study aims to characterize NDD phenotype of DEP/MS offspring during adolescence, focusing on possible female-specific sleep and behavioral alterations. To analyze sleep patterns in DEP/MS and control offspring, we performed electroencephalography and electromyography (EEG/EMG) recordings from P37 to P40. Additionally, we isolated astrocyte and microglia populations from parietal and frontal cortex tissue. Lastly, we conducted the forced-swim test to analyze depressive-like behavior, a common comorbidity in female NDD patients. We hypothesize that DEP/MS offspring will exhibit sex-specific depressive-like behavior and sleep deficits driven by changes in astrocyte gene expression.

RNAi pathway components may contribute to starvation-induced gonad abnormalities in Caenorhabditis elegans

Caenorhabditis elegans that hatch into an environment without any nutrients are arrested in the first larval stage of development, L1. Larvae can remain in L1 arrest for weeks and resume normal development once they receive food. However, many C. elegans that experience extended L1 arrest develop abnormal gonads in adulthood, including germ-cell tumors and uterine masses. These growths suggest a misregulation of cell growth. Previous results indicate that genes involved in processing somatic RNA interference (RNAi) could be causing abnormality formation. RNAi refers to a cell’s response to exogenous or endogenous double-stranded RNA. It functions as an internal regulatory mechanism as well as an immune response, allowing sequence-specific suppression of corresponding genes. We hypothesize that endogenous RNAi pathways are involved in the occurrence of starvation-induced gonad abnormalities. It is possible that aberrant small RNAs produced by somatic RNAi machinery are transported to the germline, causing abnormalities to form. We examined rrf-1, ppw-1, rde-1, dcr-1, rde-4, sid-1, alg-1, and rrf-3, which correspond to components of various RNAi pathway branches. Knockout strains and RNAi were used to evaluate the impact of these genes on gonad abnormality frequency in adults following 8 days of L1 arrest. So far, results align with previous findings about somatic RNAi and our transportation hypothesis. We expect future results to further corroborate these findings and clarify the role of different RNAi pathway branches in gonad abnormality formation. Overall, these experiments provide greater insight into the little-known mechanisms regulating pathologies that result from early-life starvation.

Optimizing Cyanobacteria Detection for Comparing Lichenized and Environmental Cyanobacterial Communities

Cyanolichens are symbiotic associations between fungi and cyanobacteria. When lichenized fungi reproduce sexually, the fungal spores are dispersed without the cyanobacteria, and they must find a new partner to form a cyanolichen thallus. However, how common these potential cyanobacterial partners are in the substrates where the cyanolichens grow is unknown. A robust sequencing procedure is necessary to compare the communities of lichenized and environmental cyanobacteria. This study aims to optimize the procedure for sequencing 1800 environmental samples from Alberta, Canada. We tested the sensitivity of the 16S rRNA and rbcLX genetic markers for cyanobacteria detection and the role of substrate depth on cyanobacterial community composition. The rbcLX genetic marker is more variable but is single-copy, while the 16S rRNA gene is less variable but exists in multiple copies. Sequencing the 16S rRNA gene may be better for detecting trace amounts of cyanobacteria in environmental samples. Additionally, cyanobacteria are expected to be more diverse in top substrate layers because they need light for photosynthesis, so sampling from deeper depths may not be necessary. We sequenced the two markers from 112 environmental samples, including 12 with known taxonomic compositions. The remaining 100 samples have unknown compositions and include both top and bottom substrate layers. We will use the sequence data to compare the detection sensitivity of the two genetic markers. Preliminary results favor the 16S rRNA gene. The results will inform the procedure for large-scale characterization of environmental cyanobacteria to understand the formation of the cyanolichen symbiosis.

Lisa’s Chalk Talk

This week in BSURF, we were tasked to present our projects in the form of a chalk talk. We had 8 minutes and a whiteboard, and had to communicate the central ideas and questions underlying our projects. Each talk was engaging and informative, and I enjoyed this dedicated time to further my understanding of the other fellows’ projects. Now, when I ask my BSURF friends about their days in the lab, I’ll have some background on the techniques they use!

For this week’s blog, I’m asked to identify a fellow’s chalk talk to reflect on. Lisa’s talk was particularly intriguing to me. Her research focuses on CRISPR-Cas9—more specifically, the guide RNAs used to direct the Cas9 protein to a DNA sequence. 

Lisa first provided background on the broader implications of her project. She explained how currently, the most pressing risk associated with the use of CRISPR is off-target DNA cuts. I learned about how Lisa’s project uses dCas-9, a deactivated form of Cas9 that finds, but doesn’t cut, a specific sequence of DNA. From my understanding, the overarching goal of her project is to gain a better understanding of different variations of Cas9 proteins. This, she explained, could have implications for clinical CRISPR use, particularly for patients who are resistant to commonly used forms of the Cas-9 protein.

The down-to-earth tone of Lisa’s presentation was what made her talk stand out. I admired her presentation skills–she presents with a confident voice, and isn’t afraid to incorporate humor into her talk. She effectively reduced complex topics into easily digestible terms, which kept the audience engaged and intrigued.

I found her topic very compelling, and I hope to be able to learn more about the CRISPR-Cas9 system in the future.

David’s Chalk Talk About Chlamy

This week, we had the privilege of learning about everyone’s projects through chalk talks: short whiteboard presentations. It was really interesting to learn about the wide variety of projects that BSURF fellows are conducting this summer. 

One such project was David’s, which involves cell division. David studies Chlamydomonas reinhardtii (also known as Chlamy), a single-celled alga. He’s investigating how the division of chloroplasts is coordinated with cell division, as chloroplasts divide independently from the rest of the cell. Because Chlamy has a single chloroplast, it is a good model organism for this question. More specifically, David is studying a protein called ARC6 that may be involved in the process. Using techniques such as protein tagging and generating mutant crosses, he investigates ARC6’s location and function.

Overall, I enjoyed David’s chalk talk and found it engaging. The way that he drew Chlamy—kind of like a cute alien—made the board fun to look at, and his other graphics also served to make his points clear. I’ve learned about cell division many times over the years, and it was interesting to learn about what is still under investigation. I look forward to learning more during the poster session! 

A Day in the Bilbo lab

I start the day by getting situated at my usual desk in Dr. Vaidyanathan’s office.

In the time I have before I dive into my lab work, I like to lay out my schedule and to-dos for the day in my bullet journal (anyone who knows me is all too aware of my obsession with good stationary). From there, I’ll go with Dr. Vaidyanathan to start our day of tasks for the project.

As someone who loves a structured routine, I’ve been really leaning into the weekly layout of the project. On Mondays, Dr. Vaidyanathan and I will typically start the day by collecting estrous smears from that week’s cohort of EEG/EMG mice. We’ll then start the EEG/EMG recordings for the mice–this marks the start of the experiment for the week!

Next, we have to image the estrous samples taken that morning. The estrous cycle is essentially the mouse equivalent of the menstrual cycle. It’s about 4 days long, and each day can be characterized into different stages. You can tell what stage in the estrous cycle a female mouse is in by examining the quantities of certain cell types in a sample taken from the vaginal epithelium–a process called vaginal cytology.

Our lab manager Dang Ngyuen (a former BSURFer himself!) trained me on using the brightfield microscope for this process. As I’ve been getting more acquainted with the lab, I’ve been able to perform some procedures with more independence. Lately, I’ve been imaging the estrous samples myself!

On Tuesdays, Dr. Vaidyanathan usually spends the day preparing next week’s mice for EEG/EMG. This part requires a lot of advanced animal handling, so I’ll shadow her for part of the process. Tuesdays typically give me a lot of free time, which I’ve been using to analyze data from the behavioral tests we conducted in the weeks prior. If there’s not much work to be done on the data, I’ll spend that time practicing MATLAB in preparation for the heavier data analysis that I’ll be doing down the line.

Wednesdays are a bit more unpredictable, but they usually end up being some of my favorite days in the lab. There’s not much to do with the cohort of mice on these days, aside from a quick check. Last Wednesday, I had the opportunity to shadow Lauren Green, another post-doc in the lab. She primarily works with zebrafish, another common model organism in neuroscience research. She taught me how to cross transgenic zebrafish and how to screen eggs for a specific genotype that would allow fluorescent tagging of microglia and serotonin-producing neurons. Then, she showed me how she uses a confocal microscopy to image these cell types in the brains of live zebrafish.

On previous Wednesdays, I’ve mostly been learning the procedure for astrocyte and microglia isolation and RNA extraction from Dang. Our plan is to run Q-PCR on RNA isolated from the cortical astrocytes of the mice to confirm that our isolation procedure did in fact isolate astrocytes. Then, although this step goes beyond the 8-week timespan of the BSURF project, we plan to perform RNA sequencing to analyze the astrocyte gene expression patterns of our treatment mice.

Thursdays tend to be another day of coding and data analysis. I’ve been working with Dr. Vaidyanathan to write a MATLAB script that will be able to efficiently compute statistics and  produce graphs from the data we’ve collected from the Forced Swim Test–which happens on Fridays.

We wrap up the experiment for that week’s cohort on Fridays. We stop the EEG/EMG recordings, and set up for the Forced Swim Test–a behavioral test meant to serve as a measure of depressive-like behavior. There’s many moving parts to this test, so Olivia, a new lab technician in training who I’ve been working closely with, helps me and Dr. Vaidyanathan with this part of the experiment.

Finishing up the Forced Swim Test is the conclusion of our week. I usually head out early, and begin with my weekend plans.

Interviewing Dr. John R. Perfect : A man changing the medical field, with one pathogen at a time

Presenting Dr.Perfect

This week, I had the honor of interviewing Dr. John R. Perfect, who serves many roles here at Duke University, with his primary role being that he is Chief of the Infectious Diseases Division at the Duke School of Medicine. He is also the Principal Investigator of my lab, “The Perfect Lab,” which focuses on the different aspects of medical mycology and works to understand fungal pathogenesis at the molecular and genetic levels. Dr. Perfect is a physician-scientist driven by passion and with one important goal in mind: “to help people.” This is his story and how he came to be the man he is today. 

He grew up in a small town in Ohio. One fun fact that Dr. Perfect enjoys sharing about himself is that his father worked as a butcher, and being a butcher’s son, allowed him to gain knowledge about meats and exposed him to blood very early in his life. I asked Dr. Perfect, “When/How did you become involved in science?”. He told me that he began thinking about careers around 7/8th grade, and at that time, he was considering three different careers: 

  1. Farmer
  2. Teacher
  3. Doctor 

However, he weighed out his career choices and realized what he truly wanted to be. He knew that to be a farmer; one needed to be married into or inherit the business because it’s expensive to run a farm. There is also a much-needed craftsmanship trait to farmers that comes in handy when a problem happens at the farm (whether it’s with the machines or livestock), and creativity has to come into action to solve it the best a person can. This was a “no” for Dr. Perfect. “Well, why not a teacher?”. Dr. Perfect has been a professor at the Duke School of Medicine school and loves to pass all his knowledge to students appreciative of it. However, Dr. Perfect does acknowledge that not all students share the same passion or ambition about school, which is reflected in their participation and commitment to their work. Teaching a class consisting of students who are all very interested and focused is a priority for Dr. Perfect to have. Otherwise, he would find it to be frustrating to teach a class with students who are not all willing to work hard and collaborate to understand the subject. Teaching at the Medical School, in classrooms where the people there have worked extremely hard to get to where they are and are motivated to make a difference in people, is one of the motivators of Dr. Perfect to give lectures when he can. Being a Doctor was the career goal he set for himself, and he sought moments when he could be granted the chance to become involved.

Young Dr. Perfect had a friend whose dad was a doctor in their small town. This doctor would often be at their soccer games and treat any injuries that the kids would sustain from the games. Dr. Perfect offered to help with physicals for the team when needed, which gave him a glimpse into helping people with the power of medicine. One thing that surprised me was that Dr. Perfect did not have much exposure to the hospital setting of medicine before medical school. He had, however, helped around his friend’s dad at the clinic (he dealt with the specialty of family medicine), but the setting and pace that medical students go through was something unknown to him which made him feel left behind compared to his other classmates who did have experience. Dr. Perfect was not discouraged and did not let his inexperience stop him. He graduated from Wittenberg University–a small liberal art college in Springfield, Ohio– with a bachelor’s degree in Art and being the first in his family. Afterward, he was on his way to attend the University of Toledo Medical Center in Ohio, where he completed 3 years of medical school. For his residency, he attended the University of Michigan for 2 years, and then he was off to Duke to fulfill a fellowship. 

I asked him, “Why work specifically with Infectious Diseases?” and he said, “I picked Infectious Diseases because I like how it is sort of a puzzle to solve within the Human Body. From detecting/narrowing down the diagnosis, testing different treatments/antibiotics out (because the bodies of different people undergo different experiences with medication, so what works for some may not work for others), and analyzing the patients’ progress until they are recovered is all a part of this big puzzle known as the human body system. Dr. Perfect loves that he has the privilege of having some control over the human body (he was a part of the team that caused children to have a better chance of reaching adulthood because, before vaccines, that wasn’t a possibility for many), and through research, he can have control over the disease and infection by “spying” on it (in a sense) and findings weapons to use against it for the good of public health. As Dr. Perfect recalled his experience with patients, he recalled a specific interaction with a patient that impacted his career. 

Dr. Perfect highlights that HIV/AIDS and COVID-19 are 2 of the biggest major outbreak in medicine. The patient that Dr. Perfect worked with had been diagnosed with HIV/AIDS, “Being at their bedside showed me a side of scared people. Especially those diagnosed first with the diseases; they went through tremendous psychological challenges (not only death) but in their families. Some of them were not prepared to face the truth of coming out of their closets (specifically gay males). Rather than their families finding out by their mouth, they found out through the diagnosis of their children, who were now infected. The male patients infected wouldn’t be protected, and what was worse was that their families rejected them after they found out they had contracted HIV/AIDS instead of providing the support they needed.” Dr. Perfect was saddened and empathized with these patients because he knew that what they needed most, at the time of their family’s rejection, was the support, kindness, and reassurance of their physician that they were going to get through it because even though there are no vaccines available to help with prevention, patients with HIV/AIDS are still able to live a fulfilling life with proper medication intake. Medication and vaccine discovery for infectious diseases is all thanks to the research that has been conducted thus far, and more is yet to be done to find better and faster methods to improve recovery. Dr. Perfect appreciates the patient interactions that as a physician, he is able to have and as a researcher, he is able to do more for his patients which is something incredible.

One of Dr.Perfect’s favorite thing about his work is having the chance to travel around the world to communicate with people about his findings. Dr.Grunwald constantly emphasizes to us the message that “What we do in the lab is useless unless we communicate that information with others.” and that is exactly what Dr. Perfect does. Dr. Perfect has visited around 55–58 countries (and counting) and acknowledges that traveling has been an immense privilege for him as he has been able to witness different cultures and meet people of different backgrounds from which he wouldn’t only educate but whom he could also learn new things from. One of the places on his bucket list is Egypt, which I hope he can accomplish soon. In contrast to his travels and interactions with Earth’s inhabitants, Dr. Perfect mentions that the thing he likes least about working in science is that “research can’t be done without money.” Grants are needed to be written, and the likeliness of those grants being funded/approved is 1/10, which is frustrating because a tremendous amount of work goes into writing them. Dr. Perfect doesn’t mind writing but hates that funding is dependent on these grants and it is not continuous. Research is expensive and a helpful tool for society, but it lacks reassurance that it might work if funding is not provided. How is one to know if the findings are successful and can save a life or if it isn’t without the research that’s done? One dream that Dr. Perfect wishes would come true is for funding to be continuous (maybe for a max of 5 years) so that he can continue conducting research with no worry of limitations for it and enjoy time doing it. Science shouldn’t be defined or limited by money because it’s impact goes way beyond that.

Lastly, one piece of advice that Dr. Perfect gave me and that helped him throughout his career is, “If you have the opportunity, then take it. Be prepared and do all that you need to do to get that position or reach that goal that brings joy to you. Work hard, and despite whatever forks may come up on the road, be flexible and overcome them because it will be worth it since you are being driven by passion and motivation. I wasn’t in just one track growing up. Sample, don’t necessarily take something just to take it but instead find stuff that you’re good at and enjoy or love doing. If it takes time, take that time to do it. Life expectancy will be pretty long.”. So with this in mind, I gained a new perspective and plan to take Dr. Perfect’s advice as I advance further in my career. I hope you all, my fellow BSURF cohort, do the same. 

Thank you, Dr. Perfect, for taking the time to sit down with me. It was truly a joy and honor to get the chance to talk to you more, and I thank you for all the work you have been able to accomplish, discoveries made, as it has helped advance medicine and helped many people along the way.


Photo received from: Dr. Perfect. (n.d.).

An interview with Dr. Vaidyanathan

It was during my first week in the Bilbo lab, eating lunch in the shared post-doc office, that I recognized Dr. Vaidyanathan’s unique passion for bringing her scientific expertise beyond the lab. She was attending a zoom meeting, strategizing about how to go about communicating the negative environmental impacts of the Mountain Valley Pipeline Project with environmental lawyers. This, I would later learn by interviewing Dr. Vaidyanathan, is just one of many examples of her dedication to scientific communication and community engagement. Dr. Trisha Vaidyanathan is a post-doctoral fellow at Dr. Staci Bilbo’s lab, and my bench mentor for my summer BSURF project. I recently had the opportunity to interview Dr. Vaidyanathan for this blog, and was able to learn more about her motivations, philosophies, and path in science. 

Dr. Vaidyanathan grew up in California and started her journey into science at the University of California, Berkeley. She noted how she didn’t know much about research at the time, and was initially interested in environmental science or art history. As her undergraduate career progressed, she began to volunteer in labs, where she was initially introduced to research. She worked mainly in human labs, focusing on topics such as sleep. Her beginnings in neuroscience was a course in psychology. Because of this course, along with a mental health advocacy group she worked with, she found herself drawn towards the psychology path. 

By the end of her undergraduate years, she had decided on a major in cognitive science–a unique mix of psychology, neuroscience, philosophy, and computer science. Finding herself enduringly interested in the questions neuroscience sought to answer, and having been introduced to the idea of a PhD by a mentor from her senior year, she graduated from UC Berkeley on the path towards graduate school. 

Hoping to gain more lab experience beyond the behavioral and computational work of her undergraduate labs, Dr. Vaidyanathan applied for and accepted a position at the National Institutes of health for a post-baccalaureate program. After a year, having strengthened her in-lab experience, Dr. Vaidyanathan entered the graduate school application process and was accepted to the University of California, San Francisco, where she began her rotation. 

Knowing she could become passionate about many topics, and having cultivated an arsenal of well-rounded lab experiences, she approached her rotation with a focus on finding a supportive lab environment and a principal investigator who would serve as an inspiring mentor. 

She found this community in the then-new lab of Dr. Kira Poskanzer. As one of the first full-time members of the Poskanzer lab, she had the unique experience of establishing the lab alongside Dr. Poskanzer. She noted that this opportunity to work directly with her principal investigator allowed her to connect with Dr. Poskanzer, who became a significant and inspiring mentor to her. An expert in the new and exciting technique of in vivo 2-photon imaging of astrocyte Ca2+ activity, Dr. Poskanzer passed on her expertise to Dr. Vaidyanathan. Becoming fascinated with the role of astrocytes in synchronous neuronal activity, and quick to draw from her own background working in sleep labs, Dr. Vaidyanathan proposed and subsequently pursued a project focused on understanding how astrocytes are involved in modulating the sleep-wake cycle. 

Talking to Dr. Vaidyanathan during our interview, it was clear that this project was both challenging and rewarding, and played a large role in her approach to her science today. She recalled the novelty of both the Poskanzer lab itself as well as the field of astrocyte research. Staring completely from scratch, she found herself troubleshooting often as she built techniques and procedures from the ground up. She remembered the frustration of lack of data, and not feeling like a successful scientist as a result. She offered a piece of advice from this anecdote: it’s okay to not get data right away. 

When I asked her about what she would change about the world of research, she emphasized the need for increasing accessibility to research, especially for underrepresented communities. Particularly, she’s passionate about ways that scientists can contribute directly and tangibly to the broader community. 

Through volunteering to assist lesson planning at local schools to helping environmental lawyers fighting against the construction of the Mountain Valley Pipeline, Dr. Vaidyanathan’s motivated to contribute her empathy and expertise beyond the lab. She’s particularly interested in how scientists can help inform policy. She recalled witnessing the need for a scientifically-informed policy during her work with a group of scientists advocating for how the Mental Health Parity and Addiction Equity act can be better enforced. 

Learning about her path, it’s no wonder how Dr. Vaidyanathan developed her creative, innovative, and enduringly patient approach to science, both inside and outside the lab. After the interview, I decided to enroll in a public policy course for my sophomore year, and felt inspired to explore ways in which I can contribute to increased communication and accessibility in research. Her story has much to offer, and I’m excited to have had the opportunity to relay it. 

Can bispecific ELP proteins be used for drug delivery?

Camila Rodriguez

Mentors: Anya Varanko, Ashutosh Chilkoti, PhD.

Department of Biomedical Engineering

Elastin-like polypeptides (ELPs) are proteins based off of tropoelastin, a subcomponent of elastin, that are able to change solubility under different temperatures. By combining these proteins with the affibodies ZEGFR and ZHER2, the proliferation of cancer can be limited much more effectively than bispecific antibodies. ELPs were combined with affibodies in E. coli plasmids to create different protein constructs, purifying the proteins using heat cycling. SK-BR-3 cancer cells positive for both EGFR and HER2 were then treated with the previous proteins to create a proliferation assay. Each construct maintained the same amount of proliferation as the control at all concentrations, resulting in no color change for the assay. This suggests that the constructs had no effect on the growth of SK-BR-3, and both affibodies were unable to block the receptors. The potential of ELPs and bispecifics still require further investigation, as it may be possible ELPs inhibit the binding of the affibodies, that ZEGFR and ZHER2 are incompatible with ELPs, or other outside factors. The use of other bispecifics, as well as maintaining temperature while performing the assay, will be explored as research in ELPs continue. 


The activation of type I interferons has long been reported to regulate pain, but the precise mechanism has remained unclear. We tested the hypothesis that type I interferons are critical pain regulators and function via a neuronal mechanism. Sensory, motor, and behavioral testing in addition to immunohistochemistry were performed on type I interferon receptor knockout (Ifnar1 KO) and wild type (WT) mice. Heightened sensitivity in KO mice suggests an importance of type I interferons in regulating pain under basal conditions. The lack of any difference in motor performance and quantity of nerve fibers in tissue of WT and Ifnar1 KO, along with RNA scope, support a neuronal-specific mechanism of interferons in regulating pain. These findings suggest that type I interferons are critical in regulating both pain and neuroinflammation by a neuronal mechanism, even under normal, healthy conditions. These findings redefine our understanding of the role of interferons in pain and could translate to improved treatment of a heterogeneous array of chronic pain.

This is long overdue…

I know, I know, this is really late. I am just now getting time to ponder of the experience I had this summer, but words cannot express how thankful I am for being able to participate in BSURF this summer. The friends I made, the faculty talks, and the research experience all made this summer very special and one that I will truly cherish. I was honestly so nervous beginning this program. I was so nervous about not being smart enough and I was nervous that I was not going to enjoy research. But with all new experiences, I believe uneasiness can be a good thing. It’s good to come out of your comfort zone, and the fact that participating in this new experience initially made me uneasy (but excited of course) meant that in some way, what I was about to do was important for my growth as an individual. I can happily say that this program did cause me to grow– in academic knowledge, confidence, knowing my strengths and weaknesses, and setting new goals for myself. Furthermore, BSURF has definitely influence my career endeavors because research is definitely something I want to do again in the future.

As I elaborated on in my previous post, one aspect that I really enjoyed about BSURF was the faculty talks. I really liked how the faculty not only talked about their research interests, but their own career paths–the ups and downs– and how it got them to where they are. This was really influential to me because I was able to see and understand that although things may not always go as planned, life works its way out.

I just want to give a special thank you to the people in my lab for making me feel welcome. I also want to thank my mentor, Connor, for teaching me about different aspects of research and allowing me to work on your project. Furthermore, I want to thank my PI, Dr. Calakos, for letting me obtain this initial research experience from your lab. Finally, I want to thank Dr. Grunwald and Jason for this summer and for facilitating my, and my fellow peers, ability to make connections with professors and important faculty in the various fields of biological sciences. Man, this was such a fun summer and I hate to see it end, but I know this experience is only the beginning and has provided me with a clearer lens of what I want to do in the future. 🙂

Final Stage: Thank You

During the poster presentation Friday, someone approached me and told me that he had read many of these blogs and liked my style, applauding my writing. Before I could really grasp that he was not simply after the 30-second rundown of my poster I had laboriously perfected the prior night, he continued through the parade of posters ephemerally as I squeaked a meek ‘thank you.’

I say it so dreamily because it certainly was one of the most touching experiences this summer, right with seeing my entire lab flood into the hall, looking around for me and Christine (who also presented under the Summer Neuroscience Program). It was somewhere in that moment that I realized they had become my family- a clutter of familar voices cutting through the mob and somehow I already know what they’re saying. An ineffable feeling that Dr. Colton is in front, like a flag-bearer in her blue blazar, and somewhere lagging behind is Hui Fang glancing around. Stuart, now unaddled by the broken A/C of the lab, is out of his lab coat and in a buttoned shirt- plaid -and shorts as things should be, and notices me first along with Angela. Joan wastes no time walking closer, steering the group in my direction, including Kendra undistracted by all the other flashy posters. Like the 5th grade science fair where your parents came despite having work, except with so, so many more questions about the science and not the closest bathroom. As BSURF concludes, I realized how many memories and experiences I have tied to this summer, and how many people I wish to thank beyond a 10′ by 5′ poster corner could.

Thank you Dr. Grunwald and Jason Long. I think you both are entirely aware of how impactful this program can be because you watch it happen every year, but for repeated emphasis, this summer has been LIFE-CHANGING. Perhaps not in a existential manner, but definitely in a navigational one. From working behind the scenes with food, finances, and fun to arranging informative experiences and talks, both of you have helped us tremendously to stay on track while still being so tolerant and flexible. I really enjoyed getting to know both of you these two months, especially in this environment where your mentorship skills really thrived. Interviewing with Dr. Grunwald had me in complete admiration from the start- both from his office’s many reptilian tanks and his scientific authority -and this has only continued to grow around your charisma towards students, and Jason’s welcoming and attentive chats. Although I had some trouble with my chalk talk, there was no dip in support, and in that atmosphere, how could I not learn to improve, to present, to communicate.

Thank you to Dr. Colton and my lab. Everyone has been incredibly friendly and helpful these two months: answering endless swarms of questions, guiding me towards what goals I should have, casual conversations and parties, and tireless jokes about my sleeping habits in and out of lab. Quite honestly, this has been the undergraduate lab experience I dreamed of, an appropriate balance of independence and mentorship, fascinating research topics with several directions that convene regularly, mellow lab environment without pressure to perform, and meetings to reinforce professionalism and ambitions while remaining friendly. I do mean it quite seriously when I claim everyone as like family, and that includes our now-gone, infant (or perhaps fetus would be more accurate?) Taylor (Good luck on college applications and the SAT/ACT!). I have picked up much from being around everyone, such as how to interact with lab members and the path to designing one’s own project about a topic. Even the finer nuances of the lab like project timelines, lab presentations, reagant costs, and technical tips and tricks to spitting out 5 Westerns in a week. I have so much more I’d like to attribute to everyone, but there will be plenty of time for me to pester the lab with them, since I will be sticking around for three more years to further look into UK114 🙂 See you in a month!

Thank you to my audience! This includes my peers, other researchers, and yes, those reading my blogs! I know how long these posts are- apologies -but I would like to ramble a bit more on how grateful I am for your support and future interactions. It is somewhat strange for me to process that my vehicle for transcribing my thoughts and project directions has actually been reviewed by a professional audience, and apparently enjoyed. Those small moments really are both moving and exciting, alerting me to just how interactive a community research can be. I hope to continue working hard to impress those looking on without deviating too far from my current style.

Weekly Highlights

“What is your name?”- a random PI grabbing a drink at the same time I was at the BioCore symposium whose name I unfortunately did not catch
“Oh, Dang”-Dang
“And where are you from, sir?”-PI
“South Carolina?”-Dang
“Oh are you from MUSC? (the Medical University of South Carolina)”-PI
“OH! Oh no. I am an undergrad.”-Dang *strangely explaining that he is not a medical student for the third time this year*

“IT’S FREEZING”-Stuart running around in lab coats for warmth trying to find out how to fix the thermostat

“Hey, Hui Fang, do you want to join a luncheon for my program?”-Dang
“What? Really?”-Hui Fang
“Uh, yeah”-Dang
“Really?!”-Hui Fang

“Good morning?”-Joan opening lab at 6 am
“Good morning Joan :)”-Dang cracking open his third Western gel
“…How long have you been here”-Joan
“I never left”-Dang

“You should sleep more Dang!”-Christine
“I feel so rested though!”-Dang
“You fell asleep three separate times during the talk”-Taylor

“What is that green ice cream?”-Marilyn
“I think it’s green tea?”-Angela
“It’s got some weird off green color. Oh Dang got some, how is it?”-Stuart
“…it has…like…no real flavor?? It is green tea I think”-Dang on his third bowl of it

“So like, no ulterior motive or anything, but could you hypothetically drink the 200 proof ethanol?”-Dang with serious but innocent inquiries
“Uh, I think? I think I asked that question when I was new too.”-Stuart

“Stuart what would weird black orbs in your culture mean?”-Dang
“Oh, is there an infection? What do they look like?”-Stuart
“Well I think they’re yeast, but they’re like orbish and black. Really round. Here let me show you, I caught it and cultured it in a well”-Dang
“You what”-Stuart
“So, I accidentally treated the same well with hydrogen peroxide meant for one of my experiments, so I think I killed them all”-Dang
“What? Are you sure they weren’t debris or anything?-Stuart
“Yeah it definitely wasn’t! There were a ton of them and they were all different sizes!”-Dang
“Hmm, well show me if you find them again I guess?”-Stuart
“So, it turns out Stuart, that they were just bubbles”-Dang
“What the heck haha you had me worried. You were trying to grow bubbles?”-Stuart


*in the midst of Lefkowitz’s talk about his career*
“Oh god I left the hot plate on”-Dang as he nervously begins staring at the clock for when he can run back to lab

“Oh thank god it didn’t explode”-Dang finding the hotplate still on with the bowl of water completely evaporated
*bowl shatters*

“zzz”-Dang asleep while waiting for chemiluminescent exposure time
*Hui Fang softly knocking outside the locked imaging room for 5 minutes*

“Now just carefully….”-Dang cracking open his first Western gel
*gel case shatters*
“…stab the gel with shrapnel…”-Dang
“How did the Western go?”-Hui Fang
“Did you learn how to solve jigsaw puzzles in your other lab?”-Dang turning around with 5 scraps of gel

“Wow we’re back at lab already?”-Dang
“You were snoring right after we left Dr. Colton’s house”-Joan

Are you a student here?”-a high schooler touring through the Bryan Research Building
“Yes, I am! A rising second-year”-Dang
“Oh wow, where did you go for undergrad?”-high schooler
“Oh, um. I actually am still an undergrad…Do I look that old?”-Dang

So you’re only a first-year?”-Dr. Colton
“Well, our lab is always open to having medical students onboard!”-Dr. Colton
“Oh. Oh no. I’m an undergraduate.”-Dang’s first interaction with Dr. Colton ever (actually in October)

Funding provided by Duke University Trinity College of Arts and Sciences. THANK YOU BSURF!!!! 

B-Surf? More like A+Surf

Up until last semester, I viewed science in one context- to learn science. I had never been exposed to the other spectrum- to do science. While we “did scientific experiments” in high school labs, it just felt like I was following instructions on cookbook. It wasn’t until I got to Duke that I actually felt like I was attempting to answer questions that hadn’t been asked before. This summer, I got to feel the satisfaction of not only asking interesting questions and even successfully answering one of them. This summer, I got to do science and nothing but science.

Funny enough, it wasn’t the doing science that I will cherish the most about this summer. The most invaluable moments are the 20 minute weekly philosophical talks about science by mentor, Mariano.

I would say one of the greatest lessons I learned this summer is that there is no capital T Truth; there are only many lowercase t truths that can suggest a capital T Truth. I knew about this saying, but getting a first hand experience of trying to reveal a truth cemented these words in me. I began to question not only if my truths were sufficient enough to infer about a Truth, but also if other things I thought were True were ever only true. I am a very trusting person, and before this summer, if you were to tell me something is science was True, I would probably shrug my shoulders and believe the Truth. Now, however, since there isn’t a Truth, I am able to critically think about whether there is even enough truths to even suggest a Truth.

Another similar (almost depressing) lessons I learned about is the vastness of the unknown. In ecology, there is what happens in the lab, what happens out in the field, and what happens in nature. No matter how hard we try, there is just no way that we can simulate exactly what happens in nature in the lab or out in the field. This hangs over each researcher’s head, because there is just isn’t a way of knowing exactly what’s happening in nature. There is no way of even predicting how much of the unknown is there. This is a scary thought, but finding comfort in the vastness of the unknown is solace in and of itself.

Honestly, I think I will remember these lessons more than the specifics about the inheritance of Arabidopsis thaliana.

I guess I would kind of say I figured out that I not only loved doing science, but almost liked learning about the drawback even more. These lessons helps to put science in context of the natural environment, and I love nature all that more after realizing the breathtaking immenseness of its complexity.

Thank you so much to Dr. Gurnwald and (future Dr.) Jason Long for allowing me to learn and do so much science. Thanks to the Donohue lab for being the kindest people.

Although I won’t be continuing this lab during the semester (I realized I am more interested in the molecular side of things), I am beyond grateful for the experiences I have had.

Also sorry for the title. I can’t help myself sometimes.


My BSURF experience has been incredibly enjoyable and rewarding.

Having grasped certain techniques, as well as a bigger picture understanding of how to plan out experiments, I now feel that I can independently ask and answer a pretty wide range of scientific questions in my lab. Considering how dependent I felt on my mentor at the beginning of the summer, this achievement seems very special indeed.

As a whole, the summer gave me a small taste of the mixed emotions that I imagine all scientists experience: the frustration that comes with a series of negative results, and the great satisfaction of finally making a significant breakthrough. After several weeks of optimizing my techniques, it started to seem as though the link I was exploring – a regulatory connection between ABL kinases and SLC7A11 – might not exist after all. Eventually, after I had convinced myself that I was most definitely wasting my time by continuing to pursue this project, I was able to show that ABL kinase inhibition does in fact cause a reduction in SCL7A11 protein levels, confirming the connection. This experience showed me the importance of sticking with a project even if you get discouraging results along the way, rather than immediately replacing it with something new.

I am very grateful to have participated in such a well-organized program and to have worked in such an outstanding lab. Thank you to Dr. Grunwald and Jason for giving me this opportunity, and for all their support throughout the summer. And of course, thank you to Dr. Pendergast and my mentor, Jill, for guiding me through my first real research experience. I look forward to continuing to work in the Pendergast lab next semester!

Goodbye BSURF

I am beyond thankful to have had the opportunity to be apart of the BSURF program. I have had the opportunity to work with some amazing researchers. I got to hear talks from amazing faculty members. I have also gotten to form bonds and make memories with the other students in my program. I am sad to see these 8 weeks come to an end.

When I first started in my lab, I was very nervous about how everything would work out but I was open to the learning experience. Over the course of the summer, I realized that I truly do enjoy working in a lab. I enjoyed planning and executing experiments. Over the summer, I had to help create a protocol and it is cool to see results come from the protocol I worked on.

Over the summer, I had to present my topic/data multiple times. Learning how to properly present data to an audience is crucial if I want to work in research in the future. Though I was nervous each time, having a solid background in my topic and tips from our program directors made me feel more confident in my presenting abilities.

As I said before, I am thankful for the opportunity I was given this summer. I would like to thank Dr. Hammer for having me in her lab this summer. I would also like to thank my mentors, Nourhan and Hsin-I for working with me and making my experience in the lab enjoyable. Finally, I would like to thank the directors for the program, Dr. Grunwald and Jason Long, for their guidance and support over the summer.

My mentors and I at the final poster session

BSURF Series Finale

I came into this summer initially wanting to focus on being able to ask tough questions in order to further myself as a scientist. When I originally came up with this goal, I thought that I would be coming up with some grand paradigm changing question, but I found that the questions I learned to ask this summer were even more valuable. I learned how to question myself at every stage of the protocol in order to understand not just how to do something, but why I was doing it, providing me with better insight into this project. So while I was not coming up with earthshattering questions, learning to critically evaluate myself and not just the world around me has increased my ability as a scientist.

Over this summer I have also learned that failure is not the end all be all. In the lab, I learned that while experiments may not always go the way that I think they should, I can still learn from them by seeing how this experiment failed, and in turn improving myself my learning how to fix it. From the talks, I learned that while some of these scientists experienced setbacks in their early years, they were still able to lead amazing careers because they did not let those setbacks define them. That has been a hard lesson for me to learn as whenever something does not go right in my life I obsess over it and think that it reflects my shortcomings as a person. But I have learned that science is built more on failure than it is by success, and a failure can be significantly more valuable than a success if you are able to learn from it.

Overall, this has been a fantastic summer and while my project did not go as expected, I still learned quite a bit in the last 8 weeks. I would like to thank Dr. G and Jason for allowing me to even be part of this program, and I would like to thank everyone at the Murphy lab for putting up with me for these last 2 months.