Category Archives: BSURF 2018

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.

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.

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.

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.

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.

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. 🙂

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
—-later—
“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
—later—
“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

SUMMER BLOOPERSHIGHLIGHTS

*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
“Yup!”-Dang
“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!!!! 

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!

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

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.