Author Archives: Piper Epstein

I’m typing this having just recently submitted my final poster draft for the research symposium, but I feel like I only just submitted my first blog post a few days ago. Reflecting on the past 8 weeks, I feel comfortable saying that my expectation for the summer as outlined by that first blog, “to grow a lot,” was achieved. My first full time “adult” job- that is, working approximately 9-5 without an onslaught of assignments, extracurriculars, and exams to keep track of- was quite the novel experience and I loved it. I could devote my full energy to a single project for two months and still have free time to visit the Farmer’s Market, hold snakes and canoe at the Eno River, and explore Durham more than I’ve ever been able to during the school year. Those experiences were all part of my growth as a person- becoming more independent and involved with my surroundings -but most of the growing I did was as a scientist. I was quite honestly pretty scared to begin research this summer. I’d had very little lab experience and a brooding fear of failure. This wasn’t immediately lost during my first few despite the welcoming and helpful mentors I found. I remember being handed a DNA extraction protocol and trying not to ask 16 thousand questions about each step. However, with each faculty talk, workshop, and new day in the lab, these nerves began to shake off. All of the faculty speakers and my lab mates recounted reassuring stories of their time as undergraduates and I got to see what their path and current “day in the life” in science was. And, as with most new things, after some practice I felt a whole lot more confident (only having to ask maybe 5 thousand questions).

The influence of this program was much less linear than I expected. I thought I’d take part and know that either “wow, I love research this is what I’m going to do forever” or “nope, definitely not for me” and go directly from there. Instead, I realized how binary that view was. Each faculty talk showed me a new area of intrigue. We were exposed to molecular genetics, ecology, microbiology, clinical research, computational biology, and more. We met people who worked in the woods, on a computer, in the hospital, and on the lab bench. In that way, B-SURF’s influence on me was more wide-sweeping, exposing me to a whole area of potential opportunities rather than a yes/no consensus. It’s honestly a little daunting to see all that’s out there but I’m excited to continue exploring with a more confident and experienced outlook. Thanks to Dr. G, Dr. Harrell, Austin, and my lab mentors for a great summer!

I enjoyed all of our faculty talks over the past few weeks, but Dr. Mohamed Noor’s presentation in particular stood out to me. Two of my friends had actually worked in Dr. Noor’s fly lab last semester. I also knew his name from a collection of emails from the biology department and my Bio 203 lab worksheets, where he was listed as one of the fly collectors for our semester lab project. The mysterious Dr. Noor was finally revealed to me in person just a few weeks ago during his talk. For some reason, I was surprised by who came in. Part of me imagined a serious, impersonal guy in a lab coat (presumptuous, I know, but something about the well known lab, books, and position as Dean seemed intimidating). I was wrong. The scientist who spoke to us was anything but impersonal and serious. He was enthusiastic, friendly, and humble. I think his enthusiasm was what stood out to me most and inspired me to write about his talk in this blog post. I can’t remember exactly the phrase he used, but his presentation was filled with him repeating “isn’t that just fascinating!” or “I just find it so cool that…” I became just as enamored with color changing caterpillars, lethal genes, and phylogenetic trees as he seemed when he explained his work. He was unapologetically excited about his work, a sentiment I want to hold with me as I navigate my time and courses at Duke and make decisions about my career path afterwards.

Having initially been unsure about his path as a student (a common theme among the faculty speakers) and even being thrust into positions like Dean of Trinity College without preemptively planning to do so perpetuated that to be successful, you don’t have to know exactly where you are going. Instead, he reminded us to just enjoy the ride and work hard because science at its core is about loving discovery- not solemn, aloof people in lab coats.

Mentors: Jun Zeng, Dr. David Lawrence

The human gut microbiome performs several important services beneficial to host health. In hematopoietic stem cell transplant (HSCT) patients, who often undergo total parenteral nutrition (TPN), this microbiome can become disrupted. However, we do not understand exactlyhow microbiome function is altered. We investigated the consequence of TPN on the gut microbiome’s ability to digest fiber and produce short chain fatty acids (SCFAs) through a fermentation experiment, testing the hypothesis that the level of fiber fermentation is lower in TPN microbiota samples than in normal diet (ND) samples due to microbiome disruption. We introduced inulin to HSCT stool samples and left them to digest for a period of 24 hours. High-Performance Anion-Exchange and Gas Chromatography analyses were used to measure concentrations of inulin and SCFAs, respectively, in the resultant solutions. We found that when introduced to inulin, the TPN samples had a greater fold change in SCFA composition compared to that of ND patients and TBD EFFECT WAITING ON RESULTS on fiber digestion. This analysis suggests that fiber supplementation in TPN patients can aid in reestablishing a healthy gut during and post-treatment and adds to our understanding of dysbiosis in human patients.

This week, we finally got to hear what everyone in the program has been up to for the last month and I’m impressed. There is such a diverse array of subjects, questions, and techniques we as a program have become involved with and I can tell how excited many of my peers are about their work.

I want to talk a bit about Natalia’s work with neuropathy at the Ji lab. I found her presentation to be informative, clear, and exciting. Natalia also happens to be working just 2 floors above me in MSRBIII, and it’s great to now understand what she’s doing after we happen to get on the same elevator heading to work. It’s also cool that one building can host so many diverse research projects: from studying mouse pain receptors to human gut bacteria and everything in between.

What especially intrigued me in Natalia’s chalk talk was the idea of sexual dimorphism. To recognize that a common and accepted method of chronic pain treatment in male mice just *doesn’t work* for female mice is fascinating to me. I also wonder- in the specific lens of neuropathy- is one sex more susceptible? And do other treatments work only on females because of divergent receptors/neurons? I know that anatomy and physiology of different sexes are divergent but I would have thought something like pain and response to pain/pain treatment would be consistent for all mice as opposed to obviously sexually dimorphic systems like the reproductive or endocrine systems. Many studies only use one sex in mice. Understanding Animal Research says 80% of drug studies only use male mice and other types of studies show the same trend (https://www.understandinganimalresearch.org.uk/news/why-we-need-female-mice-in-drug-

trials#:~:text=About%2080%25%20of%20rodent%20drug,diffe

rently%20in%20men%20and%20women). How much does this leave out of the picture? Fields dealing with sex chromosome inheritance or mating behavior shouldn’t be the only ones considering gender in their studies of mice, flies, and even human subjects (in fact, especially human subjects as they are often the final destination for our findings). This would help understand disease and biology on a deeper level, as we know many conditions (not just genetic ones) present differently in men and women.

I also appreciated this talk because it very clearly suggested the implications for the work at hand on a broad scale; Natalia detailed the significance of her (and the lab’s) work through the narrative of the opioid epidemic and finding better treatments for chronic pain. This really helped me answer the question “why care?” which is a key component in science communication. Natalia, like the rest of B-SURF, did a great job relaying her science despite only having recently discovered her specific project.

A day in the life of a microbiome scientist:

My day at the David lab consists of a lot of sample processing. Human fecal samples don’t just automatically go through a machine and become pretty strings of As, Ts, Cs, and Gs or numbers explaining their exact molecular makeup. Instead, I spend a few hours before lunch cycling through a series of steps including: adding various buffers to the samples, spinning them down, filtering them, incubating them, and transferring between many small tubes that had to be labeled earlier, and then spinning and transferring some more. In previous weeks, I was preparing samples for a machine called the HPAE which measures carbohydrate content, but this week, with my mentor out with our familiar foe Covid, I have been helping another lab mate do DNA extraction for his research. It can be a bit tedious, but after having practiced the process a few times this week I’ve become exceedingly more efficient and independent during the process, and can now perform a whole extraction myself. It’s also been an opportunity to talk to my lab members as we load and run samples almost out of muscle memory.

We then break for lunch, my favorite part of the day. Yes, I love food (especially the free food provided for lab meetings and other lab events!), but I also love getting to know my lab members. Most of us eat lunch together every day around the same time- something I’ve really come to appreciate as I get to know each of them better. They’re all exceptionally welcoming and helpful, as well as just really nice people to have random conversations with over Panda Express. After lunch, I finish up the rest of the processing and store the samples in the fridge to use later.

In the off time between sample spinning or when it’s too late to start a new batch of DNA extractions toward the end of the day, I hunker down at my desk and begin learning R. Because: what happens after all of these meticulously prepared samples go through their respective machine runs? That’s where data analysis comes in. While I have little experience with the software, many PhD students in the David lab are adept at using R to visualize and analyze data.

I follow online tutorials, resources provided by my lab mates, and use practice data files to play around with the software and figure out how to plot biological data. I’ve attached my earliest and proudest creations from such a session, but I’ve learned a lot since and hope to continue learning both wet lab and computational techniques moving forward.

My graduate mentor, Jun Zeng, is a 3rd year MGM student at the David Lab. Jun grew up in China, where he recounts loving “taking things apart” and learning how things worked. This love for discovery and exploration has carried him to where he is now, researching the microbiomes of cancer patients at Duke. This path was not always the specific plan- no one in his family had expressed a shared interest in research- but rather a product of continuously following his curiosity.

Much of that curiosity was sparked in high school, after reading the book A Short History of Everything by Bill Bryson. Bryson’s book about life and science ranging from chemistry to astronomy highlighted the wonder of science and was a strong factor in Jun pursing the field. In high school he studied slime molds: did you know that they communicate with chemical signaling? They can move?  Jun smiles talking about this work, reveling in how unique and complex the organisms were.

When he got to college at the University of Washington in Seattle, he knew he wanted to do research and overloaded his classes the first two years to get ahead on his majors Biology and Microbiology and clear up room for lab work during the rest of his time. Does he recommend this stressful, arguably fanatical decision? No. But did it let him spend the latter half of his college experience primarily in the lab, gaining an abundance of microbiology training? Yes. His lab studied bacterial competition and he was even part of finding a bacterial toxin secretion system that could be used for mitochondrial DNA editing. When asked why he reached out to this lab in particular, Jun’s child-like wonder reemerges: “It’s awesome, I mean it’s bacteria fighting each other. I thought it was cool.”

Jun started the MGM graduate program in 2019 and found his fit at the David lab. While he’s had his fair share of lab-related mishaps- such as lighting a bench with ethanol on fire- he finds joy in wet-lab experiences. He likes the process of doing experiments and prefers bench work to the more academic path of a professor. To that end, he wants to stay in the lab moving forward after graduate school whether that be in an academic lab setting as a researcher or in industry. Having received help from online groups of graduate students when he was applying for grad school, Jun also helps mentor international students from China who are applying for graduate programs in the US. He’s been an exceptionally knowledgeable, friendly, and helpful mentor for me these past few weeks and I’m excited to learn more about his experience with research!

The scene opens up to a birds-eye view of the African savannah. From afar, all seems calm: the tall grass sways in the wind as sunlight bathes the sparse trees and bushes in gold. But as you zoom in closer there’s something else: a cluster of dark shapes in motion on the horizon. Sounds of a feeding frenzy hit you before you can distinguish one animal from another in the mass: the yapping of hyenas and screeching of vultures as they descend on an fresh antelope carcass. A pride of lions pads away, licking their jowls and letting the scavengers finish the rest.

This is our classic idea of an ecosystem. It is also one of the more easily understood models of the human gut microbiome – something Dr. Lawrence David allude to during his talk this week. A complex and dynamic community of different species all fighting to survive on scraps, grow, and reproduce. Bacteria don’t quite get the David-Attenborough-narrated nature-channel-treatment, but the dynamics of this microecosystem is incredibly important to human health. Just like real ecosystems provide services like air and water filtration, the gut microbiome provides services like immune defense, fiber degradation, and provisioning of important biomolecules. In return, we provide a home in our gut and nutrients from our food for the microorganisms. Aside: this 2018 paper from the Yoder lab has an interesting take on viewing the microbiome as an ecosystem with classic ecosystem services- http://yoderlab.org/cms/wp-content/uploads/2018/03/McKenney-et-alMolEcol.2018.pdf

Lawrence’s presentation primarily focused on the food actually getting to the microbiome. But what if people aren’t eating, at least not the traditional way? In our savannah, what if the grass has dried up, depleting antelopes of their food source? Or the lions decided to go vegetarian to reduce their carbon footprints, leaving minimal antelope carcasses to feed on? We would expect the communities involved to change drastically because of a lack of food availability. Do the hyenas die out and leave space for wild dogs to proliferate?

This is the question (well… analogous to the question) that my mentor, graduate student Jun Zeng, has set out to answer. In our project, the patients in question are hematopoietic stem cell transplant (HSCT) patients. In other words, patients who have received bone marrow transplants to treat various cancers. This usually involves chemotherapy to kill off cancerous cells. Oftentimes, nausea and inflammation leave patients undergoing this process unable to eat food enterally (through the intestine) without extreme discomfort. Doctors will resort to total parenteral nutrition (TPN). Under TPN, nutrients are delivered directly into the bloodstream.

Jun has set out to answer the question: how does TPN alter the composition and function of the microbiome in HSCT patients? He’s already analyzed the compositional part of this project, utilizing 16S sequence sequencing from stool samples to determine that TPN radically alters the diversity and makeup of bacteria in the gut. I will be working on a subset of this larger project, mainly focusing on the “function” aspect. More specifically I am looking at bacteria’s ability to break down insoluble fibers in the gut and product short chain fatty acids (SCFA) in the process. SCFAs are beneficial to gut health and indicators of functioning microbiomes.

My two main questions are: do TPN patients have less dietary fiber available to their gut microbiomes? And, subsequently, do the microbiomes of patients on TPN have reduced capacity to break down dietary fiber? This first question will be helpful in confirming our assumption that less food and actual dietary fiber is able to get to the gut microbiota during TPN. If that checks out, we can then perform an experiment in which a fiber is added to the samples and then left to be degraded by the bacteria present. After some time, comparing the amount of fiber left between normal diet and TPN patient samples should help us understand if TPN promotes species less able to break down fiber. This has implications for the treatment of stem cell transplant patients and any other patient under consideration for TPN. We’ll be able to  better understand the risks associated with TPN or, potentially, inform efforts to return microbiome function with probiotics or prebiotics following treatment.

My expectation for the summer is to grow a lot. Not only will there be the growth of some friendly (and some not-so-friendly) bacteria at the David Lab, but also the more metaphysical growth of someone starting an entirely new experience.

There are moments this week when I felt that I’d bit off more than I could chew. To be a Duke student- to be part of B-SURF- often relies on exuding a confidence and competence. But thrown into a lab of complicated machines, graduate students rushing about, and a growing list of new techniques to learn, I was reminded of how unfamiliar the world of research was. I’ve had to stomach the idea of being comfortable being uncomfortable. I’ve constantly trying to convince myself: these skilled lab members were undergraduates once and they didn’t know what they were doing any more than me.

The first few days in lab I mostly worked on training modules, a comfortable start to the position. After ensuring I knew not to eat, ignite, or spill our precious samples, I was finally promoted to the classic imagine of a scientist. Adorned in gloves and equipped with my pipette, I spent the day transferring clear liquids between itty-bitty tubes. I swallowed my nerves about messing up and began to enjoy processing samples with a visiting grad student (studying mouse lemurs!) She talked about her path to research and her upcoming trip to Madagascar with other graduate students at the Lemur Center. As we talked and worked she gave me pipetting advice and my own lab mentor explained his process loading the centrifuge and keeping lab notes. We stayed late and loaded one of the now-not-so-complicated machine with the samples. By the end of the day, I was pooped. Though I still feel uncomfortable not understanding all parts of our research process, it was a day of growth for me as I realized my mentors were not expecting me to carry the project and instead allowed me to practice at my level while still aiding in the project.

I feel it in my gut that the people I’m surrounded by (and of course a healthy amount of microbiome-related puns) will guide me to grow into a more competent and more importantly, confident, scientist and person.