Category Archives: Past BSURF

Until August…

Posted on July 29, 2023 by | Leave a comment

If I tried to summarize everything I’ve learned this summer, about complex scientific techniques, about careers in research, and about myself, I think this blog post would be a novel. 

My mentor, Dr. Trisha Vaidyanathan, was the key component in making my summer experience as incredible as it was. She went beyond teaching me what I needed to know for our summer project–encouraging me to attend lab meetings, lab social events, and planning for me to shadow others in the lab to learn about their respective projects and paths.

Being able to shadow others made my summer experience all the more unique and beneficial. I was able to expand my experience further by working with techniques and model organisms different from those used in my project–ranging from in-vivo 2-photon imaging of astrocytic calcium activity in mice to breeding transgenic zebrafish. I even had the opportunity to attend a thesis dissertation by a member of the Eroglu lab!

As for my path in research, this summer has been incredibly useful in learning which aspects of science I enjoy most. Specifically, after experiencing both behavioral and molecular work, I find myself more drawn to questions at the molecular and cellular level. I intend to continue working in the Bilbo lab this coming semester, and hope to be able to further explore the molecular and cellular techniques being performed in the lab.

Outside the lab, through our BSURF programming, I learned not only about the breadth of research being done at Duke, but also about the various paths through academia, and the day-to-day lives of those who’ve chosen to pursue research. 

I’m incredibly thankful to the Bilbo Lab for welcoming me and making sure I felt comfortable in a new and intimidating environment.

I don’t think this blog post would feel complete without also talking about my BSURF friends. I couldn’t have asked for a better group of friends to spend the summer with– from our nightly group dinners, movie nights, and spontaneous Durham excursions, I always knew I had something to look forward to coming home from lab.

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Posted in BSURF 2023, Week 8

Reflecting on a talk by Dr. Chantell Evans

Posted on July 24, 2023 by | 1 comment

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.

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Posted in BSURF 2023, Week 7

Categorical Perception with Dr. Steve Nowicki

Posted on July 23, 2023 by | Leave a comment

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!

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Posted in BSURF 2023, Week 7

PRENATAL ENVIRONMENTAL TOXIN EXPOSURE AS A RISK FACTOR FOR NEURODEVELOPMENTAL DISORDER PATHOLOGY IN ADOLESCENCE

Posted on July 16, 2023 by | 1 comment

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.

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Posted in BSURF 2023, Week 6

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

Posted on July 16, 2023 by | Leave a comment

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.

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Posted in BSURF 2023, Week 6

Optimizing Cyanobacteria Detection for Comparing Lichenized and Environmental Cyanobacterial Communities

Posted on July 14, 2023 by | 1 comment

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.

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Posted in BSURF 2023, Week 6

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Lisa’s Chalk Talk

Posted on July 12, 2023 by | 1 comment

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.

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Posted in BSURF 2023, Uncategorized, Week 5

David’s Chalk Talk About Chlamy

Posted on July 9, 2023 by | Leave a comment

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! 

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Posted in BSURF 2023, Week 5

My Day in the Baugh Lab

Posted on July 2, 2023 by | Leave a comment

My schedule varies a lot depending on the day of the week: Mondays and Fridays are usually the busiest, and I hardly ever have benchwork on Wednesdays. This is because C. elegans take about three days to develop to maturity, and I usually have to wait a few days between steps. Because of this, I have a lot of experiments going on at once. In order to avoid coming in on weekends, I have to vary my weekday work accordingly.

An experiment begins when I bleach the worms, a process that allows me to dissolve the C. elegans bodies and isolate the embryos. My project studies gonad abnormalities resulting from early-life starvation, so I then leave the embryos in a starvation culture for eight days, where their development is arrested. After that, I plate the worms, now in the first stage of larval development, onto E. coli (their food), and leave them to develop for three days. Their food may include RNAi, which blocks the expression of specified genes, depending on which experiment I’m doing. Once these worms have reached maturity, I prepare a slide and look at them under a microscope, scoring how many have abnormalities, and how many appear normal. Around 30-50% of wild-type worms typically have gonad abnormalities. 

Typically, the first thing I do when I get to the lab is make a to-do list and check in with my mentor, Ivan. As the weeks have passed, I’ve become more independent, but sometimes Ivan has a new technique to teach me—and of course, things are always going wrong and I need his help to course-correct!

I usually spend the morning passaging worms, which consists of moving seven worms of a specific stage to a new plate with fresh food growing on it. This allows me to keep all nine of my strains alive and relatively in sync. In the morning I also prepare bleach plates, which I will bleach three days later. 

After lunch, I’ll usually bleach whichever strains are ready that day. This usually takes me some time, as it involves several washes and cycles in the centrifuge. At the end, I calculate the density of embryos in my resulting solution, add the desired amount into test tubes, and place them in a rotating drum.

In the afternoon, I also prepare RNAi plates and plate worms from starvation cultures, allowing them to grow to maturity.

Typically, the last thing I do is score the worms. I’ve only started scoring recently, so I’m still getting used to it, but it’s satisfying to complete the final step in each two-week experiment and finally get results. 

If I finish my benchwork before 5, I’ll typically catch up on reading, work on my experiment plan, or prepare plates for later use. After that, I head home to rest and prepare for the next day!

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Posted in BSURF 2023, Week 4

A Day in the Bilbo lab

Posted on July 2, 2023 by | 1 comment

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.

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Posted in BSURF 2023, Week 4

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

Posted on July 1, 2023 by | 1 comment

 

https://scholars.duke.edu/file/i1831252/image_1831252.jpg

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.). https://scholars.duke.edu/file/i1831252/image_1831252.jpg.

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Posted in BSURF 2023, Week 3

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A Day in the Lab: Juggling Experiments and Unravelling Mysteries

Posted on July 1, 2023 by | 1 comment

I start my day around 10-10:30am when I arrive at the lab. After settling in, my first task is to review my notes from the previous day. This helps me stay organized and recall the progress and outcomes of my ongoing experiments. Based on this information, I create a to-do list for the day, outlining the tasks I need to accomplish.

Next, I seek out my mentor, Samuel. Meeting with Samuel allows me to gain valuable insights, receive feedback on my work, and clarify any doubts or questions I may have.

Now to the real action in the lab – juggling multiple experiments with different timelines.

One of the experiments I’m currently working on involves mating and crossing strains of cells. In another area of the lab, I conduct transformation experiments. I manipulate the genetic makeup of cells by introducing foreign DNA, such as plasmids. I also perform spot assays. By spotting cells onto different plates, I observe growth patterns or changes in color. This assay enables us to identify potential phenotypes, assess antibiotic resistance, and delve deeper into various biological processes. A significant portion of my work also revolves around imaging. I prepare slides and chambers and do time course and time lapse imaging. These images provide valuable clues revealing complex systems at play.

Around 1:00 pm, I take a lunch break. Typically bringing my own lunch to the lab, I quickly heat it in the microwave and enjoy the break, often while conversing with other people in the lab. Rejuvenated and refocused after lunch, I dive back into the lab, determined to complete my tasks.

At the end of the lab day, I record any final notes. I say goodbye to everyone and leave the lab, knowing that I have made progress!

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Posted in Week 4

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An interview with Dr. Vaidyanathan

Posted on June 28, 2023 by | 1 comment

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. 

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Posted in BSURF 2023, Uncategorized, Week 3

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An Interview with Dr. Baugh

Posted on June 25, 2023 by | Leave a comment

Dr. Ryan Baugh can’t remember a time when he wasn’t interested in science. When he was young, he was “always doing stuff that seemed like a young scientist, like burning stuff and trying to make bombs, fireworks, and a hot air balloon.” When he got to college at the University of Georgia, he was interested in chemistry and physics. Still, he tried to take classes in other areas, as he thought that majoring in science was “too obvious” of a choice. Upon taking a course in genetics and learning about the central dogma, he became excited by networks of transcription factors. He decided to major in genetics partially because his university had a strong genetics department, but also because he found the subject to be a good balance of interesting, important, and pragmatic, with many future opportunities. He enjoyed hands-on work more than studying and appreciated the opportunities for creativity within research. 

Upon finishing his undergraduate education, Dr. Baugh stayed at the University of Georgia for a year, working in a genetics lab. He recommends that students considering graduate school take some time before applying, and thought that it was a great decision for him. He took the opportunity to really think about what he wanted to do and learned a lot about molecular biology, which allowed him to hit the ground running once he got to graduate school. 

After leaving the University of Georgia, Dr. Baugh completed his PhD at Harvard, studying developmental genomics in the embryos of C. elegans. During this time, he generated the “first genome-wide time series of gene expression during embryogenesis in any animal,” finding that there were thousands of differentially expressed genes. He completed his postdoc at Caltech and then came to Duke, where he continues to study C. elegans.

Dr. Baugh is most proud of having defined and stuck with an area of research: L1 arrest and nutritional control of development. He believes that the most difficult part of doing research is dealing with the inevitable frustration and setbacks that come from getting excited and disappointed by experiments. 

Dr. Baugh’s passion for his subject became abundantly clear during our conversation, which often veered toward topics and news in genetics that I found incredibly interesting, but unfortunately could not fit into this blog post. I am very grateful for the opportunity to work with him this summer, and I can’t wait to see what the next few weeks will bring!

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Posted in BSURF 2023, Week 3

An ELPnation [Explanation] of My Project

Posted on June 18, 2023 by | Leave a comment

My research project for this summer will be to analyze various elastin-like polypeptides (ELPs). ELPs are polypeptides that incorporate the 5 amino acid long sequence of Val-Pro-Gly-Xaa-Gly, where Xaa represents an unspecific amino acid. ELPs are a kind of artificial intrinsically disordered protein (IDP), which are proteins that do not fold in the typical way but rather maintain an unfolded (disordered) form that permits multivalent behavior. ELPs also change phase with lower critical solution temperature behavior, which means that they will be soluble below a critical temperature and phase separate at/above it.

So far, I have worked on cloning recombinant plasmids that contain part of the desired ELP sequence with E. coli. Each ELP sequence has an “A cut” and a “B cut” plasmid which will be ligated together in order to get the desired sequence. This is done because ELP sequences are quite repetitive and this makes it difficult for manufacturers to directly make it. E. coli is also used in order to generate the protein from the plasmid. Flasks of E. coli are given the plasmid and reproduce until they almost reach carrying capacity, at which point they are given a treatment to induce protein synthesis. This is done in order to maximize yield as a flask well below carrying capacity would not be able to produce as much protein and one at carrying capacity would not be as metabolically active. 

 

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Posted in BSURF 2023, Uncategorized, Week 2

Sleep disruption due to prenatal environmental toxin exposure and neurodevelopment disorder pathology

Posted on June 18, 2023 by | 1 comment

The prevalence of neurodevelopmental disorders (NDDs), such as Autism Spectrum Disorder (ASD) and Attention Deficit Hyperactivity Disorder (ADHD), has increased rapidly over the past two decades. As such, much research has gone into the root causes and mechanisms of these disorders. Previous studies on the genetic roots of NDDs have identified several alleles associated with NDD pathology, however, prenatal environmental stressors and toxins are thought to contribute greatly to this recent increase.

Sleep plays a critical role in synapse remodeling, especially during adolescence. Astrocytes, a type of glial cell essential to regulating neuronal activity, have recently been shown to modulate the sleep-wake cycle. Specifically, astrocytes seem to regulate both depth and duration of NREM sleep. Previous work has shown that sleep appears to be particularly sensitive to environmental stressors and toxins. 

In the case of neurodevelopmental disorders, such as autism spectrum disorder, sleep disturbances are observed in nearly 86% of patients. Thus, the project I will be working on this summer aims to investigate the mechanisms by which prenatal exposure to environmental toxins impacts the development of neurodevelopmental disorder pathology. 

In my mentor’s previous work, she identified that a prenatal combined diesel exhaust particle and maternal stress (DEP/MS) paradigm results in neurodevelopmental disorder pathology in offspring. 

Using this mouse model, we plan to address two main questions. Firstly, how does prenatal exposure to maternal stress and environmental toxins impact sleep patterns in offspring? Secondly, do we observe changes in gene expression patterns and astrocyte physiology in the brains of these mice?

We’ve begun by using electroencephalography (EEG) and electromyography (EMG) to analyze sleep patterns in DEP/MS mice offspring. By doing this, we hope to determine how time spent in NREM and REM sleep differs between control and DEP/MS mice. We then plan to isolate RNA from frontal and parietal cortical astrocytes in order to analyze gene expression patterns through quantitative real-time PCR. Additionally, building on the sex differences in NDD pathology observed in my mentor’s previous work, we plan to use the forced-swim test to measure depressive behavior in DEP/MS mice.

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Posted in BSURF 2023, Uncategorized, Week 2

Marco Polo: How Do Lichen-Forming Fungi Find Their Cyanobacterial Partners?

Posted on June 18, 2023 by | 1 comment

This summer, I will compare lichenized cyanobacteria communities to environmental cyanobacteria communities (cyanobacteria living outside the lichens) to inform how lichen-forming fungi associate with their cyanobacterial partners. For context, lichens are organisms made of symbiotic associations between algae/cyanobacteria and fungi. Fungi in lichen can reproduce sexually via fungal spores, which are essentially sterile, free of cyanobacteria, and it is largely unknown how the fungi find and associate with their symbiotic partners. In nature, fungal species have been observed associating with different cyanobacterial species, sometimes “switching” between cyanobacterial partners. The mechanism behind symbiosis formation is unclear; it is unknown where and how often the fungi find their cyanobacterial partners, and we want to know if the same cyanobacteria are found in the surrounding environment. 

My project focuses on lichens made of Peltigera, a genus of lichen-forming fungi, and Nostoc, a genus of blue-green algae or cyanobacteria. Using lichen and environmental samples, we want to ask: are lichenized cyanobacteria similar to, or different from, the environmental cyanobacteria found outside the lichens? The Lutzoni Lab collected lichen and environmental samples across Alberta, Canada, to help answer this question. The lab collected roughly 2500 lichen samples and 1800 environmental samples across 15 sites spread over five natural regions of Alberta (3 sites per natural region). The environmental samples consist of substrate sampled next to and between lichens and are split into 900 “top” and 900 “bottom” samples. The top samples were collected closer to the earth’s surface, and the bottom samples were collected deeper underground. 

This summer, I aim to answer two primary questions to determine the best method for extracting and sequencing the Nostoc DNA from lichen and environmental samples!

First, we want to know if the 16S rRNA or rbcLX gene is a more accurate marker for detecting Nostoc in the samples. The rbcLX gene is more specific to cyanobacteria and has more variation than the 16S rRNA gene, so it could more accurately classify between species of Nostoc. However, Nostoc contain one copy of the rbcLX gene compared to multiple copies of the 16S rRNA gene. The environmental samples may have low abundances of Nostoc, so sequencing the 16S rRNA gene may be more suitable for detecting the low cyanobacteria levels. To answer this question, we are testing the 16S rRNA and rbcLX approaches on 12 environmental samples which have already undergone metagenomic and metatranscriptomic analyses. By comparing the resulting 16S rRNA and rbcLX sequences to pre-existing data, we will select the marker with which we will sequence the remaining environmental samples. We hypothesize that 16S rRNA will more accurately detect the Nostoc because we are trying to detect microbes presumably in trace amounts, and because the 16S rRNA gene is the standard marker in microbiology. 

Next, we want to determine how the cyanobacterial communities in the top environmental samples compare to those of the bottom. As mentioned above, the 900 top and 900 bottom samples are from the same areas but different depths into the substrate. We want to see if the bottom cyanobacterial communities are a subset of those of the top samples, and if so, only extract DNA from the top samples to save time and money. We hypothesize that the bottom samples will be a subset of the top, and more Nostoc will be detected in the top samples because Nostoc require sunlight to photosynthesize ☀️

Lots and lots of lichen samples! 6/14/23

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Posted in BSURF 2023, Uncategorized, Week 2

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Project MutaLib

Posted on June 20, 2022 by | Leave a comment

Four different bases can be stringed together in a mind-boggling amount of variations. They form one of twenty amino acids that themselves can be combined to form various proteins. My project indirectly supports my lab, Neurotoolbox, in its endeavor to improve fluorescent proteins that are utilized for spatial and temporal resolution of neurons in the brain. There are two notable types of proteins that the lab uses. One protein can be used to activate a neuron by shining a light with a specific wavelength. The other protein can fluoresce upon activation by its respective neuron. Both of these proteins have numerous capabilities in the field of neuroscience and in identifying nerve tracts.

My project within this lab is to facilitate the pursuit of improving the biological capabilities and optimizing the performance of these proteins. My principal investigator, Yiyang Gong, provided me with a MATLAB dataset housing all the reads of a mutation-induced sequence of one of the aforementioned fluorescent proteins. There are over 350,000 different mutated sequences each with their respective coverage (number of reads/voters) and quality scores. The original sequence is known, but the issue is the successful discernment of true and fake mutations. Over 55% of the dataset has incredibly low coverage (1 or 2 reads), 15% has moderate coverage (3 reads), and the other 30% has high coverage (4 to 20 reads).

When there are few voters and an inconclusive quality score, what is the true mutation? What about if both reads have a perfect quality score yet they disagree? These are the questions I have to answer, notably when the coverage is only moderate to low (3 or less) which makes up 70% of the dataset. Through Python data analysis, probabilistic modeling, and machine learning applications, I need to clean the dataset and create a library that associates a barcode (tagged to the end of different mutated sequences) with its respective SNPs. The mutations would later be processed to determine which sets of mutations would improve the performance of the fluorescent protein (my next project after completion of this one).

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