Author Archives: Megan Jiao

Week 8: Final Reflections and Future Plans

I’ve had an amazing experience this summer in the B-SURF program. Before starting my research, I knew it would be an eye-opening experience one way or another, but I am ultimately still surprised by how much knowledge I’ve gained this summer, whether it’s in the form of lab techniques, C. elegans and genetics terminology, or simply communicating my work to both my peers and members of my lab. I’ve also discovered new things about myself that I wouldn’t have expected otherwise: for one, I enjoy working with worms more than I thought I would, and I also enjoy working with my hands. I was never really one for hands-on application of concepts from the classroom in high school, but I found myself enjoying it immensely in the lab as I did tasks like helping my mentor begin the process of setting up crosses and thinking of what sorts of genotypes the offspring would have based on Mendelian genetics.

Seeing myself improve so rapidly over the course of several weeks in regards to bench work, reading papers, communicating with my mentors, etc. was immensely gratifying. Although I entered this summer worried about how quickly I would (or would not) gain independence from my mentor, I became increasingly able to carry my own weight in the lab. After a few weeks, I felt like I had finally contributed information of worth to the projects I worked on and my lab in general. Consequently, I felt more and more integrated as a proper member of my lab both intellectually and socially as I became more independent, which greatly contributed to my overall enjoyment of my experience over time.

Something that has never failed to surprise me this summer is thinking about how truly little I know about biology and research, even with all of my improvements over time put into consideration. Compared to the other members of my lab, who have been there for years, I still know barely anything about C. elegans. Thus, every week brings with it novel experiences where I encounter new problems or new techniques and concepts that I have to ask many questions about before I can begin processing the new information. There is a steady learning curve for everything, including physical bench work, communicating with other lab members, scientific concepts and techniques, and so on. Although it has been difficult to constantly be subjected to new ideas or problems just as I began to feel comfortable, it also made my experience in the lab much more exciting and made me really start to try and think like a scientist.

As much as I enjoyed research, however, I’m not entirely sure if I’d like to pursue it as a career just yet, though I know that I’ll definitely be immersing myself in research over the course of my undergraduate studies at the very least. Even if I ultimately choose not to continue doing research in the long run, I’ll carry with me a great appreciation for scientists and all of their hard work for the rest of my life after experiencing research first-hand. Ridiculously cheesy as this is, the end is only the beginning, after all.

Thank you to Becky Kaplan and Dr. Ryan Baugh for being wonderful mentors this summer, and thank you to Dr. Ron Grunwald and Jason Long as well for organizing this program. I wish all the other B-SURF fellows good luck for whatever they may be pursuing in the future, research or otherwise, and I hope all of you have a great rest of the summer!

Week 7: Genetic Engineering and Gene Therapy with Dr. Charles Gersbach

For the past 7 weeks, I’ve thoroughly enjoyed all of the faculty seminars, which have given me both breadth and depth of knowledge in the many disciplines within biological science. I came into Duke last year with a focused interest in cell/molecular biology and genetics and apathy towards other biological areas of study such as evolutionary anthropology and ecology, but after spending a year taking biology courses and attending these faculty seminars, I’ve begun to really appreciate the diversity of biology and the worth each individual discipline contributes to science and society as a whole. I’ve also really appreciated being able to hear everybody describe their path to becoming a scientist and all of the hurdles and choices they had to make; some were more straightforward than others, but ultimately, many speakers placed an emphasis on striving to do what you enjoy, regardless of all the trials and tribulations you might encounter.

I could say plenty of good things about every seminar, but I’ll be choosing to focus on Dr. Charles Gersbach’s seminar specifically for this blog post. His talk fascinated me for a variety of reasons: for one, my dad is an engineer, so I grew up thinking that I knew a good amount about how engineers think and the type of work they did. However, he’s a structural engineer, dealing with massive amounts of steel and concrete, which is the polar opposite of Dr. Gersbach’s work with genetic engineering on the molecular level in biological systems. Being able to hear Dr. Gersbach detail a completely different type of engineering, as well as his perspective on what constitutes as engineering as the scientific community becomes increasingly interdisciplinary.

In addition to that, Dr. Gersbach’s work on gene therapy and gene editing immediately intrigued me, since I’ve been avidly interested in the topic since high school after first learning about the concept for a research paper. For a period of time, I had even considered going into his line of work as a career path before orienting myself more towards cell/molecular biology and/or clinical medicine. Regardless, I’m still deeply interested in both the technical aspects of how gene therapy is done and the potential ethical and social implications that genome editing in humans generates, should it become more precise and possibly even marketable in the future. I’m especially excited to see how geneticists will utilize the CRISPR/Cas9 system, which has immense potential, to both improve gene modification as well as discover new things about biological systems and the organisms they reside in.

I was also surprised to find out that the label “GMO” specifically indicates the insertion of genes into cells, so it doesn’t include precise modification of sequences such as changing a base from one type to another. Some of my friends are fervently anti-GMO, but I’m sure they’d be surprised to learn that plenty of foods we eat are actually genetically modified, although in a different way from the ones actually labelled as GMO.

I’m a bit sad that next week will be the end to all of these faculty seminars, but I’m still looking forward to them nonetheless. Thanks to all of the faculty who have taken time out of their day to share with us their individual paths to science and their research!


Week 6: A Perpetual Learning Process

So far this summer, I’m finding that as soon as I start feeling comfortable with my daily routine, my mentor introduces something new or I encounter new problems. Since the very beginning, the learning process has never halted, forcing me to think about how little I know about research and biology in general, even though I’ve been working in a lab for 6 weeks now and have taken 3 full years of biology courses in my life. Each week brings with it something novel, whether it’s new techniques, new ideas, or even new frustrations.

That being said, the project that I started the summer off with was very straightforward and structured, so I finished all the replications with relatively few problems a few weeks ago. Since then, I’ve moved on to working together with my mentor on her project, which she’s referred to as a “fishing expedition”: basically, we’re casting our lines out over the open sea (aka the c. elegans genome) and seeing what we get. It’s a much more open-ended experiment, and it’s come with a fair share of complications on both our parts.

For example, we’re working with mutagenized worm strains which all contain various mutations that produce the phenotype we’re looking for. However, with those mutations come several background mutations as well – mutations that result from mutagenesis but don’t contribute to the desired phenotype. These background mutations are largely neutral, but some produce detrimental effects which makes it much more difficult to proceed with certain aspects of the experiment. To combat this, we’re doing something called back crosses in an attempt to get rid of most unwanted background mutations; however, these very mutations can also prevent us from doing back crosses effectively, so it’s possible that we might be stuck with some strains with such severe mutations that they’ll never breed properly – bit of a Catch-22 there, unfortunately.

Regardless, I enjoy viewing these complications as a challenge, and although my mentor is the one thinking up all of the major solutions, I find that more and more, I’m able to find my own ways to work around smaller challenges I come up across while doing my own part in the project. Even if something can’t be solved, I still find it intriguing just to think about all the potential reasons why a problem might have arose to begin with and the sheer complexity of biological systems, even in an organism as “simple” as c. elegans.

Even with only about ten more days in the lab remaining for the summer, I’m sure I’ll still learn plenty. I’m looking forward to finishing off my B-SURF experience with a fresh perspective on biology and research as well as many great memories of all the program has had to offer these past two months!


Week 5: Chalk Talk Reflection

After listening to everyone’s chalk talks this week, I was amazed by how our project topics were so diverse, yet like Dr. Grunwald mentioned, there was a definite thread of commonality that linked all of our respective fields together. It was also fascinating to see how everybody has progressed so far in the span of 5 weeks; I still remember people voicing their worries and concerns about doing research the very first week, but clearly we’ve all improved since then to the point where we can knowledgeably present chalk talks and answer questions about our projects.

With that said, I enjoyed listening to everybody’s presentations, but one of them stood out to me in particular: I was particularly interested in Susan’s research on heart regeneration in zebrafish and the atrial/ventrial specification of genes for multiple reasons. For one, I’m potentially considering specializing in cardiology when/if I go to med school in the future. With heart disease as the leading cause of death in Americans, research into the heart and potential regeneration of heart tissue can play a vital role in improving cardiological health care in the future and possibly impact all of us, whether directly or indirectly. I also think that the genotype-to-phenotype aspect of her research is fascinating, especially since I am also doing genotype-to-phenotype research. While genes have a definite impact on phenotype, it’s intriguing to consider the broader picture of how something more abstract like environmental influences can play an important role in molecular processes such as transcription and translation as well, especially when these influences can have multigenerational effects. This is already a daunting task when considering all of this just in the context of the heart and cardiovascular system, but it’s humbling to imagine all of these possibilities applied to other relevant fields as well.

These chalk talks have made me realize both how far we’ve come as research fellows and how little we truly know about biology as a whole. While it’s important that we all specialize and become thoroughly knowledgeable in particular fields since there’s not much use in having only general knowledge, it’s fascinating to think about how we’ll all eventually grow to know so much information about so few topics (attached a relevant picture below from PhD Comics).

Week 4: A Day in the Life of a Worm Caretaker/Murderer

(I’ve probably told the “I kill worms for my job!” joke far too many times, and I’m just beating a dead horse now. Won’t do it again, sorry!)

Depending on what day of the week it is, I might be doing 8 entire hours of bench work, or I might be doing almost none at all. For my personal project, different steps of the procedure require different timings, and I also help out my mentor with her project, and she has her own planned out procedure to follow. Thus, my workload can vary a good amount from day to day.

For my project only, I have five possible activities I can do (but only the middle three are actually part of the experiment):

  • Strain maintenance, which occurs every Monday and Friday (or Tuesday/Thursday if Monday/Friday isn’t available)
  • Chunking, which I do every Monday, Tuesday, and Friday
  • Bleaching, which is usually done 3 days after chunking, so it occurs every Thursday, Friday, and the following Monday
  • M cell scoring, which is done at least a week after bleaching, so I do it on the same days of the week as bleaching
  • Spotting plates, which happens as necessary, but usually occurs once a week at least

Because of this procedure, I usually lack any bench work on Wednesdays, so I end up doing miscellaneous activities on that day, such as reading scientific literature, making sure my lab notebook is caught up, or helping my mentor with her project. Mondays and Fridays end up being my busiest days, so I’ll be describing a typical day for me on those two days of the week.

The first thing I do in the morning at 10 AM is worm maintenance. I grab my box of worm strains from the fridge kept at 20 degrees Celsius and choose one small plate from each strain to pick worms from. I then transfer 3-4 worms from each of these plates onto a new small plate using a worm picker, which is just a glass pipette with the end fused to a thin platinum wire that I coat with E. coil so the worms can stick to it.

Afterwards, I chunk worms from small plates that with plenty of larvae that are starving or near starving onto large plates, one per strain. Chunking involves cutting out a piece of the agar on a plate and transferring it onto another plate. It’s the same idea as maintenance, but it transfers many more worms at a time, and it’s used primarily for bleach preparation.

Bleaching takes me the longest out of all of the steps of the procedure. I won’t go into too much detail about it, but it involves transferring the worms on plates to conicle tubes, pouring bleach into the tubes, and lots of vortexing and centrifuging. Basically, bleaching can be thought of as a rather brutal process that forces eggs out of gravid (pregnant) worms and dissolves their bodies, along with other contaminants that may have been on the plates. It results in sterile, synchronized eggs, which means that the eggs are all the same age and the larvae that hatch from them will go through the same development stages at about the same time.

M cell scoring involves placing worms that were bleached a week prior onto slides, one per strain, and viewing them under a microscope to determine how many worms are on the slides and how many M cells they have, which determines if worms are under developmental arrest or not.

Lastly, I spot plates, which is simple: dripping E. coli in LB broth onto plates and allowing them to cool for a day before use. I usually do this after everything else, but occasionally I spot plates in between other activities.

Sometime in the middle of all of these things, I take a short 15-20 minute lunch break around noon. After I’m done with my own work, I often help my mentor with her project as well, which involves activities like categorizing worm strains to determine what can be bleached, bleaching with a few altered steps, adding food or drugs to bleached tubes of worms, spotting worms onto plates, etc. What I help her with varies widely depending on her own availability and the stage of the experiment we’re on, so I don’t have a structured schedule for working on her project as I do with my own.

After all this, I usually leave the lab anywhere between 4:30 and 5:30 PM, although I’ve stayed later in the past. Outside of the lab, I’m working on getting through all the scientific literature my mentor has sent me as well as making a spreadsheet of my data.

Week 3: Starvation and Developmental Arrest in c. elegans

Generally speaking, the Baugh lab is a c. elegans lab that observes developmental arrest (L1 arrest) in roundworms with various mutations under starvation to elucidate signaling pathways and gene regulatory mechanisms that control this arrest. These pathways and mechanisms mirror those of humans, and this research can be used to study the maintenance of homeostasis during development (adaptiveness), aging, and even cancer cell division and growth.

To describe my personal project, I first need to provide a bit of background information. When wild type (WT) c. elegans is starved, they enter a state of developmental arrest as larvae called L1 arrest. They remain in this state of arrest without growth for an extended period of time until conditions become more favorable, allowing them to recover and proceed with normal development. While they are under this developmental arrest, they do not age, so when they resume development, they also have a normal lifespan despite their previously arrested states.

This developmental arrest is controlled by insulin/insulin-like growth factor (IGF) signaling. There are two genes of special interest in this pathway: daf-2 and daf-16. daf-2 acts as a repressor to the transcription of daf-16, which regulates L1 arrest. Thus, with a daf-2 mutant, daf-16 becomes uninhibited, and the worm automatically goes into L1 arrest regardless of nutritional availability or presence of food. These mutants display a constitutive arrest phenotype, meaning that arrest always occurs no matter the circumstances. In contrast, when a daf-16 mutant faces starvation, the mutant shows an arrest defective phenotype and continues to grow and develop but dies quickly afterward due to lack of nutrition.

To determine whether larvae are arrested or not, we observe the appearance of the M cell lineage in L1 larvae. The M cell is marked by a transgene containing a GFP reporter, which causes it to glow green under a fluorescence microscope. During the L1 stage, larvae begin with a single M cell, and as they develop, the M cell divides over time to form up to 16 M cells. If properly arrested, all larvae of a particular strain should only have a single M cell. If even a single division is observed (>1 M cell), this indicates an arrest-defective phenotype in the strain.

M cell divisions in L1 stage

M cell divisions in L1 stage

My personal project involves a collaboration of sorts with a lab at MIT. Researchers at MIT have identified arrest-defective phenotypes in ssu-1 and mrp-1 mutant worms under osmotic pressure (high salt) in comparison to WT worms, which properly arrest under high salt conditions. My job is to starve strains of ssu-1 and mrp-1 mutants and score their M cells to see if they are also arrest-defective under conditions of low nutritional availability. I also starve WT worms and daf-16 mutants alongside these two strains to serve as negative and positive controls, respectively. So far, I have not observed any M cell divides in these new mutant strains, which indicates that they are not arrest-defective when starved. However, I am still in the midst of replicating the experiment to determine  whether my initial results are valid. There are many possible alternative reasons behind these results: low rate of division, slow development, or even just human error on my part among many other possibilities.

Additionally, I have been helping my mentor with one of her projects as well. Ivermectin is an antiparisitic drug that can be used to treat roundworm infections, and for c. elegans, ivermectin exposure paralyzes their pharynx, preventing them from eating food, although they can still sense it (fun fact: multiple people have accused us both of “worm torture”).

My mentor has observed that if worm larvae are exposed to ivermectin and food simultaneously for a period of time and then transferred to normal plates of food that are drug-free, they never develop and die quickly, although they are able to intake food. So far, she’s screened for mutagenized worms that might contain mutations of interest so she can better study the process behind why the larvae refuse to develop further. She’s already isolated various worm strains that have survived ivermectin exposure once, and for the past few weeks I have been helping her to put them through a second test to confirm that these strains have mutations that we’re interested in. Our next plan is to put the worms through complementation testing, which involves crossing worms together to see whether two strains contain the same gene of interest or different genes with the same effect. Eventually, we hope to elucidate the genes that regulate the mysterious halted development of ivermectin-exposed worms.

Week 2: Dr. Ryan Baugh’s Past Ambitions, Current Aspirations, and Advice for the Future

Dr. Ryan Baugh grew up in Georgia and went to the University of Georgia, majoring in genetics. He entered college on the pre-med track, but he discovered that he was more interested in research than medicine. After graduating, he took a year off and worked full time as a lab technician before attending graduate school at Harvard. His gap year allowed him to learn valuable molecular biology skills, mature personally, and define his interests for graduate school so he could hit the ground running as soon as he began his graduate experience. In graduate school, he chose to work in a model organism lab based on respect and interest in the faculty in charge. Dr. Baugh found that c. elegans research satisfied both his need for a field that was compatible with his interests and perspectives as well as biomedically relevant and fundable. He also recognized nutrient availability and starvation were overlooked in developmental biology and saw an area of opportunity in studying these features in c. elegans, leading him to his current research focus today.

Dr. Baugh’s initial and overarching goal was to find a livelihood where he could both make a living and positively contribution to society. As an undergrad, he had a wide variety of interests, but he particularly loved nature, genetics, and studies of what makes us who we are (e.g. nature vs. nurture, heredity, etc.). By studying and researching biology, he hoped to develop a meaningful, almost spiritual appreciation for nature, viewing research as a way to “[meditate] on … nature in depth”. As he progressed through his educational and academic career, his objectives became more practical, such as getting into a good graduate program, finding a good lab, publishing papers, getting a job, getting grants, getting tenure, etc. However, through all the pressures and stresses of reality, he retained certain high-minded aspirations for himself, which he still preserves to this day. Through his research, Dr. Baugh puts in his best effort to simply do the best science that he can, such as perfecting papers, conducting well-executed experiments, and obtaining significant results. In this way, he views his research as a medium of personal expression, comparing it to art. He hopes that by doing research well that he’ll be able to discover results that extend beyond his field and impact humanity.

Dr. Baugh’s primary interests in scientific research are two-part. He likes the creativity involved with brainstorming about how to approach a problem for a new project and devising new strategies or technologies. He feels a tremendous sense of satisfaction when he can understand a complex problem well enough to design an informative experiment. Additionally, it’s exciting for him to make unexpected observations during experiments that force him to challenge his assumptions. On the other hand, he also enjoys having results make sense and come together like puzzle pieces after starting from the beginning knowing very little. He finds it especially rewarding when he is able to witness a project mature and achieve good results at any point in the process after plenty of hard work and frustration. Although there are many “lows” associated with doing research, he believes that living for all of the few and far between “highs” gets him through the many moments of setbacks and tedium.

Compared to research, Dr. Baugh feels more ambivalent towards his teaching experiences. Although teaching takes a significant amount of time and effort and is hard to do well, he believes that it is under-valued within the university with little recognition for good teaching efforts. Thus, teaching can feel like a distraction from research. However, Dr. Baugh still loves talking about science and sharing his knowledge with students as an expert and role model of sorts. He feels great commitment to his students and thrives on seeing students express enthusiasm towards the class’ subject matter and influencing their career interests. He prefers teaching seminars rather than lectures because they are more freeform, with more student engagement and better opportunities to get to know the students and see how they think.

More than anything, Dr. Baugh wishes that scientific research could obtain increased funding. He believes that it’s difficult to have good conscience and effectively train students to be scientists in an environment where many who work hard to get doctorate degrees will end up with a mediocre salary and not able to pursue what they would initially want to do. Additionally, he criticizes the negativity involved in peer review, publishing papers, and obtaining grants, which he believes is caused by primarily a lack of resources. He also believes that increased funding would allow science to be more productive and contribute further to the economy and society and make research on a day to day basis a more positive experience.

Although Dr. Baugh hasn’t had any particularly bad lab disasters other than getting a piece of glass in his eye once and having to use the eye wash station, he considers his many instances where figured out or discovered something that’s already known his most embarrassing moments. In grad school, he recalls wanting a particular reagent and spending two weeks making it himself, only to realize that the reagent was available for sale. He ascribes this as part of the nature of research and a particular saying: “A few months in lab can save a couple hours in the library”, meaning that researchers can become very engaged in the research process and neglect to do basic research on the topic of interest first to see what is already known.

Dr. Baugh has the following pieces of advice for budding scientists: make sure you enjoy and have fun with research, and don’t lose sight of that. It’s important to be playful and pursue curiosity, because that’s where everything starts. There are practical real world concerns, but if you lose sight of it, you won’t have as good of a time, and you’ll also be less likely to contribute significantly. Also, to be successful in science, you need curiosity and creativity to generate ideas and identify problems, but you also need a good dose of perseverance and grit to execute and actualize your ideas.

More practically speaking, for those that choose to pursue research as a lifetime career, Dr. Baugh claims that the job in truth is highly competitive and not a good way to make a lot of money. He also found it surprising how he spent years getting an education and training in lab doing experiments with his own hands, and then once he had the opportunity to start his own lab, he acquired more managerial or administrative responsibilities such as teaching or writing grants or training others. Thus, not to be discouraging, but those who pursue research really need to find it rewarding and satisfying overall and keep in mind that things that make you successful in the training part of your career are very different than what makes you successful afterwards when you’re independent, so adaptability is a necessary trait to have.

Week 1: Learning How to Torture Worms

Whenever somebody asks me what I do for research, I always reply, “I’m killing worms” or “I’m torturing worms” just to see what sort of reaction I incite before I explain the driving purpose behind my lab in further detail. It’s much more complex than that, I say afterwards, and as I explain, I always take great satisfaction in the way people’s facial expressions morph from dubious to understanding.

I’ve experienced a similar transformation after spending a week in the Baugh lab learning new lab techniques, meeting new people, and reading plenty of scientific papers. The Baugh lab is a c. elegans lab that observes developmental arrest (L1 arrest) in roundworms with various mutations under starvation to elucidate signaling pathways and gene regulatory mechanisms that control this arrest. These pathways and mechanisms mirror those of humans, and this research can be used to study the maintenance of homeostasis during development (adaptiveness), aging, and even cancer cell division and growth.

As intriguing as the concept behind the lab is, I admittedly came back to Duke this summer to begin my first foray into scientific research with a great deal of apprehension. How would I feel about working with nearly microscopic worms for an entire 8 weeks? How much of the jargon-filled papers that I was supposed to read before starting lab was I supposed to understand? What if I turned out to be utterly incompetent and unreliable? What if I couldn’t deal with the long working hours?

Although I went into lab at first prepared to take on the worst if necessary, I ended up leaving lab each day with a new insightful, eye-opening experience. I was amazed at the way my mentor and others in the lab worked with adept efficiency and the way they casually inserted scientific jargon into their conversations with no trouble at all. I appreciated the patience my mentor displayed when I made a careless mistake, her thorough and informative responses to my frequent questions, and her willingness to take me on as a mentee even though she was plenty busy already with her own projects. I also realized after witnessing several moments of camaraderie (mostly in the form of shared anecdotes or sometimes scientific puns) that the atmosphere of the lab doesn’t have to be stiff and formal as people might expect of a place where ground-breaking research is being conducted.

I was also pleasantly surprised by how much I actually enjoyed working with worms, whether it was viewing them under a fluorescence microscope for the first time to score cells (picture below because I think it looks cool) or transferring them painstakingly from plate to plate when performing biweekly strain maintenance. More than anything this week, I particularly enjoyed the growth I personally experienced while in the lab, whether it was performing repeated techniques with more finesse each time, being able to navigate the lab more freely without supervision, reading literature with more ease, or simply becoming more knowledgeable about my personal project and the lab’s overarching purpose.

c. elegans under a fluorescence microscope

c. elegans under a fluorescence microscope

Of course, I still have quite a ways to go, but I have many expectations for these coming weeks. Although I have gotten relatively lucky this past week with making only minor mistakes in lab, I expect that many more mistakes will likely be made in the future, and while they’re likely inevitable, I hope to at the very least learn from them and prevent them from occurring again. I am also making it my goal to become as familiar as possible with my personal project in my lab and read plenty of literature regarding the two specific genes I was put in charge of testing. One of the most thrilling moments of the week for me happened when both my PI and my personal mentor told me that they both know very little regarding the genes for my project, so it’s completely uncharted territory for them, and it’ll be my job to become an “expert” on the genes. More than anything, I expect to transition from being almost totally dependent on my mentor to becoming more independent and able to carry my own weight by the end of the summer.

With that, I look forward to the great experiences the rest of the summer will provide, and I wish my fellow B-SURF fellows (pun not intended) the best of luck with their own projects!