This is a continuation of my first article from last semester where I started my undergraduate thesis writing process. You can find that here.

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January 24nd, 2024

Just submitted my methods and materials section. Honestly, at this point I’m a bit more stressed about actually finishing data collection than the actual writing. I’ve kind of reached a “well it’s just an undergraduate thesis and not the end of the world” mentality, which is helping a little. To be honest, I did have a couple stress dreams last week (one was where I was scrolling through an endless Excel sheet of data that I had to analyze), so just accepting that it’s not that deep is good to me. But we keep working. 

I also had to peer review one of my classmates’ methods section. We had this set up last semester too, where we had to peer review other people’s proposals. This semester, I’m paired with a group of other neuro students, so I feel like there’s a lot more back and forth I can actually have with them and their research. For this student, since we had similar experimental setups, I was able to see what she did well, and it also reminded me of things that I need to add to my section.

One thing I’m trying to do this semester is to work on my thesis stuff more consistently, rather than pushing it all to the few days before the deadline. For that reason, I’ve blocked off an hour every workday on my calendar as a reminder to work on my thesis, even if it’s just for 15-30 minutes. I’ll let you all know whether this is helpful or if it stresses me out more to have my thesis on my mind all the time.

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February 27, 2024

As always, problems come up right when you don’t want them to. The stereotaxic frame got broken, so we had to send it in for servicing. This means no surgery practice this month, which sets me back on my deadlines. Luckily, I’ve figured things out with my PI and my thesis class professor, but it’s still disappointing.

Still, the time will pass anyway, and I did practice with perfusions and drop fixing in the meantime. It turns out that I had gotten rusty with these basic skills, so the time spent on that still felt worthwhile.

While I’ve been waiting on unforeseen circumstances to clear up, I’ve continued working on my thesis results and discussion section. You might ask how I could write those parts without having data, but I did a method my professor calls “Mad Libs” writing, where you leave blanks where you don’t have the information yet. This has been helpful, since I have been able to get an outline of what my results and discussion sections will look like.

So, I’ll see you in a month, when I hopefully have some data I can cut my teeth on.

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March 30, 2024

Well, I’ve gotten pretty comfortable with surgeries, and next week I’m planning on doing my first optical implant. If all goes well, I can hopefully collect some data in two weeks. I’ve definitely been stressed about completing this thesis, and part of the process for me this semester is learning to deal with/live with the stress. This isn’t something I can finish in a weekend, after all, so I need to learn to work with this “unfinished task” bell dinging in my head until I turn this thing in. I really really want to have data collection done by the second week of April so we can do data analysis and I can submit the drafts to my readers. It feels like this semester has flown by faster than I thought, and I am worried about the deadline.

In terms of what else I can do on the writing side, I am working on the schematics that will take up part of my figures in my results section. This is something you never really think about when you think of writing a thesis, but working on making good figures is difficult and time intensive. However, it feels good to be able to make those to have in my paper for now.

There’s a lot going on outside of this thesis too–I’m getting ready for graduation, writing term papers, studying for tests, and looking at housing after graduation. It’s a lot to juggle, and I hope I’m doing okay. I’ve been reminding myself that I’m basically in the final lap of this process, and that I can do it.

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April 23, 2024

Finally got some data this month, and I was able to write it all up and make a complete thesis of it all. It was stressful surrounding the data collection, but actually doing it went pretty smoothly. I typed everything up today and sent it off to my first and second readers.

Really, I don’t know what to say here. After actually sending it off, I felt a little relief, but it wasn’t a super big change. That being said, I think I’m still focused on my work because I plan to continue it after graduation, and so my work doesn’t really feel finished. Still, I’m really happy that I was able to turn everything in with time to spare. By having it done about two weeks before I have to submit, this gives my readers enough time to give me feedback and turn in everything to UROP (undergraduate research office that approves undergrad theses).

Now, it’s time to focus on everything else I need to complete before the end of the semester: term papers, exams, and graduation. But tonight, instead of working on it all, I gave myself the evening off. It’s something I deserve after all this, I think.

Am I happy I did all this? Was it all worth it? I think it might be too early to tell, but I think it was well worth my time. I learned so much about research, working on a long term project, and scientific writing. But if I could go back in time and do one thing better, I would try not to stress as much about it. I think during this past year I’ve given myself so much unneeded pressure that never helped make my thesis better in the end. But I doubt that August 2023 me would have taken that advice to heart anyway. In any case, this is my last entry, because I consider this chapter of my life complete. I hope you enjoyed this mad little journal. I’m out.

The Georgia Tech Research Option is available to all undergraduate students in the College of Sciences. It includes the completion of an undergraduate thesis. Students who choose to take on all this additional work are generally considered a bit sick in the head. Through these diary entries, I hope I can provide some insight into the joys and trials of completing this process. Particularly, for those who (for some reason) want to take on the same path.

August 24, 2023

Finally figured out the direction that I want my thesis to go in! This has been stressing me out quite a bit, so I’m glad I’m able to figure things out. I talked with my PI and we sort of figured out that I can do a project that combines the calcium sensors our lab has been developing and the dopamine recordings in freely moving mice that we’ve been doing. There’s still a lot of directions this project can go, but this sounds like a good place for me to start thinking (and just as importantly, looking at sources for the background section of my thesis). What I found super helpful is that my PI gave me a set of next steps if I want to pursue this project, which alleviated a lot of my uncertainty. Here they are:

1. Get trained on stereotactic surgery (mouse brain surgery)
2. Learning how to run and handle mice in our behavior rig
3. Injecting mice with whichever thing we want to test (probably dopamine and the sensor at first)
4. Running in vivo experiments

As you can see, running experiments is step 4, after having to learn a lot of other stuff. Hopefully, I’ll be able to start that step in October/November, but if not I should be able to do it in spring. 

We also discussed how there’s a huge gap in the literature that I honestly hadn’t really considered: we don’t really know how dopamine impacts the excitability of neuron populations. This seems like something really basic to the field, but we haven’t really had the tools to measure it until very recently. I don’t want to get too deep into the particulars of the field, but basically I’m glad that we’ve found something that I can reasonably say fills a need in this field of research. In addition to that being a required part of my thesis’ introduction, it makes me feel a lot more passionate about the work. I think a big challenge of this thesis will be staying motivated as the going gets tough, so this is good.

My next steps will be to get trained on the techniques I’m planning to use and look at some papers for background.

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October 6, 2023

I have been super busy this past month and change. I have been practicing stereotactic surgery, which has proven to be really hard. While I’ve been working on experimental techniques, I’ve also been reading a ton of articles.

Right now, I have around 25 articles in my Zotero (research sorting app), and I’ve read about 7. Although I’m improving in my ability to read research articles, it’s still taking such a long time. 

Now, my literature review is due in two days, and I haven’t read all the papers yet. However, since it’s just a draft, I’ll try to use the background section of my PURA proposal as a base for it. I’m going on a trip tomorrow, so I really don’t want to work on it during my trip.

I’m going to work on it now and just submit the draft. This thesis process has taught me to just turn something in, even if it isn’t perfect.

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November 4, 2023

Well–I think I’m at the point of the semester where it all feels like I’m fighting an uphill battle. Looking at my 4 step plan from August, I’m still working through step 1. My plan of conducting actual experiments in October was a little too rosy. One thing that’s slowed my progress is that although I’ve been practicing mouse surgery, I can only pretty much do one mouse per week. I share the surgery room with other people in the lab, and with scheduling around classes and other lab tasks, that’s all the time I have for practice. 

Still, I feel like I’m making progress, slow as it is. This week, I’m going to be doing my first survival surgery, which is one step closer to being able to put in implants and biosensors into mice.

On the writing side, it’s time for me to revise my lit review, introduction, and work plan and put them together. It’s also necessary for me to get all three (all together they’re called the proposal) signed off by my research advisor and second reader. Honestly, this part kind of scares me because I feel like I haven’t gone in depth enough for my lit review in particular. I’m meeting with my advisor later this week to show him my proposal, so I’ve got to get working on this today and tomorrow (the weekend). Currently feeling stressed out. But I keep telling myself that it’ll pass.

The thing is–I really like doing research, and I find reading articles and learning more information about the topic interesting. But deadlines and expectations always scare me. Even so, I’m trying to tell myself that I have all the tools I need to succeed. I just need to be patient with myself.

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December 1st, 2023

Well, I’ve basically done all my revisions. My readers gave me some really helpful feedback, and it turned out that my proposal was in better shape than I originally thought. I just need to check some of the formatting, and then I’ll wait for the approval form to come out so I can submit it. 

One thing I noticed–that I also talked to my advisor about–is the fact that when I’ve been working on my thesis, it’s made me think about why I am doing what I’m doing. Like it’s simple enough to say I’m working on a project that uses a biosensor, but when I started writing, I started thinking more about the details in a way that I never really did while just doing bench work. Why do we choose this type of biosensor? What gives our approach the advantage over another? In what way does our experimental setup even work?

I think as undergrads, a lot of stuff is technically really complex and hard to grasp. So the researchers who are mentoring us simplify things so we can get a general gist of what’s going on. But when you’re writing your own thesis, or even making a presentation on your research, you’re encouraged to delve deeper into the reasoning behind what you do. And in that way, I think I finally kind of understand why a thesis was put into the curriculum of the research option. 

As the semester is nearing its end, I’ve been thinking a lot about what I’ve done so far. And I feel like while I’m behind on my work plan, I still feel proud about what I’ve accomplished. It’s just an undergraduate thesis–I’m not really expected to produce groundbreaking. Still, I feel like the skills I’m learning (reading journal papers, scientific writing, study design, coordinating with my research advisor) are going to be really helpful in the future.

Or, maybe I just feel like this because the pressure is off, for now. I’m going to put the final touches on my proposal now–see you next semester!

Here is my followup to this article–the finale of my undergrad thesis journey!

This semester, I started doing animal work in a research lab that uses mice as model organisms. Every time I’ve explained my training to other people, I usually get a shocked response. And I know this isn’t a common thing people do, so I wanted to give y’all a look into what it’s like working in an animal lab.

The lab I work in does research using a technique called optogenetics. Opto- means light, and genetics refers to the DNA that is changed. This might sound straight out of a sci-fi novel, but by infecting a certain brain area of healthy mice with a special virus (this doesn’t make the mice sick, by the way), the virus can insert a list of instructions written in DNA into the mouse’s own DNA. These instructions tell the cells to start producing light-sensitive proteins in their membranes.

Now, this has a very important application in neuroscience. Neurons, the unit cell of the brain, fire tiny electrical signals called action potentials. If a neuron has light sensitive proteins that respond to blue light (channelrhodopsin), it fires more often. If it has light sensitive proteins that respond to yellow light (halorhodopsin), it fires less often. Using optogenetics, you can directly measure how activation of a brain area leads to behavior in real time.

So how does that factor into what I do? So far, I’ve worked on an often-overlooked but important step: collecting samples. After you inject the virus into the brain, there’s no way to check in the live animal that you did it right. You might have put the virus in the wrong place, or the virus never got its instructions to the cells, or the equipment might be broken. The only way to know for sure that your procedure worked is to take samples of the brain, and look at them under the microscope.

To do that, we first need to collect the brains. Through a process called perfusion, the brain gets fixed in paraformaldehyde (PFA), a safer version of the formaldehyde you might remember from dissections in biology class. During drop fixing, where the brain is severed from the spinal cord and removed from the head, we store it in a test tube with more PFA.

After 48 hours, the brain is ready to be sliced. There’s a lot of ways to take brain slices, but we use a vibratome. First, we locate the area of the brain that we’re trying to reach. This is where a mouse atlas comes in handy. Using a small, vibrating blade, we make slices of 50 microns–or around the width of a human hair! These slices are then stained with dyes like DAPI (which makes neurons look blue)  and placed on microscope slides.

Finally, after all this work, we can see the fruits of our labor. In our lab, we use a confocal microscope because this type of microscope can show us thin layers of cells within thick layers of tissue. Using different colors of light, we can also check how well the light sensitive proteins were able to grow in the area of the brain we’re interested in. In the picture below, you can see the first picture that I took myself from a brain I perfused and sliced. There’s no injection in this brain, so it’s as close to a “natural” brain slice that you can get. The blue color is from the DAPI dye, which indicates the location of DNA in a nucleus. So, each tiny blue dot is a neuron.

It was hard to describe the first time I saw this image. Yeah, there were some nicks and tears in the tissue (my hands were shaky during the perfusion), but this was something that I had wholly produced myself. And now, in front of me, was a snapshot of all that this mouse was. 

See that little butterfly shaped area in the middle of the brain, right above the hole in the middle? That’s the hippocampus, where every memory is scrawled in your brain through a network of neurons. What mousy memories were kept in there? Looking at this picture, I can almost imagine what it would have been like in there when the mouse was alive. The holes in between and to the side of the “wings” are ventricles, gaps in the tissue where cerebrospinal fluid carrying nutrients and hormones was kept. I can almost imagine waves of it washing over the hippocampus, keeping this great curled machine firing, shooting sparks of electricity in patterns that say I am alive. I have lived. Here is what I have seen, heard, smelled, touched, tasted, hated, loved. 

To be honest, this work can be kind of sad. After all, all life is precious. Sometimes, it can feel almost gruesome. To perfuse a mouse, you stick a needle of fixative into its beating heart, so it evenly diffuses and preserves the entire body. The night after I read this protocol, which had a video of this process in high definition, I felt almost too nervous to sleep. When I closed my eyes, I just saw that mouse heart beating out of its chest, beating, beating, beating…

The next morning, I admitted to my principal investigator that I wasn’t sure about trying out the perfusion that day. “Everything else, I’m okay with, but the way you can see the heart pumping freaks me out. I still want to try it, but…”

He nodded. “You never really feel comfortable with this part of the work.”

After a moment, he added, more seriously, “and that’s a good thing.”

Testing on animals is a controversial subject, and I can’t claim to have the definitive opinion. But, I think my experiences give me a special point of view. In the animal labs at this institute, the animals are well cared for. Until the last day they’re with us, we treat them with respect, care, and even love (what else do you call grown adults cooing at a 2 inch long mouse washing its tiny little face with its tiny little paws?). There’s laws, regulations, committees to ensure that animals are treated ethically. They’re given pain medications after surgeries, and during procedures (surgery and perfusions) they’re put under anesthesia. Once, our lab manager stayed in the surgery room with the mouse she was operating on until night fell to make sure she was there to care for him when he woke up. 

And yet, we have to sacrifice these animals in the end, and we have complicated feelings about it. I think that’s good and necessary. If we feel sad at the animal’s death, we treat it well when it’s alive. If we feel a bit of horror at watching its life painlessly bleed away in the dissection pan, it means we placed a high value on that life in the first place. We try to perfect our surgical skills, write better protocols, and design better experiments to minimize mistakes and the number of mice who have to undergo this process. I would much prefer that than to become cold and callous. 

Because the truth is, we don’t have a better process to study the brain in vivo. Treatments for neurodegenerative disorders, like Parkinson’s and Huntington’s (two diseases targeting the brain area our lab studies), mental illnesses, and mental disorders lag far behind those for many other parts of the body. And the simple reason is that we often can’t get into the nervous system to study it without causing permanent damage. Until better options arise, this is the best way to perform this life-saving research.

Whew. Things got really serious there. But working with something as big as life and death all the time makes you think about big questions. For me, ultimately this type of research is justifiable: this is the only way to validate that the research being conducted is working properly. It’s the only way to make sure that all the weird situations we put mice in weren’t done in vain. And getting to do every step of this process, going from a live mouse to a bright image on a screen–that’s something really special. Through that intricate picture, you can almost see something persisting, living on…helping us unlock the secrets of the brain. There is something to be said, here, about loving something by studying it: giving it all your attention while taking notes, appreciating the simple symmetry of the brain slice, using the gentlest touch to mount delicate tissue onto slides, admiring the natural structural variations that nature gifts every body and every brain.

Finally, I want you to think about your daily life, and the laboratory animals that made it possible. How many medications did you take today? What about cosmetics? Vaccines? Animal testing was where many of them began. One funny thing I’ve noticed recently is that researchers who work with “animals” tend to be the most adamant about using the term “humans and non-human animals”. Other species of animals are intertwined with us in inextricable ways. And there’s really no way to really convey my gratitude to a species that can not understand it. 

I guess this article is my attempt to try.