Set up my third rotation
Table of Contents
Sunday, February 2
162.0 lbs (Day 37, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6)
I woke up pretty late this morning. Rubbing my sleepy eyes, I headed over to a nearby cafe for a latte(my favorite). There’s a really cute spot I always pass by on my way to Whole Foods, but it’s always so crowded, so I’ve been wanting to check it out. When I walked in, I was a bit surprised there weren’t any seats available, but the decor was cozy and great. The weather could have been a bit nicer, but the latte turned out pretty good. These days, instead of going through the hassle of explaining “Sungwon,” I just say “Sung” or even say the name of a friend with an easier name😜 Sometimes, even when I say “Sung,” they end up writing it as “Song,” like in that picture… I really envy people with names that are easy for English speakers to pronounce.
After that, I headed over to a brunch cafe(Plow, 1299 18th St, San Francisco, CA 94107) I hadn’t managed to try last week. Even though I got there early, it was already packed, so I ended up waiting. Luckily, I got in way faster than expected. I ordered a platter called The Plow (two eggs, your choice of house-made pork sausage, Nueske bacon, or chicken apple sausage, two lemon ricotta pancakes, and crispy potatoes), and it was amazing. The house-made sausage and lemon ricotta pancakes were especially awesome 👍 While I was enjoying the meal, my program director got back to me, and we set up a meeting for Thursday morning! Fingers crossed it all goes well.
Later on, I hit the gym with a friend and totally wrecked my legs. Lower body workouts really seem to hit harder when you’re working out with someone else. When I got home, I took a nap, did some meal prep, and then spent the whole day working on my blog. Oh, and starting this rotation, I’ve been sending my mentor weekly updates on my project progress and what I plan to do next week. After sending the weekly update, I realized I was already halfway through my rotation. Time really flies. Right now, I’m eager to settle into a lab, but since opportunities to work in such diverse labs (only a short time period) might be a once-in-a-lifetime thing, I’m determined to learn as much as I can and finish well.
Monday, February 3
163.6 lbs (Day 38, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6)
Outside of Work
I woke up around 6:30 AM and headed straight to the gym. Although it was a bit rainy(not that ideal start to Monday), I managed to get there without much trouble. I noticed that my neck stiffness has improved recently, so I slightly increased the intensity of my workout. During my overhead press, I have focused on feeling the burn in my shoulders for isolation. However, I recently heard from my primary care that the coordination between my shoulder blades and joints seems a bit off, which might cause shoulder and neck pain. To address this, I performed full-range barbell movements to help rehabilitate that rhythm, which felt like a reasonable approach.
Later in the day, I attended two classes. The first was a Responsible Conduct of Research (RCR) class via Zoom from 11:30 AM to 1:00 PM, and the second was a reaction mechanisms class from 1:00 to 2:30 PM. I always find it challenging to discuss topics like research ethics, misconduct, or plagiarism, especially in English as a non-native. About ten minutes before the RCR class ended (around 12:50 PM), I switched from my laptop to my phone so I could continue listening while I headed to the next classroom. The teaching assistants suggested that I consider becoming a TA next year (maybe? because of my active participation in asking and answering questions). I appreciate this, otherwise I have to go Parnassus campus to teach pharmD students(+ of course I like organic chemistry).
Right after class, I met with a professor whose lab I’m considering for my third rotation. It was an excellent conversation! He’s incredibly passionate about his research, and his academic journey aligns perfectly with my interests. In his first three years as a PhD student, he managed to complete the synthesis of a complex antibiotic—a process that requires up to 40 steps and had previously taken other graduate students six years to attempt. Later, he shifted his focus to incorporate more biology into his work, leading to a second, biology-intensive project that elucidated the mechanism of action of the molecule he synthesized. I found his achievements truly inspiring and exactly what I look for in a chemical biologist.
We also had an in-depth discussion about the rotation projects, and he presented two possibilities (in fact, he even mentioned the possibility of doing both simultaneously!). The first project involves using chemoproteomics in an unbiased chemical biology approach to identify protein targets. It focuses on expanding the probe library by synthesizing chiral probes with diverse structural variations. The second project is more synthesis-focused, following a traditional medicinal chemistry approach with structure-based design, especially since we already have a co-crystal structure with a previous lead compound. Although I feel comfortable with organic synthesis from my master’s work, I’m leaning toward the first project because I want to deepen my knowledge in biology and chemoproteomics.
We talked for about an hour and a half, during which the professor also gave me the opportunity to discuss my future ambitions and the different paths I could take if I eventually decide to become a professor. He believes that the biggest advantage of doing both(chemistry and biology) is the ability to work proactively, rather than being passively driven by collaborators. Although I’m a bit concerned about whether such an independent approach is feasible in Korea, it definitely seems more attractive. Beyond that, he shared several other ideas he’s currently excited about, including another synthesis project and different targets, and I felt that our research interests aligned very well. By the end of our meeting, I had decided to pursue my third rotation in his lab. I was introduced to a mentor, and we agreed to meet again around March to finalize the project details😁
Lab Work
I had planned to purify the protein pellet I got last week, but due to a packed schedule, I had to postpone the purification. My mentor and I agreed to reschedule the six-hour purification process to Wednesday since he was busy on Tuesday. Instead, I ran a reaction around 11:00 AM to test our hypothesis that leaving the reaction overnight might induce intramolecular cyclization, thereby creating a side product. After about five hours, I quenched the reaction and purified the compound and then lyophilized it. I plan to run the NMR on Wednesday(I collected approximately 30–40 mL of product across two test tubes (each with an 18 mm diameter), and complete lyophilization usually takes about two days).
Tuesday, February 4
163.2 lbs (Day 39, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6)
Outside of Work
Nothing much happened today. Despite the drizzling rain, I managed to go to the gym in the morning. After attending a journal club class in the morning, I spent the rest of the day in the lab. As soon as I got home after work, I slept again. Am I getting physically exhausted? Hmmmm I don’t really feel tired, but maybe my body thinks otherwise.
Lab Work
Today I focused on chemistry. I ran two different reactions. One reaction used a methodology I had used several times before; as a result, I was able to purify the product and get the sample lyophilized. However, the other reaction did not go well. It was about synthesizing a “vinyl sulfonyl” warhead, but the typical method used for synthesizing other warheads did not work in this case. I added 0.5 equivalents of the electrophile more after 2 hours, yet interestingly, the ratio of the starting material to other products remained unchanged. Consequently, I searched for additional references on synthesizing this type of warhead and set up two new reactions using different approaches.
Wednesday, February 5
164.4 lbs (Day 40, starting from 162.6 lbs on Dec 28) | 🏃🏻 Missed (2/6)
Outside of Work
Since I ended up leaving the lab late as usual, nothing much happened today. I woke up at a weird time because I was completely wiped out yesterday, so I couldn’t manage to go to the gym. In the afternoon, I attended my regular Reaction Mechanism class (which I have on Mondays, Wednesdays, and Fridays). Honestly, I have nothing else to report aside from working in the lab all day. I still feel that even when I’m busy, I need to find time to exercise. it really helps improve my overall condition. After work, when I had dinner, it was already 10 PM, so I just fell asleep without doing anything else.
Lab Work
Today, I finally started protein purification. The first step was nickel chromatography, and I followed the protocol already used for the wild-type version of our protein. I thought biology experiments would take a long time and be more labor-intensive😵, but as with other experiments, getting our desired product makes us very happy. What I want to emphasize is that there are plenty of opportunities to improve the protocol. I was shocked that even my mentor and the other postdoc don’t want to explore better methodologies or protocols. In my opinion, once the process is optimized, our time management and productivity will improve. During my master’s, I focused on optimizing repetitive and time-consuming procedures, and it worked. Anyway, I feel fortunate that I can make changes to improve the protocol, especially because there are many professionals with extensive experience in biology experiments whom I can ask for advice.
After a long incubation with the nickel resin and lysis buffer, finishing the column, running an SDS-PAGE, and dialyzing the desired fractions in a cold room, I ended up finishing the lab work around 9 pm. I realized that I had to use my ID to open the door in the research building since it closes after 9 p.m.🤣 Of course, I also did some chemistry. The reaction I set up yesterday did not go well. No product was formed, and the starting material remained even after using 3 equivalents of electrophile. My mentor and I decided to use DMAP to catalyze the reaction because we suspected that the instability of the electrophile might be causing the excess starting material to remain unreacted. I set up two additional reactions with DMAP, and finally, I observed a product peak on LC-MS under one condition using DCM. Surprisingly, the major M+H peak was relatively small, while the M–OH and M+Na peaks were much larger. However, the peaks were still messy, and we thought purification would be difficult, so we plan to use milder conditions next time.
Thursday, February 6
164.5 lbs (Day 41, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6)
Outside of Work
This morning, I woke up around 6:30, hit the gym, and did a lower body workout. I hadn’t done it in about a week and a half. It was really challenging but definitely worth it💪 Later in the morning, I had a meeting with the director of my program to discuss a policy I’ve mentioned several times before. To explain briefly: the policy limits the number of students a PI can accept in a year. Specifically, each PI in our program can accept up to 2.5 students—the ‘0.5’ indicates that one student must be co-advised by another PI. During the meeting, a friend who is also rotating in the same lab, and I shared our thoughts. We agreed that we didn’t want to compete with our peers. We said that if both a PI and we want to join a lab, the policy shouldn’t block us, even with the 2.5-student limit. However, due to UC’s funding issues, if a PI takes extra students, they have to cover either the second-year tuition or stipends (I’m not sure which). Since we’re only in our second rotation, we still have another chance later. We plan to have a meeting again around April or May for an update.
Today, I had lunch with my friend (the same one from the meeting), and we talked about our PhD plans, concerns, and experiences from our first rotations. It was a great conversation. I’m confident that my friend will find an excellent lab. He is smart and kind! As a side note, he, another friend, and I will be TAs for reaction mechanisms next year! Later in the day, I attended a pizza talk from 5:30 to 7:00 p.m. It was a fairly typical event; I was so preoccupied with the lab work I had done earlier that I couldn’t fully focus on the Q&A. I went home and pretty much passed out from exhaustion. While learning new things is exciting and beneficial, I often worry about missing details or misinterpreting information, especially when working in English. Biology is still relatively new to me, and learning a new technique for the first time is always somewhat stressful. 😥
Lab Work
I ran a reaction (6th attempt for the same substrate but under different conditions). This time, I added DMAP and lowered the temperature to –40°C using a mixture of acetonitrile and dry ice. I hope the lower temperature helps prevent unwanted side products. I plan to check the LC-MS results tomorrow morning. After that, I continued working on protein purification. I started by checking the dialysis, and there was no noticeable precipitation outside the dialysis chamber. I carefully decanted the solution into 15 mL tubes and ran LC-MS to check the protein (this time, we were monitoring the protein, not a small molecule—we can do this using MaxEnt). Our goal was to confirm His-tag cleavage by checking the molecular weight of the protein without the tag, and it worked!
The next step was to purify our protein again using a reverse nickel column. This process is similar to standard nickel column purification, but since our protein no longer has a His-tag, it won’t bind as strongly to the resin. We incubated the post-dialysis solution with nickel resin for about two hours before running the column. Afterward, I ran a gel. I made a small mistake by loading the same amount of ladder on both sides of our 12-well gel. Typically, we load a smaller amount in one lane to mark the loading direction, making it clear which side corresponds to which sample. Despite this, after staining the gel with Coomassie, we could clearly see the pure protein fraction. We collected the pure fractions but couldn’t perform SEC purification tomorrow due to scheduling constraints. So, we decided to run SEC next Monday. For now, we froze our samples in a 50 mL tube using liquid nitrogen and stored them at –80°C over the weekend.
Friday, February 7
163.8 lbs (Day 42, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (4/6)
Outside of Work
I freshly hit the gym in the morning. Today was packed with classes (three in total)! Literally, from 11:00 AM to 4:00 PM. I had Chem 223, Reaction Mechanisms, and an RCR discussion group. It was really heavy. As I mentioned before, Chem 223 (CCB Student Research Talks) is my favorite class. I enjoy watching the vivid presentations by my seniors and hearing all the valuable comments and feedback. To be honest, I worry about those moments when I think of an answer to a question from the audience but can’t come up with the right words to explain it. I was so nervous, but I’m sure I’ll get better with practice since I’ll be presenting my research for the rest of my life haha.
After I got off work around 6 PM, I ran into some friends and joined the group heading to In-N-Out in Daly City. Although it’s near San Francisco, it’s technically not SF. Anyway, one of my friends recommended the Animal Style fries and burger, and they were great! Next time, I’m going to try another style, maybe the Protein Style burger or even a combination.
After dinner, we planned to watch a movie in the dormitory common area, so we stopped by Target to grab some snacks. I bought a jelly, based on a friend’s recommendation. It was sour and totally my style! The movie we watched was Inception, which is my all-time number-one movie. I’ve seen it 4–5 times before, and I even have a totem like the one the main character uses to tell if he’s in the real world or a dream. I recommended Inception to my friends, and since it was on Netflix, we watched it. It was so interesting, even though I’ve seen it several times before. In my opinion, the many experiences I’ve had since the last time I watched it have given me a different perspective on the same scenes, which is great. The movie ended almost at midnight, and I went straight to bed.
Lab Work
Because classes were packed today, I only ran two reactions under conditions similar to those I have performed many times before. I managed to purify both reactions, and the samples are now being lyophilized.
Saturday, February 8
163.4 lbs (Day 43, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6)
Morning, I went to the gym with my friend (always go with him on weekends). Both of us hit the gym five times each last week and this week, which is promising! We are trying to maintain this pace throughout the year. During the workout, he explained his future plans for his PhD journey. He has almost fulfilled the graduation requirements and is considering different projects. He will be co-advised (or mentored) by a professor at Stanford to explore more theoretical aspects of his research. This conversation motivated me to think about my future more concretely.
After the gym, he introduced me to a local bakery called Neighbor Bakehouse (2343 3rd St UNIT 100, San Francisco, CA 94107). He bought two of his favorite breads as a gift for me, and they were awesome. To be honest, the sausage bread is the best I have ever tasted—crazy good! Next time, I’m definitely going to try the Malcha cream bread. We also stopped by a newly built park. It was such a wonderful day that I felt completely re-energized.
After getting back home, I took a nap (as usual), worked on an assignment for my reaction mechanism course, and then slept well.
