First Time with Cells
Sunday, May 11
167.2 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (6/6) | ★★★★★
After a refreshing rooftop workout this morning, I decided to try studying at the San Francisco Public Library (100 Larkin St, San Francisco, CA 94102). I typically work at the Hub, but I wanted to try a new spot on the weekend. When I discovered the library, it looked great, so I gave it a shot. Before heading inside, I picked up some poke and ate it in a nearby park. The atmosphere there was wonderfully relaxed, and the weather was unbelievably nice. Once I got to the library, I saw that it had plenty of seating, including large desks specifically designed for focused studying. I loved that setup (enjoyed the open, spacious feeling) and got a lot of work done, including preparing my presentation for tomorrow.
To be honest, when I start feeling tired at the Hub, I sometimes just want to go home to relax. Even though it takes time to get to this library, it’s still better than staying at the Hub because I can concentrate longer, otherwise, I’d feel guilty about wasting time commuting.
After a productive study session, I had dinner with my friend at Menya Kanemaru Golden Ramen (174 Valencia St, San Francisco, CA 94103). We ordered the Signature Donabe ramen and the garage bento, and both were delicious! The tasty food, a solid morning workout, and productive hours at the library, it was really a great day. Once I got home, I decided to do more work on my presentation for tomorrow and skip my workout so I could rest. Hopefully, all my graduate classes will be finished soon🙂
Monday, May 12
167.5 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Rest (0/6) | ★★★★
Outside of Work
Today was the first day of my third minicourse, which, looking back, is the most informative and well-organized of the three I’ve taken. My second minicourse was also a mass-spec class, but I would say it wasn’t very useful for someone who’s never used mass spectrometry before. In contrast, this third course emphasizes practical applications rather than theory and principles, which I think is sometimes better for a general audience. Below is the syllabus for the class.
BMS 270: Current Approaches to Quantitative Proteomics in Biology
Spring 2025 Module 3
Course director(s): Arun Wiita
Instructor of Record (for student study list): Arun Wiita
Other faculty: Danielle Swaney, Sanjeeva Srivastava
Days/times: 5/12-5/30/25 – MWF, 9:30-11:50
Campus: MB
Room: MH-1402/MH-1407
Description: This course will give an overview of current and emerging quantitative proteomics methods in basic science applications. The course will be a mix of lectures, paper discussions, and hands-on experience in data analysis. Topics to be covered, among others, include SILAC, post-translational modifications, affinity purification mass spectrometry, isobaric labeling, shotgun vs. targeted proteomics, data-independent acquisition, and single-cell proteomics. The goal of the course is for students to both gain a better understanding of mass spectrometry approaches as well as envision where these extremely versatile approaches could enhance their own research.
However, the course requires a team presentation, and I will need to lead the entire group in discussing the meaning of specific figures from an assigned paper, so it will be more demanding, particularly since the class meets every Monday, Wednesday, and Friday for two and a half hours.
After class, I grabbed lunch and then gave a presentation for my second minicourse, which went well. When I first arrived here, I was obsessed with my presentations and tried to memorize the entire transcript. Now, I don’t do that anymore, though I still feel I should memorize parts of it. Instead, I focus on delivering the presentation extemporaneously, which feels more natural to me (still difficult😞)
After finishing my presentation, I met with the professor in my current lab to discuss the direction of my rotation project. Later, I performed my first live-cell experiment! It was exciting, but I had to be extremely careful about contamination—working in a sterile hood is very different from chemistry labs😅 I’m sure it will take some time to adjust to these new procedures. Since it was a busy day, I went straight to bed when I got home.
Lab Work
[Biology]
- Plating 106 HEK293T Cells per Well in a 6-Well Plate
[Computation]
- Trying to Define a Covalent Bond Restraint for a Custom Ligand (Not in the CCD Library)
Tuesday, May 13
169.0 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6) | ★★★★☆
Outside of Work
After a refreshing morning workout, I didn’t have any classes today. However, tomorrow I have a mini-presentation for the third mini-course, and I also plan to attend the San Francisco Giants game for Korean Heritage Day! So I quickly wrapped up my experiment and headed to Oracle Park around 4:30 p.m.
Originally, I planned to leave early once I got the Korean Heritage uniform. Unfortunately, that wasn’t possible. The ticket we bought using the UCSF discount wasn’t eligible for the special uniform. To qualify, the ticket needs the Korean Heritage Mark, but ours didn’t have it🥲
Anyway, I ended up ordering kimchi fries (fries topped with kimchi, garlic, and spam), which they served in a small, cute baseball helmet. What shocked me most was that a player on the Giants who had never hit a home run in the entire MLB season actually hit a grand slam! It was unbelievable. Lee Jung-hoo also hit a home run, but I missed it because I had to leave early for my presentation tomorrow. Despite that, it was a great experience with my cohort, and we had a lot of fun. I’m proud of Lee Jung-hoo, he’s very popular on the Giants and loved by many fans, including the Hoo Lee Gans fan club🐔
Once I got home, I prepared for my class tomorrow. I only have to explain some figures from the assigned paper, but it’s quite stressful because the topic is completely outside my field, so I need to understand it thoroughly. In my case, unlike in Korea, I have to know the material perfectly and practice it repeatedly.
Lab Work
[Chemistry]
- Check NMR for SJ-1-36 and SJ-1-37
[Biology]
- Treat cells with drugs and collect pellets
[Computation]
- Addressing incorrect bond‐order information in Boltz-1 prediction output after treating a covalent drug as a noncanonical amino acid (PTM)
Wednesday, May 14
168.6 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Missed (1/6) | ★★★★
Outside of Work
Somehow, I managed to finish my brief presentation in this morning’s class. Surprisingly, my friend, whose parents are both Korean, got me a jersey yesterday, so I want to thank him! Today was quite busy because I had to go straight from class into a group meeting, so I didn’t have time for lunch. Anyway, the group meeting went well, and I realized that I learn something new at every one of these meetings—it’s incredibly valuable. I think the biggest strength of our current lab is our PI’s dedication; he always spends a lot of time and attention on each lab member and project.
In my brief meeting with the PI yesterday, we agreed to synthesize more warheads in case our acrylamide probes aren’t sufficient for pursuing the chemoproteomics experiment. So today I did some chemistry, which I haven’t done in a while, and I hope this will be my last time doing it during this rotation! After a busy day of lab work, I went home and went to bed early to make up for lack of sleep (only got three hours last night).
Lab Work
[Chemistry]
- SJ-1-38, 39: rxn and purification; being lyophilized
[Biology]
- Changed the cell culture media
Thursday, May 15
168.4 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6) | ★★★☆
Outside of Work
Only my second workout this week, even though today is Thursday😅 I’ll try to make up for it by going to the gym for the rest of the week. Today was busy with experiments, and I realized that there are many waiting periods in biology between experiment steps. I also feel there’s more chance for things to go wrong (more inherent variability) than in typical organic synthesis. I don’t think I like this, tbh, but it’s still better than some pure biology experiments that take weeks or months. Once I got home, I did some meal prep and went to bed early.
Lab Work
[Biology]
- Lysis, BCA, Click rxn, SDS trt.
Friday, May 16
168.0 lbs (starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6) | ★★★★☆
Outside of Work
Another success at getting to the gym today. My Monday, Wednesday, and Friday mornings are basically wiped out by minicourses🤪 I can’t wait until they’re over so I can focus solely on experiments. Today, I performed my first-ever protein transfer (gel to membrane) for a Western blot~! You know, everything seems difficult until you actually try it; once you do it, it becomes surprisingly easy, and you get better with practice. I think a valuable approach during lab classes in Korea is to watch as many complete experiments as possible from start to finish, rather than just doing a few small tasks. There are pros and cons, but being exposed to numerous techniques lowers the barrier next time I have to learn them and also eliminates the fear of the specific experiment.
After work, I enjoyed jeyuk bokkeum (제육볶음, spicy pork stir-fry) with my Korean friend, and it was so delicious! Now it’s time to seriously decide which lab to join, so I’ve emailed the professors I rotated with. I really hope everything works out. Fortunately, funding doesn’t seem to be an issue for the labs, but there’s no guarantee anywhere else, either. Still, I’m going to try my best without stressing too much. Choosing a lab will affect the next four years—or even longer—so I’ll make sure not to rush and not to give up.
Lab Work
[Biology]
- SDS-PAGE, in-gel fluorescence (TAMRA), Transfer proteins to a membrane, Stain the membrane with Ponceau, Incubate in blocking buffer over the weekend
- The IGF result was not as expected, so we will repeat the experiment using chloroacetamide warheads, expecting higher labeling efficiency due to higher electrophilicity.
Saturday, May 17
167.9 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (4/6) | ★★★★★
Busy but productive day: worked out at the gym this morning, got a haircut, and had a long catch-up call with my best friend in Korea. I also got a lot of work and reading done at the Hub, FaceTimed with my family, my aunt, uncle, and younger cousin, and then got a good night’s sleep. I’m determined to keep in closer touch with my family (whenever I do FaceTime🥹) , even though it’s not easy. They’re always supporting me, which I’m so grateful for—I feel reassured knowing there are people who back me no matter what.
From my call with my friend, I realized that many of our peers are now reaching a point of self-made success. It makes sense, after all, I’m already thirty, and it’s natural for people I know to achieve great results through their own efforts. There’s no obvious rule or criterion for success, but in my opinion, someone is successful when they accomplish what they want through fair and consistent effort. I’m lucky to have friends who are always working hard in their lives, and they keep me motivated. I need to pull myself together and finish the semester well. I miss my family and friends.
