Spring Quarter Begins
Table of Contents
Sunday, March 30
167.0 lbs (Day 93, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (7/6) | ★★★★
I finally hit 167 lbs(I think the highest weight I’ve ever been)! It still fluctuates here and there, but I’m proud that it’s been gradually increasing. I use an app called Happy Scale to track my weight trends, and honestly, it’s the best one I’ve tried so far. I’d say it’s one of those apps anyone can benefit from.
- First, whether you’re cutting or bulking, you can set your own ideal rate of change (Commitment), which helps you avoid overreacting to minor day-to-day shifts—like drinking a bit more or less water. Instead, you get a clear view of whether you’re truly trending toward your goal.
- Second, you can set reminders to weigh in, which helps with consistency.
- Lastly, it’s completely free!
My current goal is 0.25 lbs per week, and I’m aiming to hit 178 lbs eventually. That’ll take about a year. Honestly, I’m already at the heaviest I’ve ever been in my life, so I’m really looking forward to seeing how things will look a year from now. Hopefully, it’s not just fat gain hahaha..
I hit the gym(a cozy photo I took on my way home) and had a meeting with the postdoc before diving into my paper draft to get some final thoughts. As expected, there’s just something different about people who are recognized for being great at research. Talking to him in person, I could really feel the depth in both his insights and how he communicated them. Super reassuring. After that, I organized the key points from our conversation, took a short break, and finished writing my blog.
Monday, March 31
167.2 lbs (Day 94, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6) | ★★★★
The spring quarter and my new rotation finally began, starting with a refreshing workout. This quarter features a unique course system called the “minicourse.” To put it simply, the quarter is divided into three parts (Module 1 to 3):
- Module 1 (Monday, March 31 – Friday, April 18, 2025)
- Module 2 (Monday, April 21 – Friday, May 9, 2025)
- Module 3 (Monday, May 12 – Friday, May 30, 2025)
Each module runs for three weeks, and students take courses they’ve registered for during that period. As you can see in the 2025 UCSF Minicourse Listings, there are barely any courses related to CCB haha… But I think it’s a great opportunity to gain knowledge outside of my field. That said, since each course only runs for three weeks, the schedule is quite intense (and yes, it really is…).
BIOCHEM 210/BMS 270: Chronic Inflammation and Disease (2025)
Module: 1
Sponsoring Program: Tetrad/BMS
Administrator: Danny Dam
STUDY LIST INFORMATION
Course Number: BIOCHEM 210/BMS 270
Course Name: Chronic Inflammation and Disease
Units: 3
Grading Option: S/U
Course Director: Thea TIsty
Co-Director: Jean-Philippe Coppe
MORE COURSE INFORMATION
Dates: March 31, 2025 – April 18, 2025
Campus: MB
Location: BH-212, except on April 11, 2025, when it will be in room S-261
Schedule: M/W/F, 10:00am-12:00pm, except Monday 4/7/25 from 9:00am-11:00am
Minimum Class Size: 6
Maximum Class Size: 12
Chronic inflammation contributes to many leading diseases where it can result in a disruption of cellular identity/function. These include, but are not limited to, cancer, neurodegenerative diseases, heart disease, diabetes, depression, aging, kidney disease, chronic lung disease and Alzheimer’s disease. If we could understand how chronic inflammation contributes to an increase in the incidence of one of these diseases, it might provide insights on its contribution to the other diseases as well. This course will identify fundamental strategies in how to enter and study a subject area that is new to you. In addition to learning a new subject area, it will also provide fundamentals in conveying your ideas and hypotheses to scientific colleagues.
The details of the first module class are as above. Since there are only nine sessions in total, an instructor went straight into a packed lecture from the very first class. To our surprise, we were also told that each of us has to present a paper journal club-style…🤦 Thankfully, I learned some basics in pharmacy school, but presenting to others is a whole different level. To make things even more intense, my presentation is already scheduled for next Wednesday, just a little over a week away. Still, I think there’s a lot to gain if I give it my all. I don’t have a clear idea yet how to apply this to my own research, but I believe if I take thorough notes, it’ll come in handy someday. In fact, it’s often those bits and pieces that unexpectedly connect and end up helping later.
The new lab I am rotating is actually right next to the one I rotated in before, so I had seen some of the lab members around. That made it less awkward to introduce myself and settle in. But when I tried to start an experiment, I realized my bench was completely empty, so I had to ask around and set everything up from scratch, which was a bit of a hassle. However, my previous lab was pretty crowded, so I couldn’t use my bench freely. In that sense, having my own space now is kind of nice. I set up a quick reaction and did the work-up. (From tomorrow, I’ll go back to writing in my usual “Outside of Work / Lab Work” style!) One big lesson from my last lab experience is that keeping detailed records of experiments from the very beginning helps reduce mistakes and makes the whole process more structured and efficient. Since we’re not using electronic lab notebooks this time, I made an Obsidian template to document everything and I’m loving it!
Oh, and interestingly, my first day happened to be the last day for a postdoc in the lab. We went out to Somisomi(1350 4th St, San Francisco, CA 94158) for taiyaki ice cream to celebrate! I got a recommendation and went with a matcha/ube swirl ice cream and taiyaki filled with Nutella—absolutely delicious. Funny enough, I’ve never actually had this kind of “아붕” back in Korea! The postdoc is a CCB alum who just wrapped up their postdoc and is heading off on a trip. Wishing them all the best on their next journey🙏
This quarter, I promised myself I wouldn’t procrastinate and would really manage each day ahead of time. So I plan to leave work by 6 PM if possible and spend the rest of my time productively at the Hub. But… I ended up leaving after 8 PM today. It’s fine because today is the first day!
Tuesday, April 1
167.2 lbs (Day 95, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6) | ★★★☆
Outside of Work
Wrapped up another solid workout today. Honestly, this might be the longest I’ve gone without taking a break in between. Feels great! In the morning, I had our QBC Journal Club class, and a friend I rotated with previously gave the presentation. It was so great! Even though it was a bioengineering paper, he explained the key points so clearly and made it easy to follow. It is not surprising, though; I remember from our previous rotation how sharp and logical his thinking was during discussions. Definitely someone I feel will go far!
In between experiments, I tried to draft a super rough version of a paper on a new project from my previous rotation lab and sent it off. It’s definitely more convenient to have every discussion so far in one document. It makes it much clearer what’s needed and what still needs to be done. I really hope it wraps up well. Juggling multiple things at once is mentally draining. It reminds me of when I was preparing to study abroad during my master’s. It’s never easy trying to do everything perfectly without dropping the ball on any front.
Lab Work
Chemistry
- SJ-1-1(the reaction I set up yesterday) purification
- Since I switched labs, I need to be granted access again to reserve NMR time. For now, I’ll have to ask my mentor to book it for me. Planning to check it tomorrow.
Wednesday, April 2
165.7 lbs (Day 96, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6) | ★★★★
Outside of Work
Another successful workout today! My schedule is a bit tight, though—Chronic Inflammation and Diseases runs from 10:00 AM to 12:00 PM on Mondays, Wednesdays, and Fridays, and on Wednesdays, we also have lab meetings from 12:00 to 2:00 PM. I was starving by the end of it all🫠 As expected, the class is pretty intense, and I’m really starting to feel the pressure with only one week left until my presentation. The instructor mentioned they’d suggest a paper for us to present, but I haven’t heard anything yet… Looks like I’ll need to dedicate my time through the weekend.
I got a reply to the draft I sent yesterday, so I quickly responded, and after work, I finally began diving into the additional tasks I need to tackle. In short, I’m trying to calculate the Pocket-Aligned RMSD between the ground truth structure and the model-predicted structure, but due to atom labeling and numbering issues, none of the methods I’ve tried are working properly. I’m currently wrestling with ChatGPT, Claude, and Gemini to figure it out…
Lab Work
I attended my first group meeting. The group is definitely smaller, and the PI’s style is different. He points out the fine details very thoroughly. Personally, I think it’s really helpful to have someone who can regularly help assess whether what I’m doing is the best approach and provide logical, reasonable feedback. That doesn’t necessarily mean it’s not demanding, but I wouldn’t say the two are always proportional either. Overall, I think it’s a pretty good setup. Plus, getting to see everyone’s weekly progress is actually quite useful. Starting next week, I’ll be presenting too!
While it’s not directly related to my project, I decided to help synthesize an intermediate needed for my mentor’s experiment. It might indirectly benefit my own work too. Since I don’t have full access to lab resources yet, my mentor had to find the reagents for me. Unfortunately, he was in a long discussion with the PI, so I couldn’t start the reaction today. I spent most of the time planning the procedure instead.
Chemistry
- SJ-1-1 NMR check
Thursday, April 3
166.2 lbs (Day 97, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (4/6) | ★★★★
Outside of Work
Another workout success today! I haven’t mentioned it lately, but there’s actually a seminar every Thursday at noon. As I’ve said before though, chembio is already such a broad field, and when the speaker’s research isn’t related to chembio, I usually skip it. Of course, there are benefits to attending various scientific presentations, but for me, it’s more important right now to conserve my energy and focus on what I immediately need to get done.
I left work before 7 PM and headed straight to Costco to grab my usual groceries. This time, I picked up a sandwich for a quick dinner, but… ugh, definitely not a good choice. So Disappointed. They also stopped selling my favorite cioppino meal kit ㅠㅠ so sad😢 Next time, I’ll take my time and find something tastier. Oh, and while I was shopping, I watched the impeachment ruling live (11:00 AM KST, April 4). It reminded me of when I was preparing for pharmacy school and we all watched a similar broadcast together in class. I really hope Korea moves forward in a direction that’s fair and reasonable, something everyone can agree makes sense.
Lab Work
Chemistry
- SJ-1-2 run, work-up
- Technically, this is a two-step one-pot transformation from methyl ester to alkyne. But since the initial DIBAL-H reaction doesn’t seem to be going very well, I’m planning to isolate the aldehyde first.
- SJ-1-3 run
- Judging by the reaction mixture’s consistency, I already have a bad feeling… There seems to be some conversion, but even after running it longer than the reference protocol, there’s still starting material left. So, I left it overnight.
Friday, April 4
166.6 lbs (Day 98, starting from 162.6 lbs on Dec 28) | 🏃🏻 Rest (4/6) | ★★★☆
Outside of Work
I ended up skipping my workout today since I fell asleep in the early morning after wrestling with ChatGPT for hours. ㄴSadly, without any major breakthrough😭 After attending my morning class, I focused heavily on experiments throughout the day. I also kept working on my side project whenever I had a spare moment… but I hit a wall. So, I reached out to a senior CCB PhD student from a computational lab for help. They generously made time for me, and we met up after lunch to discuss it—but unfortunately, we still couldn’t solve the problem.
It seems more complex than I initially thought. None of the main texts or supporting materials in the related papers provide a clear method for calculating the metric. Even a recent preprint that used the same metric didn’t specify how it was derived. Luckily, one of my Korean PhD friends apparently worked on a similar project during a previous rotation, so we’re planning to meet next week to discuss it. For now, I think I need to put this on pause because I’ll probably have to spend this weekend preparing for next week’s presentation anyway.
Lab Work
Chemistry
- SJ-1-2 purification
- There were four spots on the TLC, and spots 2, 3, and 4 were very close together. I did my best to separate them, but I got mixtures. Before doing a re-purification, I’m considering using a different method to obtain the aldeghyde, other than the current one-pot approach. Depending on how that turns out, I’ll further purify the fractions and try to identify the spots. The yield doesn’t look promising either, so switching methods might be the better move.
- SJ-1-3 work-up
- Even after running the reaction overnight, a significant amount of starting material remained. I added more NBS along with catalytic AIBN. The starting material is now gone, but both the filtrate and the sticky solid obtained after filtration looked extremely messy on TLC. Rather than continuing with this direct bromination, I’ve decided to try a different route starting from the alcohol instead.
Saturday, April 5
166.2 lbs (Day 99, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6) | ★★★☆
Had a great workout with a friend, followed by a deep clean of the entire place. I washed all the bedding and scrubbed every corner. Doing that really clears my mind.
Since I still haven’t heard back about the paper, I couldn’t wait and kept trying the computation stuff. I feel like I’ve now pushed it as far as I can go, and I’ve decided to give up on automating the process. Even with full support from GPT and Claude, it didn’t work at all, and that’s giving me a bit of a headache. I really hope the code my friend used during their previous rotation works for my case too.
If automation’s not an option, I can always manually reassign atom pairs and edit the PDB files one by one. Actually, there aren’t that many cases to calculate, so if I had just gone manual from the start, I probably would’ve been done already… But after putting in this much time and effort, I want to and have to figure it out.
In the evening, I finalized the paper for my journal club presentation. I tried to read it, but it’s dense, and being a physiology-heavy paper, I just couldn’t stay focused. Maybe it’s because I was reading it at home. I ended up just meal-prepping and going to bed early instead. I’ll hit it hard tomorrow!
