Relaxing Halloween🎃👻

Sunday, October 26

152.5 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (7/6)

I got my first DEXA result today. It was worse than I expected, to be honest 😨, but I accepted it and aim for a satisfying improvement by the end of my bulk. I asked GPT to estimate total skeletal muscle from ALM (appendicular lean mass: arms + legs), and it came out to ~32.7–38.1 kg. Taking the midpoint is roughly the muscle mass I had five years ago… (measured on an InBody though), but I do think I look better now. The two graphs above are from the VeSync app linked to the smart scale I’ve used over the last 70 days. I’ve seen a consistent decrease in body fat, but also in “muscle mass.” That loss isn’t all true muscle (some is glycogen and water), but after a maintenance phase I’ll check how much really comes back. In hindsight, I’ve never trained to failure “really”, and during my last bulk (especially after the second rotation) my diet wasn’t consistent at all, partially due to consistent coughing. On this second attempt, I’ll do my best and leave no regrets💪

After coming home, I grabbed breakfast and went for a run. I wanted to try 10K, but I was kind of KO’d.. after 8K. For me, at least 2–3 hours seem to be needed between eating and running or lifting. Then I went to the lab, set up another reaction, and studied. It’s great that we can order custom peptides even if they’re expensive. I’ve realized the power of a well-funded lab, but I’ll make sure not to waste money; just use it as leverage for my research.

At night I cleaned the house and worked on a progress report before next week’s 4th joint meeting. I think Bill can’t make it this time, so I’m not sure if we’ll still meet on Zoom. Hopefully I can get feedback on this past month’s work.

Monday, October 27

151.8 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (1/6)

I don’t always say I went to the gym in the morning. Just assume that’s the default now😅 I’m training five to six days a week, so it’s easier to mention the day I missed. Anyway, a fresh workout to start the day, followed by an extensive workday. I bounced between the two labs, ran, purified, and characterized two compounds, and joined a DeGrado lab subgroup meeting. It was my first official (small) presentation of my thesis work to the group, so I got a lot of feedback and great practice. It really helped me firm up my approach and ideas.

For the substrate synthesis of the de novo enzyme, I would say things are on track; I expect to complete the remaining steps by mid-November. I’m loving the current setup: no need to stare at every fraction, and LC-MS makes tracking progress easy, especially when UV/TLC are not that informative. Even though I worked into the night, it didn’t feel draining at all, probably due to the relaxing work environment, or maybe it’s just the beautiful weather here that makes me genuinely happy every day🙂

Tuesday, October 28

152.1 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (2/6)

Today was pretty much the same as yesterday, except I attended journal club and went for a run after work. One thing I’d like to mention is that I’m finally going to sort my transformed yeast soon! Fingers crossed for the results I’m hoping for.

Wednesday, October 29

151.8 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (3/6)

Busy Wednesday with two failures. First, I obtained significantly less product from a certain reaction than expected, and it wasn’t pure (I need to backup the starting material). Second, during FACS on our yeast, we ran into a serious setup issue. Fortunately, I figured out the cause: massive innate spillover between the FITC and PE channels, so we’ll rerun it tomorrow. Otherwise, I attended the Shokat lab group meeting and successfully synthesized another molecule (very satisfying TLC!). It was a decent day. By the way, the first photo is of pumpkins carved in a funny way outside my housing. Halloween is almost here 😛. I don’t have specific plans this time; I chose to study at the library instead of going to the pumpkin festival with my cohort (at the same place as last year). But I’ll definitely attend Friendsgiving with my cohort this year.

Thursday, October 30

152.9 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (4/6)

Today we reran FACS and the troubleshooting I planned worked🎉 The results weren’t as satisfying as I’d hoped, but we were able to sort a few populations of interest. We’ll regrow them, induce, and run flow again to confirm those populations are not artifacts. I spent most of the afternoon digging into how to optimize induction conditions and sorting parameters. I was suddenly reminded that I’d used FACS before on T cells during a brief internship in Korea. I’m still in touch with the professor who mentored me there (basically, he is my best mentor). I never imagined I’d be using this machine again (especially during my master’s), but now it has become one of the most important techniques I need to master for my thesis. You never know where life will take you😅 For the first time in a while, I left a bit early, went for a run, and slept well.

Friday, October 31

153.5 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (5/6)

This morning at the gym I spotted a cute skeleton propped in a seated pose holding a dumbbell. Literally, Halloween decorations are everywhere😳 I didn’t get much tangible work done today. I studied protein preparation, especially cloning (Gibson vs. In-Fusion, overhang design) and expression topics, such as auto-induction. The overhang design didn’t align with my intuition, so I struggled with it for a long time. I still don’t feel I understand this seemingly simple part clearly; maybe my pride got in the way and I spent too much time on it. I prefer to dig in and understand enough before asking, but some pieces still aren’t obvious for me, so I should probably ask for help. Aside from my favorite morning class, I didn’t run experiments, and after work I went for a run. Since it’s Halloween, lots of people were in costume (even some classmates dressed up). I still don’t really get the whole Halloween vibe, and since I barely drink I don’t go to bars, so I ended the day with a quiet, weekday-like Halloween.

Saturday, November 1

153.2 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (6/6)

Weekend!… but I still went to the lab because next week (Monday and Tuesday) I’ll be at my second QBC retreat and won’t be able to look after the cells. The sorted cells grew much faster than we expected, so given next week’s schedule I stored them in the cold room for now and will restart the SD culture after the retreat.

While I was at the lab, and since I expect the entire YSD protocol (except the sequencing part) to wrap up next week, I revisited the in-silico pipeline I had built. Surprisingly, I’d forgotten a lot😨 but after a few hours, I was back up to speed and even found a promising improvement. I went back and forth between home and the lab and ended up spending about a weekday’s worth of time, but it didn’t feel demanding at all. Doing a different kind of research for the first time in a while is always engaging. After work, I went for a run: just a quick 5K on the treadmill (turns out the Megablast works really well indoors too, not just outside). Then I did some cleaning and got a good rest.