My PhD Journey in the U.S.

CCB 1st year Flask Talk

Sunday, June 1

168.2.0 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6) | ★★★★

A morning workout with a friend, then spent the rest of the day at Hub, writing my blog and preparing for my presentation (flash talk and exit talk). It was a calm and productive Sunday. I’m excited that after these two presentations, my first year will finally be done! I’m also starting to plan a vacation with my family and friends in Korea. Three weeks is enough time, though not a lot, to see everyone I know… At the very least, I’ll make sure to meet up with friends who have stayed in touch since I arrived here.

Fortunately, my cough has been getting better, although my sore throat hasn’t improved much. I’ll keep taking NSAIDs but stop using the cough suppressant. Hopefully, I’ll be fine after tomorrow’s doctor’s visit🤣

Monday, June 2

🏃🏻 Done (1/6) | ★★★★☆

Outside of Work

After finishing my morning workout, and with classes ending last week, I was able to focus solely on experiments and preparing slides. A little after 3:30, I went to my scheduled doctor’s appointment, and as expected it didn’t appear to be anything serious😌 just a lingering cough after a viral cold. Just in case, I was prescribed azithromycin; if my condition doesn’t improve or gets worse after a week, the doctor recommends taking the full five-day course. He was very thorough and answered all my questions, which put my mind at ease. It’s great to be able to see a physician for over 30 minutes, and the out-of-pocket cost for the medicine is almost nothing, thanks to insurance!

At home I rested a bit and worked on my slides again. Because this is a short Flash Talk, I’m still unsure how much background I should include. The program recommends just one slide, but it’s hard to convey the full meaning of the project like why we want to do it and why it’s interesting on a single slide. My style tends to favor detailed explanations of the logic, even if it’s sometimes too much, so I’m learning how to make the slides as compact as possible. I’m also a little worried because today I heard that the mass spectrometer I’m supposed to use is malfunctioning. I might not be able to get the proteomics raw data by the day of the presentation (this Friday). Although I have plenty to present already (synthesis, in-gel fluorescence), I’m a bit concerned because the ultimate goal is to obtain the proteomics data.

Lab Work

[Biology]

Chemoproteomics: TMT labeling, beads combination and cleavage DADPS linker, desalting

Tuesday, June 3

169.0 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6) | ★★★★

Outside of Work

Finally finished sample preparation for proteomics. It’s unbelievable how tiny the sample is. It is almost invisible! Unfortunately, the mass spectrometer is still down. The prep took almost a week, and there’s no way to check whether the peptides stayed intact at each step, with so many chances for loss. So I’m still unsure whether my peptides are intact, haha. We could monitor at a few points, but my mentor rarely does because of time constraints. It definitely takes time to get used to this prep.

In the afternoon I went to a coffee shop with the only other graduate student in the lab, and we chatted about the lab’s pros and cons. I asked many questions about lab size and other concerns, which helped me a lot. He advised me to think carefully and choose the option that benefits me most. I appreciate him taking the time.

After our chat, I read a bunch of chemoproteomics papers to prepare my exit talk and realized there are many different workflows, each with distinct pros and cons. My goal is to summarize as many as possible and highlight our strengths compared to others, especially the Cravatt Lab. I can’t imagine how long it would take to publish a complete review paper! After getting home I did meal prep, kept reading, and worked on slides. This will take longer than a few days.

Lab Work

[Biology]

Chemoproteomics: SpeedVac (got the modified peptide sample ready to go🥳)

Wednesday, June 4

167.6 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Missed (2/6) | ★★★★☆

My cough sometimes feels better, but today it got worse again🤨 I don’t want to take antibiotics, but I’ll consider them if I still feel bad over the weekend. I skipped my workout and spent the day reading and preparing my presentation. I met with the professor who may co-advise me alongside the professor whose lab I rotated in last fall, and the meeting went very well. He agreed, like the first professor, that our proposed thesis would be both promising and challenging, and we decided to move forward with joint mentorship, with the option for me to pivot to a small-molecule project later on.

I’m sad that I can’t pursue the project my current rotation PI suggested, but I’ve learned a great deal here about how to approach science, and it has been a valuable experience. I’m a bit anxious about how to deliver the news, yet all that remains is to do my best so I won’t regret the path I’ve chosen. Two leaders in the field have placed their trust in me by agreeing to this unprecedented joint mentorship, so I will work hard not to disappoint them!

Thursday, June 5

166.8 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6) | ★★★★

Outside of Work

Finally, the mass spectrometer is back, so I was able to run my sample. Hopefully I’ll see promising results tomorrow. Anyway I decided not to include this data in tomorrow’s presentation because of time constraints, so no worry. I kept practicing my Flash Talk, left work around 6 p.m., and headed to the gym for leg day😨 At night, people in the gym usually look in better shape; one person had delts so huge I couldn’t believe they were natural… like a pro bodybuilder. It was great motivation to push harder, and I had a great session.

After dinner, I kept practicing my presentation. It will be my first time presenting in front of all the professors, seniors, and my cohort, which is quite intimidating. I hope it goes well. I’m also curious about how my friends’ rotations are going. So looking forward to tomorrow!

Lab Work

[Biology] → I just realized that it’s odd to call it simply “biology,” but anyway…

Chemoproteomics: ran my sample (MS2, MS3; RTS. each in duplicate, overnight)

Friday, June 6

🏃🏻 Done (4/6) | ★★★★☆

Outside of Work

The presentation went smoothly, exactly within the time limit! I even got a question about the synthesis, the part I’m most confident in, so I was able to answer well. A year from now, I’ll give a longer version for my thesis project, so we’ll see how that goes. After our Flash Talk, I had lunch with my cohort and caught up; many of them have already finished their exit talks, and I was envious🥲

I then went to the lab and checked the proteomics results. I’ll need to dive deeper to judge whether the data are good, but the run itself was successful and can be analyzed further. My mentor gave me a brief overview of how to analyze the raw data. It is obvious that mastering proteomics analysis could take an entire PhD by itself! Later, the whole lab went to the Helen Diller Cancer Center to attend a seminar by Arvin Dar (MSKCC).

It was a great talk. These days, every chemical biology seminar seems to touch on molecular glues. My ultimate goal (just for now) is to develop a general method to make plausible molecular glues for any given protein pair, but that principle seems extremely difficult to pin down for sure. Most examples have been discovered serendipitously and only for a few proteins. Hopefully, someday I can tackle this problem at the frontier of knowledge.

After coming home, I rested, went to the gym, had dinner, relaxed watching 깡촌캉스 videos, and went to bed early. Tomorrow my cohort and I are going to the OG Pancake Place, and I’m really looking forward to it.

Lab Work

[Biology]

Chemoproteomics: analysis of the proteomics data

Saturday, June 7

168.2 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (5/6) | ★★★★★

After a quick morning workout, I headed to Millbrae Pancake House (1301 El Camino Real, Millbrae, CA 94030) with my cohort. A friend recommended it, and…wow👍 ambiance, taste, price, portions, and service were all outstanding. Parking was a bit tough and the line was long (thankfully my friend signed us in early), but everything else was near perfect. Even the “side” dishes came out as large as main courses! People say this place is classic American dining, and I totally agree. I love the place. I’d honestly recommend anything on the menu, but the hash browns, which have a crispy outside and a fluffy inside, were incredible. We filled two tables with food, took a photo to celebrate the end of the quarter, and headed home. It’s strange to realize almost a whole year has flown by.

After a short rest, I met a friend at a nearby café, intending to study, but we ended up deep in research talk. Lately, I find other people’s projects fascinating. Probably this is because I’m constantly convincing myself why my own work matters, and naturally, I’m curious how others frame their questions and solve them. I don’t always grasp every detail, but it’s still fun. Later, I lay down in the field near my place for the first time, listening to music and staring at the sky while a cool breeze blew over me. It was the most vivid feeling of “leisure” I’ve had in ages. A perfectly restful day.