January Gone Already😐
Table of Contents
Sunday, January 26
163.5 lbs (Day 30, starting from 162.6 lbs on Dec 28) | 🏃🏻 Missed (5/6)
A peaceful and warm Sunday☀️ My friend and I went to a local brunch place(Cracked & Battered, 1434 18th St, San Francisco, CA 94107). To be honest, we originally planned to go to a different place, but we kind of decided on this one because at the previous place, we would have had to wait for an hour. So, we promised to go there next time. The food was delicious, especially the waffle and chicken combination—it was so good! I think the wonderful weather might have contributed to this nice experience.
After that, I headed straight to the Hub and finished my reaction mechanism assignment. On top of that, I worked on writing a blog post (which was so difficult to make up for because I had postponed it a lot this week… 😭). After getting back home, I cut my hair. This time, I tried the shortest length I’ve ever had. Usually, I like to push down the top part to make it flat while lifting up the front to style it, but the top part is too short, making it difficult to flatten my hair even with a hairdryer. Now, I’m considering trying a different style😇 I feel like this length (1 and a half inches on top) is too short for me. I spent over two hours trying to find a solution, but I couldn’t find it. In the end, I just did some meal prep and went to bed.
Monday, January 27
161.6 lbs (Day 31, starting from 162.6 lbs on Dec 28) | 🏃🏻 Rest (0/6)
Outside of Work
This morning, I went to UCSF Bayfront Primary Care, where I’d been before, and had a great experience. I asked many questions about my insurance coverage, including the benefit of Gardasil, the well-known HPV vaccine. Typically, Gardasil is recommended for people under 26, based on sexual activity considerations, but those aged 26 to 45 can still benefit. Because my student insurance covers it fully, I decided to get vaccinated. I’ll have to return for the second and third doses two and six months from now, respectively. Oh, and I also got a tetanus shot for free.
I also asked about getting a body composition test—something to measure body fat and muscle. The clinic only has a DEXA scan, which is accurate and quite expensive, and I don’t really need that level of detail. Instead, I’ll probably just use a simple, free measurement tool at the gym. Lastly, I asked about arranging dental and vision appointments. The doctor said he would send me a message through the MyChart app to set those up. I also mentioned some shoulder discomfort I’ve had for six months, especially when doing overhead presses. The discomfort is in the back of my left shoulder blade. Although it’s been improving, I still want to see a physical therapist (PT). The doctor said he would help arrange an appointment.
Later in the day, I attended my reaction mechanisms class. This session was taught by one of my seniors from college in Korea. He was very enthusiastic and had prepared excellent materials, so everyone in our cohort enjoyed it. I was proud of him for doing such a great job teaching. I finished work around 6 p.m., went home, took a shower, ate dinner, did some laundry, and took care of other chores. I also worked on my blog again. I wasn’t able to finish my latest post last week, but I’m planning to publish it by tomorrow.
Also, as I mentioned yesterday, I don’t like my current hairstyle, so I decided to trim the top part of my hair with scissors to create a flat look. However, things turned out very unexpectedly to be a disaster. Haa… The top is now so short that my scalp is visible. Consequently, I had no choice but to buy hats from Amazon immediately😭 I might have to wear a hat all day for two or more weeks.
BUT Good news! When I checked my mailbox, I found a letter from the Social Security Office. I was thrilled to see that I finally received my Social Security Number (SSN). I tried to register for online payments on the PG&E website using my new SSN, but I ran into an error linking my existing payment account to the new number. I’ll contact their service center to resolve that. I also plan to let my program manager know that I now have my SSN so I won’t need any additional emergency loans. I can repay any existing loans once I receive my stipend😄
Lab Work
I missed part of the lab meeting because my primary care appointment was at 10 a.m., which was the same time the meeting started. I arrived around 11:15 a.m. and caught the remainder of the session. Our MD-PhD student presented her research in detail. The discussion was very active, with lots of exchanging ideas, and it felt like a really productive meeting.
After class, I checked four NMR samples, including two from a recent reaction I completed (I plan to confirm the results via LC-MS later). Regarding protein expression, I transformed a plasmid (generated previously by site-directed mutagenesis) into competent bacterial cells and incubated them overnight at 37°C. On Wednesday, I’ll move on to induce protein expression with IPTG. By Thursday or Friday, I expect to start purifying the protein of interest.
Tuesday, January 28
162.8 lbs (Day 32, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6)
Outside of Work
I started my day feeling fresh by going to the gym around 6:30 a.m. Unfortunately, I sprained my neck(again….) while doing a shrug for my upper trapezius. I often sprain the left side of my neck, so I asked the doctor yesterday why it keeps happening. I don’t have a clear answer yet, but I’m sure that topical pain relievers, such as 30% salicylic acid or diclofenac gel, can help ease the pain. I used to avoid medications, but nowadays I think using the right type and amount of medication is beneficial, especially topical ones given that they usually have fewer systemic side effects. After the injury, I wrapped up my workout quickly and switched to cardio instead of weightlifting.
Later in the morning, I grabbed coffee and spoke with a current graduate student about the lab atmosphere, the ongoing research, and my own situation. I hope to join their lab, to be honest, but my program’s current policy is somewhat problematic now. I’ll need to speak with my program director to see if there’s a possibility of an exception. One of the things I really appreciate about this lab is the people. They’re very kind, and whenever I see them, they always say hello first. That welcoming environment makes me feel better, even when I’m preoccupied with my projects or personal issues.
Right after the conversation, I went to a QBC journal club. The first presenter was a member of my cohort, and the presentation was excellent. I understood over 80% of the concepts, which involved a serendipitous discovery of a molecule group targeting an unusual E3 ligase. This compound induces the degradation of a nuclear pore protein, which could potentially be a strategy to block certain proteins from leaving or entering the nucleus.
After the journal club, I grabbed lunch on campus in the Genetics Hall, where there were focaccia provided by seminar organizers. The seminar following the journal club was about the ribosome, which interested me since my current rotation project involves eukaryotic translation initiation factors (eIF4E). It ties directly into ribosome function, so I really enjoyed that seminar.
+ I finally created an online account for my PG&E (gas and electricity) bills after calling the service center. After a 30-minute wait, I spoke with a representative who informed me that I didn’t need my Social Security number to set up the account. I had tried enrolling online before, but I failed because there was a blank field asking for my SSN. That made me think that the absence of an SSN was the problem. But my phone number alone was sufficient! All I had to do was make a call. Anyway, I’m relieved to have set up the account because paying by phone has been both costly (an extra $1 or $2 per transaction) and time-consuming.
Lab Work
The first thing I did was analyze the NMR data of some compounds I synthesized. Some of the proton peaks were unusual, but both my mentor and I agreed that they matched the expected compound overall. After reviewing the data, I set up the same reaction again but used starting material with different stereochemistry. I had previously used the (S)-form; today, I used the (R)-form. I also ran another reaction with a different substrate and coupling partner. Then I checked the reactions by LC-MS, and I ended up purifying two out of the three. As I mentioned, they were essentially the same reactions but with different stereochemistry. Once they were purified, I set all four compounds aside for overnight lyophilization.
Yesterday, I transformed a plasmid containing the eIF4E truncated mutant into competent bacteria. The cells grew overnight, so I checked the colonies, and they looked good. Before heading home, I inoculated a colony into 75 mL of LB medium with 0.1% of a carb antibiotic (to maintain selection). I left it shaking overnight at 37 °C in the incubator(mini culture).
Wednesday, January 29
163.2 lbs (Day 33, starting from 162.6 lbs on Dec 28) | 🏃🏻 Missed (1/6)
Outside of Work
I wasn’t feeling well, especially with my left neck, so I decided not to go to the gym today. Afternoon, I took my usual reaction mechanism class. It was great again. We built a reaction model of a typical Diels-Alder reaction using sticks and clay😆 The class was also very informative, just like Monday’s class. I hope future lectures by other professors will be just as good.
At 3 p.m., I went to a lab meeting. A second-year CCB senior student presented his work, and it was amazing. He answered all the questions from the other members with solid evidence from the literature. I can’t believe the difference between him and me is only one year haha. I was so impressed that after the lab meeting, I spontaneously complimented him on his preparedness and presentation skills. Thanks to his presentation, I was motivated once again to do my best, and I look forward to getting my own research project soon, to which I will dedicate myself with a happy mind.
Lab Work
In the morning, I purified the reaction that I had set up yesterday and then lyophilized it. Before the lab meeting, I transferred the mini culture I made yesterday into larger culture containers (10 mL of culture for each of two 1 L TB containers containing 0.1% carbenicillin antibiotic). I checked the OD of these samples using a Nanodrop. When we observed that the OD had reached approximately 0.6, we moved them temporarily to the cold room and added solid IPTG (50mg for a liter) to induce the desired protein. We then incubated the cultures overnight at 18°C in a shaker. It is interesting and beneficial to compare the similar, yet somewhat different, methods used to obtain protein in both my current and previous labs. I hope to use this experience to develop a more optimal protocol soon.
Thursday, January 30
163.2 lbs (Day 34, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6)
Outside of Work
I went to the gym today, but I didn’t push myself too hard because of my neck pain. I did a full-body workout using lighter weights and added some cardio. I believe that doing something is better than doing nothing, and even a light workout definitely improves my mood compared to going long periods without exercising.
Today, the BBC Journal Club focused on chemical biology, so I attended the session. The lecture, titled “Altering the H3 Methylation Landscape through Degradation of Methyl-Lysine Reader Proteins,” was given by Lindsey Ingerman James from UNC Chapel Hill. It was very well-structured and explained the general concepts so clearly that I believe even people outside of CCB could understand it. I also found it interesting that a lot of medicinal chemistry work can be done in academia. Perhaps because the lecturer is from the pharmacy department rather than a typical chemistry department.
I wasn’t feeling very well, so after the seminar I quickly had lunch with leftovers from yesterday’s lab meeting, then went home and took a short, one-hour nap. I’ve noticed that when I feel this way during work hours, it’s a clear sign that my body needs some rest. If I ignore these signals and keep pushing myself, I’ll likely end up with a cold or body aches. So, whenever possible, I try to relax when I feel this way.
Lab Work
I checked the cultures and centrifuged them to obtain the pellet. I transferred the pellet to a 50 mL Falcon tube, froze it using liquid nitrogen, and stored it in a -80°C freezer since we have a three-step purification process for our protein. We will continue the purification on Monday.
I also ran a reaction, purified the product, and examined the NMR spectra of two compounds. Strangely, one of them displayed a spectrum that differed from the expected (S)-form, even though we didn’t introduce any external chiral environment. I plan to check the remaining compounds tomorrow and then discuss this discrepancy with my mentor. Additionally, when I examined the lyophilized samples, I became uncertain about the compound concentration. I had recovered the final compounds from the NMR sample (which was in DMSO) by performing a single round of lyophilization, using 3 mL each of ACN and water as additives before freezing. Today, I suspected that this method might have removed all the residual DMSO, given the unusually sticky consistency of some final compounds (normally a fluffy white solid).
I asked one of my colleagues how he handled this issue when he worked at a pharmaceutical company. He mentioned that using an overnight flow of gas (either air or an inert gas) through the sample can help remove as much residual DMSO as possible. After that, you can add ethyl acetate and diethyl ether before lyophilizing again. I hadn’t considered that approach before, but it seemed reasonable. Unfortunately, using an overnight inert gas flow is challenging in our lab due to an issue with my bench, and using air isn’t ideal either because I believe my compound is unstable (it contains a cysteine-reactive warhead). I searched for various lyophilization methods but couldn’t decide which one would be best. I plan to discuss this with my mentor and the other postdocs in the lab tomorrow.
Finally, my mentor and I finalized the list of warheads. I realized that I still have many warheads to synthesize🫠 We ordered some reagents and even found a few additional warheads already in the lab. I will begin synthesizing them next week. I also created a “warheads table” on PowerPoint, which looks nice. I hope I can complete the synthesis of all these warheads and that at least one of them will successfully label our mutant protein by the end of the rotation!
Friday, January 31
162.8 lbs (Day 35, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6)
Outside of Work
It’s a rainy☔️ morning, though I definitely prefer sunny days since rainy weather makes it difficult to get to the gym. Despite human’s(?) natural inclination to stay in bed early in the morning, I managed to head to the gym at 7:00 and did some cardio because my neck still felt a bit strained. I then attended my usual two classes on Friday. Between classes, I grabbed a sandwich from Subway with my cohort. We chatted about our rotations and our interview experiences(hard to believe it’s already been about a year ) as we noticed the in-person interviews were starting in the lobby. After work, nothing particularly happened. I’m not sure if it was due to my neck strain, but I’ve felt especially tired this week; perhaps that’s why I ended up dozing off as soon as I got home for three days in a row.
Lab Work
Today, I checked two NMR spectra. Unlike previous instances where the (S)- and (R)- forms showed noticeable differences, today’s data were unusual(just the same; actually, it is common). My mentor and I reviewed every possibility including rechecking earlier NMR, LC-MS results, and our synthetic procedure. We concluded that although the HATU reaction is generally reliable and the overnight reaction is a dependable option, the unique hydroxy group on benzoxazole can trigger an intramolecular side reaction. This side reaction could produce a compound that has the exact same mass as the desired product but exhibits a slightly different NMR pattern. Although we were unable to identify the side product, we agreed that attempting to quench the reaction within an hour might be worth trying.
In addition, I assisted with some lab cleaning and investigated the best approach for lyophilizing DMSO. I considered two methods:
- Method 1: Using DMSO mixed with water (or water/ACN if solubility in water is an issue). For example, a solution of about 10% DMSO in water.
- Method 2: Using pure DMSO without any additives.
After discussing with my mentor and a postdoc, they recommended the second option(pure DMSO). Their reasoning was that adding water decreases the melting point of the solution, which can hinder its removal by sublimation. I understand that a lower melting point can be problematic. However, I found in the literature that many researchers (myself included) have used the first method. The rationale behind adding water is that, during freeze-drying, vapor pressure is also crucial. Since DMSO has a much lower vapor pressure than water, it is difficult to remove on its own. Adding water can increase the overall vapor pressure of the solution and potentially speed up the process.
Since there isn’t a widely accepted analysis on this matter, I decided to test both methods. I used exactly 0.5 mL of DMSO for both the (S)- and (R)- compounds, adding water to only one of them. I will determine the amount of DMSO removed by comparing the sample’s weight before dissolving it in DMSO and after retrieval post-lyophilization, and I plan to compare the efficiency of the two methods on Monday!
Saturday, February 1
162.5 lbs (Day 36, starting from 162.6 lbs on Dec 28) | 🏃🏻 Done (4/6)
I woke up around 8 AM and quickly had breakfast. In preparation for the reaction mechanism study group, I worked on some problems on an assignment. At 10 AM, I headed to the study group. When I arrived, only one of my friends was there. It turns out that the rest of the group had been hanging around until late last night. I didn’t attend the party because I wasn’t feeling well and needed some rest. Although I really like my cohort🥹 and enjoy hanging out with them, these days I feel like I need some time for myself.
Shortly after, three more friends arrived, and we had an in-depth discussion. I felt that my explanation of the concepts wasn’t as clear or well-structured as it could have been. I believe this wasn’t just a language issue but also a lack of experience in answering the many possible questions about the principles I’ve learned. It seems obvious that I can become more familiar with these concepts by continually thinking about, organizing, and reviewing the material.
After finishing the assignment, which is due next Monday, I headed straight to the gym. There, I ran into my Korean friend whom I’ve mentioned before(he’s pursuing his PhD in bioengineering, and we occasionally work out together 💪). We exercised and then had a late lunch at a local spot near campus. I’m pretty sure that the ahi taco is one of the top five American dishes I’ve ever tasted.
During lunch, he offered some advice about my rotation situation. Although things weren’t going exactly as I had hoped, he told me that the situation wasn’t that bad at all. He reassured me that the third rotation would be a good experience, especially since I had already completed my master’s in Korea—relatively a hierarchical environment where expressing one’s opinions was quite challenging. I agreed with him and started feeling more positive about my future. I know, In the end, the most important thing is to follow my passion and demonstrate my diligence, enthusiasm, and ability, rather than constantly searching for an external solution.
When I got back home and was taking a shower, the head attachment on the shower hose broke🫤 But I managed to adjust the hole where the water was coming out, so the water flow wasn’t as bad as I had expected when it first broke. I submitted a maintenance request to get it fixed(thanks always). Despite the unexpected event, I still rested well and even managed to finish next week’s assignment. Whenever I study organic chemistry, time just flies by, and I don’t have to put in extra effort to stay focused. I wish that all my work would feel as engaging and effortless as this. In that world, I wouldn’t have to struggle every day to get things done. I’d simply be following my interests. What a dream!
