Happy Birthday🥳

Sunday, October 19

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

Usual Sunday: morning workout (first time in a while doing “Stairway to Heaven”), meal prep, writing a blog, and a good rest. It’s already the end of week 9 of my cut. I feel great, but I’m eager to finish the cut and start bulking. Considering my current body weight, wrapping up next week (about 10 weeks total) seems reasonable. So I booked a DEXA scan for next Sunday to check body composition. I considered skipping it, but my $20 body-comp scale isn’t very reliable; you can track trends, but with electrodes only on the bottom so the upper body is theoretically hard to measure. This will be my first DEXA to set an exact starting point. It’s not perfect either, but I will do it at the end of the bulk. I’m not sure when that will be, since this time I will gain at a very conservative pace, about 0.5% of body weight per month. Looking forward to the results!

Monday, October 20

155.1 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (1/6)

Today we had a Shokat Lab group meeting where one of my CCB cohort mates (also a second-year) presented. She did a nice job. She began with a chalk talk, followed by some data on slides. Usually two to three people present at a meeting, but this time it was just one. I’m increasingly aware that my turn is coming up😳 I’ll make the talk as easy to follow as possible, since my current direction is quite different from most lab members. I also need to revise my thesis proposal… lots to do!

In the afternoon I organized all the notes I took last week while shadowing a postdoc on yeast surface display prep. He had shared a YSD summary document, so I edited and improved it with what I actually observed. He will be leaving in a few months, and then I’ll be the only one in the lab who can run this experiment, so I’m making sure I understand every aspect of it.

After organizing my notes, I ran a PCR, but no band showed up!? Even stranger, the DNA ladder didn’t appear either. I didn’t know why at the time (I figured it out later). I got off work around 6:30 and went for a run to clear my mind. I’m trying to run as often as I can, but when I’m stressed it’s hard, even though I know I always feel better afterward. Thinking about it, preventing excessive stress in every part of my life seems to really matter.

Tuesday, October 21

155.1 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (2/6)

Just kept going experiment toward yeast surface display. Today I set up a yeast miniculture and digested the vector, followed by an EtOH precipitation. On Thu we’ll do the transformation by electroporation. It will be a long day!

After work, I went for a run (I’m trying to run at least three times a week). Chinatown isn’t far from campus, and I was tempted to get a warm soup because of a bit chilly outside; maybe I used the run as an excuse to eat😛 I went to Hon’s Wun-Tun House (733 Washington St, San Francisco, CA 94108). To be honest, there was a very loud group that made me a little uncomfortable. The wontons and soup were decent, but the bathroom wasn’t good, so I don’t think I’ll go back (maybe try different food at lunch?). To be honest, there are plenty of other options to try in Chinatown.

Wednesday, October 22

154.9 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (3/6)

Today we had a DeGrado Lab group meeting. It was great to hear a completely different angle on protein design, but I had to head out in the middle of the meeting for flow-cytometry training. The UCSF Flow Core, which manages and runs the flow cytometers and their applications, led the session. The instructor was friendly and very knowledgeable, and I learned a lot about the instrument. The training was ~$240/hour, which seemed expensive (even though the lab pays), but it was definitely worth it. Tomorrow is FACS (fluorescence-activated cell sorting) training, which is one of the main applications of flow cytometry that lets you sort cells based on user-defined parameters. I’m looking forward to it!

After that, I checked the OD of the miniculture and inoculated fresh cells into a new 200 mL culture for electroporation. I also stored the EtOH-precipitated vector in the cold room and got off work a bit early. In the evening I had a reservation at Via Aurelia (300 Toni Stone Xing Suite A, San Francisco, CA 94158) for a birthday. We truly enjoyed the warm, kind atmosphere and the delicious food. I highly recommend it for an anniversary or any special occasion, and they’re open past 10 pm, which is convenient. Food Rec.: PICI ALL’AGLIONE (hand-formed long noodles with “overcooked” heirloom tomato, garlic, and pangrattato). We expected a simple tomato pasta, but the server highly recommended it and it turned out to be a banger👍 Should try it!

Thursday, October 23

155.7 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (4/6)

Today I had another flow-cytometry training, this time focused on FACS. Thanks to yesterday’s general session, I could pick up almost all aspects of sorting (basically the same concepts, just a sorting step added). Since we’re working with yeast, we need extra wash steps, which adds a bit of complexity but nothing major.

In the afternoon I ran a gel again with help from a graduate student. He recommended using more DNA stain (CyberSafe), and it worked! It turned out that the amount I used was only about 40% of the vendor’s recommendation. Lesson learned: even when I’m learning from someone experienced, I still ㅗ double-check the vendor manuals and choose whichever settings are better between the lab protocol and the defaults. Because the yeast culture OD was much lower than expected, a postdoc and I started the electroporation transformation at 6:30 pm. We finished around 10:30😵 Long day, but I’m excited to see transformants soon!

Friday, October 24

154.6 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (5/6)

Today was the last weekday of my cut. I’m slightly short of my goal, so I decided to skip carbs today. In the past I’ve gone two or three days without carbs with no issues, probably because I don’t have a metabolic condition like diabetes.

Recently I picked up another side project from a postdoc who mentored me during my DeGrado rotation: synthesizing substrates for a de novo enzyme he designed to catalyze a specific reaction. He’s wrapping up his manuscript and asked for help a few days ago. I agreed because he’s helped me a lot, and it’s a good way to use my organic chemistry skills. I ran the first reaction this morning.

After that, I took a RIPS class, then watched the skit we filmed for the upcoming QBC retreat with a few cohort mates. Seeing everyone act was hilarious😆 Our main director (also a cohort mate) edited all the scenes, and the result was way better than I expected (she is so talented!) I’m excited to see it at the retreat. After the watch party, we had lunch together.

In the afternoon, I checked the OD of the yeast cultures (transformants plus a negative control), and it was reassuring to see the transformant culture much higher than the control, suggesting the transformation worked. After taking the number of cells needed to cover all of the library diversity with 95% confidence, we induced the transformants. Next week, we’ll check induction and do FACS.

To wrap up the day I checked the reaction I set up this morning; it didn’t look good… I should have used a different base given the characteristic of nucleophile, which is different from phenoxide. Multiple spots on TLC were frustrating for what I thought was a straightforward transformation. I’ll find a more relevant reference and try again.

Saturday, October 25

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

I hit the milestone I set when I started this cut🙂 165.5 lb on Aug 19 to 153.0 lb on Oct 25 (about 5.7 kg down). Excited to see the DEXA results tomorrow, and I will share a summary of my 10-week cut next week. I went back to my original PPL split twice per week, so I got in a second leg day this week. Since I’m keeping total leg volume similar to my previous split, I don’t feel much pressure from having two leg days. Maybe I’m just not strong enough yet to feel big fatigue😅 We’ll see if the higher frequency makes my legs stronger.

After my workout I stopped by both labs. I checked the chemical reaction I set up last night, and again, it didn’t look great😨 (I found another route. Don’t worry). In the other lab I took out the induced yeast and stored it at 4 ^oC. Next week will be busy. I took a quick shower and had brunch, headed to my favorite library and almost finished a blog post, then went home and did meal prep (about a 30% calorie increase to find maintenance) for the bulking phase. Afterward, I went to Costco, did a quick run, had dinner, got some work done, and slept well! A productive Saturday.