05 Jul Eleanor Rosen, Briney Lab Scripps Research – week 2

Sunday, June 28,

Sunday started with a slow morning where, after we all got up, I made pancakes and bacon for everyone, and then we all sat down to work on our Pinterest blogs. Around noon, Zoe, Jennie, and I went to the Hillcrest farmers market, where we unashamedly spent a lot of money on food; our excuse is that we were trying new foods that are hard to find back home. After that, we went toTarget, and Trader Joe’s to pick up some essentials for the week. After coming home, we relaxed until the others came home from the beach. During dinner, Kaila and I got into a little bit of a water balloon fight (Jennie started it), which ended with us drenching each other with the hose and being locked out of the house till we dried off. It was really funny, to say the least. We all went to bed early to prepare for the week ahead.

   Boba that Zoe and I got at the farmers market

Monday, June 29

We started the morning in the lab by looking at the sequenced DNA we got last week. We uploaded the DNA to Geniuses, where we took the sequence and entered it into the National Library of Medicine BLAST. From there, we were given the strains of HIV that it showed the most similarities with. After that, we went to a lab meeting between both the Briney lab and the Ward lab, where we listened to two presentations from grad students, the first was about influenza-A, and the second was about analyzing a paper from a lab at Stanford. Both presentations were really interesting, but were definitely hard to grasp the full concept. After the meeting, we started the tedious process to make sure the sequence we had matched the sequence given to us from the database. This literally meant looking at 2,000 AGCT’s and seeing if they matched 2,000 more. The good news is they did. We left the lab for the day and tried out taking the trolley home. It was really cool to figure out public transport on our own. After getting home, Belle, Zoe, and I got boba; we then had family dinner and ended the night early. 

Our Agar plates from Tuesday

Tuesday, June 30

When we arrived at the lab on Tuesday, we were put to work making 10 liters of media, which is a compound of water, NaCl, yeast extract, and Tryptone. We let that mix, then portioned it into bottles, and took them down to the autoclave, which sterilizes them. The media is essentially Gatorade; it’s full of nutrients and sugars to help the cells grow.  After lunch, we began with the physical Gibson assembly, which meant taking HiFi DNA assembly and a vector, then adding the HIV and Hauntavirus in. This was then put in the thermocycler at 50*c for 40 minutes. While we waited for that, we went down to the autoclave, removed our media, and set that out to cool. We then took notes on the overall process of heat-shock transformation, which is essentially the process that enables bacterial cells to take up circular plasmid DNA with genes of interest. We took the DNA out of the thermocycler and cooled it down. We then added the competent cells. This mixture was then heat-shocked at 42*c, we then added the growth medium and put them on a shaker plate for 30 minutes. This is then put on agar plates to incubate overnight and see what grows. We then headed home for the evening, where we relaxed, watched a show, and had an early bedtime.

Wednesday, July 1,

Wednesday, we arrived at the lab,b and Jonathan presented us with our plates from yesterday to see what grew. Absolutely nothing. After that, we went to check on the media we made on Tuesday. We went to make sure that it went well and no bacteria grew. Well, the good news is we can grow bacteria; the bad news is that we grew it in the media. Turns out the autoclave broke and didn’t get up to temperature. So we had to redo seven liters of media. This meant washing all the beakers, then redoing the whole process. Once the media was made, we went with Nathan and Umair to go look at Ebola on the electron microscope, where the guy who was studying it joined us. After getting the program set up to run photos, we walked around that area of campus and found some Greek food that Umair ate. After that, we looked at all the photos that had been processed by the microscope and headed back to the lab. Nate then showed us his project, which is coming up with antibodies for different strains of Ebola. After work, we headed home, where I made gnocchi for dinner. Stella and I had a great time listening to music and making pasta. The night ended with Zoe and me doing the dishes in the yard. 

Our failed media

I got permission from the lab to take Thursday off, so for the long weekend, I was invited to join an old friend for their family vacation to San Francisco. It was nice to relax and get to see people I hadn’t seen in a while.