28 Jun Eleanor Rosen, Briney Lab Scripps Research: week 1

Hi, my name is Eleanor Rosen, and I will be spending the summer in San Diego at Scripps Research in the Briney lab. Where we will be studying immunology, mainly by creating antibodies.

Saturday, June 20, 

Belle and I arrived at the house around midday, where we met the other girls and settled in. We then all went to Costco for the weekly grocery shopping. We then made dinner as a family, and learned really fast that we all get along really well. After dinner, we headed to the beach, where we got to watch our first sunset of the summer. We ended the night with an episode of a show and an early bedtime. 

First beach sunset

Sunday, June 21,

After a relaxing morning at the house, we set off to visit the Hillcrest farmers’ market and enjoyed some food and the sun. We had an early dinner and headed to the beach for the evening. After coming home, we enjoyed a relaxing evening and went to bed early. 

Kaila and I at the farmers market

Monday, June 22,

Monday was our first day at the lab. We started the morning with HR orientation, we got logged into the programs we need, and took a quick tour of the campus. After that, Belle, Liliana, and I headed to our lab, where we met up with Terrence Messmer, who showed us where we were working and had us start doing our training, which taught us safety in the lab. After that, he took us on a tour of the lab, showing us the safety equipment, and gave us safety goggles and lab notebooks. Thus ended our first day in the lab. We went home and chilled at the house, Stella made dinner,r and we ended the night relaxing on the couch.

Us at our desks in the lab

Tuesday, June 23,

Tuesday morning started with 4 hours of note-taking of everything they do in the lab. We started by reading the foundational papers on the basics of what goes on in the lab. We learned about what they are finding antibodies for, the different kinds of antibodies, as well as how they code them. We were then given a slideshow to take notes from. The slideshow explained the processes of building antibodies and how it works in the lab. The lab uses B-cell immunology mainly, which uses adaptive immunology, so it’s highly specific to each antibody, and the basis of vaccination. We learned about B-cell development, and how it’s from bone marrow, then taken through a process to see if it is usable. We then learned about antibody structure, and how it is built of a light chain and a heavy chain, with a constant region and a Fab region, making it so that they can adjust to whatever antigens they are bonding to. We then learned about molecular cloning, which is how they get the DNA to build proteins and antibodies. Taking DNA from E. coli because of its high doubling time, you can grow cells much faster. This DNA is then put in mammalian cells to be used for protein production. The slideshow then covered PCR and primer design, and the whole process of Gibson assembly. The last part of the slideshow was talking about antibody production in mammalian cells, which is how they finish the process and get antibodies in the end. After notes, we took a lunch break to prepare for an exciting afternoon. One of our mentors, Nathan Liend,o took us to the other side of campus to try and look at antibodies for T-cell leukemia, which, if successful,d we would be the first people to ever see said antibodies. He prepared the disk that would be used by covering it in a radioactive material, then blasting it with plasma. We then headed back to the Briney lab to go over the slideshow, where they clarified our questions and told us more about what we are doing. We then walked back to get to use the Electron microscope, which was really cool technology. We got the photos processed, and then ended our day with that. After work, we came home and surprised Liliana with decorations and brownies for her birthday.

the inside of the electron microscope

Wednesday, June 24,

We started the morning with learning how to pippet and use a centrifuge, which was really cool. Both instruments are basic ones used in the lab, but were definitely on my list of pens to use. It was really fun to use them. On Wednesday, we went to our first lab meeting, where one of the grad students was practicing his defence. It was really cool to get to see what other people are doing in the lab. We were then introduced to a project that Benjamin Nemoz is working on, which is developing antibodies for the Hauntavirus (yes, the one from the cruise ship). We were given 21 sets and told to make primers for them. They showed us the technology we will be using and the requirements for primer design. After work, we came home, and Zoe, Kail, and I went on a walk to get boba and limes for dinner. We ended the night eating ceviche and watching a show.

pipet practice

Thursday, June 25,

Thursday was a lot of staring at screens. We spent the whole morning trying to create primers, which proved to be very tedious, but it was interesting to see how computers work to create them. They have to follow specific measurements, and have a certain TM, and GC%, which was really hard to get all 3 to work together at once. After lunch, we worked with mentor Nathan Liendo and his other intern, Umair, to create buffers. These buffers were fun to make because they felt like we were mixing random things, even though two of them were mainly salt. After work, we walked to UCSD to go home with Stella and Kaila. We went home, and I made dinner, and we ate it having a picnic in the back yard.

Notes on the process

Friday, June 26,

Friday was our first day of doing real lab work. After coming into the lab, Jonathan Hurtado set us up with a kit for a Miniprep to extract DNA from E. coli cells. It was funny, he handed us the kit and went “ break things”, things meaning cells. We started by centrafuging so the cells would form a pellet at the bottom and the media would rise to the top, we then disposed of the media keeping the cells, we then added another solutio nthat made the cells split from the DNA which we centrafuged the cell debris to the bottom and kept the dna, which was then washed and purified with a vacuum, and centrifuged again. In the end,d we measured how much we had and set them on ice and put them away, they might later go for sequencing. After a lunch break,k we did some more reading, and Nathan asked us to do Maxipreps with him. We worked on the two preps with Umair, who kept us entertained with his overuse of ethanol in the lab. The Maxipreps had the same system as the Minipreps, just with a higher amount of DNA in the end. In the end,d we watched Jonathan do transfections, which is how they add the DNA into mammalian cells. It was a great day to end the week; we all left the lab really happy and proud of ourselves. After work we went to the movies to celebrate Liliana’s birthday, it was a fun evening out in San Diego.

us doing the Minipreps

Saturday, June 27,

After a chill morning at home,e we all ventured to the Little Italy farmers market, where we found some good food, and had a good time. After that, we walked along the Embarcadero and saw the US Navy Memorial there. We took the trolley home and all relaxed for a while. While the others napped, Belle, Zoe, and I adventured around the neighborhood and got boba before coming home. We had a nice chill day to end the week. 

us at the navy memorial