19 Jul Eleanor Rosen, Briney lab TSRI- Week 4

This was my 4th week in the lab. I’m so sad I only have a week left. It’s been so fun getting to see what everyone does, and exploring San Diego and the lab a bit more. This week we spent a lot of time continuing our projects, and getting to work with new people. Jonathan was gone this week so we had to pause on our hantavirus project, but we got to do some new work with other viruses.

Monday, July 13,

We have begun to learn that Mondays and Fridays are slow in the lab. Monday morning we attended the Briney/Ward lab meeting, where we listened to two presentations, one on the flu, and the other on malaria. We were also told to “stay in science”, and are officially now known as Nathan’s kids in the labs. After lunch we joined Dani on her work for the afternoon, this involved a lot of shadowing, and learning new processes. We got to venture into the backrooms of the chemistry building to use the microfluidizer, which is a machine that uses high amounts of pressure to process fluids. We used it to separate proteins from cells, this was then centrifuged to create a pellet of the cells we don’t want. After this we headed back to the lab, where we went into the tissue culture room to watch Dani do a process known as cell splitting, it was a complicated process, but to simplify it we had to separate the cells from the bottom of the container they were growing on, then get them into another container, then add media to help them keep growing. We then waited for our centrifuge to finish, and then filtered it, and set our proteins to rotate overnight. After leaving the lab we took the trolley home. Zoe and I headed to Target, and we all just had a nice evening at home. 

Me working with Dani at the microfluidizer 

Tuesday, July 14,

Tuesday morning was spent in the BSL2 room with another person in the lab Morgan. It was our first time getting to use the hoods ourselves, the hoods are sterile environments, so each one gets a bleach bucket, where all your waste goes, and everything gets sprayed with ethanol before entering. Today we continued working with our 38 antibodies.  We each got 13 of them and began by putting them in clean tubes to be spun down. We did this so we would get a cell pellett, and we put them in new tubes because the cells got bacteria . After spinning them down we put them through a filter, and then added a protein (protein a)  to them. The finished tubes were put to spin overnight in the cold room. We went on an adventure to figure out where to watch the world cup. It turned out that we had the wrong day, so we headed back to the lab. In the afternoon we spent some time shadowing Morgan and her work. We watched her get B-cells out of a mouse spleen, which was a complicated process and I didn’t really know what was going on in it. She meshed the spleen through a filter, then added a buffer, and centrifuged, she then added an “antibody cocktail” and centrifuged again, the last step we saw her do was set it up to go through a magnet that pulls them through. It was confusing since it wasn’t our traditional work in the lab, but we got to learn more and see more which was wonderful. After work we took Stella’s car to the carwash, and took a late evening trip for mango sticky rice and ice cream.

My work in the hood  

Wednesday, July 15,

Wednesday morning we began by harvesting the proteins from the transfections we did with Raiza on Friday. We started by spinning down the mixture so the cell debris made a pellet at the bottom, we then filtered the rest of the cell debris out of the supernatant. Then we added different beads to each one, and all four got a chemical (sodium azide) that will kill everything. While they were filtering we went down to the lab meeting where Terrance got the whole leb thai food, and Nathan presented, his presentation was mainly what we have been working on so it was nice to finally understand a presentation. After we finished up harvesting, we set them to roll overnight. We then headed to another part of campus to watch the last 20 minutes of the world cup game. (Argentina won!!!). We then spent the afternoon in the lab working on our blogs, because most of the people in the lab went home early. After work Zoe, Belle and I spent the evening reading, before an early night.

Filtering our proteins

Thursday, July 16,

Thursday morning we went down to the beach before work again. We started by continuing harvesting our 38 antibodies. This meant putting them in columns, and letting the liquid flow through while the beads get stopped in the filter. Nathan gave us a whiteboard presentation of what exactly we were going to be doing. Once we let all the excess media flow through the column, we then added PBS which washed the beads. After that flowed through we added an elution buffer, which separated the antibodies from the beads they binded to. This was then filtered through, leaving the beads on the filter, and letting the antibodies and buffer follow into another container which had a basic solution so the antibodies couldn’t be damaged. These were then stored in the coldroom. We then left the lab for the day and went home to enjoy our last second to last night of all of us in the house. We ended the night with a midevening drive for boba.

Harvesting antibodies

Friday, July 17,

Friday was easily the best day in the lab so far. When we got to the lab we did a little bit of work with dani, we did the final stage of the gibson assembly process. Liliana poured beads on the plates, and I added the bacteria. Before we had even finished this terrace came and told us that we needed to finish the harvesting of our proteins. Finishing this process took all day. We first spent almost two hours in the cold room. Which is basically a giant room full of random projects that is kept at 4*c, we all were wearing multiple pairs of gloves, and ended the time in the cold room with bright red noses. While we were there we put the proteins in a column. We did what we had done with Nathan the day before but on a larger scale. So we filtered them, then added PBS, and cleaned the beads. Belle and liliana began working with Nathan on finishing the harvesting for our 38 antibodies. I spent more time in the cold room with terrance, so we added the elution buffer. Finally we got to leave the cold room and start centrefuging. We had to pass it through the filter, so it took forever because you could only fit so much of the solution in the conicales. After we finally passed it all through we added 2 rounds of wash with pbs, finally we tested the concentration. Terrnace began setting up the AKTA (or the truth) that measures the usable protein based on size, but he wouldn’t run it until later in the night. Oh and we learned our hard work for the past two weeks paid off and our 38 antibodies are usable. We then headed home for our last night as a family. We had dinner at home, then went to the beach to take pictures and enjoy the night. We then went to a dessert store. And ended the night late at home.

centrefuge 

Saturday, July 18,

Saturday we got up and I made our last big pancake breakfast, we then said goodbye to Stella and Kaila. We spent midday in Balboa Park with Izzy, and made sure to check out the free exhibits at the science museum. We also went to see the odyssey in theaters, which was absolutely incredible, and well worth the hype.

Sunday, July 12,

Sunday was our last designated beach day as a big group. So after we all posted our blogs for the week we headed to the beach. It was a great day relaxing in the sun. In the evening we did group grocery shopping, and headed home for the evening.

     Zoe and i made a sandcastle on Kaila’s feet as she slept