Hello, I have officially finished my 6-week neuroscience internship under Cassandra White in the Jin Lab at Scripps Research! By the time you read this, I will be on my way back through the hot desert to Colorado. This has been such an incredible experience and I am definitely going to remember my time here for the rest of my life.
Me giving my presentation.
On Monday I went to my last lab meeting and actually gave a small presentation. It was my mentor’s week to discuss her project during lab meeting and she asked me to give a quick 10-minute presentation about my time in San Diego and everything I have learned while in the lab. Afterward, I got to run a qPCR with the samples that I made through reverse transfection and lysis last week. A qPCR is more sensitive than a normal PCR and will usually provide more consistent results. qPCR is a quantitative reaction that couples the amplification of a target DNA sequence with the creation of graphs. On these graphs, the x-axis is the number of PCR cycles and the y-axis is the fluorescence from the amplification reaction. To run a qPCR you need to pipette tiny amounts of your samples into 384 well plates. The tiny wells are really difficult to get bubbles out of, I definitely learned that the hard way. In the afternoon I started another neuron tracing image.
My 9 samples.
All of the bands that I extracted DNA from.
On Tuesday my mentor came in late so I took an hour in the morning to walk around the Scripps and the Skaggs Graduate School Campus. If you walk directly up the hill from the Dorris Neuroscience Center and cross the road you can overlook the Torrey Pines Golf Course and the ocean. After I got back I took a final for an online class that I took over the summer and went through the first step of cloning with Cassie. We ran this in the thermocycler and ran the samples on an E-gel. There was a whole collection of bands on the gel and I extracted them for DNA. The E-gel is inside a plastic casing and to get to the bands you need to crack open the front cover, I’ve done this a few times now but it definitely takes some strength to break the plastic without hurting the gel. You also have to put the gel over a red light to see the bands, you can’t look at the light without eye protection so I have to wear red light glasses while cutting the bands (they make everything bright orange). I had 9 samples plus 1 balance to extract. I got to trace a few neurons on Tuesday as well.
On Wednesday I started off the morning by running the tapestation on two samples of cDNA that I extracted yesterday. Afterward, I ran a 1% gel on the same samples from Tuesday to see if using a 1% gel resulted in clearer bands than a 2% gel. If the bands looked the same on both we weren’t going to purify them but they looked different so I did another gel purification. I only had to extract 4 samples this time which were much more manageable than 9. I nanodroped the new samples and used them in a PCR. This PCR was more complicated than the ones I usually do, there were more components and each sample needed specific amounts of specific things so I couldn’t make one big master mix. While that PCR was running I split cells in the TC hood and watched Cassie make the media for her cells. After I left for the day Cassie ran the completed PCR on a gel.
Thursday was a fairly quiet day, I started by watching Cassie do something called Qubit Quantification. Qubit is just
another way to determine the concentration of DNA in a sample, it’s similar to the nanodrop but is better at reading lower concentrations. They also had a special intern lunch with a bunch of games and raffle drawings. I did make myself eat the lunch I brought from home instead of the food they had at the event. Somehow I ended up making 8 servings of pasta for lunch this week and it was my personal mission to try and finish all of the pasta before I left (I was unsuccessful). After the lunch, I split some more cells and called it a day.
Friday was officially my last day in the lab, I think the universe could tell that it was celebratory because there wasn’t any traffic on the way to work for the first time this week! I got to split my last set of cells and go to an Olympic-themed happy hour that one of the labs at the DNC put on.
Last sunset picture!
My dad is getting to San Diego on Saturday and we are going to start our drive back on Sunday, I should hopefully be home by Monday. I’m going to spend Saturday hiking one last time and packing/cleaning everything up. Thank you so much to everyone who made it possible for me to have this incredible experience. Thank you to Sarah Holbrooke, the Hacker Family, the Jin Lab, and everyone who followed the blogs. I will see you at the Pinhead Presentations in the fall!
Signing out as a neuroscientist,
-Siena
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