Wednesday, July 23, 2014

DNA Sequencing

I woke up today at 8:00 AM, got ready, and went to breakfast. Soon after I went to class and walked with Katherine and Alexa. Then they went to class and I kept walking my way and caught up with Dani and Kaitlyn because our classes are in the same building. When I got to class we did an hour lecture and then to the lab until lunch. In the lecture Dr. Fineschi talked about the different RNAs there are and what they do. They are mRNA (messenger), rRNA (ribosomal), tRNA (transfer). The mRNA is transported in the cytoplasm and tRNA has a complementary way with the mRNA codon. She also talked about ribosomes. They keep the mRNA in place, they allow mRNA and tRNA alignment, catalyze the formation of bonds between successive amino acids that are carried by tRNA.

I learned that Fredrick Sanger won two noble prizes, noble in chemistry 1958 for the structure of insulin and noble in chemistry 1975 for DNA sequencing. He also invented DNA sequencing. She told us that large scale DNA sequencing uses the dideoxy method with some improvements for increased efficiency and speed. Before we left to go to the lab we sequenced DNA off of DNA sequence paper from a while back. It was fun because we were all confused at the beginning but then got used to it. But it didn't work because Dr. Fineschi gave us the wrong sequence. But I learned that scientists sequence 200 genes at a time because there are a lot of genes to sequence.

 When we went  to the lab and extracted DNA from our mutant in the environmental plates and used PCR to amplify the rpoB gene. Next we mixed the 3 different colonies in 3 different tubes with lysis in it. After that we put the sample tubes into the thermocycler because the lysis solution needs to be heated up in order to be activated. As we waited, we put 40 mL of water into 3 separate tubes labeled for red, blue, and environmental. After we put the water in, we put the diluted samples into the tube that matched the label. Then we used a pipette and inserted 2.5 mL of the lysed dilution into the tac bead tube. Next, we added 17.5 mL of primer and then 5.0 mL of water. Next, we put it into the centrifuge for the short cycle and then put it in the thermocycler.

Dawn, the TA, Helping my Partner Sofi
Then I went to lunch and had meatloaf and fruit. After I came from lunch our class went to the lab first and before class Dani brought me a milkshake. I thought that was nice of her to bring me one since I didn't get to go with her and Kaitlyn during lunch. For the next part of the lab we got three more tubes and put 4.0 mL of loading dye and 1.0 mL of PCR in each one. We labeled the tubes red, blue, and environmental. Then we loaded the solution into the gel. The purpose of this lab was to verify if there was data from our samples. Our plans for tomorrow is to go to a sequencing facility to see how it actually works.

At dinner we all ate in the main dining hall. I ate fruit, rice, chicken nuggets, and for desert I had one scoop of cotton candy ice cream in a cone. At dinner we made a lot of jokes and laughed almost the whole time we were there. I ate with Alexa, Jimmy, Oyin, Dani, and Kaitlyn. Then we left and I went to my room for a while until I went to go play soccer with Jimmy and some more people from the program. I had fun and we stayed until 8:45 PM. Sadly my team lost but it's okay because I still had fun playing with them. But ending the night with my Chicago Family is the best thing every night.

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