First Week Blog

First Week Learning

    This week, I learned about PCR, gel electrolysis, overlap, and restriction enzymes. We did some amplified some left + tet, and tried to combine the left + tet with the right. Despite the group’s best efforts, we were unsuccessful with getting a good sample of left + tet + right. While the experiments were happening, however, I was busy learning how to do said experiments - so I’ll go over what I leaned. 

Gel Electrolysis 

    I learned how to make a gel to read how many base pairs a sequence of DNA has. First, you figure out how dense you want the gel, based on what DNA you’re trying to read. Afterwards, you make the gel by combining agarose and TAE, boiling it for 5 minutes, then let it harden from a liquid to a  gel while you have a comb inserted in it to make wells. After the gel is hardened, you can load your sample(s) of DNA into the wells - loading the first or second well with your ladder. The ladder is used as a scale to read how many base pairs you have. After your samples of DNA are loaded, you put some TAE over the gel and into the water wells until the gel is slightly covered. Then, you plug in your machine and run electricity through the gel to sort of unfurl the DNA. From there, based on the ladder and your sample, you can approximate the number of base pairs in a sequence of DNA. 

I'll go over a different procedure next week, and try to keep this a weekly addition to the blog that people can read in layman's terms. 

Theory

    The basics of what I learned in lab about what we're doing in one part of lab is trying to get Deinococcus radiodurans (henceforth known as D rad ) to uptake a linear plasmid with the gene coding for Tet r/a from Lux s. Right now in lab, we're still around the beginning, and working on building the genetic sequence for D rad to uptake. So far, as stated above, the groups have been able to combine the left fragment and tet, the right fragment and tet, but not both the right fragment and the left fragment with tet. When I say fragment, I'm referring to a 1000 base pair sequence of DNA put on either end of tet r/a to let cell read it. When I think of this, I think of an DNA as an old film reel, where each part of the movie is important, some parts more important than others, but most required for it to work. When editing old film, people would cut out parts of the film, and manually put in the next scenes. You can think of the new gene being expressed like a new scene in the movie, but replaced with a separate scene. 

    Well, it's 11:58, and I would like to write more but have a deadline - so will make it up with an even longer entry next week. Keep tuned y'all.

Kieran