July 12, 2009
I forgot to update this after I set a PR in the gym on Wednesday, but I think I remember it well enough to write about it. Originally, we had planned to do Zercher squats, but instead we decided to box squat onto a high box instead. We hadn’t squatted heavy in a while and high box squats allow us to use heavier weights than we can use for Zerchers. Since I’m fairly tall and have different proportions from Alex and James, who are shorter than me, I had to add a 25 pound bumper plate on our “box” so that it was a half an inch to an inch above parallel. The box was actually four 45lb bumper plates and one 25lb bumper plate, so I used an additional one to get above parallel. This lets me get used to using higher weight so that when I free squat to parallel or lower, I won’t be feeling the weight for the first time on my back. Also, my depth wasn’t too shallow anyway, so I didn’t mess up my movement pattern.
When I squatted onto the box, I could feel that I was several inches higher than normal because I usually go several inches below parallel. I figured that I could easily do 225lbs for a triple. After a bunch of warm up sets, I did 225lbs for a triple and it was clean. Alex approved and told me 275lbs should be doable, too. I then did 250lbs for a triple, which was also pretty easy. When I tried 275lbs, I felt like it was heavy, especially because the fatigue was setting in. Regardless, I got 275lbs for a pretty clean triple. Alex suggested 295lbs, but after 275lbs, I was pretty spent so I told him I’d take 285lbs. It felt a lot heavier than 275lbs, even though it was only 10lbs heavier. I got it for a double; the second rep was a grinder. I went for a third, but I couldn’t get it up so Alex had to help me a bit. He told me he barely helped, but I definitely could not have pushed through it by myself. I call 285lbs for a double a fake PR. It’s a PR because it’s the best I’ve ever done, but I’ve also never done high box squats before. However, it’s the most weight I’ve handled on my back, so it’s a PR in that sense. The next day, my legs were mad sore.
If you’ve read my other posts, you know that a lot of what I’ve been doing at work has been manual labor. I suppose there’s nothing inherently wrong with that, because I’m helping out the lab, I’m making money, and Andy says I’m building character. However, I felt like I wasn’t using my head enough and most people could do what I was doing. I think that’s something I’m not comfortable with: doing something that anyone/most people can do. That may have been why I took linear algebra and am going to take multivariable, even though I had the option of never taking a math again. I’m not satisfied if I only know as much as everyone else, or just the minimum.
Anyway, on Friday I actually used my brain and when Sara told me to do something and I was confused. This confusion was actually a good thing, because this meant that I was trying to understand something new. What Sara asked me to do was test out some primers. The first task I had to take care of was to prepare two 96-well PCR plates with the right DNA in the wells and the primer mix. We wanted to use one type of forward primer for one plate and another type of forward primer for the other plate, but keep everything else the same (i.e. corresponding wells on the plates would have the same reverse primer, same DNA polymerase, same solution, etc.). What amazes me about PCR is that we use such small amounts of DNA, but when we run them on gels, we still get images. The protocol we use calls for 5microliters of green taq polymerase, 1 microliter of a forward primer, 1 microliter of a reverse primer, 1 microliter of deionized/distilled (or sterile) water, and 2 microliters of 10nanogram per microliter concentration of DNA. The total volume is 10 microliters and we still get usable data.
Anyway, the part that confused me was interpreting the gel images that we got after we ran the DNA for about 40minutes on a gel. Sara asked me to pick out primer pairs that “worked.” She asked me to look for double bands on the heterozygotes and primers that are allele-specific to B73 or P39/Tx303 (lines of maize). I was totally confused and had no idea what to do. I sat there scribbling things on a piece of paper while looking at the computer screen for a good ten minutes and I was lost. I asked Jason, a Ph. D. student, if he could explain what I was looking for. Sara told him to explain to me what we had just done by using the primers and running them on a thermocycler. He explained how we had a QTL with two markers on either side of the region of the chromosome that we suspect contains the gene for the trait we’re studying, and hopefully the polymorphism, too. Our primers that we picked anneal to the markers when we run them on PCR and amplify that segment. Depending on the primers that we run them with and whether we have homozygotes or hets, when the amplified segments are run on a gel, we can see whether the primers have amplified the region we want, and only the region we want. If the primers are not allele-specific enough, they’re not useful to us. We also need the primers to amplify the hets. This was why when I put the DNA in the wells of the PCR plates, I created “fake hets” by mixing the DNA of two different lines of maize. We are interested in the hets, because if we find hets, that means that between the two markers that we picked, there was an instance of crossover. This helps us narrow down where the gene (and SNP) is in the region we’ve identified. Then, we can pick new markers for next year and cross the offspring to further narrow down the region.
When I was at work, I was still really confused and asked Jason and Sara for some reading I can do. Sara lent me one of her textbooks that she used last semester, so I’ve been reading that. It’s on population genetics so only the introduction to genetics is useful for me. She also gave me a title of another genetics textbook that might be more relevant to what I’m confused about. The more I learn, the more I’m interested, so maybe I will continue working in this lab during the semester. I haven’t completely decided yet, though, because I’m already expecting to have more work than last year.
Erwa said,
July 16, 2009 at 6:12 PM
“96-well PCR plates” just reminded of freshman bio class. I remember on a test there was a diagram of some DNA analysis stuff and I think one of the questions was to explain what was going on. I remember I didn’t do any of the research we were supposed to do on genetics and didn’t know anything about DNA analysis. So I just looked at the picture and saw lots of well plates and I made some stuff up that sounded plausible in my mind and I remember I still got most of the credit for the question haha. But I think I did pretty poorly on that test overall.
Andy said,
July 17, 2009 at 10:46 PM
Ewwww population genetics. I did something very remotely related to that this year in Java, where we attempted to solve the Traveling Salesman Problem: writing an algorithm for the computer to determine the shortest route between a set of points. We used genetic algorithms and populated gene pools to create the fittest (fastest gene).
I know what you mean when you say that you don’t want to do something that everyone else can do. It shows that you aspire to learn, despite not having to learn, and intellectual curiosity will get you far. However, that being said, I definitely agree with the cliche that manual labor builds character – especially the kind that is purely physical and even looked down upon by the middle class. Custodians have it tough, and sometimes, it’s good to do a little (or a lot) of cleaning yourself. It teaches you to appreciate the hard work that other people put in, and also makes you realize how lucky you are to be able to have a future not filled with manual labor that doesn’t stimulate your brain.