In this lab, we were running fake patient blood samples through a process called gel electrophoresis to determine if they had cancer. Gel electrophoresis is a process where electric currents are run through a buffer to either a positive or negative conductor, so you can see how far DNA travels. The DNA is located in small wells that are in a rectangular piece of 1% agarose gel. Since DNA is negatively charged, we put it in wells that are closer to the negative side and watch it travel to the positive side, since opposites attract. We use agarose because there are microscopic pores that the DNA can travel through. We stained the DNA so we could see it in the gel. We used seven wells, one for the control DNA ladder, two for positive leukemia samples, one for a negative leukemia sample, and 4 patient blood samples. As you can see, it appears that two patients did have leukemia, as their DNA bands matched with the positive samples. This lab was really interesting to do as we were actually able to see how the DNA traveled with our naked eyes. The whole process was really fascinating as I did not know that it was possible to see individual DNA fragments. However, it was pretty hard to actually see the DNA bands and the whole process was somewhat prone to error, especially when loading DNA into the wells.
Spot on CML Lab
We went on a lab tour and looked at very powerful microscopes. This particular piece of equipment costs over $650,000, and is an x-ray crystallography machine. Its purpose is to create 3D models of proteins and etcetera. The process of using the machine is very complicated and time-consuming. The first step, to obtain pure crystals of protein and a precipitant, is the least certain step. Protein and solution are subject to crystallization techniques, which takes lots of time. Bigger proteins may not even crystallize. The reason that protein crystals are required is because the protein molecules in a crystal are arranged in a lattice structure, so the x-rays are reflected back in the same order. The x-ray machine works by bombarding the protein crystals with c-rays and recording the diffraction patterns. Then, a computer converts that into a 3D shape, following a mathematical formula, and the protein is mapped. The whole process can last from a couple weeks to a couple decades. I was really surprised at how the x-ray crystallography machine worked. I could never have thought that diffracting x-rays would allow for such depth in viewing proteins. It was really interesting listening to Dr. Stoddard talk about his experiences going to the Soviet Union and sending his x-ray crystallography experiments to space as well, especially on the reasons why he had to go to the Soviet Union and how he almost got stuck in it during the collapse.
X-ray crystallography