By Vinzente Fedele
On March 2nd, 2015, I joined the Advanced Science Research (ASR) class in visiting the Harlem DNA Lab. I met Ms. Lee, who explained and directed the lab. She started the activity by asking us simple questions about DNA, and how it’s used to create proteins. She discussed the ALU gene located on the 16th chromosome of some people. She explained that scientists are not aware of the function of this gene; in fact, this gene might not have a function. Nearly 100% of the genes within all human beings are the same with a very small percentage making us different. However, some genes within the larger percentage are usually found within certain groups of people for whatever reason. She called this larger percentage the ”junk DNA” because scientists have not found any use for it. If you are in Mr.Kerzner’s AP Biology class, you will be doing this same experiment in class. You should be aware that I’ll ruin the surprise of the ALU gene at the end of this story!
The procedure began with each person rinsing his or her mouth with a .09% saline solution. This is a salt solution that matches the amount of salt within all of our cheek cells. We used the same percentage because too much or too little salt within the solution would shrink or bloat the cells, possibly making them useless for the lab. After rinsing, I spit the solution back into the paper cup. I used a pipette to move some of the solution with cheek cells into a tube, and I placed my tube, along with the others, into a centrifuge: a machine which spins samples at great speed. For most people, the cells clumped together as expected, but my cells were “floaters” for some reason, meaning that the cells did not clump. When we were instructed to remove some of the liquid from the tube, I accidentally lost my sample and had to repeat the beginning steps. Fortunately, my second sample was not a floater, and I obtained a nice little clump like everyone else.
To read the segment where the ALU gene would be located, I had to use something called polymerase chain reaction (PCR). ). I had heard about PCR when it was mentioned by other students, but I had never really gotten the idea until this trip. Ms. Lee gave everyone a small tube with a solution containing the material needed for PCR, to place his or her sample inside. The solution had a pink bioluminescence, which was used to allow the DNA to glow once it was placed in gel electrophoresis. After another use of the centrifuge, Ms. Lee placed everyone’s sample inside a machine with a name that I do not recall. She showed us a video of what would happen to the DNA as the machine did its job. The PCR contained enzymes which would divide each half of the double helix, and then continuously make copies of the target segment.
By the time that the machine finished, each tube contained not only the DNA, but billions of copies of the target segment. The final step of this entire procedure was placing the DNA inside gel electrophoresis. This was actually my first time using gel electrophoresis. Using a pipette I removed my sample containing the many copies of my DNA segment, and I slowly placed the DNA into the cell or chamber corresponding to my number. The cell in the gel electrophoresis is a rectangular box which holds the DNA. Within a short amount of time, the samples were ready to be examined. The gel electrophoresis showed bands as the DNA was dragged downward by electrical forces. Ms. Lee went through each sample and told us if it was positive homozygous, negative homozygous, or heterozygous.
If you recall from freshman biology, sex cells are “haploid,” meaning that they only contain half of the DNA found in somatic cells throughout the body, so each “common-bred” human has half of its DNA from each parent. An organism which is homozygous for a gene has obtained the specific gene from both of its parents. Intuitively, an organism which is heterozygous for the same gene has received only a single copy from either parent. “Positive homozygous” meant that the gene was present, while “negative homozygous” meant that the gene was not present. Before the examination of the gel electrophoresis happened, I asked Ms. Lee where this gene was found and whose it was, but she decided to not reveal any information to me until the end of the process. Interestingly, while my DNA did not contain the ALU gene, the class contained a decent number of students who were either heterozygous or positive homozygous. Ms. Lee asked these people to raise their hands, and what everyone noticed was that those with the ALU gene were either Asian or Latino with a mestizo appearance. At this point, Ms. Lee revealed that the ALU gene was largely found in Central Asia. She also mentioned that her husband, who is South Korean, also has the ALU gene.
This visit allowed me to finally have experience using gel electrophoresis. At the same time I was also able to learn something interesting about some of my classmates, in that those with the ALU gene share a common ancestor. If you would like to visit the Harlem DNA lab in the future, be sure to speak to one of the science teachers, AP biology students or ASR students for more information.