Research Project Individual Blog Post #2

As we approached our gel results for looking at skeletal muscles samples from 6 different organisms which are deer, elk, Moose, Caribou, bear, and finally chicken. We were faced with the challenge that 5 of our samples (deer, elk, moose, caribou, and bear) shared many bands. We believe that was due to the fact that they are all mammals. In addition, the deer, moose, elk, and caribou share many phenotypes and look very similar then they must be closer together on a phylogenetic tree. Nonetheless, it was easy to distinguish the chicken skeletal muscle sample as the outgroup since it only shared one band with all of the other samples. However, for the other 5 samples, we see lots of similarities and very few differences which will be a problem in determining each organism place on the phylogenetic tree. My question for other groups is did you measure all the bands in every lane or did you choose certain bands to measure in your gels?

 Another challenge we had which could also cause us some error is that we had a lot of smearing in our gels. We couldn’t tell if there is one big band or 2 bands in a certain lane as a result of the smearing. The smearing was caused by having too much protein present. I believe what caused this is the chunks of skeletal muscles we used at the beginning of the experiment were too big. This led to having a big amount of proteins extracted and when running the gel caused smearing. Another source of error can be as a result of having a really faint band that we could believe it is a band while it may not be. I tried to count how many bands each lane has and each time I did it, I ended up having a different number of bands in each lane. The appearance of faint bands is the outcome of not having enough amount of a certain protein in a skeletal muscle sample. Furthermore, seeing very faint bands could be also the result of a problem in staining the gel. Perhaps there is some contamination in the dye we used and it didn’t stain the gel very well. Moreover, the loading of samples in the gel could be a source of error too because the gel is very thin and could be punctured easily. Nonetheless, it could be that we loaded too much of one sample, the existence of bubbles in a well, and even that we loaded the sample above the gel well given that wells are small and mistakes can happen.