Gene Evolution Lab Report

The Relationship between Gene Copy Number, Amylase Concentration, and Gene Evolution

Matthew Fantauzzi
400007178
Shawn Hercules - L15
25 November 2015
Abstract
In this lab, students were experimenting to determine if a relationship exists between gene copy number, amylase concentration, and gene evolution. At the same time, this lab was designed to introduce university freshman to the etiquette and conventions used in a formal research setting. The methods used ranged from sample production, dilution techniques, and the use of scientific machinery to determine individual results. The experiment took place over multiple weeks. Individually, I was testing to determine if my ancestry has any bearing on my genetic makeup; I approached
the experiment by hypothesizing that high ancestral starch diets would result in a higher level of amylase and AMY1A gene copies in my own genome. My results indicated otherwise, as it was determined that I have an average amount of gene copies and salivary amylase concentration.
Introduction
McMaster University is an institution based in research expertise, credibility, and innovation.
In order to retain this status, it is necessary for undergraduate students to be exposed to a research environment early and thoroughly, allowing for these young scholars to begin developing their skills and etiquette within a lab. Most importantly, however, it allows for students to begin asking their own questions within the field of biology, creating the scientific inquiry and drive needed to push the future of research. The experiment being discussed in this paper is an entry level lab; simple enough to be completed by individuals without prior experience in a laboratory, but still engaging enough to encourage pursuit of further
studies. In this set of experiments, the question being researched is “is there an association between enzyme production, gene copy number, and gene evolution?” (Tracey, 2015). To answer this question, salivary amylase, the enzyme responsible for the breaking down of starch, was used to test whether or not individual ancestry had any bearing on how genes are expressed. The amount of amylase in an individual’s saliva is a result of the AMY1A gene; each person has this gene in their genome, but the way in which it is expressed differs from individual to individual (Morris et al, 2013). Research has shown that certain groups of people have more AMY1A gene copies than others (Perry et al, 2007), and it is suggested that the reasoning behind this lies in the individual's background. It is seen that people from populations which have historically consumed a large amount of starch as part of their diet have more copies of the AMY1A gene, while those from areas with very little starch consumption had less copies. This makes it evident that gene expression and replication is influenced by external factors, and that changes in DNA can be passed onto offspring. George Perry proves this point in his paper, in which he completes a similar experiment but on a larger scale and with more accurate results. The methods are fairly similar between Perry’s approach and the process used within this lab, allowing a comparison to be made, and, more notably, a concrete agreement among results. Using the data collected by Perry and other researchers, I hypothesized that my AMY1A gene count and therefore amylase concentration would be higher than the average person. I made this conclusion based on the fact that my ancestry has roots in the European continent, specifically in Ireland and Italy. Both of these regions, as is with most of Europe, contain diets with a high amount of starch consumption. Therefore, it would make logical sense and align with Perry’s findings that my AMY1A gene count would be high as a result of gene evolution. To test my hypothesis, I tested the variables of amylase concentration and AMY1A gene copies directly, using techniques involving spectrophotometric data, gel electrophoresis interpretations, and PCR duplications. Over the process of the experiment, it was necessary to keep in mind sources of error and external factors that may have hindered the results, which will be examined in the discussion portion of the report. With all these points kept in mind, my results are certainly interesting.
Discussion
This set of experiments contained two purposes within its process, the first of which was answering the research question involving gene evolution. Interestingly, my hypothesis was incorrect. I predicted that, due to my family line, I would be a carrier of a large amount of AMY1A genes, and therefore a high concentration count. Although my hypothesis was logical, the results I obtained were surprisingly somewhat contradictory. As seen in the results and appendix sections of this report, my amylase concentration was .4961 mg/mL and the number of gene copies for the AMY1A gene was 1. Both of these values are close to that of the average person, that is, they would be deemed moderate. This would go against my claim that my levels would be considered high. However, I believe that there are more factors affecting these results, which disallow them to be one hundred percent accurate. First of all, the methods completed throughout the labs, although basic, contain room for error, especially for someone new to the environment.
For example, lab 4 was very pipette heavy, requiring a dilution to be completed to specific values. It would be really quite easy for myself or any individual new to the lab to make an error in either volume, concentration, or timing that would cause the results to be warped. Similarly, in labs where machines are being used for readings, issues could have occurred, causing the results to be incorrect. For example, multiple times throughout the labs, a spectrophotometer was used to determine absorbance values, thus providing knowledge on another variable. If the spectrophotometer was read incorrectly, or the test tube was not properly cleaned, then the reading would be wrong, resulting in skewed results. To further add to this claim, by looking at Figure 4 in the appendix, it can be seen that the error bars indicate a very large margin of error. This indicates that some individuals either had incorrect results, or that other anomalies were at play. Overall, it would seem that inexperience can cause a lot of issues which can greatly skew
results. Another issue of this experiment was that it did not take into consideration any strict guidelines. Since an individual’s saliva was being tested, it would be necessary to ensure that the individual keeps a constant diet, sleep schedule, and exercise regime to ensure that there is no outside influence on the level of amylase present at the time of sampling. It is entirely possible that an individual can receive a particularly high or low concentration despite their normal levels being different due to outside factors. Fortunately, gene count number would almost certainly not be affected by external influence.
With some sources of errors discussed, my results can now be looked at from that lens of thought. I do not believe that my findings reflect or disprove the hypothesis brought forth by Perry in his journal article. Although the nature of scientific research allows for changes in what is known as fact, my deviation from the accepted theory is simply an anomaly caused by the aforementioned errors and one other key factor: my hypothesis was not based in concrete fact. Although it is generally seen that people of similar descent to myself would have high amylase levels, it is entirely possible and even likely given my results that my particular lineage may not follow that trend. Therefore, it can be stated that my results show very little to no relation to that of Perry’s and thus, would not disprove it. In the scope of my experiment, it would appear that gene copy numbers are not affected by external factors of gene evolution, but as implied above, this can very easily be discredited as a misstep. Despite all the issues, the methods in this set of experiments were all very good at accomplishing their purpose. They remained simple enough for beginners to complete, yet still provided mostly accurate results. However, improvements do exist in the procedure that could improve the scientific accuracy of the results. First and foremost, multiple trials of each lab should have been used. An individual sample with its corresponding results are not valid enough to make any single conclusion. If each lab was repeated three to five times, with the results being averaged out, the conclusion being made would be more valid and reliable. This would ensure that errors and anomalies could not largely affect the results. Another improvement would be to establish stricter quality control between lab parts. Due to beginner naivety and ignorance, a lot of simple errors could have been made, which may have never been noted. By having more experienced experimenters working more closely with each individual student, less inaccuracies would occur, resulting in a stronger conclusion. Both of these points would greatly improve the experiments, but they would require a lot more time and resources that students and TAs alike do not have.