ALU PCR LAB

Tak Maga
09.26.2017
STEM BIOlOGY AND BIOTECHNOLOGY
INTRODUCTION AND PURPOSE

This lab was conducted in order to provide the students with experience in common
laboratory techniques, such as PCR and gel electrophoresis, determine the origin of our
individual DNA, and to ascertain whether the population was evolving.

HYPOTHESIS

If my DNA underwent the process of the lab, I believe that it would establish that my
DNA had European and Asian origin.

PROCEDURE

All procedures and materials were conducted according to Alu PCR Lab. Bay Area
Biotechnology Education Consortium, 2017.

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DATA

2 1

A
A B
B
C
C
D
D E
E F
F G
G
H
H

Figure 1: Results of 2% agarose gel running at 150v for 20 min (1 towards 2), and
stained using gel red for 72 hrs. Lanes 1a and 2a have a 100 bp ladder. Lanes 1 b-h and
2b-h have 20 microliters of a 50 microliters DNA/10 microliters loading dye solution.
Land 1b had my dna. This is viewed over a UV light.

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 Figure 2: Close up view of the lane containing my DNA. There are no
observable bands in the lane.

ANALYSIS

As seen from Figure 1, there were no conclusive results from this lab. None of the
lanes in this gel produced bands indicative of the presence of the Alu repeats. However,
the 100 bp ladders ( in lanes 1a and 2a) did show bands. This means that there were
errors made when forming the DNA sample. There are many possible areas in which this
may be possible. Starting with the beginning of the lab, it is likely that some samples did
not have enough cheek cells in order to produce enough DNA. Throughout the process,
many amounts of liquids were transported between tubes, providing a base for
inaccurate measurement and cross-contamination. During the PCR process, there may
have been times when the PCR tube was not fully iced, creating more areas for error. All
of these possible methods in which we could have erred are, in all probability,
responsible for the lack of results. However, there is also the chance that there is an
error in the lab procedure, given the sheer number of failed groups.

This lack of results means that the hypothesis can neither be confirmed nor
denied, returning a result of inconclusive. Further tests would be need to do this. If the
lab did work, then further investigations could lead to online databases where the origin
of the DNA could be traced. This is not possible with the data available.

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 In the interest of learning about the mathematical methods of analysis, a fictional
data set was produced, as shown in figure 3.

Alleles Number of Students

(+,+) 15

(+,-) 10

(-,-) 12

Figure 3: Table describing the amount of students that have been found to have each set
of alleles in a fictional population.

Using this hypothetical data, we then proceeded to analyze it in order to learn the proper
procedures. Our first method of analysis was to calculate the frequencies of both positive
(+) and negative (-) alleles this can be found by finding the number of alleles in
question and dividing it by the total amount of alleles.

The total amount of alleles is the amount of students in the population (37) multiplied by
the 2, which is the number of alleles per person. This means that the total amount of
alleles is 74.

There are two groups of students that have positive (+) alleles. The first group have
(+,+), meaning that for every student in this group, there are 2 + alleles. This means that
15 multiplied by 2 is 30. To this number is added the number of positive alleles in the
second group. The second group is (+,-) meaning that for every student in this group,
there is only one + allele. This process yields us the number of 10. (10 multiplied by 1).
Adding these numbers together provides the result of 40. Put over the total amount of
alleles (74) and divided means that the frequency of positive alleles is around 0.54.

The frequency of negative alleles can be found using one of two methods. One method is
to repeat the same process as the positive alleles. We would then use the third and

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second groups instead of the first and second groups. The second method is to subtract
the positive allele frequency from 1. This is because all the alleles in this population are
either positive or negative, and so therefore we can establish that that any allele that is
not positive must be negative. So, the population that is not part of the 0.54 must be part
of the rest, which comes out to 0.46. Both methods result in this outcome. Both positive
and negative frequencies are rounded.

The second part of the analysis is to find out whether the population is in equilibrium,
using the equation p2+pq+q2=1. Variables p and q are the individual frequencies of the
alleles, with p equaling + and q equaling -. Therefore, p multiplied by p would be the
theoretical frequency of a (+,+) genotype, p multiplied by q would be a (+,-) genotype, and
q multiplied by q a (-,-) genotype. All of these totaled should equal 1, which encompasses
all genotypes.a (+,+) genotype, p multiplied by q is theoretically the (+,-) frequency, and q
by q is the (-,-) frequency. Doing this math with p equalling 0.54, and q = 0.46, we get
0.2916+0.4968+0.2116=1. Expounding on this, we find that 11 students would be in the
first group, 18 in the second group, and 8 in the third. We find this by multiplying the
expected frequency by 37, the number of students in the population. However, it is
noticed that the expected frequencies of the the group are not the same as are actually
found. The percentage of students in the first group is actually 0.41, and 0.27 for the
second, then 0.32 for the third. This considerable difference of numbers means that the
population is not in Hardy-Weinberg, and therefore still is evolving.

CONCLUSION

Throughout this lab, the large amount of mishaps that may have occurred leads me to
state my claim that to conduct PCR lab is difficult with our experience. Our lab consisted
of obtaining a sample of our DNA, then conducting PCR to replicate it. Then, we did gel
electrophoresis to find out whether our genotype had Alu repeats. Our data was highly
inconclusive, with only 5 students obtaining results. This means that the large majority
of students did not perform it correctly, showing its difficulty. Another point to make is
the number of areas in which an error could have easily occurred. Therefore, it is
possible to say that there is a high level of difficulty associated with doing a PCR lab with
our level of experience.

REFERENCES

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Alu PV92 PCR. Bay Area Biotechnology Education Consortium, 2017.

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