Lab 10: Bioinformatics

Caroline Hernandez-Casner
Micro 2141
CRN: 16077
November 16, 2015

Introduction:
Microorganisms can be identified in many ways but one in particular is by
DNA sequencing. Once the microorganism has been isolated, its DNA then can also
be isolated and looked at. This processes helps to save money and time compared
to biochemical tests. This is because less tests are needed to be done in order to
identify the microorganism. In order to use DNA Sequencing to identify a
microorganism, one would have to align all of the sequences which is very time
consuming but fortunately there is a BLAST search tool provided by the National
Institute of Health (NIH). This allows for the comparison of one specific DNA
sequence to all known DNA sequences. The sequence that the search tool
specifically looks for is the 16S RNA sequence. This sequence codes for ribosomes
and because all cellular life has ribosomes, the specific DNA sequence that is being
observed, can be compared to all types of cellular life. All the information gathered
is then used to create a phylogenic tree which helps to explain which organisms are
most closely related evolutionarily. It is hypothesized that the BLAST test will
provide at least one identical DNA sequence that matches the unknown DNA
sequence, it will also provide many similar DNA sequences.
Methods and Procedure:
First a series of biochemical tests were performed on the unknown
microorganism which identified the unknown microorganism and then a BLAST
search was done in order to confirm the results. In order to perform a BLAST search
on an unknown microorganism, internet explorer was used. The unknown
microorganism was isolated and then the DNA sequence was isolated. The isolate
DNA sequence was then entered into BLAST website, under a BLAST nucleotide
search. After the search was conducted, the BLAST page provided a color key of
alignment scores. It also provided a description of all of the alignments. This
description was used to identify the unknown DNA sequence by comparing it to the
DNA sequences it most closely resembles.

Results:

Figure 1:
Figure 1 shows the biochemical tests performed on several different microorganisms.
Figure 2 is the color key alignment for
Pseudomonas.

Figure 2:

Figure 3:
Figure 3 shows two similar DNA
sequences to Pseudomonas.

Figure 4:
Figure 4 is a picture of the phylogenic tree of Pseudomonas.
Conclusion:
For this experiment, a BLAST test was performed in order to identify two unknown
microorganisms. Figure 1 shows multiple biochemical test performed on multiple
microorganism. Although microorganisms can be identified through biochemical
tests alone, it is not always accurate due to contamination and it is costly and
timely to perform. Figure 2 is an image of the first unknown microorganisms color
key. The color key indicates how many similar sequences there were to the
unknown sequence as well as how long the query was, which is the length of the
sequence. The length of this sequence was 1457 nucleotides long. Figure 3 are
images of the first two similar sequences. As you can see, the first similar sequence
has no gaps and 1457/1457 identities. This means that is exactly the same as the
unknown. This figure also indicates what the unknown is which is Pseudomonas. The
second similar sequence, in figure 3, is very close to the Pseudomonas DNA
sequence but has one gap, indicating that it has one difference. After the unknown
was discovered to be Pseudomonas a phylogenic tree was produced, which is
indicated in figure 4. This phylogenic tree is used to show the relation of
Pseudomonas to other similar microorganisms evolutionarily. The hypothesis was
mainly supported by figure 3, because it indicated that the BLAST test found an
exact match of DNA sequence to the unknown that was being observed.
References:
Laboratory 10: Bioinformatics. General Microbiology Laboratory, 1-6.