Questions 1, 2 and 6 are short answer questions and should be answered in complete sentences. Each
short answer question is worth 3.3 points. Questions 3, 4 and 5 are long response questions. Your
answer to each should be 100 – 200 words. Each long response question is worth 10 points.
1. What kind of patient samples are used for the purpose of identifying possible pathogens?
For identifying possible pathogens, patient samples used include blood, stool, sputum, urine, and
other body fluids.
2. What is the first thing you must do once you enter the lab – before you start the virtual
experiment?
Before starting the virtual experiment, safety is the utmost priority by donning a pair of gloves.
3. What does PCR do, how does it work, and why is it useful?
The PCR is a process or technique that allows amplification of DNA with short strands by making many
copies up to billions of such DNA strand through repeated heating and cooling processes. During the
heating process at 95 degrees centigrade and followed by cooling of the chromosomes, the primers are
softened and combine to the original DNA strands. The DNA polymerase then binds and are able to copy
each strand of the DNA producing mostly subunits of ribosomal DNA or 16s rDNA with different
sequences depending on the species of the bacteria. The amplified strands of the DNA facilitates analysis
of the DNA sequences which then helps identification of specific bacteria .
4. How do you separate the desired DNA from all others?
Separation of desired DNA from all others is done through the process of purification using microfilter
or gel and running the sample in a microconcentrator column by centrifuge process. The process will
trap the PCR products or the desired DNA, setting aside the materials that are not needed in the
collection tubes for discard which may contain primers, nucleotides, and other undesired small
compounds. The column containing the PCR products will be then attached to the inverted tube and
once again centrifuged after adding buffers to loosen the DNA. The collection tube will then contain
mostly 1,500bp-long 16S rDNA with little contamination of long-stranded DNA.
5. Why is it possible to use a DNA sequence to identify bacteria?
Every bacterium follows a unique DNA sequence. By studying the pattern of the sequence information
in each tube, the bacteria will be identified by matching the sequence of their 16SrDNA to the DNA
sequence of the other previously identified bacteria with known sequences in the database. The use of
tools like Basic Local Alignment Search Tool (BLAST) can facilitate the matching process. The sequence
is unique to every species making the identification of the bacteria possible by matching the pattern of the
DNA sequence. Perfect match DNA sequence would indicate the bacteria is identical to that in the
database while a sequence pattern with some differences may indicate a variation of species or could be
a new species which needs further assessment.
6. What bacteria was isolated from Sample D – Blood Sample?
The bacterium isolated from Sample D was Salmonella Typhimurium.