Virtual Lab

Punzalan, Nicole D.

VIRTUAL BACTERIAL IDENTIFICATION (20 pts)

SOURCE: https://media.hhmi.org/biointeractive/vlabs/bacterial_id/index.html

Welcome to the Virtual Bacterial Identification Lab. The purpose of the lab is to familiarize you
with the science and techniques used to identify different types of bacteria based on their DNA sequence.
Not long ago, DNA sequencing was a time-consuming, tedious process. With readily available commercial
equipment and kits, it is now routine. The techniques used in this lab are applicable in a wide variety of
settings, including scientific research and forensic labs.
Basic Steps
 Prepare a sample from a patient and isolate whole bacterial DNA.
 Make many copies of the desired piece of DNA.
 Sequence the DNA.
 Analyze the sequence and identify the bacteria.

The piece of DNA used for identifying bacteria is the region that codes for a small subunit of the
ribosomal RNA (16S rRNA). We will refer to this piece as 16S rDNA. Different bacterial species have
unique 16S rDNA sequences. The identification relies on matching the sequence from your sample
against a database of all known 16S rDNA sequences.
Learning Output

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 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 .

3. 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.

4. How does an automatic DNA sequencer work?
In an automatic DNA sequencer, just as in any DNA sequencer, the DNA is injected into the gel
wells at the top of the tank, and a negative charge is applied to that end of the tank. The negative charge
provides a strong impetus for the DNA strands to travel different distances, to the end of the tank.
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.
Punzalan, Nicole D.

LAB DISEASE (30 pts)

Source: https://www.learner.org/wp-content/interactive/envsci/disease/disease.html?initLesson=1

1. LESSON: VIRGIN FIELD
A. DISEASE: KOLD
B. POPULATION DENSITY: MEDIUM
C. POPULATION MIXING: MEDIUM

Output:

A. Open Details. Take a picture of Details:

B. Click Run, wait until your data stops. Take a picture of your screen.
2. LESSON: VACCINATION
A. DISEASE: IMPFLUENZA
B. POPULATION DENSITY: MEDIUM
D. VACCINATED: NONE

Output:



3. LESSON: PANDEMIC
A. DISEASE: IMPFLUENZA
B. POPULATION DENSITY: HIGH
D. VACCINATED: NONE

Output:



Punzalan, Nicole D.

VIRTUAL LABS

Source: https://virtuallab.nmsu.edu

At the home page, there are many topics listed. Click on the following subtopics and perform the virtual
lab.
1] BACTERIA SAMPLING (Using Various Disposable Lab Equipments) (10 pts)
Output: Summary and Reflection

Ma’am, I really can’t access the third part of this activity.
2] GRAM STAINING (10 pts)

Under the following subtopics, take 1 picture and upload:
1. Laboratoray info

Upload your output here
2. Gram Stain info

3. Slide Prep
4. Gram Staining
5. On your own: (Take a picture of the last step where it says Good Job!)

3] USING THE MICROSCOPE (16 pts)

Under the following subtopics, take 1 picture and upload:
1. Introduction
Type your output here
2. Setting up
3. Low magnification
4. High magnification
5. Oil immersion
6. Discussing results
7. Clean up
8. Conclusion

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Punzalan, Nicole D.

5. Why is it possible to use a DNA sequence to identify bacteria?

Output: Summary and Reflection

2] GRAM STAINING (10 pts)

1. Laboratoray info

2. Gram Stain info

3] USING THE MICROSCOPE (16 pts)

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