Name: Barte, Aira Chrissel G.

Section: MEXE-1304
Subject: SCI-402 General Biology

I. Activity Title:
“LAB Simulation - Virtual Bacterial Identification”

II. Objective:
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.

III. Tools, Materials, and Equipment:

The Virtual BACTERIAL ID LAB - by Howard Hughes Medical Institute

IV. Procedure:

1. Read the “Intro” on the virtual lab website

2. Click on the animation part to enter the lab.
3. Click on the specific object at the animation to follow the step by step process of the
activity
4. As you reached the “6. Sequencing analysis”, follow the steps found on the Notebook tab
of the web page.
5. Answer the following questions below.
• What kind of patient samples are used for the purpose of identifying possible
pathogens?
• What does PCR do, how does it work, and why is it useful?
• How do you separate the desired DNA from all others?
• How does an automatic DNA sequencer work?
• Why is it possible to use a DNA sequence to identify bacteria?
6. Place 3 screenshot for each animation process

V. Questions and Answers:

What kind of patient samples are used for the purpose of identifying possible pathogens?
- They used fluid from lymph node, stool, urine, blood, and sputum sample for the
purpose of identifying possible.
What does PCR do, how does it work, and why is it useful?
- Polymerase chain reaction (PCR) is a common laboratory technique used to make many
copies (millions or billions!) of a particular region of DNA. In PCR, single-stranded
DNA is made by heating a chromosome fragment to 95°C. It is then cooled so that the
primers anneal to the original DNA strands and DNA polymerase can bind and copy
each strand. With repeated heating and cooling, millions and even billions of copies of
 DNA can be made in a few hours. Before the advent of PCR, making sufficient copies
of DNA for sequencing was a tedious process. Now, PCR makes obtaining copies of
DNA from a small original sample routine, with far-reaching consequences. PCR is
used in many research labs, and it also has practical applications in forensics, genetic
testing, and diagnostics. For instance, PCR is used to amplify genes associated with
genetic disorders from the DNA of patients (or from fetal DNA, in the case of prenatal
testing). PCR can also be used to test for a bacterium or DNA virus in a patient's body:
if the pathogen is present, it may be possible to amplify regions of its DNA from a
blood or tissue sample. PCR is used in many areas of biology and medicine, including
molecular biology research, medical diagnostics, and even some branches of ecology.

How do you separate the desired DNA from all others?

- Running a gel is actually one method of purification. Once the PCR product is in the
gel, you can cut out the band corresponding to the PCR product and isolate the DNA
from the gel.
How does an automatic DNA sequencer work?
- 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.
Why is it possible to use a DNA sequence to identify bacteria?
- DNA sequence is particularly useful in identifying unusual bacteria that are difficult to
identify by conventional methods. It can also provide accurate identification of isolate
with atypical phenotypic characteristics.
VI. Screenshots: (Label or categorize it properly)
VII. Conclusion/s: (What can you say about the activity? Summarize your learnings or learning
experience)

Performing this experiment enable us to be familiarize with the science and techniques
used to identify different types of bacteria based on their DNA sequence. We are able to learn
performing in a virtual lab wherein we can do tasks using only our laptops. Also, we are able to
identify bacteria using DNA sequence. It also gives information about PCR (polymerase chain
reaction), how does it work and its use in identifying bacteria.