BIOTECHNOLOGY II

LABORATORY WORK 1
September 26, 2010

From:
Usman AZIZ
Adil BHATTI

To:
Ms. Moniza
Biotechnology II
INTRODUCTION

An ordinary visit, not-the-first time sneak peeks, to Laboratories in Bio-

Physics Department of COMSATS. The purpose of the labs and their work
progress are in fields such as Microbiology, Genetics, and other works related
to these fields such as cancer, viruses etc. The details of these works and
labs are defined below. The apparatus, the projects involved in these labs
and what role they play in the Bioinformatics will be our concern.

MIRCOBIOLOGY LAB

This lab deals in with microorganisms such as viruses, bacteria, protozoa etc,
their properties such as pathogenicity and creation of vaccines against
viruses. The work environment is controlled as not to contaminate the
outside environment and most significantly the personnel working in that
area, as any infiltration of pathogens inside the human body has drastic
effects, may be lethal too.

Projects________________________________________________

• “Development of integrated The project is defined to detect

whole cell GFB based elements both macronutrients and
biosensor to detect bio micronutrients, which are not
available organophosphate essential such as element
from environment.” (This cadmium, arsenic, mercury etc.
project is HEC funded) Their high quantity can be harmful
and lethal for example Napoleon
Details of the above project: Bonaparte, famous French military
personnel died because of arsenic
Usage of organophosphate is in the poisoning.
pesticides, but apart from being
useful in terminating field bugs, it Their usage is in industries to
is also a carcinogen, yet harmful to manufacture pesticides,
certain organisms including poor preservatives etc., but these
human beings. industrial products are some
The project involves a chip based environmental killers. They can be
biosensor unlike conventional detected using Atomic Absorption
method it uses no training of Photometry, which is a tiresome
personnel, less man power is and time wasting stuff.
required and the results are rapid
and its easy to use. • “Surveillance and source
tracking of diarrhea causing
• “Development of integrated bacterial pathogens in
whole cell GFB based Pakistan”
biosensor to detect heavy
metals from environment” Details of the above project:

Details of the above project: Bacterial pathogens especially

which are sourced from the recent

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flood incident happening in
Pakistan. Diarrhea, or loose
motions one say, is the extreme
discharge of water from the body,
which leads to dehydration of
bodily fluids. It’s caused by viruses,
protozoa, and some five or more
types of bacteria including: E. coli, • “Investigation of Whooping
Vibrio Cholera, Salmonella and its cough (Pertussis) infection”
variants and others.
Details of the above project:
The procedure involves actively
monitoring of disease from The work is on the causes of the
contaminated sources like water or infection and the feasible
food, uncooked meat and fouled effectiveness of vaccines and to
diary products. develop more effective control for
the spread of this infection.

Equipements____________________________________________

Microscope An instrument to see objects too small for the

naked eye. The science of investigating small
objects using such an instrument is called
microscopy. Microscopic means invisible to the
eye unless aided by a microscope.

Gel Electrophoresis deoxyribonucleic acid (DNA), ribonucleic acid

(RNA), or protein molecules using an electric field
applied to a gel matrix. DNA Gel electrophoresis
is usually performed for analytical purposes,
A technique used for often after amplification of DNA via PCR.
the separation of

Fluorometer of fluorescence: its intensity and wavelength

distribution of emission spectrum after excitation
by a certain spectrum of light. These parameters
are used to identify the presence and the amount
of specific molecules in a medium. Modern
fluorometers are capable of detecting fluorescent
molecule concentrations as low as 1 part per
A device used to trillion.
measure parameters

Spectrophotometer

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 Perhaps the most common application of
spectrophotometers is the measurement of light
It’s a photometer (a absorption.
device for measuring
light intensity) that The use of spectrophotometers spans various
can measure scientific fields, such as physics, chemistry,
intensity as a biochemistry, and molecular biology. They are
function of the light widely used in many industries including printing
source wavelength. and forensic examination.

Centrifuge perpendicular to the axis. The centrifuge works

using the sedimentation principle, where the
centripetal acceleration causes more

A piece of
equipment, generally
driven by an electric
motor (some older
models were spun by dense substances to separate out along the
hand), that puts an radial direction (the bottom of the tube). By the
object in rotation same token, lighter objects will tend to move to
around a fixed axis, the top (of the tube; in the rotating picture, move
applying a force to the centre).

It’s used in DNA hybridization technique

Hybridization Oven providing constant temperature and continuous
shaking

Thermal Cycler Machine or DNA Amplifier) is a laboratory

apparatus used to amplify segments of DNA via
the polymerase chain reaction (PCR) process. The
device has a thermal block with holes where
tubes holding the PCR reaction mixtures can be
inserted. The cycler then raises and lowers the
temperature of the block in discrete, pre-
(Also known as a programmed steps.
Thermocycler, PCR

Biosafety Cabinet for safely working with materials contaminated

with (or potentially contaminated with)
pathogens in the laboratory. Several different
types exist, differentiated by the specifics of
An enclosed, construction. The one in the lab was Class I for
ventilated workspace non-pathogenic organisms.

Role of Bioinformatics of that laboratory:

It was aimed to establish or provide a library of bacterial pathogens and

compile their data to provide helpful material for other work projects and

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enhance their participation in the field of Bioinformatics. Gene sequencing of
these pathogens are done and saved for future works.

CANCER GENETICS LAB

The research and work is been done in breast, and head & neck tumors.
Cancer is a polygenic disorder. The process is carried by expression analysis
and tumor analysis in relation to disease progression. Tumors are screened in
metastasis with respect to these cancers. Up regulation of suppressor genes
with the help pf other molecules provide a cure for these cancer, the purpose
is also to detect the stages and assist in de regulation of the metastasis
process.

Metastasis which is the clonal expansion of cancer cells, Metastasis

Suppressor Gene NM23 as well as BRCA1, the main focus is stage 1 of the
cancer. It can also be reduced by limiting cell to cell adhesion of the cancer
cells.

Equipments_____________________________________________

Gel Doc Also known as Gel Documentation System,

Gel Image System or Gel Imager, is widely
used in molecular biology laboratories for the
imaging and documentation of nucleic acid and
protein polyacrylamide or agarose gels typically
stained with ethidium bromide or other
fluorophores such as

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SYBR Green. ultraviolet (UV) light transilluminator, a hood to
Generally, a Gel Doc shield external light sources and a camera for
is composed of an image capturing.

Incubator microbiological cultures or cell cultures. The

incubator maintains optimal temperature,
humidity and other conditions such as the carbon
dioxide (CO2) and oxygen content of the
atmosphere inside. Incubators are essential for a
lot of experimental work in cell biology,
microbiology and molecular biology and are used
to culture both bacterial as well as eukaryotic
cells. The one used in lab was specially purposed
A device used to for the incubation of mammalian cells.
grow and maintain

Real-time PCR Machine that amplifies and detects DNA. It

Instrument combines the functions of a thermal cycler and a
fluorimeter, enabling the process of real-time
PCR.

Other equipements included Horizontal Gel tank and OGGE for multiple
samples.

Role of Bioinformatics of that laboratory:

Primer designing and the role gene database for research.

POINT OF VIEW FOR LABORATORIES

Bioinformatics is a diverse subject, including some major field such as

microbiology, genetics, computer programming and etc. The visit to these
laboratories has provided us with views that there are so many fields to
choose from the Bioinformatics program. Bioinformatics alone touches most
of the biological studies. The sandwich of computers and biology has
provided us with diverse knowledge to tackle with most nature born problem
in the environment. There is not much to say as this was the first visit, later
as our visit to other labs will enhance and broaden our thoughts, the views
will definitely become more complex and better.

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