Transcript Genes and Chips

Genes and Chips
Genes….
 The proper and harmonious
expression of a large number of
genes is a critical component of
normal growth and development and
the maintenance of proper health.
Disruptions or changes in gene
expression are responsible for many
diseases.
 Gene expression is a highly complex
and tightly regulated process that
allows a cell to respond dynamically
both to environmental stimuli and to
its own changing needs.
In short…
 Not only do genes have an ‘on’ and
an ‘off’
 They also have volume control
This means…
 All cells in an organism contain the
same genes
 Different genes are expressed in
different tissues under different
conditions
Induced (expressed) Gene:
Gene A ------- Lots of mRNA A
Repressed (not expressed) Gene:
Gene B ……..sadly, no mRNA B
To Determine which genes are
expressed under which
circumstances:
 A microarray is a tool for analyzing
gene expression that consists of a
small membrane or glass slide
containing samples of many genes
arranged in a regular pattern.
How they work:
Why they are REALLY
important….
 Survey a large number of genes
quickly or when the sample to be
studied is small.
 Assay gene expression within a single
sample or to compare gene
expression in two different cell types
or tissue samples, such as in healthy
and diseased tissue.
 Functions of new genes can be
determined based on similarities in
expression patterns with those of
known genes.
 Reveal new patterns of coordinated
gene expression across gene families.
 Knowledge of these interrelationships among genes
Practical applications…
 Comparative Genomic Hybridization
--tumor classification, risk, and
prognosis
 Expression Analysis
--drug and therapy development
and response
 Mutation/Polymorphism Analysis
--tracking disease progression
In this experiment:
 Identify the major steps of the chip
process
 Identify the primary colors that a chip
shows
 Understand the reasons for the
presence/absence/intensity of a
particular color
You will need:
 Chip slide
 Marker
 Access to hybridization solutions
What to do:
1.
2.
3.
4.
DO NOT TOUCH surface of slide
Mark each spot with a number (1-6)
Move to water bath area
Use the dropper bottles to spot the
appropriate gene solution onto each
labeled slide spot
5. Successful print = hardened and dry
spots
 6. Carefully drop 1-2 drops of
hybridizing solution onto each spot,
making sure not to touch tip of bottle
to DNA spots
 7. Visualize results by setting slide on
white paper
How to read them…
 The mRNA used in this lab was
isolated from 6 genes found in both
normal and cancerous lung cells
 Expressed genes, because we are
NOT using lasers, will be seen as
either pinks, purples, and blues
Important Stuff….
 Many students may have the view
that only important cancer genes are
those that are highly expressed, so it
must be explained that:
 Highly expressed normal genes may
prevent cancer
 Minimally expressed genes may be
important
 “Housekeeping genes” may be expressed
in either cell type
As the lab is written:
 Everyone gets the same result, so
basically everyone is testing the same
individual
 Students who don’t follow protocol
can still “get the right results,” and
therefore understanding is unclear
So….
 Did some research and discovered
how the solutions were
produced…various combinations of
water, phenophthalein, and
thymolphthalein…by altering the
combinations different “color” results
can be achieved.
 Student groups can have different
“patients” to diagnose