Toxicology: Toxicogenomics: microarray

1. ZY-408 T : TOXICOLOGY II
CH:3 TOXICOGENOMICS :
MICROARRAY
BY:
EDEN D’SOUZA
M.SC. II
DEPT. OF ZOOLOGY
A.K.I.’S POONA COLLEGE

2. MICROARRAY ANALYSIS
• A grid of DNA segments of known sequence that is used to test and map DNA
fragments, antibodies, or proteins.
• The human genome contains approximately 21,000 genes. At any given moment,
each of our cells has some combination of these genes turned on, and others are
turned off. How do scientists figure out which are on and which are off?
• Scientists can answer this question for any cell sample or tissue by gene
expression profiling, using a technique called microarray analysis.
• Microarray analysis involves breaking open a cell, isolating its genetic contents,
identifying all the genes that are turned on in that particular cell, and generating
a list of those genes.
• DNA microarray analysis is a technique that scientists use to determine whether
genes are on or off.
• Scientists know a gene is on in a cell if its mRNA is present.

3. GENE EXPRESSION
VALUES FROM
MICROARRAY
EXPERIMENTS CAN BE
REPRESENTED AS
HEAT MAPS
TO VISUALIZE THE
RESULT OF DATA
ANALYSIS.

4. HOW DOES IT WORK?
• A DNA micorarray allows scientists to perform an
experiment on thousands of genes at the same
time.
• Each spot on a microarray contains multiple
identical strands of DNA.
• The DNA sequence on each spot is unique.
• Each spot represents one gene.
• Thousands of spots are arrayed in orderly rows
and columns on a solid surface (usually glass).
• The precise location and sequence of each spot is
recorded in a computer database.
• Microarrays can be the size of a microscope slide,
or even smaller.

5. TYPICAL DUAL-COLOUR
MICROARRAY EXPERIMENT

6. USES / APPLICATIONS
• Microarray technology provides a unique tool for the determination of gene
expression at the level of messenger RNA (mRNA).
• The simultaneous measurement of the entire human genome (thousands of
genes) will facilitate the uncovering of specific gene expression patterns that are
associated with disease.
• One important application of microarray technology, within the context of
neurotoxicological studies, is its use as a screening tool for the identification of
molecular mechanisms of toxicity.
• Such approaches enable researchers to identify those genes and their products
(either single or whole pathways) that are involved in conferring resistance or
sensitivity to toxic substances.

7. TYPES OF MICROARRAYS INCLUDE:
• DNA microarrays, such as cDNA microarrays, oligonucleotide microarrays, BAC microarrays and
SNP microarrays
• MMChips, for surveillance of microRNA populations
• Protein microarrays
• Peptide microarrays, for detailed analyses or optimization of protein–protein interactions
• Tissue microarrays
• Cellular microarrays (also called transfection microarrays)
• Chemical compound microarrays
• Antibody microarrays
• Glycan arrays (carbohydrate arrays)
• Phenotype microarrays
• Reverse Phase Protein Microarrays, microarrays of lysates or serum
• Interferometric reflectance imaging sensor (IRIS)

8. TWO AFFYMETRIX
CHIPS.
A MATCH IS SHOWN AT
BOTTOM LEFT FOR SIZE
COMPARISON 

9. DNA MICROARRAY
• A DNA microarray (also commonly known as DNA chip or biochip) is a collection
of microscopic DNA spots attached to a solid surface.
• Scientists use DNA microarrays to measure the expression levels of large
numbers of genes simultaneously or to genotype multiple regions of a genome.
Each DNA spot contains picomoles (10 moles) of a specific DNA sequence, known
as probes (or reporters or oligos).
• DNA microarray analysis is one of the fastest-growing new technologies in the
field of genetic research. Scientists are using DNA microarrays to investigate
everything from cancer to pest control. You can use a DNA microarray to
investigate the differences between a healthy cell and a cancer cell.

10. Summary of DNA Microarrays.
Within the organisms, genes are
transcribed and spliced to produce
mature mRNA transcripts (red). The
mRNA is extracted from the
organism and reverse transcriptase
is used to copy the mRNA into
stable ds-cDNA (blue). In
microarrays, the ds-cDNA is
fragmented and fluorescently
labelled (orange). The labelled
fragments bind to an ordered array
of complementary oligonucleotides,
and measurement of fluorescent
intensity across the array indicates
the abundance of a predetermined
set of sequences. These sequences
are typically specifically chosen to
report on genes of interest within
the organism's genome.

11. PROTEIN MICROARRAY
• A protein microarray (or protein chip) is a high-throughput method used to track
the interactions and activities of proteins, and to determine their function, and
determining function on a large scale.[1] Its main advantage lies in the fact that
large numbers of proteins can be tracked in parallel. The chip consists of a
support surface such as a glass slide, nitrocellulose membrane, bead, or
microtitre plate, to which an array of capture proteins is bound.[2] Probe
molecules, typically labeled with a fluorescent dye, are added to the array. Any
reaction between the probe and the immobilised protein emits a fluorescent
signal that is read by a laser scanner.[3] Protein microarrays are rapid, automated,
economical, and highly sensitive, consuming small quantities of samples and
reagents.

12. HYBRIDIZATION OF THE TARGET TO THE PROBE

13. APPLICATIONS
• There are five major areas where protein arrays are being applied: diagnostics,
proteomics, protein functional analysis, antibody characterization, and treatment
development
• Diagnostics involves the detection of antigens and antibodies in blood samples;
the profiling of sera to discover new disease biomarkers; the monitoring of
disease states and responses to therapy in personalized medicine; the
monitoring of environment and food. Digital bioassay is a en example of using
protein microarray for diagnostic purposes. In this technology, an array of
microwells on a glass/polymer chip are seeded with magnetic beads (coated with
fluorescent tagged antibodies), subjected to targeted antigens and then
characterised by a microscope through counting fluorescing wells. A cost-
effective fabrication platform (using OSTE polymers) for such microwell arrays
has been recently demonstrated and the bio-assay model system has been
successfully characterised.

14. • Proteomics pertains to protein expression profiling i.e. which proteins are
expressed in the lysate of a particular cell.
• Protein functional analysis is the identification of protein–protein interactions
(e.g. identification of members of a protein complex), protein–phospholipid
interactions, small molecule targets, enzymatic substrates (particularly the
substrates of kinases) and receptor ligands.
• Antibody characterization is characterizing cross-reactivity, specificity and
mapping epitopes.
• Treatment development involves the development of antigen-specific therapies
for autoimmunity, cancer and allergies; the identification of small molecule
targets that could potentially be used as new drugs.

15. THE STEPS REQUIRED IN A MICROARRAY
EXPERIMENT

16. REFERENCES:
• http://learn.genetics.utah.edu/content/labs/microarray/
• https://einstein.pure.elsevier.com/en/publications/use-of-microarray-technologies-in-toxicology-
research-2
• https://en.wikipedia.org/wiki/Microarray