dna microarray

MICROARRAY

MicroarrayMicroarray

Just a bunch of dots…

Or a smooth comprehensive data

MICROARRAY

Study the expression of genes at once

Study the expression of genes at once

Involves placing thousands of gene

sequences in known locations on a glass slide

called a gene chip

Involves placing thousands of gene

sequences in known locations on a glass slide

called a gene chip

A sample containing DNA or RNA is placed in contact with the

gene chip.

A sample containing DNA or RNA is placed in contact with the

gene chip.

Complementary base pairing between the

sample and the gene sequences

on the chip produces light

that is measured. 

Complementary base pairing between the

sample and the gene sequences

on the chip produces light

that is measured. 

HistoryHistory

Evolved from Southern Blot

Miniaturized microarrays were introduced in 1995 (Science 1995;270:467)

1980s - better surface technologies, more powerful robots for arraying, better nucleic acid dye labeling techniques and improved computational power and automated analyzers have vastly improved the power and efficiency of microarray, while also lowering the cost of these analyses

HistoryHistory

Used to analyze many different systems, including the classification of microbes and human microbial pathogens, cellular responses to pathogens, drug and toxic exposures, tumor classification, single nucleotide polymorphism detection, the detection of gene fusions, comparative genomic hybridization, alternative splicing detection (exon junction array/exon arrays) and gene expression profiling via analyzing global mRNA levels

Classification of microbes and human microbial pathogens Classification of microbes and human microbial pathogens

Cellular responses to pathogensCellular responses to pathogens

Drug and toxic exposuresDrug and toxic exposures

Tumor classification Tumor classification

Detection of gene fusions Detection of gene fusions

How does the equipment look like?

How is the technique done?

ApplicationsApplications

Microarray Analyses of Shrimp Immune ResponsesMicroarray Analyses of Shrimp Immune ResponsesTakashi Aoki, Han-Ching Wang, Sasimanas Unajak

Mudjekeewis D. Santos, Hidehiro Kondo, Ikuo Hirono2010

Shrimp Aquaculture

Shrimp Aquaculture

Shrimp Aquaculture

Shrimp Aquaculture diseases

Environmental factors

Antibiotic use

Several problems include:

ObjectiveObjective

Review the gene expression profile of shrimp in response to some of the problems using microarray analysis

Immune-related gene expression following WSSV infectionImmune-related gene expression following WSSV infection

Immune-related gene expression following YHV infectionImmune-related gene expression following YHV infection

Immune-related gene expression following Vibrio infectionImmune-related gene expression following Vibrio infection

6 Categories of Shrimp Immune Responses against different stimuli:

Immune-related gene expression following ImmunostimulationImmune-related gene expression following Immunostimulation

Immune-related gene expression following antibiotic treatmentImmune-related gene expression following antibiotic treatment

Immune-related gene expression following environmental stressImmune-related gene expression following environmental stress

White Spot Syndrome VirusWhite Spot Syndrome Virus(WSSV)(WSSV)

Immune-related gene expression following WSSV infectionImmune-related gene expression following WSSV infection

Microarray results, together with the results of other shrimp gene studies, indicated not only the importance of innate immunity for defense against WSSV, but also the novel

antiviral functions of known and unknown proteins in innate immunity.

Yellow Head VirusYellow Head Virus(YHV)(YHV)

Immune-related gene expression following YHV infectionImmune-related gene expression following YHV infection

-Over ten responsive genes were shrimp immune-related genes

- Five genes showed relatively consistent high expression throughout the YHV infection

VibrioVibrio infection infection

Immune-related gene expression following Vibrio infectionImmune-related gene expression following Vibrio infection

-Suggests that different immune modulation responses can be triggered by different pathogens

-Hemocyanin expression was significantly suppressed in WSSV treated shrimp, whereas it was up regulated in inactivated

Vibrio

Immune-related gene expression following ImmunostimulationImmune-related gene expression following Immunostimulation

- Analysis showed that PG administration up-regulated the expression of immune-related genes

Immune-related gene expression following antibiotic treatmentImmune-related gene expression following antibiotic treatment

-For therapeutic and prophylactic purposes

-Expression of genes in the shrimp lymphoid organ including those that are involved in immune response were altered after

the administration of antibiotics

Immune-related gene expression following antibiotic treatmentImmune-related gene expression following antibiotic treatment

Immune-related gene expression following environmental stressImmune-related gene expression following environmental stress

Immune-related gene expression following environmental stressImmune-related gene expression following environmental stress

-Stress should decrease the ability of shrimp to defend themselves against pathogens

-Shrimp physical condition, the immune response, and environmental stress are closely related

ConclusionConclusion

Effective tool in elucidating and understanding the mechanisms of shrimp responses to viral and bacterial

infection, antibiotic treatment and environmental stress.

The technique is an indispensable tool in the study of shrimp and should reveal breakthrough information that

could lead to novel applications