Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A
microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest.
Microarrays are used in
microbial ecology, especially with the recent increase in
microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. See also:
Metagenomics: Theory, Methods and ApplicationsA phylogenetic microarray that has been developed by the Andersen laboratory, the
PhyloChip, is an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods.
A functional gene array that has been developed by the Zhou laboratory, the
GeoChip, is an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer oligonucleotide probes and covers more than 10,000 gene sequences in 150 gene categories involved in carbon, nitrogen, sulfur, and phosphorus cycling, metal resistance and reduction, and organic contaminant degradation. GeoChip can be used as a generic tool for microbial community analysis, and also link microbial community structure to ecosystem functioning.
from Gary L. Andersen
in Environmental Molecular MicrobiologyFurther reading:
Labels: DNA microarray, DNA microarrays, GeoChip, microarray, Microarrays, PhyloChip, Phylogenetic microarray
Epigenetics"This volume is an excellent collection of advanced review papers on different aspects of the emerging research field of
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from S.K. Basu and A. Goyal, Agriculture and Agri-Food Canada writing in
Crop Science (2009) 49: 1937-1938 read more ...Labels: Book on epigenetics, book review, books, epigenetics