C Garrett Miyada | PubMed Health

PubMed2006

The affymetrix GeneChip platform: an overview.

The intent of this chapter is to provide the reader with a review of GeneChip technology and the complete system it represents, including its versatility, components, and the exciting applications that are enabled by this platform. The following aspects of the technology are reviewed: array design and manufacturing, target preparation, instrumentation, data analysis, and both current and future applications. There are key differentiators between Affymetrix' GeneChip technology and other microarray-based methods. The most distinguishing feature of GeneChip microarrays is that their manufacture is directed by photochemical synthesis. Because of this manufacturing technology, more than a million different probes can be synthesized on an array roughly the size of a thumbnail. These numbers allow the inclusion of multiple probes to interrogate the same target sequence, providing statistical rigor to data interpretation. Over the years the GeneChip platform has proven to be a reliable and robust system, enabling many new discoveries and breakthroughs to be made by the scientific community.

Animals↗

PubMed2003

Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa.

Pseudomonas aeruginosa is a ubiquitous environmental bacterium capable of causing a variety of life-threatening human infections. The genetic basis for preferential infection of certain immunocompromised patients or individuals with cystic fibrosis by P. aeruginosa is not understood. To establish whether variation in the genomic repertoire of P. aeruginosa strains can be associated with a particular type of infection, we used a whole-genome DNA microarray to determine the genome content of 18 strains isolated from the most common human infections and environmental sources. A remarkable conservation of genes including those encoding nearly all known virulence factors was observed. Phylogenetic analysis of strain-specific genes revealed no correlation between genome content and infection type. Clusters of strain-specific genes in the P. aeruginosa genome, termed variable segments, appear to be preferential sites for the integration of novel genetic material. A specialized cloning vector was developed for capture and analysis of these genomic segments. With this capture system a site associated with the strain-specific ExoU cytotoxin-encoding gene was interrogated and an 80-kb genomic island carrying exoU was identified. These studies demonstrate that P. aeruginosa strains possess a highly conserved genome that encodes genes important for survival in numerous environments and allows it to cause a variety of human infections. The acquisition of novel genetic material, such as the exoU genomic island, through horizontal gene transfer may enhance colonization and survival in different host environments.

Bacterial Proteins↗