For DNA analysis, polymerase chain reaction (PCR) methods exist that can selectively enrich the unique biomarker sequence of an organism. This sequence amplification allows the representative pathogen sequences to be identified by more common laboratory methods, such as mass spectrome-try, optical spectroscopy, and gel and capillary electrophoresis. More specifically, optical analysis methods have been combined with PCR to form a real-time PCR assay. Real-time PCR methods allow the fluorescent response to correlate directly to the biomarker sequence amplification, which increases exponentially with the PCR process, essentially signaling the presence of the gene targets of an organism as the PCR process is ongoing. This method is now a widely adopted assay for preliminary analysis of pathogens, with results reported within a few hours. In few notable applications, this method has been used for multiplexed analysis of water-borne pathogens (Bopp et al., 2003; LaGier et al., 2004). Another novel extension of nucleic acid amplification includes a RNA amplification method, signaling the presence of pathogen and allowing determination of viability (Min and Baeumner, 2002; Baeumner et al., 2003).
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