PCR-based methods have proven to be sensitive, but two rounds of amplification (nested PCR) are often needed to detect the presence of Plasmodium DNA.
DNA digestion seems to occur more quickly, and PCR-based methods have proven to vary considerably between different laboratories.
Culture-based methods have proven successful to document bacterial community changes on bleached and diseased corals [25], [48] [50], but the difficulties associated with culturing marine bacteria coupled with a bias towards groups of bacteria that readily grow on general culture media limits the usefulness of such methods in describing bacterial diversity in environmental samples [7], [51], [52].
Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced.
Previously, only microsatellite-based methods have proven useful for molecular epidemiologic studies of Coccidioides spp., which provide adequate separation across geographically diverse samples (17 ) and identifying clonal isolates (genotypically identical) recovered from the same patient (18 ).
In general, PCR-based methods have proven to be very effective for the quantitative analysis of gene copy number or mRNA, especially when only a limited amount of tissue is available [ 39, 40], while recent publications have shown that total RNA isolated from FFPE tissue samples can be used for reliable gene expression analysis [ 22, 41].
Unfortunately, many of these rate based methods have not proven to be as successful as intended because of factors external to the reservoir.
Those methods have proven to be particularly effective and yielded a clearer biological view of the system than single source based methods.
