There are several ways to interrogate a cell for changes induced by artificial or natural agents during a biological process. One way is to look for changes in cellular transcript levels that may indicate changes in the corresponding proteins. In another instance, the focus may be on the presence or absence of a viral or bacterial pathogen. In this case, detecting not only the presence but also the level of the pathogen provides valuable information in devising a treatment regimen. Alternatively, looking for an increase in the level of expression from a transgene or the inhibition of expression of an endogenous gene by an siRNA may be the question of interest. In all cases, quantitative real-time PCR technology can be utilized to provide the required information. Successful implementation of the technology requires users to have a basic background in the theoretical principles of real-time PCR as well as their practical application to the project at hand. The goal of this introductory chapter is to provide a basic foundation in the use of real-time PCR. Some of the following chapters will expand on topics presented here and add necessary new information required for a full understanding of this powerful technique.

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