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Development of A New Instrument to Identify Microbial Genome

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Rapid identification and tracing the origin of pathogenic bacteria are imperative in response to a bioterrorist attack or an infectious disease outbreak. Pulsed-Field Gel Electrophoresis (PFGE) fingerprinting is frequently used for these tasks, particularly for tracing bacterium origins. However, the short fragment bands are lost in PFGE when extended separation times are used to resolve the long DNA molecules, thus reduce the detection specificity, because the lengths of the short fragments provide additional genotype information that could be critical to discriminate two similar genomes. Another drawback of PFGE is that the electrophoresis is too slow. In a rapid (24-hour) PFGE method the electrophoresis takes 14-18 hours. Additionally, the intra- and inter-laboratory reproducibility of PFGE also needs to be improved. Although diverse approaches such as entropic traps and DNA prisms have been explored for DNA separations, none have thus far been practically utilized. We have recently discovered a new and efficient technique to resolve broad size ranges of DNA molecules. In this application we propose to construct a novel instrument to demonstrate the proof-of-principle of this new technique for high-speed and accurate microbial identification.
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