A portable quantitative polymerase chain reaction platform (qPCR) for rapid detection of pathogens impacting model organisms in animal facilities

Project Summary In recent years there have been growing concerns about the rigor and reliability of data originating from common and critical animal model experimentation. In fact, a core principal of science – reproducibility – has been called into question largely due to challenges in replicating biologically complicated animal experiments. We have developed a fast, portable, quantitative PCR (the current universal “gold standard” method) device for use in a wide variety of diagnostic settings. We believe that our rapid, handheld, battery-powered and wireless device has the potential to empower rapid diagnostics around the world. In this proposal we aim to validate the use of our prototype device using real-world samples for microbial pathogen detection. Regarding our innovative technology, we have taken a fundamentally different approach to heating and cooling the sample being amplified, avoiding the standard Peltier heating block. The heat transfer is so efficient that we are able to perform a heating and cooling cycle in as little as 15 seconds (possibly even faster), resulting in a 40-cycle run finishing in about 11 minutes. In essence, this means you can get a quantitative answer regarding the presence and abundance of your target pathogen with ultimate sensitivity significantly faster than the current state of the art. Looking deeper into the root causes of animal-derived data variability is pointing to several possible environmental and biological causes. In terms of the biology, microbes that live inside or outside of the body are proving to have clear and present effects on experimental outcomes, yielding data that is inconsistent and questionable. In particular, when the studies of interest are translational by design, and therefore intended to benefit / improve human health, there is even greater cause for concern. We are poised to test our device to identify and quantify the presence (or absence) of pathogens in an fully operating academic animal facility at UC Berkeley. Together with the Office of Laboratory Animal Care, we have identified two important and tractable pathogens as good candidates for initial proof of principle studies: Helicobacter species (bacteria) in mice and B. dendrobatidis, a fungus affecting amphibians.