HelioCLEAN: miniaturized system for rapid monitoring of foodborne pathogens

In this project, our major goal of this project is to design, develop and validate an innovative, rapid, and highly selective portable foodborne pathogen detection system, HelioCLEAN. This system will help promote public health by preventing foodborne related contamination, as well as enhance supply chain efficiency, and provide cost-effective testing solutions for the end-to-end agricultural applications. To achieve this major goal, we will focus on the following objectives:1. Developing a High-Efficiency Microbial Extraction ProtocolDesign and optimize a microbial extraction process capable of retrieving pathogens from various agricultural sample matrices (e.g., soil, milk, meat, vegetables) with high recovery rates (>60%) and viability (>50%).Demonstrate detection of one or more bacteria inoculated to three or more food products.2. Create and Validate CRISPR-Based Pathogen Detection ProbesDesign specific CRISPR-based detection probes for the identification of key model microbes (e.g., E. coli, Salmonella with a confusion matrix >90% that gives true detection from the diagonal)Optimize reagent concentrations, detection thresholds, and system configurations for accuracy and minimization of false positives or negatives (<10%).Implement and optimize the photo-controlled reaction to improve the detection specificity and simplify the action required during chip operation.3. Integrate Detection Components into a Portable Microfluidic SystemDevelop a fully integrated microfluidic device to house the detection system, enabling on-site testing and real-time results. (<15cmx10cm). Build a supporting portable microsystem (total footprint <0.1m3) to support the extraction and necessary electrical/optical components.Validate system performance, generate the final data report using three or more target microbes against three or more sample matrices, including performance metrics such as sensitivity, specificity, time efficiency, limit of detection, accuracy, precision, linearity or ruggedness