The use of nucleic acid-based approaches for detection and quantification of molecular targets in biology allows for rapid responses and potentially improved outcomes, whether it be successful treatment in human health situations, or protection of the environment. However, these approaches are often complex, requiring centralized laboratory facilities and skilled personnel. The use of simpler molecular approaches could allow these tests to be conducted in the field or at the point-of-care. Traditional nucleic acid-based approaches are also highly targeted, allowing the user to detect only a few targets per experiment. The use of higher-throughput technologies could allow full panel screening of many targets and samples in a single experiment. In this dissertation, the development and use of these simpler and high-throughput approaches has been shown for a number of biological applications relevant to human health and the environment. Direct nucleic acid amplification without sample processing has the potential to greatly reduce the time-to-results by allowing detection of molecular targets in the field or at the point-of-care. This was shown to be important for rapid detection of environmental DNA (eDNA) from aquatic invasive species, antimicrobial resistance genes (ARG) to rapidly determine treatment options, and human microRNAs directly from body fluids for diagnosis of diseases, cancers, or environmental exposure to toxicants. Similarly, higher-throughput molecular approaches were determined to be important for detection ARG panels in environmental and human samples to assess whether sources are anthropogenic or part of the natural resistome as well as for quantification of microRNA panels to determine differential expression of microRNAs in response to environmental toxicants and members of the gut microbiome. Overall the development and use of these techniques can enhance a number of biological applications, resulting in improved environments and human health.
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