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CC BY V4.0, Open Access
Thesis
DEVELOPMENT AND DEPLOYMENT OF A RAPID DETECTION SYSTEM FOR SALMONID ENVIRONMENTAL DNA WITH CRISPR-CAS12A
Washington State University
Master of Science (MS), Washington State University
05/2024
DOI:
https://doi.org/10.7273/000006918
Abstract
Pacific salmon and trout are ecologically, economically, and culturally invaluable to their native waters. In recent history, a wide range of threats including climate change, habitat destruction and loss and invasions of non-native species have severely impacted many populations of Pacific salmon and trout. Large-scale efforts to conserve, restore, and protect salmon and trout require consistent and extensive monitoring to assess success and areas for improvement. One such monitoring strategy uses the detection of environmental DNA (eDNA), an organism’s DNA suspended in its occupied habitat medium. Utilized by many for its cost-effective and simple deployment, eDNA provides a binary present or absent indication for a target species. Traditionally, eDNA samples are processed in a sterile laboratory with results visualized via qPCR. However, many groups lack access to equipment such as qPCR, leading to extended wait-periods to receive results when samples are outsourced to dedicated laboratories. Therefore, a simplified and rapid method to detect eDNA would be of great benefit. CRISPR-Cas12a nucleic acid detection was employed to detect specific sequences from salmon and trout species. The technology was then paired with Loop Mediated Isothermal Amplification to sensitively detect a target species’ eDNA. Field-capable protocols were designed and tested for the option to obtain real-time streamside results. The technology was piloted on the Snake River, detecting Chinook salmon in correspondence with positive identification from a nearby fish ladder. Subsequently, an invasive species identification study deployed CRISPR-eDNA assays to detect the presence of brook trout and cutthroat trout in a Washington State Stream. Chinook salmon were successfully detected in the Snake River, and brook trout and cutthroat trout were identified as occupying the same spatial range within the study area. This body of work provides a foundation for improving the simplicity and efficiency of environmental DNA sampling.
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Details
- Title
- DEVELOPMENT AND DEPLOYMENT OF A RAPID DETECTION SYSTEM FOR SALMONID ENVIRONMENTAL DNA WITH CRISPR-CAS12A
- Creators
- Tholen Blasko
- Contributors
- Michael P Phelps (Chair)Caren S Goldberg (Committee Member)Amber L Adams-Progar (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- Department of Animal Sciences
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University
- Number of pages
- 93
- Identifiers
- 99901125940201842
- Language
- English
- Resource Type
- Thesis