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FINDeM: A CRISPR-based, molecular method for rapid, inexpensive, and field-deployable organism detection.
  • +4
  • Brandon Hoenig,
  • Jakub Zegar,
  • Michel Ohmer,
  • Macie Chess,
  • Brady Porter,
  • Myah Madril,
  • Corinne Richards-Zawacki
Brandon Hoenig
University of Pittsburgh, Pymatuning Lab of Ecology

Corresponding Author:[email protected]

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Jakub Zegar
University of Mississippi
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Michel Ohmer
University of Mississippi
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Macie Chess
Duquesne University
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Brady Porter
Duquesne University
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Myah Madril
University of Pittsburgh
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Corinne Richards-Zawacki
University of Pittsburgh, Pymatuning Lab of Ecology
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Abstract

The field of ecology has undergone a molecular revolution, with researchers increasingly relying on DNA-based methods for organism detection. Unfortunately, these techniques often require expensive equipment, dedicated laboratory spaces, and specialized training in molecular and computational techniques; limitations effectively excluding field researchers, underfunded programs, and citizen scientists from contributing to cutting-edge science. It is for these reasons that we have designed a simplified, inexpensive method for field-based molecular organism detection – FINDeM (Field-deployable Isothermal Nucleotide-based Detection Method). In this approach, DNA is extracted using chemical cell lysis and a cellulose filter disc, followed by two body-heat inducible reactions – recombinase polymerase amplification and a CRISPR-cas12a fluorescent reporter assay – to amplify and detect target DNA, respectively. Here, we demonstrate FINDeM in detecting Batrachochytrium dendrobatidis, the causative agent of amphibian chytridiomycosis, and show that this approach can identify single-digit DNA copies from epidermal swabs in under one hour using low-cost supplies and field-friendly equipment.
Dec 2023Published in Methods in Ecology and Evolution volume 14 issue 12 on pages 3055-3067. 10.1111/2041-210X.14236