BIT 495/595: Environmental DNA Analysis and Applications

Course Overview:

  • This course covers environmental DNA (eDNA) and applications of this tool to environmental and ecological research questions. The use of eDNA is expanding rapidly. It is being used to address challenges like biodiversity assessment, detecting invasive species, tracking rare species, and characterizing ecosystem functions. The course will explore examples of these applications and technologies and approaches that make them possible such as metabarcoding, metagenomics, next-generation sequencing, and bioinformatics. The course incorporates opportunities to analyze current primary literature and gain hands-on experience with eDNA collection and isolation, barcode amplification, sequencing library preparation, metabarcode analysis, and measuring biodiversity and community composition. This is an opportunity to learn about emerging biotechnology while practicing authentic exploratory science in a collaborative, supportive learning environment.

Lecture/Discussion Topics:

  • Biodiversity assessment
    • Metabarcoding, metagenomics, traditional survey methods
  • Functional characterization of communities
    • Metagenomics, metatranscriptomics, inferring gene functions
  • Targeted species detection
    • Primer design and validation, qPCR, traditional survey methods
  • Other topics covered throughout
    • eDNA collection/filtering/extraction strategies
    • Basic linear modeling
    • Bioinformatics

Lab Skills Practiced:

  • eDNA collection, filtering, and extraction
  • PCR amplification for metabarcoding
  • DNA purification and sequencing library preparation
  • Metabarcoding analysis (e.g., alpha and beta diversity and taxonomic abundance)

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