Weekly Advisor Meeting

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Published

November 13, 2025

Today’s goal is to recap what I’ve been up to for the last 2 weeks and work through the validation chapter

Recap since October 23rd

  1. Gave the guest lecture on November 3rd to Alison’s ecotoxicology class
  2. Gave the guest lecture on Noveber 7th to Eli & Kristi’s ENV 100 class
  3. Found my original MS thesis proposal and started cleaning it up.
    1. It contains the Biomarker & Yellow Island eDNA projects.
    2. Can I keep it like that, or should I adjust it to Biomarkers & DNA Methylation?
  4. In compliance with the SAFS warning letter, I will have my draft MS proposal to the committee by end of day Friday, Nov 14th

Current Work

DNA Methylation Analysis

  1. Currently on Raven working through a stripped down version of the code from your project-mytilus repo.

    1. There a ton of sequences that I don’t know where they came from - what are they?

    2. Process is trimming and aligning with Bismark is next - will hopefully be able to start that today. Should I move that part of the process to Klone?

    3. Related, I ran a single sample (239/ low PAH) up through Bismark, but I don’t really understand the report.

  1. Experimental design.
    1. Ariana & I walked through building a lab based experiment that would be cool, but after thinking through it further it doesn’t align with the goal to validate the novel biomarkers.
    2. Chatted with Alison on Nov 3rd and it is possible that if I identify a handful of sites to go pick up the samples, WDFW may be able to give me their extras from the February 2026 pickup. Not a guarantee.
    3. What would it take to get a field- based exposure experiment up and running? Is it possible to pilot 1-3 local sites this winter (December - February)?