Advisor 1v1: February 11, 2026

1v1
Author

CM

Published

February 10, 2026

Agenda

  1. Update on written deliverables (MS proposal, PhD proposal, Biomarker manuscript)
  2. Mussel pilot experiment takeaways
  3. Mussel Experiment for Chapters 3 & 4
  4. DNA Methylation Analysis
  5. NW CASC Fellowship

Updates

Written Deliverables

MS Proposal

  • Submission deadline: February 20, 2026
  • No committee feedback on the draft as of 2/10. Email reminder sent to committee on 2/10 extending the feedback window to 2/15.
  • The draft can be found at this link.

PhD Proposal

  • No current submission deadline. The bypass window (2/15) is too close and no one but Alison has seen the manuscript (required in package).
  • Goal: Have Bypass Package complete and submitted by March 13th, ahead of the May 15th deadline (next available).
  • The draft can be found at this link.

Mussel Biomarker Manuscript

  • Submission Deadline to ICB: April 1, 2026 with preference for earlier if possible
  • To be completed by February 15: Updated results with the corrected spatial analyses, and a complete abstract.
  • Next steps (before committee receipt):

    • Add figures directly into draft

    • Put together a ‘support’ folder of the manuscript figures, supplementary information, and results for review with a link to the code in the existing repo.

  • The draft can be found at this link.

Mussel Pilot Experiment Takeaways

Summary Stats

  • Experiment Duration: 33 days (December 24, 2025 - January 25, 2026)
  • Experiment Goal: Determine mussel’s in- lab thermal tolerance. Can the mussels survive for 30- days or more under chronic exposure to increasing temperatures.

Experiment Setup

  • 75 mussels, bagged in groups of 15, acclimated to 11° C with no food for 7 days
  • On Day 7, 45 mussels were moved to a 11° C treatment and 30 mussels were moved to a 15° C treatment; all were fed per Shellfish Diet 1800 instructions on Day 8.
  • Daily water temperature, salinity and mortality checks were performed.
  • Weekly water changes and feeding were performed
    • Water changes were PRN, no less than once a week, and became more frequent with 20° C and 22° C temperatures.
  • Elevated temperature regime:

    • Day 7 - 15° C

    • Day 14 - 18° C

    • Day 21 - 20° C

    • Day 27 - 22° C

Experiment Outcome: 50% mortality reached in temp tx on Day 30, three days after 22° C exposure.

Takeaways

  • 22° C after consistent exposure to elevated temperatures is too far
  • 20° C may be the maximum temperature
  • Multi- stressor experiment may require a decrease to 18° C for longevity, or 20° C (or higher) temperatures in acute exposures instead of chronic exposure

Next Steps

  • Finish setting up the repo documentation.
  • Complete the resazurin analysis.

DNA Methylation Analysis

  • Status: On hold until MS Proposal submission and mussel experiment ordering/ setup is completed
  • Anticipated Restart: February 20, 2026
  • Plan of attack for March 15th Completion of the Steps Below:

    • Re-familiarize myself with where I left off in late 2025 and backup the large files.

    • Move through the initial Bismark pipeline (which I believe I finished) into optimizing alignment parameters and using that outcome for subsequent steps.

    • Quantify methylation levels and visualize using IGV or JBrowse.

    • Get feedback on initial results from Steven and/or other lab members before moving into downstream analyses.

Mussel Experiment for Chapters 3 & 4

Research Questions

  • How does thermal stress modify mussel physiological responses to legacy contaminant or metal exposure across environmentally relevant temperature regimes?

  • Which physiological and molecular mechanisms are associated with survival, stress tolerance, and sublethal impairment under combined legacy contaminant, metal and temperature stress?

  • Does exposure to legacy contaminants and/ or metals under elevated temperature induce changes in DNA methylation, and are differentially methylated loci associated with genes involved in stress response, detoxification, or thermal tolerance?

Setup and Methods Overview: Ideal

  • Treatments (high, low and control, n=15)
    • Temperature - 11° C and 20° C
      • Based on pilot study thresholds
      • Could be replaced with resazurin stress assay to simulate acute heat stress once a test run of full time to reach plateau is identified.
    • Cadmium (metal) - low concentration & 25% above environmentally found concentrations
      • Based on WDFW data from 2015 - 2022 and literature
    • PAH mixture - low concentration & 25% above environmentally found concentrations at sites like Elliott Bay and Commencement Bay versus those at Hood Canal
      • Based on WDFW data from 2015 - 2022 and literature
  • Measurements to be Taken
    • Morphometrics - beginning and end only (LxWxH, △ weight as proxy for tissue weight)
    • Respiration or metabolism - at timepoints defined below
    • Biomarkers, P450 and SOD- at time points defined below
    • Gill or mantle tissue dissection for molecular sequencing- at time points defined below
  • Experiment Duration: Minimum 30 days, Ideal- 45-60 days which is approximately 1/2 of outplanting season
  • Timepoints for Sampling (~7)
    • Day 0, 7, 14,21,28, 41 and end if exceeding 30 days
  • Sample Requirement: ~14lb of mussels
    • 2lbs yields ~70 mussels
    • 15 treatments requiring minimum 8 samples per timepoint (7) of destructive sampling

      • ~840 mussels + 10% for initial condition and mortality

      • ~930 mussels (35 mussels/ lb)

In Progress

  • Lab risk assessment form from EH&S. It’s diagnostic, not a requirement

  • A summary of risk and physical mitigation techniques must be on file (only part not included in standard lab handbooks/ MSDS sheets/ existing ‘harmful agents’ exposure protocols

  • Located chemical vendor for legacy contaminants & potential ‘granting’ of chemicals

    • Cambridge Isotope Laboratories

      • Grant request application (will complete regardless of choice)

      • PAH contaminants range in price, for single agents to mixtures, from ~$200 - $2000 with the average mixtures running ~$1000.

      • An option would be to get input from Alison and Mariko (WDFW) on maybe 1-3 specifics that would cost ~$450 (for 3).

      • Alternatively, since PCBs are also a heavy- hitter, and skew slightly lower in price

    • ThermoFisher is the vendor for cadmium

      • The formats (powder or foils?) unsure of the impact of difference

      • No prices available without contact with them

Next Steps

  • Confirm design options and requirements for moving forward
  • Connect with Jon W to assess physical setup and limitations
  • Provide a budget, supply requirements for assessment

NW CASC Fellowship

  • A version of my Chapter 3 draft can be used for this, reasoning is below application specs.
  • Deadline for submission: March 9, 2026 The Research Fellowship call is at this link and the pdf of the call overview is at this link.
  • Funding range: $5,000 - $65,000 with an averaged awarded amount of $30,000 for graduate students (not including tuition/ fees cost) for 1 year of fellowship.
    • Higher amounts go to Postdocs per the fellowship FAQ/ website
  • Full proposal requires the following pieces:
    • Completed online application that identifies the NW CASC Actionable Science Agenda item being addressed, specific output/ outcomes of the work, identification of external partners, requested funding and budget, and leveraged support description.
    • Proposal (3 page max, excluding references) with standard requirements + plan for interaction with NW CASC stakeholder (WDFW and UW-T for my thought)
    • Budget + Justification
    • Letter of support from PI
    • Letter of application from prospective fellow (2 page max)
    • Statement of Support from external partner (WDFW in accepted list)
    • CV of prospective fellow
  • NW CASC Actionable Science Alignment
    • Managing the Ecological Impacts of Extreme Heat in the Northwest (ActionableScience Agenda5)

      • Key Research Needs: Ranked from most applicable to least

      • Characterize the interactive ecological effects of extreme heat and other anthropogenic, biotic and abiotic disturbances and stressors

      • Assess and improve the effectiveness and accessibility of existing tools to measure and predict general and extreme heat exposure and impacts

      • Understand the mechanisms and drivers of interspecific and intraspecific variation in sensitivity and adaptive capacity to extreme heat

      • Key Capacity- building Needs: Ranked from most applicable to least

      • Improve, operationalize and expand the accessibility of existing tools and datasets

      • Support long-term and post-event rapid ecological and microclimate monitoring

    • Priority ecosystem: Coastal
      • Marine coastlines and nearshore habitats, Rocky intertidal zones, Estuaries, Sandy coastlines
    • Climate-Linked Drivers of Ecological Change

      • Increasing Temperatures: Warmer winters, summer heat extremes and heat domes, changes in growing seasons

      • Land use changes and additional stressors categories may also apply

Next Steps

  • Info-session on Thursday 2/12- I am registered and will attend.