Advisor 1v1: February 11, 2026

1v1
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.