Agenda

1. Updates

   1. Shifting 4/21 meeting (1030-1130) to Wednesday or Thursday of the same week

   2. Biomarker Manuscript

   3. Plan for Methylation Manuscript completion NLT June 10, 2026

   4. Committee email re: status update

2. Methylation Analysis Resources

3. Today’s Goals for Working Session

Agenda Topic 1

Something

Agenda Topic 2

Something

Agenda Topic 3

Something

Agenda Topic 4

Something

For Next Week:

Focus for the Week:

1. Realign outcomes (or products), direction, and deliverables with Steven.

2. TKO this Biomarker manuscript draft.

3. Keep the methylation analysis moving forward.

Progress Made:

1. Realignment. After a great meeting on Wednesday with Steven and Chelsea, the department GPC, I believe we have a solid working plan for alignment and moving forward.

2. Biomarkers. I have completed the first step of critically reviewing the state of the draft, identified what can get it to committee- ready status, and began work on the first of 3 categories of refinement.

   1. The three categories are writing, citing, and clarifying. I broke down the first major WDFW report I cite into it’s ‘backing’ scientific lit on Thursday and Friday.

   2. I then shifted to the clarification notes and began focusing on the argument and narrative breakdowns. This helped me identify that I was burying the lead - the big takeaway from this work is that while contamination is clearly characterized across Puget Sound, the biological outcomes were much more variable using traditional tools, so turning the monitoring program into a bio-monitoring program is more complex than anticipated despite having traditionally validated tools.

3. Methylation analysis. Analysis up through methylKit is complete, and base scripts for the methylKit steps are 90% ready to go. Additionally, I created a project log and running questions list to help me prepare for my weekly working sessions with Steven.

Challenges:

The largest challenge this week was getting my To-Do list and my sense of overwhelm under control - I’ll explain a bit more about that below.

Synthesis:

Spending the time to really sit in the current ‘state of the union’ allowed me to think more critically about the work I’m engaged in, the supports I will need, and how to better benchmark my progress and day-to-day capacity.

Next Week:

Weekly working sessions with Steven start next week. This will help move the methylation analysis and manuscript forward so it doesn’t lag in the way the biomarkers manuscript has.

So, How Exactly are We Making the Realignment Stick?

Ferris Bueller’s Day Off is a quintessential 1980s movie most fondly summarized by the fun of playing hooky and driving around in a vintage convertible, and the lines, “Life moves pretty fast. If you don’t stop and look around once in a while, you could miss it.”

This sentiment is easily translated to taking a break, but it also applies to gaining broader clarity and alignment with your goals and the process to achieve them; task overwhelm obscures the finish line, and we need to stop and look around at what we’re doing. I was reminded this week, that taking the time to just let it rip - write it all down, confront what is spiraling and do something about it - it the ultimate first step in actually getting the work done.

For this whole thing to work, you have to know your goals and what life area you are trying to clarify progress around; obviously this is my lab notebook, so we’re focused on my Master’s work. You cannot successfully redesign every area of your life at one time, I don’t care how motivated you are at midnight on a Tuesday with a blank Notion landing page and YouTube waiting for you…

My three major goals for Spring Quarter, in order of priority are:

1. Completed, polished draft of the biomarker manuscript.
2. Completed, polished draft of the methylation manuscript.
3. Clearly drafted introduction and a clearly outlined Chapter 3 & 4 of my PhD proposal.

Each of these will take multiple steps and even more tasks to complete; this is how I do that.

Step 1 of 7 is to pick the two to three categories of one goal you want to prioritize first, and then one to two categories that will follow the completion of the first goal. The key to this being successful is extremely clear categories based on your hierarchical goal list. For example, a complete biomarker manuscript is my first goal, but not a clear category. The manuscript goal can be broken into three categories:

1. Line edit- level of my writing to assess for alignment with the key results and larger narrative.
2. Critical review of citations (currently only 24 of the 67 papers I’ve read are in the draft) and their applicability to the manuscript. This to be done by major section (intro, methods, results, conclusion).
3. Sufficient visualizations to tell the story, not overwhelm the manuscript. I think 3-5 plots/ maps is the target number based on the analysis and result.

Step 2 of 7 is taking the time to just brain dump all that is swirling in your mind - even if it’s not goal- related; we’re multi-faceted, work with that and not against it. This parctice prevents tunnel vision, poor prioritization, and action paralysis (both the failure to start & the narrowing of focus to minutia rather than broader task, a.k.a. tunnel vision).

Step 3 of 7 is organizing that list into the categories you defined earlier - Do Not Create New Ones - this will help you separate the important from the peripheral. My biggest pitfall has been deciding on the categories after looking at the list, not beforehand. Most of my overwhelm and aspirational sense of productivity comes from making this mistake. We have identified the big priorities, stick to them! This part feels like you’re going backwards because the list grows wildly but it stops the lie you tell yourself that “it’s only three things, why can’t I get three things done.” In fact, it is 10 things slotted into a time block built for two things. 

Worth a pause and a callout - this is no place to let embarrassment, shame, or disappointment takeover. Get your Hercules on, wrangle that Cerberus, and get back to business. The energy wasted by chastising yourself is clouding your judgement. Instead, get into the practice of completing a post-mortem for goal or milestone achievement to help separate the story from the facts.

Step 4 of 7. A mentor told me that only putting deadlines on your calendar, ones that you may or may not meet, is a surefire way to lose motivation because you are unintentionally reinforcing the narrative that you are a person who does not complete things. To combat that, take your expanded task list, assigned to your top goal and goal categories, and add the actual steps to your calendar along with the ‘big’ deadline. Now you have proof and reinforcement that you are a person who completes things - even if the major deadline is shifted.

Step 5 of 7. Arguably more important than planning your process, is planning your inspriration. You will not always feel as ready to get it done as you do today, so plan for it. I take great inspiration from sports, sports theory, and coaches talks when I can’t get focused on the tasks in front of me. I find personal and creative inspiration by looking to writers, artists, and creators; typically as far away from obvious science as possible. I look to painters, sculptures, the fashion icons - designers and critics, mostly. The pursuit of translating the beauty of the human experience provides me both a grounding and an expansiveness that allows my brain to get to the outcome I’m seeking.

Once you identify what motivates you and when, it’s important that you start putting together a few things you can read, a few you can see, and a few more that you can listen to depending on your preferred method. I have content in folders, digital bookmark lists, YouTube playlists, podcast lists, a couple of vision boards, and hand-written quotes from folks I admire. The key here is to put them where you can see them.

Step 6 of 7. We’ve got our goals, assigned a date for the deliverables for each category, and added a motivation plan for when we need a little help; now we refine. The hardest of the steps is this one. Walk away from it, come back a few hours later and be honest with a side of grace - we cannot plan in a vacuum, which is what we just did. Take a realistic look at your schedule and start moving and shaking. For example, I know heavy meeting days present me two challenges, (1) re-engaging my focus as I shift tasks, and (2) getting into deep work when I know it’s on a timetable bounded by others.

Creating plots and maps are multi-step things I can pick-up and drop without significant re-engagement time, so shifting my visualizations tasks to meeting days keeps my progress moving forward. The writing and clarifying tasks require significant engagement, and regular disruptions present progress paralysis for me, so I block morning or guaranteed non-meeting time to work on those. In addition, I don’t let my 3-hour time block, for example, to go unplanned. Typically, I plan the specifics just before starting the block, accounting for my mood and motivation. The big caveat being that the task category was defined on the calendar so I know the focus of the block. And, finally…

Step 7 of 7 is to remember to reward yourself for the things you’ve completed. Give yourself a chance to look back and say, “I really have done well.” I have a physical jar, the Victory Jar, where once a day I add a ‘win’ of any size, across any area of my life. Once in awhile I re-read some of them, but once a quarter I put all of them together and read them when I do my quarterly post-mortem. This is the evidence that reinforces that I am exactly who I think I am.

Hopefully this gave you a sense of my planning, motivation, and reinforcement practice, as well as maybe a takeaway or two. I thought it was a good time to share since I am making a large pivot and have to commit or end up really disappointed in myself when I finally stop to notice the opportunity passed me by.

Agenda

1. Update on written deliverables outlined in Alert letter
   1. Biomarker manuscript
   2. WDFW Mussel methylation manuscript
2. DNA Methylation analysis progress
3. Stretch Goal: PhD Proposal
4. GPC Meeting
   1. Expectations & Alignments
   2. Status of deliverables in Alerts
   3. Moving Forward
   4. Decisions, Questions, Action Items

Updates

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.

Established Protocol Adjustments

1. Most of the mussels were on the larger side of the ‘large’ classification outlined in the protocol, so I measured using ImageJ as outlined, and used calipers to measure length, width, and height (in mm) to also proxy volume.
2. The seawater used for the working solution was at a salinity of 27 psu, aligned with the target for the 30-day experiment. This is an adjustment for record- keeping rather than to the protocol itself.
3. I purposefully selected mussels as follows:
   1. The heat treated mussels were similar in size, so one of the control treatment groups were specifically chosen to match size
   2. One exceptionally large mussel was chosen to see if size had an effect on the assay results
   3. All mussels used in a ‘seawater-only’ control for the assay were as identical in size as possible.
4. I loaded a plate in triplicate for all values based on unclear expectations for the activity. In addition to that, the following changes to the plate load were:
   1. Two full rows of resazurin-only wells to ensure there was an accurate “blank” or control value to subtract background fluorescence from.
   2. Two full rows of seawater-only wells to verify any measured fluorescence from the seawater itself was negligible.

Setup

Before complete take- down of the 30- day survival experiment, mussels were collected (as seen below) and held in their respective tank water before being measured, photographed, and put into their assigned individual containers. A total of 12 mussels were assessed; the two remaining from the elevated temperature treatment and ten from the control temperature.

Mussels were measured two ways: first using calipers to measure width, height, and length, and second, was using ImageJ software. Mussels ranged in length from 46 mm to 96 mm with a median length of

Total working solution volume was determined using three ways: first, using caliper measurements as a proxy for volume (length x width x height) and converted to cm³ and summed for total mL; second, using the area measurement tool in ImageJ and converting the same as the first method; and finally, mechanical adding of water to a cup until the mussel was completely submerged, and then measuring that volume using a graduated cylinder. The first and third methods were closely aligned, the second was below required volume. I believe this was because I didn’t also measure width in ImageJ- this will be revisited post- analysis as a check for future experiments.

Mussels were in their treatment solution at room temperature (20° C) for approximately 35 minutes before being placed in the cold room for T₁ and T₂ sampling.

Moving through the experiment, there was not much notable color change in the well plates (as seen in the plate image below). This could indicate a longer testing period, or that room- temperature incubation wasn’t as effective as using the incubator.

Since this was the first time Resazurin was used with mussels in the lab, I ran all samples in triplicate to see if there were any significant deviations in activity. There was some deviation, but two of the three measurements per time cycle were identical or near- identical, so I felt confident in the readings and will run samples in a single- load versus a duplicate or triplicate in future work.

Finally, the plates at T₅ are below, as is a representative image of the color change observed in the sample cups.

TL; DR - Experiment Stats

• 12 total samples assessed across four 96-well plates. Each plate contained the following configuration:

  • 4 mussels in Resazurin (Rows A-D)

  • 2 mussels in seawater- only, no Resazurin (Rows E-F)

  • 2 Resazurin- only ‘blanks’, no mussels (Rows G-H)

  • All samples loaded 180 µL in triplicate, this required four total plates

• Total experiment time (including setup and cleanup) was from 1120 - 1834

  • Mussels ranged in length from 46 mm to 96 mm with a median size of 54 mm

  • Total working solution (850 mL) was calculated based on the following volumes:

    • 9 of 12 mussels required ~50 mL solution for submersion

    • 1 of 12 mussels required 300 mL solution for submersion

    • 2 of 12 mussels required 0 mL solution since they were seawater- only controls

    • 2 of 2 Resazurin-only controls (no mussels) required 10 mL solution

    • 10% additional solution (~150 mL) for slightly larger mussels and in case of mistakes/ re-run potential

  • Metabolic activity assessed from 1255 - 1757

  • T₀ measured at 1255, T₁ - T₄ measured at hour intervals with the final T₅ measurement at 1757

  • 2 mussels from the increased temperature treatment (22° C)

    • 1 of 2 mussels didn’t survive (mortality at T₃)

    • 1 of 2 mussels survived for the duration of the experiment

  • 10 mussels from the control temperature (11° C)

    • 10 out of 10 mussels survived for the duration of the experiment

• Noticeable color change didn’t occur in most samples despite increasing activity values from the plate reader

• Duration of experiment may not have reached an activity plateau indicating the need for longer experimental duration, increased incubation temperatures, or a combination to properly stress the organisms into increased or ‘maintained’ metabolic stress response.

• Next steps: clone the training repo and run the analysis and visualization scripts.

Focus for the Week: Primary goals and priorities for the past week.

Progress Made: What moved forward?

Challenges: What slowed things down?

Synthesis: How does this week connect to the larger project?

Next Week: Planned tasks and questions.

Blog Reflection

Read my post here.

Course Reflection

Welcome to the Arena: DNA 101

Before any game begins, you need a field. In biology, that’s DNA.

DNA is a double-stranded playbook carrying every instruction an organism needs. Within it, genes are individual plays—schemes for building proteins, running the metabolism, repairing cells, and orchestrating life itself. But here’s the twist: just because a play exists in the book doesn’t mean the team uses it every game.

And that is where epigenetics comes in.

Meet the Coaching Staff: What Is Epigenetics?

Epigenetics is the study of how organisms change gene expression without altering the DNA sequence itself. These changes are induced by the environment and allow organisms to remain plastic, flexible, and ready to win.

Think of it as the coaching staff deciding which plays to run, how often, and under what conditions. Just because Pete Carroll didn’t activate Beast Mode in Super Bowl 49 doesn’t mean that Marshawn Lynch wasn’t ready to get the job done.

Marine organisms live in environments that shift dramatically due to elevated water temperatures, ocean acidification, reduced oxygen, and pollution. Many are sessile and can’t walk off the field or swap arenas, so instead, they rely on epigenetics to make on-the-fly adjustments. We’re going to focus on marine invertebrates, but if you want to know more, check out the Coach’s Challenges for where you can find more information.

Let’s check out a few audibles available to our favorite marine organisms.

Nick Saban, Defense: DNA Methylation

Nick Saban is famous for “the process” that has built a dynasty in Alabama: focus, precision, shutting down what doesn’t serve the system and elevating what brings the team together. That’s DNA methylation: chemical tags (a.k.a. methyl groups) get added to DNA like a defensive scheme, dictating whether genes are expressed or not.

Oysters, mussels, and corals have used methylation to withstand environmental changes and alter their energy allocation during stressful events. It’s strict, strategic, and controlled. Most mammals have a ton of methylation in their genome—upwards of 70%—because we’re complex and biologically fussy, but marine invertebrates (like oysters, mussels, and corals) are just trying to meet the big basic biological goals: survive long enough to reproduce before you die. DNA methylation helps them do this.

Jessica Campbell, Agility: Histone Modifications

Histones are the proteins DNA wraps around; loosen them and gene expression can ramp up; tighten them and it can slow down. While Jessica Campbell may be the first woman coach in the NHL, she’s not new to this—she’s true to this. She’s fast, agile, and manipulates space in the barn better than most.

She’s histone modification: creating openings you didn’t see coming, or locking down a play you thought was available. Histone modifications work the same way.

Geno Auriemma, Court Vision: Chromatin Remodeling

If DNA methylation is discipline and histones are agility, chromatin remodeling is pure coaching genius. If we’re talking about coaching genius, we must be talking about 12-time NCAA champion (and champion-maker), UCONN Women’s Basketball Head Coach Geno Auriemma. Coach Auriemma doesn’t change who you are, he changes how the pieces are arranged so you shine; just ask the 45 WNBA players (26 went first pick) from his Huskies — see Bird, Taurasi, and Moore et al. for proof.

Chromatin is the molecular complex made up of DNA and proteins in the nucleus of a cell. Remodeling physically shifts entire DNA regions by putting them in either zone or stacked play (spaced out or bunched together). Marine species use this when facing extreme stress, like heat waves; they restructure their genome’s landscape the way Geno restructures an offense.

The Utility Players: Non-Coding RNAs

Non-coding RNAs are a little less well understood, but generally, they regulate gene expression by intercepting signals, amplifying others, or turning certain genes on or off at key moments. As the least studied mechanism of epigenetics, the sky is the limit for adding to our understanding of how this mechanism works.

While not exactly coaches, think about non-coding RNAs like A’ja Wilson and Alex Ovechkin: players who are leaders, versatile, impactful, impossible to ignore. They do the gritty work that changes the outcome of the game.

Training Camp: Environmental Stressors

Coach Saban says your environment shapes your commitment. Marine organisms live that reality more literally than any athlete ever will. Since the epigenetic mechanisms we covered earlier are largely induced by the environment, their “training camps” look like marine heatwaves, ocean acidification, and pollution exposure.

These pressures trigger epigenetic responses that help organisms survive the moment or prepare their young for upcoming challenges.

In-Season Adjustments vs Building a New Team: Acclimatization vs Adaptation

Acclimatization is a short-term change, like Lewis Hamilton switching from medium compound tires to inters for rain on the track in Miami—we all know Florida rain only lasts a brief stint. Adaptation is long-term, across generations, like Ferrari designing an entirely new car concept for the next season.

Epigenetics sits between these:

• Sometimes it’s reversible, like changing tires in a race (acclimatization)
  
• Sometimes it influences offspring—think F2 and F3 drivers moving into F1 seats (parental effects)
  
• Sometimes it persists across generations—think Schumacher and Sainz (transgenerational inheritance)

Marine species often “preload” offspring with epigenetic cues so they’re ready for warming waters or increased acidity. It’s like when LeBron sends a plume of chalk into the air before a game or you hear those opening notes of Enter Sandman at a Virginia Tech football game; the ritual signals what’s to come and, just like sport, we may not always win, but we can’t win if we aren’t prepared.

When Does Acclimatization Become Adaptation?

I’m sure you’re asking: if epigenetics keeps making the same play, at what point does it become a permanent part of the playbook?

There are plenty of reasons why we would expect epigenetics to be part of the answer to how marine organisms withstand environmental changes, but there is so much more to understand before we can make such a blanket statement—I mean, there are still Dallas Cowboy fans despite evidence that they won’t see a Super Bowl anytime soon.

Game Time: Analytics & Officiating

The Expansion Era: Where Epigenetics Is Heading

Epigenetics isn’t static; it’s evolving like sports themselves. We’re entering a future of innovation in data collection methods, even more open-source data from around the globe, and innovative analysis techniques. The future is as bright as Josh Naylor’s with the Mariners!

This is the age of the rookies: Michael Penix Jr. (#GoDawgs), Matthew Schaefer, Paige Bueckers, Kimi Antonelli — athletes rewriting their sports in real time. Epigenetics is undergoing that same explosive transformation.

Add new tools, third-generation sequencing, and a wealth of open-source data—that’s just like electronic line judging in tennis (except for the French Open), the new concussion helmets in the NFL, and more investment in youth sports across the US.

We are rewriting our understanding of resilience, inheritance, vulnerability, and survival. Marine organisms are already doing it. Now, science is catching up.

Because when it comes to life on a changing planet, epigenetics isn’t just a game. It’s the whole season, the draft, the practice, the film, and the long, hard work that lets life show up ready to play when the whistle blows.

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

Here are the questions/ chapters we were kicking around last meeting:

New (to me) Literature

Reviewing Mytilus trossulus genome literature, I came across a ton of cool papers that I want to discuss in the context of pollutant work, resilience, and hitting a knowledge gap that isn’t a chasm or a dead end. The 3 below are just a few that are interesting to me.

• [Paper 1: Breton et al. (2006) Comparative analysis of gender-associated complete mtDNA genomes in marine mussels] (https://github.com/ChrisMantegna/labnotebook/blob/main/resources/Breton%20et%20al.%20-%202006%20-%20Comparative%20Analysis%20of%20Gender-Associated%20Complete%20Mitochondrial%20Genomes%20in%20Marine%20Mussels%20(%20Myti.pdf)
• Paper 2: Breton et al. (2021) Did doubly uniparental inheritance (DUI) of mtDNA originate as a cytoplasmic male sterility (CMS) system?
• Paper 3: Chelyadina et al. (2022) Effects of heavy metals on sex inversion of the mussel Mytilus galloprovincialis in coastal zone of the Black Sea

Post- Meeting Notes

Steven and I discussed framing my PhD proposal and have settled on this path to explore. We’ll refine as we move forward, and as I learn to read my own handwriting a little better!

The overarching theme is: Exploring xenobiotic effects and consequences in mussels (to mussel physiology)

• Chapters 1 & 2 (my MS work) remain the biomarker and DNA methylation work, respectively

  • Can the mussels from the WDFW Nearshore Monitoring Program be used to assess the impact of contaminants on the mussels using traditional biomarkers?

  • Can epigenetics (DNA Methylation) be used to identify novel biomarkers of PAH exposure in mussels?

• Chapter 3 is lab testing the results of the Chapter 2

  • Utilize ‘new’ mussels to test the outcomes of the mussels that show differential methylation from Chapter 2.

  • Short- term (1-3 month) and longer term (3-6 month) lab- based exposure and response experiments designed to characterize the metabolic threshold of mussels exposed to known contaminant mixtures that mimic those in Puget Sound.

    • Clarify stress induced DMLs and their pathways. Do they align with the DMLs in Chapter 2?

• Chapter 4 is a larger synthesis of the knowledge gained in Chapters 2 and 3.

  • What are the contaminants inducing in mussels that can have broader population or ecosystem implications?

    • This can be assessed through a variety of field- based experiments

      • Outplanting primed and non-primed mussels to assess response at sites with higher or lower contaminant burdens.

      • Reciprocal outplanting - mussels outplanted at high contaminant sites are moved to sites with low contamination and vice versa.

Do’s & Dont’s

DO start with the most basic setup you need to get started

DON’T sink a ton of time world- building before you’ve tested it out

DO spend time sketching out what you need

DON’T buy templates unless they are absolutely everything you’ve ever wanted

DO build a main dashboard and 1-2 pages to begin

DON’T create a new page for everything or you’ll never find it properly again

DO explore the automations and connections that can be made to your existing tools

DON’T try to make everything fit into Notion

DO set a trial period so you can assess what is working and what isn’t

DON’T only open Notion to create the tool or tweak the tool

Give Notion a test drive and tell me what you think! What do you like, dislike, or want to know more about?

Goals for Today’s Meeting

• Overview of work to date

  • MS research progress

• Review requirements for MS to PhD bypass

  • Review current research

  • Review places of expansion from MS to PhD

  • Discuss potential to bypass

• Bypass requirements

  • Deliverables & Asks

• My academic year goals

Committee Members

What I’ve been up to

MS Research Questions

Main Question: Can long-running mussel outplant data from WDFW’s Nearshore Monitoring Program be leveraged to link contaminant exposure to physiological and epigenetic responses in Mytilus trossulus?

Do established biomarkers in M. trossulus show reproducible exposure–response associations with site-level contaminant burdens and classes?

Which exposure-associated methylation signatures and pathways in M. trossulus could inform the development of candidate molecular biomarkers?

Current Research

Last week recap

• Milestones form updated

  • Please sign the Docusign form sent via email so I can update the tracker

  • Committee meeting set of October 9th at 12pm

  • Only remaining ‘overdue’ milestone is my MS proposal, will become a moot point when I submit my bypass

New this week

• Biomarker paper update
  • Working the plotting through Friday (10/3)
  • Drafting discussion/ intro through Monday (10/5)
  • Goal - draft to you and Alison by committee meeting on 10/9
    • Not as a part of the meeting
• Bypass package scope refinement
  • Not sure how to really package this, so I need so help thinking through scoping the work. The research assumptions and questions below are where I think it works.
  • My goal is to have a working presentation to you for review by COB on 10/07.
    • Will build based on how we adjust the questions/ assumptions below

Research Questions

1. What is the community composition of the nearshore ecosystem in Puget Sound?

   1. Are there any temporal similarities or differences across the sound? Anything not expected?

   2. Can we identify any trends that point toward resilience or adverse response to human impacts? 

2. What is the impact of legacy contaminants and heavy metals on foundational nearshore organisms?

   1. How does regional (and nationally established and backed) biennial monitoring support conservation strategy development in Puget Sound?

   2. Can that monitoring model be leveraged to also infer organismal impact?

      1. If so, does organismal impact align with the contamination profiles at each monitored site?

3. How do we identify data-driven opportunities in conservation ecology and utilize those to prepare the next generation of conservation ecologists?

   1. What is the current state of conservation ecology? Is it effective? How do we know?

      1. Scoped to historical efficacy, collegiate preparation and inclusion, and new data techniques to bring together all the pertinent information to make decisions.

      2. Looking through the data and practitioners - not policy even though I will have to address 

   2. What teaching methods will support the learning and research for the next group of conservationists?

   3. Where are the new and the established conservationists aligned or mismatched with current conservation professionals?

      1. Social expectation - changes in workload versus personal time, work ethic?, compensation, and societal acceptance or celebration of the work

      2. Educational expectation - what skills are new folks coming in with, is it mismatched to what is needed, how does the UG degree provide (or not) the skills to be successful, and is there commentary on how that has changed over time?

      3. Urgency - efficacy is the question of the hour as we are losing time to ‘reverse’ or ‘stop’ change. Can we stop it, should we stop it, and how does multiple knowledge systems’ incorporation into the application of the data (and how its gathered) alter or confirm the future of conservation?

Research Assumptions

• Assessing the nearshore environment from ecosystem level to organismal impact is thorough but incomplete without considering how the human element impacts the ecosystem.

• Conservation Ecology is the end focus - what can my work do to bring together/ or bridge the existing data, identify where data is incomplete, or support the folks who want data-driven actions/ solutions to conservation

• We are not working with micro-plastics. Contamination work is the only axis of alteration we are assessing directly.

Things to Consider

• Where are the gaps in my approach?

• Can I launch an eDNA bio blitz where WDFW is outplanting the mussels if we find interesting correlations from the biomarker work and the DNA methylation work?

• What are the other axes of human impact in conservation ecology that I’m overlooking OR need to address?