Integrating Epigenetic Mechanisms

Plan of the Week: March 16 - 22, 2026

• I am feeling marginally better, and since I didn’t map the week on Sunday, the plan today is to keep it low key so I don’t put myself back at square one.
• Monday: Map the week, catch up on UW-RUA work, confirm my spring/ summer tide schedule, build base histone and chromatin knowledge notes.
• Tuesday: UW-RUA work, no science.
• Wednesday: Return to epigenetic mechanisms to outline new Chapter 3 for my proposal.
• Thursday: Biomarker manuscript
• Friday: Biomarker manuscript
• Saturday: Return to Chapter 3 outline and start drafting options for the introduction and methods.
• Sunday: Continue Chapter 3 work.

Missing from the plan is the DNA Methylation work - it will be worked into the other priorities as time permits, or be a focus for spring break week next week.

Plan of the Day

• I originally slated time today to work on biomarkers, but I want to finish the chromatin work so I can mull over the mechanisms while working on the biomarker manuscript.
• Today is chromatin’s day to shine… again!
  • Compile current notes, identify basic biology, any applicable marine invert knowledge, and develop some questions around the mechanism in the context of my work.
• I did not get through finalizing my chromatin notes and outlining Chapter 3, so I’m going to focus on that before moving into Biomarker work.
  • First, review existing notes. Second, pull the questions out and put them with the rest and format notes like the others. Third, use the questions and notes to identify alternate ways to work with open source data for Chapter 3.
• After note taking, I will begin outlining a plan for Chapter 3.
  • Pivoting to a bioinformatics chapter rather than a lab based one will allow me to make better decisions for the experiments, more strongly tie the mechanisms to the outcomes, and pull together the complete work cleanly.

Projects Touched Today

• PhD Proposal
• Foundational Knowledge
• DNA Methylation

Progress Notes

• I started by wondering how I ever made it out of Catholic school with this handwriting!
  • My Chromatin notes are a bit all over the place, so after a quick review I identified some gaps I have in understanding. I’m filling those in as best as I can to knock out the cleaner notes.
  • I moved my questions over to the running doc and realized that chromatin remodeling is possibly the most straightforward of all of the mechanisms.
• When I shifted over to DNA methylation, I found myself with more analysis/ workflow questions than mechanistic questions.
  • I pivoted to creating a more comprehensive checklist and process to follow for myself since it is easy for me to rattle a few high-level steps, but unpacking them has been a process.
  • I then created a decision outline with some guiding questions for the analysis.
  • For both I chose to start at the point of sequences in hand - I will need to go back and make a section for sampling/ experimental design. Probably when I work on the methods for the manuscript.
  • This exercise took an embarassingly long time, but really helped me get down to the ‘bones’ of the process and set myself up to comprehensively answer any questions with something more robust than “that’s how my lab does it”.
• For all of my explainers/ note docs I am certain there is plenty of room to make them better, and when the time is appropriate, I will, but for now I need to get back to basics and reinforce information or decisions I have been treating as ‘set-in-stone’ facts.
• I was feeling pretty ‘ready to apply’ this reinforced knowledge and quickly learned that sorting through old code and outputs after dinner is a recipe for instant despair.
  • I went back to the DNA methylation analysis work to see where I left off and possibly move forward… I did this because evening writing is often akin to trying to sharpen a pencil with a blade of grass - not smart. So, I thought, maybe tangible do X get Y work would do it. Instead, I am now questioning every decision and trying to figure out how my maping efficiency has not gotten above 27%, and if that is even a problem… Key sign to pack it up for the day.

Products & Word Count

• Doc 6- Chromatin Explainer: 498 words
• Doc 7- DNA Methylation Analysis Checklist: 573 words
• Doc 8- DNA Methylation Analysis Decisions: 875 words

Today’s total: 1946 words

Monthly total to date: 8538 words

Annual total to date: 30,233 words

Annual target total to date: 39,000 words

Tomorrow’s Plan

• Friday starts with creating a specific task list for the biomarker manuscript, executing a reasonable amount of it, and then turning my attention to methylation.