Advisor Working Session: April 15, 2026

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Working Session
Published

April 14, 2026

Agenda

  1. Updates

    1. Biomarker Manuscript

  2. Methylation Results and Methods Drafting

Updates 1: Biomarker Manuscript

Status: Emailed draft on 4/18 to Steven only

Added to Google Drive on 4.19.26 when the WiFi was stable

Item 2: Methylation Methods Drafting

This is the link to the drafted Methods Section.

Status: Initial draft

Item 2: Methylation Results Drafting

I put together the table of DMLs from your 1055.tab file.

The quick stats are below from my 4/15 Daily Post

  • The annotated gene list is in Steven’s notebook post. A quick review shows the following:
    • 12 of 17 DMLs mapped to genes that are hypo-, hyper- methylated, or both.
    • 4 are hyper-methylated, 6 are hypo-methylated, and 2 have both instances.
    • The magnitudes of methylation in either direction are the same.
    • 10/12 have a characterized gene function, and 2/10 are uncharacterized.

DML Table

DML_ID Chromosome Start End p_value q_value Meth_Diff Methylation_Status Sample_ID Gene_ID Functional_Annotation
517209 NC_086373.1 90626338 90626340 3.96E-16 1.16E-11 56.32 Hypermethylated LOC134690221 GRAM domain-containing protein 4-like; membrane-associated signaling or vesicle trafficking
606937 NC_086373.1 105503509 105503511 2.40E-19 4.17E-14 -57.86 Hypomethylated LOC134695637 Otoferlin-like; vesicle-mediated transport and sensory signaling
907320 NC_086374.1 34742951 34742953 8.09E-19 1.10E-13 58.27 Hypermethylated LOC134707074 Receptor-type tyrosine-protein phosphatase N2-like; cell signaling and differentiation
1500842 NC_086375.1 31938079 31938081 6.89E-24 8.98E-18 -60.69 Both LOC134711256 Cancer-related nucleoside-triphosphatase homolog; DNA/RNA metabolism and stress response
1551568 NC_086375.1 43581688 43581690 3.47E-25 6.02E-19 58.20 Both LOC134711256 Cancer-related nucleoside-triphosphatase homolog; DNA/RNA metabolism and stress response
1859027 NC_086375.1 90876604 90876606 1.04E-18 1.32E-13 55.88 Hypermethylated LOC134712818 Uncharacterized protein
1914146 NC_086376.1 5631156 5631158 3.19E-18 2.92E-13 59.00 Hypermethylated LOC134714536 Coatomer subunit epsilon-like; intracellular vesicle trafficking
2751840 NC_086378.1 6633121 6633123 1.21E-17 7.20E-13 -55.24 Hypomethylated LOC134720671 Roundabout homolog 1-like; cell migration and guidance signaling
3165089 NC_086379.1 1603830 1603832 4.36E-22 2.52E-16 -60.82 Hypomethylated LOC134724475 Uncharacterized protein
3382604 NC_086379.1 47961734 47961736 3.43E-19 5.77E-14 56.45 Both LOC134725187 Membrane protein BRI3-like; signaling and membrane dynamics
3464660 NC_086379.1 64017640 64017642 3.94E-28 1.72E-21 -63.60 Both LOC134725187 Membrane protein BRI3-like; signaling and membrane dynamics
3940870 NC_086381.1 21212100 21212102 1.86E-17 1.06E-12 -56.07 Hypomethylated LOC134685297 Tumor protein p53-inducible protein 11-like; stress response and apoptosis

Issue with DML Result Write-up

  1. No sample IDs or clear files to figure it out without going through an generating for myself.

Deliverables for Next Week

Next Meeting: April 28th @ 10am

Items:

  1. Treat DMLs as hyper= high PAH, hypo= low PAH when writing the results
  2. Curate the supporting papers and add a link to the Zotero folder to the agenda
    1. Focus is dominantly in oysters re: DMLs
    2. Supporting evidence is within other bivalves re: immune function, pesticide and microplastic exposure,
  3. NSF Activity Report and GSAR ready for next week
  4. Consider using the extracted DNA from these samples for my first Promethion run once the equipment is up and running.