---
title: "Masters/Bypass Progress and Planning"
author: "Kathleen Durkin"
date: "last-modified"
categories: ["monthly goals"]
format:
  html:
    toc: true
engine: knitr
---

Overview of 2024.10.25 meeting with Steven to discuss/plan Masters/bypass completion.

## AU24

-   Finalize masters committee. Discussing with Kerry on Tuesday (10/29), I think (hope) she'll agree to join my committee! If not, Jackie would also fit.

-   Have first committee meeting. **What materials/slides do I need to prepare for this?**

    -   Need to prepare material overviewing my current degree progress and plans for completion

-   Submit Plan of Study. Currently need 5.5 credits to complete masters requirements (4.5 if CENV 590 can by counted toward degree -- would need approval). **What other courses would be beneficial for proposed study?**

-   Thesis focus: role of multiple epigenetic mechanisms and their interactions in environmental memory/stress response in marine invertebrates.

    -   E5: miRNA, miRNA + RNA expression, miRNA/siRNA + DNA methylation

-   Q: **How is collaborative work handled for thesis? E.g., to what extent can E5 work be included in thesis?**

    -   E5 work that I've completed is fully eligible

### Thesis progress and brainstorming

Chapter 1: corals deep-dive (+ deep-dive-expression)

I've currently completed miRNA/siRNA characterization and preliminary expression work. I'm in the process of characterizting patterns of sncRNA + mRNA coexpression. Will also incorporate DNA methylation mapping and sncRNA/methylation interaction analysis.

-   were methylation samples sent out? for deep dive

-   could also include coral hDNA methylation in this if I receive the SIFP

-   logical expansion into PhD thesis is looking at time series data

Chapter 2: environmental memory in oysters

-   we have data for oysters under OA exposure. Described in parents, but not yet touched children. In parents have gene expression and methylation (plus lncRNA from the RNAseq data)

-   so I could look into **heritability of methylation in oysters**

-   methylation data from the offspring already exists!! (i.e., the samples have already been sequenced)

-   side note: lab has already looked into barcoding bisulfite-converted DNA, but had limited success because their gene of interest was very long and bisulfite treatment degrades high-molecular-weight DNA. It would be interesting to develop some kind of screening protocol to screen for methylation patterns associate with resilience. (e.g., for broodstock screening)

### To-Do:

E5:

-   For each miRNA, calculate correlation coefficent with each gene

-   Look into miRNA binding again (get software from Jill?)

-   interactions with lncRNA (get data from Zach). Could also do binding here, since lncRNAs may be sponges, precursors, etc.

-   cross-species stuff could be interesting -- gene orthologs? but can be back burner for now

-   correlation between methylation in an miRNA-coding region and expression of that miRNA.

General:

-   can bring Hollie in now for committee

-   schedule meeting with steven, weekly thursdays at 11

## WI25

-   Full draft of Masters Proposal

-   Q: **To what extant can your thesis work deviate from submitted Proposal?**

## SP25/SU25

-   Submit finalized Masters Proposal

## SU25

-   Possibly Smithsonian fellowship (coral hDNA methylation), 10wks

    -   **How would funding for the remaining \~4wks work for this?**

## AU25

-   MS exam + bypass
