January

goals, daily
Author

Megan Ewing

Published

January 22, 2025

It’s January 22nd. Clearly, “posting in my notebook more” is not a resolution I’m great at following. I am thankful for Google calendar, my notes app, and BeReal and their ability to let me see what I was doing on any given day, so with that, here’s what I’ve been up to since our last meeting:

Jan. 1

Happy New Year :) Nice day up at Crystal Mountain.

Jan. 2

Canvas pages for classes got posted. Reviewing those to prep for class. Coordinating some logistics stuff with Jose and Celeste for 270.

Working on WAS travel app.

Jan. 3-5

My mom’s 60th birthday! I’m out of town.

Jan 6.

First day of 270, went to the lecture to meet the students.

Lab meeting.

Wrapped up WAS travel app

Jan 7.

Readings for snow hydro class, first day of lecture

270 meeting with jose and celeste

GIS class

Homework

Past Two Weeks (from 1/23 meeting) Starts Here

Jan 8.

Office hours, homework

Jan 9.

Snow hydro class

Read: Gonadal rematuration of sex-specific reproductiv impairment in Manila clams under ocean acidificataion

(which then sparked some questions by Mac to be answered by the next paper re: measuring sex steroids in bivalves)

Read: Possible roles of sex steroids in the control of reproduction in bivalves

Jan. 10

Meeting with Mac to go over results. Here’s the notes from that:

- Methods look good for thesis. Will need to get to 1 paragraph for ms

Intro : summarize larken paper findings, “we found differences in larval between primed and unprimed differences. This begs the question of what is happening in these eggs that leads to these differences. I took the data from these eggs and looked at RNA seq analysis.”

  • why is knowing the mechanism important

  • figures (larval growth and survivorship, egg size)

  • what parental priming is and why it matters.

  • biological marker. Genes fro successful priming

For results: look for protein domains

- Results missing

  • Log2fold change — give biologically meaningful definition (more expressed in control, less expressed, etc)

  • How many annotated, how many go terms, enrichment results (or lack thereof)

  • rRNA — eating up the read counts

  • Incl. distribution of RNA type (stacked bar plot)

  • Look at p value for the rRNA between treatment

  • Add in mito, rRNA, and protein-coding (by proportion)

  • Move enrichment info to results (last sentence of methods.

For results: look for protein domains.

use pFam database to determine protein domains for uncharacterized genes using amino acid sequences provided in annotation file

From main manuscript

- Fig 3b

- Fig 5

Mention how many of the RNA egg samples we had egg size data for.

Look for papers where there aren’t very many differentially expressed genes — how do they report their results.

If not transcriptional differences, maybe epigenetic mechs explain phenotype

Jan. 11-12

Snowboard and work at snowboard shop.

Learned how to play the card game “Golf” aka “Tamoul”

Jan. 13

Review 270 lab 1 materials

Jan. 14

snow hydro reading

snow hydro lecture

snow hydro homework…

Jan. 15

finish snow hydro homework

Office hours

First 270 lab

Jan. 16

Snow hydro reading

snow hydro lecture

lab meeting

read: modern phylogenomics: building phylogenetic trees using the multi species coalescent model

Jan. 17

weekly TA meeting

270 lab

Jan. 18-19

Chores and work at the shop

read (well.. skimmed and took relevant information to prep for meeting with luke):

Jan. 20

Met with Luke to discuss methods for ch. 1 and what I’m going to do with my gene list of gametogenesis genes once I have it, in order to have information that is meaningful.

Theres this thing called a robinson-foulds tree distance which I can use to identify outlier genes against a statistically significant threshold. This will leave me with a list of genes that aren’t well conserved ie. genes that might have duplication (like dmrt in some bivalves), genes that have been lost or indicate convergent evolution, genes that have been actively selected for/against.

So I end up with a gene list with 20,000+ genes (or even 200), I can find which genes are meaningful evolutionary and can select those to map onto a known phylogeny of bivalves (like the figures in Nicolini et al. 2023)

Going to use these to redraft / revise my methods in my proposal and have set a date to revisit with luke by Feb. 14

Also graded some 270 assignments

Jan. 21

I dropped snow hydro :D

Was taking too much of my time for a 3 credit class, and the topics for the class once all the material was posted seemed to be more of a physics of snowpacks rather than snows influence on normal hydrology topics. Juice was not worth the squeeze…

Met with celeste to prep some of the 270 materials for the week and learn how to use the autoclave

filled out travel pre-authorization request for aquaculture 2025 on treq

GIS class

Next Two Weeks’ Targets….

Now that I’ll have more time since no snow hydro lecture readings or homework, i’ll have some time to get back to my own work :D

Jan. 24:

  • 270 lab and TA meeting.

  • grade 270 stuff

Jan. 27-31:

  • Address action items from meeting with Mac

    • protein domains – [pFAM database for uncharacterized genes (n=16)

    • add in meaningful definition of log2fold change in results

    • indicate how many annotated, how many go terms, and (lack of) enrichment in results

    • include distribution of RNA type (stacked bar plot)

    • look at pvalue for rRNA between treatments

      • will need to re run chi square for this

    • add in mito, rRNA, and protein coding (similar to stacked bar plot, but pie chart)

    • move enrichment info to results instead pof methods

    • add in info on how mnay RNA egg samples we had egg size data for (will add in info about egg samples we did have to intro when summarizing / referencing Larken paper findings)

  • TA stuff

Feb 3-7:

  • Now that rphil methods results are updated, will draft intro and discussion. some talking points:

    • summarize larken paper findings, “we found differences in larval between primed and unprimed differences. This begs the question of what is happening in these eggs that leads to these differences. I took the data from these eggs and looked at RNA seq analysis.”

      - why is knowing the mechanism important

- figures (larval growth and survivorship, egg size)

- what parental priming is and why it matters.

- biological marker. Genes fro successful priming

    • dicussion: parental priming, OA on bivalves, offspring health, etc. also, if not transcriptional differences explaining the phenotype found in Larken MS, perhaps epi mechanisms?

  • TA stuff

Feb 10-14 (slight preview):

  • Switching gears from rphil back to proposal – will be focusing this week on the phylogenomics stuff discussed with Luke to get an updated methods to discuss with him for our 2/14 meeting.