May 2025 Goals

May 2025 goals and daily notebook entries.

Goals

Writing and manuscripts

  1. Dissertation edits - check w Hollie
    • For AST chapter, shorten discussion to focus on nutrient implications for miRNA discussion
  2. AST manuscript writing - polishing for publication, maybe submit to JEB?
  3. Mcap 2023 manuscript writing - methods and results
  4. CBASS - stats results

Sample processing

  1. Train Flo re molecular work
  2. e5 lipid/metabolite protein assays
  3. Anything else lab needs

Data analysis

  1. AST 2021
    • phys univariate statistics. Remove Feb to see if this impacts stats at all
    • DESeq2 + GO enrichment for ambient Feb, June, and August to tell seasonal story of gene expression.
    • Exclude Feb time point and only include molecular for June + August amb and heat and run PERMANOVA. This will tell us if we care about treatment, time, or the interaction at all when looking at summer time points.
    • Do DESeq2 + GO enrichment for June + August amb and heat (exclude Feb)
    • mRNA-miRNA interactions - predicting interactions with miranda and correlations. network changes between june and aug amb v heat. short term network changes between june and august and long term network changes between feb, june, aug –> see how we can compare these statistically. look at papers that have done this stuff before and look at their stats
  2. Mcap 2023
    • clarification of polyadenlation - polyA v ribofree MZT and ZGA
    • subsetting genes of interest in Ayers et al. 2023
    • look at polyAD and polyA in relation to miRNAs
    • Process miRNA data once its back from Azenta
  3. e5 deep dive - check w Kathleen
  4. e5 molecular mechanisms - check w Kathleen

Field work / travel

  1. Help Zoe with her experiment
  2. Epimar?

Daily log

20250501

  • Accepted Upenn job!
  • Looking at AST 2021 phys with Feb removed
  • BES symposium

20250502

  • Nothing

20250503

  • Nothing

20250504

  • Nothing

20250505

  • AST DEGs June and August amb v heat
  • AST WGCNA for mRNAs and miRNAs
  • AST correlation of mRNA and miRNA module eigengenes
  • AST correlation of mRNA and miRNA by Condition

20250506

  • Shipping stuff to Ariana
  • Moving stuff from Andromeda to Unity via Globus
  • AST correlation of mRNA and miRNA by Condition

20250507

  • Helped Zoe with experiment setup
  • CBASS meeting

20250508

  • Helped Flo with extractions
  • Apul miRNA-lncRNA PCCs + plots
  • Katie meeting

20250509

  • e5 meeting

20250510

  • Nothing

20250511

  • Nothing

20250512

  • Lab meeting
  • Helped Zoe
  • Wrote down Barott lab project ideas

20250513

  • Coding for AST - looking at correlations between conditions

20250514

  • Coding for AST - looking at correlations between conditions
  • HMW DNA extraction
  • Submitted review for Microbial Ecology

20250515

  • Coding for AST
  • Helped Zoe

20250516

  • Helped Zoe

20250517

  • Graduation!

20250518

  • Nothin

20250519

  • Lab meeting
  • Helped Zoe
  • AST writing for seasonal enrichment
  • AST treatment GO enrichment

20250520

  • AST treatment GO enrichment
  • Helped Zoe

20250521

  • AST paper writing
  • Helped Zoe

20250522

  • Helped Zoe

20250523

  • Helped Zoe

20250524

  • Looked for apartments
  • Packed for epimar

20250525

  • Travel

20250526

  • Travel

20250527 - 20250530

  • Epimar

20250531

  • Travel

How did I do on my goals this month?

This month was chaotic.

Writing and manuscripts

  1. Dissertation edits - done
  2. AST manuscript writing - polishing for publication, maybe submit to JEB? - still stuck on whether to use the 3’UTR or full CDS as the miRNA target site?
  3. Mcap 2023 manuscript writing - methods and results - no
  4. CBASS - stats results - not really

Sample processing

  1. Train Flo re molecular work - kinda
  2. e5 lipid/metabolite protein assays - don’t need to do anymore
  3. Anything else lab needs - helped with various things

Data analysis

  1. AST 2021
    • phys univariate statistics. Remove Feb to see if this impacts stats at all - done
    • DESeq2 + GO enrichment for ambient Feb, June, and August to tell seasonal story of gene expression. - done
    • Exclude Feb time point and only include molecular for June + August amb and heat and run PERMANOVA. This will tell us if we care about treatment, time, or the interaction at all when looking at summer time points.
    • Do DESeq2 + GO enrichment for June + August amb and heat (exclude Feb) - done
    • mRNA-miRNA interactions - predicting interactions with miranda and correlations. network changes between june and aug amb v heat. short term network changes between june and august and long term network changes between feb, june, aug –> see how we can compare these statistically. look at papers that have done this stuff before and look at their stats - kinda done? Working on it
  2. Mcap 2023 - nothing really
    • clarification of polyadenlation - polyA v ribofree MZT and ZGA
    • subsetting genes of interest in Ayers et al. 2023
    • look at polyAD and polyA in relation to miRNAs
    • Process miRNA data once its back from Azenta
  3. e5 deep dive - check w Kathleen - no
  4. e5 molecular mechanisms - check w Kathleen - no

Field work / travel

  1. Help Zoe with her experiment - yes
  2. Epimar - yes

Overall, busy month.

Written on May 1, 2025