All Projects To Do List

This post lists all my ongoing projects and to-do list.

Mcap 2020

Final manuscript

  • Revise text for length and format
  • Submit manuscript to Current Biology

Hawaii 2023

Analysis and writing

  • Process all samples for larval symbiont cell density in the lab at UW
  • Revise analysis of rapid light curves from phenoplate data and send results to UTS collaborators
  • Analyze larval size and symbiont cell density data
  • Finalize RNAseq differential gene expression and functional enrichment analyses
  • Finalize ITS2 analysis
  • Revise lipidomic analyses for differential lipids and SAM modeling methods
  • Finalize metabolomics analysis
  • Conduct WGCNA correlation analyses between lipidomic and RNAseq datasets across temperature, parental phenotypes, and ITS2
  • Conduct WGCNA correlation analyses of lipid and RNAseq datasets across parental phenotypes, symbiont cell density, phenoplate metrics, and ITS2
  • Storyboard manuscript with collaborators
  • Finalize methods section

Moorea 2023

Data collection and analysis

  • Analyze Sanger DNA sequences for Acropora, Pocillopora, and Porites sepecies identification
  • Decide on samples to process for RNAseq and/or stable isotope metabolomics depending on species DNA identification
  • Update methods section

E5 Physiology

Final manuscript

  • Add correlation analyses of phys and light/temp to results and methods section
  • Finish writing discussion section
  • Send draft of full manuscript to coauthors
  • Revise manuscript and post on bioRxiv
  • Submit manuscript

E5 Molecular

Data analysis

  • Conduct multi-omic analysis using DIABLO method for the deep dive expression project
  • Assist Jill with sending samples to UW facility for metabolomics and lipidomics processing
  • Analyze metabolomic and lipidomic data when made available
  • Conduct time series WGCNA between RNAseq and physiology

Resazurin methods manuscript

Analysis and writing

  • Obtain size data for all oysters (Noah in progress)
  • Re-analyze data for metabolic rates and survival after size normalization
  • Introduction
  • Methods
  • Results
  • Discussion

Oyster 2024 Stress Hardening

Data collection and analysis

  • Goose Point
    • Measure size of June 2024 oysters prior to outplant from images
    • Measure size of December 2024 oysters from images
    • Analyze growth rates from June to September to December
    • Analyze survival data from June to September to December time points
  • Westcott
    • Analyze growth and survival data from Westcott 12/17/2024 assessment (Grace in progress)
  • Point Whitney
    • Conduct spring assessment of siblings outplanted at Point Whitney
    • Consolidate and clean oysters at Point Whitney and move broodstock from Point Whitney to UW
    • Clean and inventory supplies
    • Transfer HUDLs to other facilities if we decide not to keep them
    • Move 2024 USDA seed out of heath trays and into larger cages or upwellers when they outgrow the current trays
    • Analyze temperature data from December 2024 logger download
  • Story board potential manuscripts and decide on timeline for continuing assessments of oysters at all sites
  • Record methods for all efforts
  • Organize GitHub repository

Oyster Lifestage Carry Over

Analysis and writing

  • Analyze qPCR data
  • Storyboard potential manuscript
  • Analyze final time point growth data
  • Organize GitHub repository
  • Introduction
  • Methods
  • Results
  • Discussion

10K Seed

Data collection and analysis

  • Re-analyze data after size normalization (Noah in progress)
  • Conduct spring growth and survival of outplants at Baywater shellfish
  • Pending outplant data, storyboard potential manuscripts or additional analyses
  • Move animals at Point Whitney to new bags and count the number alive at Point Whitney to track winter survival

PolyIC Larvae

Data collection and experiments

  • Test RNA extractions of shelled larvae and seed using Zymo Quick RNA test kits
  • Design January 2025 resazurin stress testing experiment
  • Transport seed samples from Point Whitney to UW lab for January 2025 testing
  • Conduct testing in the lab and resazurin assay in January

Oyster 2025 Stress Hardening

Planning

  • Design spring-summer oyster stress hardening projects
  • Design spring-summer oyster spawning/larval projects

Planning and funding

  • Talk with the Coral Resilience Lab about upcoming work and potential projects
  • Work on grant applications with Steven and Hollie
  • Perspectives manuscript with Yaamini

Student projects

  • Test/optimize enzyme assays in the lab on test oysters
  • Conduct lab based stress hardening trials
  • Plan student projects

Outreach and education

  • Create and publish Reva Atea spring issue of communications magazine
  • Work with Bellingham Technical College to plan summer internship for WSG project
  • Work with Bellingham Technical College to set up winter/spring stress hardening trials for WSG project
Written on December 12, 2024