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

Mcap 2020

In review!

• Revise by mid March 2020 at the latest

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
• ITS2 sequencing analysis

E5 Physiology

Final manuscript

• Finish writing discussion section
• Send draft of full manuscript to coauthors
• Revise manuscript and post on bioRxiv
• Submit manuscript

E5 Molecular

Data analysis

• Examine neural networks and SEM modeling for time series multiomic modeling analyses
• Analyze metabolomic and lipidomic data when made available
• Trial machine learning approaches to predict mRNA from features of other omics
• Multi-omic WGCNA analysis

E5 Nom Nom

Data analysis

• Analyze PR rates data set

Resazurin methods manuscript

Analysis and writing

• Introduction
• Methods
• Results
• Discussion

Oyster 2024 Stress Hardening

Data collection and analysis

• Goose Point
  • Measure size of December 2024 oysters from images (Noah K. in progress) and analyze
• Point Whitney
  • Conduct spring assessment of siblings outplanted at Point Whitney
  • 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
• Record methods for all efforts
• Plan spring field assessments

Oyster Lifestage Carry Over

Analysis and writing

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

10K Seed

Data collection and analysis

• Conduct spring growth and survival of outplants at Baywater shellfish
• Pending outplant data, storyboard potential manuscripts or additional analyses

PolyIC Larvae

Data collection and experiments

• Conduct testing in the lab and resazurin assay in January-February
• Measure size from December and January images for growth (Madeline)

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

Outreach and education

• Create and publish Reva Atea spring issue of communications magazine