I’m an NSF Postdoctoral Research Fellow in Biology now! This means my main focus will be anything and everything green crab. My other postdoc scholar and Ph.D work is now relegated to side project land. Still, I feel like a panicking droid since at the end of this month I go on leave for over two weeks.

March Goals recap

Coral Transcritomics:

• I finished all of my outstanding analyses! I have one more analysis I would like to complete, but I think the manuscript would be okay without it (but…I think it will be really cool if I can figure out why I keep getting R errors)
• Shared my findings with Maggie and Ann, and wrote a summary of these findings for Maggie to send to collaborators
• Outlined discussion points

Hawaii Gigas Methylation:

• …didn’t do anything for this project. It’s taken a backseat to some more interesting developments in the Virginica project

Virginica Methylation and Expression:

• I didn’t update the results with initial mixOmics analysis
• But I did revise gene-based transcriptional noise model and conducted variance partitioning analyses!
• I didn’t do any other modeling or methods investigation.
• Assigned creating a SNP list from EpiDiverse output to Steven so I could focus on modeling

Green Crab Pilot Experiment:

• …again, didn’t do anything related to this project

Other:

• Completed my NSF PRFB start paperwork!
• Addressed eelgrass transcriptomics reviewer comments and formatted the Github repository for publication
• Got two summer interns: one SSF student and a PEP student!

April Goals

Green Crab Summer Experiment:

• Create experimental plan and timeline
• Meet with SSF and PEP students to plan summer projects
• Coordinate logistics for summer experiments with various parties

Green Crab Pilot Experiment:

• Update experimental methods
• Finish demographic data analysis
• Survivorship analysis
• Time-to-right analysis
• Test respirometry analysis
• Update methods and results
• Determine workflow for metabolomics sample processing
• Order materials for metabolomics samples

Coral Transcriptomics:

• Finalize methods and results
• Outline full discussion

Virginica Methylation and Expression:

• Update results with initial mixOmics analysis
• Remove SNPs from methylation analysis and all downstream analyses
• Look into spurious transcription methods

Hawaii Gigas Methylation:

• Add Rajan’s edits as comments to the draft manuscript
• Review EpiDiverse output and create a new SNP list
• Rerun methylKit
• Conduct a randomization test for DML identification
• Update methods and results

Other:

• Create budget spreadsheet for remaining PDS funds
• Create budget spreadsheet for NSF PRFB
• Mindful productivity module 1

Deep Freeze

Things that are not immediate enough to be on the backburner, so they’re stuck in the deep freeze.

Killifish Methylation and Expression:

I’ll return to this when I have a good draft of the coral paper.

• Pathway analysis for RNA-Seq data
• Determine protocol for SNP identification
• Conduct in silico RRBS digestion
• Characterize DEG that overlap between populations
• Quantify gene expression variability
• Visualize DEG data

Zebrafish DNMT:

I’ll think about this once I have a robust killifish paper draft.

• Identify a stress condition to use for the zebrafish based on disease factors or conditions that are known to induce changes in methylation
• Determine physiological endpoints to assess for embryos
• Construct a project timeline