I keep thinking that after each chaotic week of this experiment, that the next week is the one that will bring a stable routine and a chance to do something that isn’t mess around with live animals all day. Not that live animals are bad, but I sure do miss my computer. I’ll (obviously) re-evaluate this statement in February when I’m tired of staring at a screen.

Spoiler alert: I’ll be nostalgic for experimental chaos!

June Goals recap

Green Crab Pilot Experiment:

• Sent my samples for metabolomics and lipidomics sequencing!!
• Started the respirometry data analysis! Not done yet, but my preliminary results show that there is a point to doing respirometry…and that’s pretty darn exciting.

West Coast Green Crab Experiment:

• Set up ESL and bought all necessary experimental materials
• Receive the Washington crabs!! Measured, labelled, and took leg joints for genotyping for all the crabs with the help of an amazing crew.
• Managed to start the treatments after a grueling few days at ESL!

Summer Students:

• Finalized summer projects for Lauren and Julia
• Julia got a (much-needed) extension on her thesis proposal so Carolyn and I have more time to write her letter of support

Hawaii Gigas Methylation:

• Started revising my previous methylKit results! Then the experiment got extremely chaotic and I paused this work.

July Goals

Green Crab Pilot Experiment:

• Seriously actually finish the respirometry analysis

West Coast Green Crab Experiment:

• Just. keep. swimming.

Summer Students:

• Write Julia’s letter of support for her proposal
• Assist students with their independent projects and analysis
• Introduce students to other people they can network with at WHOI
• Help students write an abstract for a conference of their choice

Coral Transcriptomics:

• Rework analysis with additional dataset
• Re-try KOG analysis
• Dig into gene lists
• Start discussion

Hawaii Gigas Methylation:

• Add Rajan’s edits as comments to the draft manuscript
• Finish methylKit contingency tests
• Conduct a randomization test for DML identification
• Integrate with other epigenetic datasets
• Update methods and results

Other:

• Review paper for Evolutionary Applications
• Review paper for Aquaculture
• Start draft of Evolution Symposium
• Revise CV
• Revise research statement
• Revise teaching statement

Deep Freeze

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

Virginica Methylation and Expression:

I’ll return to this when I have an updated discussion for the Hawaii paper.

• Update methods and results from quadratic addition to transcriptional noise model
• Compare transcriptional noise analysis with Liew and Aranda papers

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