Had first committee meeting (01/09) with Steven Roberts, Hollie Putnam, and Amy Van Cise. Slides can be found here

Big takeaways…

  • Timeline: Since I’m going to bypass to the PhD, it seems most strategic for me to focus on wrapping up my first chapter (mussel heat stress) over the next couple of months, while continuing to formulate a solid dissertation proposal for my bypass application. Need to think about timeline in conjunction with funding, teaching, courses, planned travel/activities. Lay everything out to decide when exams and other milestones can be feasubly met.

  • Chapter 2 Focus: Total reframe of the system for my second chapter seems necessary. Still focusing on lncRNAs, but now working with coral data Hollie mentioned (includes stress element with control). Should be considering a more narrow focus for lncRNA analysis.
    • Are there specific tissues that would best answer whether or not lncRNAs are environmentally sensitive?
    • Or specific tissues involved in a biological process that might rely on lncRNAs for regulation? Basically needs to be set up so that a biologically motivated question is being answered with lncRNA data. More specific and direct as opposed to a shot-gun approach of “what did we see after inspecting the data”. A good first step in this would be completing a differential expression analysis for the CEABiGR data to get a feel for what the lncRNA expression landscape looks like.

  • Chapter 1 Considerations: Need to get ahead of temperature choices since the max and min of the temperature treatments are not the same. Absolutely should finish the lab work ASAP to move forward with quntification and analysis (HIGH PRIORITY).

  • Overall Thesis/Dissertation Topic: Need to define resilience in the context of my project. Should create a conceptual diagram of how everything fits together.
    • Am I talking about molecular resilience or a more ecological definition? (Ecological resilience conveyed by molecular mechanisms?)
    • How will these chapters fit together? Increasing complexity by adding pieces of the expression landscape?
    • What is the focus beyond lncRNAs? Is it additional ncRNAs (miRNA, siRNA)?
  • Statistical Analyses: What sort of stats can I be using to analyze this work. Is it stats focused or mechanism focused? Both?
    • Should consider taking additional courses in stats to support this work. It’s more than likely that.

I’m really pleased with where this meeting has me headed. It will be nice to jump right into corals, and it has me thinking about what a potential chapter line up might look like.

  1. Mussel heat stress
  2. Coral lncRNAs
  3. Coral miRNAs & siRNAs
  4. Putting this work together toward some global analysis incorporating environmental data?

If you couldn’t tell from that last one, I’m still interesting in seeing what a seascape genomics project could look like with this type of expression data combined with spatial or environmental data.