Overview of 2024.10.25 meeting with Steven to discuss/plan Masters/bypass completion.
AU24
Finalize masters committee. Discussing with Kerry on Tuesday (10/29), I think (hope) she’ll agree to join my committee! If not, Jackie would also fit.
Have first committee meeting. What materials/slides do I need to prepare for this?
- Need to prepare material overviewing my current degree progress and plans for completion
Submit Plan of Study. Currently need 5.5 credits to complete masters requirements (4.5 if CENV 590 can by counted toward degree – would need approval). What other courses would be beneficial for proposed study?
Thesis focus: role of multiple epigenetic mechanisms and their interactions in environmental memory/stress response in marine invertebrates.
- E5: miRNA, miRNA + RNA expression, miRNA/siRNA + DNA methylation
Q: How is collaborative work handled for thesis? E.g., to what extent can E5 work be included in thesis?
- E5 work that I’ve completed is fully eligible
Thesis progress and brainstorming
Chapter 1: corals deep-dive (+ deep-dive-expression)
I’ve currently completed miRNA/siRNA characterization and preliminary expression work. I’m in the process of characterizting patterns of sncRNA + mRNA coexpression. Will also incorporate DNA methylation mapping and sncRNA/methylation interaction analysis.
were methylation samples sent out? for deep dive
could also include coral hDNA methylation in this if I receive the SIFP
logical expansion into PhD thesis is looking at time series data
Chapter 2: environmental memory in oysters
we have data for oysters under OA exposure. Described in parents, but not yet touched children. In parents have gene expression and methylation (plus lncRNA from the RNAseq data)
so I could look into heritability of methylation in oysters
methylation data from the offspring already exists!! (i.e., the samples have already been sequenced)
side note: lab has already looked into barcoding bisulfite-converted DNA, but had limited success because their gene of interest was very long and bisulfite treatment degrades high-molecular-weight DNA. It would be interesting to develop some kind of screening protocol to screen for methylation patterns associate with resilience. (e.g., for broodstock screening)
To-Do:
E5:
For each miRNA, calculate correlation coefficent with each gene
Look into miRNA binding again (get software from Jill?)
interactions with lncRNA (get data from Zach). Could also do binding here, since lncRNAs may be sponges, precursors, etc.
cross-species stuff could be interesting – gene orthologs? but can be back burner for now
correlation between methylation in an miRNA-coding region and expression of that miRNA.
General:
can bring Hollie in now for committee
schedule meeting with steven, weekly thursdays at 11
WI25
Full draft of Masters Proposal
Q: To what extant can your thesis work deviate from submitted Proposal?
SP25/SU25
- Submit finalized Masters Proposal
SU25
Possibly Smithsonian fellowship (coral hDNA methylation), 10wks
- How would funding for the remaining ~4wks work for this?
AU25
- MS exam + bypass