Mon. Sept 24, 2018

My goals for today

  1. Lab meeting @ 10
  2. Meet with Steven to decide projects to focus on
  3. SAFS kickoff @ 2-5

Notes from lab meeting

  • Sam’s working on oyster transcriptome and genome assembly
  • Kaitlyn’s working on oyster proteomics temperature x time series analysis
    • pharmacokinetics toolkit applicable? (Brent asked)
    • RNA-seq time series analysis tool applicable?
  • Yaamini’s working on reviewer comments for JSR submission on oyster broodstock DMR comparison under OA conditions
    • what is the best way to vaildate methylation levels?
      • MSP vs. MBD or both? Need data relevant to physiology
  • Brent’s working on lots of grants and coordinating Pt. Whitney setup
    • Pt. Whitney: need to set a date, set up CO2 tanks
      • monitoring Geoduck over time by
        • measuring respiration weekly
        • hemolymph sampling (how contaminated with sea water will this be?)
          • where’s the best place to poke?
            • heart (Brent tried, not best survival rate)
            • aductor muscle (maybe too small, size of an eraser)
            • siphon
          • ELISA for vitellogenin to tell dev. stage
            • can we order an commercial ELISA kit to test on Geoduck?
            • can we test kit with old hemolymph sample where vitellogenin was expressed?
          • [SRM]https://pubs.acs.org/doi/full/10.1021/pr400444m)
        • non-lethal gonad biopsy (Emma’s paper)
        • histology? at least on some for validation of dev. stage
  • Laura’s working on summer histology analysis on OWL (protocol on Git). Austrailia work was temp. association with spawning and using histology to quantify eggs to tell stage: brooder vs. non-brooder. Also doing OA Oly. RNAseq data analysis pipeline
  • Emma’s working on hatchery microbiome with OA conditioned Geoduck. Comparing traditional assembly to MOCAT to 6-Gill and digging into unaligned reads. Larvae at pH 8.2 had ciliates in seawater, ciliates didn’t grow at lower pH treatments.

Notes from meeting with Steven

  • Geoduck project options:
    • OA methylation data analysis
      • Have RRBS data from many different days.
        • figure out comparisons to do
        • what data is good (i.e. minimum # of loci/sample)
        • samlpe descriptions in Ronnit’s notebook
    • Geoduck transcriptome analysis for evolutionary comparison or alt. splicing comparison
      • Lots of illumina data from many tissue samples from the same individual
        • one tissue is the crystalline style (precursor of the thyroid)
        • Analysis = running trinity and BLAST
          • Check Steven’s lab notebook entry on this

my thoughts on metrics for monitoring OA effects



Written on September 24, 2018