Shelly’s Notebook: Thur. Sept. 19, 2019 Pt. Whitney Juvenile Var.low pH experiment

Water chemistry

  • Took discrete measurements and TA around 2:30pm
    • for TA, I took directly from the discrete measurment water after filtering it through 20uM. The discrete measurement water samples were directly from the headers and inside the silos (using clean TA cups)
    • everything looked as it should
  • @5:40pm calibrated B5 which was off by 0.08. All other probes were within 0.01.

Animal check

  • Tote B5 had a pretty low water level and Matt and I weren’t really sure why. He said the header upstairs was overflowing so he turned that down and it should give more water to the totes. He also turned the pump up a little bit. The animals in B3 were still receiving water although the flow felt a little weaker by the touch. I doubt it has been like this for a whole week, it seems anomlymous.
  • uc?export=view&id=1qJcx4kZI58M1znUqjQizEcRYnqCE292a
  • Algae line looked a little clogged, like it wasn’t really flowing. However disconnecting from the tote inflow pipe looked like it was dispensing the same volume as the lines going into the conical headers. Also algae came out from the tap near the pump head itself when turned on. So all good here.

Respirometry and sampling

  • filled 5L beakers with 1-2L 1uM FSW.
  • Submerged vials in well plate holders
  • turned off flow in silos and removed manifolds
  • took 1 animal/silo with transfer pipette spoon and then used 2 transfer pipettes like chopsticks to transfer the animal into the corresponding submerged vial
    • Did this for all silos, took about 20 minutes
      • Turned flow back on immediately after transferring animals and adjusted to 7mL/sec.
    • Noticed animals in low pH treatment had very fragile shells and are a little white like Sam has previously seen
      • it seemed like animals from ambient parents were more fragile (many broken shells on the sand surface.
  • Ran 1 respirometry trial around 5pm for about 30 minutes.
    • SDR plate positions here (A1 = bottom right corner):
      • uc?export=view&id=1-pLPP4zsD3X0uyL_HakmZWjEp5Eqm5SG
      • on SDR plate: uc?export=view&id=1TBMmtUUk-HM8rBXHE348p2JbSacWTSfq
  • After trial, emptied vials and animals onto a well plate lid (to track their positions; A1 = upper right corner and order listed on size measurement data table linked below) for shell length measurements
  • uc?export=view&id=1nT7hq6Htii_Wnno32OnSO6ripnLZ5uyx
  • Got wet weight for each animal by transfering animals onto paper towel (using the transfer pipette chopstick method) to gently blot off excess water. Then transferred animal into tared snap cap tube, recorded weight, and immediately froze in liquid N2.

Geoduck genome call at 12pm

  • We shared our progress with our three different DM methods:
    • loci (Steven)
    • DMGs (Hollie)
    • DMRs (Shelly)
  • CONCLUSIONS:
    • DMLs are more just for curiousity and confirming sites for other methods at this point
    • DMRs need to be more stringently defined
      • I will continue working on this
    • We will focus on DMGs now (Hollie is leading this effort)
      • She will make a heatmap with treatment averages of % gene body methylation (with and without filtering for low variance)
      • Then she will do GO enrichment

from shellytrigg https://ift.tt/30daYKF
via IFTTT