Laura’s Notebook: Oly OA gonad histology & spawning data options

I’ve come full circle with my data from the Olympia oyster adult OA exposure project from 2017. After agonizing over the data for months (…years?), I’m moving forward with population-specific analysis, focusing on the effect of low pH on gonad & fecundity, with some minor findings regarding the offspring. Until a couple days ago I was all set to just use data from the 6C pre-treatment temperature groups (overwintered at 6C), but since we are now looking at population specific effects I may want to include the 10C groups (overwintered at 10C). The reasons to include both temperature groups are a) very simliar gonad results in both groups, b) more spawning data which support the population-specific reproduction theme, and c) I can refer to this paper when I write my QuantSeq paper (since RNA from larvae was from 10-low pH and 6-amb pH). If I go this route I will not analyze the 10C survival/growth data.

I’ve prepared some new figure options, particularly for the gonad histology data:

6C gonad data only, showing dominant stage, sex, and example gonad tissue

Gonad stage before pH treatment (n=54) and after 52 days in ambient pH (7.82±0.02, n=39) and low pH (7.31±0.02, n=39) for all populations combined. Gonad differed significantly between pH treatments (𝝌2=9.79, p=0.032), and between pre-treatment and ambient pH (𝝌2=6.61, p=0.146)


Shelly’s Notebook: Mon. Jan 28, 2019, Geoduck Broodstock DNA extraction from Hemocytes

Kaitlyn and I isolated DNA from four Jan. 4 hemocyte samples. Two samples were from Tank 2 (low pH) and two were from Tank 3 (ambient) treated animals. We used the EZNA kit and followed the manual with the following exceptions:

  • We started on step 2 because we had cells not tissue, so no tissue homogenization was necessary
  • Heat block in rm 213 was 59-65C instead of 60C because the digital setting was a few degrees off from the alcohol thermometer.
  • In step 6, the volumes transferred were:
    • 250uL for sample 16
    • 300uL for sample 15
    • 350uL for sample 26
    • 400uL for sample 25
  • We eluted with 2 x 50uL elution buffer warmed to 70C.

Then used 1 uL of each sample for Qubit BR.

Standard 2 read 98 ng/uL and 102 ng/uL, so average is 100 ng/uL which is what it should be.

Here are the following qubit readings for the samples:

Animal ID Tank Treatment Conc. (ng/ul) Total DNA (ng)
15 3 amb 12.3 1230
16 3 amb 56 5600
025 2 low (pH 6.8) 8.3 830
026 2 low (pH 6.8) 7.4 740

We will send these for WGBS sequencing.

from shellytrigg