Added a little to the oyster discussion, then went down a slight tangent looking for and then looking into the histology report results from the samples taken for this project. (Update March 26, 2021 –> will not use histology report results for the paper. Don’t have access to report results and also it doesn’t fit in with the proteomic results in the paper)
Oyster paper: here
Oyster paper GitHub repo: here
Rhonda’s original project GitHub repo: here
I added a little to the discussion about infuences on oyster susceptibility to ciliates and other pathogens (salinity, seasonality, temperature), so that’s good.
I then started thinking more about the salinity and realized I didn’t have anything in the oyster rearing methods about what salinity they were kept at. So I dug around the RobertsLab/project-pacific.oyster-larvae to see if I could find anything. I couldn’t.
I came across the reports directory which I have been in before and remembered not having access to the Histology reports from this project. Samples were taken on Days 5 and 8 of the experiemnt for proteomics AND for histology. I made a GitHub issue asking about the reports here, but it’s not a big deal.
I looked through an old .pdf version of Rhonda’s 2015 paper, and found that she’d written out about the histology report results. The histology report apparently includes information on digestive gland quality, and presence or absence of bactieral infections and protozoan ciliates. Essentially the results are:
ciliates: none on day 5; 44% infected on day 8
digestive gland quality: above average quality on day 5 (32% high quality; 36% medium; 32% low; 0% very low), and slight improvement by day 8 (48% high quality; 32% medium; 16%low; 4% very low)
bacteria: none on day 5; none on day 8
ciliates: none on day 5; none on day 8
digestive gland quality: overall poor quality on day 5 (4% high quality; 8% medium quality; 28% low quality; 60% very low quality); huge improvement by day 8 (44% high quality; 36% medium quality; 20% low quality; 0% very low quality)
bacteria: none on day 5 and none on day 8
Update March 26, 2021
Not going to use histology report reults for the paper becuase it doesn’t fit in with the proteomic results that I have since the proteomics results pool the sample days. Would be way too confusing to try to fit in the paper.