Grace’s Notebook: 4/28/2017

Histology: Finished up the histology slide images of Oly and gigas gonad tissue. I uploaded the images into folders in the GitHub repository here. Additionally, I sent off the next batch of histology cassettes to be made into histology slides.

Oysters: Fed the oysters in the tank algae paste. Let sit for 1 hour. Measured salinity: 30. Started a feed log in order to keep track of salinity and feeding schedule.

Grace’s Notebook: Oly Histology Slides Thoughts

I took pictures of the tissues of a few histology slides from Laura’s O. lurida project.

Below are some thoughts I have on what we may be looking at using my past experience of looking at geoduck gonad histology, and using the histological work from two papers (Oates 2013 thesis) (Moore et al., 2016) found from a recent literature search on specifically O. lurida gonadal histology. Also, Brent came over and helped a lot. (Link to google drive folder)





Ones I’m unsure about:



Histology from Moore et al. 2016:



Grace’s Notebook: April 14, 2017

  1. SRA Data: Sean showed me the process of downloading SRA data directly into my folder in Scaphapoda using command line. Link to Sean’s explanation of the process here.
  2. Histology Images: I took some pictures of Laura’s oly histology slides. There’s a folder here that includes two papers that I found which have oly histology images of gonads, and a folder of the images I have taken so far, labeled as the slides are labeled.
  3. Proteomics paper refs: I was sent a newer revision of the Timmins-Schiffman et al. proteomics paper with a request to update the references. I used paper pile originally, so in an attempt to not waste too much time, I uploaded the word doc to my google drive. Then I right-clicked on the file in order to open it using google docs. All of the comments, images, and tables from word was present in the google doc. The only thing that wasn’t transferred was the line numbers. I updated the references using paper pile, then downloaded as a word doc to send back to Emma.



April 11, 2017

Set up an iPod camera on a microscope for nearing histology work: IMG_3122

There is a glare, so either will have to be blocked by hand, or turn off overhead lights. Here is a google drive folder with some histology images.

Finished up some summary data for Rhonda’s oyster seed morphology:

Screen Shot 2017-04-11 at 12.19.23 PM


April 4, 2017

Looked into some options for cell phone adapters for microscopes. Found a promising one from Gosky Universal.

Revisited edits to the “Differential response to stress in Ostrea lurida as measured by gene expression” paper. More needs to be done.

Started cleaning/organizing refrigerator in FTR 209. Added general shelf contents to the lab inventory spreadsheet under the “Refrigerator Rm 209” tab.

Fish Sample Integrity: Coho liver samples and Rainbow Trout tissue

Information from Dr. Abraham Aviv, Rutgers
Samples were provided by SR Lab

First analysis phase: DNA integrity

9 samples degraded: loss of margins of the dense DNA band (crown) and presence of high intensity tail (smear)Aviv_fishsamples_DNAintegrity

Rest are ok.

Up next: measuring terminal restriction fragment length (telomere length: TL) in the good samples
Issue: whether or not TL will be within range to use Southern blot methodology

Manchester, Histology send off, and Oyster morphology

Yesterday morning Yaamini and I met Olivia at 8am at Manchester. We cleaned algae lines and filters. We performed water chemistry. Next week Yaamini will join us again, but will be mostly there to observe how well Olivia and I can perform the tasks, as we will do them ourselves while Yaamini and Laura are away.

Yesterday I sent out histology samples of gigas and olys from Laura and Yaamini’s projects. For future reference, this is what the histology filled-out form looks like that accompanies the samples.

Today I have continued Rhonda’s oyster seed measurements. I am currently beginning Tube 3, screen size 710-1000.