Yaamini’s Notebook: March 2018 Goals

[Insert something witty about March Madness]

February Goals Recap:

  • I made progress on my DNR paper! I now have a solid figure, and relatively complete methods and results sections.
  • Started putting things in my paper repository. I haven’t sorted through anything, but most of what I think will be important is there.
  • Analyzed my reproductive output data. While there was no difference in egg production between females exposed to the different pH treatments, there was a significant difference in hatch rates. Any cross with a female exposed to low pH had a significantly lower hatch rate.
  • Decided not to start any labwork with the C. gigas histology samples just yet. If we find something interesting int he C. virginica gonad samples, then we can think about the C. gigas gonad samples.
  • Met with Tim to discuss the best way to analyze my gonad histology data. We started an R Script with a binomial glm that I’ll modify in the near future.
  • Wrapped up the C. virginica labwork!
  • Updated my section of the People page. It now includes my research interests, other interests, reasons to contact me, and my contact information!

March Goals:


  • Write my discussion, introduction and abstract (i.e. finish the paper)
  • Finalize paper repository contents and supplemental information section
  • Send draft to Alex and Micah (after Steven, Emma and Brent give the all-clear)


  • Finish analyzing gonad histology data
  • Analyze larval mortality data
  • Put together my NSA presentation!


  • Set up C. viriginica data analysis pipeline using oil spill samples


  • Read papers
  • Draft introduction


  • Schedule time every day to read at least one paper. I hate reading, but I need to do it! It’ll be my version of #MarchMadness.
  • Come up with broad project ideas for my next chapter. Current ideas include incorporating “-omics” data into climate change predictions (à la Dr. Rachel Bay), examining epigenetic signatures of marine invasions AND climate-related stressors, and/or doing more work outside of controlled hatchery and lab settings. Reading should help with this.

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Yaamini’s Notebook: Remaining Analyses Part 20

This series has (finally) come to an end

I showed Steven, Emma, and Brent my heatmap options and we decided to include all peptide abundance data, not to cluster rows, and to go with the purple-green color scheme.


I sent the figure to my friend with red-green confusion, and he said he could understand it! In my R Script, I started playing around with other modifications.

The first thing I did was switch out complicated protein names for common names. I created a .csv file that matched protein name, common name, and peptides. I also added an asterisk to the end of each peptide that exhibited differential abundance. I used the common name and peptide to identify rows in the heatmap. I also added a title and tried making some of the font size bigger. pheatmap is not a package that’s easy to manipulate if you want to change the aesthetics of your plot. I’ll probably have to do more work in Powerpoint, Photoshop or InDesign (which sucks because that’s not reproducible).

For now, here’s my figure!


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Laura’s Notebook: Terminating 3-month Oly temp/food treatment

It’s been 3~ months since Olys went into their temperature / feeding treatments. I’ve been collecting gonad samples for histology every 2-3 weeks. Today I did a 6th sampling from treatments and “wild” (aka directly from Mud Bay) and moved animals into their spawning buckets. Details …

Sampled gonad tissue for 2 things today: 1) histology and 2) lipid & glycogen content

To accomplish this, I shucked the oyster, removed the gill tissue as usual by grabbing with gripped tweeers and tearing back the tissue (usually removes cleaniy, without removing any gonad). Then, I used dissecting scissors to bisect the whole visceral mass into two sections. The cut was made perpendicular to and midway along the anterior/posterior axis, as shown below. The anterior section was fixed for histology, and the posterior placed into a labeled 2mL tube for glycogen/lipid analysis. Oysters were sampled in batches of 5 (from each replicate), and immediately walked to the -80 in Rick’s building to freeze. The posterior section was selected for lipid/glycogen analysis, as it was free of gill or palp tissue (not always the case in the anterior section). Mantle tissue on dorsal/ventral planes of visceral mass was not intentionally removed. Frozen gonad samples were labeled with their designated histology sample number (from 241-290; there are no frozen gonad tissue samples #1-239).

Bottom prong of tweezer indicating where transverse cut will be made: img_3715


Final Mud Bay sampling, retrieved HOBO loggers

As usual, I collected 10 oysters from Mud Bay during low tide (today, ~8:30pm), and took back to the hatchery for sampling. Tonight I also retrieved the 2 HOBO data loggers. One HOBO was installed at a shallow depth, accessible around ~2’, close to where I harvested oysters throughout the winter (labeled “Mud Bay Shallow”). The other was installed at a low tidal elevation near the main channel, away from my sampling site (labeled “Mud Bay Deep”).

Moved animals to spawning buckets

Decided on 4 spawning buckets/treatment. This results in ~45-50 animals per spawning bucket and I was able to simply split the 4 bags in each treatment rep. This makes it easy to keep track of replicates from the treatment to the spawning stage. For example, in treatment A1 there were 4 backs (#1, 15, 5, 15). These were split into 2 spawning buckets (#1 + 16, #5 + 15).

First, I counted the # oysters in each treatment bag, and measured volume displacement. Volume displacement was measured using a 1000mL graduate cylinder filled to ~500mL, then I removed the oysters from their bag and trasferred to the grad. cylinder, and measured final volume. I selected 2-bag spawning “pairs” using volume displacement to acheive consistent volume across reps.

In summary: For each treatment (A, B, C, D) I have 4 replicate spawning buckets: 2 from treatment replicate 1 (e.g. A1-1, A1-2 … D1-1, D1-2), and 2 from treatment replicate 2 (e.g. A2-1, A2-2 … D2-1, D2-2). All buckets were installed with air stones. Avtech loggers were placed back in their respective treatments.


Terminated experiment, adjusted things

Turned chiller in low temp up 1degC. Plan is to increase temperature on low temp by 1degC per day unti it reaches 10degC, then all buckets will be increased by 1degC/day until 18degC is acheieved on ~3/10. Ryan said he would turn temp up for me.
Turned up low food algae dosing rate to match high fodd rate (175 on peristaltic dosing pump).

Next steps & To-Do’s

I expect to get larvae during the week of 3/26
Will visit Manchester on Tuesdays (and maybe Sundays too) to clean broodstock, check mortality.
Inventory the # of 1L silos, estimate now many I will need, and build more.
Get OA system back up and running.
Plan OA stress trials for larvae

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