Laura’s Notebook: Moved Olympia oyster seed to Manchester dock

My post-set Oly’s have been housed in upwelling silos in a tank at Manchester, fed algae produced by PSRF, since July. It’s time to get them out of there, since PSRF is really only producing algae for me, and they have potential plans to turn the water off for re-plumbing projects, etc. My task for today is to move the oysters to cages hanging off the dock.

Step 1) Acclimate Olys to ambient water temperature

Since settlement the Oly tank has had the heated water line, which is ~14degC, and warms up to ~16 in the tank. The ambient line is ~13degC, so the temperature off the dock will be around 13degC (~55degF). Last Thursday, to acclimate the Olys to the slightly cooler water temperature, I cracked the ambient line open a bit, and turned the heated line down. On Monday Stuart increased the ambient line flow and turned the heated line off.

Step 2) Build envelopes to house separate Oly groups

I have 21 Oly groups, and need to keep them separate. I built envelopes in 2 mesh sizes: ~1600um (window screen), 450um. Some groups’ oysters have grown large enough to safely fit in ~1600um window screen, while some still have a few that are very small. Stuart advises that these small oysters will not likely make it through the winter, and growth will be minimal off the dock, since available algae is low starting in October. I’m going to give the small guys a chance, and will check them in early November to see if they have grown large enough to transition them to larger screen. If not, I may have to cull them, since the fine mesh size requires regular cleaning.

Step 3) Screen oysters to determine envelope size needed, add to envelope

I screened my oysters first through 1600, catching anything that fell through on 450. If no oysters fell through I put them into the 1600 window screen. Created tags using pieces of pvc pipe with black sharpie labels. Will need to keep an eye on condition of tags. Then using the impuse sealer I closed the envelopes, and gave the oysters a last meal while I prepared the rest of the envelopes.

Making many envelopes took time. Here are images of the almost-final product, where oysters+tag (pvc piece labeled w/ sharpie) are in an envelope and I am using the impulse sealer to close the open end of the bag. Pro tip: when using the impuse sealer on mesh, press and hold until the red light turns off, continue to hold down for a few seconds to let the newly melted plastic cool. If you release right away, you will likely tear a hole in the envelope.


Step 4) Move oyster envelopes to dock

There are 3 cages already hanging off the dock with my Oly broodstock (and a few Pacifics). I zip-tied the Oly packages to the inside of one cage, laying the most dense groups down flat. I’ll grap a photo of the setup next week when I go out to clean.

from LabNotebook


Yaamini’s Notebook: October Goals

October Goals

screen shot 2017-10-02 at 1 39 40 pm

September Goals Recap:

  • I presented a preliminary analysis of my SRM data at PCSGA!
  • The DNR paper got split into two separate papers. I added SRM methods to the oyster paper but have not updated any SRM results. The associated repository can be found here.
  • Steven suggested not revising the proposal, so I didn’t
  • I sent an email to schedule my first committee for the end of October/beginning of November. To prepare for my meeting, I cleaned up the project-oyster-oa repo. The repository has very clear README files and project/file descriptions!

October Goals:

This month is all about the DNR project!

  • Figure out what happened with my technical replicates
  • Revise the oyster paper introduction and methods, start writing results and discussion
  • Submit a NSF GRFP proposal
  • Have my committee meeting and submit milestone paperwork
  • Prepare for WSN
  • Low priority: Metaanalysis and Manchester
    • I can start reviewing papers and writing an introduction. If there are any interesting questions I think we should tackle with the dataset, then I can consult with Steven and start analyses
    • Analyze histology images


Laura’s Notebook: Initial results from geoduck SRM data

Check out my recent Jupyter Notebook entry where I perform a full SRM Analysis.

And for a preview of the SRM results and how they correlate to the environmental summary data, here are (slightly modified) slides from my presentation at the PCSGA 2017 conference:

Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15

from LabNotebook

Laura’s Notebook: October Goals

This is vast. Lots to do.

Small To Do:

  • Email Abigail re: GROW program
  • Email re: Oly session @ NSA 2018 – deadline FRIDAY
  • Register for Parasites once add code comes through
  • Book return ferries @ 7am on Friday!
  • Learn how to tag notebook posts
  • Take geoduck proteomics poster to WA Co-op once location confirmed (I think SAFS somewhere)

Large To-Do:

  • Geoduck proteomics
    • Clean up scripts from SRM analysis
    • Quickly summarize everything done to raw data for analysis so I don’t forget
      • DIA
      • SRM
    • Figure out which vials to throw away from SRM run:
      • “D”
      • “E”
      • Autosampler vials (highly unlikely we’ll need these again)
      • KEEP: completely digested peptides (“F”), other 1/2 of sample not digested, is there another vial of quantifed but un-digested proteins?
    • More analysis for SRM:
      • Figure out how to calculate distances between tech reps, to numerically validate my removal of poor-quality reps
      • Generate Linear Response Plot, as per Emma: Peak area on the y, amount of peptide (moles) on the x. Don’t know absolute quantity of experimental peptides, could make the x-axis relative quantity or something. Can generate plots like these in MSstats.
      • Determine if abundance difference is “biologically relevant,” aka look to lit for abundance values to see what is low, normal, high (if possible!)
      • See if I can bring DIA results into SRM analysis (at very least, compare 3 proteins in DIA data)
      • Consider implications: HSP70 is not highly specific, since some interference w/ gigas in dilution curve
    • Start drafting geoduck proteomics
      • Outline everything
      • Methods detailed
      • Full lit review
  • Record podcast pilot with Megan
    • Read Megan’s paper
    • Rent mic from UW tech resources for this
    • Where to record?
  • Meet with Brent re: Oly genetics paper
    • See if he has scripts for calling loci
    • Gather existing write-up for 1st genetic testing
  • Start drafting GROW application
    • Need project description from Abigail
  • Grant Apps:
  • Oly experiment:
    • Make sure I’m organized
    • Write-up 1-stop shopping list of Oly project including:
      • Experiment summary
      • Samples collected
      • Data collected
      • Treatments, populations, etc.
    • Figure out how/when to transport Oly samples from Manchester/Rick’s -80
    • Meet with STATS resource to figure out how to analyze Oly larval survival – parse out survival data to 224um, to juvenile, by time for reps
  • For Committee:
    • Schedule 1st meeting – mid October
    • Complete committee sheet for SAFS
    • Complete PhD timeline
    • Presentation for committee meeting: 20-30 mins, to include:
      • Overall goals of PhD
        • Research interests
        • Motivation
        • Post-graduation ideals
      • Proposed timeline, travel, etc.
      • What I’ve done to date
        • Chapter 1 – Proteomics
        • Chapter 2 – Oly OA/T experiment Generation 1
      • What I plan to do
        • Chapter X – Oly OA/T experiment Generation 2
        • Chapter X – Oly OA/T experiment, wild generation OR hatchery-produced F1’s (repeat experiment, using silos only for larvae!)
        • Chapter X – Oly genetics wild vs. hatchery (?)
        • Chapter X – Project in Australia on reproductive peptides
        • Chapter X – Could I do a geoduck genetics wild vs. hatchery? (or, what is “baseline”?)
      • Grants & Fellowships
      • Extra curriculars

from LabNotebook

Grace’s Notebook: Wednesday, September 27, 2017

Today I tried really hard to get this titrator working. I still have some parts that I’m not sure how to fit together… Here’s what it looks like so far:


I just need to figure out how to get the probe set-up, and how to get the Rondolino to have power… I’ve followed the instructions over and over, but it still isn’t turning on.

Yaamini’s Notebook: Lab Notebook Maintenance

We interrupt your regularly scheduled lab notebook perusing for some maintenance.


In preparation for my first committee meeting, I’m tackling the long-outstanding task of reorganizing the project-oyster-oa repository. While I shuffle things around and add files, links in this lab notebook will definitely break! All links will be repaired by the beginning of October.


Grace’s Notebook: Tuesday, September 26, 2017

The Traceable VWR Digital Thermometer needs a 9-volt battery in order for me to test if it works.

I am unsure how to test if the Accumet Eletrode (Fisher Scientific) pH probe works, because there is no manual, and there is nothing that I can see to plug it into.

Same as above with the Honeywell Probe Analyzer. No manual, no connecting cords…

I put the rest of the supplies from Manchester away, and updated the Roberts Lab Inventory. There are some things I’m not sure what to do with: some bottles of chemicals, a container of oyster shells, and all the empty storage bins.

I put purple tape on the handles of all the tools in the tool bag, and reorganized a little so that all the tools (wrenches, screwdrivers, hammer, etc.) are in the bag and all the smaller things, like the sealants, screws, tape, etc., is in the box.

Then, I unpacked more of the Titrator and read more of the manual. Having a hard time finding the connector cable for the terminal to the titrator…