Wed. Nov 14, 2018

Geoduck Broodstock Experiment

FFAR meeting notes

  • Can’t untangle effects from high/low pH or static/fluctuating, so include additional fluctuating low pH treatment with new geoduck
    • Hollie has a code for this
  • Why is the oxygen low on Nov 10? What is the saturation of water at 9-10C and salinity @ 29 PSU ?

  • continuous feeding:
    • bringing peristatic pump
    • there are also programmable pumps

To-do on Friday Nov 16

  1. water chemistry
    • discrete measurements
      • pH tris curve
    • titrator
      • pH cal
      • CRM
      • water samples
  2. automate data download
    • enable remote access to router
    • test data download from dry lab building
  3. calibrate temp probes

  4. Set up tanks 5 and 6 with gas
    • need to order more pumps
    • do we have probes for these?
  5. take hemolymph samples AND label all animals
    • supplies needed:
      • liquid nitrogen carrier
      • at least 150 microfuge colored LABELLED tubes replace (need to order more)
      • needles
      • syringes
      • centrifuge (can we set the freezer to 4C and put it in there?)
      • styrofoam containers for carrying samples on ice to centrifuge (ice packs in freezer in garage)
      • p1000 and tips for transferring lymph
      • towels to put animals on during samlping
  6. Think about respirometry
    • Presens is expensive, and preferred to stay in the dry lab
    • carting water (for containers and water bath) is lots of labor
    • need a solution

Need to order:

  • 4 submersible pumps (Drs. Foster & Smith)
  • 1.7 mL microfuge tubes 500ct Rainbow Pack (VWR cat no. 87003-296) $24.14 (https://us.vwr.com/store/product/4674613/vwr-microcentrifuge-tubes-polypropylene)
  • calcium assay 96-well $215 (cayman chemical) https://www.caymanchem.com/product/701220

Oyster seed Proteomics manuscript next steps (decided after meeting with Kaitlyn):

  1. compare ASCA proteins with uniquely clustered proteins (Kaitlyn will look into this)
    • what do their abundances look like?
      • make raw abundance line plots facetted by protein
    • does the GO enrichment change when ASCA and cluster proteins are combined?
  2. does hierarchical clustering change when day 0 is removed? (Kaitlyn will try this)

  3. begin identifying and locating data files that we need to deposit in public protein repository (i.e. ProteomeXchange and PeptideAtlas) (I will start this)
    • see what Emma’s paper (and supplementary materials) included: Raw data can be accessed via ProteomeXchange under identifier PXD004921. Raw data can be accessed in the PeptideAtlas under accession PASS00943 and PASS00942. Code used to perform enrichment analysis is available in a corresponding GitHub repository (https://github.com/ yeastrc/compgo-geoduck-public) as is the underlying code for the end user web-interface (http://yeastrc.org/compgo_ geoduck/pages/goAnalysisForm.jsp).
    • add file names and location, links to a googlesheet
    • confirm with Emma what files need to be made available
    • confirm with Rhonda where files are if we can’t find them
    • do we include a fasta file of the peptides ID’d by mass spec?
  4. add updated NMDS with only silo 3 and 9 to manuscript draft (Kaitlyn will do this)

  5. For supplementary table of all proteins detected:
    • re-do the BLAST of CHOYP protein sequences to 2018 UniProt database (for reproducibility and to use up-to-date info)
    • ask Steven about files related to SQLShare from April 26, 2017
      • need to regenerate ‘table_blastout_gigatonpep-uniprot’
      • need fasta file of the peptides ID’d by mass spec
      • need 2018 Uniprot DB - make a simplified supplementary table containing CHOYP IDs, UniProt Accessions, e.val, Protein names, Gene names
  6. Low priority: do we need to explain we did 2 x 4 treatments, or just say we did 1 x 2 treatments?
    • do we have survival data for other silos to compare to silo 2, 3, and 9?
    • Can we rule out silo 2 as an anomoly or should we include it?
  7. Low priority: re-focus the intro


Written on November 14, 2018