October Goals

This is vast. Lots to do.

Small To Do:

  • Email Abigail re: GROW program
  • Submit back-log of reimbursements for Manchester & shellfish club
  • 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)
  • Submit geoduck project presentation for GSS
  • Throw away some geoduck vials (D, E, autosampler vials) & organize others (original samples, quantified proteins, digested peptides)

Large To-Do:

Geoduck proteomics

  • Clean up scripts from SRM analysis
  • Figure out which vials to throw away from SRM run:
    • Throw away: “D”, “E”, Autosampler vials (highly unlikely we’ll use these again, since they sat around and not enough volume to re-run, and PRTC was messed up
    • KEEP: 1) other 1/2 of sample not digested, 2) protein in solution from quantification step, 3) completely digested peptides (“F”)
  • 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 paper
    • Outline everything
    • SRM Methods detailed
    • DIA Methods detailed
    • Full lit review
  • Document steps from Vantage -> Replicate Review. Write notebooks for:
    • How to create Skyline project file with .raw SRM data including PRTC
    • Calculating predicted RT
    • Pick peaks & adjust retention time ranges using predicted RT
    • Remove peaks, replicates, and transitions/peptides that are poor quality, as determined via: RT, dilution curve
    • Export abundance data as report & re-format slightly
    • Data analysis in R
  • Document steps from Lumos -> selecting proteins for SRM
    • Download & convert .raw files to .mzML
    • Prep files for PECAN, including using Protein Digestion Simulator
    • Run PECAN (at least include PECAN input files, commands, and lessons learned)
    • Create Skyline Project & export report
    • Calculate error rate
    • Data analysis in R (not excel!)

Record podcast pilot with Megan

  • Read Megan’s paper
  • Rent mic from UW tech resources for this
  • Where to record?

Oly genetics hatchery vs. wild

  • Meet with Brent re: Oly genetics paper, see if he has scripts for calling loci
  • Gather materials from 1st genetic testing
  • Read Fischer et al. 2012

Application things

  • Start drafting GROW application
  • Get project description from Abigail
  • NSA travel grant, other?
  • Dive grant: http://www.wdhof.org/wdhof-scholarshipDesc.aspx
  • differed UW FINS for Vegas - Apply in January
  • Coenv travel fund, due Oct. 27

Oly experiment:

  • Transition Oly’s to ambient T
  • Make screen envelopes and move olys to dock, affix to cage (move on Thursday 10/5).
  • 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 academic 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

Scientific Diving

  • Find local vendor that sells dry suits, try on to determine size
  • Purchase gear
  • Start weekly dives with Will beginning early-mid October - starting Nov. 8th
Written on September 27, 2017