Feb ‘23 Goals

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February ‘23 Goals

Primary Focus

Conduct 1st Committee Meeting

  • Write committee agreements (complete on 01FEB23)
  • Build ‘committee presentation’ blog post (here) (complete on 05FEB23)
  • Host meeting (complete on 06FEB23)
  • Integrate feedback into master’s thesis committee meeting #1 blog (complete on 07FEB23)

DNA/RNA Extraction Protocols

  • Research DNA/RNA extraction kits (compete on 05FEB23)
  • Buy Quick-DNA/RNA Miniprep Plus Kit , 10 preps ($106.70, requested 08FEB23 on Hall Grant Budget)
  • Receive kits (complete on 23FEB23)
  • Draft protocol (complete on 15FEB23 )
  • Locate (… or buy or borrow) 300uL/500uL & 1000uL pipettes & tips
  • Protocol dry-run walk-thru with IBIS mentee
  • Edit/amend protocol
  • Trial methods with subset of samples Note: We originally thought about using Callum’s coral fragments for the trial, but these were not held at -80C, and therefore the RNA step would not work properly

Get Sequencing Quotes

  • Get general idea of costs ( $80/sample for 16S & $200/sample for RNAseq )
  • Answer/identify common quote questions:
    • What type of library prep is needed?
    • What is the minimum number of reads per sample?
    • How many samples to sequence?
  • UW Northwest Genomics Center
  • Azenta Life Sciences (previously Genewiz)
  • Univ. of Texas
  • Mr. DNA Lab
  • FYR Diagnostics (20% off promo)

Supporting Roles

  • Complete SMEA/FISH 539 coursework
  • Ongoing coordinating for GSIS speaker Dr. Nicola S. Smith
  • Ongoing participation in Student Advisory Council
    • CoEnv Strategic Planning student working group
    • CoEnv Assistant Dean of Diversity Equity & Inclusion (ADDEI) hire student input
  • Ongoing mentoring with IBIS mentee Nora Hessen
    • develop project (DNA/RNA extraction & alpha & beta diversity analysis!)
    • lab training & certificates
    • brainstorming & meeting every Wednesday for 2hrs
  • Apply for FHL Marine Botany TAship
  • Apply for WSG Grad Student Assistant, locally sourced seafood project

Apply for PCC Climate Solutions Project Funding

$5k max for solutions-based projects, capstone programs (IBIS), outreach efforts with community organizations and partners. Can be used for Financial Support, Training, Publication & Travel. Rolling application. Would like to apply for this to be used to help IBIS mentee, via more sequencing or publication? Need to brainstorm how to angle ‘solutions-based’ project.

Looking Ahead…

gantt-timeline

Spring 2023

March

  • pick a sequening service
  • finalize extraction strategy (how many samples, from which treatments)
  • extract DNA/RNA from samples Note: this will be a subset of samples, likely the control vs. highest treatments
  • send for sequencing ( 2-4 weeks )
  • setup Linux Subsystem for Windows in preparation of Bioinformatics Course
  • March 27 Spring Quarter begins : Dr. Robert’s Bioinformatics Course

April

  • receive trial sequences
  • analyze the sequences in Bioinformatics course
  • 2nd round DNA/RNA extraction, & send for sequencing

May

  • analyze sequences with Nora for IBIS project (QA/QC… both run same analysis and see if we get same result?)

  • Celebrate IBIS mentee project completion
  • assess how we proceed with extraction & sequencing (did we see something interesting to warrant paying for more sequences? do we need to think about finding additional funding to pay for more sequencing?)
  • continue bioinformatics pipelines

Summer 2023

June

  • June 9th Spring Quarter ends
  • June 20th Summer A term begins
  • FHL Marine Botany TAship?
  • begin drafting manuscript(s)

July

  • July 19th Summer A term ends
  • continue drafting manuscript
  • continue bioinformatics pipelines

Aug

  • continue drafting manuscript
  • continue bioinformatics pipelines

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