Utilizing biochemical biomarkers to characterize Mytilus trossulus response to pollutants in Puget Sound waterways

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This work is being conducted in collaboration with the Washington Department of Fish & Wildlife. The samples are a subset of mussels from the 2021/22 mussel outplanting for the ongoing 'Mussel Watch' program.

Team

Chris Mantegna, UW SAFS, Contact: mantegna@uw.edu
Mariko Langeness, WDFW
Molly Shuman-Goodier, WDFW
Danielle Nordstrom, WDFW
Steven Roberts, UW SAFS
Alison Gardell, lead PI, UW Tacoma

Undergraduate Support

Ly Vuthy
Noah Krebs

Project Dates

Mussels from the 2021/22 outplanting season
Bench work September 2023 - February 2024
Analysis and writing February 2024 - April 2026

Kits

1. Pierce BCA Protein Assay Kits
2. Cayman SOD

Protocols

1. Dissection
2. BCA- see Pierce protocol above
3. p450
4. SOD

Repo Contents

Data

Folders

start_here: raw data
cleaned: raw data with names and format cleaned up for tidyverse manupulation
interim_df: log- transformed data and index creation
plotting: interim data where table structure has been manipulated for visualizations
don't_use: exactly what it sounds like\

Code:

00-data_cleaning: initial data cleaning.
01-01.1-exploratory_stats: exploratory stats and visualizations.
02-ibr_cci_creation: creating the integrated biomarker response score (IBR) and Contaminant Class Indices (CCI).
03-03.2-analyses: KW comparisons, correlations, and spatial analyses.
04-visualizations and 11-11.1-visualizations: initial analysis visualizations - not used in end products.
12-12.2-visualizations: visualizations to support the manuscript and/or the supplement.\ 13-modeling_biomarkers: early attempt to fit biomarkers and contaminant concentrations into a non-linear model, not used.\ 99-junkyard`: code remnants for other processes that were not effective for this work, not used.

Output

Exploratory: all visualizations used to clarify the data before transformation.
Figures: visualizations that can or will be used in the manuscript.
Man_viz: visualizations that can or will be used in the manuscript.
Spatial Stats: spatial analysis outputs, tables and plots to be overlayed in GIS.
Tables: significant results tables for KW comparisons, correlations, and spatial stats.

Images

Bench processing photos.

Protocols

Protocols in .pdf format.