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, UW Tacoma

Undergraduate Support

Ly Vuthy
Noah Krebs

Project Dates

Mussels from the 2021/22 outplanting season
Bench work December 2022 - February 2024
Analysis and writing February 2024 - March 2024

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

Output

Exploratory

All visualizations used to clarify the data

Figures

Visualizations that can or will be used in the manuscript

Miscellaneous

Screenshots or snippets of code used in issue pposting

Tables

Raw tables, prior to formatting, that will be used in the manuscript

Code:

01-explore: initial data exploration.
02-correlations: Spearman's Correlation of all sites and grouped by laitudinal region.
03-map: Washington state map of biomarker values plotted by coordinates of sites.
04-spatial: Geospatial statistical analysis of the biomarkers.
05-analytes: Individual and summed analyte comparisons to biomarker data.
06 - 09: Docs to be removed or reworked.

Data

Primary analysis file

All work to date utilizing biomarkerfull.csv
latitude - latitude
longitude - longitide
site_name - name of cage location given to us from WDFW
site_number - number assigned by our team for labeling ease
sample - sample number assigned by our tean for dissection labeling
p450 - final cytochrome p450 activity in (activity/ (mg/protein)). All values post standardization by BCA assay values for each tissue sample.
SOD - final superoxide dimutase activity in (activity/ (mg/protein)). All values post assay and standardization by BCA assay values for each tissue sample.
weight_initial - full weight of the frozen mussel in (mg) prior to dissection.
length - full length of the frozen mussel in (mm) prior to dissection.
width - width of the frozen mussel in (mm) prior to dissection.
height - full height of the frozen mussel in (mm) prior to dissection.
weight_final - weight of the shells scraped clean in (mg) post dissection.
weight_change - the calculation in (mg) of weight_initial - weight_final.
condition_factor - a unitless calculation of the approximate tissue weight/ length. Tissue weight is the weight_change value in this data set.
avg_thickness - the average in (mm) of four pre-determined measurements per valve of each sample.

Not for analysis

These files are individual files with raw data, not used in analysis but in creating the analysis files