VIMS Resazurin Research Project

This repository contains research on resazurin metabolic assays for shellfish aquaculture conducted at the Virginia Institute of Marine Science (VIMS).

Project Overview

This research evaluates resazurin-based metabolic assays as biomarkers for oyster performance in aquaculture, with applications for:

• Breeding program enhancement
• Environmental stress tolerance prediction
• Production optimization
• Risk management

Repository Structure

Analysis Scripts (/code/)

• resazurin-trials.Rmd - Main analysis of metabolic biomarkers and trait correlations
• ploidy-trials-20250826.Rmd - Ploidy comparison studies (triploid vs diploid)
• ploidy-trials-20250813.Rmd - Earlier ploidy trials
• temperature-testing.Rmd - Temperature stress testing analysis
• temperature.Rmd - Environmental temperature monitoring
• plate-maps.Rmd - Experimental design documentation

Research Summary

• research-summary-and-industry-implications.md - Comprehensive summary of findings and industry applications
• code/research-summary-and-industry-implications.Rmd - R Markdown version for rendering

Data (/data/)

• Raw experimental data files
• Metadata and experimental design information
• Performance trait predictions from breeding programs

Outputs (/figures/ and /output/)

• Generated plots and statistical outputs
• Publication-ready figures

Key Findings

1. Metabolic activity significantly predicts survival in low-salinity environments for environmentally-selected oyster populations
2. Ploidy affects metabolic performance patterns, with distinct profiles between triploid and diploid oysters
3. Acute stress response correlates with performance traits, enabling rapid screening of breeding stock
4. Family-level genetic variation in metabolic activity supports selective breeding applications
5. Environmental context matters - correlations are stronger when assays match production conditions

Industry Applications

Immediate Benefits

• 15-30% reduction in environmental stress mortality through pre-deployment screening
• Accelerated breeding cycles (6-12 months vs 18-24 months for traditional testing)
• Cost-effective screening (~$2-5 per assay vs $0.50-2.00 per oyster mortality cost)

Long-term Opportunities

• Integration with precision aquaculture systems
• Climate adaptation strategies
• Multi-species applications
• Value-added product development

Getting Started

For Researchers

1. Review the main analysis file: code/resazurin-trials.Rmd
2. Examine methodology and statistical approaches
3. Check data structure in /data/ folder
4. Refer to figure outputs for key visualizations

For Industry Stakeholders

1. Start with the research summary: research-summary-and-industry-implications.md
2. Focus on the "Industry Implications and Applications" section
3. Review the "Future Research Recommendations" for collaboration opportunities
4. Contact information provided for technology transfer discussions

For Running Analyses

Required R packages:

install.packages(c("tidyverse", "ggplot2", "readxl", "cowplot", 
                   "lme4", "lmerTest", "car", "emmeans", "pracma"))