Marine Biology: Mammalian (Dolphins and Sea Lions) Chemistry and Genomics  (Hybrid)

Course Description:

Marine mammal physiology and overall health are closely influenced by water quality and environmental exposures—factors that are particularly impactful for animals inhabiting semi-enclosed or non-open sea environments for extended periods. The exposome, or cumulative measure of environmental exposures, encompasses a range of factors including diet, pathogens, and contaminants such as persistent organic pollutants (POPs), which are known to possess mutagenic, carcinogenic, and endocrine-disrupting properties. 

This hybrid research course investigates the impact of environmental exposures on marine mammals, particularly dolphins and sea lions, through the assessment of water quality in various locations within the San Diego Bay, including animal pens, adjacent waters, and potential pollution sources. The course meets four times per week—twice virtually and twice in person in a laboratory setting. 

A key component of the course involves the deployment of Composite Integrative Passive Samplers (CIPS) at selected sites. These advanced sensors capture both hydrophilic and lipophilic compounds and enable the characterization of over 1,000 chemical entities, including known carcinogens, mutagens, and other persistent organic pollutants. In addition to chemical profiling of seawater, students will collect data on standard water quality parameters such as pH, salinity, temperature, dissolved oxygen, and conductivity. 

Biological sampling will include bay mussels and oysters collected from study sites. Their tissues will undergo chemical content analysis and metagenomic sequencing to quantify the presence of microbial communities, including bacteria, viruses, and parasites. Depending on the outcomes of the chemical and microbiological analyses, archived biological specimens from marine mammals (e.g., blood, brain, and blubber samples) will be utilized for comparative chemical assessments. These analyses aim to deepen our understanding of how industrial pollutants affect the health of marine mammals residing in the San Diego Bay. 

By the end of the course, students will be able to: 

• Identify marine mammal species using genotyping techniques and phylogenetic analysis. 
• Formulate testable scientific hypotheses and design statistically robust experiments. 
• Critically evaluate primary scientific literature related to molecular biology and environmental health. 
• Demonstrate understanding of key molecular biology concepts, including DNA and RNA structure, transcription, and gene expression analysis. 
• Extract and assess the quality and integrity of RNA and DNA from biological samples. 
• Interpret tissue-specific analytical chemistry data to assess environmental exposures. 
• Perform metagenomic sequencing using Nanopore technology. 
• Apply fundamental bioinformatics tools to analyze sequencing data and determine biological significance. 
• Design and present a scientific research poster in a formal seminar setting. 

Course Topics: 

• Anatomy and physiology of marine mammals 
• Microdissection techniques for marine mammal and invertebrate tissues 
• Genotype–phenotype relationships and their biological implications 
• Comparative analysis of DNA and RNA structure and function 
• Principles of analytical chemistry with a focus on primary organic pollutants 
• Fundamentals of microbiology in marine environments 
• Introduction to metagenomics and microbial community profiling 
• The central dogma of molecular biology: DNA → RNA → Protein 
• Experimental design and hypothesis-driven research methodology 
• Applications of biostatistics and bioinformatics in environmental and molecular biology 
• Introduction to Nanopore sequencing technology and its research applications 
• Quantitative and qualitative data analysis in biological research 
• Scientific communication through written reports and oral presentations 

Quarter Dates, Schedules, and Deadlines