Dolphins Metagenomics

Course Description:

Marine mammal physiology and overall health can be significantly affected by water quality and environmental exposures among animals that spend long time in enclosed areas. Exposome encompasses diet, pathogens, and persistent organic industrial pollution, which cause mutations, cancers and endocrine disruption. To better understand the effects of environmental exposures and health risk to dolphins, we use environmental chemistry data and correlate it with metagenomics: chemical analysis of animal pens, surrounding areas, and potential sources of pollution within the San Diego Bay will be assessed along with metagenomic sequencing data from intestines and waste to quantify microorganism composition, including bacterial, viral, and parasite profiles of twelve adult female and male dolphins.  During the 10-weeks hybrid research course that meets twice per week – once virtually, and once in-person (lab), students will process tissues and biological samples, extract DNA, perform library prep, and obtain metagenomics data via long-sequence reads methodology.  Metagenomic profiling will be corelated to concentrations of >200 primary contaminants measured in and around dolphin facility in San Diego Bay. This data will also be compared to metagenomics sequencing of resident bivalves (mussels and oysters) from the area. This work will help better understand the environmental pollution – metagenome associations within at-risk dolphin population form San Diego Bay.

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

• Identify marine mammal species by genotyping and phylogenetic analysis
• Develop testable scientific hypothesis and design a statistically relevant experiment
• Critically assess primary scientific literature
• Become familiar with molecular biology concepts including DNA and RNA structure, transcription, and gene expression quantification
• Isolate and assess the quality of RNA and DNA
• Analyze tissue-specific analytical chemistry data
• Perform metagenomics sequencing (Nanopore)
• Apply fundamental bioinformatics analysis to infer biological relevance
• Design a scientific poster and present their findings in a formal science seminar setting

Course Topics: 

• Marine mammal anatomy and physiology
• Micro-dissection of marine mammal and invertebrate tissues
• Genotype vs phenotype
• DNA vs RNA
• Analytical Chemistry – primary organic pollutants
• Microbiology
• Metagenomics
• Central dogma
• Experimental design
• Biostatistics and Bioinformatics
• Nanopore Sequencing
• Data analysis
• Science communication (written and oral)

Quarter Dates, Schedules, and Deadlines