The Molecular Ecology Lab in La Jolla is developing several new applications to aid research of marine species. These include:
Single Nucleotide Polymorphism (SNP) discovery and genotyping: SNPs are the most common type of genetic variation in most genomes, but have not been used extensively for population genetics studies of nonmodel organisms. Technological advances now make it possible to use these markers effectively, and the Molecular Ecology Laboratory is among the first labs to develop and apply SNPs for marine organisms. SNP genotyping will allow us to obtain genetic information from >50 loci simultaneously for each individual, providing greater statistical power and genome coverage in our population studies. We have developed a set of 21 SNP assays for sperm whale population studies, and are continuing to develop technologies for rapid screening of targeted and random genetic loci to find novel SNPs in sperm whales and other organisms, through a grant from the Marine Mammal Commission.
Ancient DNA analysis: Our new ancient DNA laboratory within the new clean room facility provides a PCR product free space for extraction and amplification of DNA from historical and preshistoric hard tissue samples (e.g., bone, tooth, and baleen). The space is physically separated from the other laboratories, and users of the space follow clean room and ancient-DNA extraction practices to prevent cross-contamination of samples. Extracted DNA is typically highly degraded and at low concentration, so we use quantitative PCR (below) of a small mitochondrial DNA fragment to assess the utility of samples prior to sequence analysis.
Quantitative PCR (qPCR) analysis: Quantitative PCR can be used to estimate the amount of starting material (DNA) in a PCR reaction very precisely, and at very low starting concentration. We use fluorescent dyes that fluoresce only when bound to double stranded DNA (e.g., Pico-Green and Sybr-Green) to measure the change in fluorescence at each cycle in the PCR, and extrapolate the starting DNA concentration by comparison to a standard curve. We recently acquired a quantiative PCR instrument to allow these types of studies.
qPCR can also be used to measure the relative expression levels of RNA in tissues via rtPCR, and to measure relative abundances of DNA, for example when measuring viral load in tissues of infected animals.