My dissertation is focused on investigating the biological impacts of climate change in the ecologially and economically important California market squid, Doryteuthis opalescens.
The California opalescent (market) squid is a primary forage species for fish, sharks, mammals, and seabirds in the California Current and also is one of California’s largest fishery species. These squid lay eggs that are attached to the seafloor for the duration of development (~1 month at 11˚C), where they are exposed to variations in temperature, pH, and oxygen as a result of upwelling and longer-term events such as El Nino/La Nina events (ENSO). Investigating the transcriptional and signaling mechanisms that allow these squid to thrive and develop at lower oxygen and pH conditions may provide insight to understand and predict future acclimation or adaptation to climate change in the ocean. In collaboration with Mike Navarro and the Levin lab, we exposed squid embryos to constant low-pH, low-oxygen conditions during development. We are currently investigating the gene expression response of these squid, with particular attention to pathways that regulate development. For a cartoon depiction of the “super” market squid life cycle and fishery, check out this squidtoons comic, created by collaborator Garfield Kwan.
The adult and developmental transcriptomes are nearing completion and data will be shared soon. Contact me for more details.
De novo transcriptomics
Along the way to my main project on market squid, I developed a python framework for automated de novo transcriptome assemblies, MakeMyTranscriptome. This pipeline leverages popular quality control, assembly, annotation, and expression tools to produce high-quality de novo reference assemblies with minimal user input. The goal here is to help biologists just getting into transcriptomics produce high quality references from their data, which can then be used for additional downstream analyses. The framework operates as a “black box” for those unfamilar with python and coding, but offers complete flexibility and customization for advanced users. Coming soon.
If you don’t know anything about mantis shrimp, check out this Oatmeal comic for a fun introduction.
In collaboration with Maya deVries and Jennifer Taylor, I am investigating the transcriptome response of Neogonodactylus bredini to high temperature and low pH conditions. Their larger project is focused on impacts of warming and ocean acidification on the carapace and smashing appendage. Contact me for more details.
I was fortunate to be funded by an NSF IGERT to SIO for Global Change, Ecosystems and Society, an NSF GRFP, and the San Diego Diversity Fellowship for six years during my PhD, including a small research grant of $12k from a network of local donors. Many thanks to all who have made it possible for me to work on such interesting questions.