Student Seminar: Brian Granger

October 17th, 2012

Speaker: Brian Granger
Advisers: John Finnerty and Daniel Segrè
Title: Construction of Transcriptomic Databases and Analyses, and Virtual Metabolic Interactions of Microbes.

My research has two separate aspects which I would eventually like to bring together. The first aspect of my research is to understand cnidarian organisms, such as coral and sea anemones, and especially how they respond to stress and develop into different body plans throughout their life. To this effect the coral Pocillopora damicornis, and the parasitic sea anemone Edwardsiella lineata have had their transcriptomes sequenced, assembled, and stored in databases along with annotation from NCBI, amiGO, KEGG and Pfam. These databases are available for querying through an online web interface, and have already offered insights about the coral’s ability to deal with environmental stressors, and the sea anemone’s ability to modify it’s body plan for it’s various life stages, including a novel parasite form. The secondary aspect of my research involves understanding the microbes involved in an environmental system and being able to model their dynamics, and in particular, their symbiosis in system of microbes. A modeling system for metabolic models has been made called COMETS (Computation Of Microbial Ecosystems in Time and Space) which allows for simulation of many organisms at a time in a 2 dimensional environment with a pooled media where metabolites can be exchanged and diffused. This system allows for testing of theoretical microbe combinations in a virtual petri dish which may not otherwise be possible to conduct in a lab. Eventually this platform may be able to simulate a coral animal, and the consortium of microbes that live in and on it, along with the intracellular symbiotic algae, and be able to track the exchange of metabolites between all of them, and how this might change under various conditions.