Graduation date: 2007Cnidarians, such as anemones and corals, engage in an intracellular symbiosis with photosynthetic dinoflagellates. Corals form both the trophic and structural foundation of reef ecosystems. Despite their environmental importance, little is known about the molecular basis of this symbiosis. In this dissertation we explored the cnidariandinoflagellate symbiosis from two perspectives: 1) by examining the gene, CnidEF, which was thought to be induced during symbiosis, and 2) by profiling the gene expression patterns of a coral during the break down of symbiosis, which is called bleaching. The first chapter characterizes a novel EF-hand cDNA, CnidEF, from the anemone Anthopleura elegantissima. CnidEF was found to contain two EF-hand motifs. A combination of bioinformatic and molecular phylogenetic analyses were used to compare CnidEF to EF-hand proteins in other organisms. The closest homologues identified from these analyses were a luciferin binding protein involved in the bioluminescence of the anthozoan Renilla reniformis, and a sarcoplasmic calciumbinding protein involved in fluorescence of the annelid worm Nereis diversicolor. Northern blot analysis refuted link of the regulation of this gene to the symbiotic state. The second and third chapters of this dissertation are devoted to identifying those genes that are induced or repressed as a function of coral bleaching. In the first of these two studies we created a 2,304 feature custom DNA microarray platform from a cDNA subtracted library made from experimentally bleached Montipora capitata, which was then used for high-throughput screening of the subtracted library. In the second of these studies we used this array to profile the gene expression of bleached samples collected in Pilaa Bay, Kauai, HI. In both studies we detected a large number of host genes that displayed statistically different ratios of expression between the control and bleached groups of corals. The identified repressed genes included a novel carbohydrate associated protein (CnidCAP) putatively involved in host/symbiont specificity and recognition. Our data, particularly the emergence of CnidCAP, suggest that host/symbiont specificity in corals is homologous to the complement pathway active in innate immunity in animals. In addition, we have isolated many novel, unidentified genes that may prove useful as markers of coral stress.