FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression.

BACKGROUND: While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. RESULTS: We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. Steps are taken to ensure that the annotation is self-consistent and that the structure of GO is used to identify higher level functions that may not be annotated directly. An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. In a case study, a set of genes, that had statistically significant regression between gene expression levels and environmental temperature along the Atlantic Coast, shows a statistically significant (P < 0.001) enrichment in genes associated with amine metabolism. CONCLUSION: The methods described have application for functional genomics studies, particularly among non-model organisms. The web interface for FunnyBase can be accessed at http://genomics.rsmas.miami.edu/funnybase/super_craw4/. Data and source code are available by request at jpaschall@bioinfobase.umkc.edu.

Solar UV radiation enhances the toxicity of arsenic in Ceriodaphnia dubia.

Extensive research exists regarding the toxicity of metals (including arsenic) to aquatic invertebrates. However, there has been little consideration of potential synergies between metals and ultraviolet (UV) radiation--despite considerable debate on this topic in human health research. Ultraviolet radiation is nearly ubiquitous in the natural environment, but it is generally overlooked as a confounding variable in toxicological assessments. We evaluate synergies between arsenic and solar UV radiation using the crustacean, Ceriodaphnia dubia. Both laboratory (with simulated solar radiation) and outdoor (with natural solar radiation) factorial experiments were performed with two intensities of UV (low and high) and four arsenic concentrations (0, 1, 1.25 and 1.5 mg/l). The laboratory experiment was multigenerational, examining survival and fecundity effects. The combination of high UV + 1.5 mg/l As adversely impacted survival; whereas, High UV + 0 mg/l As and Low UV + 1.5 mg/l As treatments did not. These results suggest synergism. This pattern was consistent for all three generations. Fecundity effects were not consistent across generations, and arsenic was demonstrated to have a greater impact than UV. Outdoor experiments were limited to assessing survival. Exposures in September 1999 resulted in a pattern similar to that in the laboratory exposure. High UV + 1.5 mg/l As treatment elicited diminished survival as compared to high UV + 0 mg/l As and low UV + 1.5 mg/l As. These results indicate that a synergistic effect between arsenic and UV exposure is possible under ambient conditions and within a relatively narrow dose range. The mechanism of this effect is unknown but could include synergistic genotoxic or oxidative stress. These findings point to the importance of using realistic UV exposures when determining criteria for protection of aquatic life.