Implications of informatics approaches in ecological research

The LifeWatch approach to the exploration of distributed species information

This paper introduces a new method of automatically extracting, integrating and presenting information regarding species from the most relevant online taxonomic resources. First, the information is extracted and joined using data wrappers and integration solutions. Then, an analytical tool is used to provide a visual representation of the data. The information is then integrated into a user friendly content management system. The proposal has been implemented using data from the Global Biodiversity Information Facility (GBIF), the Catalogue of Life (CoL), the World Register of Marine Species (WoRMS), the Integrated Taxonomic Information System (ITIS) and the Global Names Index (GNI). The approach improves data quality, avoiding taxonomic and nomenclature errors whilst increasing the availability and accessibility of the information.

Beyond xeroderma pigmentosum: DNA damage and repair in an ecological context. A tribute to James E. Cleaver

The ability to repair DNA is a ubiquitous characteristic of life on Earth and all organisms possess similar mechanisms for dealing with DNA damage, an indication of a very early evolutionary origin for repair processes. James E. Cleaver's career (initiated in the early 1960s) has been devoted to the study of mammalian ultraviolet radiation (UVR) photobiology, specifically the molecular genetics of xeroderma pigmentosum and other human diseases caused by defects in DNA damage recognition and repair. This work by Jim and others has influenced the study of DNA damage and repair in a variety of taxa. Today, the field of DNA repair is enhancing our understanding of not only how to treat and prevent human disease, but is providing insights on the evolutionary history of life on Earth and how natural populations are coping with UVR-induced DNA damage from anthropogenic changes in the environment such as ozone depletion.

Gene-class analysis of expression patterns induced by psychoactive pharmaceutical exposure in fathead minnow (Pimephales promelas) indicates induction of neuronal systems

Psychoactive pharmaceuticals are among the most frequently prescribed drugs, contributing to persistent measurable concentrations in aquatic systems. Typically, it is assumed that such contaminants have no human health implications because they exist in extremely low concentrations. We exposed juvenile fathead minnows (Pimephales promelas) to three pharmaceuticals, fluoxetine, venlafaxine and carbamazepine, individually and in a mixture, and measured their effect on the induction of gene expression in fish brains using microarray analysis. Gene expression changes were accompanied by behavioral changes and validated by qPCR analysis. Gene Set Enrichment Analysis was used to perform gene-class analysis of gene expression, testing for enrichment of gene sets known to be involved in human neuronal development, regulation and growth. We found significant enrichment of gene sets for each of the treatments, with the largest induction of expression by the mixture treatment. These results suggest that the psychoactive pharmaceuticals are able to alter expression of fish genes associated with development, regulation and differentiation of synapses, neurons and neurotransmitters. The results provide a new perspective for the consideration of potential consequence for human health due to environmental exposure to unmetabolized psychoactive pharmaceuticals.