Phylogenetic Focusing Reveals the Evolution of Eumetazoan Opsins

Phylogenetic analyses of gene trees commonly begin by searching large molecular datasets from the taxa of interest using some known query sequence. Resulting sequences that exceed some threshold are then concatenated, aligned, and analyzed phylogenetically. This approach has revealed much about the evolutionary history of gene families, but several problems are apparent. Here we apply a new approach that we call Phylogenetic Focusing that circumvents some issues related to global search strategies. Our approach first circumscribes the largest possible orthogroup containing the gene family of interest and then proceeds to focus in on the gene family of interest based on iterative rounds of phylogenetic analyses. We demonstrate this approach by using the phylogeny of eumetazoan rhodopsin class GPCRs to focus in on a clade containing melatonin receptors, opsins, and other genes. Our results clarify the evolutionary history of eumetazoan rhodopsin class GPCRs, the subclade containing opsins, and provide new hypotheses on the functional significance of these genes in cnidarians

Monitoring and Scoring Counter-Diffusion Protein Crystallization Experiments in Capillaries by in situ Dynamic Light Scattering

In this paper, we demonstrate the feasibility of using in situ Dynamic Light Scattering (DLS) to monitor counter-diffusion crystallization experiments in capillaries. Firstly, we have validated the quality of the DLS signal in thin capillaries, which is comparable to that obtained in standard quartz cuvettes. Then, we have carried out DLS measurements of a counter-diffusion crystallization experiment of glucose isomerase in capillaries of different diameters (0.1, 0.2 and 0.3 mm) in order to follow the temporal evolution of protein supersaturation. Finally, we have compared DLS data with optical recordings of the progression of the crystallization front and with a simulation model of counter-diffusion in 1D

Recreational boating site choice and the impact of water quality

This paper examines whether water quality has an effect on recreational boating activity. The analysis is based on survey data collected by face-to-face interviews with recreational visitors to 10 waterway sites across Ireland. We model the respondent's choice decision to travel to a specific site for the purposes of beginning their recreational boating activity. Water quality data is from European Union Water Framework Directive monitoring stations. Across recreational sites, which have generally high water quality levels within our sample, we find that boaters favour sites with better water quality; as indicated by biological oxygen demand and phosphates metrics. We also find that for each additional 10 km distance from respondents' homes the probability that a site is visited declines by up to 10%. Preferences for other site attributes, such as boat slipways, parking and toilet facilities, were counter to expectation but reflects the fact that all boat users do not necessarily access or need all facilities provided