Diversity of hard-bottom fauna relative to environmental gradients in Kongsfjorden, Svalbard

A baseline study of hard-bottom zoobenthos in relation to environmental gradients in Kongsfjorden, a glacial fjord in Svalbard, is presented, based on collections from 1996 to 1998. The total species richness in 62 samples from 0 to 30 m depth along five transects was 403 species. Because 32 taxa could not be identified to species level and because 11 species are probably new to science, the total number of identified species was 360. Of these, 47 species are new for Svalbard waters. Bryozoa was the most diverse group. Biogeographic composition revealed features of both Arctic and sub-Arctic properties of the fauna. Species richness, frequency of species occurrence, mean abundance and biomass generally decreased towards the tidal glaciers in inner Kongsfjorden. Among eight environmental factors, depth was most important for explaining variance in the composition of the zoobenthos. The diversity was consistently low at shallow depths, whereas the non-linear patterns of species composition of deeper samples indicated a transitional zone between surface and deeper water masses at 15–20 m depth. Groups of “colonial” and “non-colonial” species differed in diversity, biogeographic composition and distribution by location and depth as well as in relation to other environmental factors. “Non-colonial” species made a greater contribution than “colonial” species to total species richness, total occurrence and biomass in samples, and were more influenced by the depth gradient. Biogeographic composition was sensitive to variation of zoobenthic characteristics over the studied depth range. A list of recorded species and a description of sampling sites are presented

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Interannual changes in zooplankton on the West Spitsbergen Shelf in relation to hydrography and their consequences for the diet of planktivorous seabirds

The purpose of the work was to determine how atmospheric and oceanic processes (the North Atlantic Oscillation (NAO) and the Arctic Ocean Oscillation (AOO)) influence hydrography and zooplankton on the West Spitsbergen Shelf (WSS), and the impacts of the processes on chick meals of zooplanktivorous little auks Alle alle. There were distinct Atlantic and Arctic oceanographic domains on the shelf resulting from the presence of the West Spitsbergen Current and the Sørkapp Current, which contain different proportions of Calanus finmarchicus and C. glacialis. The abundance of warm- and cold-water species varied as a result of an interplay between processes in the atmosphere and ocean. In the Arctic domain, on which the study focused, the NAO impacted oceanography, zooplankton, and consequently little auk chick meals, with time-lags of 4–7 years. The diet of little auk chicks was more energy-rich when C. glacialis stage 5 in the Arctic community were more easily available. To date, the changes in zooplankton abundance on the WSS have not posed a threat to the ability of little auks to feed their chicks lipid-rich Arctic copepods