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

Geographic and seasonal patterns and limits on the adaptive response to temperature of European Mytilus spp. and Macoma balthica populations

Seasonal variations in seawater temperature require extensive metabolic acclimatization in cold-blooded organisms inhabiting the coastal waters of Europe. Given the energetic costs of acclimatization, differences in adaptive capacity to climatic conditions are to be expected among distinct populations of species that are distributed over a wide geographic range. We studied seasonal variations in the metabolic adjustments of two very common bivalve taxa at European scale. To this end we sampled 16 populations of Mytilus spp. and 10 Macoma balthica populations distributed from 39° to 69°N. The results from this large-scale comprehensive comparison demonstrated seasonal cycles in metabolic rates which were maximized during winter and springtime, and often reduced in the summer and autumn. Studying the sensitivity of metabolic rates to thermal variations, we found that a broad range of Q10 values occurred under relatively cold conditions. As habitat temperatures increased the range of Q10 narrowed, reaching a bottleneck in southern marginal populations during summer. For Mytilus spp., genetic-group-specific clines and limits on Q10 values were observed at temperatures corresponding to the maximum climatic conditions these geographic populations presently experience. Such specific limitations indicate differential thermal adaptation among these divergent groups. They may explain currently observed migrations in mussel distributions and invasions. Our results provide a practical framework for the thermal ecophysiology of bivalves, the assessment of environmental changes due to climate change and its impact on (and consequences for) aquaculture

Effect of species invasion on transport of solutes at different levels of soft sediment macrofauna diversity: results from an experimental approach

Different irrigation or ventilation strategies by macrofauna may provide a competitive advantage to tolerant species invading impacted benthic systems and alter benthic-pelagic coupling. To comparatively analyze the effects of an exotic and a native polychaete burrower on sedimentwater exchanges, two laboratory experiments were performed. In the first experiment, the invasive spionid polychaete Marenzelleria neglecta was added to defaunated sediments and fluxes of the inert tracer (bromide, Br−) were measured to quantify the effects of irrigation by the worm on the tracer transport. In the second experiment, M. neglecta or the native polychaete Hediste diversicolor were introduced to a relatively diverse Baltic soft-bottom macrofauna community. The effect of species on fluxes of reactive solutes (ammonium, NH4+, and phosphate, PO43−) and transport rates of Br− was estimated. The results indicate different invasion effects depending on the characteristics of the recipient habitat. In defaunated sediments, a single specimen of M. neglecta significantly enhanced originally low solute exchange rates. Total tracer flux was significantly enhanced over diffusive flux by a factor of 1.6 ± 0.14 (n = 3). In natural sediments, on the other hand, the addition of either M. neglecta or H. diversicolor had no statistically significant effects on benthic fluxes. Tracer flux estimates between control and treatment incubations differed by less than 10% on average, and both reactive solutes tended to increase by 10 to 40% after additions. One specimen of M. neglecta in cores with defaunated sediment generated approximately 20% of the tracer flux produced by the relatively diverse macrofauna community. Estimated net tracer fluxes in two experiments corresponded well with the number of adult polychaetes found in sediments (r2 = 0.73, p = 0.005, n = 12). The invasive M. neglecta produced a small effect on fluxes in biodiverse sediments, comparable to those of H. diversicolor, but it may deeply alter porewater chemistry in azoic sediment. As M. neglecta tolerates chemically reduced and sulphidic conditions, its bioirigation may favor sediment reoxidation and ultimately the recolonization by less tolerant, native species

Nitrogen processes in coastal and marine ecosystems

Nature of the problem • Nitrogen (N) inputs from human activities have led to ecological deteriorations in large parts of the coastal oceans along European coastlines, including harmful algae blooms and anoxia. • Riverine N-loads are the most pronounced nitrogen sources to coasts and estuaries. Other signifi cant sources are nitrogen in atmospheric deposition and fi xation. Approaches • Th is chapter describes all major N-turnover processes which are important for the understanding of the complexity of marine nitrogen cycling, including information on biodiversity. • Linkages to other major elemental cycles like carbon, oxygen, phosphorus and silica are briefl y described in this chapter. • A tentative budget of all major sources and sinks of nitrogen integrated for global coasts is presented, indicating uncertainties where present, especially the N-loss capacity of ocean shelf sediments. • Finally, specifi c nitrogen problems in the European Regional Seas, including the Baltic Sea, Black Sea, North Sea, and Mediterranean Sea are described. Key fi ndings/state of knowledge • Today, human activity delivers several times more nitrogen to the coasts compared to the natural background of nitrogen delivery. Th e source of this is the land drained by the rivers. Th erefore, the major European estuaries (e.g. Rhine, Scheldt, Danube and the coastlines receiving the outfl ow), North Sea, Baltic Sea, and Black Sea as well as some parts of the Mediterranean coastlines are aff ected by excess nutrient inputs. • Biodiversity is reduced under high nutrient loadings and oxygen defi ciency. Th is process has led to changes in the nutrient recycling in sediments, because mature communities of benthic animals are lacking in disturbed coastal sediments. Th e recovery of communities may not be possible if high productivity and anoxia persist for longer time periods. Major uncertainties/challenges • Th e magnitude of nitrogen sources are not yet well constrained. Likewise the role of nutrient ratios (N:P:Si ratios) may be a critical variable in the understanding of the development of harmful algae blooms. • Whether only inorganic forms of nitrogen are important for productivity, or whether organic nitrogen is also important is not well understood and needs future attention. Recommendations • For the future it will be necessary to develop an adaptive transboundary management strategy for nitrogen reduction. Th e starting point for such regulation is located in the catchments of rivers and along their way to the coastal seas. • An overall reduction of nitrogen inputs into the environment is urgently necessary, especially in the case of diff use nitrogen inputs from agricultural activities.Chapter 8:info:eu-repo/semantics/publishe

Tasting the wealth of seafood biodiversity in Europe: a MARBEF outreach initiative

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