The 2015 Annual Meeting of SETAC German Language Branch in Zurich (7-10 September, 2015): ecotoxicology and environmental chemistry-from research to application

This report provides a brief review of the 20th annual meeting of the German Language Branch of the Society of Environmental Toxicology and Chemistry (SETAC GLB) held from September 7th to 10th 2015 at ETH (Swiss Technical University) in Zurich, Switzerland. The event was chaired by Inge Werner, Director of the Swiss Centre for Applied Ecotoxicology (Ecotox Centre) Eawag-EPFL, and organized by a team from Ecotox Centre, Eawag, Federal Office of the Environment, Federal Office of Agriculture, and Mesocosm GmbH (Germany). Over 200 delegates from academia, public agencies and private industry of Germany, Switzerland and Austria attended and discussed the current state of science and its application presented in 75 talks and 83 posters. In addition, three invited keynote speakers provided new insights into scientific knowledge ‘brokering’, and—as it was the International Year of Soil—the important role of healthy soil ecosystems. Awards were presented to young scientists for best oral and poster presentations, and for best 2014 master and doctoral theses. Program and abstracts of the meeting (mostly in German) are provided as Additional file 1

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

SETAC GLB and SETAC Europe SAC : a liaison promoting the next generation of ecotoxicologists and environmental chemists

This commentary is an introduction for students to the Society of Environmental Toxicology and Chemistry (SETAC) and its Student Advisory Council (SAC). As young academics face challenges while trying to develop their careers, SETAC and the SAC help facilitate student involvement in the various communities within the society that can help to develop the students’ careers within the environmental sciences [e.g. the German Language Branch (GLB)]. This piece would also like to emphasize and pay homage to the continual cooperation between the SAC and the ESEU, which provides a scientifc platform to communicate internationally and beyond the borders of SETAC, as well as ofer heartfelt congratulations from the SAC to the GLB for their “20 Years SETAC GLB” and deep gratitude for their strong advocacy and support of the SAC.nonPeerReviewe

CO2_2 fluxes before and after partial deforestation of a Central European spruce forest

A seven year CO$_2$-flux dataset measured in a 70 year old spruce monoculture is presented, of which 22% was deforested three years after the start of the measurements to accelerate regeneration towards natural deciduous vegetation. An eddy covariance (EC) system, mounted on top of a tower within the spruce forest, continuously sampled fluxes of momentum, sensible heat, latent heat and CO$_2$. After clear-cutting, a second EC station with an identical set of instruments was installed inside the deforested area. In total, we examined an EC dataset including three years before (forest) and four years after partial deforestation (forest and deforested). Full time series and annual carbon budgets of the net ecosystem exchange (NEE) and its components gross primary production (GPP) and total ecosystem respiration (Reco) were calculated for both EC sites. Soil respiration was measured with manual chambers on average every month after the deforestation at 75 measurement points in the forest and deforested area. Annual sums of NEE measured above the forest indicated a strong carbon sink of -660 (-535) g C m$^{-2}$ y$^{-1}$ with small interannual variability ±78 (72) g C m$^{-2}$ y$^{-1}$ (values in brackets including correction for self-heating of the open-path gas analyzer). In the first year after partial deforestation, regrowth on the clearcut consisted mainly of grasses, with beginning of the second year shrubs and young trees became increasingly important. The regrowth of vegetation is reflected in the annual sums of NEE, which decreased from a carbon source of 521 (548) g C m$^{-2}$ y$^{-1}$ towards 82 (236) g C m$^{-2}$ y$^{-1}$ over the past four years, due to an increase in the magnitude of GPP from 385 (447) to 892 (1036) g C m$^{-2}$ y$^{-1}$

CO2 fluxes before and after partial deforestation of a spruce forest

Forest ecosystems are a sink for atmospheric CO2, but can weaken or turn into a source due to disturbances such as deforestation. Later, the recovering vegetation may be a weaker or stronger sink than the original forest. Changes in albedo additionally modify the total climate effect.We present seven years of flux measurements sampled above a spruce (picea abies) monoculture at the ICOS associate station candidate DE-RuW (50°30'N, 06°19'E, 600 m a.s.l.). The monoculture originally covered the whole headwater catchment (38.5 ha), which is highly instrumented in the framework of TERENO (TERrestrial ENvironmental Observatories). Three years after the start of measurements, 9 ha outside the main footprint of the tower were deforested to promote natural succession towards deciduous forest. A second eddy-covariance station was installed in the centre of the clearcut and soil respiration of both ecosystems measured manually at monthly intervals. Finally, we compared the climate effect due to changed CO2 sequestration with the biophysical one due to changed albedo.Annual sums of NEE measured above the forest showed a strong carbon sink with small inter-annual variability (-660±78 g C m-2 y-1). Over the four years since deforestation, the initially almost bare clearcut overgrew with grasses, shrubs and young deciduous trees (mostly rowan, sorbus aucuparia). The recovery is reflected by annual sums of NEE, which decreased from a carbon source of +521 g C m-2 y-1 towards almost neutral (+83 g C m-2 y-1). Soil respiration of the clearcut resembled the one of the forest floor during the first two years, but then became significantly higher during summer months as GPP increased. In terms of global radiative forcing, an immediate biophysical cooling effect of the deforested area, due to higher albedo of the soil and recovering vegetation, still overrides the cumulating biochemical effect of the missing CO2 sink