ALBERT

Description: Major overturn within a magma chamber can bring together felsic and mafic magmas, prompting de-volatilisation and acting as the driver for Plinian eruptions. Until now identification of mixing has been limited to analysis of lavas or individual crystals ejected during eruptions. We have recovered partially developed cumulate material (‘live’ cumulate mush) from pyroclastic deposits of major eruptions on Tenerife. These samples represent “frozen” clumps of diverse crystalline deposits from all levels in the developing reservoir, which are permeated with the final magma immediately before eruptions. Such events therefore record the complete disintegration of the magma chamber, leading to caldera collapse. Chemical variation across developing cumulus crystals records changes in melt composition. Apart from fluctuations reflecting periodic influxes of mafic melt, crystal edges consistently record the presence of more felsic magmas. The prevalence of this felsic liquid implies it was able to infiltrate the entire cumulate pile immediately before each eruption. Scientific Reports 2 doi: 10.1038/srep00731

Description: Using models and ecological data, this study shows that the eastern Pacific Ocean population of leatherback sea turtles could well face extirpation owing to climate change. However, the findings indicate that it may be possible to sustain a viable nesting population in Costa Rica throughout this century by cooling nests. Nature Climate Change 2 814 doi: 10.1038/nclimate1582

Description: Based on a given time series, the data-driven Langevin equation (dLE) estimates the drift and the diffusion field of the dynamics, which are then employed to reproduce the essential statistical and dynamical features of the original time series. Because the propagation of the dLE requires only local information, the input data are neither required to be Boltzmann weighted nor to be a continuous trajectory. Similar to a Markov state model, the dLE approach therefore holds the promise of predicting the long-time dynamics of a biomolecular system from relatively short trajectories which can be run in parallel. The practical applicability of the approach is shown to be mainly limited by the initial sampling of the system’s conformational space obtained from the short trajectories. Adopting extensive molecular dynamics simulations of the unfolding and refolding of a short peptide helix, it is shown that the dLE approach is able to describe microsecond conformational dynamics from a few hundred nanosecond trajectories. In particular, the dLE quantitatively reproduces the free energy landscape and the associated conformational dynamics along the chosen five-dimensional reaction coordinate.

Description: Background: Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recruited their original biota from the same source, but their geological evolution eventually constituted sharp environmental barriers, restricting genetic exchange between the individual basins. Therefore, DHABs are unique model systems to assess the effect of geological events and environmental conditions on the evolution and diversification of protistan plankton. Here, we examine evidence for isolated evolution of unicellular eukaryote protistan plankton communities driven by geological separation and environmental selection. We specifically focused on ciliated protists as a major component of protistan DHAB plankton by pyrosequencing the hypervariable V4 fragment of the small subunit ribosomal RNA. Geospatial distributions and responses of marine ciliates to differential hydrochemistries suggest strong physical and chemical barriers to dispersal that influence the evolution of this plankton group. Results: Ciliate communities in the brines of four investigated DHABs are distinctively different from ciliate communities in the interfaces (haloclines) immediately above the brines. While the interface ciliate communities from different sites are relatively similar to each other, the brine ciliate communities are significantly different between sites. We found no distance-decay relationship, and canonical correspondence analyses identified oxygen and sodium as most important hydrochemical parameters explaining the partitioning of diversity between interface and brine ciliate communities. However, none of the analyzed hydrochemical parameters explained the significant differences between brine ciliate communities in different basins. Conclusions: Our data indicate a frequent genetic exchange in the deep-sea water above the brines. The "isolated island character" of the different brines, that resulted from geological events and contemporary environmental conditions, create selective pressures driving evolutionary processes, and with time, lead to speciation and shape protistan community composition. We conclude that community assembly in DHABs is a mixture of isolated evolution (as evidenced by small changes in V4 primary structure in some taxa) and species sorting (as indicated by the regional absence/presence of individual taxon groups on high levels in taxonomic hierarchy).

Description: Principal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a low-dimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the small-amplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and well-resolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.

Description: Principal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a low-dimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the small-amplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and well-resolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.

Description: This report provides a brief review of the 16th annual meeting of the German Language Branch of the Society of Environmental Toxicology and Chemistry (SETAC GLB) held from September 18th to 20th 2011 at the University Koblenz-Landau at Campus Landau. The event was organized by Carsten Bruhl and Ralf B. Schafer and many members and students of the Institute for Environmental Sciences under the main theme "EcoTOXICOlogy and Environmental CHEMISTRY: Crossing borders". Almost 300 participants enjoyed the scientific program that included 54 oral and 70 poster presentations under seven session themes. In addition, four invited keynote speakers and a plenary discussion on biodiversity with representatives from government, academia and industry provided new insights. The best oral and poster presentations of the meeting were awarded together with the annual young scientist award of SETAC GLB for the best diploma and doctoral thesis. The reader of the meeting (mostly in German) including the program and all abstracts is freely available as Supplemental Material.

Description: In several neurodegenerative diseases, like Huntington's disease (HD), treatments are still lacking. To determine whether a treatment is effective, sensitive disease progression biomarkers are especially needed for the premanifest phase, since this allows the evaluation of neuroprotective treatments preventing, or delaying disease manifestation. On the basis of a longitudinal study we present a biomarker that was derived by integrating behavioural and neurophysiological data reflecting cognitive processes of action control. The measure identified is sensitive enough to track disease progression over a period of only 6 month. Changes tracked were predictive for a number of clinically relevant parameters and the sensitivity of the measure was higher than that of currently used parameters to track prodromal disease progression. The study provides a biomarker, which could change practice of progression diagnostics in a major basal ganglia disease and which may help to evaluate potential neuroprotective treatments in future clinical trials. Scientific Reports 3 doi: 10.1038/srep01797

Description: Nature Geoscience 6, 545 (2013). doi:10.1038/ngeo1837 Authors: Daniele Bianchi, Eric D. Galbraith, David A. Carozza, K. A. S. Mislan & Charles A. Stock Throughout the ocean, countless small animals swim to depth in the daytime, presumably to seek refuge from large predators. These animals return to the surface at night to feed. This substantial diel vertical migration can result in the transfer of significant amounts of carbon and nutrients from the surface to depth. However, its consequences on ocean chemistry at the global scale have remained uncertain. Here, we determine the depths of these diel migrations in the global ocean using a global array of backscatter data from acoustic Doppler current profilers, collected between 1990 and 2011. We show that the depth of diel migration follows coherent large-scale patterns. We find that migration depth is greater where subsurface oxygen concentrations are high, such that seawater oxygen concentration is the best single predictor of migration depth at the global scale. In oxygen minimum zone areas, migratory animals generally descend as far as the upper margins of the low-oxygen waters. Using an ocean biogeochemical model coupled to a general circulation model, we show that by focusing oxygen consumption in poorly ventilated regions of the upper ocean, diel vertical migration intensifies oxygen depletion in the upper margin of oxygen minimum zones. We suggest that future changes in the extent of oxygen minimum zones could alter the migratory depths of marine organisms, with consequences for marine biogeochemistry, food webs and fisheries.