Facing glycosphingolipid–Shiga toxin interaction: dire straits for endothelial cells of the human vasculature

The two major Shiga toxin (Stx) types, Stx1 and Stx2, produced by enterohemorrhagic Escherichia coli (EHEC) in particular injure renal and cerebral microvascular endothelial cells after transfer from the human intestine into the circulation. Stxs are AB₅ toxins composed of an enzymatically active A subunit and the pentameric B subunit, which preferentially binds to the glycosphingolipid globotriaosylceramide (Gb3Cer/CD77). This review summarizes the current knowledge on Stx-caused cellular injury and the structural diversity of Stx receptors as well as the initial molecular interaction of Stxs with the human endothelium of different vascular beds. The varying lipoforms of Stx receptors and their spatial organization in lipid rafts suggest a central role in different modes of receptor-mediated endocytosis and intracellular destiny of the toxins. The design and development of tailored Stx neutralizers targeting the oligosaccharide–toxin recognition event has become a very real prospect to ameliorate or prevent life-threatening renal and neurological complications.     

Memory processes during sleep: beyond the standard consolidation theory

Two-step theories of memory formation suggest that an initial encoding stage, during which transient neural assemblies are formed in the hippocampus, is followed by a second step called consolidation, which involves re-processing of activity patterns and is associated with an increasing involvement of the neocortex. Several studies in human subjects as well as in animals suggest that memory consolidation occurs predominantly during sleep (standard consolidation model). Alternatively, it has been suggested that consolidation may occur during waking state as well and that the role of sleep is rather to restore encoding capabilities of synaptic connections (synaptic downscaling theory). Here, we review the experimental evidence favoring and challenging these two views and suggest an integrative model of memory consolidation.     

Forecasting the Dubai financial market with a combination of momentum effect with a deep belief network

Applying recent advances in machine learning techniques, we propose a hybrid model to forecast the Dubai financial market general index. Particularly, we exploit a deep belief networks model that applies a restricted Boltzmann machine as its main component in combination with momentum effects. We also introduce an innovative way of selecting the inputs by using momentum effects. With this hybrid methodology we generate a prediction model along with a comparison of three different linear models. The results obtained from the hybrid model are better and more stable than the three linear models. The findings support that the hybrid model we applied will find their way into finance because of their reliability and good performance.     

Spatially scaled response of a Lazuli Bunting population to fire

We examined the response of Lazuli Bunting ( Passerina amoena ) to fire in Gambel oak ( Quercus gambelii ) woodland at Camp Williams, Utah, during 1993–1998. Overall, Lazuli Bunting abundance on the study area increased significantly during the 2 years after a stand-replacing wildfire, which covered 800 ha of Gambel oak woodland. This increase suggested that Lazuli Buntings respond positively to fire. However, a comparison of pre- and postfire abundance of Lazuli Bunting for 2 groups of monitoring plots with different fire histories showed that abundance was significantly greater during the post-fire period for both burned and unburned plots. When we examined our data at a spatial scale appropriate to Lazuli Bunting, we found that post-fire increases observed on unburned plots were limited to plots in close proximity to the burned area. A comparison of pre- and post-fire abundance of Lazuli Bunting for 3 groups of monitoring plots located at various distances from the burned area revealed that post-fire abundance was similar only for plots within the fire boundary and for those ≤1000 m from the fire boundary; plots located >1000 m from the fire boundary had fewer individuals per plot post-fire. However, prefire Lazuli Bunting abundance was similar among all 3 categories. This differential, spatially scaled response of Lazuli Bunting to fire at the landscape level may support a hierarchical view of habitat selection.     

Proteome survey reveals modularity of the yeast cell machinery

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.     

Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline

The chemical composition of the Bannock basin has been studied in some detail. We recently showed that unusual microbial populations, including a new division of Archaea (MSBL1), inhabit the NaCl-rich hypersaline brine. High salinities tend to reduce biodiversity, but when brines come into contact with fresher water the natural haloclines formed frequently contain gradients of other chemicals, including permutations of electron donors and acceptors, that may enhance microbial diversity, activity and biogeochemical cycling. Here we report a 2.5-m-thick chemocline with a steep NaCl gradient at 3.3 km within the water column betweeen Bannock anoxic hypersaline brine and overlying sea water. The chemocline supports some of the most biomass-rich and active microbial communities in the deep sea, dominated by Bacteria rather than Archaea, and including four major new divisions of Bacteria. Significantly higher metabolic activities were measured in the chemocline than in the overlying sea water and underlying brine; functional analyses indicate that a range of biological processes is likely to occur in the chemocline. Many prokaryotic taxa, including the phylogenetically new groups, were confined to defined salinities, and collectively formed a diverse, sharply stratified, deep-sea ecosystem with sufficient biomass to potentially contribute to organic geological deposits.     

Insights into the dynamics of mantle plumes from uranium-series geochemistry

The long-standing paradigm that hotspot volcanoes such as Hawaii or Iceland represent the surface expression of mantle plumes--hot, buoyant upwelling regions beneath the Earth's lithosphere--has recently been the focus of controversy. Whether mantle plumes exist or not is pivotal for our understanding of the thermal, dynamic and compositional evolution of the Earth's mantle. Here we show that uranium-series disequilibria measured in hotspot lavas indicate that hotspots are indeed associated with hot and buoyant upwellings and that weaker (low buoyancy flux) hotspots such as Iceland and the Azores are characterized by lower excess temperatures than stronger hotspots such as Hawaii. This direct link between buoyancy flux and mantle temperature is evidence for the existence of mantle plumes.