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.     

Nonsense-mediated decay approaches the clinic

Nonsense-mediated decay (NMD) eliminates mRNAs containing premature termination codons and thus helps limit the synthesis of abnormal proteins. New results uncover a broader role of NMD as a pathway that also affects the expression of wild-type genes and alternative-splice products. Because the mechanisms by which NMD operates have received much attention, we discuss here the emerging awareness of the impact of NMD on the manifestation of human genetic diseases. We explore how an understanding of NMD accounts for phenotypic differences in diseases caused by premature termination codons. Specifically, we consider how the protective function of NMD sometimes benefits heterozygous carriers and, in contrast, sometimes contributes to a clinical picture of protein deficiency by inhibiting expression of partially functional proteins. Potential 'NMD therapeutics' will therefore need to strike a balance between the general physiological benefits of NMD and its detrimental effects in cases of specific genetic mutations.     

Presynaptic induction of heterosynaptic associative plasticity in the mammalian brain

The induction of associative synaptic plasticity in the mammalian central nervous system classically depends on coincident presynaptic and postsynaptic activity. According to this principle, associative homosynaptic long-term potentiation (LTP) of excitatory synaptic transmission can be induced only if synaptic release occurs during postsynaptic depolarization. In contrast, heterosynaptic plasticity in mammals is considered to rely on activity-independent, non-associative processes. Here we describe a novel mechanism underlying the induction of associative LTP in the lateral amygdala (LA). Simultaneous activation of converging cortical and thalamic afferents specifically induced associative, N-methyl-D-aspartate (NMDA)-receptor-dependent LTP at cortical, but not at thalamic, inputs. Surprisingly, the induction of associative LTP at cortical inputs was completely independent of postsynaptic activity, including depolarization, postsynaptic NMDA receptor activation or an increase in postsynaptic Ca2+ concentration, and did not require network activity. LTP expression was mediated by a persistent increase in the presynaptic probability of release at cortical afferents. Our study shows the presynaptic induction and expression of heterosynaptic and associative synaptic plasticity on simultaneous activity of converging afferents. Our data indicate that input specificity of associative LTP can be determined exclusively by presynaptic properties.