Conserved and species-specific alternative splicing in mammalian genomes

Background  

Alternative splicing has been shown to be one of the major evolutionary mechanisms for protein diversification and proteome expansion, since a considerable fraction of alternative splicing events appears to be species- or lineage-specific. However, most studies were restricted to the analysis of cassette exons in pairs of genomes and did not analyze functionality of the alternative variants.     

Current theories for mechanism of stomatal opening: Influence of blue light; mesophyll cells,and sucrose

Since the late 1960s, researchers have observed that starch in the chloroplasts of the guard cells breaks down during the day and accumulates in the dark. Based on this, carbohydrates have historically been regarded as the primary osmotica modulating stomatal opening. However, the discovery of an important role for potassium uptake has led to the replacement of that starch-sugar hypothesis. Current research now focuses mainly on how K⁺ is transported in and out of cells when the stomata open or close. However, questions remain concerning photoreceptors, and the functioning of guard cell chloroplasts is still disputed. Coincidentally, some recent study results have again suggested that sucrose may play a major role in guard cell osmoregulation, thus supporting the original theory of starch-sugar involvement.     

Exploring the Influence of TorsinA Expression on Protein Quality Control

DYT1 dystonia is caused by a glutamic acid deletion (ΔE) in the endoplasmic reticulum (ER) protein torsinA. Previous studies suggest that torsinA modulates the aggregation of cytosolic misfolded proteins and ER stress responses, although the mechanisms underlying those effects remain unclear. In order to investigate the bases of these observations, we analyzed the interaction between torsinA expression, protein aggregation and ER stress in PC6.3 cells. Unexpectedly, we found that expression of torsinA(wt) or (ΔE) does not influence the inclusion formation by an expanded polyglutamine reporter protein in this cellular model. Furthermore, torsinA does not prevent the activation of ER stress induced by thapsigargin or the reducing agent DTT. Interestingly, DTT induces post-translational changes in torsinA, more prominently for torsinA(wt) than (ΔE). This work highlights the importance of model system selection for the study of torsinA function. Furthermore, it provides additional evidence suggesting that torsinA is sensitive to changes in the cellular redox potential.     

Recognition of heteropolysaccharide alginate by periplasmic solute-binding proteins of a bacterial ABC transporter

Alginate is a heteropolysaccharide that consists of β-D-mannuronate (M) and α-L-guluronate (G). The Gram-negative bacterium Sphingomonas sp. A1 directly incorporates alginate into the cytoplasm through the periplasmic solute-binding protein (AlgQ1 and AlgQ2)-dependent ABC transporter (AlgM1-AlgM2/AlgS-AlgS). Two binding proteins with at least four subsites strongly recognize the nonreducing terminal residue of alginate at subsite 1. Here, we show the broad substrate preference of strain A1 solute-binding proteins for M and G present in alginate and demonstrate the structural determinants in binding proteins for heteropolysaccharide recognition through X-ray crystallography of four AlgQ1 structures in complex with saturated and unsaturated alginate oligosaccharides. Alginates with different M/G ratios were assimilated by strain A1 cells and bound to AlgQ1 and AlgQ2. Crystal structures of oligosaccharide-bound forms revealed that in addition to interaction between AlgQ1 and unsaturated oligosaccharides, the binding protein binds through hydrogen bonds to the C4 hydroxyl group of the saturated nonreducing terminal residue at subsite 1. The M residue of saturated oligosaccharides is predominantly accommodated at subsite 1 because of the strict binding of Ser-273 to the carboxyl group of the residue. In unsaturated trisaccharide (ΔGGG or ΔMMM)-bound AlgQ1, the protein interacts appropriately with substrate hydroxyl groups at subsites 2 and 3 to accommodate M or G, while substrate carboxyl groups are strictly recognized by the specific residues Tyr-129 at subsite 2 and Lys-22 at subsite 3. Because of this substrate recognition mechanism, strain A1 solute-binding proteins can bind heteropolysaccharide alginate with different M/G ratios.     

Use of basidiomycetes in industrial waste processing and utilization technologies: fundamental and applied aspects (review)

This review provides an analysis of recent data on the mechanisms of degradation of lignocellulosic materials and xenobiotics by basidiomycetes. Special attention is given to the analysis of the current state of research of ligninolytic enzymes and their involvement in the degradation ofxenobiotics. Data on the practical use of basidiomycetes for bioconversion of industrial wastes are systematized. The most promising areas of bioconversion technologies are considered, such as contaminated water purification (including wastewater), cleanup of soils contaminated with heavy metals and xenobiotics, and degradation of difficult-to-degrade substrates (lignin and lignocellulose wastes, low-energy coal, and synthetic polymers).     

Behavior in the forced-swimming test and expression of BDNF and Bcl-xl genes in the rat brain

A single exposure of rats to the forced-swimming stress decreased BDNF mRNA levels in the cortex and increased Bcl-xl gene expression in the hippocampus and amygdala 24 h after the stress. The animals demonstrated a depressive-like behavior and elevated blood corticosterone level. There was a significant negative correlation between BDNF mRNA level in the cortex and immobility time during swimming. Repeated exposure to swimming stress caused the elevation of the hippocampal BDNF mRNA level assessed 24 h after the second swimming session. The data suggest that stress-induced down-regulation of cortical BDNF gene expression and behavioral despair in the forced-swimming test may be interrelated. The increase in the BDNF and Bcl-xl mRNA levels may contribute to the mechanisms protecting the brain against negative effects of stress.     

Autonomous learning of load and traffic patterns to improve cluster utilization

Adaptive clustering aims at improving cluster utilization for varying load and traffic patterns. Locality-based least-connection with replication (LBLCR) scheduling that comes with Linux is designed to help improve cluster utilization through adaptive clustering. A key issue with LBLCR, however, is that cluster performance depends much on a single threshold value that is used to determine adaptation. Once set, the threshold remains fixed, regardless of the load and traffic patterns. If a cluster of PCs is to adapt to different traffic patterns for high utilization, a good threshold has to be selected and used dynamically. We present in this paper an adaptive clustering framework that autonomously learns and adapts to different load and traffic patterns at runtime with no administrator intervention. The cluster is configured once and for all. As the patterns change, the cluster automatically expands/contracts to meet the changing demands. At the same time, the patterns are proactively learned so that when similar patterns emerge in the future, the cluster knows what to do to improve utilization. We have implemented this autonomous learning method and compared it with LBLCR using published Web traces. Experimental results indicate that our autonomous learning method produces high performance scalability and adaptability for different patterns. On the other hand LBLCR-based clustering suffers from performance scalability and adaptability for different traffic patterns since it is not designed to obtain good threshold values and use them at runtime.     

Effects of tunable excitation in carotenoids explained by the vibrational energy relaxation approach

Carotenoids are fundamental building blocks of natural light harvesters with convoluted and ultrafast energy deactivation networks. In order to disentangle such complex relaxation dynamics, several studies focused on transient absorption measurements and their dependence on the pump wavelength. However, such findings are inconclusive and sometimes contradictory. In this study, we compare internal conversion dynamics in \(\beta\)-carotene, pumped at the first, second, and third vibronic progression peak. Instead of employing data fitting algorithms based on global analysis of the transient absorption spectra, we apply a fully quantum mechanical model to treat the high-frequency symmetric carbon–carbon (C=C and C–C) stretching modes explicitly. This model successfully describes observed population dynamics as well as spectral line shapes in their time-dependence and allows us to reach two conclusions: Firstly, the broadening of the induced absorption upon excess excitation is an effect of vibrational cooling in the first excited state (\(S_{1}\)). Secondly, the internal conversion rate between the second excited state (\(S_{2}\)) and \(S_{1}\) crucially depends on the relative curve displacement. The latter point serves as a new perspective on solvent- and excitation wavelength-dependent experiments and lifts contradictions between several studies found in literature.