Zooming in on protein–RNA interactions: a multilevel workflow to identify interaction partners

Interactions between proteins and RNA are at the base of numerous cellular regulatory and functional phenomena. The investigation of the biological relevance of non-coding RNAs has led to the identification of numerous novel RNA-binding proteins (RBPs). However, defining the RNA sequences and structures that are selectively recognised by an RBP remains challenging, since these interactions can be transient and highly dynamic, and may be mediated by unstructured regions in the protein, as in the case of many non-canonical RBPs. Numerous experimental and computational methodologies have been developed to predict, identify and verify the binding between a given RBP and potential RNA partners, but navigating across the vast ocean of data can be frustrating and misleading. In this mini-review, we propose a workflow for the identification of the RNA binding partners of putative, newly identified RBPs. The large pool of potential binders selected by in-cell experiments can be enriched by in silico tools such as catRAPID, which is able to predict the RNA sequences more likely to interact with specific RBP regions with high accuracy. The RNA candidates with the highest potential can then be analysed in vitro to determine the binding strength and to precisely identify the binding sites. The results thus obtained can furthermore validate the computational predictions, offering an all-round solution to the issue of finding the most likely RNA binding partners for a newly identified potential RBP

Assessment of the influence of electric arc furnace slag as a non-conventional filler for Nitrile Butadiene Rubber

Reinforcement of polymers by the addition of particles filler is a complex phenomenon that depends mainly on the hydrodynamic effect and a complex interplay between polymer, filler, and interfacial region. Mineral fillers are usually adopted as low-cost extenders due to their lower cost. In this study, the influence of a waste material such as electric arc furnace steel slag is assessed as filler for Nitrile-Butadiene Rubber following experimental procedures and analytical calculations adopted for traditional fillers. It was found that the slag content affects the static and the dynamic properties by increasing the material's capability to storage and dissipate energy. In addition to an important contribution of the hydrodynamic effect, the presence of an increasing immobilized rubber fraction around the slag particles (quantified by a differential scanning calorimetry analysis) plays a central role. The slag stiffens the NBR composite; the increase of static tensile and dynamic shear storage moduli was found to be consistent with the Halpin-Tsai and Guth-Gold prevision models respectively. Moreover, the non-linear dynamic behavior was found to be well-fitted by the Kraus equation models. The reinforcing ability of the slag particles as filler was confirmed by the negative slope of the Kraus plot on swelling data

Heavy Metals in Soil and Salad in the Proximity of Historical Ferroalloy Emission

Emissions of manganese (Mn), lead (Pb), iron (Fe), zinc (Zn), copper (Cu) from ferro-alloy operations has taken place in Valcamonica, a pre-Alp valley in the province of Brescia, Italy, for about a century until 2001. Metal concentrations were measured in the soil of local home gardens and in the cultivated vegetables. Soil analysis was carried out using a portable X-Ray Fluorescence (XRF) spectrometer in both surface soil and at 10 cm depth. A subset of soil samples (n = 23) additionally was analysed using the modified BCR sequential extraction method and ICP-OES for intercalibration with XRF (XRF Mn = 1.33 * total OES Mn – 71.8; R = 0.830, p < 0.0001). Samples of salads (Lactuca sativa and Chichorium spp.) were analyzed with a Total Reflection X-Ray Fluorescence (TXRF) technique. Vegetable and soil metal measurements were performed in 59 home gardens of Valcamonica, and compared with 23 gardens from the Garda Lake reference area. Results indicate significantly higher levels of soil Mn (median 986 ppm vs 416 ppm), Pb (median 46.1 ppm vs 30.2 ppm), Fe (median 19,800 ppm vs 13,100 ppm) in the Valcamonica compared to the reference area. Surface soil levels of all metals were significantly higher in surface soil compared to deeper soil, consistent with atmospheric deposition. Significantly higher levels of metals were shown also in lettuce from Valcamonica for Mn (median 53.6 ppm vs 30.2) and Fe (median 153 vs 118). Metals in Chichorium spp. did not differ between the two areas. Surface soil metal levels declined with increasing distance from the closest ferroalloy plant, consistent with plant emis- sions as the source of elevated soil metal levels. A correlation between Mn concentrations in soil and lettuce was also observed. These data show that historic ferroalloy plant activity, which ended nearly a decade before this study, has contributed to the persistence of increased Mn levels in locally grown vegetables. Further research is needed to assess whether this increase can lead to adverse effects in humans and plants especially for Mn, an essential element that can be toxic in humans when exceeding the homeostatic ranges

Lovastatin Modulates Glycogen Synthase Kinase-3β Pathway and Inhibits Mossy Fiber Sprouting after Pilocarpine-Induced Status Epilepticus

This study was undertaken to assay the effect of lovastatin on the glycogen synthase kinase-3 beta (GSK-3β) and collapsin responsive mediator protein-2 (CRMP-2) signaling pathway and mossy fiber sprouting (MFS) in epileptic rats. MFS in the dentate gyrus (DG) is an important feature of temporal lobe epilepsy (TLE) and is highly related to the severity and the frequency of spontaneous recurrent seizures. However, the molecular mechanism of MFS is mostly unknown. GSK-3β and CRMP-2 are the genes responsible for axonal growth and neuronal polarity in the hippocampus, therefore this pathway is a potential target to investigate MFS. Pilocarpine-induced status epilepticus animal model was taken as our researching material. Western blot, histological and electrophysiological techniques were used as the studying tools. The results showed that the expression level of GSK-3β and CRMP-2 were elevated after seizure induction, and the administration of lovastatin reversed this effect and significantly reduced the extent of MFS in both DG and CA3 region in the hippocampus. The alteration of expression level of GSK-3β and CRMP-2 after seizure induction proposes that GSK-3β and CRMP-2 are crucial for MFS and epiletogenesis. The fact that lovastatin reversed the expression level of GSK-3β and CRMP-2 indicated that GSK-3β and CRMP-2 are possible to be a novel mechanism of lovatstain to suppress MFS and revealed a new therapeutic target and researching direction for studying the mechanism of MFS and epileptogenesis

A circular economy virtuous example-use of a stabilized waste material instead of calcite to produce sustainable composites

This work reports and analyzes the mechanical properties of some composites obtained using stabilized waste with epoxy resins E-227. For comparison, correspondent composite samples were realized using calcite as a filler. The recovered stabilized waste was obtained by means of a new method to stabilize municipal solid waste incineration (MSWI) fly ash (FA), based on the use of bottom ash (BA). The aim of this paper is to show that the stabilization process, which can be considered a zero-waste treatment, produces inert materials, that can be reused as a filler. The production of new filler was made on a pilot plant, designed to verify the transferability of the proposed stabilization technology. Mechanical analysis revealed that flexural modulus raises by increasing the filler content around 30% wt, independently of filler type, stabilized sample or calcium carbonate. Mechanical properties are lower in the samples with the high amount of filler due to the crowding effect. The morphology of composite materials showed a non-homogeneous dispersion of particles in stabilized sample filler, characterized by large particle agglomerates. Finally, according to the ESCAPE simplified method, the obtained composites result more sustainable in comparison with the corresponding ones produced by using natural resources (like calcite). These findings open new possibilities for the reuse of the stabilized material, in frame of circular economy principles, with environmental and economic advantage

Extraordinary optical transmission in one-dimensional gold gratings: near- and far-field analysis

One-dimensional arrays of nanoslits fabricated on silicon nitride membranes show extraordinary optical transmission. Optical characterization techniques have been used to characterize the transmission spectra and the near-field optical configuration. Experimental results have been compared with numerical simulations in order to elucidate the different modes of light propagation. Near- and far-field optical distribution is studied as a function of the polarization of light. (c) 2011 Optical Society of Americ