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

waste silica sources as heavy metal stabilizers for municipal solid waste incineration fly ash

Abstract The present work discusses a new method, based on the use of silica fume, for heavy metal stabilization. The inertization procedure is reported and compared with other technologies, involving the employ of amorphous silica as stabilizing agent for municipal solid waste incinerator fly ash treatment (i.e. colloidal silica and rice husk ash). The obtained final materials are characterized in terms of chemical composition and phase analysis. The reported method, realized at room temperature, employs all waste or by-product materials. As a consequence it appears to be economically and environmentally sustainable

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

Foundry sand alkali activation for sustainable construction

Please click Additional Files below to see the full abstract

Integrated management of ash from industrial and domestic combustion : a new sustainable approach for reducing greenhouse gas emissions from energy conversion

This work supports, for the first time, the integrated management of waste materials arising from industrial processes (fly ash from municipal solid waste incineration and coal fly ash), agriculture (rice husk ash), and domestic activities (ash from wood biomass burning in domestic stoves). The main novelty of the paper is the reuse of wood pellet ash, an underestimated environmental problem, by the application of a new technology (COSMOS-RICE) that already involves the reuse of fly ashes from industrial and agricultural origins. The reaction mechanism involves carbonation: this occurs at room temperature and promotes permanent carbon dioxide sequestration. The obtained samples were characterized using XRD and TGA (coupled with mass spectroscopy). This allowed quantification of the mass loss attributed to different calcium carbonate phases. In particular, samples stabilized using wood pellet ash show a weight loss, attributed to the decomposition of carbonates greater than 20%. In view of these results, it is possible to conclude that there are several environmental benefits from wood pellet ash reuse in this way. In particular, using this technology, it is shown that for wood pellet biomass the carbon dioxide conversion can be considered negative

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

Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins

BACKGROUND: Avidin is a chicken egg-white protein with high affinity to vitamin H, also known as D-biotin. Many applications in life science research are based on this strong interaction. Avidin is a homotetrameric protein, which promotes its modification to symmetrical entities. Dual-chain avidin, a genetically engineered avidin form, has two circularly permuted chicken avidin monomers that are tandem-fused into one polypeptide chain. This form of avidin enables independent modification of the two domains, including the two biotin-binding pockets; however, decreased yields in protein production, compared to wt avidin, and complicated genetic manipulation of two highly similar DNA sequences in the tandem gene have limited the use of dual-chain avidin in biotechnological applications. PRINCIPAL FINDINGS: To overcome challenges associated with the original dual-chain avidin, we developed chimeric dual-chain avidin, which is a tandem fusion of avidin and avidin-related protein 4 (AVR4), another member of the chicken avidin gene family. We observed an increase in protein production and better thermal stability, compared with the original dual-chain avidin. Additionally, PCR amplification of the hybrid gene was more efficient, thus enabling more convenient and straightforward modification of the dual-chain avidin. When studied closer, the generated chimeric dual-chain avidin showed biphasic biotin dissociation. SIGNIFICANCE: The improved dual-chain avidin introduced here increases its potential for future applications. This molecule offers a valuable base for developing bi-functional avidin tools for bioseparation, carrier proteins, and nanoscale adapters. Additionally, this strategy could be helpful when generating hetero-oligomers from other oligomeric proteins with high structural similarity