Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection.

To globally profile circRNAs, we employ RNA-Sequencing paired with chimeric junction analysis for alpha-, beta-, and gamma-herpesvirus infection. We find circRNAs are, as a population, resistant to host shutoff. We validate this observation using ectopic expression assays of human and murine herpesvirus endoribonucleases. During lytic infection, four circRNAs are commonly induced across all subfamilies of human herpesviruses, suggesting a shared mechanism of regulation. We test one such mechanism, namely how interferon-stimulation influences circRNA expression. 67 circRNAs are upregulated by either interferon-ß or -γ treatment, with half of these also upregulated during lytic infection. Using gain and loss of function studies we find an interferon-stimulated circRNA, circRELL1, inhibits lytic Herpes Simplex Virus-1 infection. We previously reported circRELL1 inhibits lytic Kaposi sarcoma-associated herpesvirus infection, suggesting a pan-herpesvirus antiviral activity. We propose a two-pronged model in which interferon-stimulated genes may encode both mRNA and circRNA with antiviral activity. This is critical in cases of host shutoff, such as alpha- and gamma-herpesvirus infection, where the mRNA products are degraded but circRNAs escape.

RNA Structure Prediction, Analysis, and Design: An Introduction to Web-Based Tools.

Understanding RNA structure has become critical in the study of RNA in their roles as mediators of biological processes. To aid in these studies, computational algorithms that utilize thermodynamics have been developed to predict RNA secondary structure. Due to the importance of intermolecular interactions, the algorithms have been expanded to determine and predict RNA-RNA hybridization. This chapter discusses popular webservers with the tools for RNA secondary structure prediction, RNA-RNA hybridization, and design. We address key features that distinguish common-functioning programs and their purposes for the interests of the user. Ultimately, we hope this review elucidates web-based tools researchers may take advantage of in their investigations of RNA structure and function.

Uptake of potentially toxic elements by edible plants in experimental mining Technosols: preliminary assessment.

A study was carried out to evaluate the absorption of potentially toxic elements from mining Technosols by three types of vegetable plants (broccoli (Brassica oleracea var. italica), lettuce (Lactuca sativa) and onion (Allium cepa)), the different parts of which are intended for human and farm animal consumption (leaves, roots, edible parts). The preliminary results obtained highlight the importance of the design of the mining Technosols used for agricultural purposes, obtained from soils and sediments of mining origin and amended with residues of high calcium carbonate concentrations (limestone filler and construction and demolition wastes). The experiment was carried out in a greenhouse, and the total metal(loid)s concentration (As, Pb, Cd, Cu, Fe, Mn and Zn) of the soil, rhizosphere, aqueous leachates and plant samples was monitored, the translocation and bioconcentration factors (TF and BCF, respectively) being calculated. The characterization of the soils included a mobilization study in media simulating different environmental conditions that can affect these soils and predicting the differences in behavior of each Technosol. The results obtained showed that the levels of potentially toxic elements present in the cultivated species are within the range of values mentioned in the literature when they were cultivated in soils with calcareous amendments. However, when the plants were grown in contaminated soils, the potentially toxic elements levels varied greatly according to the species, being higher in onions than in lettuce. Experiments with the use of lime filler or construction and demolition wastes for soil remediation result in crops that, in principle, do not present health risks and are similar in development to those grown on non-contaminated soil.

Assessment of risk from lead intake in mining areas: proposal of indicators.

This study discusses an estimate of the risk associated with the intake of soil contaminated by lead, based on the nature of the source, through a detailed study of the parameters that can influence the bioaccessibility of the element from soil intake. Statistical variables that are related to the solubility and bioavailability of lead are used for this purpose. This includes considering the values of pH, electrical conductivity, particle size, mineralogical composition and the bioaccessibility/bioasimilability of lead. Obtaining an algorithm, represented by different probability distributions of the parameters considered, needs a thorough knowledge of the source materials, which may allow estimating/evaluating the intake health risk provided by the concentration of the metal present. The selected materials are from sites affected by mining activities in the Region of Murcia (SE of Spain) and soils in nearby areas, using a total of 186 samples. Soil samples, once screened and homogenized, were parameterized by determining pH, electrical conductivity, granulometry, both total and water-extractable Pb content. Oral bioaccessibility tests were also performed, and a detailed mineralogical analysis by X-ray diffraction was carried out.

Phytoremediation of potentially toxic elements using constructed wetlands in coastal areas with a mining influence.

This paper proposes the use of wetlands as a phytoremediation strategy for areas of mining and maritime influence in the southeast of Spain. Potentially toxic elements (PTEs) tolerant and salinity-resistant macrophytes (Phragmites australis, Juncus effusus and Iris pseudacorus) have been used. The experiment is carried out in an aerobic artificial wetland using representative sediments affected by mining activities in the study area. Selected species were placed in pots containing substrates made with different mixtures of topsoil and/or peat, mining residues (black or yellow sand). After six months, rhizosphere, root and aerial parts were collected. A transfer study of As, Pb, Zn and Cu is performed, determining contents in rhizosphere and plant (aerial and underground part). From these data, the TF and BCF were calculated for each plant in 15 different substrates. The work is complemented by an initial study of scanning electron microscopy (SEM-EDX) of plants. The obtained results indicate a tolerance of the metallophytes to these PTEs, which may favour the obtaining of a naturalized habitat that acts as an effective protective barrier to the ecosystem, that is easy to maintain and that avoid the risk of transfer to the trophic chain. The use of these species can be a complement to the chemical stabilization proposed for the whole area and carried out in experimental plots. Because they are perennial plants, it is necessary to continue with the experiments and obtain results in a longer period of time that allows to evaluate yield and stabilization.