World reference base for soil resources 2014 International soil classification system for naming soils and creating legends for soil maps

The first edition of the World Reference Base for Soil Resources (WRB) was released at the 16th World Congress of Soil Science at Montpellier in 1998. At the same event, it was also endorsed and adopted as the system for soil correlation and international communication of the International Union of Soil Sciences (IUSS). The second edition of the WRB was released at the 18th World Congress at Philadelphia in 2006. After an additional eight years of intensive worldwide testing and data collection, the third edition of the WRB is presented. This publication builds on and reflects the valuable work of the authors of the earlier drafts and editions of the WRB, as well as the experiences and contributions of many soil scientists who participated in the work of the IUSS Working Group on the WRB. The WRB is a soil classification system for naming soils and creating soil map legends. It is hoped that this publication will contribute to the understanding of soil science in the general public and in the scientific community.JRC.H.5-Land Resources Managemen

Conformation Effects of CpG Methylation on Single-Stranded DNA Oligonucleotides: Analysis of the Opioid Peptide Dynorphin-Coding Sequences

Single-stranded DNA (ssDNA) is characterized by high conformational flexibility that allows these molecules to adopt a variety of conformations. Here we used native polyacrylamide gel electrophoresis (PAGE), circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy to show that cytosine methylation at CpG sites affects the conformational flexibility of short ssDNA molecules. The CpG containing 37-nucleotide PDYN (prodynorphin) fragments were used as model molecules. The presence of secondary DNA structures was evident from differences in oligonucleotide mobilities on PAGE, from CD spectra, and from formation of A-T, G-C, and non-canonical G-T base pairs observed by NMR spectroscopy. The oligonucleotides displayed secondary structures at 4°C, and some also at 37°C. Methylation at CpG sites prompted sequence-dependent formation of novel conformations, or shifted the equilibrium between different existing ssDNA conformations. The effects of methylation on gel mobility and base pairing were comparable in strength to the effects induced by point mutations in the DNA sequences. The conformational effects of methylation may be relevant for epigenetic regulatory events in a chromatin context, including DNA-protein or DNA-DNA recognition in the course of gene transcription, and DNA replication and recombination when double-stranded DNA is unwinded to ssDNA

Conductance and Ion Selectivity of a Mesoscopic Protein Nanopore Probed with Cysteine Scanning Mutagenesis

Nanometer-scale proteinaceous pores are the basis of ion and macromolecular transport in cells and organelles. Recent studies suggest that ion channels and synthetic nanopores may prove useful in biotechnological applications. To better understand the structure-function relationship of nanopores, we are studying the ion-conducting properties of channels formed by wild-type and genetically engineered versions of Staphylococcus aureus α-hemolysin (αHL) reconstituted into planar lipid bilayer membranes. Specifically, we measured the ion selectivities and current-voltage relationships of channels formed with 24 different αHL point cysteine mutants before and after derivatizing the cysteines with positively and negatively charged sulfhydryl-specific reagents. Novel negative charges convert the selectivity of the channel from weakly anionic to strongly cationic, and new positive charges increase the anionic selectivity. However, the extent of these changes depends on the channel radius at the position of the novel charge (predominately affects ion selectivity) or on the location of these charges along the longitudinal axis of the channel (mainly alters the conductance-voltage curve). The results suggest that the net charge of the pore wall is responsible for cation-anion selectivity of the αHL channel and that the charge at the pore entrances is the main factor that determines the shape of the conductance-voltage curves

MicroRNAs as Predictors of Lung-Cancer Resistance and Sensitivity to Cisplatin

Background: Platinum-based chemotherapy, cisplatin (DDP) specifically, is the main strategy for treating lung cancer (LC). However, currently, there is a lack of predictive drug-resistance markers, and there is increased interest in the development of a reliable and sensitive panels of markers for DDP chemotherapy-effectiveness prediction. MicroRNAs represent a perspective pool of markers for chemotherapy effectiveness. Objectives: Data on miRNAs associated with LC DDP chemotherapy response are summarized and analyzed. Materials and methods: A comprehensive review of the data in the literature and an analysis of bioinformatics resources were performed. The gene targets of miRNAs, as well as their reciprocal relationships with miRNAs, were studied using several databases. Results and Discussion: The complex analysis of bioinformatics resources and the literature indicated that the expressions of 12 miRNAs have a high predictive potential for LC DDP chemotherapy responses. The obtained information was discussed from the point of view of the main mechanisms of LC chemoresistance. Conclusions: An overview of the published data and bioinformatics resources, with respect to the predictive microRNA markers of chemotherapy response, is presented in this review. The selected microRNAs and gene panel have a high potential for predicting LC DDP sensitiveness or DDP resistance as well as for the development of a DDP co-therapy

Sodium Lignosulfonate Effect on Physiological Traits of Cucumis sativus L. Seedlings

The application of pulp and paper mill sludge to agricultural soils is commonly considered as a strategy to improve soil properties, promote plant growth, and reduce the demand for costly chemical fertilization. The aim of this study was to evaluate if sodium lignosulfonate (sLS), one of the sludges of pulp production, may affect the biomass production, the respiration (R) and net CO2 assimilation rate (An) at the leaf level, and the content and accumulation of trace elements in the leaves of cucumbers grown under a sufficient nutrient supply or soil nutrient deficit. A pot culture experiment was conducted using sLS application rates of 0, 1.0, 2.5, 5.0, and 10 vol% to sandy loam soil. The decline in nutrient availability caused an increase in the R/An ratio and dramatically depressed biomass accumulation. The leaf Fe, Ni, Cr, Co, Al, and Pb contents were lower under low nutrient availability than under sufficient nutrient supply. Although sLS was not very effective in lessening the negative effect of nutrient deficiency on biomass accumulation, it reduced respiratory carbon losses and cell membrane permeability in the leaves of cucumbers grown under nutrient deficit. The reduction in the toxic level of leaf Mn in seedlings grown under sufficient nutrient availability and the toxic level of leaf Fe under a nutrient deficit might also be considered as a positive effect of the sLS application to sandy soil

Sodium Lignosulfonate Effect on Physiological Traits of <i>Cucumis sativus</i> L. Seedlings

The application of pulp and paper mill sludge to agricultural soils is commonly considered as a strategy to improve soil properties, promote plant growth, and reduce the demand for costly chemical fertilization. The aim of this study was to evaluate if sodium lignosulfonate (sLS), one of the sludges of pulp production, may affect the biomass production, the respiration (R) and net CO2 assimilation rate (An) at the leaf level, and the content and accumulation of trace elements in the leaves of cucumbers grown under a sufficient nutrient supply or soil nutrient deficit. A pot culture experiment was conducted using sLS application rates of 0, 1.0, 2.5, 5.0, and 10 vol% to sandy loam soil. The decline in nutrient availability caused an increase in the R/An ratio and dramatically depressed biomass accumulation. The leaf Fe, Ni, Cr, Co, Al, and Pb contents were lower under low nutrient availability than under sufficient nutrient supply. Although sLS was not very effective in lessening the negative effect of nutrient deficiency on biomass accumulation, it reduced respiratory carbon losses and cell membrane permeability in the leaves of cucumbers grown under nutrient deficit. The reduction in the toxic level of leaf Mn in seedlings grown under sufficient nutrient availability and the toxic level of leaf Fe under a nutrient deficit might also be considered as a positive effect of the sLS application to sandy soil

TLR2 and endosomal TLR-mediated secretion of IL-10 and immune suppression in response to phagosome-confined Listeria monocytogenes.

Listeria monocytogenes is a facultative intracellular bacterial pathogen that escapes from phagosomes and induces a robust adaptive immune response in mice, while mutants unable to escape phagosomes fail to induce a robust adaptive immune response and suppress the immunity to wildtype bacteria when co-administered. The capacity to suppress immunity can be reversed by blocking IL-10. In this study, we sought to understand the host receptors that lead to secretion of IL-10 in response to phagosome-confined L. monocytogenes (Δhly), with the ultimate goal of generating strains that fail to induce IL-10. We conducted a transposon screen to identify Δhly L. monocytogenes mutants that induced significantly more or less IL-10 secretion in bone marrow-derived macrophages (BMMs). A transposon insertion in lgt, which encodes phosphatidylglycerol-prolipoprotein diacylglyceryl transferase and is essential for the formation of lipoproteins, induced significantly reduced IL-10 secretion. Mutants with transposon insertions in pgdA and oatA, which encode peptidoglycan N-acetylglucosamine deacetylase and O-acetyltransferase, are sensitive to lysozyme and induced enhanced IL-10 secretion. A ΔhlyΔpgdAΔoatA strain was killed in BMMs and induced enhanced IL-10 secretion that was dependent on Unc93b1, a trafficking molecule required for signaling of nucleic acid-sensing TLRs. These data revealed that nucleic acids released by bacteriolysis triggered endosomal TLR-mediated IL-10 secretion. Secretion of IL-10 in response to infection with the parental strain was mostly TLR2-dependent, while IL-10 secretion in response to lysozyme-sensitive strains was dependent on TLR2 and Unc93b1. In mice, the IL-10 response to vacuole-confined L. monocytogenes was also dependent on TLR2 and Unc93b1. Co-administration of Δhly and ΔactA resulted in suppressed immunity in WT mice, but not in mice with mutations in Unc93b1. These data revealed that secretion of IL-10 in response to L. monocytogenes infection in vitro is mostly TLR2-dependent and immune suppression by phagosome-confined bacteria in vivo is mostly dependent on endosomal TLRs

Design and Immunological Properties of the Novel Subunit Virus-like Vaccine against SARS-CoV-2

The COVID-19 pandemic is ongoing, and the need for safe and effective vaccines to prevent infection and to control spread of the virus remains urgent. Here, we report the development of a SARS-CoV-2 subunit vaccine candidate (Betuvax-CoV-2) based on RBD and SD1 domains of the spike (S) protein fused to a human IgG1 Fc fragment. The antigen is adsorbed on betulin adjuvant, forming spherical particles with a size of 100–180 nm, mimicking the size of viral particles. Here we confirm the potent immunostimulatory activity of betulin adjuvant, and demonstrate that two immunizations of mice with Betuvax-CoV-2 elicited high titers of RBD-specific antibodies. The candidate vaccine was also effective in stimulating a neutralizing antibody response and T cell immunity. The results indicate that Betuvax-CoV-2 has good potential for further development as an effective vaccine against SARS-CoV-2

Chapter 11 - Regional assessment of soil changes in Europe and Eurasia

In Europe and Eurasia, the inherent complexity and spatial variability of soil makes the evaluation of the impact of any change difficult. Transformations of features such as texture and mineralogical composition will only occur over geological time spans while properties such as pH, organic matter content or microbial activity will show a more rapid reaction. In addition, the response of a particular soil type may be both positive and negative depending on the function in question. For example, rising temperatures and precipitation may support increased agricultural productivity on soils previously deemed marginal, but such a transformation can lead to a deterioration of soil biological diversity and an increased risk of erosion. Quantitative assessments of future trends in soil characteristics and properties are limited. As a consequence, this chapter provides an outlook only for a selected number of issues. Considerably more effort is required to model changes in the state of soil conditions in relation to drivers such as changes in land use and climate. Based on the above finding, an assessment  is made of the status and trend of the ten soil threats in order of importance for the region. At the same time an indication is given of the reliability of these estimates.JRC.H.5-Land Resources Managemen