MtDNA metagenomics reveals large‐scale invasion of belowground arthropod communities by introduced species

Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large‐scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil‐dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate human‐mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.     

Identification of naturally processed ligands in the C57BL/6 mouse using large-scale mass spectrometric peptide sequencing and bioinformatics prediction

Most major histocompatibility complex (MHC) class I–peptide-binding motifs are currently defined on the basis of quantitative in vitro MHC–peptide-binding assays. This information is used to develop bioinformatics-based tools to predict the binding of peptides to MHC class I molecules. To date few studies have analyzed the performance of these bioinformatics tools to predict the binding of peptides determined by sequencing of naturally processed peptides eluted directly from MHC class I molecules. In this study, we performed large-scale sequencing of endogenous peptides eluted from H2K^b and H2D^b molecules expressed in spleens of C57BL/6 mice. Using sequence data from 281 peptides, we identified novel preferred anchor residues located in H2K^b and H2D^b-associated peptides that refine our knowledge of these H2 class I peptide-binding motifs. The analysis comparing the performance of three bioinformatics methods to predict the binding of these peptides, including artificial neural network, stabilized matrix method, and average relative binding, revealed that 61% to 94% of peptides eluted from H2K^b and H2D^b molecules were correctly classified as binders by the three algorithms. These results suggest that bioinformatics tools are reliable and efficient methods for binding prediction of naturally processed MHC class I ligands. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Solubility behaviour of phosphofructokinase from haemolysate of erythrocytes, reticulocytes and bone marrow cells in poly (ethylene glycol) solutions.

The precipitation profiles of phospofructokinase obtained by addition of poly(ethylene glycol) to haemolysates of erythrocytes, reticulocytes and bone marrow are displaced towards higher polymer concentrations when the pH decreases from 6 to 5 or increases from 6 to 8. In the pH range 5 to 8, the concentration of polymer required to provide any level of precipitation follows the order erythrocytic less than reticulocytic less than bone marrow phosphofructokinase. The precipitation of erythrocytic and reticulocytic phosphofructokinase is enhanced by the presence of F6P and ATP. No effect is observed for bone marrow phosphofructokinase. These results are consistent with an isoenzymatic variation of phosphofructokinase in erythrocytes, reticulocytes and bone marrow cells.     

A comprehensive phenotypic CRISPR-Cas9 screen of the ubiquitin pathway uncovers roles of ubiquitin ligases in mitosis

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The influence of climatic legacies on the distribution of dryland biocrust communities

Predicting the distribution of biocrust species, mosses, lichens and liverworts associated with surface soils is difficult, but climatic legacies (changes in climate over the last 20 k years) can improve our prediction of the distribution of biocrust species. To provide empirical support for this hypothesis, we used a combination of network analyses and structural equation modelling to identify the role of climatic legacies in predicting the distribution of ecological clusters formed by species of mosses, lichens and liverworts using data from 282 large sites distributed across 0.6 million km² of eastern Australia. Two ecological clusters contained 87% of the 120 moss, lichen and liverwort species. Both clusters contained lichen, moss and liverwort species, but were dominated by different families. Sites where the air temperature increased the most over 20k years (positive temperature legacies) were associated with reductions in the relative abundance of species from the lichen (Peltulaceae and Teloschistaceae) and moss (Bryaceae) families (Cluster A species), greater groundstorey plant cover and lower soil pH. Sites where precipitation has increased over the past 20k years (positive precipitation legacy) were associated with increases in the relative abundance of lichen (Cladoniaceae, Lecideaceae and Thelotremataceae) and moss (Pottiaceae) families (Cluster B species) and lower levels of soil pH. Sites where temperatures have increased the most in the past 20k years suppressed the negative effects of plant cover on Cluster B by reducing plant cover. Increased intensity of grazing suppressed the negative effect of soil pH and the positive effect of soil carbon, on the relative abundance of Cluster B taxa. Finally, increasing temperature and precipitation legacies reduced the negative effect of soil pH on Cluster B. Understanding of the importance of climatic legacies improves our ability to predict how biocrust assemblies might respond to ongoing global environmental change associated with increasing land use intensification, increasing temperature and reduced rainfall.