Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture

Management of soil biological resources to optimise plant production, efficiency of nutrient inputs, and system sustainability is an emerging opportunity for pastoral agriculture. To achieve these goals, suitable tools that can assess the functional state of the soil ecosystem must be developed and standardised approaches to their application adopted. Towards this end, we have undertaken comprehensive, high-density functional-gene microarray analysis (GeoChip5) of environmental DNA (eDNA) extracted from 50 pastoral soils. When combined with soil, environmental and management metadata, the information can be used to provide insights into soil biological processes spanning greenhouse gas emissions, through to natural suppression of plant root diseases. To provide an example of a structured workflow of analysis in a pastoral system context, we analysed the GeoChip data using a combination of approaches spanning routine univariate methods through to more complex multivariate and network-based analysis. Analyses were restricted to comparing effects of land-use (dairy or ‘other’ farming systems), and exploring relationships of the GeoChip data with the soil properties from each sample. These exemplar analyses present a pathway for the application of eDNA approaches (GeoChip or others) to deliver outcomes for pastoral agricultural in New Zealand. © 2016 The Royal Society of New Zealand

The RKIP (Raf-1 Kinase Inhibitor Protein) conserved pocket binds to the phosphorylated N-region of Raf-1 and inhibits the Raf-1-mediated activated phosphorylation of MEK

The Raf-MEK-ERK pathway regulates many fundamental biological processes, and its activity is finely tuned at multiple levels. The Raf kinase inhibitory protein (RKIP) is a widely expressed negative modulator of the Raf-MEK-ERK signaling pathway. We have previously shown that RKIP inhibits the phosphorylation of MEK by Raf-1 through interfering with the formation of a kinase-substrate complex by direct binding to both Raf-1 and MEK. Here, we show that the evolutionarily conserved ligand-binding pocket of RKIP is required for its inhibitory activity towards the Raf-1 kinase mediated activation of MEK. Single amino acid substitutions of two of the conserved residues form the base and the wall of the pocket confers a loss-of-function phenotype on RKIP. Loss-of-function RKIP mutants still appear to bind to Raf-1. However the stability of the complexes formed between mutants and the N-region Raf-1 phosphopeptide were drastically reduced. Our results therefore suggest that the RKIP conserved pocket may constitute a novel phosphoamino-acid binding motif and is absolutely required for RKIP function. (C) 2008 Elsevier Inc. All rights reserve

Sulfasalazine prevents T-helper 1 immune response by suppressing interleukin-12 production in macrophages

Interleukin-12 (IL-12) plays a pivotal role in the development of T-helper 1 (Th1) immune response, which may be involved in the pathogenesis of chronic inflammatory autoimmune disorders. In this study we investigated the effects of sulfasalazine, a drug for treating inflammatory bowel disease and rheumatoid arthritis, on the production of IL-12 from mouse macrophages stimulated with lipopolysaccharide (LPS). Sulfasalazine potently inhibited the production of IL-12 in a dose-dependent manner, in part through the down-regulation of nuclear factor κB (NFκB) activation in IL-12 p40 gene. Activation of macrophages by LPS resulted in markedly enhanced binding activities to the κB site, which significantly decreased upon addition of sulfasalazine as demonstrated by an electrophoretic gel shift assay. Importantly, macrophages pretreated with sulfasalazine either in vitro or in vivo reduced their ability to induce interferon-γ (IFN-γ) and increased the ability to induce IL-4 in antigen-primed CD4+ T cells. From these results, sulfasalazine may induce the Th2 cytokine profile in CD4+ T cells by suppressing IL-12 production in macrophages, and sulfasalazine-induced inhibition of IL-12 production in macrophages may explain some of the known biological effects of sulfasalazine