Public participation in soil surveys: lessons from a pilot study in England.

In many countries there are policies in place that impact on soils, but very few legislative or policy tools specifically for the protection of soil. Recent EU legislative proposals on soil protection have been met with opposition on the grounds of excessive cost and resource demands. With the need for evidence based policy, and recognition that involving the public in environmental monitoring is an effective way of increasing understanding and commitment, there has been growing interest in soil surveys. In addition, it is accepted that the success of environmental policies depends greatly on how effectively scientists, regulators, stakeholders, and society communicate. This paper presents the Open Air Laboratories (OPAL) Soil and Earthworm Survey as an example of public participation in soil surveys that aims to integrate the above. It is demonstrated how such surveys generate data that can be used to prioritise soil assessment, in order to address some of the concerns and objections to soil protection policies. Lessons from this pilot study in England highlight that with strategic planning of civic participation activities, this approach can deliver improvements in the quality of the evidence collected and allow for effective public involvement in policymaking and implementation, on top of direct educational benefits.

Land use and soil characteristics affect soil organisms differently from above-ground assemblages.

BACKGROUND: Land-use is a major driver of changes in biodiversity worldwide, but studies have overwhelmingly focused on above-ground taxa: the effects on soil biodiversity are less well known, despite the importance of soil organisms in ecosystem functioning. We modelled data from a global biodiversity database to compare how the abundance of soil-dwelling and above-ground organisms responded to land use and soil properties. RESULTS: We found that land use affects overall abundance differently in soil and above-ground assemblages. The abundance of soil organisms was markedly lower in cropland and plantation habitats than in primary vegetation and pasture. Soil properties influenced the abundance of soil biota in ways that differed among land uses, suggesting they shape both abundance and its response to land use. CONCLUSIONS: Our results caution against assuming models or indicators derived from above-ground data can apply to soil assemblages and highlight the potential value of incorporating soil properties into biodiversity models.

From chemical risk assessment to environmental quality management: the challenge for soil protection.

The 40 years that have passed since the beginning of the 'environmental revolution' has seen a large increase in development of policies for the protection of environmental media and a recognition by the public of the importance of environmental quality. There has been a shift from policy in reaction to high profile events, then to control of releases to single environmental media, and to the present position of moving toward integrated management of all environmental media at present. This development has moved away from classical chemical risk assessment toward environmental holism, including recognition of the ecological value of these media. This work details how policy developments have taken place for air and water, with examples from the USA and EU, in order to compare this with policy development regarding soil. Soil, with quite different policy frameworks and distinct uses, understanding, and threats compared to other environmental media, is currently attracting attention regarding the need for its protection independent of use. Challenges for soil policy are identified and evaluated, and recommendations on how these challenges can be overcome are discussed with relevance to water and air protection policy.

Independent transcriptomic and proteomic regulation by type I and II protein arginine methyltransferases.

Protein arginine methyltransferases (PRMTs) catalyze the post-translational monomethylation (Rme1), asymmetric (Rme2a), or symmetric (Rme2s) dimethylation of arginine. To determine the cellular consequences of type I (Rme2a) and II (Rme2s) PRMTs, we developed and integrated multiple approaches. First, we determined total cellular dimethylarginine levels, revealing that Rme2s was ∼3% of total Rme2 and that this percentage was dependent upon cell type and PRMT inhibition status. Second, we quantitatively characterized in vitro substrates of the major enzymes and expanded upon PRMT substrate recognition motifs. We also compiled our data with publicly available methylarginine-modified residues into a comprehensive database. Third, we inhibited type I and II PRMTs and performed proteomic and transcriptomic analyses to reveal their phenotypic consequences. These experiments revealed both overlapping and independent PRMT substrates and cellular functions. Overall, this study expands upon PRMT substrate diversity, the arginine methylome, and the complex interplay of type I and II PRMTs.

Multiple classes of MSL binding sites target dosage compensation to the X chromosome of Drosophila.

MSL complexes bind hundreds of sites along the single male X chromosome to achieve dosage compensation in Drosophila. Previously, we proposed that approximately 35 "high-affinity" or "chromatin entry" sites (CES) might nucleate spreading of MSL complexes in cis to paint the X chromosome. This was based on analysis of the first characterized sites roX1 and roX2. roX transgenes attract MSL complex to autosomal locations where it can spread long distances into flanking chromatin. roX1 and roX2 also produce noncoding RNA components of the complex. Here we identify a third site from the 18D10 region of the X chromosome. Like roX genes, 18D binds full and partial MSL complexes in vivo and encompasses a male-specific DNase I hypersensitive site (DHS). Unlike roX genes, the 510 bp 18D site is apparently not transcribed and shows high affinity for MSL complex and spreading only as a multimer. While mapping 18D, we discovered MSL binding to X cosmids that do not carry one of the approximately 35 high-affinity sites. Based on additional analyses of chromosomal transpositions, we conclude that spreading in cis from the roX genes or the approximately 35 originally proposed "entry sites" cannot be the sole mechanism for MSL targeting to the X chromosome.

Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression.

Recent studies of histone methylation have yielded fundamental new insights pertaining to the role of this modification in gene activation as well as in gene silencing. While a number of methylation sites are known to occur on histones, only limited information exists regarding the relevant enzymes that mediate these methylation events. We thus sought to identify native histone methyltransferase (HMT) activities from Saccharomyces cerevisiae. Here, we describe the biochemical purification and characterization of Set2, a novel HMT that is site-specific for lysine 36 (Lys36) of the H3 tail. Using an antiserum directed against Lys36 methylation in H3, we show that Set2, via its SET domain, is responsible for methylation at this site in vivo. Tethering of Set2 to a heterologous promoter reveals that Set2 represses transcription, and part of this repression is mediated through the HMT activity of the SET domain. These results suggest that Set2 and methylation at H3 Lys36 play a role in the repression of gene transcription.

Resetting the histone code at CDKN2A in HNSCC by inhibition of DNA methylation.

Head and neck squamous cell carcinoma (HNSCC) is the fifth most frequent cancer in the US. Several genetic and epigenetic alterations are associated with HNSCC tumorigenesis, including inactivation of CDKN2A, which encodes the p16 tumor suppressor, in cell lines and primary tumors by DNA methylation. Reactivation of tumor suppressor genes by DNA-demethylating agents and histone deacetylase (HDAC) inhibitors shows therapeutic promise for other cancers. Therefore, we investigated the ability of these agents to reactivate p16 in Tu159 HNSCC cells. Treatment of cells with 5-aza-2'deoxycytidine (5-aza-dC) increases CDKN2A expression and slightly increases histone H3 acetylation at this gene. No reactivation of CDKN2A is observed upon treatment with the HDAC inhibitor trichostatin A (TSA), but synergistic reactivation of CDKN2A is observed upon sequential treatment of Tu159 cells with both 5-aza-dC and TSA. Silencing of CDKN2A in Tu159 cells is correlated with increased methylation of histone H3 at lysine 9 and decreased methylation at lysine 4 relative to the upstream p15 gene promoter. Interestingly, global levels of H3-K9 methylation are decreased upon treatment with 5-aza-dC. Together these data indicate that DNA methylation is a dominant epigenetic mark for silencing of CDKN2A in Tu159 tumor cells. Moreover, changes in DNA methylation can reset the histone code by impacting multiple H3 modifications.

Soil quality assessment under emerging regulatory requirements.

New and emerging policies that aim to set standards for protection and sustainable use of soil are likely to require identification of geographical risk/priority areas. Soil degradation can be seen as the change or disturbance in soil quality and it is therefore crucial that soil and soil quality are well understood to protect soils and to meet legislative requirements. To increase this understanding a review of the soil quality definition evaluated its development, with a formal scientific approach to assessment beginning in the 1970s, followed by a period of discussion and refinement. A number of reservations about soil quality assessment expressed in the literature are summarised. Taking concerns into account, a definition of soil quality incorporating soil's ability to meet multifunctional requirements, to provide ecosystem services, and the potential for soils to affect other environmental media is described. Assessment using this definition requires a large number of soil function dependent indicators that can be expensive, laborious, prone to error, and problematic in comparison. Findings demonstrate the need for a method that is not function dependent, but uses a number of cross-functional indicators instead. This method to systematically prioritise areas where detailed investigation is required, using a ranking based against a desired level of action, could be relatively quick, easy and cost effective. As such this has potential to fill in gaps and compliment existing monitoring programs and assist in development and implementation of current and future soil protection legislation.