Investigating the of Water treatment residuals on Phosphorus mobility derived from biosolid application to Willow coppice

Short rotation willow coppice (SRWC) treatment of biosolids is limited by the oversupply of biosolid derived phosphorus; this can lead to eventual losses of phosphorus to water. Water treatment residuals (WTR), a by-product of potable water treatment, have been identified as a viable soil amendment for mitigation of phosphorus loss. WTR exploit the capacity of internally held aluminium oxide-hydroxide complexes to immobilise labile phosphorus. However indiscriminate additions to plots can result in inadequate control or excessive immobilization of soluble P, leading to crop deficiencies. Four commercially grown common willow (Salix) genotypes (Terra Nova, Endeavour, Resolution and Tora) were grown in soil amended with WTR at five different application rates (0, 10, 25, 50 and 100 tonne ha-1 air-dry basis) in a glasshouse pot experiment. The effects of application rates on plant yields, tissue P concentrations, P uptake and soil labile P availability were measured. Results indicate labile P was reduced with increasing WTR application rates, without any negative agronomic impacts.

Do leaves of plants on phosphorus-impoverished soils contain high concentrations of phenolic defence compounds?

<p>Prominent theories of plant defence have predicted that plants growing on nutrient-poor soils produce more phenolic defence compounds than those on richer soils. Only recently has the Protein Competition Model (PCM) of phenolic allocation suggested that N and P limitation could have different effects because the nutrients are involved in different cellular metabolic processes. 2. We extend the prediction of the PCM and hypothesize that N will have a greater influence on the production of phenolic defensive compounds than P availability, because N limitation reduces protein production and thus competition for phenylalanine, a precursor of many phenolic compounds. In contrast, P acts as a recyclable cofactor in these reactions, allowing protein and hence phenolic production to continue under low P conditions. 3. We test this hypothesis by comparing the foliar concentrations of phenolic compounds in (i) phenotypes of 21 species growing on P-rich alluvial terraces and P-depleted marine terraces in southern New Zealand, and (ii) 87 species growing under similar climates on comparatively P-rich soils in New Zealand vs. P-depleted soils in Tasmania. 4. Foliar P concentrations of plants from the marine terraces were about half those of plants from alluvial soils, and much lower in Tasmania than in New Zealand. However, foliar concentrations of N and phenolic compounds were similar across sites in both comparisons, supporting the hypothesis that N availability is a more important determinant of plant investment in phenolic defensive compounds than P availability. We found no indication that reduced soil P levels influenced plant concentrations of phenolic compounds. There was wide variation in the foliar N and P concentrations among species, and those with low foliar nutrient concentrations produced more phenolics (including condensed tannins). 5. Our study is the first trait comparison extending beyond standard leaf economics to include secondary metabolites related to defence in forest plants, and emphasizes that N and P have different influences on the production of phenolic defence compounds. © 2009 British Ecological Society.p>

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

<p>MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.p><p>RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.p><p>AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).p><p>
p>

Availability of stage at diagnosis, cancer treatment delay and compliance with cancer guidelines as cancer registry indicators for cancer care in Europe:Results of EUROCHIP-3 survey

EUROCHIP (European Cancer Health Indicators Project) focuses on understanding inequalities in the cancer burden, care and survival by the indicators "stage at diagnosis," "cancer treatment delay" and "compliance with cancer guidelines" as the most important indicators. Our study aims at providing insight in whether cancer registries collect well-defined variables to determine these indicators in a comparative way. Eighty-six general European population-based cancer registries (PBCR) from 32 countries responded to the questionnaire, which was developed by EUROCHIP in collaboration with ENCR (European Network of Cancer Registries) and EUROCOURSE. Only 15% of all the PBCR in EU had all three indicators available. The indicator "stage at diagnosis" was gathered for at least one cancer site by 81% (using TNM in 39%). Variables for the indicator "cancer treatment delay" were collected by 37%. Availability of type of treatment (30%), surgery date (36%), starting date of radiotherapy (26%) and starting date of chemotherapy (23%) resulted in 15% of the PBCRs to be able to gather the indicator "compliance to guidelines". Lack of data source access and qualified staff were the major reasons for not collecting all the variables. In conclusion, based on self-reporting, a few of the participating PBCRs had data available which could be used for clinical audits, evaluation of cancer care projects, survival and for monitoring national cancer control strategies. Extra efforts should be made to improve this very efficient tool to compare cancer burden and the effects of the national cancer plans over Europe and to learn from each other. © 2012 UICC.

Accessibility and availability of smoking-related associations in smokers

<p>A free association test was used in the present study to examine the availability and accessibility of positive vs negative smoking-related information in the long-term memories of smokers. Participants were asked to generate smoking-related associations across a 4-minute interval. Although smokers generated more positive smoking-associations than non-smokers, both groups produced a greater number of negative than positive associations per se. Of particular interest was the finding that whilst the ratio of positive/negative associations generated was constant across time in non-smokers, this ratio varied in smokers. Specifically, smokers generated proportionately more of their available positive associations and proportionately less of their negative associations in the early time interval. It is suggested that these results not only indicate a greater availability of positive smoking-associations in smokers compared to non-smokers, but also a greater accessibility too. It is proposed that positive smoking associations are more automatically activated than negative associations in smokers, even though they have generally more negative associations available.p>

Manipulation of intracellular glycerol and erythritol enhances germination of conidia at low water availability

The insect pathogen Beauveria bassiana, Metarhizium anisopliae and Paecilomyces farinosos can be effective biocontrol agents when relative humidity (RH) is close to 100%. At reduced water availability, germination of propagules, and therefore host infection, cannot occur. Cultures of B. bassiana, M. anisopliae and P. farinosus were grown under different conditions to obtain conidia with a modified polyol and trehalose content. Conidia with higher intracellular concentrations of glycerol and erythritol germinated both more quickly and at lower water activity (a(w)) than those from other treatments. In contrast, conidia containing up to 235.7 mg trehalose g-1 germinated significantly (P < 0 05) more slowly than those with an equivalent polyol content but less trehalose, regardless of water availability. Conidia from control treatments did not germinate below 0.951 - 0.935 a(w) (≡ 95.1 - 93.5% RH). In contrast, conidia containing up to 164.6 mg glycerol plus erythritol g-1 germinated down to 0.887 a(w) (≡ 88.7% RH). These conidia germinated below the water availability at which mycelial growth ceases (0.930 - 0.920 a(w)). Germ tube extension rates reflected the percentage germination of conidia, so the most rapid germ tube growth occurred after treatments which produced conidia containing the most glycerol and erythritol. This study shows for the first time that manipulating polyol content can extend the range of water availability over which fungal propagules can germinate. Physiological manipulation of conidia may improve biological control of insect pests in the field.

Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015: elaboration and explanation

<p>Protocols of systematic reviews and meta-analyses allow for planning and documentation of review methods, act as a guard against arbitrary decision making during review conduct, enable readers to assess for the presence of selective reporting against completed reviews, and, when made publicly available, reduce duplication of efforts and potentially prompt collaboration. Evidence documenting the existence of selective reporting and excessive duplication of reviews on the same or similar topics is accumulating and many calls have been made in support of the documentation and public availability of review protocols. Several efforts have emerged in recent years to rectify these problems, including development of an international register for prospective reviews (PROSPERO) and launch of the first open access journal dedicated to the exclusive publication of systematic review products, including protocols (BioMed Central's Systematic Reviews). Furthering these efforts and building on the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines, an international group of experts has created a guideline to improve the transparency, accuracy, completeness, and frequency of documented systematic review and meta-analysis protocols--PRISMA-P (for protocols) 2015. The PRISMA-P checklist contains 17 items considered to be essential and minimum components of a systematic review or meta-analysis protocol.This PRISMA-P 2015 Explanation and Elaboration paper provides readers with a full understanding of and evidence about the necessity of each item as well as a model example from an existing published protocol. This paper should be read together with the PRISMA-P 2015 statement. Systematic review authors and assessors are strongly encouraged to make use of PRISMA-P when drafting and appraising review protocols.p>

The histone demethylase JMJD2A/KDM4A links ribosomal RNA transcription to nutrients and growth factors availability

<p>The interplay between methylation and demethylation of histone lysine residues is an essential component of gene expression regulation and there is considerable interest in elucidating the roles of proteins involved. Here we report that histone demethylase KDM4A/JMJD2A, which is involved in the regulation of cell proliferation and is overexpressed in some cancers, interacts with RNA Polymerase I, associates with active ribosomal RNA genes and is required for serum-induced activation of rDNA transcription. We propose that KDM4A controls the initial stages of transition from 'poised', non-transcribed rDNA chromatin into its active form. We show that PI3K, a major signalling transducer central for cell proliferation and survival, controls cellular localization of KDM4A and consequently its association with ribosomal DNA through the SGK1 downstream kinase. We propose that the interplay between PI3K/SGK1 signalling cascade and KDM4A constitutes a mechanism by which cells adapt ribosome biogenesis level to the availability of growth factors and nutrients.p>

Availability and transfer to grain of As, Cd, Cu, Ni, Pb and Zn in a barley agri-system: Impact of biochar, organic and mineral fertilizers

<p>With biochar becoming an emerging soil amendment and a tool to mitigate climate change, there are only a few studies documenting its effects on trace element cycling in agriculture. Zn and Cu are deficient in many human diets, whilst exposures to As, Pb and Cd need to be decreased. Biochar has been shown to affect many of them mainly at a bench or greenhouse scale, but field research is not available. In our experiment we studied the impact of biochar, as well as its interactions with organic (compost and sewage sludge) and mineral fertilisers (NPK and nitrosulfate), on trace element mobility in a Mediterranean agricultural field (east of Madrid, Spain) cropped with barley. At harvesting time, we analysed the soluble fraction, the available fraction (assessed with the diffusive gradients in thin gels technique, DGT) and the concentration of trace elements in barley grain. No treatment was able to significantly increase Zn, Cu or Ni concentration in barley grain, limiting the application for cereal fortification. Biochar helped to reduce Cd and Pb in grain, whereas As concentration slightly increased. Overall biochar amendments demonstrated a potential to decrease Cd uptake in cereals, a substantial pathway of exposure in the Spanish population, whereas mineral fertilisation and sewage sludge increased grain Cd and Pb. In the soil, biochar helped to stabilise Pb and Cd, while marginally increasing As release/mobilisation. Some of the fertilisation practises or treatments increased toxic metals and As solubility in soil, but never to an extent high enough to be considered an environmental risk. Future research may try to fortify Zn, Cu and Ni using other combinations of organic amendments and different parent biomass to produce enriched biochars.p>

Effect of weather and the hybrid energy storage on the availability of standalone microgrid

<p>This paper presents a model for availability analysis of standalone hybrid microgrid. The microgrid used in the study consists of wind, solar storage and diesel generator. Boolean driven Markov process is used to develop the availability of the system in the proposed method. By modifying the developed model, the relationship between the availability of the system with the fine (normal) weather and disturbed (stormy) weather durations are analyzed. Effects of different converter technologies on the availability of standalone microgrid were investigated and the results have shown that the availability of microgrid increased by 5.80 % when a storage system is added. On the other hand, the availability of standalone microgrid could be overestimated by 3.56 % when weather factor is neglected. In the same way 200, 500 and 1000 hours of disturbed weather durations reduced the availability of the system by 5.36%, 9.73% and 13.05 %, respectively. In addition, the hybrid energy storage cascade topology with a capacitor in the middle maximized the system availability.p>

Using Vibrational Infrared Biomolecular Spectroscopy to Detect Heat-Induced Changes of Molecular Structure in Relation to Nutrient Availability of Prairie Whole Oat Grains on a Molecular Basis

Background To our knowledge, there is little study on the interaction between nutrient availability and molecular structure changes induced by different processing methods in dairy cattle. The objective of this study was to investigate the effect of heat processing methods on interaction between nutrient availability and molecular structure in terms of functional groups that are related to protein and starch inherent structure of oat grains with two continued years and three replication of each year. Method The oat grains were kept as raw (control) or heated in an air-draft oven (dry roasting: DO) at 120 °C for 60 min and under microwave irradiation (MIO) for 6 min. The molecular structure features were revealed by vibrational infrared molecular spectroscopy. Results The results showed that rumen degradability of dry matter, protein and starch was significantly lower (P <0.05) for MIO compared to control and DO treatments. A higher protein α-helix to β-sheet and a lower amide I to starch area ratio were observed for MIO compared to DO and/or raw treatment. A negative correlation (−0.99, P < 0.01) was observed between α-helix or amide I to starch area ratio and dry matter. A positive correlation (0.99, P < 0.01) was found between protein β-sheet and crude protein. Conclusion The results reveal that oat grains are more sensitive to microwave irradiation than dry heating in terms of protein and starch molecular profile and nutrient availability in ruminants.