Municipal sludge as source of nitrogen and phosphorus in perennial pasture Eragrostis curvula production: Agronomic benefits and environmental impacts

Land application of sludge has been shown to improve soil properties and aid crop growth, but the possibility of constituent nutrients such as nitrogen and phosphorus reaching environmentally toxic levels has caused governing authorities to set limits to how much sludge can be applied to agronomic land. The high nitrogen utilisation potential of pasture grasses suggests that more sludge can be used in this cropping system without the risk of excess nitrates. This study investigates the effect of exceeding the South African sludge application limit on hay yield, soil nitrates and phosphorus. Field plots were arranged in a complete block design comprising 4 replications of 4 treatments planted to Eragrostis curvula. The treatments consisted of 0, 4, 8 and 16 Mg∙ha-1 anaerobically digested sludge. Soil samples were collected before treatment application and at the end of each growing season for N, P, NO3-, NH4+, and Bray-1P analyses. Plant samples were collected at flowering stage for hay yield and N and P uptake determination. Statistical analyses were conducted using analysis of variance (ANOVA) and general linear model (GLM) procedures of Windows SAS 9.0 to evaluate the effect of sludge application rates on hay yield. Results over 4 growing seasons indicate that exceeding the recommended limit increased hay yield by 4% in a dry season (11.7 vs. 12.36 Mg∙ha-1) and by 16% in a wet season (14.19 vs. 17.31 Mg∙ha-1) and also increased nitrogen uptake by 15%. Sludge applied at double the recommended limit did not cause the accumulation of nitrate and ammonium in the soil, however, both total and Bray-1P were doubled. The study shows that the potential long-term environmental risk of doubling the sludge application rate norm would be from labile P accumulation in the soil profile despite a sludge P:Fe molar ratio of less than unity.Keywords: sludge, Eragrostis curvula, nitrogen, phosphorus, leachin

Comparison of methods for determining unsaturated hydraulic conductivity in the wet range to evaluate the sensitivity of wetting front detectors

The design of passive lysimeters or wetting front detectors determines the tensions at which they collect a water sample from an unsaturated soil. When deployed in the field to help manage irrigation, it is necessary to know the minimum flux of water that can be sampled by a passive lysimeter and how this relates to the drainage flux at field capacity. This requires a good estimate of the unsaturated hydraulic conductivity characteristic, K(h), in the wet range (< 10 kPa). We compared various field, laboratory and theoretical approaches for obtaining the K(h) function and compared these to a reference K(h) function derived by applying inverse modelling approaches to field drainage experimental data. The Van Genuchten model and three of the pedotransfer models produced K(h) functions with a root mean square error of less than 5% compared to the reference, and appear to be simple methods of obtaining a reasonable estimate of unsaturated hydraulic conductivity. However, despite the goodness of fit, there can be a 10-fold difference in conductivity at a given tension < 10 kPa estimated from the different methods. Moreover, water content at field capacity depends entirely on whether field capacity is defined as time elapsed after saturation, a set tension or a minimum flux.Keywords: inverse modelling, instantaneous profile method, pedotransfer functions, wetting front detector, field capacity, HYDRUS-2

Irrigation scheduling research: South African experiences and future prospects

Many scheduling approaches have been developed with Water Research Commission funding over the past 4 decades and deployed with varying levels of success; 2 approaches have won prestigious international awards. Soil-based approaches which include measurement of matric potential (tensiometry), water content (neutron probes, capacitance sensors) and depth of wetting (wetting front detectors) have been relatively well accepted by farmers. Atmospheric-based approaches apply, through biophysical modelling of the soil-crop-atmosphere system, thermodynamic limits to the amount of water that can evaporate from a cropped surface under particular environmental conditions. Modelling approaches have been quite empirical or somewhat more mechanistic, generic or crop specific, with pre-programmed (e.g. irrigation calendars) or real-time output. Novel mechanisms have been developed to deliver recommendations to farmers, including resource-poor irrigators. Although general adoption of objective irrigation scheduling in South Africa is still low, the high cost of electricity and nitrogen, and scarcity of water is reviving the interest of consultants and irrigators in the application of these tools to use water more efficiently. Where adoption has been relatively high, intensive support and farmer-researcher-consultant interactions have been key contributing factors. We propose 4 avenues in the R&D domain to ensure responsible water utilisation. Firstly, there is a need to continue to advance existing soil-water measurement technology; and secondly, to further develop new and emerging technologies, like the use of remote sensing. Thirdly, the user-friendliness should be improved as should systems that support existing scheduling tools; and finally, we need to appreciate that farmers are intuitively adaptive managers, and we need to develop simple monitoring tools and conceptual frameworks that enable structured learning.Keywords: BEWAB; CANESIM; PUTU; SWB; wetting front detecto

A double-ended queue with catastrophes and repairs, and a jump-diffusion approximation

Consider a system performing a continuous-time random walk on the integers, subject to catastrophes occurring at constant rate, and followed by exponentially-distributed repair times. After any repair the system starts anew from state zero. We study both the transient and steady-state probability laws of the stochastic process that describes the state of the system. We then derive a heavy-traffic approximation to the model that yields a jump-diffusion process. The latter is equivalent to a Wiener process subject to randomly occurring jumps, whose probability law is obtained. The goodness of the approximation is finally discussed.Comment: 18 pages, 5 figures, paper accepted by "Methodology and Computing in Applied Probability", the final publication is available at http://www.springerlink.co

Developmental morphology of cover crop species exhibit contrasting behaviour to changes in soil bulk density, revealed by X-ray computed tomography

Plant roots growing through soil typically encounter considerable structural heterogeneity, and local variations in soil dry bulk density. The way the in situ architecture of root systems of different species respond to such heterogeneity is poorly understood due to challenges in visualising roots growing in soil. The objective of this study was to visualise and quantify the impact of abrupt changes in soil bulk density on the roots of three cover crop species with contrasting inherent root morphologies, viz. tillage radish (Raphanus sativus), vetch (Vicia sativa) and black oat (Avena strigosa). The species were grown in soil columns containing a two-layer compaction treatment featuring a 1.2 g cm-3 (uncompacted) zone overlaying a 1.4 g cm-3 (compacted) zone. Three-dimensional visualisations of the root architecture were generated via X-ray computed tomography, and an automated root-segmentation imaging algorithm. Three classes of behaviour were manifest as a result of roots encountering the compacted interface, directly related to the species. For radish, there was switch from a single tap-root to multiple perpendicular roots which penetrated the compacted zone, whilst for vetch primary roots were diverted more horizontally with limited lateral growth at less acute angles. Black oat roots penetrated the compacted zone with no apparent deviation. Smaller root volume, surface area and lateral growth were consistently observed in the compacted zone in comparison to the uncompacted zone across all species. The rapid transition in soil bulk density had a large effect on root morphology that differed greatly between species, with major implications for how these cover crops will modify and interact with soil structure

Genome-wide methylation analysis identifies genes silenced in non-seminoma cell lines

Silencing of genes by DNA methylation is a common phenomenon in many types of cancer. However, the genome wide effect of DNA methylation on gene expression has been analysed in relatively few cancers. Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. Previous analyses have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. The genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours’ biology have not yet been established. In this study, genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data from primary tumours to address this question. Genome methylation was analysed using the Illumina infinium HumanMethylome450 bead chip system and gene expression was analysed using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Regulation by methylation was confirmed by demethylation using 5-aza-2-deoxycytidine and reverse transcription–quantitative PCR. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested played a role in their silencing in yolk sac tumour cells and many of these genes were also differentially expressed in primary tumours. Genes silenced by methylation in the various GCT cell lines were identified. Several pluripotency-associated genes were identified as a major functional group of silenced genes

Mutagenesis Objective Search and Selection Tool (MOSST): an algorithm to predict structure-function related mutations in proteins

<p>Abstract</p> <p>Background</p> <p>Functionally relevant artificial or natural mutations are difficult to assess or predict if no structure-function information is available for a protein. This is especially important to correctly identify functionally significant non-synonymous single nucleotide polymorphisms (nsSNPs) or to design a site-directed mutagenesis strategy for a target protein. A new and powerful methodology is proposed to guide these two decision strategies, based only on conservation rules of physicochemical properties of amino acids extracted from a multiple alignment of a protein family where the target protein belongs, with no need of explicit structure-function relationships.</p> <p>Results</p> <p>A statistical analysis is performed over each amino acid position in the multiple protein alignment, based on different amino acid physical or chemical characteristics, including hydrophobicity, side-chain volume, charge and protein conformational parameters. The variances of each of these properties at each position are combined to obtain a global statistical indicator of the conservation degree of each property. Different types of physicochemical conservation are defined to characterize relevant and irrelevant positions. The differences between statistical variances are taken together as the basis of hypothesis tests at each position to search for functionally significant mutable sites and to identify specific mutagenesis targets. The outcome is used to statistically predict physicochemical consensus sequences based on different properties and to calculate the amino acid propensities at each position in a given protein. Hence, amino acid positions are identified that are putatively responsible for function, specificity, stability or binding interactions in a family of proteins. Once these key functional positions are identified, position-specific statistical distributions are applied to divide the 20 common protein amino acids in each position of the protein's primary sequence into a group of functionally non-disruptive amino acids and a second group of functionally deleterious amino acids.</p> <p>Conclusions</p> <p>With this approach, not only conserved amino acid positions in a protein family can be labeled as functionally relevant, but also non-conserved amino acid positions can be identified to have a physicochemically meaningful functional effect. These results become a discriminative tool in the selection and elaboration of rational mutagenesis strategies for the protein. They can also be used to predict if a given nsSNP, identified, for instance, in a genomic-scale analysis, can have a functional implication for a particular protein and which nsSNPs are most likely to be functionally silent for a protein. This analytical tool could be used to rapidly and automatically discard any irrelevant nsSNP and guide the research focus toward functionally significant mutations. Based on preliminary results and applications, this technique shows promising performance as a valuable bioinformatics tool to aid in the development of new protein variants and in the understanding of function-structure relationships in proteins.</p