A note on the Hybrid Soil Moisture Deficit Model v2.0

peer-reviewedThe Hybrid Soil Moisture Deficit (HSMD) model has been used for a wide range of applications, including modelling of grassland productivity and utilisation, assessment of agricultural management opportunities such as slurry spreading, predicting nutrient emissions to the environment and risks of pathogen transfer to water. In the decade since its publication, various ad hoc modifications have been developed and the recent publication of the Irish Soil Information System has facilitated improved assessment of the spatial soil moisture dynamics. In this short note, we formally present a new version of the model (HSMD2.0), which includes two new soil drainage classes, as well as an optional module to account for the topographic wetness index at any location. In addition, we present a new Indicative Soil Drainage Map for Ireland, based on the Irish Soil Classification system, developed as part of the Irish Soil Information System

Pathways for Nutrient Loss to Water; Slurry and Fertilizer Spreading

End of project reportThere are almost 150,000 farms in Ireland and these contribute substantial quantities of N and P to inland and coastal waters. Some of these nutrients are carried from wet soils by overland flow and by leaching from dry soils. Farm practice can reduce the loss from farms by judicious management of nutrients. Improvements are required to diminish export of nutrients without impairing operations on the farm. Literature regarding nutrient loss from agriculture was reviewed in this project and maps were prepared to predict best slurry spreading times around Ireland. Two further maps were prepared to show slurry storage requirement on farms

Agriculture, meteorology and water quality in Ireland: a regional evaluation of pressures and pathways of nutrient loss to water

peer-reviewedThe main environmental impact of Irish agriculture on surface and ground water quality is the potential transfer of nutrients to water. Soil water dynamics mediate the transport of nutrients to water, and these dynamics in turn depend on agro-meteorological conditions, which show large variations between regions, seasons and years. In this paper we quantify and map the spatio-temporal variability of agro-meteorological factors that control nutrient pressures and pathways of nutrient loss. Subsequently, we evaluate their impact on the water quality of Irish rivers. For nitrogen, pressure and pathways factors coincide in eastern and southern areas, which is reflected in higher nitrate levels of the rivers in these regions. For phosphorus, pathway factors are most pronounced in north-western parts of the country. In south-eastern parts, high pressure factors result in reduced biological water quality. These regional differences require that farm practices be customised to reflect the local risk of nutrient loss to water. Where pathways for phosphorus loss are present almost year-round—as is the case in most of the north-western part of the country—build-up of pressures should be prevented, or ameliorated where already high. In south-eastern areas, spatio-temporal coincidence of nutrient pressures and pathways should be prevented, which poses challenges to grassland management

The Effects of Peripheral Canopy on DGPS Performance on Forest Roads

The purpose of this study was to evaluate differential global positioning system (DGPS) positional accuracy on Irish forest roads with typical peripheral canopies. The peripheral canopy obstruction at 20 forest road sites in Roundwood State Forest, was determined using a hand-held clinometer and magnetic compass. This simple field technique permitted quantification of the canopy obstruction using graphical means and resulted in a graphical skyplot of each site. The equipment, one Trimble ProXRS DGPS unit and two Trimble 4000SSi units permitted determination of the DGPS accuracy (average of 2.9 m) and precision (average of 2.1 m) with a range of peripheral canopies. DGPS performance was quantified in terms of the average absolute error in positional dilution of precision (PDOP) (DPDOP = 1.6). The relationship between DPDOP and percentage of open sky was found to be statistically significant (r = 0.706, r = 0.001). Statistical analysis also indicated a strong relationship between relative precision and DPDOP (r = 0.796, r = 0.000). Satellite constellation in the measurement period was not the sole factor affecting DGPS useability. Three distinct classes of peripheral obstruction at road sites were defined (Class I: 100-66 %; Class II: 65-33 %; Class III: 32-0 % obstruction) and it was found that both DGPS accuracy (3.70 m, 3.23 m, 1.91 m, respectively) and precision (4.10 m, 2.43 m, 0.83 m, respectively) improved with decreasing peripheral obstruction. These classes may be used as a means of predicting signal attenuation which might be expected under particular forest canopy conditions elsewhere

Visual drainage assessment: A standardised visual soil assessment method for use in land drainage design in Ireland

peer-reviewedThe implementation of site-specific land drainage system designs is usually disregarded by landowners in favour of locally established ‘standard practice’ land drainage designs. This is due to a number of factors such as a limited understanding of soil–water interactions, lack of facilities for the measurement of soil’s physical or hydrological parameters and perceived time wastage and high costs. Hence there is a need for a site-specific drainage system design methodology that does not rely on inaccessible, time-consuming and/or expensive measurements of soil physical or hydrological properties. This requires a standardised process for deciphering the drainage characteristics of a given soil in the field. As an initial step, a new visual soil assessment method, referred to as visual drainage assessment (VDA), is presented whereby an approximation of the permeability of specific soil horizons is made using seven indicators (water seepage, pan layers, texture, porosity, consistence, stone content and root development) to provide a basis for the design of a site-specific drainage system. Across six poorly drained sites (1.3 ha to 2.6 ha in size) in south-west Ireland a VDA-based design was compared with (i) an ideal design (utilising soil physical measurements to elucidate soil hydraulic parameters) and (ii) a standard design (0.8 m deep drains at a 15 m spacing) by model estimate of water table control and rainfall recharge/drain discharge capacity. The VDA method, unlike standard design equivalents, provided a good approximation of an ideal (from measured hydrological properties) design and prescribed an equivalent land drainage system in the field. Mean modelled rainfall recharge/drain discharge capacity for the VDA (13.3 mm/day) and ideal (12.0 mm/day) designs were significantly higher (P < 0.001, s.e. 1.42 mm/day) than for the standard designs (0.5 mm/day), when assuming a design minimum water table depth of 0.45 m

Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.

MOTIVATION: Protein-protein interactions (PPI) play a crucial role in our understanding of protein function and biological processes. The standardization and recording of experimental findings is increasingly stored in ontologies, with the Gene Ontology (GO) being one of the most successful projects. Several PPI evaluation algorithms have been based on the application of probabilistic frameworks or machine learning algorithms to GO properties. Here, we introduce a new training set design and machine learning based approach that combines dependent heterogeneous protein annotations from the entire ontology to evaluate putative co-complex protein interactions determined by empirical studies. RESULTS: PPI annotations are built combinatorically using corresponding GO terms and InterPro annotation. We use a S.cerevisiae high-confidence complex dataset as a positive training set. A series of classifiers based on Maximum Entropy and support vector machines (SVMs), each with a composite counterpart algorithm, are trained on a series of training sets. These achieve a high performance area under the ROC curve of ≤0.97, outperforming go2ppi-a previously established prediction tool for protein-protein interactions (PPI) based on Gene Ontology (GO) annotations. AVAILABILITY AND IMPLEMENTATION: https://github.com/ima23/maxent-ppi. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Pathways for nutrient loss to water with emphasis on phosphorus

Teagasc wishes to acknowledge the support of the Environmental Research Technological Development and Innovation (ERTDI) Programme under the Productive Sector Operational Programme which was financed by the Irish Government under the National Development Plan 2000-2006.End of project reportThe main objective of this project was to study phosphorus (P) loss from agricultural land under a range of conditions in Ireland, to quantify the main factors influencing losses and make recommendations on ways to reduce these losses. This report is a synthesis of the main conclusions and recommendations from the results of the studies. The final reports from the individual sub-projects in this project are available from the EPA (www.epa.ie).Environmental Protection Agenc

Assessment of the Environmental Impact of Food Consumption in Ireland-Informing a Transition to Sustainable Diets

Dietary changes are required to mitigate the climatic impact of food consumption. Food consumption databases can support the development of sustainable food based dietary guidelines (SFBDG) when linked to environmental indicators. An improved knowledge base is crucial to the transition to sustainable diets, and multiple environmental indicators should be considered to ensure this transition is evidence based and accounts for trade-offs. The current study aimed to quantify the environmental impact of daily diets across population groups in Ireland. Nationally representative food consumption surveys for Irish children (NCFSII; 2017-2018), teenagers (NTFSII; 2019-2020), and adults (NANS; 2008-2010) were used in this analysis. Blue water use (L) and greenhouse gas emissions (GHGe; kgCO2eq) were assigned at food level to all surveys. Cropland (m2), nitrogen (kgN/t), and phosphorous use (kgP/t) were assigned at the agricultural level for adults. Multiple linear regressions, Spearman correlations, and ANCOVAs with Bonferroni corrections were conducted. Higher environmental impact diets were significantly associated with demographic factors such as age, education status, residential location, and sex, but these associations were not consistent across population groups. The median greenhouse gas emissions were 2.77, 2.93, and 4.31 kgCO2eq, and freshwater use per day was 88, 144, and 307 L for children, teenagers, and adults, respectively. The environmental impact of the Irish population exceeded the planetary boundary for GHGe by at least 148% for all population groups, however the boundary for blue water use was not exceeded. Meat and meat alternatives (27-44%); eggs, dairy, and dairy alternatives (15-21%); and starchy staples (10-20%) were the main contributors to GHGe. For blue water use, the highest contributors were meat and meat alternatives in children; savouries, snacks, nuts, and seeds in teenagers; and eggs, dairy, and dairy alternatives in adults (29-52%). In adults, cropland use, nitrogen use, and phosphorous use exceeded planetary boundaries by 277-382%. Meat, dairy, and grains were the main contributors to cropland, nitrogen, and phosphorous use (79-88%). The quantified environmental impact of Irish diets provides a baseline analysis, against which it will be possible to track progress towards sustainable diets, and the basis for the development of Sustainable Food Based Dietary Guidelines in Ireland

Old Drugs To Treat Resistant Bugs: Methicillin-Resistant Staphylococcus aureus Isolates with mecC Are Susceptible to a Combination of Penicillin and Clavulanic Acid.

β-Lactam resistance in methicillin-resistant Staphylococcus aureus (MRSA) is mediated by the expression of an alternative penicillin-binding protein 2a (PBP2a) (encoded by mecA) with a low affinity for β-lactam antibiotics. Recently, a novel variant of mecA, known as mecC, was identified in MRSA isolates from both humans and animals. In this study, we demonstrate that mecC-encoded PBP2c does not mediate resistance to penicillin. Rather, broad-spectrum β-lactam resistance in MRSA strains carrying mecC (mecC-MRSA strains) is mediated by a combination of both PBP2c and the distinct β-lactamase encoded by the blaZ gene of strain LGA251 (blaZLGA251), which is part of mecC-encoding staphylococcal cassette chromosome mec (SCCmec) type XI. We further demonstrate that mecC-MRSA strains are susceptible to the combination of penicillin and the β-lactam inhibitor clavulanic acid in vitro and that the same combination is effective in vivo for the treatment of experimental mecC-MRSA infection in wax moth larvae. Thus, we demonstrate how the distinct biological differences between mecA- and mecC-encoded PBP2a and PBP2c have the potential to be exploited as a novel approach for the treatment of mecC-MRSA infections.This work was supported by a Medical Research Council (MRC) Partnership Grant (G1001787/1) held between the Department of Veterinary Medicine, University of Cambridge (M. A. H.), the School of Clinical Medicine, University of Cambridge (S. J. P.), the Moredun Research Institute (R. N. Z.) and the Wellcome Trust Sanger Institute (J. P. and S. J. P.).This is the author accepted manuscript. The final version is available from American Society for Microbiology via http://dx.doi.org/10.1128/AAC.01469-1

Donor plasmids for phenotypically neutral chromosomal gene insertions in Enterobacteriaceae

Recombineering using bacteriophage lambda Red recombinase (λ-Red) uses homologous recombination to manipulate bacterial genomes and is commonly applied to disrupt genes to elucidate their function. This is often followed by the introduction of a wild-type copy of the gene on a plasmid to complement its function. This is often not, however, at a native copy number and the introduction of a chromosomal version of a gene can be a desirable solution to provide wild-type copy expression levels of an allele in trans. Here, we present a simple methodology based on the λ-Red-based 'gene doctoring' technique, where we developed tools used for chromosomal tagging in a conserved locus downstream of glmS and found no impact on a variety of important phenotypes. The tools described provide an easy, quick and inexpensive method of chromosomal modification for the creation of a library of insertion mutants to study gene function