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Keenan K.,Queens University of Belfast | Mcginnity P.,University College Cork | Cross T.F.,University College Cork | Crozier W.W.,Agri Food and Biosciences Institute | Prodohl P.A.,Queens University of Belfast
Methods in Ecology and Evolution

Summary: We present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (θ, GST) and population differentiation statistics (DJost, GST ', χ2 test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective. diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F-statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co-dominant marker types (e.g. allozymes, SNPs). Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity. Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis. © 2013 British Ecological Society. Source

Barry C.D.,Queens University of Belfast | Barry C.D.,Agri Food and Biosciences Institute | Foy R.H.,Queens University of Belfast
Journal of Environmental Quality

Lowland waters in Northern Ireland experience elevated agricultural phosphorus (P) inputs, and in response a variety of control measures targeting farm nutrient management have been implemented. Their efficacy in lowering nitrogen (N) and P exports and improving water quality is examined in 40 headwater streams from 1990 to 2009, and to 2014 for 24 of these. Over this period manure production in the study catchments declined by 7%, but regional chemical fertilizer inputs declined by 37% for N and 79% for P, and the regional nutrient surplus was lowered by 18% for N and 49% for P. Diminished pollution by organic wastes meant that 85% of streams exhibited chemistry suitable for salmonids in 2009 compared to 40% in 1990. Flow-weighted mean concentrations (FWMCs) of nutrients declined between 1990 and 2009, and their correlations with catchment stocking rates became stronger over time. For catchments with manure inputs < 16.6 kg P ha-1, total P and nitrate FWMCs declined from 123 ± 19 μg P L-1 and 1.92 ± 0.5 mg N L-1 in 1990 at rates of 2.2 ± 0.5 and 30 ± 10 μg L-1 yr-1, respectively. For catchments with higher manure inputs the respective rates of decline were greater at 5.8 ± 1.0 μg P L-1 yr-1 and 160 ± 20 μg N L-1 yr-1 from 1990 concentrations of 270 ± 25 μg P L-1 and 5.99 ± 0.4 mg N L-1. Although now lower, P concentrations in the more highly stocked catchments still exceed regional nutrient standards so that the identification of further factors impinging on nutrient losses is critical if such standards are to be achieved. © American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. 5585 Guilford Rd., Madison, WI 53711 USA. All rights reserved. Source

Marassi C.D.,Federal University of Fluminense | Medeiros L.,Federal University of Fluminense | McNair J.,Agri Food and Biosciences Institute | Lilenbaum W.,Federal University of Fluminense
Acta Tropica

The objective was to evaluate the use of two indirect IgG-ELISA tests (with recombinant proteins MPB70 or MPB83, respectively, as capture antigens) as confirmatory tests for diagnosis of bovine tuberculosis in a herd of naturally infected dairy cows. Results for ELISA-MPB70 and ELISA-MPB83 were similar (kappa statistic. =0.92) on Days 0 (day of intradermal injection with purified protein derivatives, PPD), 7, and 21. The kappa statistic between ELISA and the Comparative Intradermal Tuberculin Test, as well as ELISA sensitivity and specificity (relative to culture or PCR as standards) were: 0.7, 34.4% and 75% on Day 0; 0.25, 53.8% and 66.6% on Day 7; and 0.01, 1.8% and 77.7% on Day 21, respectively. In conclusion, although ELISAs using MPB70 or MPB83 as antigens were not reliable indicators of infection status, especially on Days 7 and 21, they were of potential value as complementary tools to intradermal PPD testing. © 2011 Elsevier B.V. Source

McLea L.,Queens University of Belfast | Ball M.E.E.,Queens University of Belfast | Ball M.E.E.,Agri Food and Biosciences Institute | Kilpatrick D.,Agri Food and Biosciences Institute | Elliott C.,Queens University of Belfast
British Poultry Science

1. Crude glycerol from biodiesel production was offered ad libitum to broiler chickens in a 21-d feeding and digestibility trial. The study was designed as a 3*2+ factorial design with 3 concentrations (33, 67, 100 g/kg) of glycerol from 2 sources, A and B (PRS Environmental Ltd and John Thompson and Sons Ltd) and a control diet. The diets were formulated to contain apparent metabolisable energy (AME) of 12.95 MJ/kg (assuming 14.6 MJ/kg for glycerol). 2. No significant interactions occurred, so only the main effects were discussed. At 7-14 d, feed conversion ratio (FCR) showed a significant linear response with increased glycerol inclusion. However quadratic responses on FCR were observed for the 21-28 d period and 7-28 d. 3. Glycerol digestibility was significantly greater with birds offered the 67 g/kg and 100 g/kg glycerolbased diets in contrast to the digestibility of 33 g/kg glycerol-based diets. 4. Glycerol inclusion level also had an effect on AME, which increased linearly with increasing glycerol inclusion. Birds offered the diets containing glycerol also required less energy per unit gain in contrast to birds offered the control diet. 5. When examining the effect of source of glycerol, source A glycerol resulted in the highest AME (15.20 vs. 14.72 MJ/kg). There was no significant effect of glycerol source on the other performance parameters. 6. Glycerol digestibility was significantly greater with glycerol from source B (John Thompson and Sons, Ltd) with a mean value of 0.848 in contrast to source A (PRS Environmental), which had a somewhat lower mean glycerol digestibility of 0.757. 7. In conclusion, glycerol source did not affect performance and increasing level of glycerol improved FCR, with 67 g/kg inclusion resulting in the most efficient conversion of feed to gain without any negative effects upon nutrient digestibility. © 2011 British Poultry Science Ltd. Source

Whelan A.O.,Veterinary Laboratories Agency | Clifford D.,Veterinary Laboratories Agency | Upadhyay B.,Veterinary Laboratories Agency | Breadon E.L.,Agri Food and Biosciences Institute | And 3 more authors.
Journal of Clinical Microbiology

The tuberculin skin test has been used for the diagnosis of bovine and human tuberculosis (TB) for over a hundred years. However, the specificity of the test is compromised by vaccination with the Mycobacterium bovis-derived vaccine strain bacille Calmette-Guérin (BCG). Since current promising vaccines against bovine TB are based on heterologous prime-boost combinations that include BCG, there is a need for diagnostic tests for differentiating infected from vaccinated animals (DIVA). The application of antigens such as ESAT-6 and CFP-10 for DIVA has so far been realized largely through their application in the blood-based gamma interferon release assay. In the current study, we have reassessed the potential of such antigens as skin test reagents for DIVA in cattle. A cocktail of the Mycobacterium tuberculosis complex recombinant protein antigens ESAT-6, CFP-10, MPB70, and MPB83 elicited delayed-type hypersensitivity (DTH) skin test responses in 78% of naturally infected tuberculin-positive cattle. Importantly, this cocktail induced no skin responses in BCG-vaccinated cattle despite them being sensitized for strong tuberculin responses. Further optimization of skin test antigen combinations identified that the inclusion of Rv3615c (Mb3645c) enhanced skin test sensitivity in naturally infected cattle without compromising specificity. In addition, we demonstrate for the first time the utility of synthetic peptides as promising skin test antigens for bovine TB for DIVA. Our data provide a promising basis for the future development of skin tests for DIVA with practical relevance for TB diagnosis in both veterinary and clinical settings. Copyright © 2010, American Society for Microbiology. All Rights Reserved. Source

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