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Keenan K.,Queen's 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.,Queen's University of Belfast
Methods in Ecology and Evolution | Year: 2013

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.


Kennedy R.J.,Agri Food and Biosciences Institute | Rosell R.,Agri Food and Biosciences Institute
Fisheries Management and Ecology | Year: 2012

A severe fish kill event caused by agricultural pollution impacted 2.4km of the River Blackwater, Northern Ireland, in August 2007. A post-kill monitoring programme sampled existing monitoring sites in the fish kill zone as well as upstream and downstream control sites. Post-kill monitoring in combination with historical background data facilitated an assessment of the extent and severity of the disturbance episode on local salmonid populations. Subsequent recovery patterns indicated that total salmonid abundance returned to control levels within 1year. Total salmonid biomass recovered within 2years, whereas brown trout age structure took up to 3years to return to background levels. Recovery dynamics were dominated by large-scale directional migrations rather than random local movements. This included an initial autumnal immigration of 0+ age class brown trout, Salmo trutta L., in late 2007 followed by spawning migrations of adult migratory salmonids. The significance of relatively rapid natural recovery patterns is discussed in the context of potential management options such as restocking. © 2011 Blackwell Publishing Ltd.


Muller C.,University College Dublin | Muller C.,Justus Liebig University | Laughlin R.J.,Agri Food and Biosciences Institute | Christie P.,Agri Food and Biosciences Institute | Watson C.J.,Agri Food and Biosciences Institute
Soil Biology and Biochemistry | Year: 2011

The effects of repeated synthetic fertilizer or cattle slurry applications at annual rates of 50, 100 or 200m3ha-1yr-1 over a 38 year period were investigated with respect to herbage yield, N uptake and gross soil N dynamics at a permanent grassland site. While synthetic fertilizer had a sustained and constant effect on herbage yield and N uptake, increasing cattle slurry application rates increased the herbage yield and N uptake linearly over the entire observation period. Cattle slurry applications, two and four times the recommended rate (50m3ha-1yr-1, 170kgNha-1), increased N uptake by 46 and 78%, respectively after 38 years. To explain the long-term effect, a 15N tracing study was carried out to identify the potential change in N dynamics under the various treatments. The analysis model evaluated process-specific rates, such as mineralization, from two organic-N pools, as well as nitrification from NH4 + and organic-N oxidation. Total mineralization was similar in all treatments. However, while in an unfertilized control treatment more than 90% of NH4 + production was related to mineralization of recalcitrant organic-N, a shift occurred toward a predominance of mineralization from labile organic-N in the cattle slurry treatments and this proportion increased with the increase in slurry application rate. Furthermore, the oxidation of recalcitrant organic-N shifted from a predominant NH4 + production in the control treatment, toward a predominant NO3 - production (heterotrophic nitrification) in the cattle slurry treatments. The concomitant increase in heterotrophic nitrification and NH4 + oxidation with increasing cattle slurry application rate was mainly responsible for the increase in net NO3 - production rate. Thus the increase in N uptake and herbage yield on the cattle slurry treatments could be related to NO3 - rather than NH4 + production. The 15N tracing study was successful in revealing process-specific changes in the N cycle in relationship to long-term repeated amendments. © 2011 Elsevier Ltd.


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 | Year: 2010

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.


O'Rourke S.M.,University College Dublin | Foy R.H.,Agri Food and Biosciences Institute | Watson C.J.,Agri Food and Biosciences Institute | Ferris C.P.,Agri Food and Biosciences Institute | Gordon A.,Agri Food and Biosciences Institute
Journal of Environmental Quality | Year: 2010

The increasing use of concentrate feedstuffs within Northern Ireland dairy systems has resulted in significant farm gate phosphorus (P) surpluses, and these have contributed to increased soil P levels and risk of P loss to overland flow. However, the P content of feed concentrates can be lowered without compromising animal performance. This study focuses on P losses from grassland and evaluates how adjusting the P content of manure impacts on the P composition and concentration in overland flow. Dairy cows were off ered diets containing 5.3 to 3.0 g P kg-1 dry matter (DM) and produced manures with a range of P contents. Manure was applied at a rate of 50 m3 ha-1 to 0.5-m2 grassland plots, and simulated rainfall (40 mm h -1) was applied repeatedly 2, 9, 28, and 49 d after during the summer, winter, and spring. Decreasing the P content in the diet, from the highest to the lowest P treatment (43%), produced aproportionately greater reduction in manure TP content (63%), but reductions were not exclusively in the water-soluble fraction. Following surface applications of manure, P concentrations in overland flow increased in all seasons (P < 0.001), while the greatest impact of varying the manure P content was most evident during the first simulated overland flow event. When diet P content was reduced from 5.4 to 3.0 g P kg-1 DM, a statistically significant reduction in runoff P concentration was observed in all seasons. Elevated P concentrations in overland flow were observed for 28 d in spring and 9 d in summer and winter. The large drop in P concentrations between simulated rainfall events on Day 2 and Day 9 suggests that increasing the time interval between manure application and the generation of overland flow has a greater impact on P losses than does varying the dietary P content. Copyright © 2010 by the American Society of Agronomy.


Kelly A.K.,University College Dublin | McGee M.,Teagasc | Crews D.H.,Colorado State University | Fahey A.G.,University College Dublin | And 2 more authors.
Journal of Animal Science | Year: 2010

This study examined the relationship of feed efficiency and performance with feeding behavior, blood metabolic variables, and various body composition measurements in growing beef heifers. Individual DMI and growth were measured in yearling Limousin × Holstein-Friesian heifers [n = 86; initial BW = 191.8 (SD = 37) kg] fed a TMR diet comprising 70:30 concentrate:corn silage on a DM basis (ME of 2.65 Mcal/kg of DM; DM of 580 g/kg) for 82 d. Meal duration (min/d) and meal frequency (events/d) were calculated for each animal on a daily basis using an Insentec computerized feeding system. Physical measurements as well as ultrasonic fat and muscle depths were recorded on 3 equally spaced occasions during the experimental period. Blood samples were collected by jugular venipuncture on 4 equally spaced occasions and analyzed for plasma concentrations of IGF-I, insulin, leptin, and various metabolites. Phenotypic residual feed intake (RFI) was calculated for all animals as the residuals from a multiple regression model regressing DMI on ADG and midtest BW 0.75. Overall, ADG, DMI, feed conversion ratio (FCR), and RFI were 1.51 (SD = 0.13), 6.74 (SD = 0.99), 4.48 (SD = 0.65), and 0.00 (SD = 0.48) kg/d, respectively. Residual feed intake was positively correlated with DMI (r = 0.47) and FCR (r = 0.46), but not with ADG or midtest BW. Positive correlations (ranging from r = 0.27 to r = 0.63) were estimated between ultrasonic measures of final lumbar fat and lumbar fat accretion over the test period and DMI, FCR, and RFI. The inclusion of gain in lumbar fat to the base RFI model increased R 2 (0.77 vs. 0.80) value for the degree of variation in DMI not explained by midtest BW and ADG alone. The Pearson rank correlation between RFI and carcass-adjusted RFI (RFI c) was high (r = 0.93). From the plasma analytes measured, NEFA (r = -0.21; P < 0.05) and β-hydroxybutyrate (r = 0.37; P < 0.05) concentrations were correlated with RFI. Plasma leptin (r = 0.48), glucose:insulin (r = -0.23), NEFA (r = -0.32), and β-hydroxybutyrate (r = 0.25) were associated with FCR. However, systemic IGF-I and insulin were unrelated (P > 0.05) to any measure of feed efficiency. The feeding behavior traits of eating rate, daily feeding events, and nonfeeding events were positively correlated (P < 0.05) with RFI and RFI c. This multifactorial study provides new information on some of the biological processes responsible for variation in feed efficiency in beef cattle. © 2010 American Society of Animal Science.


McLea L.,Queen's University of Belfast | Ball M.E.E.,Queen's University of Belfast | Ball M.E.E.,Agri Food and Biosciences Institute | Kilpatrick D.,Agri Food and Biosciences Institute | Elliott C.,Queen's University of Belfast
British Poultry Science | Year: 2011

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.


Barry C.D.,Queen's University of Belfast | Barry C.D.,Agri Food and Biosciences Institute | Foy R.H.,Queen's University of Belfast
Journal of Environmental Quality | Year: 2016

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.


Foy R.H.,Agri Food and Biosciences Institute | Ball M.E.,Agri Food and Biosciences Institute | George J.,Agri Food and Biosciences Institute
Poultry science | Year: 2014

Microbial phytases increase the bioavailability of phytate P in poultry diets, and a survey was undertaken to determine if their use had lowered the P composition of broiler litter in Northern Ireland compared with standard values of litter composition listed in the current United Kingdom fertilizer recommendations. Litter samples were collected from a total of 20 units across Northern Ireland in 2010 and analyzed for DM, N, phosphate (P2O5), potash (K2O), magnesium oxide (MgO), water-soluble P (WSP), ammonium N (NH4N), and uric acid N. Dry matter of litter was positively correlated (P < 0.001) with N (r(2) = 0.65), P2O5 (r(2) = 0.63), K2O (r(2) = 0.56), and MgO (r(2) = 0.58). Negative correlations were observed between litter DM and WSP (r(2) = 0.45, P < 0.001) and NH4N (r(2) = 0.22, P = 0.038) contents. A standardized litter composition with a 60% DM gave a phosphate content of 13.7 kg/t that was 45% lower than the fertilizer book value (RB209), but there were only slight differences (<3%) between book values and DM standardized values for N and potash contents. Uric acid and NH4 contents were similar to published values. Mean N:P ratio (by weight) of litter increased from 3.7 in 2004 to 5.0 in 2010, lowering the risk of oversupply of P if land applications are targeted to meet N supply. Using the standard RB209 values to plan land applications of broiler litter to meet crop P demands risks undersupplying P, and there is a need for the regulatory values to be modified in light of the changing composition of broiler litter. ©2014 Poultry Science Association Inc.


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 | Year: 2011

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.

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