• Temporal patterns of inflammatory gene expression in local tissues after banding or burdizzo castration in cattle

      Pang, Wanyong; Earley, Bernadette; Sweeney, Torres; Gath, Vivian; Crowe, Mark A (Biomed Central, 2009-09-23)
      Background: Castration of male cattle has been shown to elicit inflammatory reactions and acute inflammation is initiated and sustained by the participation of cytokines. Methods: Sixty continental × beef bulls (Mean age 12 ± (s.e.) 0.2 months; Mean weight 341 ± (s.e.) 3.0 kg) were blocked by weight and randomly assigned to one of three treatments (n = 20 animals per treatment): 1) untreated control (Con); 2) banding castration at 0 min (Band); 3) Burdizzo castration at 0 min (Burd). Samples of the testis, epididymis and scrotal skin were collected surgically from 5 animals from each group at 12 h, 24 h, 7 d, and 14 d post-treatment, and analysed using real-time PCR. A repeated measurement analysis (Proc GLM) was performed using SAS. If there was no treatment and time interaction, main effects of treatment by time were tested by ANOVA. Results: Electrophoresis data showed that by 7 d post-castration RNA isolated from all the testicle samples of the Burd castrated animals, the epididymis and middle scrotum samples from Band castrates were degraded. Transitory effects were observed in the gene expression of IFN-γ, IL-6, IL-8 and TNF-α at 12 h and 24 h post treatment. Burd castrates had greater (P < 0.05) testicular IFN-γ mRNA levels compared with Band and Con animals, but lower (P < 0.05) testicular TNF-α mRNA levels compared with Con animals. Band castrates had greater (P < 0.05) testicular IL-6 mRNA levels than Burd castrates at 12 h post-castration. Burd castrates had greater (P < 0.05) testicular IL-8 mRNA levels than Band and Con animals at 24 h post-castration. In the epididymis, Burd castrates had greater (P < 0.05) IL-6 mRNA (both at 12 h and 24 h post treatment) and IL-8 mRNA (12 h post treatment) levels compared with Band and Con animals; Burd castrates had greater (P = 0.049) IL-10 mRNA levels than Band castrates at 12 h post-castration. Conclusion: Banding castration caused more inflammatory associated gene expression changes to the epididymis and scrotum than burdizzo. Burdizzo caused more severe acute inflammatory responses, in terms of pro-inflammatory cytokine gene expression, in the testis and epididymis than banding.
    • Temporal trends in bulk milk antibodies to Salmonella, Neospora caninum, and Leptospira interrogans serovar hardjo in Irish dairy herds

      O'Doherty, E.; Sayers, Riona; O'Grady, L. (Elsevier, 2012-10-29)
      Bulk milk samples were collected from 309 Irish dairy herds at four time points during 2009 and tested for antibodies to Salmonella spp., N. caninum, and L. hardjo, three abortifacient agents in Irish dairy herds. Of the 312 study herds, 49% vaccinated against Salmonella and 76% vaccinated against L. hardjo. In unvaccinated herds, the overall prevalence of antibody positive herds was 49% for Salmonella, 19% for N. caninum and 86% for L. hardjo. There was no association between both testing positive for and incidence of Salmonella or L. hardjo on sample date and calving season. A significant association was found between sample date and both testing positive for [p = <0.0001 OR = 2.41 (95% CI 1.54–3.80)] and incidence [p = 0.001 OR = 3.10 (95% CI 1.72–5.57)] of N. caninum. No association with region of Ireland was found for either testing positive for or incidence of N. caninum, or L. hardjo. There was however a tendency towards a higher incidence of Salmonella in regions of Ireland with higher cattle densities.
    • Temporal trends in bulk milk antibodies to Salmonella, Neospora caninum, and Leptospira interrogans serovar hardjo in Irish dairy herds

      O'Doherty, Eugene; Sayers, Riona; O'Grady, L. (Elsevier, 2012-10-29)
      Bulk milk samples were collected from 309 Irish dairy herds at four time points during 2009 and tested for antibodies to Salmonella spp., N. caninum, and L. hardjo, three abortifacient agents in Irish dairy herds. Of the 312 study herds, 49% vaccinated against Salmonella and 76% vaccinated against L. hardjo. In unvaccinated herds, the overall prevalence of antibody positive herds was 49% for Salmonella, 19% for N. caninum and 86% for L. hardjo. There was no association between both testing positive for and incidence of Salmonella or L. hardjo on sample date and calving season. A significant association was found between sample date and both testing positive for [p = <0.0001 OR = 2.41 (95% CI 1.54–3.80)] and incidence [p = 0.001 OR = 3.10 (95% CI 1.72–5.57)] of N. caninum. No association with region of Ireland was found for either testing positive for or incidence of N. caninum, or L. hardjo. There was however a tendency towards a higher incidence of Salmonella in regions of Ireland with higher cattle densities.
    • Temporal trends in reproductive performance in Irish dairy herds and associated risk factors

      Mee, John F (Biomed Central, 2004-03-01)
      Irish dairy herd fertility has been declining since the 1980s. The extent, nature and causes of this decline in fertility and the current status of Irish dairy herd fertility were described. An increase in calving interval of approximately one day per year has been recorded. The principal components of this trend have been an increased incidence of postpartum endocrinopathies, reduced expression of oestrus and a fall in conception rate. Both submission rate and calving-to-service interval have increased slightly over time. Significant risk factors associated with these trends have been strain substitution within the Holstein-Friesian breed and single trait selection for milk production. Critically, these changes have been reflected in loss of body condition. Contributory factors included increased herd size and possibly increased use of DIYAI. The most recent Irish study showed that 48% of cows conceived to first service and 14% of cows were not pregnant at the end of the industry-average 15-week spring breeding season. However, the top quartile of herds achieved a first-service conception rate of 59%, illustrating the wide variation between herds. These phenotypic trends were attributed to both genetic and environmental factors and their interactions. Recent Irish dairy herd fertility performance falls short of the targets set for seasonal compact calving.
    • A theoretical and practical analysis of the optimum breeding system for perennial ryegrass

      Conaghan, P.; Casler, M.D. (Teagasc (Agriculture and Food Development Authority), Ireland, 2011)
      The goal of plant breeding is to effectively and efficiently select for the best phenotypes leading to the development of improved cultivars. The objectives for this review are to describe and critically evaluate breeding methods appropriate to the improvement of perennial ryegrass (Lolium perenne L.) in a long-term breeding programme. The optimum breeding system is dependent on the traits for improvement, and the available physical and human resources. Forage dry matter yield, persistency, disease resistance, nutritional value and seed yield are considered among the most important traits for improvement. Careful consideration should be given to the expression of the trait under the management regime imposed in the breeding programme and under real-world sward conditions in the target sowing region. Recurrent selection programmes for intrapopulation improvement are most appropriate for breeding perennial ryegrass. Three distinct types of recurrent selection may be implemented: (i) phenotypic recurrent selection, (ii) genotypic recurrent selection and (iii) marker-assisted selection. Genotypic recurrent selection will be a necessary part of the breeding system if forage yield is a trait for improvement. Genotypic recurrent selection may be practiced using full-sib or half-sib families, each with their own advantages and disadvantages. Phenotypic recurrent selection in tandem (i.e., within-family selection) or in succession with genotypic recurrent selection should be used to improve traits that have a high-correlation between performance from spaced plants and from sward plots. Genome-wide selection represents the most interesting and exciting potential application of marker-assisted selection, although it remains to be seen how beneficial it will be in practice.
    • Transcriptome Analysis of CD4+ T Cells in Coeliac Disease Reveals Imprint of BACH2 and IFNγ Regulation

      Quinn, Emma M; Coleman, Ciara; Molloy, Ben; Castro, Patricia Dominguez; Cormican, Paul; Trimble, Valerie; Mahmud, Nasir; McManus, Ross (PLOS, 2015-10-07)
      Genetic studies have to date identified 43 genome wide significant coeliac disease susceptibility (CD) loci comprising over 70 candidate genes. However, how altered regulation of such disease associated genes contributes to CD pathogenesis remains to be elucidated. Recently there has been considerable emphasis on characterising cell type specific and stimulus dependent genetic variants. Therefore in this study we used RNA sequencing to profile over 70 transcriptomes of CD4+ T cells, a cell type crucial for CD pathogenesis, in both stimulated and resting samples from individuals with CD and unaffected controls. We identified extensive transcriptional changes across all conditions, with the previously established CD gene IFNy the most strongly up-regulated gene (log2 fold change 4.6; Padjusted = 2.40x10-11) in CD4+ T cells from CD patients compared to controls. We show a significant correlation of differentially expressed genes with genetic studies of the disease to date (Padjusted = 0.002), and 21 CD candidate susceptibility genes are differentially expressed under one or more of the conditions used in this study. Pathway analysis revealed significant enrichment of immune related processes. Co-expression network analysis identified several modules of coordinately expressed CD genes. Two modules were particularly highly enriched for differentially expressed genes (P<2.2x10-16) and highlighted IFNy and the genetically associated transcription factor BACH2 which showed significantly reduced expression in coeliac samples (log2FC -1.75; Padjusted = 3.6x10-3) as key regulatory genes in CD. Genes regulated by BACH2 were very significantly over-represented among our differentially expressed genes (P<2.2x10-16) indicating that reduced expression of this master regulator of T cell differentiation promotes a pro-inflammatory response and strongly corroborates genetic evidence that BACH2 plays an important role in CD pathogenesis.
    • Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

      O’Loughlin, Aran; Lynn, David J; McGee, Mark; Doyle, Sean; McCabe, Matthew; Earley, Bernadette; Teagasc Walsh Fellowship Programme (Biomed Central, 2012-06-18)
      Background: Weaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessation of the maternal-offspring bond and is often accompanied by housing. While much recent research has focused on the physiological response of the bovine immune system to stress in recent years, little is known about the molecular mechanisms modulating the immune response. Therefore, the objective of this study was to provide new insights into the molecular mechanisms underlying the physiological response to weaning at housing in beef calves using Illumina RNA-seq.Results: The leukocyte transcriptome was significantly altered for at least 7 days following either housing or weaning at housing. Analysis of differentially expressed genes revealed that four main pathways, cytokine signalling, transmembrane transport, haemostasis and G-protein-coupled receptor (GPRC) signalling were differentially regulated between control and weaned calves and underwent significant transcriptomic alterations in response to weaning stress on day 1, 2 and 7. Of particular note, chemokines, cytokines and integrins were consistently found to be up-regulated on each day following weaning. Evidence for alternative splicing of genes was also detected, indicating a number of genes involved in the innate and adaptive immune response may be alternatively transcribed, including those responsible for toll receptor cascades and T cell receptor signalling.Conclusions: This study represents the first application of RNA-Seq technology for genomic studies in bovine leukocytes in response to weaning stress. Weaning stress induces the activation of a number of cytokine, chemokine and integrin transcripts and may alter the immune system whereby the ability of a number of cells of the innate and adaptive immune system to locate and destroy pathogens is transcriptionally enhanced. Stress alters the homeostasis of the transcriptomic environment of leukocytes for at least 7 days following weaning, indicating long term effects of stress exposure in the bovine. The identification of gene signature networks that are stress activated provides a mechanistic framework to characterise the multifaceted nature of weaning stress adaptation in beef calves. Thus, capturing subtle transcriptomic changes provides insight into the molecular mechanisms that underlie the physiological response to weaning stress.
    • Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes

      Moran, Bruce; Cummins, Sean B; Creevey, Christopher J.; Butler, Stephen T. (Biomed Central, 2016-08-11)
      Background The transition between pregnancy and lactation is a major physiological change for dairy cows. Complex systemic and local processes involving regulation of energy balance, galactopoiesis, utilisation of body reserves, insulin resistance, resumption of oestrous cyclicity and involution of the uterus can affect animal productivity and hence farm profitability. Here we used an established Holstein dairy cow model of fertility that displayed genetic and phenotypic divergence in calving interval. Cows had similar genetic merit for milk production traits, but either very good genetic merit for fertility traits (‘Fert+’; n = 8) or very poor genetic merit for fertility traits (‘Fert-’; n = 8). We used RNA sequencing to investigate gene expression profiles in both liver and muscle tissue biopsies at three distinct time-points: late pregnancy, early lactation and mid lactation (-18, 1 and 147 days relative to parturition, respectively). Results We found 807 and 815 unique genes to be differentially expressed in at least one time-point in liver and muscle respectively, of which 79 % and 83 % were only found in a single time-point; 40 and 41 genes were found differentially expressed at every time-point indicating possible systemic or chronic dysregulation. Functional annotation of all differentially expressed genes highlighted two physiological processes that were impacted at every time-point in the study, These were immune and inflammation, and metabolic, lipid and carbohydrate-binding. Conclusion These pathways have previously been identified by other researchers. We show that several specific genes which are differentially regulated, including IGF-1, might impact dairy fertility. We postulate that an increased burden of reactive oxidation species, coupled with a chronic inflammatory state, might reduce dairy cow fertility in our model.
    • Trends in milk production, calving rate and survival of cows in 14 Irish dairy herds as a result of the introgression of Holstein-Friesian genes

      Evans, Ross D; Dillon, Pat; Buckley, Frank; Berry, Donagh P.; Wallace, M.; Ducrocq, V.; Garrick, D. J. (Cambridge University Press, 2006-08)
      Trends in milk production, calving rates, and survival were monitored on a potential 5580 primiparous and multiparous Holstein-Friesian dairy cows across 14 Irish seasonal spring-calving dairy farms between the years 1990 and 2001. Over this period calving rate to first service (CALV1) reduced by 0·96% per year (55 to 44%; P< 0·001), calving rate to first and second service (CALV12) reduced by 0·84% per year ( 77 to 70%; P< 0·001) and herd average parity number reduced by 0·10 lactation per year (4·3 to 3·5; P<0·001). The proportion of North American Holstein Friesian (NAHF) genes in the cows increased by 5·5% per year (8 to 63%; P<0·001), while pedigree index for milk yield (PIMILK) of the cows increased by 25 kg per year ( P<0·001). The predicted difference of the sires of the cows for calving interval and survival increased by 0·5 days (P<0·001) and reduced by 0·12% ( P<0·001) per year, respectively. A negative association was found between increased phenotypic milk yield, NAHF and PIMILK and reduced calving rates as assessed by CALV1 and CALV12. Increased proportion of NAHF genes exhibited a negative effect on survival ( P<0·001) whereas increased levels of heterosis had a positive impact on survival ( P<0·001). The results of the present study indicate that in seasonal calving herds in Ireland a need for direct selection on traits related to fertility and survival is required to arrest and reverse the declining trends in calving rates and survival.
    • Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

      Creevey, Christopher J.; Doerks, Tobias; Fitzpatrick, David A.; Raes, Jeroen; Bork, Peer (PLOS, 2011-08-05)
      Single copy genes, universally distributed across the three domains of life and encoding mostly ancient parts of the translation machinery, are thought to be only rarely subjected to horizontal gene transfer (HGT). Indeed it has been proposed to have occurred in only a few genes and implies a rare, probably not advantageous event in which an ortholog displaces the original gene and has to function in a foreign context (orthologous gene displacement, OGD). Here, we have utilised an automatic method to identify HGT based on a conservative statistical approach capable of robustly assigning both donors and acceptors. Applied to 40 universally single copy genes we found that as many as 68 HGTs (implying OGDs) have occurred in these genes with a rate of 1.7 per family since the last universal common ancestor (LUCA). We examined a number of factors that have been claimed to be fundamental to HGT in general and tested their validity in the subset of universally distributed single copy genes. We found that differing functional constraints impact rates of OGD and the more evolutionarily distant the donor and acceptor, the less likely an OGD is to occur. Furthermore, species with larger genomes are more likely to be subjected to OGD. Most importantly, regardless of the trends above, the number of OGDs increases linearly with time, indicating a neutral, constant rate. This suggests that levels of HGT above this rate may be indicative of positively selected transfers that may allow niche adaptation or bestow other benefits to the recipient organism.
    • Urine patch distribution under dairy grazing at three stocking rates in Ireland

      Dennis, S.J.; Moir, J.L.; Cameron, K.C.; Di, H.J.; Hennessy, D.; Richards, Karl G. (Teagasc (Agriculture and Food Development Authority), Ireland, 2011)
      Nitrate pollution of water is a serious global environmental issue. Grassland agriculture is a major source of diffuse nitrate pollution, with much of this nitrate originating from the urine patches of grazing animals. To study nitrate losses from grassland it is necessary to consider the areas of grassland that are affected by urine separately from the remainder of the pasture. Urine patches can be observed in the field as areas of vigorously growing pasture, however the pasture may continue to respond for several months, making it difficult to determine when the observed patch was actually deposited. A global positioning system was used to record the location of all urine and dung patches in a pasture at every second grazing on an Irish dairy farm during the grazing season. Any patches reappearing were removed from the data, allowing the fresh urine patches to be identified. Dairy cows deposited 0.359 urine patches per grazing hour, a value that may be used to predict the distribution of urine patches under any grazing regime. This equated to 14.1 to 20.7% of the soil surface being wet by urine annually at stocking rates of 2.0 to 2.94 cows per hectare, consistent with previous research. These values may be used in conjunction with values for nitrate loss from urine and non-urine areas to calculate nitrate losses from grazed pasture at a range of stocking rates.
    • Use of different wood types as environmental enrichment to manage tail biting in docked pigs in a commercial fully-slatted system

      Chou, Jen-Yun; D'Eath, Rick B.; Sandercock, Dale A.; Waran, Natalie; Haigh, Amy; O'Driscoll, Keelin; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; Scotland's Rural College (Elsevier, 2018-04-07)
      Provision of adequate environmental enrichment on pig farms is a legal requirement under current EU legislation and also alleviates the risk of tail biting. Wood is an organic alternative where loose bedding, which has been identified as the optimal enrichment, is not possible on fully-slatted floors since it may disrupt the slurry system. The study compared four different wood types (beech (Fagus sylvatica), larch (Larix decidua), spruce (Picea sitchensis), and Scots pine (Pinus sylvestris L.)) as enrichment, taking into account the qualities of the wood, economic considerations, and effectiveness at reducing damaging behaviours and lesions. A total of 800 tail docked finisher pigs on an Irish commercial farm were used. Eight pens were provided with each wood type (25 pigs/pen), and the study was conducted over 2 replicates in time. In each pen a single wooden post was presented to the pigs in a metal dispenser with two lateral chains during the finisher period (12–22 weeks of age). The rate of wear, moisture content, and hardness of the wood along with lesion scorings and behavioural observation on pigs were monitored. Spruce was consumed more quickly than other wood types in terms of weight loss and reduction in length (P < 0.001), resulting in a greater cost per pig. Pigs were observed interacting with the spruce more frequently than the other wood types (P < 0.05). Pigs also interacted with the wood more often than the chains in spruce allocated pens (P < 0.001). Overall the interaction with wood posts did not decline significantly across time. However, there was no difference in the frequency of harmful behaviours (tail/ear/flank-biting) observed between wood types, and also no difference in the effectiveness of the different types of wood in reducing tail or ear damage. There was a positive correlation between ear lesion and tear-staining scores (rp= 0.286, P < 0.01), and between tail lesion and tail posture scores (rp= 0.206, P < 0.05). Wood types did not affect visceral condemnation obtained in the slaughterhouse. Wood is a potentially suitable enrichment material, yet the wood species could influence its attractiveness to pigs.
    • Validation and Improvement of the Beef Production Sub-index in Ireland for Beef Cattle

      Drennan, Michael J; McGee, Mark; Clarke, A. M.; Kenny, D.A.; Evans, R.D.; Berry, Donagh P. (Teagasc, 2009-12-01)
      The objectives of the following study were to: a. Quantify the effect of sire genetic merit for BCI on: 1. feed intake, growth and carcass traits of progeny managed under bull or steer beef production systems. 2. live animal scores, carcass composition and plasma hormone and metabolite concentrations in their progeny. b. Compare the progeny of : 1. Late-maturing beef with dairy breeds and 2. Charolais (CH), Limousin (LM), Simmental (SM) and Belgian Blue (BB) sires bred to beef suckler dams, for feed intake, blood hormones and metabolites, live animal measurements, carcass traits and carcass value in bull and steer production systems.
    • Validation of national genetic evaluations for maternal beef cattle traits using Irish field data

      McHugh, Noirin; Cromie, A.R.; Evans, R.D.; Berry, Donagh P. (American Society of Animal Science, 2014-11-24)
      Genetic evaluations provide information to aid in breeding decisions that increase long-term performance of animals and herds. However, to date no study has been undertaken to investigate the accuracy of the Irish maternal genetic evaluations in beef cattle. The objective, therefore, of this study was to quantify the relationship between phenotypic performance and measures of genetic merit for predominantly maternal-related traits in Irish beef cattle. The association between animal EBV for calving interval, age at first calving, and both direct and maternal weaning weight with the respective phenotypic performance was quantified using a fixed effects model; the expectation for the regression coefficient of phenotypic performance on EBV was one. The association between genetic merit for cow survival, perinatal mortality, calving assistance, and calving dystocia with the log of the odds of the respective trait was quantified using logistic regression. The association analyses were conducted using field data on up to 38,619 records from 5,236 herds. Age at first calving increased linearly by 0.32 ± 0.15 (P = 0.03) days per day increase in EBV for age at first calving. Calving interval increased by, on average, 0.58 ± 0.16 (P = 0.002) days per day increase in EBV for calving interval although the association differed by parity with a greater association in pluriparae. Weaning weight increased linearly by 1.74 ± 0.09 and 0.84 ± 0.16 kg (P < 0.001) per kilogram increase in EBV for direct and maternal weaning weight, respectively. The log of the odds of a cow surviving to next lactation increased linearly by 0.16 ± 0.03 (P < 0.001) per unit increase in EBV for cow survival. The log of the odds of an assisted calving or dystocia both increased linearly by 0.21 ± 0.01 and 0.24 ± 0.01, respectively, per unit increase in EBV for direct calving difficulty (P < 0.001). The log of the odds of a dead calf at birth increased linearly by 0.93 ± 0.13 (P < 0.001) per unit increase in EBV for calf mortality. Results from this study show that selection of breeding animals for favorable maternal genetic attributes will result in favorable improvements in performance and profitability.
    • Variance components for susceptibility to Mycobacterium bovis infection in dairy and beef cattle

      Richardson, Ian W.; Bradley, Dan G.; Higgins, Isabella M.; More, Simon J.; McClure, Jennifer; Berry, Donagh P. (Biomed Central, 2014-11-18)
      Background Infection of livestock with bovine tuberculosis (bTB; Mycobacterium bovis) is of major economical concern in many countries; approximately 15 000 to 20 000 cattle are infected per year in Ireland. The objective of this study was to quantify the genetic variation for bTB susceptibility in Irish dairy and beef cattle. Methods A total of 105 914 cow, 56 904 heifer and 21 872 steer single intra-dermal comparative tuberculin test records (i.e., binary trait) collected from the years 2001 to 2010 from dairy and beef herds were included in the analysis. Only animal level data pertaining to periods of herd bTB infection were retained. Variance components for bTB were estimated using animal linear and threshold mixed models and co-variances were estimated using sire linear mixed models. Results Using a linear model, the heritability for susceptibility to bTB in the entire dataset was 0.11 and ranged from 0.08 (heifers in dairy herds) to 0.19 (heifers in beef herds) among the sub-populations investigated. Differences in susceptibility to bTB between breeds were clearly evident. Estimates of genetic correlations for bTB susceptibility between animal types (i.e., cows, heifers, steers) were all positive (0.10 to 0.64), yet different from one. Furthermore, genetic correlations for bTB susceptibility between environments that differed in herd prevalence of bTB ranged from 0.06 to 0.86 and were all different from one. Conclusions Genetic trends for bTB susceptibility observed in this study suggest a slight increase in genetic susceptibility to bTB in recent years. Since bTB is of economic importance and because all animals are routinely tested at least once annually in Ireland and some other countries, the presence of genetic variation for bTB susceptibility suggests that bTB susceptibility should be included in a national breeding program to halt possible deterioration in genetic susceptibility to bTB infection.
    • The variation in morphology of perennial ryegrass cultivars throughout the grazing season and effects on organic matter digestibility

      Beecher, Marion; Hennessy, Deirdre; Boland, T. M.; McEvoy, Mary; O'Donovan, Michael; Lewis, Eva (Wiley, 2013-09-19)
      The grass plant comprises leaf, pseudostem, true stem (including inflorescence) and dead material. These components differ in digestibility, and variations in their relative proportions can affect sward quality. The objective of this study was to determine the change in the proportion and organic matter digestibility (OMD) of leaf, pseudostem, true stem and dead components of four perennial ryegrass cultivars (two tetraploids: Astonenergy and Bealey and two diploids: Abermagic and Spelga) throughout a grazing season. The DM proportions and in vitro OMD of leaf, pseudostem, true stem and dead in all cultivars were determined during ten grazing rotations between May 2011 and March 2012. There was an interaction between rotation and cultivar for leaf, pseudostem, true stem and dead proportions. In May and June, Astonenergy had the highest leaf and lowest true stem proportion (P < 0·05). From July onwards, there was no difference in leaf or true stem proportion between cultivars. Bealey had the highest annual mean OMD (752 g kg−1) and Spelga the lowest (696 g kg−1; P < 0·05). The OMD followed the order leaf > pseudostem > true stem > dead. Bealey had the highest combined leaf and pseudostem proportion 0·92, which explains why it had the highest OMD. In this study, the tetraploid cultivars had the highest leaf and pseudostem proportion and OMD. For accurate descriptions of a sward in grazing studies and to accurately determine sward morphological composition, pseudostem should be separated from true stem, particularly during the reproductive stage when true stem is present.
    • Variation in the Ovine Abomasal Lymph Node Transcriptome between Breeds Known to Differ in Resistance to the Gastrointestinal Nematode

      Ahmed, Albin M.; Good, Barbara; Hanrahan, James P.; McGettigan, Paul; Browne, John; Keane, Orla M; Bahar, Bojlul; Mehta, Jai; Markey, Bryan; Lohan, Amanda; Sweeney, Torres (PLoS, 2015-05-15)
      Texel lambs are known to be more resistant to gastrointestinal nematode (GIN) infection than Suffolk lambs, with a greater ability to limit infection. The objectives of this study were to: 1) profile the whole transcriptome of abomasal lymph node tissue of GIN-free Texel and Suffolk lambs; 2) identify differentially expressed genes and characterize the immune-related biological pathways and networks associated with these genes. Abomasal lymph nodes were collected from Texel (n = 6) and Suffolk (n = 4) lambs aged 19 weeks that had been GIN-free since 6 weeks of age. Whole transcriptome profiling was performed using RNA-seq on the Illumina platform. At the time of conducting this study, a well annotated Ovine genome was not available and hence the sequence reads were aligned with the Bovine (UMD3.1) genome. Identification of differentially expressed genes was followed by pathway and network analysis. The Suffolk breed accounted for significantly more of the differentially expressed genes, (276 more highly expressed in Suffolk v 162 in Texel; P < 0.001). The four most significant differentially expressed pathways were all related to immunity and were classified as: Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses, Activation of IRF by Cytosolic Pattern Recognition Receptors, Role of RIG-I-like Receptors in Antiviral Innate Immunity, and Interferon Signaling. Of significance is the fact that all of these four pathways were more highly expressed in the Suffolk. These data suggest that in a GIN-free environment, Suffolk lambs have a more active immune profile relative to the Texel: this immune profile may contribute to the poorer efficiency of response to a GIN challenge in the Suffolk breed compared to the Texel breed.
    • Variations in travel time for N loading to groundwaters in four case studies in Ireland:Implications for policy makers and regulators

      Fenton, Owen; Coxon, Catherine E.; Haria, Atul H.; Horan, Brendan; Humphreys, James; Johnson, Paul; Murphy, Paul; Necpalova, Magdalena; Premrov, Alina; Richards, Karl G. (School of Agriculture, Food Science and Veterinary Medicine, University College Dublin in association with Teagasc, 2009)
      Mitigation measures to protect waterbodies must be implemented by 2012 to meet the requirements of the EU Water Framework Directive. The efficacy of these measures will be assessed in 2015. Whilst diffuse N pathways between source and receptor are generally long and complex, EU legislation does not account for differences in hydrological travel time distributions that may result in different water quality response times. The “lag time” between introducing mitigation measures and first improvements in water quality is likely to be different in different catchments; a process that should be considered by policy makers and catchment managers. Many examples of travel time variations have been quoted in the literature but no Irish specific examples are available. Lag times based on initial nutrient breakthrough at four contrasting sites were estimated to a receptor 500 m away from a source. Vertical travel times were estimated using a combination of depth of infiltration calculations based on effective rainfall and subsoil physical parameters and existing hydrological tracer data. Horizontal travel times were estimated using a combination of Darcian linear velocity calculations and existing tracer migration data. Total travel times, assuming no biogeochemical processes, ranged from months to decades between the contrasting sites; the shortest times occurred under thin soil/subsoil on karst limestone and the longest times through thick low permeability soils/subsoils over poorly productive aquifers. Policy makers should consider hydrological lag times when assessing the efficacy of mitigation measures introduced under the Water Framework Directive. This lag time reflects complete flushing of a particular nutrient from source to receptor. Further research is required to assess the potential mitigation of nitrate through denitrification along the pathway from source to receptor.
    • Veterinary dairy herd fertility service provision in seasonal and non-seasonal dairy industries - a comparison

      Mee, John F (Biomed Central, 2010-04-01)
      The decline in dairy herd fertility internationally has highlighted the limited impact of traditional veterinary approaches to bovine fertility management. Three questionnaire surveys were conducted at buiatrics conferences attended by veterinary practitioners on veterinary dairy herd fertility services (HFS) in countries with a seasonal (Ireland, 47 respondents) and non-seasonal breeding model (The Netherlands, 44 respondents and Portugal, 31 respondents). Of the 122 respondents, 73 (60%) provided a HFS and 49 (40%) did not. The majority (76%) of all practitioners who responded stated that bovine fertility had declined in their practice clients' herds with inadequate cow management, inadequate nutrition and increased milk yield as the most important putative causes. The type of clients who adopted a herd fertility service were deemed more educated than average (70% of respondents), and/or had fertility problems (58%) and/or large herds (53%). The main components of this service were routine postpartum examinations (95% of respondents), fertility records analysis (75%) and ultrasound pregnancy examinations (69%). The number of planned visits per annum varied between an average of four in Ireland, where breeding is seasonal, and 23 in Portugal, where breeding is year-round. The benefits to both the practitioner and their clients from running a HFS were cited as better fertility, financial rewards and job satisfaction. For practitioners who did not run a HFS the main reasons given were no client demand (55%) and lack of fertility records (33%). Better economic evidence to convince clients of the cost-benefit of such a service was seen as a major constraint to adoption of this service by 67% of practitioners.
    • Web-based Tools for the Analysis of DNA Microarrays

      Geeleher, P.; Golden, A.; Hinde, J.; Morris, Dermot G. (Teagasc, 2008-01-01)
      DNA microarrays are widely used for gene expression profiling. Raw data resulting from microarray experiments, however, tends to be very noisy and there are many sources of technical variation and bias. This raw data needs to be quality assessed and interactively preprocessed to minimise variation before statistical analysis in order to achieve meaningful result. Therefore microarray analysis requires a combination of visualisation and statistical tools, which vary depending on what microarray platform or experimental design is used.Bioconductor is an existing open source software project that attempts to facilitate analysis of genomic data. It is a collection of packages for the statistical programming language R. Bioconductor is particularly useful in analyzing microarray experiments. The problem is that the R programming language’s command line interface is intimidating to many users who do not have a strong background in computing. This often leads to a situation where biologists will resort to using commercial software which often uses antiquated and much less effective statistical techniques, as well as being expensively priced. This project aims to bridge this gap by providing a user friendly web-based interface to the cutting edge statistical techniques of Bioconductor.