• Identification of possible cow grazing behaviour indicators for restricted grass availability in a pasture-based spring calving dairy system

      Werner, Jessica; Umstatter, Christina; Kennedy, Emer; Grant, Jim; Leso, Lorenzo; Geoghegan, Anne; Shalloo, Laurence; Schick, Matthias; O'Brien, Bernadette; Science Foundation Ireland; et al. (Elsevier, 2018-12-05)
      Precision livestock farming uses biosensors to measure different parameters of individual animals to support farmers in the decision making process. Although sensor development is advanced, there is still little implementation of sensor-based solutions on commercial farms. Especially on pasture-based dairy systems, the grazing management of cows is largely not supported by technology. A key factor in pasture-based milk production is the correct grass allocation to maximize the grass utilization per cow, while optimizing cow performance. Currently, grass allocation is mostly based on subjective eye measurements or calculations per herd. The aim of this study was to identify possible indicators of insufficient or sufficient grass allocation in the cow grazing behaviour measures. A total number of 30 cows were allocated a restricted pasture allowance of 60% of their intake capacity. Their behavioural characteristics were compared to those of 10 cows (control group) with pasture allowance of 100% of their intake capacity. Grazing behaviour and activity of cows were measured using the RumiWatchSystem for a complete experimental period of 10 weeks. The results demonstrated that the parameter of bite frequency was significantly different between the restricted and the control groups. There were also consistent differences observed between the groups for rumination time per day, rumination chews per bolus and frequency of cows standing or lying.
    • Identifying Single Copy Orthologs in Metazoa

      Creevey, Christopher J.; Muller, Jean; Doerks, Tobias; Thompson, Julie D.; Arendt, Detlev; Bork, Peer; European Union; Science Foundation Ireland; LSH-2004-1.1.5-3; 07/SK/B1236A (PLOS, 2011-12-01)
      The identification of single copy (1-to-1) orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene. Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence. To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis) to 99.8% (human) with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.
    • Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue

      Johnston, Dayle; Earley, Bernadette; Cormican, Paul; Murray, Gerard; Kenny, David A.; Waters, Sinead M.; McGee, Mark; Kelly, Alan K; McCabe, Matthew; Department of Agriculture, Food and the Marine; et al. (Biomed Central, 2017-05-02)
      Background Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Results Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences. Conclusions The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD.
    • Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

      McCabe, Matthew; Cormican, Paul; Keogh, Kate; O'Connor, Aaron; O'Hara, Eoin; Palladino, Rafael Alejandro; Kenny, David A.; Waters, Sinead M.; Science Foundation Ireland; Teagasc Walsh Fellowship Programme; et al. (PLOS, 2015-07-30)
      Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.
    • Impact of agronomic practices of an intensive dairy farm on nitrogen concentrations in a karst aquifer in Ireland

      Huebsch, Manuela; Horan, Brendan; Blum, P.; Richards, Karl G.; Grant, Jim; Fenton, Owen; Teagasc Walsh Fellowship Programme (Elsevier, 24/09/2013)
      Exploring the relationship between agricultural nitrogen loading on a dairy farm and groundwater reactive nitrogen concentration such as nitrate is particularly challenging in areas underlain by thin soils and karstified limestone aquifers. The objective of this study is to relate changes in detailed agronomic N-loading, local weather conditions, hydrogeological and geological site characteristics with groundwater N occurrence over an 11-year period on an intensive dairy farm with free draining soils and a vulnerable limestone aquifer. In addition, the concept of vertical time lag from source to receptor is considered. Statistical analysis used regression with automatic variable selection. Four scenarios were proposed to describe the relationships between paddock and groundwater wells using topographic and hydrogeological assumptions. Monitored nitrate concentrations in the studied limestone aquifer showed a general decrease in the observed time period (2002–2011). Statistical results showed that a combination of improved agronomic practices and site specific characteristics such as thicknesses of the soil and unsaturated zone together with hydrogeological connections of wells and local weather conditions such as rainfall, sunshine and soil moisture deficit were important explanatory variables for nitrate concentrations. Statistical results suggested that the following agronomic changes improved groundwater quality over the 11-year period: reductions in inorganic fertiliser usage, improvements in timing of slurry application, the movement of a dairy soiled water irrigator to less karstified areas of the farm and the usage of minimum cultivation reseeding on the farm. In many cases the explanatory variables of farm management practices tended to become more important after a 1- or 2-year time lag. Results indicated that the present approach can be used to elucidate the effect of farm management changes to groundwater quality and therefore the assessment of present and future legislation implementations.
    • Impact of three inactivated bovine viral diarrhoea virus vaccines on bulk milk p80 (NS3) ELISA test results in dairy herds

      Sayers, Riona; Sayers, Gearoid; Graham, David A.; Arkins, S.; Irish Dairy Levy Research Trust (Elsevier, 2015-03-25)
      Bovine viral diarrhoea virus (BVDV) is endemic in many countries and vaccines are used as a component of control and eradication strategies. Surveillance programmes to detect exposure to BVDV often incorporate the use of bulk milk (BM) testing for antibodies against BVDV p80 (NS3), but vaccination can interfere with these results. The aim of this study was to evaluate whether BVDV vaccines would confound BM testing for specific antibodies in a nationally representative group of commercial dairy farms in the Republic of Ireland. A total of 256 commercial dairy herds were included in the statistical analysis. Quarterly BM or serum samples from selected weanling heifers (unvaccinated homeborn youngstock) were assessed by ELISA for antibodies against the BVDV p80 subunit and whole virus. Wilcoxon ranksum and receiver operating characteristic (ROC) analyses were used to examine differences among groups vaccinated with one of three commercially available inactivated BVDV vaccines. Two of the three vaccines showed evidence of interference with ELISA testing of BM samples. ROC analysis highlighted that one vaccine did not reduce the discriminatory power of the BVDV p80 ELISA for identification of herds with evidence of recent BVDV circulation, when compared with unvaccinated herds; thus, administration of this vaccine would allow uncomplicated interpretation of BM ELISA test results in vaccinated seropositive herds. Seasonal differences in BM antibody results were identified, suggesting that the latter half of lactation is the most suitable time for sampling dairy herds containing predominantly spring calving cows. The results of the present study are likely to prove useful in countries allowing vaccination during or following BVDV eradication, where BM testing is required as part of the surveillance strategy.
    • Implementing biosecurity measures on dairy farms in Ireland

      Sayers, Riona; Sayers, Gearoid; Mee, John F; Good, Margaret; Bermingham, Mairead L; Grant, Jim; Dillon, Pat; Irish Dairy Levy Research Trust (Elsevier, 2012-12-29)
      Dairy farms in Ireland are expanding in preparation for a new era of unrestricted milk production with the elimination of the European Union (EU) production quotas in 2015. Countries experiencing a changing agricultural demographic, including farm expansion, can benefit from documenting the implementation of on-farm biosecurity. The objectives of this study were to document and describe influences on biosecurity practices and related opinions on dairy farms. A representative response rate of 64% was achieved to a nationwide telesurvey of farmers. A 20% discrepancy was found between self-declared and truly ‘closed’ herds indicating a lack of understanding of the closed herd concept. Although >72% of farmers surveyed considered biosecurity to be important, 53% stated that a lack of information might prevent them from improving their biosecurity. Logistic regression highlighted regional, age, and farm-size related differences in biosecurity practices and opinions towards its implementation. Farmers in the most dairy cattle dense region were three times more likely to quarantine purchased stock than were their equivalents in regions where dairy production was less intense (P = 0.012). Younger farmers in general were over twice as likely as middle-aged farmers to implement biosecurity guidelines (P = 0.026). The owners of large enterprises were almost five times more likely to join a voluntary animal health scheme (P = 0.003), and were over three times more likely to pay a premium price for health accredited animals (P = 0.02) than were those farming small holdings. The baseline data recorded in this survey will form the basis for more detailed sociological and demographic research which will facilitate the targeting of future training of the farming community in biosecurity.
    • The Imprinted Retrotransposon-Like Gene PEG11 (RTL1) Is Expressed as a Full-Length Protein in Skeletal Muscle from Callipyge Sheep

      Byrne, Keren; Colgrave, Michelle L.; Vuocolo, Tony; Pearson, Roger; Bidwell, Christopher A.; Cockett, Noelle E.; Lynn, David J; Fleming-Waddell, Jolena N.; Tellam, Ross L (PLOS, 2010-01-08)
      Members of the Ty3-Gypsy retrotransposon family are rare in mammalian genomes despite their abundance in invertebrates and some vertebrates. These elements contain a gag-pol-like structure characteristic of retroviruses but have lost their ability to retrotranspose into the mammalian genome and are thought to be inactive relics of ancient retrotransposition events. One of these retrotransposon-like elements, PEG11 (also called RTL1) is located at the distal end of ovine chromosome 18 within an imprinted gene cluster that is highly conserved in placental mammals. The region contains several conserved imprinted genes including BEGAIN, DLK1, DAT, GTL2 (MEG3), PEG11 (RTL1), PEG11as, MEG8, MIRG and DIO3. An intergenic point mutation between DLK1 and GTL2 causes muscle hypertrophy in callipyge sheep and is associated with large changes in expression of the genes linked in cis between DLK1 and MEG8. It has been suggested that over-expression of DLK1 is the effector of the callipyge phenotype; however, PEG11 gene expression is also strongly correlated with the emergence of the muscling phenotype as a function of genotype, muscle type and developmental stage. To date, there has been no direct evidence that PEG11 encodes a protein, especially as its anti-sense transcript (PEG11as) contains six miRNA that cause cleavage of the PEG11 transcript. Using immunological and mass spectrometry approaches we have directly identified the full-length PEG11 protein from postnatal nuclear preparations of callipyge skeletal muscle and conclude that its over-expression may be involved in inducing muscle hypertrophy. The developmental expression pattern of the PEG11 gene is consistent with the callipyge mutation causing recapitulation of the normal fetal-like gene expression program during postnatal development. Analysis of the PEG11 sequence indicates strong conservation of the regions encoding the antisense microRNA and in at least two cases these correspond with structural or functional domains of the protein suggesting co-evolution of the sense and antisense genes.
    • Improved detection of biomarkers in cervico-vaginal mucus (CVM) from postpartum cattle

      Adnane, Mounir; Kelly, Paul M; Chapwanya, Aspinas; Meade, Kieran G; O'Farrelly, Cliona; The Algerian Ministry for High Education and Scientific Research; University of Tiaret, Algeria; Department of Agriculture, Food and the Marine, Ireland; ofarrecl-HRB-HRA_POR/2012/37; 13/S/472 (Biomed Central, 2018-09-29)
      Background In the postpartum cow, early diagnosis of uterine disease is currently problematic due to the lack of reliable, non-invasive diagnostic methods. Cervico-vaginal mucus (CVM) is an easy to collect potentially informative source of biomarkers for the diagnosis and prognosis of uterine disease in cows. Here, we report an improved method for processing CVM from postpartum dairy cows for the measurement of immune biomarkers. CVM samples were collected from the vagina using gloved hand during the first two weeks postpartum and processed with buffer alone or buffer containing different concentrations of the reducing agents recommended in standard protocols: Dithiothriotol (DTT) or N-Acetyl-L-Cysteine (NAC). Total protein was measured using the bicinchoninic acid (BCA) assay; interleukin 6 (IL-6), IL-8 and α1-acid glycoprotein (AGP) were measured by ELISA. Results We found that use of reducing agents to liquefy CVM affects protein yield and the accuracy of biomarker detection. Our improved protocol results in lower protein yields but improved detection of cytokines and chemokines. Using our modified method to measure AGP in CVM we found raised levels of AGP at seven days postpartum in CVM from cows that went on to develop endometritis. Conclusion We conclude that processing CVM without reducing agents improves detection of biomarkers that reflect uterine health in cattle. We propose that measurement of AGP in CVM during the first week postpartum may identify cows at risk of developing clinical endometritis.
    • Improvement of dry-cured Iberian ham sensory characteristics through the use of a concentrate high in oleic acid for pig feeding

      Jurado, A.; Garcia, C.; Timon, M.L.; Carrapiso, A.I. (Teagasc, Oak Park, Carlow, Ireland, 2008)
      The aim of this study was to investigate the sensory characteristics of dry-cured hams from confined Iberian pigs fed on a high oleic (HO) concentrate (HO-Pienso hams), and to study how different the characteristics of these hams are from those of Iberian hams from the best grade (Montanera hams, from extensively reared pigs). Nearly half of the fatty acids studied were similar in HO-Pienso and Montanera hams. No differences were found for 18:1, but some major fatty acids of subcutaneous fat of Iberian hams were different between the HO-Pienso and the Montanera hams (C16:0, C18:0, C18:2). The descriptive test revealed that 15 of the 23 sensory characteristics were not significantly different between both groups of hams. No sensory differences appeared for fat appearance or lean texture characteristics, but lean appearance, oiliness, saltiness and the most intensively perceived characteristics of odour and flavour were significantly different. These differences in the sensory traits between Montanera and Pienso hams were not as marked as found in previous studies. Therefore, the use of a concentrate high in oleic acid enables simulation, at least in part, of the sensory characteristics, especially texture.
    • Improving Farm Sustainability: Practical Tools for Farmers

      Teagasc (Teagasc, 2019-05-03)
      Irish agriculture rightly has a global reputation for high environmental standards. However, these standards continue to become more stringent, and the expansion in dairying since milk quota removal is adding further pressure. Early action is key to meeting the environmental challenges of reducing greenhouse gas and ammonia emissions, increasing carbon capture, improving water quality, protecting and improving biodiversity. There are a range of farm practices that dairy farmers can implement easily on their farms that can combine profitability gains while contributing to meeting these sustainability challenges. Some of these are outlined in this practical guide of what you can do on your farm to help meet the environmental challenges.
    • Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection

      Berry, Donagh P.; Kearney, J.F.; Department of Agriculture, Food and the Marine; European Union; RSF-06-0353; RSF-06-0428 (Cambridge University Press, 2011-02)
      The objective of this study was to quantify the accuracy achievable from imputing genotypes from a commercially available low-density marker panel (2730 single nucleotide polymorphisms (SNPs) following edits) to a commercially available higher density marker panel (51 602 SNPs following edits) in Holstein–Friesian cattle using Beagle, a freely available software package. A population of 764 Holstein–Friesian animals born since 2006 were used as the test group to quantify the accuracy of imputation, all of which had genotypes for the high-density panel; only SNPs on the low-density panel were retained with the remaining SNPs to be imputed. The reference population for imputation consisted of 4732 animals born before 2006 also with genotypes on the higher density marker panel. The concordance between the actual and imputed genotypes in the test group of animals did not vary across chromosomes and was on average 95%; the concordance between actual and imputed alleles was, on average, 97% across all SNPs. Genomic predictions were undertaken across a range of production and functional traits for the 764 test group animals using either their real or imputed genotypes. Little or no mean difference in the genomic predictions was evident when comparing direct genomic values (DGVs) using real or imputed genotypes. The average correlation between the DGVs estimated using the real or imputed genotypes for the 15 traits included in the Irish total merit index was 0.97 (range of 0.92 to 0.99), indicating good concordance between proofs from real or imputed genotypes. Results show that a commercially available high-density marker panel can be imputed from a commercially available lower density marker panel, which will also have a lower cost, thereby facilitating a reduction in the cost of genomic selection. Increased available numbers of genotyped and phenotyped animals also has implications for increasing the accuracy of genomic prediction in the entire population and thus genetic gain using genomic selection.
    • Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes

      Berry, Donagh P.; McParland, Sinead; Kearney, J.F.; Sargolzaei, Mehdi; Mullen, Michael P.; Department of Agriculture, Food and the Marine, Ireland; Science Foundation Ireland; European Union; RSF-06-0353; RSF-06-0428; et al. (Cambridge University Press, 2014-04-09)
      The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n = 3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n = 5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the withinanimal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, ⩾96% accuracy.
    • Incorporating white clover (Trifolium repens L.) into perennial ryegrass (Lolium perenne L.) swards receiving varying levels of nitrogen fertilizer: Effects on milk and herbage production

      Egan, M.; Galvin, Norann; Hennessy, Deirdre; Teagasc Walsh Fellowship Programme; Irish Dairy Levy (Elsevier, 2018-02-04)
      White clover (Trifolium repens L.; clover) can offer a superior nutritional feed compared with perennial ryegrass (Lolium perenne L.; PRG) and offers an additional or alternative source (or both) of N for herbage production. The objective of this study was to investigate the effect of including clover into PRG swards receiving 150 (Cl150) or 250 kg of N/ha (Cl250) compared with a PRG-only sward receiving 250 kg of N/ha (Gr250) on herbage production, milk production, and herbage dry matter intake (DMI) in an intensive grass-based spring calving milk production system over 2 full lactations. A farm systems experiment was established in February 2013, and conducted over 2 grazing seasons [2013 (yr 1) and 2014 (yr 2)]. In February 2013 (yr 1), 42 Holstein-Friesian spring-calving dairy cows, and in February 2014 (yr 2), 57 Holstein-Friesian spring-calving dairy cows were allocated to graze the Cl150, Cl250, and Gr250 swards (n = 14 in yr 1 and n = 19 in yr 2) from February to November, at a stocking rate of 2.74 cows/ha. Herbage DMI was estimated twice in yr 1 (May and September) and 3 times in yr 2 (May, July, and September). Treatment did not have a significant effect on annual herbage production. Sward clover content was greater on the Cl150 treatment than the Cl250 treatment. The cows grazing both clover treatments (Cl250 and Cl150) produced more milk than the cows grazing Gr250 from June until the end of the grazing season. A significant treatment by measurement period interaction was observed on total DMI. In May, the cows on the Cl250 treatment had the greatest DMI. In July, the cows on the clover treatments had greater DMI than those on the Gr250 treatment, whereas in September, the cows on the Cl150 treatment had the lowest DMI. In conclusion, including clover in a PRG sward grazed by spring-calving dairy cows can result in increased animal performance, particularly in the second half of lactation. Reducing N fertilizer application to 150 kg of N/ha on grass-clover swards did not reduce herbage production compared with grass-only swards receiving 250 kg of N/ha. White clover can play an integral role in intensive grazing systems in terms of animal performance and herbage production.
    • Increased detection of mastitis pathogens by real-time PCR compared to bacterial culture

      Keane, Orla M; Budd, Kathleen E; Flynn, James; McCoy, Finola (British Veterinary Association, 2013-08-23)
      Rapid and accurate identification of mastitis pathogens is important for disease control. Bacterial culture and isolate identification is considered the gold standard in mastitis diagnosis but is time consuming and results in many culture-negative samples. Identification of mastitis pathogens by PCR has been proposed as a fast and sensitive alternative to bacterial culture. The results of bacterial culture and PCR for the identification of the aetiological agent of clinical mastitis were compared. The pathogen identified by traditional culture methods was also detected by PCR in 98 per cent of cases indicating good agreement between the positive results of bacterial culture and PCR. A mastitis pathogen could not be recovered from approximately 30 per cent of samples by bacterial culture, however, an aetiological agent was identified by PCR in 79 per cent of these samples. Therefore, a mastitis pathogen was detected in significantly more milk samples by PCR than by bacterial culture (92 per cent and 70 per cent, respectively) although the clinical relevance of PCR-positive culture-negative results remains controversial. A mixed infection of two or more mastitis pathogens was also detected more commonly by PCR. Culture-negative samples due to undetected Staphylococcus aureus infections were rare. The use of PCR technology may assist in rapid mastitis diagnosis, however, accurate interpretation of PCR results in the absence of bacterial culture remains problematic.
    • Infection exposure, detection and causes of death in perinatal mortalities in Polish dairy herds

      Jawor, Paulina; Król, Dawid; Mee, John F.; Sołtysiak, Zenon; Dzimira, Stanisław; Larska, Magdalena; Stefaniak, Tadeusz; The National Centre for Research and Development; PBS2/A8/20/2013; PBS2/A8/24/2013 (Elsevier, 2017-07-29)
      The objective of this study was to determine the prevalence and types of infections in perinatal mortality (PM) cases from Polish dairy farms and the relevance of the presence of infection to the cause of death. This prospective longitudinal study was carried out on 121 PM and 21 control calves with a gestation of ≥260 days. Six control calves were euthanized and examined using the same protocol as for PM calves. Material was collected over a 20-month period between November 2013 and June 2015. The PM and control calves were collected from 29 to 5 herds, respectively. Blood samples from calves were tested for antibodies to Neospora caninum, glycoprotein B of BoHV-1, BVDV and SBV using ELISAs and Leptospira hardjo and Leptospira pomona with the microscopic agglutination test. Brain and kidney samples from all PM and six euthanized control calves were tested using real time PCR to detect Neospora caninum, pathogenic Leptospira spp., BoHV-1 and SBV; brain was examined histopathologically for detection of N. caninum cysts. Samples from eight inner organs from all PM and six control calves were cultured aerobically, anaerobically and microaerobically. Ear samples from all PM and control calves were tested for BVDV using an antigen ELISA. In total, 21.5% of PM calves were infected (antigen and/or antibody-positive) in utero; none of the control calves were infected. Direct evidence of infection (culture, Ag-ELISA, PCR, histopathology) was detected in 9.1% of PM calves. Gestation length in infected singletons was shorter than in uninfected singletons (274 ± 8 vs. 279 ± 7 days; P < 0.01). The odds ratio for diagnosis of infection in single pregnancies ≤275 days was 3.75 (95% CI:1.2–12.1), (P < 0.05). Infection was the cause of death in 10% of calves. The most common infections detected in these Polish PM calves were parasitic (11.6% of PM cases), viral (7.4%) and bacterial (5%). This study demonstrated that indirect evidence of infection is detected more frequently than direct, coinfection is rare, infection is rarely accompanied by gross lesions and is rarely a cause of death in cases of PM.
    • Influence of feeding systems on the eating quality of beef

      Troy, Declan J.; Murray, Brendan; O'Sullivan, Aileen; Mooney, Teresa; Moloney, Aidan P; Kerry, Joseph P. (Teagasc, 2002-10)
      The objective was to determine pre-slaughter factors which may enhance the eating quality of beef and to assist the Irish beef production chain to exploit these factors to produce beef of higher quality and increased consumer acceptability. The effects of pre-slaughter growth rate, high energy diets, feed type and age at slaughter on beef quality were examined.
    • Influence of testing procedure on evaluation of white clover (Trifolium repens L.)

      Gilliland, T. J.; McGilloway, D.; Conaghan, P. (Teagasc, Oak Park, Carlow, Ireland, 2009)
      This study examined data sets derived from the white clover cultivar evaluation programmes of AFBI (N. Ireland), and DAFF (Republic of Ireland) to determine whether elite performing genotypes are identifiable, independent of test procedure and leaf size factors. Genetic variation in yield and persistency, independent of the leaf size continuum effect, was observed. Identification of elite cultivars by breeders or testers therefore required readjustment of assessment standards to account for the mostly curvilinear relationships between performance and leaf size. The different testing procedures, involving cutting or grazing at different heights, frequencies and nitrogen rates changed the relative performances between the cultivars, making it difficult to predict performance potential beyond specific test conditions. The underlying causes for these changes in rankings was considered, including sensitivity to season and location, the antagonistic affects of defoliation pressure and companion grass competition, the independence of different seasonal profiles and the probable role of other morphological characteristics. In is concluded that testing authorities must calculate the management by leaf size relationships to adjust pass/fail standards if elite performing cultivars are to be correctly indentified.
    • InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

      Breuer, Karin; Foroushani, Amir K.; Laird, Matthew R; Chen, Carol; Sribnaia, Anastasia; Lo, Raymond; Winsor, Geoffrey L; Hancock, Robert E.W.; Brinkman, Fiona S. L.; Lynn, David J; et al. (Oxford University Press, 2012-11-24)
      InnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism.
    • Insemination factors affecting the conception rate in seasonal calving Holstein-Friesian cows

      Buckley, Frank; Mee, John F; O'Sullivan, Kathleen; Evans, R. D.; Berry, Donagh P.; Dillon, Pat; AIB Bank; Holstein UK and Ireland; National AI Co-ops; Dairy Levy Research Trust (EDP Sciences, 2003-11)
      Differences in conception rate to first service between artificial inseminations (AI) carried out by commercial AI operators (CAI) or do-it-yourself operators (DIY), between natural service (NAT) and AI, between different AI sires, and between fresh and frozen-thawed semen, on Irish commercial dairy farms, were studied using logistic regression. The study comprised 12 933 potential first inseminations from 77 spring-calving dairy herds. The data were recorded during 1999 and 2000. Amongst the total, 4 394 cows had repeated records across the two years. Adjustment variables included: herd, year, parity, calving period, calving to service interval, herd size, proportion of North American Holstein-Friesian genes, peak milk yield, semen fresh or frozen-thawed status, AI sire and a cow history variable to account for the correlation structure that may exist between performance records of cows present in both years of the study. Interactions of interest were tested but were non-significant. No significant association was observed between the category of AI operator and the likelihood of conception rate to first service (PREG1). The variation in PREG1 observed within the category of operator (CAI and DIY) was investigated using the Levene test for homogeneity of variance. There was no difference between the level of variation observed within CAI and DIY operators. There were significant differences in the likelihood of PREG1 between different AI sires. Amongst the 40 most commonly used AI sires, 3 sires had a lower likelihood of PREG1 (P < 0.05) when compared to the reference AI sire (sire with PREG1 similar to the mean of the group). There was a tendency for a reduced likelihood of PREG1 with the use of fresh semen compared to frozen-thawed semen ( , P = 0.067). Amongst the adjustment variables in the model, those significantly associated with the likelihood of PREG1 included the herd, calving period, calving to first service interval and peak milk yield. No significant difference in the likelihood of PREG1 was observed between AI and NAT.