• Paratuberculosis sero-status and milk production, SCC and calving interval in Irish dairy herds

      Hoogendam, K; Richardson, Esther K. B.; Mee, John F (Biomed Central, 2009-04-01)
      The objective of this study was to investigate the impact of paratuberculosis sero-status on milk yield, fat, protein, somatic cell count and calving interval in Irish dairy herds. Serum from all animals over 12 months of age (n = 2,602) in 34 dairy herds was tested for antibodies to Mycobacterium avium subsp. paratuberculosis using an ELISA. Herds were categorised by sero-status into positive, non-negative and negative, where a positive herd contained two or more positive cows, a non-negative herd contained only one positive cow and a negative herd contained no positive cows. Data at animal, parity and herd-level were analysed by multiple regression using general linear models. Positive herds (mean herd size = 129 cows) and non-negative herds (81 cows) were larger than negative herds (72 cows) (P < 0.01). Negative herds had the highest economic breeding index (EBI), while positive herds had the highest estimated breeding value (EBV) for milk yield. There was no significant effect of paratuberculosis sero-status at animal, parity or herd-level on milk yield, milk fat or protein production, somatic cell count score (SCCS) or calving interval. Negative herds tended to have a lower SCCS than positive and nonnegative herds (P = 0.087). This study only examined the effects of paratuberculosis sero-status but did not examine the clinical effects of Johne's disease at the farm or dairy industry levels.
    • PastureBase Ireland: A grassland decision support system and national database

      Hanrahan, Liam; Geoghegan, Anne; O'Donovan, Michael; Griffith, Vincent; Ruelle, Elodie; Wallace, Michael; Shalloo, Laurence (Elsevier, 2017-03-22)
      PastureBase Ireland (PBI) is a web-based grassland management application incorporating a dual function of grassland decision support and a centralized national database to collate commercial farm grassland data. This database facilitates the collection and storage of vast quantities of grassland data from grassland farmers. The database spans across ruminant grassland enterprises – dairy, beef and sheep. To help farmers determine appropriate actions around grassland management, we have developed this data informed decision support tool to function at the paddock level. Individual farmers enter data through the completion of regular pasture cover estimations across the farm, allowing the performance of individual paddocks to be evaluated within and across years. To evaluate the PBI system, we compared actual pasture cut experimental data (Etesia cuts) to PBI calculated outputs. We examined three comparisons, comparing PBI outputs to actual pasture cut data, for individual DM yields at defoliation (Comparison 1), for cumulative annual DM yields including silage data (Comparison 2) and, for cumulative annual DM yields excluding silage data (Comparison 3). We found an acceptable accuracy between PBI outputs and pasture cut data when statistically analyzed using relative prediction error and concordance correlation coefficients for the measurement of total annual DM yield (Comparison 2), with a relative prediction error of 15.4% and a concordance correlation coefficient of 0.85. We demonstrated an application of the PBI system through analysis of commercial farm data across two years (2014–2015) for 75 commercial farms who actively use the system. The analysis showed there was a significant increase in DM yield from 2014 to 2015. The results indicated a greater variation in pasture growth across paddocks within farms than across farms.
    • Pathogen profile of clinical mastitis in Irish milk-recording herds reveals a complex aetiology

      Keane, Orla M; Budd, Kathleen E; Flynn, James; McCoy, Finola (British Veterinary Association, 2013-05-21)
      Effective mastitis control requires knowledge of the predominant pathogen challenges on the farm. In order to quantify this challenge, the aetiological agents associated with clinical mastitis in 30 milk-recording dairy herds in Ireland over a complete lactation were investigated. Standard bacteriology was performed on 630 pretreatment quarter milk samples, of which 56 per cent were culture-positive, 42 per cent culture-negative and 2 per cent contaminated. Two micro-organisms were isolated from almost 5 per cent of the culture-positive samples. The bacteria isolated were Staphylococcus aureus (23 per cent), Streptococcus uberis (17 per cent), Escherichia coli (9 per cent), Streptococcus species (6 per cent), coagulase-negative Staphylococci (4 per cent) and other species (1 per cent). A wide variety of bacterial species were associated with clinical mastitis, with S aureus the most prevalent pathogen overall, followed by S uberis. However, the bacterial challenges varied widely from farm to farm. In comparison with previous reports, in the present study, the contagious pathogens S aureus and Streptococcus agalactiae were less commonly associated with clinical mastitis, whereas, the environmental pathogens S uberis and E coli were found more commonly associated with clinical mastitis. While S aureus remains the pathogen most commonly associated with intramammary infection in these herds, environmental pathogens, such as S uberis and E coli also present a considerable challenge.
    • Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures

      Foroushani, Amir B. K.; Brinkman, Fiona S. L.; Lynn, David J; Teagasc Walsh Fellowship Programme; AllerGen 12B&B2; Genome Canada; Michael Smith Foundation for Health Research; RMIS6018 (PeerJ, 2013-12-19)
      Motivation. Predominant pathway analysis approaches treat pathways as collections of individual genes and consider all pathway members as equally informative. As a result, at times spurious and misleading pathways are inappropriately identified as statistically significant, solely due to components that they share with the more relevant pathways. Results. We introduce the concept of Pathway Gene-Pair Signatures (Pathway-GPS) as pairs of genes that, as a combination, are specific to a single pathway. We devised and implemented a novel approach to pathway analysis, Signature Over-representation Analysis (SIGORA), which focuses on the statistically significant enrichment of Pathway-GPS in a user-specified gene list of interest. In a comparative evaluation of several published datasets, SIGORA outperformed traditional methods by delivering biologically more plausible and relevant results. Availability. An efficient implementation of SIGORA, as an R package with precompiled GPS data for several human and mouse pathway repositories is available for download from http://sigora.googlecode.com/svn/.
    • Performance and carcass traits of progeny of Limousin sires differing in genetic merit

      Keane, Michael G.; Diskin, Michael G. (Teagasc, Oak Park, Carlow, Ireland, 2007)
      Genetic indices for growth and carcass classification are published for beef sires used in Ireland for artificial insemination (AI). The objective of this study was to compare growth and carcass traits of progeny of Limousin sires of low and high genetic index for growth. A total of 70 progeny (42 males and 28 females) out of predominantly Holstein-Friesian cows by 7 AI Limousin sires were reared together to slaughter. The 7 sires were classified as low (n=3) or high (n=4) index based on their published genetic index for growth. The male progeny were reared entire and all animals were slaughtered at about 20 months of age. Carcasses were classified for conformation and fatness, and a rib joint (ribs 6 to 10) was separated into fat, muscle and bone. Growth rate did not differ significantly between the index groups but tended to be higher for the high index progeny. This higher growth rate, combined with a significantly higher kill out proportion, resulted in carcass weight andcarcass weight per day of age being significantly higher for the high index progeny. Carcass conformation and fat class were not affected by genetic index, nor was the composition of the rib joint. Compared with males, females had a significantly lower growth rate and kill out proportion and, consequently, had a significantly lower carcass weight. The proportions of fat and bone in the rib joint were significantly higher, and the proportion of muscle was significantly lower for females than for males. It is concluded that carcass weight reflected sire group genetic index for growth but feed intake, carcass classification and rib joint composition were not affected.
    • Performance and feed intake of five beef suckler cow genotypes and pre-weaning growth of their progeny

      Murphy, B.M.; Drennan, Michael J; O'Mara, Frank P.; McGee, Mark; Teagasc Walsh Fellowship Programme (Teagasc, Oak Park, Carlow, Ireland, 2008)
      The effect of beef suckler cow genotype on feed intake, performance, milk yield and on pre-weaning growth of their progeny was determined over four lactations. The five cow genotypes examined were Limousin (L), Charolais (C), Limousin × Holstein-Friesian (LF), Limousin × (Limousin × Holstein-Friesian) (LLF) and Simmental × (Limousin × Holstein-Friesian) (SLF). The herd calved in spring and the progeny spent from April until weaning (October/ November) at pasture with their dams. Live weight (kg) at the start of the indoor winter period was greater (P < 0.001) for C (702) than L (616) cows who in turn were heavier than LF (552) and LLF (574), with SLF (582) being intermediate. Silage dry matter (DM) intake (kg /day) was greater (P < 0.01) for C and SLF cows than L and LLF, whereas LF were inter-mediate. Dry matter intake (kg/day) of zero-grazed grass did not differ (P > 0.05) between the genotypes but followed a similar trend to grass silage intake. The decrease in live weight over the indoor winter period was greater (P < 0.01) for L and C cows than for LLF and SLF, whereas LF were intermediate. The increase in live weight during the grazing season was greater (P < 0.01) for C cows than all except L, which were intermediate. Calving difficulty score was greater (P < 0.01) for C cows than LLF, L and SLF, whereas LF were intermediate. Birth weight of calves from LF cows was lower (P < 0.001) than C with L being intermediate, but greater than LLF, with SLF being intermediate. Milk yield (kg/day) was higher (P < 0.001) for LF (9.7) and SLF (8.7) cows than the other genotypes (5.5 to 7.0), which did not differ significantly. Pre-weaning live-weight gain was greater (P < 0.001) for progeny of LF cows than all other genotypes except SLF, which in turn were greater than L and C, with LLF being intermediate. In conclusion, calf pre-weaning growth was higher for cow genotypes with higher milk yield, which was also associated with higher cow DM intake.
    • Perinatal immuno/inflammatory responses in the presence or absence of bovine fetal infection

      Jawor, Paulina; Mee, John F; Stefaniak, Tadeusz; The National Centre for Research and Development; PBS2/A8/20/2013 (Biomed Central, 2018-11-01)
      Background It is known that the bovine fetus can mount an immune and inflammatory reaction to infection, but it is not known whether there is a contemporaneous maternal response. Nor is it known whether the response of calves which die perinatally, with or without infection, differs from that of live perinates. Hence, the objective of this study was to determine if acute phase reactant and immunoglobulin concentrations differed between calves (and their dams) in three groups: live calves (CC; n = 21) and dead calves with (PM INF+; n = 22) or without (PM INF-; n = 89) in utero infection. In calf plasma, serum amyloid A, haptoglobin, immunoglobulins M, G1 and G2 and interleukin-6 were measured. In dam serum, SAA and Hp was measured and in amniotic and abomasal fluid, IL-6 was measured. Results Live calves had higher plasma concentrations of SAA and IL-6 than dead calves with (PM INF+) or without (PM INF-) in utero infection. Calves in the PM INF-, but not PM INF+ group, had higher Hp concentrations than calves in the CC group. Calves in the PM INF+ group had higher IgG1 concentrations than calves in the PM INF- and CC groups. Except for higher IgG1 and IgG2 concentrations, biomarker values did not differ significantly between dead calves with or without in utero infection. Live calves had higher IL-6 concentrations in abomasal fluid compared to PM INF- calves. There were no significant differences in blood biomarker concentrations between dams of the three groups of calves. Amniotic fluid IL-6 concentrations were higher from the dams of control calves than the dams of uninfected calves. Conclusions Differences in biomarkers (higher Hp and IgG1; lower SAA and IL-6) between perinatal mortalities and live perinates probably reflect differences between these two groups in age at sampling (SAA and IL-6) and in utero infection (IgG1). Out of the six analytes measured in calves, only IgG1 and IgG2 were biomarkers of (chronic) in utero infection.
    • Peripheral and gastrointestinal immune systems of healthy cattle raised outdoors at pasture or indoors on a concentrate-based ration

      Lejeune, Alexandre; Monahan, Frank J; Moloney, Aidan P; Earley, Bernadette; Black, Alistair D; Campion, Deirdre P; Englishby, Tanya; Reilly, Petrina; O'Doherty, John V.; Sweeney, Torres (Biomed Central, 2010-03-31)
      Background: Despite an increasing preference of consumers for beef produced from more extensive pasture-based production systems and potential human health benefits from the consumption of such beef, data regarding the health status of animals raised on pasture are limited. The objective of this study was to characterise specific aspects of the bovine peripheral and the gastrointestinal muscosal immune systems of cattle raised on an outdoor pasture system in comparison to animals raised on a conventional intensive indoor concentrate-based system. Results: A number of in vitro functional tests of immune cells suggested subtle differences between the animals on the outdoor versus indoor production systems. There was a decrease in the number of neutrophils and monocytes engaged in phagocytosis in outdoor cattle (P < 0.01 and P < 0.05, respectively) in comparison to those indoors. Following mitogen stimulation, a lower level of interferon-γ was produced in leukocytes from the outdoor animals (P < 0.05). There was evidence of a gastrointestinal nematode infection in the outdoor animals with elevated levels of serum pepsinogen (P < 0.001), a higher number of eosinophils (P < 0.05) and a higher level of interleukin-4 and stem cell factor mRNA expression (P < 0.05) in the outdoor animals in comparison to the indoor animals. Lower levels of copper and iodine were measured in the outdoor animals in comparison to indoor animals (P < 0.001). Conclusion: Despite distinctly contrasting production systems, only subtle differences were identified in the peripheral immune parameters measured between cattle raised at pasture in comparison to animals raised on a conventional intensive indoor concentrate-based production system.
    • Physiological and behavioural aspects of housing stress in cattle

      Earley, Bernadette; Gupta, Sandeep; Murray, Margaret; Prendiville, Daniel J.; European Union (Teagasc, 2008-12-01)
      The effect of various space allowances on pituitary, adrenal, immune responses and performance was investigated in 72 Holstein x Friesian bulls. Bulls (403 ± 3.5 kg) were blocked by weight and randomly assigned into two groups (familiar, F and unfamiliar, UF) x three (1.2, 2.7 and 4.2 m2 per bull; n = 24 bulls per space allowance) treatments and housed for 83 days in 18 pens (n = 4 per pen). Blood samples were collected on day –1, 0, 3, 14, 36 and 77 with respect to mixing and housing on day 0. The bulls were administered with adrenocorticotrophic hormone (ACTH) on day 3 and corticotrophin-releasing hormone (CRH) on days 14, 36 and 77. The basal cortisol concentrations were not affected (P>0.05) by mixing of familiar and unfamiliar bulls. On day 3, basal cortisol was greater (P<0.05) in the bulls housed at 1.2 than those at 2.7 and 4.2 m2 space allowances while no effect was observed in ACTH-induced plasma cortisol concentration among treatments. Following CRH administration there was no effect (P>0.05) of treatment and treatment x time on ACTH. On day 14, interferon-? production was lower (P<0.05) in the bulls housed at 4.2 vs 2.7 m2 and was intermediate but not (P>0.05) different for those housed at 1.2 m2. Bulls housed at either space allowances had (P<0.05) neutrophilia, lymphopenia, eosinopenia and decreased haemoglobin on day 3 compared with day 0. The liveweight gain from days 0 to 83 was lower (P< 0.05) in bulls housed at 1.2 compared with those at 2.7 and 4.2 m2. Housing bulls at 1.2 m2 space allowance had a detrimental effect on their growth and was associated with an acute rise in plasma cortisol concentration (on day 3) compared with space allowances of 2.7 and 4.2 m2/bull.
    • Physiological and behavioural aspects of housing stress in cattle.

      Earley, Bernadette; Gupta, Sandeep; Murray, Margaret; Prendiville, Daniel J. (Teagasc, 2008-12-01)
      The effect of various space allowances on pituitary, adrenal, immune responses and performance was investigated in 72 Holstein x Friesian bulls.The effect of transporting bulls for 12-h by road previously housed for 96 days at three space allowances (1.2, 2.7, 4.2 m2 per bull) on adrenal, haematological, immune responses, body temperature and performance was investigated. The effect of repeated regrouping and relocation (R&R) on behaviour of steers was investigated. The effect of repeated regrouping and relocation (R&R) of cattle on hypothalamicpituitary- adrenal (HPA) axis, immune function, blood biochemical, hematological variables and ADG, was investigated.
    • Pig Farmers' Conference 2012: Proceedings from the Teagasc National Pig Conferences

      Lawlor, Peadar G; McKeon, Michael; Quinn, Amy; Norris, David; Owens, David; Boyle, Laura; McCutcheon, Gerard; Clarke, Seamas (Teagasc, 2012-10)
      Proceedings from the Teagasc National Pig Conferences which took place on 23 October in the Horse and Jockey Hotel, Tipperary and the 24 October in the Cavan Crystal Hotel, Cavan
    • Pig producer perspectives on the use of meat inspection as an animal health and welfare diagnostic tool in the Republic of Ireland and Northern Ireland

      Devitt, Catherine; Boyle, Laura; Teixeira, Dayane L.; O'Connell, Niamh E.; Hawe, M.; Hanlon, A.; Department of Agriculture, Food and the Marine; RSF 11/S/107 (Biomed Central, 2016-02-09)
      Background Currently, there is growing interest in developing ante and post mortem meat inspection (MI) to incorporate measures of pig health and welfare for use as a diagnostic tool on pig farms. However, the success of the development of the MI process requires stakeholder engagement with the process. Knowledge gaps and issues of trust can undermine the effective exchange and utilisation of information across the supply chain. A social science research methodology was employed to establish stakeholder perspectives towards the development of MI to include measures of pig health and welfare. In this paper the findings of semi-structured telephone interviews with 18 pig producers from the Republic of Ireland and Northern Ireland are presented. Results Producers recognised the benefit of the utilisation of MI data as a health and welfare diagnostic tool. This acknowledgment, however, was undermined for some by dissatisfaction with the current system of MI information feedback, by trust and fairness concerns, and by concerns regarding the extent to which data would be used in the producers’ interests. Tolerance of certain animal welfare issues may also have a negative impact on how producers viewed the potential of MI data. The private veterinary practitioner was viewed as playing a vital role in assisting them with the interpretation of MI data for herd health planning. Conclusions The development of positive relationships based on trust, commitment and satisfaction across the supply chain may help build a positive environment for the effective utilisation of MI data in improving pig health and welfare. The utilisation of MI as a diagnostic tool would benefit from the development of a communication strategy aimed at building positive relationships between stakeholders in the pig industry.
    • Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen

      McGovern, Emily; McCabe, Matthew; Cormican, Paul; Popova, Milka; Keogh, Kate; Kelly, Alan K; Kenny, David A.; Waters, Sinead M. (Springer Nature, 2017-10-12)
      Methane generated during enteric fermentation in ruminant livestock species is a major contributor to global anthropogenic greenhouse gas emissions. A period of moderate feed restriction followed by ad libitum access to feed is widely applied in cattle management to exploit the animal’s compensatory growth potential and reduce feed costs. In the present study, we utilised microbial RNA from rumen digesta samples to assess the phylogenetic diversity of transcriptionally active methanogens from feed-restricted and non-restricted animals. To determine the contribution of different rumen methanogens to methanogenesis during dietary restriction of cattle, we conducted high-throughput mcrA cDNA amplicon sequencing on an Illumina MiSeq and analysed both the abundance and phylogenetic origin of different mcrA cDNA sequences. When compared to their unrestricted contemporaries, in feed-restricted animals, the methanogenic activity, based on mcrA transcript abundance, of Methanobrevibacter gottschalkii clade increased while the methanogenic activity of the Methanobrevibacter ruminantium clade and members of the Methanomassiliicoccaceae family decreased. This study shows that the quantity of feed consumed can evoke large effects on the composition of methanogenically active species in the rumen of cattle. These data potentially have major implications for targeted CH4 mitigation approaches such as anti-methanogen vaccines and/or tailored dietary management.
    • Plane of nutrition before and after 6 months of age in Holstein-Friesian bulls: II. Effects on metabolic and reproductive endocrinology and identification of physiological markers of puberty and sexual maturation

      Byrne, Colin J; Fair, Seán; English, Anne-Marie; Urh, C.; Sauerwein, H.; Crowe, Mark A; Lonergan, P.; Kenny, David A.; Department of Agriculture, Food and the Marine; 11/S/116 (Elsevier, 2018-02-04)
      The aim of this study was (1) to examine the effect of plane of nutrition during the first and second 6 mo of life on systemic concentrations of reproductive hormones and metabolites in Holstein-Friesian dairy bulls, and (2) to establish relationships with age at puberty and postpubertal semen production potential. Holstein-Friesian bull calves (n = 83) with a mean (standard deviation) age and body weight of 17 (4.4) d and 52 (6.2) kg, respectively, were assigned to a high or low plane of nutrition for the first 6 mo of life. At 24 wk of age, bulls were reassigned, within treatment, either to remain on the same diet or to switch to the opposite diet until puberty, resulting in 4 treatment groups: high-high, high-low, low-low, and low-high. Monthly blood samples were analyzed for metabolites (albumin, urea, total protein, β-hydroxybutyrate, glucose, nonesterified fatty acid, triglycerides and creatinine), insulin, insulin-like growth factor-1, leptin, adiponectin, FSH, and testosterone. A GnRH challenge was carried out at 16 and 32 wk of age (n = 9 bulls per treatment). Blood was collected at 15-min intervals for 165 min, with GnRH administered (0.05 mg/kg of body weight, i.v.) immediately after the third blood sample. Blood samples were subsequently analyzed for LH, FSH, and testosterone. Stepwise regression was used to detect growth and blood measurements to identify putative predictors of age at puberty and subsequent semen quality traits. Metabolic hormones and metabolites, in general, reflected metabolic status of bulls. Although FSH was unaffected by diet, it decreased with age both in monthly samples and following GnRH administration. Testosterone was greater in bulls on the high diet before and after 6 mo of age. Testosterone concentrations increased dramatically after 6 mo of age. Luteinizing hormone was unaffected by diet following GnRH administration but basal serum LH was greater in bulls on a high diet before 6 mo of age. In conclusion, the plane of nutrition offered before 6 mo of age influenced metabolic profiles, which are important for promoting GnRH pulsatility, in young bulls
    • Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples.

      Mullen, Michael P.; Creevey, Christopher J.; Berry, Donagh P.; McCabe, Matthew; Magee, David A; Howard, Dawn J.; Killeen, Aideen P.; Park, Stephen D. E.; McGettigan, Paul; Lucy, Matt C.; et al. (Biomed Central, 2012-01-11)
      Background: The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility. Results: In total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952) of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612) were intronic and 9% (n = 464) were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS). Significant (P < 0.01) mean allele frequency differentials between the low and high fertility groups were observed for 720 SNPs (58 NSS). Allele frequencies for 43 of the SNPs were also determined by genotyping the 150 individual animals (Sequenom® MassARRAY). No significant differences (P > 0.1) were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total). Conclusions: The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post-natal growth and development and subsequent lactogenesis and fertility. We have identified a large number of variants segregating at significantly different frequencies between cattle groups divergent for calving interval plausibly harbouring causative variants contributing to heritable variation. To our knowledge, this is the first report describing sequencing of targeted genomic regions in any livestock species using groups with divergent phenotypes for an economically important trait.
    • Polymorphisms in bovine immune genes and their associations with somatic cell count and milk production in dairy cattle

      Beecher, Christine; Daly, Mairead; Childs, Stuart; Berry, Donagh P.; Magee, David A; McCarthy, Tommie V; Giblin, Linda (Biomed Central, 05/11/2010)
      Background: Mastitis, an inflammation of the mammary gland, is a major source of economic loss on dairy farms. The aim of this study was to quantify the associations between two previously identified polymorphisms in the bovine toll-like receptor 2 (TLR2) and chemokine receptor 1 (CXCR1) genes and mammary health indictor traits in (a) 246 lactating dairy cow contemporaries representing five breeds from one research farm and (b) 848 Holstein-Friesian bulls that represent a large proportion of the Irish dairy germplasm. To expand the study, a further 14 polymorphisms in immune genes were included for association studies in the bull population. Results: TLR4-2021 associated (P < 0.05) with both milk protein and fat percentage in late lactation (P < 0.01) within the cow cohort. No association was observed between this polymorphism and either yield or composition of milk within the bull population. CXCR1-777 significantly associated (P < 0.05) with fat yield in the bull population and tended to associate (P < 0.1) with somatic cell score (SCS) in the cows genotyped. CD14-1908 A allele was found to associate with increased (P < 0.05) milk fat and protein yield and also tended to associate with increased (P < 0.1) milk yield. A SERPINA1 haplotype with superior genetic merit for milk protein yield and milk fat percentage (P < 0.05) was also identified. Conclusion: Of the sixteen polymorphisms in seven immune genes genotyped, just CXCR1-777 tended to associate with SCS, albeit only in the on-farm study. The lack of an association between the polymorphisms with SCS in the Holstein-Friesian data set would question the potential importance of these variants in selection for improved mastitis resistance in the Holstein-Friesian cow.
    • Post-epidemic Schmallenberg virus circulation: parallel bovine serological and Culicoides virological surveillance studies in Ireland

      Collins, Áine B; Barrett, Damien; Doherty, Michael L.; Larska, M.; Mee, John F; Teagasc Walsh Fellowship Programme; National Centre for Research and Development (NCBiR), Poland; PBS2/A8/24/2013 (Biomed Central, 2016-10-18)
      Background Schmallenberg virus (SBV) emerged in northern-Europe in 2011 resulting in an epidemic of ruminant abortions and congenital malformations throughout the continent. In the years following the epidemic there have been reports of SBV overwintering and continued circulation in several European countries. When the population-level of immunity declines in exposed regions, re-introduction of SBV could result in further outbreaks of Schmallenberg disease. The aims of this study were to determine the SBV seroprevalence in previously exposed Irish dairy herds in 2014 and to investigate if SBV continued to circulate in these herds in the three years (2013–2015) following the Irish Schmallenberg epidemic. Whole-herd SBV serosurveillance was conducted in 26 herds before (spring) and following the 2014 vector-season (winter), and following the 2015 vector-season (winter). In spring 2014, 5,531 blood samples were collected from 4,070 cows and 1,461 heifers. In winter 2014, 2,483 blood samples were collected from 1,550 youngstock (8–10 months old) and a subsample (n = 933; 288 cows, 645 heifers) of the seronegative animals identified in the spring. Youngstock were resampled in winter 2015. Culicoides spp. were collected in 10 herds during the 2014 vector-season and analysed for SBV; a total of 138 pools (3,048 Culicoides) from 6 SBV vector species were tested for SBV RNA using real-time PCR. Results In spring 2014, animal-level seroprevalence was 62.5 % (cows = 84.7 %; heifers = 0.6 %). Within-herd seroprevalence ranged widely from 8.5 %–84.1 % in the 26 herds. In winter 2014, 22 animals (0.9 %; 10 cows, 5 heifers, 7 youngstock) originating in 17 herds (range 1–4 animals/herd) tested seropositive. In winter 2015 all youngstock, including the 7 seropositive animals in winter 2014, tested seronegative suggesting their initial positive result was due to persistence of maternal antibodies. All of the Culicoides pools examined tested negative for SBV-RNA. Conclusions SBV appears to have recirculated at a very low level in these herds during 2013 and 2014, while there was no evidence of SBV infection in naïve youngstock during 2015. A large population of naïve animals was identified and may be at risk of infection in future years should SBV re-emerge and recirculate as it has done in continental Europe.
    • Post-Transcriptional Dysregulation by miRNAs Is Implicated in the Pathogenesis of Gastrointestinal Stromal Tumor [GIST]

      Kelly, Lorna; Bryan, Kenneth; Kim, Su Young; Janeway, Katherine A.; Killian, J. Keith; Schildhaus, Hans-Ulrich; Miettinen, Markku; Helman, Lee; Meltzer, Paul S.; van de Rijn, Matt; et al. (PLOS, 2013-05-24)
      In contrast to adult mutant gastrointestinal stromal tumors [GISTs], pediatric/wild-type GISTs remain poorly understood overall, given their lack of oncogenic activating tyrosine kinase mutations. These GISTs, with a predilection for gastric origin in female patients, show limited response to therapy with tyrosine kinase inhibitors and generally pursue a more indolent course, but still may prove fatal. Defective cellular respiration appears to underpin tumor development in these wild-type cases, which as a group lack expression of succinate dehydrogenase [SDH] B, a surrogate marker for respiratory chain metabolism. Yet, only a small subset of the wild-type tumors show mutations in the genes coding for the SDH subunits [SDHx]. To explore additional pathogenetic mechanisms in these wild-type GISTs, we elected to investigate posttranscriptional regulation of these tumors by conducting microRNA (miRNA) profiling of a mixed cohort of 73 cases including 18 gastric pediatric wild-type, 25 (20 gastric, 4 small bowel and 1 retroperitoneal) adult wild-type GISTs and 30 gastric adult mutant GISTs. By this approach we have identified distinct signatures for GIST subtypes which correlate tightly with clinico-pathological parameters. A cluster of miRNAs on 14q32 show strikingly different expression patterns amongst GISTs, a finding which appears to be explained at least in part by differential allelic methylation of this imprinted region. Small bowel and retroperitoneal wild-type GISTs segregate with adult mutant GISTs and express SDHB, while adult wildtype gastric GISTs are dispersed amongst adult mutant and pediatric wild-type cases, clustering in this situation on the basis of SDHB expression. Interestingly, global methylation analysis has recently similarly demonstrated that these wild-type, SDHB-immunonegative tumors show a distinct pattern compared with KIT and PDGFRA mutant tumors, which as a rule do express SDHB. All cases with Carney triad within our cohort cluster together tightly.
    • Post-weaning growth, ultrasound and skeletal measurements, muscularity scores and carcass traits and composition of progeny of five beef suckler cow genotypes

      Murphy, B.M.; Drennan, Michael J; O'Mara, Frank P.; McGee, Mark; Teagasc Walsh Fellowship Programme (Teagasc, Oak Park, Carlow, Ireland, 2008)
      Post-weaning growth, ultrasound and skeletal measurements, muscularity scores, and carcass traits and composition of the progeny of spring-calving Limousin (L), Charolais (C), Limousin × Holstein-Friesian (LF), Limousin × (Limousin × Holstein-Friesian) (LLF) and Simmental × (Limousin × Holstein-Friesian) (SLF) cow genotypes was determined over 3 years. Bull and heifer progeny were slaughtered at ~460 and ~610 days of age, respectively. Post-weaning growth did not differ significantly between the genotypes. Progeny from LF and SLF cows had the highest (P<0.001) carcass gain per day of age, whereas progeny from L and C cows had the highest (P < 0.01) carcass conformation score and lowest (P < 0.001) fat score. The proportion of meat in the car¬cass was higher (P < 0.001) and bone lower (P < 0.001), and meat to bone ratio higher (P < 0.001) for the progeny of L cows than all other genotypes, which were similar. Carcass fat proportion was similar for progeny of L and C cows and lower (P < 0.001) than LLF and SLF, with LF being intermediate. The progeny from L cows tended to have the greatest proportion of hind-quarter in the carcass. Genotype effects were mini¬mal when the proportion of high-value cuts was expressed relative to weight of meat in the carcass and hind-quarter. In conclusion, there was no effect of cow genotype on the performance of their progeny from weaning to slaughter. However, crossbred cows with good maternal (milk) traits produced progeny with a higher carcass weight per day of age, whereas the purebred continental cows produced progeny with superior carcass classification traits.
    • Post-weaning performance and carcass characteristics of steer progency from different suckler cow breed types

      Drennan, Michael J; McGee, Mark; Keane, Michael G. (Teagasc (Agriculture and Food Development Authority), Ireland, 2005-04)
      In two experiments a total of 44 steer progeny of spring-calving Charolais (C) and Hereford × Friesian (HF) suckler cows and C sires were slaughtered at approximately 2 years of age. Following weaning they were offered silage and 1 kg of concentrate per head daily during a 5 month winter after which they spent 7 months at pasture. In Experiment 1, animals were given a silage/concentrate diet during a finishing period of either 95 or 152 days. In Experiment 2, steers were offered either a daily diet of silage plus 6 kg of concentrates or concentrates to appetite plus 5 kg of silage (fresh weight) during the final 140-day finishing period. Following slaughter, an 8-rib pistola from each animal was dissected. For the two experiments combined C and HF progeny had carcass weights of 372 and 385 (s.e. 6.1) kg, proportions of carcass as pistola of 467 and 454 (s.e. 2.8) g/kg and pistola meat proportions of 676 and 642 (s.e. 5.1) g/kg, respectively. All fat traits were lower for the C than HF progeny but there was no difference in carcass conformation score. Increasing slaughter weight increased carcass weight (P < 0.001), kidney plus channel fat weight (P < 0.001), and pistola fat proportion (P < 0.001) and decreased the proportions of carcass as pistola (P < 0.05), pistola meat (P < 0.01), and bone (P < 0.05). In conclusion, breed type had no effect on carcass growth but the C progeny had higher meat yield than the HF. Increasing slaughter weight increased fatness and reduced meat yield.