• An observational study on passive immunity in Irish suckler beef and dairy calves: Tests for failure of passive transfer of immunity and associations with health and performance

      Todd, C. G.; McGee, Mark; Tiernan, Katie; Crosson, Paul; O’Riordan, Edward G.; McClure, J.; Lorenz, Ingrid; Earley, Bernadette; Department of Agriculture, Food and the Marine; 11/S/131 (Elsevier, 2018-07-25)
      The study objectives were to: 1) evaluate the diagnostic performance of passive immunity tests for classification of failure of passive transfer (FPT) risk, based on their relationships with calf health and performance, and 2) describe the epidemiology of morbidity and mortality in suckler beef and dairy calves under Irish conditions. A total of 1392 suckler beef calves (n = 111 farms) and 2090 dairy calves (84 farms) were included in this observational study. Blood samples were collected by jugular venipuncture. Serum samples were analysed for total IgG concentration using an ELISA assay, total protein concentration by clinical analyser (TP – CA), globulin concentration, zinc sulphate turbidity (ZST) units, total solids percentage by Brix refractometer (TS – BRIX), and total protein concentration by digital refractometer (TP – DR). Crude and cause-specific morbidity, all-cause mortality, and standardised 205-day body weight (BW) were determined. Generalised linear mixed models were used to evaluate associations between suckler beef and dairy calves for morbidity, mortality, growth and passive immunity. Receiver operating characteristic (ROC) curves were constructed to determine optimal test cut-offs for classification of health and growth outcomes. Overall, 20% of suckler beef and 30% of dairy calves were treated for at least one disease event by 6 mo. of age. Suckler beef calves had greater odds of bovine respiratory disease (BRD; odds ratio (OR), 95% confidence interval (CI): 2.8, 1.2–6.5, P = 0.01), navel infection (5.1, 1.9–13.2, P < 0.001), and joint infection/lameness (3.2, 1.3–7.8, P = 0.01) during the first 6 mo. of life than dairy calves. In addition, from birth to 6 mo. of age, suckler beef calves had greater rates of navel infection (incidence rate ratio (IRR), 95% CI: 3.3, 1.3–8.4, P = 0.01), but decreased rates of diarrhoea (0.9, 0.2–0.9, P = 0.03) compared to dairy calves. Optimal test cut-offs for classification of morbidity and mortality outcomes in suckler beef calves ranged from 8 to 9 mg/ml ELISA, 56 to 61 g/l TP – CA, 26 to 40 g/l globulin, 12 to 18 ZST units, 8.4% TS – BRIX, and 5.3 to 6.3 g/dl TP – DR. Optimal test cut-offs for classification of morbidity and growth outcomes in dairy calves ranged from 10 to 12 mg/ml ELISA, 57 to 60 g/l TP – CA, 29 to 34 g/l globulin, 19 ZST units, 7.8 to 8.4% TS – BRIX, and 5.7 to 5.9 g/dl TP – DR.
    • An observational study using blood gas analysis to assess neonatal calf diarrhea and subsequent recovery with a European Commission-compliant oral electrolyte solution

      Sayers, Riona; Kennedy, Aideen E.; Krump, Lea; Sayers, Gearoid; Kennedy, Emer; Epsilion Ltd.; IV20151256 (American Dairy Science Association, 2016-04-06)
      An observational study was conducted on dairy calves (51 healthy, 31 with neonatal diarrhea) during outbreaks of diarrhea on 4 dairy farms. Clinical assessment scores (CAS) were assigned to each healthy and diarrheic calf [from 0 (healthy) to 4 (marked illness)]. Blood gas analysis [pH, base excess (BE), Na+, K+, Ca2+, Cl−, glucose, total hemoglobin, standard HCO3−, strong ion difference (SID), and anion gap (AG)] was completed for each calf. Repeated measurements were taken in healthy animals, and pre- and postintervention measurements were taken for diarrheic calves. The mean CAS of diarrheic calves was 1.7, with 51, 30, 17, and 2% of calves scoring 1, 2, 3, and 4, respectively. The mean value for blood pH, BE, AG, and SID was 7.26, −4.93 mM, 16.3 mM, and 38.59 mM, respectively. Calves were administered an oral rehydration and buffering solution (ORBS; Vitalife for Calves, Epsilion Ltd., Cork, Ireland) and reassessed. The mean CAS decreased to 0.38 (65% of calves scored 0 and 35% scored 1) at 6 to 18 h posttreatment and to 0.03 (98% of calves scored 0 and 2% scored 1) within 24 to 48 h. Significant increases in mean value for pH, BE, HCO3−, Na+, and SID, and significant decreases in AG, K+, Ca2+, and total hemoglobin were recorded posttreatment. The correlation estimates indicated that pH, HCO3−, and BE were strongly correlated with CAS, with values exceeding 0.60 in all cases. Administration of an ORBS with a high SID and bicarbonate buffer demonstrated rapid recovery from a diarrheic episode in dairy calves.
    • Observed progeny performance validates the benefit of mating genetically elite beef sires to dairy females.

      Berry, D P; Ring, S C; Science Foundation Ireland; Department of Agriculture, Food and Marine; 16/RC/3835 (Elsevier for American Dairy Science Association, 2020-01-13)
      While several studies in cattle have confirmed the improved performance achievable from selection on total merit indexes, these studies have solely been confined to specific-purpose beef or dairy total merit indexes. Validation studies of total merit indexes used to select beef sires for use on dairy females are lacking. The objective here was to fill this void by quantifying the performance of beef × dairy progeny where the sire excels in either a total merit index encompassing calving performance and beef performance traits (dairy-beef index; DBI) or excels in a subindex based solely on calving performance (CLV); for comparative purposes, these beef × dairy progeny were also compared with dairy × dairy progeny. A total of 123,785 calving records from 101,773 dairy cows calving in 3,065 dairy herds were used; of these, 48,875 progeny also had carcass information. The beef sires were stratified into 5 equally sized groups based separately on their DBI or CLV. Linear and threshold mixed models were used to compare calving and carcass performance of all 3 sire genotypes. Of the 415 sires that ranked in the highest of the 5 strata on the CLV subindex, only 52% of them ranked in the highest stratum for the DBI. The percentage of primiparae requiring any assistance at calving was 2 to 3 percentage units greater for the higher DBI sires relative to both the higher CLV beef sires and the dairy sires (not ranked on anything); no difference existed in multiparae. The extent of calving difficulty in primiparae was, however, less in higher DBI beef sires relative to both the higher CLV beef sires and the dairy sires, although the differences were biologically small. Perinatal mortality was greatest in the beef sires relative to the dairy sires, but no difference existed between the high CLV or high DBI beef sires. No difference in progeny gestation length was evident between the high DBI or high CLV beef sires, although both were >2 d longer than progeny from dairy sires. The higher DBI sires produced progeny with heavier, more conformed carcasses relative to the progeny from both high CLV beef sires and dairy sires. No differences existed between the progeny of the beef sires ranked highly on the CLV versus those ranked highly on the DBI for the probability of achieving the specification for carcass weight (between 270 and 380 kg) or fat score; the higher DBI animals, however, had a 4 to 10% greater probability of achieving the minimum carcass conformation required. In all instances, the beef sires had a greater probability of achieving all specifications relative to the progeny from the dairy sires with the difference for conformation being particularly large. Results indicate that more balanced progeny can be generated using a DBI, helping meet the requirements of both dairy and beef producers. Ignoring market failure across sectors, using higher DBI sires could increase dairy herd profit by 3 to 5% over and above the status quo approach to selection in dairy (i.e., CLV subindex).
    • Offspring subcutaneous adipose markers are sensitive to the timing of maternal gestational weight gain

      Giblin, Linda; Darimont, Christian; Leone, Patricia; McNamara, Louise B.; Blancher, Florence; Berry, Donagh P.; Castaneda-Gutierrez, Euridice; Lawlor, Peadar G; Teagasc Walsh Fellowship Programme (Biomed Central, 08/03/2015)
      Background Excessive maternal weight gain during pregnancy impacts on offspring health. This study focused on the timing of maternal gestational weight gain, using a porcine model with mothers of normal pre-pregnancy weight. Methods Trial design ensured the trajectory of maternal gestational weight gain differed across treatments in early, mid and late gestation. Diet composition did not differ. On day 25 gestation, sows were assigned to one of five treatments: Control sows received a standard gestation diet of 2.3 kg/day (30 MJ DE/day) from early to late gestation (day 25–110 gestation). E sows received 4.6 kg food/day in early gestation (day 25–50 gestation). M sows doubled their food intake in mid gestation (day 50–80 gestation). EM sows doubled their food intake during both early and mid gestation (day 25–80 gestation). L sows consumed 3.5 kg food/day in late gestation (day 80–110 gestation). Offspring body weight and food intake levels were measured from birth to adolescence. Markers of lipid metabolism, hypertrophy and inflammation were investigated in subcutaneous adipose tissue of adolescent offspring. Results The trajectory of gestational weight gain differed across treatments. However total gestational weight gain did not differ except for EM sows who were the heaviest and fattest mothers at parturition. Offspring birth weight did not differ across treatments. Subcutaneous adipose tissue from EM offspring differed significantly from controls, with elevated mRNA levels of lipogenic (CD36, ACACB and LPL), nutrient transporters (FABP4 and GLUT4), lipolysis (HSL and ATGL), adipocyte size (MEST) and inflammation (PAI-1) indicators. The subcutaneous adipose depot from L offspring exhibited elevated levels of CD36, ACACB, LPL, GLUT4 and FABP4 mRNA transcripts compared to control offspring. Conclusions Increasing gestational weight gain in early gestation had the greatest impact on offspring postnatal growth rate. Increasing maternal food allowance in late gestation appeared to shift the offspring adipocyte focus towards accumulation of fat. Mothers who gained the most weight during gestation (EM mothers) gave birth to offspring whose subcutaneous adipose tissue, at adolescence, appeared hyperactive compared to controls. This study concluded that mothers, who gained more than the recommended weight gain in mid and late gestation, put their offspring adipose tissue at risk of dysfunction.
    • Offspring subcutaneous adipose markers are sensitive to the timing of maternal gestational weight gain

      Giblin, Linda; Darimont, Christian; Leone, Patricia; McNamara, Louise B.; Blancher, Florence; Berry, Donagh P.; Castaneda-Gutierrez, Euridice; Lawlor, Peadar G; Teagasc Walsh Fellowship Programme (Biomed Central, 08/03/2015)
      Background Excessive maternal weight gain during pregnancy impacts on offspring health. This study focused on the timing of maternal gestational weight gain, using a porcine model with mothers of normal pre-pregnancy weight. Methods Trial design ensured the trajectory of maternal gestational weight gain differed across treatments in early, mid and late gestation. Diet composition did not differ. On day 25 gestation, sows were assigned to one of five treatments: Control sows received a standard gestation diet of 2.3 kg/day (30 MJ DE/day) from early to late gestation (day 25–110 gestation). E sows received 4.6 kg food/day in early gestation (day 25–50 gestation). M sows doubled their food intake in mid gestation (day 50–80 gestation). EM sows doubled their food intake during both early and mid gestation (day 25–80 gestation). L sows consumed 3.5 kg food/day in late gestation (day 80–110 gestation). Offspring body weight and food intake levels were measured from birth to adolescence. Markers of lipid metabolism, hypertrophy and inflammation were investigated in subcutaneous adipose tissue of adolescent offspring. Results The trajectory of gestational weight gain differed across treatments. However total gestational weight gain did not differ except for EM sows who were the heaviest and fattest mothers at parturition. Offspring birth weight did not differ across treatments. Subcutaneous adipose tissue from EM offspring differed significantly from controls, with elevated mRNA levels of lipogenic (CD36, ACACB and LPL), nutrient transporters (FABP4 and GLUT4), lipolysis (HSL and ATGL), adipocyte size (MEST) and inflammation (PAI-1) indicators. The subcutaneous adipose depot from L offspring exhibited elevated levels of CD36, ACACB, LPL, GLUT4 and FABP4 mRNA transcripts compared to control offspring. Conclusions Increasing gestational weight gain in early gestation had the greatest impact on offspring postnatal growth rate. Increasing maternal food allowance in late gestation appeared to shift the offspring adipocyte focus towards accumulation of fat. Mothers who gained the most weight during gestation (EM mothers) gave birth to offspring whose subcutaneous adipose tissue, at adolescence, appeared hyperactive compared to controls. This study concluded that mothers, who gained more than the recommended weight gain in mid and late gestation, put their offspring adipose tissue at risk of dysfunction.
    • On farm welfare assessment of beef cattle using an environmentally-based welfare index and investigation of the human-animal relationship

      Earley, Bernadette; Mazurek, Mickael; Murray, Margaret; Prendiville, Daniel J.; European Union (Teagasc, 2009-01-01)
      On farm welfare assessment of beef cattle using an environmentally-based welfare index and investigation of the human-animal relationship. Study 1. Animal welfare index (AWI): an on-farm survey of beef suckler farms in Ireland. Study 2. Investigation and specificity of behavioural fear responses of heifers to different fear-eliciting situations involving humans.
    • An on-farm investigation of beef suckler herds using an animal welfare index (AWI)

      Mazurek, Mickael; Prendiville, Daniel J.; Crowe, Mark A; Veissier, Isabelle; Earley, Bernadette (Biomed Central, 2010-12-13)
      Background: Beef suckler farms (194 farms throughout 13 counties) were assessed once with housed cattle and once with cattle at grass using an animal welfare index (AWI). Twenty-three of the 194 farms were revisited a year later and re-evaluated using the AWI and the Tier-Gerechtheits-Index 35L/2000 (TGI35L/2000). Thirty-three indicators were collected in five categories: locomotion (5 indicators); social interactions (between animals) (7), flooring (5), environment (7) and Stockpersonship (9). Three indicators relating to the size of the farm were also collected. Improving animal welfare is an increasingly important aspect of livestock production systems predominantly due to increased consumer concern about the source of animal products. The objectives were (i) to evaluate animal welfare of Irish beef suckler herds using an animal welfare index (AWI), (ii) to examine correlations between parameters, how they influence the AWI and investigate the applicability of the parameters used, (iii) to investigate the impact of the activity of the farmer (full-time or part-time), the interest of the farmer and the number of animals on the AWI. Results: The mean AWI was 65% and ranged from 54% to 83%. The grazing period represented 16.5% of the total points of the AWI. Seventy percent of the farms were rated as "Very Good" or "Excellent". There was no difference (P > 0.05) in AWI between full-time and part-time farmers. Part-time farmers had greater (P = 0.01) "social interactions": calving (P = 0.03) and weaning (P < 0.001) scores. Full-time farmers had cleaner animals (P = 0.03) and their animals had less lameness (P = 0.01). The number of animals on-farm and the interest of the Stockperson were negatively and positively correlated (P = 0.001), respectively, with the AWI. A hierarchical classification was performed to examine how the indicators influenced the AWI. Conclusion: The AWI was easily applicable for an on-farm evaluation of welfare. The Stockpersonship was an important factor in determining the AWI (11% of the total variation) more specifically, the interest of the farmer. Part and full-time farming did not differ (P > 0.05) in AWI scores. This method could, with further development, be used in countries with both intensive and/or extensive production systems and would require substantially less resources than animal-based methods.
    • Optimal system of contract matings for use in a commercial dairy population

      McParland, Sinead; Kearney, K. F.; Lopez-Villalobos, N.; Berry, Donagh P. (Teagasc (Agriculture and Food Development Authority), Ireland, 2009)
      Managing the contribution of prominent animals to the pedigree of livestock populations is a topic of increasing importance worldwide. The aim of this study was to evaluate methods of controlling the accumulation of inbreeding in the Irish Holstein-Friesian population through the methodology used to arrange contract matings. Two non-random mating systems were investigated, linear programming (LP) and sequential programming (SEQ); these were compared with random mating (RAN) and mating of the best sires to the best dams (TOP). All mating systems were compared across a range of objectives: to maximise genetic merit for the economic breeding index (EBI) used in Ireland, to minimise population coancestry with breeding females (R-value), and a dual objective of simultaneously maximising EBI and minimising coancestry with breeding females. Algorithms were developed to identify elite dams and sires from the national herd for use in the contract mating programme. One thousand contract matings were generated using each selection method, with the aim of producing 83 test sires (the number of bulls which it is feasible to test annually in Ireland) for use in a progeny testing scheme. The top 1,000 matings, as selected by the LP and SEQ methods, performed similarly when maximising the dual objective (average progeny EBI of €145 and an average coancestry of the progeny to the population of breeding females of 0.93%). The TOP and RAN methods both selected phantom progeny with higher coancestry with the breeding female population (1.21% and 1.34%, respectively) than the LP and SEQ methods. However the matings from the TOP method generated progeny of higher genetic merit (EBI = €199), whilst the progeny generated from the RAN method had lower genetic merit (EBI = €127) than those selected by the LP or SEQ methods.
    • Optimising The Response To Supplementary Concentrates By Beef Cattle In Winter

      Keane, Michael G.; Drennan, Michael J; Moloney, Aidan P (Teagasc, 2008-01-01)
      Concentrates are a major component of feed costs in winter finishing of beef cattle. Two separate experiments were carried out to evaluate the response to increasing supplementary concentrate level with grass silage and the effects of feeding the silage and concentrates separately or as a total mixed ration (TMR). In experiment 1, a total of 117 finishing steers (initial live weight 538 kg, s.d. 35.5) were assigned to a preexperimental slaughter group of 9 animals and to 6 feeding treatments of 18 animals each. The feeding treatments were: 1) silage (SO) only offered ad libitum, 2) SO plus a low level of concentrates offered separately (LS), 3) SO plus a low level of concentrates offered as a TMR (LM), 4) SO plus a medium level of concentrates offered separately (MS), 5) SO plus a medium level of concentrates offered as a TMR (MM), and 6) concentrates ad libitum plus a restricted silage allowance (AL). Low and medium target concentrate levels were 3 and 6 kg dry matter (DM) per head daily. When silage and concentrates were fed separately, the daily concentrate allowance was given in one morning feed. The animals were individually fed for a mean period of 132 days. After slaughter, carcasses were weighed and graded and the ribs joint was dissected into its component tissues. Silage DM intake decreased but total DM intake increased with increasing concentrate level. Live weight gains for SO, LS, LM, MS, MM and AL were 0.34, 0.86, 0.86, 1.02, 1.00 and 1.12 (s.e. 0.064) kg/day, respectively. Corresponding carcass weight gains were 0.25, 0.58, 0.58, 0.71, 0.68 and 0.82 (s.e. 0.028) kg/day. All measures of fatness increased, ribs joint bone proportion decreased, and muscle proportion was not significantly affected by dietary concentrate level. There were no significant interactions between concentrate level and method of feeding. Compared with offering the feeds separately, feeding a TMR increased silage DM intake by proportionately 0.06 and total DM intake by proportionately 0.04. Otherwise, method of feeding had no significant effect on performance, slaughter or carcass traits. Mean rumen pH decreased while ammonia concentration tended to increase with increasing concentrate level. Total volatile fatty acids and the acetate to propionate ratio were lowest for SO. Method of feeding had no significant effect on rumen fermentation.
    • Outdoor grazing of dairy cows on pasture versus indoor feeding on total mixed ration: Effects on gross composition and mineral content of milk during lactation

      Gulati, Arunima; Galvin, Norann; Lewis, Eva; Hennessy, Deirdre; O'Donovan, Michael; McManus, Jennifer J.; Fenelon, Mark A.; Guinee, Timothy P.; Department of Agriculture, Food and the Marine; Dairy Levy Trust Co-Operative Society Limited; et al. (Elsevier, 2017-08-15)
      The influence of feeding system and lactation period on the gross composition, macroelements (Ca, P, Mg, and Na), and trace elements (Zn, Fe, Cu, Mo, Mn, Se, and Co) of bovine milk was investigated. The feeding systems included outdoor grazing on perennial ryegrass pasture (GRO), outdoor grazing on perennial ryegrass and white clover pasture (GRC), and indoors offered total mixed ration (TMR). Sixty spring-calving Holstein Friesian dairy cows were assigned to 3 herds, each consisting of 20 cows, and balanced with respect to parity, calving date, and pre-experimental milk yield and milk solids yield. The herds were allocated to 1 of the 3 feeding systems from February to November. Milk samples were collected on 10 occasions over the period June 17 to November 26, at 2 or 3 weekly intervals, when cows were on average 119 to 281 d in lactation (DIL). The total lactation period was arbitrarily sub-divided into 2 lactation periods based on DIL, namely mid lactation, June 17 to September 9 when cows were 119 to 203 DIL; and late lactation, September 22 to November 26 when cows were 216 to 281 DIL. With the exception of Mg, Na, Fe, Mo, and Co, all other variables were affected by feeding system. The GRO milk had the highest mean concentrations of total solids, total protein, casein, Ca, and P. The TMR milk had the highest concentrations of lactose, Cu, and Se, and lowest level of total protein. The GRC milk had levels of lactose, Zn, and Cu similar to those of GRO milk, and concentrations of TS, Ca, and P similar to those of TMR milk. Lactation period affected all variables, apart from the concentrations of Fe, Cu, Mn, and Se. On average, the proportion (%) of total Ca, P, Zn, Mn, or Se that sedimented with the casein on high-speed ultracentrifugation at 100,000 × g was ≥60%, whereas that of Na, Mg, or Mo was ≤45% total. The results demonstrate how the gross composition and elemental composition of milk can be affected by different feeding systems.
    • 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.
    • 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 BV, 2017-04-15)
      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.
    • Phosphorus and nitrogen losses from temperate permanent grassland on clay-loam soil after the installation of artificial mole and gravel mole drainage

      Valbuena-Parralejo, N.; Fenton, Owen; Tuohy, Patrick; Williams, M.; Lanigan, Gary; Humphreys, James; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the MArine; RSF11152 (Elsevier, 2018-12-14)
      Mole (M) and gravel-mole (GM) drainage systems improve the permeability of soils with high clay contents. They collect and carry away infiltrating water during episodic rainfall events. Characterisation of nutrient fluxes (concentration and flows) in overland flow (OF) and in mole drain flow (MF) across sequential rainfall events is important for environmental assessment of such drainage systems. The objective of this study is to assess the impact of drainage systems on soil nutrient losses. Three treatments were imposed on grazed permanent grassland on a clay loam soil in Ireland (52°30′N, 08°12′W) slope 1.48%: undrained control (C), mole drainage (M) and gravel mole drainage (GM). Plots (100 m × 15 m) were arranged in a randomized complete block design with four replicated blocks. Nitrogen (N) and phosphorus (P) concentrations in OF, MF and groundwater (GW) were measured from each plot over 15 consecutive rainfall events. The results showed that M and GM (P < 0.05) deepened the watertable depth and decreased OF. M and GM increased losses of nitrate-N (22%) and ammonium-N (14%) in GW. Nitrate-N concentrations from all the flow pathways (mean and standard error (s.e.): 0.99 s.e. 0.10 mg L−1) were well below the 11.3 mg L−1 threshold for drinking water. Ammonium-N concentrations from all the flow pathways (mean: 0.64 s.e. 0.14 mg L−1) exceeded drinking water quality standards. On the other hand M and GM lowered total P losses (mean annual losses from C, M and GM: 918, 755 and 853 s.e. 14.1 g ha−1 year−1) by enhancing soil P sorption. Hence M and GM can be implemented on farms under similar management to that described in the present study with a minor impact on N (increased concentration on averaged 18% to GW) and P (reduced by on avenged 114 g ha−1 year−1).