• Labour efficiency on-farm

      O'Brien, Bernadette; Gleeson, David E; O'Donovan, K.; Ruane, D.; Kinsella, J.; Mee, John F; Boyle, Laura; McNamara, John G. (Teagasc, 2007-01-01)
      Improvements in milking efficiency have a greater influence than any other aspect of the dairy farmers work on overall farm labour inputs (Whipp, 1992). In order to facilitate the examination of milking process labour inputs, the milking process may be divided into the following three components: herding pre and post milking (transfer of cows to and from the milking parlour); milking (milking tasks / work routines within the parlour); and washing (washing of milking machine and yard). Meanwhile, within milking specifically, the number of cows milked per operator per hour is the best measure of both the performance of the operator and the milking installation (Clough, 1978). This is affected by the following three factors: the milking times of the cows, the number and arrangement of the milking units, and the operator’s work routine (Whipp, 1992). The addition of extra milking units will only increase milking performance if the operator has idle time during milking (Hansen, 1999).
    • Land Drainage - A farmer’s practical guide to draining grassland in Ireland

      Tuohy, Patrick; Fenton, Owen; O'Loughlin, James; Humphreys, James (Teagasc, 30/07/2013)
      No drainage work should be carried out before the drainage characteristics of the soil are established by a site and soil test pit investigation. • Two types of drainage system exist: a groundwater drainage system and a shallow drainage system. The design of the system depends entirely on the drainage characteristics of the soil. • Distinguishing between the two types of drainage systems essentially comes down to whether or not a permeable layer is present (at a workable depth) that will allow the flow of water with relative ease. If such a layer is evident, a piped drain system at that depth is likely to be effective. If no such layer is found during soil test pit investigations, it will be necessary to improve the drainage capacity of the soil. This involves a disruption technique such as moling, gravel moling or subsoiling in tandem with collector drains. • Drains are not effective unless they are placed in a free draining soil layer or complimentary measures (mole drainage, subsoiling) are used to improve soil drainage capacity. If water is not moving through the soil in one or other of these two ways, the water table will not be lowered. • Outfall level must not dictate the drainage system depth. If a free draining layer is present, it must be utilised. • Drain pipes should always be used for drains longer than 30 m. If these get blocked it is a drainage stone and not a drainage pipe issue. • Drainage stone should not be filled to the top of the field trench except for very limited conditions (the bottom of an obvious hollow). Otherwise it is an extremely expensive way of collecting little water. • Most of the stone being used for land drainage today is too big. Clean aggregate in the 10–40 mm (0.4 to 1.5 inch approx) grading band should be used. Generally you get what you pay for. • Subsoiling is not effective unless a shallow impermeable layer is being broken or field drains have been installed prior to the operation. Otherwise it will not have any long-term effect and may do more harm than good. • Most land drainage systems are poorly maintained. Open drains should be clean and as deep as possible and field drains feeding into them should be regularly rodded or jetted.
    • Leukocyte profile, gene expression, acute phase response, and metabolite status of cows with sole hemorrhages

      O'Driscoll, Keelin; McCabe, Matthew; Earley, Bernadette; Marie Curie Intra-European Fellowship; 252611 (Elsevier, 2017-08-23)
      Sole hemorrhages result from disruption to normal claw horn formation and are caused by a variety of internal and external factors. Evidence suggests that they are painful, although they do not usually cause clinical lameness and are difficult to detect by observing cow gait. Little is known about how or whether sole hemorrhages affect the cow systemically. This study compared hematology profile, leukocyte gene expression, and physiological responses of cows with no/mild hemorrhages (category 1; n = 17), moderate hemorrhages (category 2; n = 18), and severe hemorrhages (category 3; n = 12). At approximately 100 d in milk, all cows in the study herd (n = 374) were locomotion scored before hoof examination. The cows included in the study were not clinically lame and had no other hoof disorder. Blood samples were taken from all cows within 24 h of selection. Leukocyte counts were obtained using an automated cell counter, cortisol and dehydroepiandrosterone (DHEA) concentration by ELISA, and plasma haptoglobin, urea, total protein, creatine kinase and glucose were analyzed on a clinical chemistry analyzer. Expression of 16 genes associated with lameness or stress were estimated using real-time quantitative PCR. Data from cows within each category were compared using the Mixed procedure in SAS (version 9.3; SAS Institute Inc., Cary, NC). Fixed effects included hemorrhage severity category and lactation number, with days in milk and body condition score included as covariates. Locomotion score worsened as sole hemorrhage category worsened. Locomotion score of category 1 cows tended to be lower than that of category 2 cows and was lower than that of category 3 cows. The locomotion score of category 3 cows was also greater than that of categories 1 and 2 combined. Category had no effect on leukocyte number, on any of the individual leukocyte cell numbers or percentages, cortisol or DHEA concentration, cortisol:DHEA ratio, or relative expression of any of the genes investigated, and we detected no differences in plasma glucose, protein, or creatine kinase concentrations between categories. However, category 3 cows had greater plasma concentrations of haptoglobin and tended to have lesser concentrations of plasma urea than category 1 and 2 cows. The differences in gait between cows with no or minor sole hemorrhages and cows with severe hemorrhages indicate that hemorrhages may be associated with discomfort or pain. Nevertheless, the only physiological measure that changed with increasing locomotion score was plasma haptoglobin concentration. Haptoglobin has previously been found to be elevated in lame cows, and thus shows promise as a marker for limb pain.
    • Linkage between predictive transmitting ability of a genetic index, potential milk production, and a dynamic model

      Ruelle, Elodie; Delaby, Luc; Shalloo, Laurence; Department of Agriculture, Food and the Marine; 11/S/132 (Elsevier, 2019-01-26)
      With the increased use of information and communication technology–based tools and devices across traditional desktop computers and smartphones, models and decision-support systems are becoming more accessible for farmers to improve the decision-making process at the farm level. However, despite the focus of research and industry providers to develop tools that are easy to adopt by the end user, milk-production prediction models require substantial parameterization information for accurate milk production simulations. For these models to be useful at an individual animal level, they require the potential milk yield of the individual animals (and possibly potential fat and protein yields) to be captured and parameterized within the model to allow accurate simulations of the interaction of the animal with the system. The focus of this study was to link 3 predicted transmitting ability (PTA) traits from the Economic Breeding Index (PTA for milk yield, fat, and protein) with potential index parameters for milk, fat, and protein required as inputs to a herd-based dynamic milk model. We compiled a data set of 1,904 lactations that included different experiments conducted at 2 closed sites during a 14-yr period (2003–2016). The treatments implied different stocking rates, concentrate supplementation levels, calving dates, and genetic potential. The first step, using 75% of the data randomly selected, was to link the milk, fat, and protein yields achieved within each lactation to their respective PTA value, stocking rate, parity, and concentrate supplementation level. The equations generated were transformed to correspond to inputs to the pasture-based herd dynamic milk model. The equations created were used in conjunction with the model to predict milk, fat, and protein production. Then, using the remaining 25% data of the data set, the simulations were compared against the actual milk produced during the experiments. When the model was tested, it was capable of predicting the lactation milk, fat, and protein yield with a relative prediction error of <10% at the herd level and <13% at the individual animal level.
    • Live animal measurements, carcass composition and plasma hormone and metabolite concentrations in male progeny of sires differing in genetic merit for beef production

      Clarke, Anne Marie; Drennan, Michael J; McGee, Mark; Kenny, David A.; Evans, R. D.; Berry, Donagh P. (Cambridge University Press, 2009-07)
      In genetic improvement programmes for beef cattle, the effect of selecting for a given trait or index on other economically important traits, or their predictors, must be quantified to ensure no deleterious consequential effects go unnoticed. The objective was to compare live animal measurements, carcass composition and plasma hormone and metabolite concentrations of male progeny of sires selected on an economic index in Ireland. This beef carcass index (BCI) is expressed in euros and based on weaning weight, feed intake, carcass weight and carcass conformation and fat scores. The index is used to aid in the genetic comparison of animals for the expected profitability of their progeny at slaughter. A total of 107 progeny from beef sires of high (n = 11) or low (n = 11) genetic merit for the BCI were compared in either a bull (slaughtered at 16 months of age) or steer (slaughtered at 24 months of age) production system, following purchase after weaning (8 months of age) from commercial beef herds. Data were analysed as a 2 × 2 factorial design (two levels of genetic merit by two production systems). Progeny of high BCI sires had heavier carcasses, greater (P < 0.01) muscularity scores after weaning, greater (P < 0.05) skeletal scores and scanned muscle depth pre-slaughter, higher (P < 0.05) plasma insulin concentrations and greater (P < 0.01) animal value (obtained by multiplying carcass weight by carcass value, which was based on the weight of meat in each cut by its commercial value) than progeny of low BCI sires. Regression of progeny performance on sire genetic merit was also undertaken across the entire data set. In steers, the effect of BCI on carcass meat proportion, calculated carcass value (c/kg) and animal value was positive (P < 0.01), while a negative association was observed for scanned fat depth pre-slaughter and carcass fat proportion (P < 0.01), but there was no effect in bulls. The effect of sire expected progeny difference (EPD) for carcass weight followed the same trends as BCI. Muscularity scores, carcass meat proportion and calculated carcass value increased, whereas scanned fat depth, carcass fat and bone proportions decreased with increasing sire EPD for conformation score. The opposite association was observed for sire EPD for fat score. Results from this study show that selection using the BCI had positive effects on live animal muscularity, carcass meat proportion, proportions of high-value cuts and carcass value in steer progeny, which are desirable traits in beef production.
    • Long-term effects of prior diets, dietary transition and pregnancy on adipose gene expression in dairy heifers

      Waerp, Hilde K.; Waters, Sinead M; McCabe, Matthew S.; Cormican, Paul; Salte, Ragnar; The Research Council of Norway; 199448 (Public Library of Science (PLoS), 2019-07-03)
      Adipose tissue is highly involved in whole-body metabolism and is the main site for lipid synthesis, storage and mobilization in ruminants. Therefore, knowledge about adipose tissue responses to different diets is important, especially in growing heifers as the feeding regimes of replacement heifers affect their future success as dairy cows. However, at gene expression level such knowledge is limited. As part of a larger feed trial, adipose tissue biopsies from 24 Norwegian Red heifers were collected at 12 months of age (12MO) and at month seven of gestation (PREG) and analyzed by next-generation mRNA sequencing. Between these two sampling points, all heifers had gone through a successful conception and a feed change from four dietary treatments of high or low energy (HE/LE) and protein (HP/LP) content (treatments LPHE, HPHE, LPLE and HPLE) to a low-energy, low-protein pregnancy feed given to all animals. Gene expression differences between different feed treatments at 12MO are described in an earlier publication from our group. The main objectives of this study were to investigate the long-term effects of diets differing in protein and energy density level on gene expression in adipose tissue of growing replacement dairy heifers. To achieve this, we examined the post-treatment effects between the treatment groups at month seven of gestation; 6 months after the termination of experimental feeding, and the long-term gene expression changes occurring in the adipose tissue between 12MO and PREG. Post-treatment group comparisons showed evidence of long-term effects of dietary treatment on adipose gene expression. Differences between protein treatments were smaller than between energy treatments. Adipose gene expression changes from 12MO to PREG were much larger for the HE than the LE treatments and seemed to mostly be explained by the characteristics of the diet change. 97 genes displayed a unidirectional expression change for all groups from 12MO to PREG, and are considered to be treatment-independent, possibly caused by pregnancy or increased age. This study provides candidate genes and key regulators for further studies on pregnancy preservation (TGFB1, CFD) and metabolic regulation and efficiency (PI3K, RICTOR, MAP4K4,) in dairy cattle.
    • Long-term stability of RNA in post-mortem bovine skeletal muscle, liver and subcutaneous adipose tissues

      Bahar, Bojlul; Monahan, Frank J; Moloney, Aidan P; Schmidt, Olaf; MacHugh, David E; Sweeney, Torres; National Development Plan 2000-2006; Teagasc Walsh Fellowship Programme (Biomed Central, 2007-11-29)
      Background: Recovering high quality intact RNA from post-mortem tissue is of major concern for gene expression studies in animals and humans. Since the availability of post-mortem tissue is often associated with substantial delay, it is important that we understand the temporal variation in the stability of total RNA and of individual gene transcripts so as to be able to appropriately interpret the data generated from such studies. Hence, the objective of this experiment was to qualitatively and quantitatively assess the integrity of total and messenger RNA extracted from bovine skeletal muscle, subcutaneous adipose tissue and liver stored at 4°C at a range of time points up to 22 days post-mortem. These conditions were designed to mimic the environment prevailing during the transport of beef from the abattoir to retail outlets. Results: The 28S and 18S rRNA molecules of total RNA were intact for up to 24 h post-mortem in liver and adipose tissues and up to 8 days post-mortem in skeletal muscle. The mRNA of housekeeping genes (GAPDH and ACTB) and two diet-related genes (RBP5 and SCD) were detectable up to 22 days post-mortem in skeletal muscle. While the mRNA stability of the two housekeeping genes was different in skeletal muscle and liver, they were similar to each other in adipose tissue. After 22 days post-mortem, the relative abundance of RBP5 gene was increased in skeletal muscle and in adipose tissue and decreased in liver. During this period, the relative abundance of SCD gene also increased in skeletal muscle whereas it decreased in both adipose tissue and liver. Conclusion: Stability of RNA in three tissues (skeletal muscle, subcutaneous adipose tissue and liver) subjected to long-term post-mortem storage at refrigeration temperature indicated that skeletal muscle can be a suitable tissue for recovering biologically useful RNA for gene expression studies even if the tissue is subjected to post-mortem storage for weeks, whereas adipose tissue and liver should be processed within 24 hours post-mortem.
    • Machine learning algorithms for the prediction of conception success to a given insemination in lactating dairy cows

      Henpstalk, K.; McParland, Sinead; Berry, Donagh P.; European Commission (Elsevier for American Dairy Science Association, 2015-06)
      The ability to accurately predict the conception outcome for a future mating would be of considerable benefit for producers in deciding what mating plan (i.e., expensive semen or less expensive semen) to implement for a given cow. The objective of the present study was to use herd- and cow-level factors to predict the likelihood of conception success to a given insemination (i.e., conception outcome not including embryo loss); of particular interest in the present study was the usefulness of milk mid-infrared (MIR) spectral data in augmenting the accuracy of the prediction model. A total of 4,341 insemination records with conception outcome information from 2,874 lactations on 1,789 cows from 7 research herds for the years 2009 to 2014 were available. The data set was separated into a calibration data set and a validation data set using either of 2 approaches: (1) the calibration data set contained records from all 7 farms for the years 2009 to 2011, inclusive, and the validation data set included data from the 7 farms for the years 2012 to 2014, inclusive, or (2) the calibration data set contained records from 5 farms for all 6 yr and the validation data set contained information from the other 2 farms for all 6 yr. The prediction models were developed with 8 different machine learning algorithms in the calibration data set using standard 10-times 10-fold cross-validation and also by evaluating in the validation data set. The area under curve (AUC) for the receiver operating curve varied from 0.487 to 0.675 across the different algorithms and scenarios investigated. Logistic regression was generally the best-performing algorithm. The AUC was generally inferior for the external validation data sets compared with the calibration data sets. The inclusion of milk MIR in the prediction model generally did not improve the accuracy of prediction. Despite the fair AUC for predicting conception outcome under the different scenarios investigated, the model provided a reasonable prediction of the likelihood of conception success when the high predicted probability instances were considered; a conception rate of 85% was evident in the top 10% of inseminations ranked on predicted probability of conception success in the validation data set.
    • Major management factors associated with the variation in reproductive performance of Irish dairy herds

      Buckley, Frank; Dillon, Pat; Mee, John F (Teagasc, 2007-01-01)
      The results highlight the importance of BCS in achieving good reproductive performance. The likelihood of reproductive success was best predicted by BCS around the time of breeding and, for cows calving in good BCS (3.0 or greater) the level of BCS loss between calving and first service. A low BCS pre-calving (<2.75) was associated with prolonged calving to first service, and calving to conception intervals. Very high BCS pre-calving (>3.5) results in excessive BCS loss (>0.5) post-calving. On the basis of these findings a pre-calving BCS of no greater than 3.25 is a sensible target for pasture-based spring calving systems in Ireland. It is necessary to maintain BCS at 2.75 or greater during the breeding season, and loss of body condition between calving and first service should be restricted to 0.5 BCS units.
    • Management practices as risk factors for the presence of bulk milk antibodies to Salmonella, Neospora caninum and Leptospira interrogans serovar hardjo in Irish dairy herds

      O'Doherty, Eugene; Berry, Donagh P.; O'Grady, Luke; Sayers, Riona (Cambridge University Press, 2014-03-24)
      A survey of management practices in 309 Irish dairy herds was used to identify risk factors for the presence of antibodies to Salmonella, Neospora caninum and Leptospira interrogans serovar hardjo in extensively managed unvaccinated dairy herds. A previous study documented a herd-level seroprevalence in bulk milk of 49%, 19% and 86% for Salmonella, Neospora caninum and leptospira interrogans serovar hardjo, respectively in the unvaccinated proportion of these 309 herds in 2009. Association analyses in the present study were carried out using multiple logistic regression models. Herds where cattle were purchased or introduced had a greater likelihood of being positive to leptospira interrogans serovar hardjo (P<0.01) and Salmonella (P<0.01). Larger herds had a greater likelihood of recording a positive bulk milk antibody result to leptospira interrogans serovar hardjo (P<0.05). Herds that practiced year round calving were more likely to be positive to Neospora caninum (P<0.05) compared to herds with a spring-calving season, with no difference in risk between herds that practiced split calving compared to herds that practiced spring calving. No association was found between presence of dogs on farms and prevalence of Neospora caninum possibly due to limited access of dogs to infected materials including afterbirths. The information from this study will assist in the design of suitable control programmes for the diseases under investigation in pasture-based livestock systems.
    • Management practices as risk factors for the presence of bulk milk antibodies to Salmonella, Neospora caninum and Leptospira interrogans serovar hardjo in Irish dairy herds

      O'Doherty, Eugene; Berry, Donagh P.; O'Grady, Luke; Sayers, Riona (Cambridge University Press, 2014-03-24)
      A survey of management practices in 309 Irish dairy herds was used to identify risk factors for the presence of antibodies to Salmonella, Neospora caninum and Leptospira interrogans serovar hardjo in extensively managed unvaccinated dairy herds. A previous study documented a herd-level seroprevalence in bulk milk of 49%, 19% and 86% for Salmonella, Neospora caninum and leptospira interrogans serovar hardjo, respectively in the unvaccinated proportion of these 309 herds in 2009. Association analyses in the present study were carried out using multiple logistic regression models. Herds where cattle were purchased or introduced had a greater likelihood of being positive to leptospira interrogans serovar hardjo (P<0.01) and Salmonella (P<0.01). Larger herds had a greater likelihood of recording a positive bulk milk antibody result to leptospira interrogans serovar hardjo (P<0.05). Herds that practiced year round calving were more likely to be positive to Neospora caninum (P<0.05) compared to herds with a spring-calving season, with no difference in risk between herds that practiced split calving compared to herds that practiced spring calving. No association was found between presence of dogs on farms and prevalence of Neospora caninum possibly due to limited access of dogs to infected materials including afterbirths. The information from this study will assist in the design of suitable control programmes for the diseases under investigation in pasture-based livestock systems.
    • Managing variability in decision making in swine growing-finishing units

      Agostini, Piero D.S.; Manzanilla, Edgar G; de Blas, Carlos; Fahey, Alan G.; da Silva, Caio A; Gasa, Josep; Spanish Ministerio de Ciencia e Innovación; Agencia Española de Cooperación Internacional para el Desarrollo; AGL2011-29960 (Biomed Central, 2015-09-01)
      Analysis of data collected from pig farms may be useful to understand factors affecting pig health and productive performance. However, obtaining these data and drawing conclusions from them can be done at different levels and presents several challenges. In the present study, information from 688 batches of growing-finishing (GF) pigs (average initial and final body weight of 19.1 and 108.5 kg respectively) from 404 GF farms integrated in 7 companies was obtained between July 2008 and July 2010 in Spain by survey. Management and facility factors associated with feed conversion ratio (FCR) and mortality were studied by multiple linear regression analysis in each single company (A to G) and in an overall database (OD). Factors studied were geographic location of the farm, trimester the pigs entered the farm, breed of sire and sex segregation in pens (BREGENSEG), use of circovirus vaccine, number of origins the pigs were obtained from, age of the farm, percentage of slatted floor, type of feeder, drinker and ventilation, number of phases and form of feed, antibiotic administration system, water source, and number and initial weight of pigs. Results In two or more companies studied and/or in OD, the trimester when pigs were placed in the farm, BREGENSEG, number of origins of the pigs, age of the farm and initial body weight were factors associated with FCR. Regarding mortality, trimester of placement, number of origins of the pigs, water source in the farm, number of pigs placed and the initial body weight were relevant factors. Age of the farm, antibiotic administration system, and water source were only provided by some of the studied companies and were not included in the OD model, however, when analyzed in particular companies these three variables had an important effect and may be variables of interest in companies that do not record them. Conclusions Analysing data collected from farms at different levels helps better understand factors associated with productive performance of pig herds. Out of the studied factors trimester of placement and number of origins of the pigs were the most relevant factors associated with FCR and mortality.
    • Manipulating the ensilage of wilted, unchopped grass through the use of additive treatments

      McEniry, Joseph; O'Kiely, Padraig; Clipson, Nicholas J.W.; Forristal, P.D.; Doyle, Evelyn M.; Teagasc Walsh Fellowship Programme (Teagasc, Oak Park, Carlow, Ireland, 2007)
      Baled silage composition frequently differs from that of comparable conventional precision-chop silage. The lower final concentration of fermentation products in baled silage makes it more conducive to the activities of undesirable microorganisms. Silage additives can be used to encourage beneficial microbial activity and/or inhibit detrimental microbial activity. The experiment was organised in a 2 (chop treatments) × 6 (additive treatments) × 2 (stages of ensilage) factorial arrangement of treatments (n = 3 silos/treatment) to suggest additive treatments for use in baled silage production that would help create conditions more inhibitory to the activities of undesirable microorganisms and realise an outcome comparable to precision-chop silage. Chopping the herbage prior to ensiling, in the absence of an additive treatment, improved the silage fermentation. In the unchopped herbage, where the fermentation was poorer, the lactic acid bacterial inoculant resulted in an immediate increase (P < 0.001) in lactic acid concentration and a faster decline (P < 0.001) in pH with a subsequent reduction in butyric acid (P < 0.001) and ammonia-N (P < 0.01) concentrations. When sucrose was added in addition to the lactic acid bacterial inoculant, the combined treatment had a more pronounced effect on pH, butyric acid and ammonia-N values at the end of ensilage. The formic acid based additive and the antimicrobial mixture restricted the activities of undesirable microorganisms resulting in reduced concentrations of butyric acid (P < 0.001) and ammonia-N (P < 0.01). These additives offer a potential to create conditions in baled silage more inhibitory to the activities of undesirable microorganisms.
    • Manipulation of grass supply to meet feed demand

      French, Padraig; Hennessy, Deirdre; O’Donovan, Michael; Laidlaw, S. (Teagasc, 2006-01-01)
      Grazed grass is generally the cheapest form of feed available for beef and milk production in Ireland. Grass growth is variable during the year with a peak in May/June and a secondary peak in August. There is little net growth from December to February. Grass growth is also variable across the country with higher grass growth in the south and south-west (14 to 15 t DM/ha/year) compared with approximately 11 t DM/ha/year in the north-east (Brereton, 1995). There is poor synchrony between grass supply and feed demand on beef and dairy farms. The feed demand curve for a calf to two year old beef system shows feed demand decreasing as grass supply increases, and grass supply decreasing as feed demand increases. Similarly, the feed demand curve of a spring calving dairy herd shows poor synchrony with grass supply, with a surplus of grass from about mid-April to mid-August, and a deficit for the rest of the year. Traditionally surplus grass produced during May and June is conserved as silage or hay and fed back to cattle and dairy cows during the deficit times of the year.
    • Measurements of the acid-binding capacity of ingredients used in pig diets

      Lawlor, Peadar G; Lynch, P Brendan; Caffrey, Patrick J.; O'Reilly, James J; O'Connell, M. Karen (Biomed Central, 2005-08-01)
      Some feed ingredients bind more acid in the stomach than others and for this reason may be best omitted from pig starter foods if gastric acidity is to be promoted. The objective of this study was to measure the acid-binding capacity (ABC) of ingredients commonly used in pig starter foods. Ingredients were categorised as follows: (i) milk products (n = 6), (ii) cereals (n = 10), (iii) root and pulp products (n = 5), (iv) vegetable proteins (n = 11), (v) meat and fish meal (n = 2), (vi) medication (n = 3), (vii) amino acids (n = 4), (viii) minerals (n = 16), (ix) acid salts (n = 4), (x) acids (n = 10). A 0.5 g sample of food was suspended in 50 ml distilled de-ionised water with continuous stirring. This suspension was titrated with 0.1 mol/L HCl or 0.1 mol/L NaOH so that approximately 10 additions of titrant was required to reach pH 3.0. The pH readings after each addition were recorded following equilibration for three minutes. ABC was calculated as the amount of acid in milliequivalents (meq) required to lower the pH of 1 kg food to (a) pH 4.0 (ABC-4) and (b) pH 3.0 (ABC-3). Categories of food had significantly different (P < 0.01) ABC values. Mean ABC-4 and ABC-3 values of the ten categories were: (i) 623 (s.d. 367.0) and 936 (s.d. 460.2), (ii) 142 (s.d. 79.2) and 324 (s.d. 146.4), (iii) 368 (s.d. 65.3) and 804 (s.d. 126.7), (iv) 381 (s.d. 186.1) and 746 (s.d. 227.0), (v) 749 (s.d. 211.6) and 1508 (s.d. 360.8), (vi) 120 (s.d. 95.6) and 261 (s.d. 163.2), (vii) 177 (s.d. 60.7) and 1078 (s.d. 359.0), (viii) 5064 (s.d. 5525.1) and 7051 (s.d. 5911.6), (ix) 5057 (s.d. 1336.6) and 8945 (s.d. 2654.1) and (x) -5883 (s.d. 4220.5) and -2591 (s.d. 2245.4) meq HCl per kg, respectively. Within category, ABC-3 and ABC- 4 values were highly correlated: R2 values of 0.80 and greater for food categories i, iv, v, vi, vii and viii. The correlation between predicted and observed ABC values of 34 mixed diets was 0.83 for ABC-4 and 0.71 for ABC-3. It was concluded that complete diets with low ABC values may be formulated through careful selection of ingredients. The final pH to which ABC is measured should matter little as ABC-3 and ABC-4 are highly correlated.
    • Measuring labor input on pasture-based dairy farms using a smartphone

      Deming, J.; Gleeson, David E; O'Dwyer, T.; O'Brien, Bernadette; Kinsella, J.; Dairy Research Ireland; Teagasc Walsh Fellowship Programme (Elsevier, 2018-07-19)
      With the cessation of milk quotas in the European Union, dairy herd sizes increased in some countries, including Ireland, with an associated increase in labor requirement. Second to feed costs, labor has been identified as one of the highest costs on pasture-based dairy farms. Compared with other European Union countries, Ireland has historically had low milk production per labor unit; thus, optimization of labor efficiency on farm should be addressed before or concurrently with herd expansion. The objective of this study was to quantify current levels of labor input and labor efficiency on commercial pasture-based dairy farms and to identify the facilities and management practices associated with increased labor efficiency. Thirty-eight dairy farms of varying herd sizes, previously identified as labor-efficient farms, were enrolled on the study and data were collected over 3 consecutive days each month over a 12-mo period, starting in May 2015 and finishing in August of 2016. This was achieved through the use of a smartphone application. For analysis purposes, farms were categorized into 1 of 3 herd size categories (HSC): farms with <150 cows (HSC 1), 150–249 cows (HSC 2), or ≥250 cows (HSC 3). Overall farm labor input increased with HSC with 3,015, 4,499, and 6,023 h worked on HSC 1, 2, and 3, respectively. A higher proportion of work was carried out by hired staff as herd size increased. Labor efficiency was measured as total hours input to the dairy enterprise divided by herd size. Labor efficiency improved as herd size increased above 250 cows with 17.3 h/cow per yr observed for HSC 3; labor efficiency was similar for HSC 1 and 2, at 23.8 and 23.3 h/cow per yr, respectively. A large range of efficiency was observed within HSC. The labor requirements had a distinct seasonal pattern across the 3 HSC with the highest input observed in springtime (February to April) primarily due to calving and calf-care duties, milking, and winter feeding. The lowest input was observed in wintertime (November to January) when cows were dry. Particular facilities and management practices were associated with efficiency within certain tasks, the most notable in regard to milking and winter feeding practices. Additionally, the most efficient farms used contractors to perform a higher proportion of machinery work on farm than the least efficient farms.
    • Meat provenance: Authentication of geographical origin and dietary background of meat

      Monahan, Frank J.; Schmidt, Olaf; Moloney, Aidan P; European Union; Department of Agriculture, Food and the Marine; FOOD-CT-2005–006942; 06/R&D/D/481; Teagasc Walsh Fellowship Programme (Elsevier, 2018-05-30)
      The authenticity of meat is now an important consideration in the multi-step food chain from production of animals on farm to consumer consumption of the final meat product. A range of techniques, involving analysis of elemental and molecular constituents of meat, fingerprint profiling and multivariate statistical analysis exists and these techniques are evolving in the quest to provide robust methods of establishing the dietary background of animals and the geographical origin of the meat derived from them. The potential application to meat authentication of techniques such as stable isotope ratio analysis applied to different animal tissues, measurement in meat of compounds directly derived from the diet of animals, such as fatty acids and fat soluble vitamins, and spectroscopy is explored. Challenges pertaining to the interpretation of data, as they relate to assignment of dietary background or geographical origin, are discussed.
    • A mechanistic model for electricity consumption on dairy farms: Definition, validation, and demonstration

      Upton, John; Murphy, Michael D.; Shalloo, Laurence; Groot Koerkamp, Peter W.G.; De Boer, Imke J.M.; INTERREG IVB North-West Europe (Elsevier, 2014-06-07)
      Our objective was to define and demonstrate a mechanistic model that enables dairy farmers to explore the impact of a technical or managerial innovation on electricity consumption, associated CO2 emissions, and electricity costs. We, therefore, (1) defined a model for electricity consumption on dairy farms (MECD) capable of simulating total electricity consumption along with related CO2 emissions and electricity costs on dairy farms on a monthly basis; (2) validated the MECD using empirical data of 1 yr on commercial spring calving, grass-based dairy farms with 45, 88, and 195 milking cows; and (3) demonstrated the functionality of the model by applying 2 electricity tariffs to the electricity consumption data and examining the effect on total dairy farm electricity costs. The MECD was developed using a mechanistic modeling approach and required the key inputs of milk production, cow number, and details relating to the milk-cooling system, milking machine system, water-heating system, lighting systems, water pump systems, and the winter housing facilities as well as details relating to the management of the farm (e.g., season of calving). Model validation showed an overall relative prediction error (RPE) of less than 10% for total electricity consumption. More than 87% of the mean square prediction error of total electricity consumption was accounted for by random variation. The RPE values of the milk-cooling systems, water-heating systems, and milking machine systems were less than 20%. The RPE values for automatic scraper systems, lighting systems, and water pump systems varied from 18 to 113%, indicating a poor prediction for these metrics. However, automatic scrapers, lighting, and water pumps made up only 14% of total electricity consumption across all farms, reducing the overall impact of these poor predictions. Demonstration of the model showed that total farm electricity costs increased by between 29 and 38% by moving from a day and night tariff to a flat tariff.
    • Merging and characterising phenotypic data on conventional and rare traits from dairy cattle experimental resources in three countries

      Banos, G.; Coffey, Mike P.; Veerkamp, Roel F.; Berry, Donagh P.; Wall, E.; European Union; RERAD; KBBE-211708 (Cambridge University Press, 2012-01)
      This study set out to demonstrate the feasibility of merging data from different experimental resource dairy populations for joint genetic analyses. Data from four experimental herds located in three different countries (Scotland, Ireland and the Netherlands) were used for this purpose. Animals were first lactation Holstein cows that participated in ongoing or previously completed selection and feeding experiments. Data included a total of 60 058 weekly records from 1630 cows across the four herds; number of cows per herd ranged from 90 to 563. Weekly records were extracted from the individual herd databases and included seven traits: milk, fat and protein yield, milk somatic cell count, liveweight, dry matter intake and energy intake. Missing records were predicted with the use of random regression models, so that at the end there were 44 weekly records, corresponding to the typical 305-day lactation, for each cow. A total of 23 different lactation traits were derived from these records: total milk, fat and protein yield, average fat and protein percentage, average fat-to-protein ratio, total dry matter and energy intake and average dry matter intake-to-milk yield ratio in lactation weeks 1 to 44 and 1 to 15; average milk somatic cell count in lactation weeks 1 to 15 and 16 to 44; average liveweight in lactation weeks 1 to 44; and average energy balance in lactation weeks 1 to 44 and 1 to 15. Data were subsequently merged across the four herds into a single dataset, which was analysed with mixed linear models. Genetic variance and heritability estimates were greater (P,0.05) than zero for all traits except for average milk somatic cell count in weeks 16 to 44. Proportion of total phenotypic variance due to genotype-by-environment (sire-by-herd) interaction was not different (P.0.05) from zero. When estimable, the genetic correlation between herds ranged from 0.85 to 0.99. Results suggested that merging experimental herd data into a single dataset is both feasible and sensible, despite potential differences in management and recording of the animals in the four herds. Merging experimental data will increase power of detection in a genetic analysis and augment the potential reference population in genome-wide association studies, especially of difficult-to-record traits.
    • Messenger RNA Sequence Rather than Protein Sequence Determines the Level of Self-synthesis and Antigen Presentation of the EBV-encoded Antigen, EBNA1

      Tellam, Judy T; Lekieffre, Lea; Zhong, Jie; Lynn, David J; Khanna, Rajiv; National Health & Medical Research Council Australia; 496684 APP1005091; 496712 (PLOS, 2012-12-27)
      Viruses establishing persistent latent infections have evolved various mechanisms to avoid immune surveillance. The Epstein-Barr virus-encoded nuclear antigen, EBNA1, expressed in all EBV-associated malignancies, modulates its own protein levels at quantities sufficient to maintain viral infection but low enough so as to minimize an immune response by the infected host cell. This evasion mechanism is regulated through an internal purine-rich mRNA repeat sequence encoding glycine and alanine residues. In this study we assess the impact of the repeat's nucleotide versus peptide sequence on inhibiting EBNA1 self-synthesis and antigen presentation. We demonstrate that altered peptide sequences resulting from frameshift mutations within the repeat do not alleviate the immune-evasive function of EBNA1, suggesting that the repetitive purine-rich mRNA sequence itself is responsible for inhibiting EBNA1 synthesis and subsequent poor immunogenicity. Our comparative analysis of the mRNA sequences of the corresponding repeat regions of different gammaherpesvirus maintenance homologues to EBNA1 highlights the high degree of identity between the nucleotide sequences despite very little homology in the encoded amino acid sequences. These studies demonstrate the importance of gammaherpesvirus purine-rich mRNA repeat sequences on antigenic epitope generation and evasion from T-cell mediated immune control, suggesting novel approaches to prevention and treatment of latent infection by this class of virus.