• 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.
    • Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

      Bouwman, Aniek C.; Hayes, Ben J.; Purfield, Deirdre C; Berry, Donagh P.; Chamberlain, Amanda J.; Hurtado Ponce, Carla; Sargolzaei, Mehdi; Schenkel, Flavio S.; Sahana, Goutam; Govignon-Gion, Armelle; et al. (Nature Publishing Group, 2018-02-19)
      Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
    • Meta-analysis of the effect of white clover inclusion in perennial ryegrass swards on milk production

      Dineen, Michael; Delaby, Luc; Gilliland, T.; McCarthy, B.; Teagasc Walsh Fellowship Programme; Irish Dairy Levy (Elsevier, 2017-11-23)
      There is increased demand for dairy products worldwide, which is coupled with the realization that consumers want dairy products that are produced in a sustainable and environmentally benign manner. Forage legumes, and white clover (Trifolium repens L.; WC) in particular, have the potential to positively influence the sustainability of pasture-based ruminant production systems. Therefore, there is increased interest in the use of forage legumes because they offer opportunities for sustainable pasture-based production systems. A meta-analysis was undertaken to quantify the milk production response associated with the introduction of WC into perennial ryegrass swards and to investigate the optimal WC content of dairy pastures to increase milk production. Two separate databases were created. In the grass-WC database, papers were selected if they compared milk production of lactating dairy cows grazing perennial ryegrass-WC (GC) swards with that of cows grazing perennial ryegrass-only swards (GO). In the WC-only database, papers were selected if they contained milk production from lactating dairy cows grazing on GC swards with varying levels of WC content. Data from both databases were analyzed using mixed models (PROC MIXED) in SAS (SAS Institute, Cary, NC). Within the grass-WC database, where mean sward WC content was 31.6%, mean daily milk and milk solids yield per cow were increased by 1.4 and 0.12 kg, respectively, whereas milk and milk solids yield per hectare were unaffected when cows grazed GC compared with GO swards. Stocking rate and nitrogen fertilizer application were reduced by 0.25 cows/ha and 81 kg/ha, respectively, on GC swards compared with GO swards. These results highlight the potential of GC production systems to achieve similar levels of production to GO systems but with reduced fertilizer nitrogen inputs, which is beneficial from both an economic and environmental point of view. In the context of increased demand for dairy products, there may be potential to increase the productivity of GC systems by increasing fertilizer nitrogen use to increase stocking rate and carrying capacity while also retaining the benefit of WC inclusion on milk production per cow.
    • Meta-analysis to investigate relationships between somatic cell count and raw milk composition, Cheddar cheese processing characteristics and cheese composition

      Geary, Una; Lopez-Villalobos, N.; O'Brien, Bernadette; Garrick, Dorian J.; Shalloo, Laurence (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      The relationship between elevated somatic cell count (SCC) and raw milk composition, cheese processing and cheese composition, was investigated by meta-analysis using available literature representing 45 scientific articles. With respect to raw milk composition there was a significant positive relationship between SCC and the protein and fat contents and a significant negative relationship between SCC and the lactose content. In relation to cheese processing, there was a significant negative relationship between SCC and recoveries of protein and fat. As SCC increased cheese protein content declined and cheese moisture content increased.
    • A method for assessing liner performance during the peak milk flow period

      Penry, J. F.; Upton, John; Leonardi, S.; Thompson, P. D.; Reinemann, D. J. (Elsevier, 2017-11-06)
      The objective of this study was to develop a method to quantify the milking conditions under which circulatory impairment of teat tissues occurs during the peak flow period of milking. A secondary objective was to quantify the effect of the same milking conditions on milk flow rate during the peak flow rate period of milking. Additionally, the observed milk flow rate was a necessary input to the calculation of canal area, our quantitative measure of circulatory impairment. A central composite experimental design was used with 5 levels of each of 2 explanatory variables (system vacuum and pulsator ratio), creating 9 treatments including the center point. Ten liners, representing a wide range of liner compression (as indicated by overpressure), were assessed, with treatments applied using a novel quarter-milking device. Eight cows (32 cow-quarters) were used across 10 separate evening milkings, with quarter being the experimental unit. The 9 treatments, with the exception of a repeated center point, were randomly applied to all quarters within each individual milking. Analysis was confined to the peak milk flow period. Milk flow rate (MFR) and teat canal cross sectional area (CA) were normalized by dividing individual MFR, or CA, values by their within-quarter average value across all treatments. A multiple explanatory variable regression model was developed for normalized MFR and normalized CA. The methods presented in this paper provided sufficient precision to estimate the effects of vacuum (both at teat-end and in the liner mouthpiece), pulsation, and liner compression on CA, as an indicator of teat-end congestion, during the peak flow period of milking. Liner compression (as indicated by overpressure), teat-end vacuum, vacuum in the liner mouthpiece, milk-phase time, and their interactions are all important predictors of MFR and teat-end congestion during the peak milk flow period of milking. Increasing teat-end vacuum and milk-phase time increases MFR and reduces CA (indicative of increased teat-end congestion). Increasing vacuum in the liner mouthpiece also acts to reduce CA and MFR. Increasing liner compression reduces the effects of teat-end congestion, resulting in increased MFR and increased CA at high levels of teat-end vacuum and milk-phase time. These results provide a better understanding of the balance between milking speed and milking gentleness.
    • The microbiological and chemical composition of baled and precision-chop silages on a sample of farms in County Meath

      McEniry, Joseph; O'Kiely, Padraig; Clipson, Nicholas J.W.; Forristal, P.D.; Doyle, Evelyn M.; Teagasc Walsh Fellowship Programme; (Teagasc, Oak Park, Carlow, Ireland, 2006)
      Baled and precision-chop silages were examined on a sample of farms in the Irish midlands to determine microbiological and chemical composition at feedout. Silage making practices and chemical composition were similar to those in national surveys. Wilting was an integral part of baled silage production and was reflected in a more restricted fermentation (higher pH and water-soluble carbohydrates, with lower fermentation acids and buffering capacity) compared to precision-chop silage. Yeast numbers were higher in baled silage, suggesting a more aerobic environment within the bale. Although the fermentation appeared similar in the outer and inner horizons of baled silage, yeast, lactic acid bacteria and Enterobacteria numbers were higher in the outer horizon suggesting less exacting anaerobiosis adjacent to the surface of the bale.
    • Microevolution of antimicrobial resistance and biofilm formation of Salmonella Typhimurium during persistence on pig farms

      Tassinari, Eleonora; Duffy, Geraldine; Bawn, Matt; Burgess, Catherine; McCabe, Evonne M.; Lawlor, Peadar G.; Gardiner, Gillian; Kingsley, Robert A.; BBSRC Institute Strategic Programme Microbes in the Food Chain; Teagasc Walsh Fellowship Programme; et al. (Springer Nature, 2019-06-20)
      Salmonella Typhimurium and its monophasic variant S. 4,[5],12:i:- are the dominant serotypes associated with pigs in many countries. We investigated their population structure on nine farms using whole genome sequencing, and their genotypic and phenotypic variation. The population structure revealed the presence of phylogenetically distinct clades consisting of closely related clones of S. Typhimurium or S. 4,[5],12:i:- on each pig farm, that persisted between production cycles. All the S. 4,[5],12:i:- strains carried the Salmonella genomic island-4 (SGI-4), which confers resistance to heavy metals, and half of the strains contained the mTmV prophage, harbouring the sopE virulence gene. Most clonal groups were highly drug resistant due to the presence of multiple antimicrobial resistance (AMR) genes, and two clades exhibited evidence of recent on-farm plasmid-mediated acquisition of additional AMR genes, including an IncHI2 plasmid. Biofilm formation was highly variable but had a strong phylogenetic signature. Strains capable of forming biofilm with the greatest biomass were from the S. 4,[5],12:i:- and S. Typhimurium DT104 clades, the two dominant pandemic clones found over the last 25 years. On-farm microevolution resulted in enhanced biofilm formation in subsequent production cycle.
    • MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking

      Vegh, Peter; Magee, David A.; Nalpas, Nicolas C.; Bryan, Kenneth; McCabe, Matthew S.; Browne, John A.; Conlon, Kevin M.; Gordon, Stephen V.; Bradley, Daniel G.; MacHugh, David E.; et al. (Elsevier, 2014-11-05)
      Mycobacterium bovis, the causative agent of bovine tuberculosis, a major problem for global agriculture, spreads via an airborne route and is taken up by alveolar macrophages (AM) in the lung. Here, we describe the first next-generation sequencing (RNA-seq) approach to temporally profile miRNA expression in primary bovine AMs post-infection with M. bovis. One, six, and forty miRNAs were identified as significantly differentially expressed at 2, 24 and 48 h post-infection, respectively. The differential expression of three miRNAs (bta-miR-142-5p, bta-miR-146a, and bta-miR-423-3p) was confirmed by RT-qPCR. Pathway analysis of the predicted mRNA targets of differentially expressed miRNAs suggests that these miRNAs preferentially target several pathways that are functionally relevant for mycobacterial pathogenesis, including endocytosis and lysosome trafficking, IL-1 signalling and the TGF-β pathway. Over-expression studies using a bovine macrophage cell-line (Bomac) reveal the targeting of two key genes in the innate immune response to M. bovis, IL-1 receptor-associated kinase 1 (IRAK1) and TGF-β receptor 2 (TGFBR2), by miR-146. Taken together, our study suggests that miRNAs play a key role in tuning the complex interplay between M. bovis survival strategies and the host immune response.