• 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, E.; Berry, Donagh P.; O'Grady, L.; 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, L.; 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, N.W.J.; Forristal, P.D.; Doyle, E.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.
    • Merging and characterising phenotypic data on conventional and rare traits from dairy cattle experimental resources in three countries

      Banos, G.; Coffey, M. P.; Veerkamp, R. 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.; et al; Purfiled, Deirdre C; Berry, Donagh P.; Department of Agriculture, Food and the Marine, Ireland; Science Foundation Ireland; German Federal Ministry of Education and Research; Deutsche Forschungsgemeinschaft; Breed4Food; European Commission; Dairy Futures Cooperative Research Centre; Genome Canada project; 11/S/112; 14/IA/2576; 0315527B; PA 2789/1-1; BO-22.04-011-001-ASG-LR; 317697 (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 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, D.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.
    • 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, N.W.J; Forristal, P.D.; Doyle, E.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.
    • MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model.

      Lawless, Nathan; Reinhardt, Timothy A.; Bryan, Kenneth; Baker, Mike; Pesch, Bruce; Zimmerman, Duane; Zuelke, Kurt; Sonstegard, Tad; O'Farrelly, Cliona; Lippolis, John D.; Lynn, David J.; Teagasc Walsh Fellowship Programme; United States Department of Agriculture; Teagasc; 3625-32000-102-00 (Genetics Society of America, 2014-01-27)
      Bovine mastitis is an inflammation-driven disease of the bovine mammary gland that costs the global dairy industry several billion dollars per annum. Because disease susceptibility is a multi-factorial complex phenotype, an integrative biology approach is required to dissect the molecular networks involved. Here, we report such an approach, using next generation sequencing combined with advanced network and pathway biology methods to simultaneously profile mRNA and miRNA expression at multiple time-points (0, 12, 24, 36 and 48h) in both milk and blood FACS-isolated CD14+ monocytes from animals infected in vivo with Streptococcus uberis. More than 3,700 differentially expressed (DE) genes were identified in milk-isolated monocytes (MIMs), a key immune cell recruited to the site of infection during mastitis. Up-regulated genes were significantly enriched for inflammatory pathways, while down-regulated genes were enriched for non-glycolytic metabolic pathways. Monocyte transcriptional changes in the blood, however, were more subtle but highlighted the impact of this infection systemically. Genes up-regulated in blood-isolated-monocytes (BIMs) showed a significant association with interferon and chemokine signalling. Furthermore, twenty-six miRNAs were differentially expressed in MIMs and three in BIMs. Pathway analysis revealed that predicted targets of down-regulated miRNAs were highly enriched for roles in innate immunity (FDR < 3.4E-8) in particular TLR signalling, while up-regulated miRNAs preferentially targeted genes involved in metabolism. We conclude that during S. uberis infection miRNAs are key amplifiers of monocyte inflammatory response networks and repressors of several metabolic pathways.
    • Mid-infrared prediction of lactoferrin content in bovine milk: potential indicator of mastitis

      Soyeurt, H.; Bastin, C.; Colinet, F. G.; Arnould, V. M.-R.; Berry, Donagh P.; Wall, E.; Dehareng, F.; Nguyen, H. N.; Dardenne, P.; Schefers, J.; Vandenplas, J.; Weigel, K.; Coffey, M.; Theron, L.; Detilleux, J.; Reding, E.; Gengler, N.; McParland, Sinead; European Union; National Fund for Scientific Research; 211708; KBBE-2007 (Cambridge University Press, 2012-04-27)
      Lactoferrin (LTF) is a milk glycoprotein favorably associated with the immune system of dairy cows. Somatic cell count is often used as an indicator of mastitis in dairy cows, but knowledge on the milk LTF content could aid in mastitis detection. An inexpensive, rapid and robust method to predict milk LTF is required. The aim of this study was to develop an equation to quantify the LTF content in bovine milk using mid-infrared (MIR) spectrometry. LTF was quantified by enzyme-linked immunosorbent assay (ELISA), and all milk samples were analyzed by MIR. After discarding samples with a coefficient of variation between 2 ELISA measurements of more than 5% and the spectral outliers, the calibration set consisted of 2499 samples from Belgium (n = 110), Ireland (n = 1658) and Scotland (n = 731). Six statistical methods were evaluated to develop the LTF equation. The best method yielded a cross-validation coefficient of determination for LTF of 0.71 and a cross-validation standard error of 50.55 mg/l of milk. An external validation was undertaken using an additional dataset containing 274 Walloon samples. The validation coefficient of determination was 0.60. To assess the usefulness of the MIR predicted LTF, four logistic regressions using somatic cell score (SCS) and MIR LTF were developed to predict the presence of mastitis. The dataset used to build the logistic regressions consisted of 275 mastitis records and 13 507 MIR data collected in 18 Walloon herds. The LTF and the interaction SCS × LTF effects were significant (P < 0.001 and P = 0.02, respectively). When only the predicted LTF was included in the model, the prediction of the presence of mastitis was not accurate despite a moderate correlation between SCS and LTF (r = 0.54). The specificity and the sensitivity of models were assessed using Walloon data (i.e. internal validation) and data collected from a research herd at the University of Wisconsin – Madison (i.e. 5886 Wisconsin MIR records related to 93 mastistis events – external validation). Model specificity was better when LTF was included in the regression along with SCS when compared with SCS alone. Correct classification of non-mastitis records was 95.44% and 92.05% from Wisconsin and Walloon data, respectively. The same conclusion was formulated from the Hosmer and Lemeshow test. In conclusion, this study confirms the possibility to quantify an LTF indicator from milk MIR spectra. It suggests the usefulness of this indicator associated to SCS to detect the presence of mastitis. Moreover, the knowledge of milk LTF could also improve the milk nutritional quality.
    • Mid-infrared spectrometry of milk as a predictor of energy intake and efficiency in lactating dairy cows

      McParland, Sinead; Lewis, Eva; Kennedy, Emer; Moore, S. G.; McCarthy, B.; O'Donovan, Michael; Butler, Stephen T.; Pryce, J. E.; Berry, Donagh P.; Department of Agriculture, Food and the Marine, Ireland; Marie Curie project International Research Staff Exchange Scheme SEQSEL; 13/S4/96 (Elsevier for American Dairy Science Association, 2014-09)
      Interest is increasing in the feed intake complex of individual dairy cows, both for management and animal breeding. However, energy intake data on an individual-cow basis are not routinely available. The objective of the present study was to quantify the ability of routinely undertaken mid-infrared (MIR) spectroscopy analysis of individual cow milk samples to predict individual cow energy intake and efficiency. Feed efficiency in the present study was described by residual feed intake (RFI), which is the difference between actual energy intake and energy used (e.g., milk production, maintenance, and body tissue anabolism) or supplied from body tissue mobilization. A total of 1,535 records for energy intake, RFI, and milk MIR spectral data were available from an Irish research herd across 36 different test days from 535 lactations on 378 cows. Partial least squares regression analyses were used to relate the milk MIR spectral data to either energy intake or efficiency. The coefficient of correlation (REX) of models to predict RFI across lactation ranged from 0.48 to 0.60 in an external validation data set; the predictive ability was, however, strongest (REX = 0.65) in early lactation (<60 d in milk). The inclusion of milk yield as a predictor variable improved the accuracy of predicting energy intake across lactation (REX = 0.70). The correlation between measured RFI and measured energy balance across lactation was 0.85, whereas the correlation between RFI and energy balance, both predicted from the MIR spectrum, was 0.65. Milk MIR spectral data are routinely generated for individual cows throughout lactation and, therefore, the prediction equations developed in the present study can be immediately (and retrospectively where MIR spectral data have been stored) applied to predict energy intake and efficiency to aid in management and breeding decisions.
    • The miRNAome of the postpartum dairy cow liver in negative energy balance

      Fatima, Attia; Lynn, David J; O'Boyle, Padraic; Seoighe, Cathal; Morris, Dermot; Teagasc Walsh Fellowship Programme (Biomed Central, 2014-04-12)
      Background: Negative energy balance (NEB) is an altered metabolic state in high yielding cows that occurs during the first few weeks postpartum when energy demands for lactation and maintenance exceed the energy supply from dietary intake. NEB can, in turn, lead to metabolic disorders and to reduced fertility. Alterations in the expression of more than 700 hepatic genes have previously been reported in a study of NEB in postpartum dairy cows. miRNAs (microRNA) are known to mediate many alterations in gene expression post transcriptionally. To study the hepatic miRNA content of postpartum dairy cows, including their overall abundance and differential expression, in mild NEB (MNEB) and severe NEB (SNEB), short read RNA sequencing was carried out. To identify putative targets of differentially expressed miRNAs among differentially expressed hepatic genes reported previously in dairy cows in SNEB computational target identification was employed. Results: Our results indicate that the dairy cow liver expresses 53 miRNAs at a lower threshold of 10 reads per million. Of these, 10 miRNAs accounted for greater than 95% of the miRNAome (miRNA content). Of the highly expressed miRNAs, miR-122 constitutes 75% followed by miR-192 and miR-3596. Five out of thirteen let-7 miRNA family members are also among the highly expressed miRNAs. miR-143, down-regulated in SNEB, was found to have 4 putative up-regulated gene targets associated with SNEB including LRP2 (low density lipoprotein receptor-related protein 2), involved in lipid metabolism and up-regulated in SNEB. Conclusions: This is the first liver miRNA-seq profiling study of moderate yielding dairy cows in the early postpartum period. Tissue specific miR-122 and liver enriched miR-192 are two of the most abundant miRNAs in the postpartum dairy cow liver. miR-143 is significantly down-regulated in SNEB and putative targets of miRNA-143 which are up-regulated in SNEB, include a gene involved in lipid metabolism.
    • Modelling fat and protein concentration curves for Irish dairy cows

      Quinn, N.; Killen, L.; Buckley, Frank (Teagasc, Oak Park, Carlow, Ireland, 2006)
      The objective of this study was to acquire a well-fitting, single-equation model that would represent the fat and protein concentration curves of milk from Irish dairy cows. The dataset consisted of 16,086 records from both spring and autumn calving cows from both experimental and commercial herds. Many models cited in the literature to represent milk yield were examined for their suitability to model constituent curves. Models were tested for goodness-of-fit, adherence to the assumptions of regression analysis, and their ability to predict total fat and protein concentration for an entire lactation. Wilmink’s model best satisfied these criteria. It had the best Mean Square Prediction Error (goodness-of-fit) value, it satisfied the assumptions of regression analysis (multicollinearity, heteroskedasticity, autocorrelation and normality of distribution), and it predicted the actual concentration of the constituents to within 0.01 percentage point.
    • Molecular Genetic Typing of Staphylococcus aureus from Cows, Goats, Sheep, Rabbits and Chickens

      Smyth, Davida S.; Hartigan, Patrick J.; Meaney, William J; Smyth, Cyril J. (Teagasc, 2006-12-01)
      S. aureus can also cause a number of infections in animals such as tick-associated pyaemia in lambs, staphylococcosis in rabbits, septicaemia, abscesses and chondronecrosis in chickens and pneumonia and osteomyelitis complex in turkeys. S. aureus is the most frequent cause of bovine mastitis, a disease that is of economic importance worldwide (Beck et al., 1992). Typically staphylococcal mastitis is chronic in nature, with subclinical mastitis being the most common form.
    • N leaching to groundwater from dairy production involving grazing over the winter on a clay-loam soil

      Necpalova, Magdalena; Fenton, Owen; Casey, I.; Humphreys, James; Department of Agriculture, Food and the Marine, Ireland; RSF07-511 (Elsevier B. V., 15/08/2012)
      This study investigated concentrations of various N species in shallow groundwater (< 2.2 m below ground level) and N losses from dairy production involving grazing over the winter period on a clay loam soil with a high natural attenuation capacity in southern Ireland (52˚51’N, 08˚21’W) over a two year period. A dense network of shallow groundwater piezometers was installed to determine groundwater flow direction and N spatial and temporal variation. Estimated vertical travel times through the unsaturated zone (<0.5 yr, time lag) allowed the correlation of management with groundwater N within a short space of time. There was a two way interaction of the system and sampling date (P < 0.05) on concentrations of DON, oxidised N and NO3--N. In contrast, concentrations of NH4+-N and NO2--N were unaffected by the dairy system. Grazing over the winter had no effect on N losses to groundwater. Mean concentrations of DON, NH4+-N, NO2--N and NO3--N were 2.16, 0.35, 0.01 and 0.37 mg L-1 respectively. Soil attenuation processes such as denitrification and DNRA resulted in increased NH4+-N levels. For this reason, DON and NH4+-N represented the highest proportion of N losses from the site. Some of the spatial and temporal variation of N concentrations was explained by correlations with selected chemical and hydro-topographical parameters (NO3--N/Cl- ratio, distance of the sampling point from the closest receptor, watertable depth, depth of sampling piezometer, DOC concentration). A high explanatory power of NO3--N/Cl- ratio and the distance of the sampling point from the closest receptor indicated the influence of point sources and groundwater-surface water interactions.