• Short Communication: The effect of dry period duration and dietary energy density on the rennet gelation properties of milk in early lactation

      Butler, Stephen T.; de Feu, M.A.; O'Brien, Bernadette; Guinee, Timothy P.; Murphy, J.J. (American Dairy Science Association and Elsevier Inc., 2010-02)
      This study was carried out to examine the effects of decreasing dry period duration (DP) and altering the energy density of the diet during early lactation on the rheological characteristics of milk. Forty mature Holstein-Friesian cows were used in a completely randomized design with a 2 × 2 factorial arrangement of treatments. Cows were randomly assigned to one of two dry period treatments and one of two nutritional treatments. The dry period treatments were continuous milking (CM) or an 8-week standard dry period (SDP), and the nutritional treatments were a standard energy diet (SE) or a high energy diet (HE). Actual dry period lengths were 6.3 ± 1.7 days and 62.1 ± 1.9 days for cows for the CM and SDP treatments, respectively. Milk samples were collected at 2, 6 and 10 weeks postpartum. The concentration of fat, protein and lactose was determined in each sample. The rennet gelation properties were measured at 31 ° C using dynamic low-amplitude strain oscillatory rheometry. The following parameters were obtained from the resultant elastic shear modulus (G′): gelation time (GT), maximum curd firming rate (CFRmax) and gel strength (GS). Reducing dry period duration from 62 to 6 days resulted in increases in milk protein concentration (31.8 vs. 34.7 g/kg; P < 0.001), CFRmax (2.58 vs. 3.60 Pa/min; P < 0.001) and GS (69.4 vs. 90.5 Pa; P = 0.003). Raising the dietary energy density decreased percentage milk fat (43.1 vs. 37.7 g/kg; P < 0.001) but otherwise had no effect. GS was correlated with CFRmax (r = 0.98; P < 0.001), and both variables were correlated with milk protein concentration (r = 0.71; P < 0.001, and r = 0.73; P < 0.001, respectively). The results indicate that decreasing the duration of DP increased milk protein concentration and improved the rennet gelation properties of milk, but that dietary energy density had little effect.
    • Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle

      Berkowicz, Erik W; Magee, David A; Sikora, Klaudia M.; Berry, Donagh P.; Howard, Dawn J.; Mullen, Michael Paul; Evans, Ross D.; Spillane, Charles; MacHugh, David E (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 2010-09)
      The imprinted insulin-like growth factor 2 gene (IGF2) encodes a fetal mitogenic hormone protein (IGF-II) and has previously been shown to be associated with performance in dairy cattle. In this study we assessed genotype-phenotype associations between four single nucleotide polymorphisms (SNPs) located within the bovine IGF2 locus on chromosome 29 and a range of performance traits related to milk production, animal growth and body size, fertility and progeny survival in 848 progeny-tested Irish Holstein-Friesian sires. Two of the four SNPs (rs42196909 and IGF2.g-3815A>G), which were in strong linkage disequilibrium (r 2=0.995), were associated with milk yield (Pf0.01) and milk protein yield (Pf0.05); the rs42196901 SNP was also associated (Pf0.05) with milk fat yield. Associations (Pf0.05) with milk fat percentage and milk protein percentage were observed at the rs42196901 and IGF2.g-3815A>G SNPs, respectively. The rs42196909 and IGF2.g-3815A>G SNPs were also associated with progeny carcass conformation (Pf0.05), while an association (Pf0.01) with progeny carcass weight was observed at the rs42194733 SNP locus. None of the four SNPs were associated with body size, fertility and progeny survival. These findings support previous work which suggests that the IGF2 locus is an important biological regulator of milk production in dairy cattle and add to an accumulating body of research showing that imprinted genes influence many complex performance traits in cattle.
    • Single nucleotide polymorphisms in the insulin-like growth factor 1 (IGF-1) gene are associated with performance in Holstein-Friesian dairy cattle

      Mullen, Michael Paul; Berry, Donagh P.; Howard, Dawn J.; Diskin, Michael G.; Lynch, Ciaran O.; Giblin, Linda; Kenny, David A.; Magee, David A; Meade, Kieran G; Waters, Sinead M. (Frontiers Media SA, 16/02/2011)
      Insulin-like growth factor 1 (IGF-1) has been shown to be associated with fertility, growth, and development in cattle. The aim of this study was to (1) identify novel single nucleotide polymorphisms (SNPs) in the bovine IGF-1 gene and alongside previously identified SNPs (2) determine their association with traits of economic importance in Holstein-Friesian dairy cattle. Nine novel SNPs were identified across a panel of 22 beef and dairy cattle by sequence analysis of the 5′ promoter, intronic, and 3′ regulatory regions, encompassing ∼5 kb of IGF-1. Genotyping and associations with daughter performance for milk production, fertility, survival, and measures of body size were undertaken on 848 Holstein-Friesian AI sires. Using multiple regression analysis nominal associations (P < 0.05) were identified between six SNPs (four novel and two previously identified) and milk composition, survival, body condition score, and body size. The C allele of AF017143 a previously published SNP (C-512T) in the promoter region of IGF-1 predicted to introduce binding sites for transcription factors HSF1 and ZNF217 was associated (P < 0.05) with increased cow carcass weight (i.e., an indicator of mature cow size). Novel SNPs were identified in the 3′ region of IGF-1 were associated (P < 0.05) with functional survival and chest width. The remaining four SNPs, all located within introns of IGF-1 were associated (P < 0.05) with milk protein yield, milk fat yield, milk fat concentration, somatic cell score, carcass conformation, and carcass fat. Results of this study further demonstrate the multifaceted influences of IGF-1 on milk production and growth related traits in cattle.
    • Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

      Doran, Anthony G; Creevey, Christopher J. (Biomed Central, 2013-02-08)
      Background: Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results: Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions: SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.
    • Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

      Doran, Anthony G; Creevey, Christopher J. (Biomed Central, 2013-02-08)
      Background: Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results: Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions: SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.
    • Spatial patterns of Fasciola hepatica and Calicophoron daubneyi infections in ruminants in Ireland and modelling of C. daubneyi infection

      Naranjo-Lucena, Amalia; Munita Corbalán, María P; Martínez-Ibeas, Ana M; McGrath, Guy; Murray, Gerard; Casey, Mícheál; Good, Barbara; Sayers, Riona; Mulcahy, Grace; Zintl, Annetta; European Union; Department of Agriculture, Food and the Marine, Ireland; 635408); 13/S/405 (Biomed Central, 2018-09-29)
      Background Fasciola hepatica has always represented a threat to Irish livestock because the Irish climate is highly suitable for the main local intermediate host of the parasite, the snail Galba truncatula. The recent clinical emergence of infections due to Calicophoron daubneyi has raised the question of whether the two parasites, which share a niche during part of their life-cycles, interact in some way. Here, we used geographical information systems (GIS) to analyse the distribution of both parasites in cattle and sheep. We also developed the first predictive model of paramphistomosis in Ireland. Results Our results indicated that, in cattle, liver fluke infection is less common than rumen fluke infection and does not exhibit the same seasonal fluctuations. Overall, we found that cattle had a higher likelihood of being infected with rumen fluke than sheep (OR = 3.134, P < 0.01). In addition, infection with one parasite increased the odds of infection with the other in both host species. Rumen fluke in cattle showed the highest spatial density of infection. Environmental variables such as soil drainage, land cover and habitat appeared to be the most important risk factors for C. daubneyi infection, followed by rainfall and vegetation. Overall the risk of infection with this parasite was predicted to be higher in the west of the country. Conclusions This study shows differences between the infection rates and spatial patterns of bovine and ovine infections with F. hepatica and C. daubneyi in Ireland. Whether the reasons for this are due to susceptibility, exposure and/or management factors is yet to be determined. Furthermore, the rumen fluke model indicates distinct risk factors and predicted distribution to those of F. hepatica, suggesting potential biological differences between both parasite species.
    • Stakeholder involvement in establishing a milk quality sub-index in dairy cow breeding goals: a Delphi approach

      Henchion, Maeve; McCarthy, M.; Resconi, Virginia C.; Berry, Donagh P.; McParland, Sinead; Department of Agriculture, Food and the Marine, Ireland; 11/SF/311 (Cambridge University Press, 17/11/2015)
      The relative weighting on traits within breeding goals are generally determined by bio-economic models or profit functions. While such methods have generally delivered profitability gains to producers, and are being expanded to consider non-market values, current approaches generally do not consider the numerous and diverse stakeholders that affect, or are affected, by such tools. Based on principles of respondent anonymity, iteration, controlled feedback and statistical aggregation of feedback, a Delphi study was undertaken to gauge stakeholder opinion of the importance of detailed milk quality traits within an overall dairy breeding goal for profit, with the aim of assessing its suitability as a complementary, participatory approach to defining breeding goals. The questionnaires used over two survey rounds asked stakeholders: (a) their opinion on incorporating an explicit sub-index for milk quality into a national breeding goal; (b) the importance they would assign to a pre-determined list of milk quality traits and (c) the (relative) weighting they would give such a milk quality sub-index. Results from the survey highlighted a good degree of consensus among stakeholders on the issues raised. Similarly, revelation of the underlying assumptions and knowledge used by stakeholders to make their judgements illustrated their ability to consider a range of perspectives when evaluating traits, and to reconsider their answers based on the responses and rationales given by others, which demonstrated social learning. Finally, while the relative importance assigned by stakeholders in the Delphi survey (4% to 10%) and the results of calculations based on selection index theory of the relative emphasis that should be placed on milk quality to halt any deterioration (16%) are broadly in line, the difference indicates the benefit of considering more than one approach to determining breeding goals. This study thus illustrates the role of the Delphi technique, as a complementary approach to traditional approaches, to defining breeding goals. This has implications for how breeding goals will be defined and in determining who should be involved in the decision-making process.
    • Strategies to alleviate reproductive wastage in dairy cows

      Butler, Stephen T. (Teagasc, 2007-01-01)
      grass-based systems of production. A series of studies were carried out to (i) improve our understanding of the physiological basis of poor reproductive performance; (ii) examine management and nutritional strategies to improve fertility; and (iii) examine the potential role of extended lactation to mitigate the effects of poor reproductive performance. A comprehensive characterization of the North American and New Zealand strains of Holstein-Friesian cow was carried out. North American cows produce a greater volume of milk, but yield a similar amount of fat and protein on a grass-based diet. Dry matter intake was greater for the larger NA strain, but energy balance did not differ during the first 20 weeks of lactation. Circulating concentrations of metabolic hormones and metabolites during the early lactation period were indicative of lesser bioenergetic status in the NZ strain compared to the NA strain. During established lactation, circulating concentrations of insulin-like growth factor-I (IGF-I) were greater in the NZ strain. Liver biopsies collected at day 35 and day 150 postpartum indicated that the greater circulating concentration of IGF-I was due to greater hepatic mRNA abundance of IGF-I and acid labile subunit (ALS). Embryos were collected from both strains after superovulation. A greater proportion of the embryos recovered were transferable in the NZ strain compared with the NA strain, indicating that the previously reported differences in reproductive performance were manifest as early as 7 days post-insemination. Collectively, the results of the study indicate that the NZ strain are genetically better equipped to survive on a pasture-based seasonal calving system. A study was carried out to examine the effect of dry period duration and dietary energy density on milk production, bioenergetic status and postpartum ovarian function. Omitting the dry period and increasing dietary energy density both resulted in improved energy balance and metabolic status, but omitting the dry period reduced the postpartum interval to resumption of cyclicity whereas increasing dietary energy density had no effect. Omitting the dry period reduced the inherent drive to produce milk, and allowed the cow to fully meet nutritional requirements from voluntary dry matter intake. Increased dietary energy density also allowed the cow to more closely meet nutritional requirements from a higher energy density diet, albeit at a greater milk yield. The results suggest that the mechanism by which a cow arrives at a particular energy balance status may be as important as energy balance per se. One of the main energy costs associated with lactation is milk fat. Trans 10, cis 12 conjugated linoleic acid (CLA) is a geometric and positional isomer of linoleic acid that reduces milk fat synthesis in a dose dependent manner. Supplementing cows with CLA resulted in improved energy balance status during the transition period and reduced postpartum body condition score loss. Some indices of reproductive performance were also improved. In seasonal systems, cows that fail to become pregnant by the end of the breeding season are typically culled and replaced. When reproductive performance is poor, this represents a major cost on dairy farms. A study was carried out to examine the feasibility of extending the lactation to 22 months, resulting in a calving interval of 24 months instead of 12 months. High yielding cows produced the equivalent of 2 normal lactations in an extended lactation system. An economic analysis indicated that an efficient spring calving system with a compact calving pattern and a 12 month calving interval is still the most profitable, but with high yielding cows extending the lactation of non-pregnant cows is more profitable than culling and replacing.
    • Stress and immunological response of heifers divergently ranked for residual feed intake following an adrenocorticotropic hormone challenge

      Kelly, A. K; Lawrence, P.; Earley, Bernadette; Kenny, David A.; McGee, Mark (Biomed Central, 2017-08-08)
      Background When an animal is exposed to a stressor, metabolic rate, energy consumption and utilisation increase primarily through activation of the hypothalamic-pituitary-adrenal (HPA) axis. Changes to partitioning of energy by an animal are likely to influence the efficiency with which it is utilised. Therefore, this study aimed to determine the physiological stress response to an exogenous adrenocorticotropic hormone (ACTH) challenge in beef heifers divergently ranked on phenotypic residual feed intake (RFI). Results Data were collected on 34 Simmental weaning beef heifers the progeny of a well characterized and divergently bred RFI suckler beef herd. Residual feed intake was determined on each animal during the post-weaning stage over a 91-day feed intake measurement period during which they were individually offered adlibitum grass silage and 2 kg of concentrate per head once daily. The 12 highest [0.34 kg DM/d] and 12 lowest [−0.48 kg DM/d] ranking animals on RFI were selected for use in this study. For the physiological stress challenge heifers (mean age 605 ± 13 d; mean BW 518 ± 31.4 kg) were fitted aseptically with indwelling jugular catheters to facilitate intensive blood collection. The response of the adrenal cortex to a standardised dose of ACTH (1.98 IU/kg metabolic BW0.75) was examined. Serial blood samples were analysed for plasma cortisol, ACTH and haematology variables. Heifers differing in RFI did not differ (P = 0.59) in ACTH concentrations. Concentration of ACTH peaked (P < 0.001) in both RFI groups at 20 min post-ACTH administration, following which concentration declined to baseline levels by 150 min. Similarly, cortisol systemic profile peaked at 60 min and concentrations remained continuously elevated for 150 min. A RFI × time interaction was detected for cortisol concentrations (P = 0.06) with high RFI heifers had a greater cortisol response than Low RFI from 40 min to 150 min relative to ACTH administration. Cortisol response was positively associated with RFI status (r = 0.32; P < 0.01). No effect of RFI was evident for neutrophil, lymphocytes, monocyte, eosinophils and basophil count. Plasma red blood cell number (6.07 vs. 6.23; P = 0.02) and hematocrit percentage (23.2 vs. 24.5; P = 0.02) were greater for low than high RFI animals. Conclusions Evidence is provided that feed efficiency is associated with HPA axis function and susceptibility to stress, and responsiveness of the HPA axis is likely to contribute to appreciable variation in the efficiency feed utilisation of cattle.
    • Studies of Autumn calving suckler cows, bulls at pasture and winter grazing

      Black, Alistair D; O’Riordan, Edward G.; Weldon, B.; French, Padraig (Teagasc, 2010-09)
      Most beef and dairy cows are spring calving leading to distinct seasonality of supply. Calving a proportion of the beef herd in the autumn would lead to a more uniform annual supply of cattle for slaughter and potentially increase the proportion of grazed grass in the diet of the suckler progeny. Autumn calving sucklers also facilitate the use of AI, which should enhance the product quality. This project aimed to address the technical aspects of autumn calving sucklers, which differ from those of spring calvers. The currently available international energy models were evaluated for autumn calving lactating suckler cows using the type of cow typically found in Irish suckler herds (Experiment 1). The winter accommodation of the suckler cow and calf unit and its impact on cow reproductive performance was evaluated (Experiment 2). The final part of the project evolved into component studies to determine the effect of supplementary feed on the performance of grazing bulls (Experiment 3), and the consequences of weanling cattle grazing pasture in winter as an alternative to housing them in winter (Experiments 4 to 7).
    • Studies relating to Polyunsaturated Fatty Acid (PUFA) Supplementation and Fertility in Cattle

      Childs, Stuart; Kenny, D.A.; Sreenan, J.M.; Diskin, Michael G. (Teagasc, 2007-01-01)
      Reproductive inefficiency has a significant impact on the economic performance of both dairy and beef herds, particularly in seasonal calving systems. Nutrition plays a fundamental role in reproduction. Furthermore, there is emerging evidence that supplemental dietary polyunsaturated fatty acids (PUFA) may increase cow fertility independent of their role as energy substrates. A number of studies have reported enhanced reproductive performance in dairy cows following dietary supplementation with sources of n-3 PUFA. However the possible mechanisms involved have not been identified and there is some inconsistency in the published literature on this topic. The objective of the research reported was to conduct a holistic examination of the effects of dietary long-chain n-3 PUFA supplementation on metabolic and reproductive responses in cattle. Such information is essential for the appropriate formulation of diets to enhance cow reproductive performance and in particular embryo survival.
    • Studies relating to protein expression in the uterus of the cow

      Costello, L.M.; Hynes, A.C.; Diskin, Michael G.; Sreenan, J.M.; Morris, Dermot G. (Teagasc, 2007-01-01)
      Embryo loss is a major cause of reproductive wastage in the cow. The majority of embryo loss occurs in the first 16 days after fertilisation when the embryo is critically dependent on the maternal uterine environment for survival. Despite the central role of uterine fluid in the normal growth and development of the embryo, there is limited information on the protein composition of these fluids. The main objectives of the studies in this thesis were to examine the protein composition of the bovine uterus during the oestrous cycle and to examine the relationship between the concentration of systemic progesterone and uterine protein expression in the cow. In the first study, the concentration of retinol-binding protein (RBP) in the bovine uterus was found to vary across the cycle and was 5-15-fold higher (P<0.001) on Day 15 than Days 3, 7 and 11. Additionally, the concentration of uterine RBP seems to be regulated in a local manner as the concentration in the uterine horn ipsilateral to the corpus luteum (CL) was more than 2-fold higher (P<0.001) than the contralateral horn on Day 15. This indicates that RBP is possibly regulated by a local increase in the concentration of progesterone. Uterine and plasma concentrations of RBP were similar on days 3 to 11, however, uterine RBP concentrations were 6-15 fold higher than blood plasma RBP concentrations on day 15. This shows evidence of active transport and/or synthesis of proteins into the uterus which previously were thought to be due to transduation of plasma. There was no relationship between the concentration of systemic progesterone and concentration of RBP on day 7 (P>0.05) of the cycle, which was surprising given that previous studies have indicated that uterine RBP gene expression was positively associated with the concentration of systemic progesterone. In the second study, IGF binding protein 2 (IGFBP-2), IGFBP-3, IGFBP-4 and IGFBP-5 were identified in uterine fluid on days 3, 7, 11 and 15 of the oestrous cycle. There was a local effect on the concentration of IGFBPs where the concentration was greater on the ipsilateral side than that on the contralateral side for IGFBP-2 (P<0.05), 3 (P<0.01) and 5 (P<0.01) on day 15. This difference is a further indication of a local controlling mechanism regulating proteins between the uterine horns. Similar to RBP expression this study could find no significant relationship between the concentration of systemic progesterone and IGFBP concentrations on Day 7 of the oestrous cycle. In the third study, changes in the global pattern of uterine proteins between Days 3 and Day 15 of the oestrous cycle were examined using two-dimensional electrophoresis (2-DE). Six proteins were found to be upregulated on Day 15 compared to Day 3. Three proteins of these were identified as aldose reductase, plakoglobin and heat shock protein 27 while the other three proteins were identified as bovine serum albumin. Aldose reductase, an enzyme directly involved in the production of sorbitol and indirectly of fructose, was 10-fold higher (P<0.0001) on Day 15 compared to Day 3. Plakoglobin (Pg) was upregulated 2.3-fold (P<0.0001) on Day 15 compared to Day 3. Pg is a component of cellular junctions and its up-regulation may have a role in the uterine glandular epithelium. Heat shock protein 27 (Hsp27) was higher on Day 15 than on Day 3 (P<0.01) and Hsp27 was 1.4-fold higher in the ipsilateral compared to the contralateral uterine horn (P<0.01). Hsp27 may be secreted in response to potential stresses in the uterus or act as a molecular chaperone. On Day 7 there was no difference (P<0.05) in the pattern of proteins secreted between cows with low (2.7±0.10ng/ml) and high (4.8±0.13 ng/ml) concentrations of systemic progesterone on Day 7. The results of these studies have shown that dramatic changes occur in protein expression across the bovine oestrous cycle. Additionally, it emphasises the need for gene studies to be followed with protein studies as an adjunct or complementary tool. Proteins have a wide range of essential roles in the uterus and together these studies provide novel information on protein expression in the uterus of the cow.
    • A study of the somatic cell count (SCC) of Irish milk from herd management and environmental perspectives

      O'Brien, Bernadette; Berry, Donagh P.; Kelly, Philip M.; Meaney, William J; O'Callaghan, Edmond J (Teagasc, 2009-12-01)
      The objective of this study was to investigate the herd management practices associated with somatic cell count (SCC) and total bacteria count (TBC), to geographically analyse SCC on a national basis, to investigate cow factors associated with SCC and to estimate the milk loss associated with high SCC across parities. From the 400 farms surveyed during farm visits throughout spring and winter, a profile of herd management was developed and the associations between management practices and milk SCC and TBC were established. Management practices associated with low SCC included the use of dry cow therapy, participation in a milk recording scheme, the use of teat disinfection post-milking, a higher frequency of cleaning and increased farm hygiene. Management practices associated with low TBC included the use of heated water in the milking parlour, participation in a milk recording scheme, tail clipping of cows at a frequency greater than once per year and increased farm hygiene. The spatial analysis showed that the south of the country had the greatest density of milk-recording herds. Approximately 60% of all herds in the study were from four counties (Cork, Kerry, Limerick and Tipperary). Average bulk tank SCC increased from 110,264 cells/mL in 2003 to 118,782 cells/mL in 2005, followed by a decrease to 108,454 cells/mL in 2007. Spatial clustering of high SCC scores was not observed (i.e., SCC on one farm was not related to SCC on other farms), which is consistent with mastitis being a herd problem as opposed to an area-based problem. SCC increased with parity from 97,000 cells/mL in parity 1 to 199,000 cell/mL in parity 6. SCC decreased between the period 5 to 35 days in milk (DIM) and 36 to 65 DIM, and increased thereafter. Cows calving in the months of January and September were associated with lower average 305 day SCC. The rate of increase in SCC from mid to late lactation was greatest in older parity animals. There was a test day milk loss of 1.43, 2.08, 2.59, 2.56 and 2.62 litres (parities 1 to 5, respectively) associated with an increase of SCC category from <51,000 to >400,000 cells/mL. When SCC was adjusted (test day SCC/dilution estimate, and test day SCC + (-ß)(test day milk yield)) to account for milk yield, similar trends in milk loss were observed. Alternatively, adjusting SCC (SCC*test day milk yield/mean test day milk yield) to account for milk yield showed an increase in test day milk with increasing SCC category. The results from this study highlight that adherence to best milking/farming practice will help reduce SCC and TBC on farms. The results contribute to the knowledge relating to SCC through increasing the accuracy of milk loss due to SCC and management practices associated with SCC. The results in the study can also be used in the development of strategies to reduce SCC on farms.
    • A survey of biosecurity-related practices, opinions and communications across dairy farm veterinarians and advisors

      Sayers, Riona; Good, M.; Sayers, Gearoid (Elsevier, 2014-02-25)
      Biosecurity at farm-level can often be poorly implemented, and lack of information has been cited by many studies as a potential explanation. Veterinary practitioners (VPs) and dairy advisors (DAs) play a central role in the provision of animal health and management services to dairy farmers. The objective of this study was to document and compare biosecurity-related practices and opinions across VPs and DAs in Ireland. A selection of veterinary experts (VEs) from outside of Ireland was also surveyed. Questionnaires were completed and response rates of 47% (VPs), 97% (DAs), and 65% (VEs) were achieved. Significant differences were identified in the promotion and implementation of biosecurity between VPs and DAs, with a higher proportion of VPs regularly receiving requests from (P = 0.004), and dispensing advice to (P < 0.0001), their farm clients. Communication between DAs and VPs was sub-optimal with over 60% of each group not in regular communication with each other. With regard to the main farmer motivation for biosecurity implementation, the majority of VPs (62%) prioritised external factors such as ‘economic benefit’ and ‘mandatory obligation’, while the majority of DAs prioritised health/animal-related factors (69%), which were similar to those of farmers (83.1%), although they remained significantly less likely (OR = 1.8) than farmers to choose such motivators (P = 0.005). Inconsistencies in the implementation of, and in opinions relating to, farm biosecurity were highlighted across all the groups surveyed emphasising the need for standardised information and improved communication.
    • Temporal patterns of inflammatory gene expression in local tissues after banding or burdizzo castration in cattle

      Pang, Wanyong; Earley, Bernadette; Sweeney, Torres; Gath, Vivian; Crowe, Mark A (Biomed Central, 2009-09-23)
      Background: Castration of male cattle has been shown to elicit inflammatory reactions and acute inflammation is initiated and sustained by the participation of cytokines. Methods: Sixty continental × beef bulls (Mean age 12 ± (s.e.) 0.2 months; Mean weight 341 ± (s.e.) 3.0 kg) were blocked by weight and randomly assigned to one of three treatments (n = 20 animals per treatment): 1) untreated control (Con); 2) banding castration at 0 min (Band); 3) Burdizzo castration at 0 min (Burd). Samples of the testis, epididymis and scrotal skin were collected surgically from 5 animals from each group at 12 h, 24 h, 7 d, and 14 d post-treatment, and analysed using real-time PCR. A repeated measurement analysis (Proc GLM) was performed using SAS. If there was no treatment and time interaction, main effects of treatment by time were tested by ANOVA. Results: Electrophoresis data showed that by 7 d post-castration RNA isolated from all the testicle samples of the Burd castrated animals, the epididymis and middle scrotum samples from Band castrates were degraded. Transitory effects were observed in the gene expression of IFN-γ, IL-6, IL-8 and TNF-α at 12 h and 24 h post treatment. Burd castrates had greater (P < 0.05) testicular IFN-γ mRNA levels compared with Band and Con animals, but lower (P < 0.05) testicular TNF-α mRNA levels compared with Con animals. Band castrates had greater (P < 0.05) testicular IL-6 mRNA levels than Burd castrates at 12 h post-castration. Burd castrates had greater (P < 0.05) testicular IL-8 mRNA levels than Band and Con animals at 24 h post-castration. In the epididymis, Burd castrates had greater (P < 0.05) IL-6 mRNA (both at 12 h and 24 h post treatment) and IL-8 mRNA (12 h post treatment) levels compared with Band and Con animals; Burd castrates had greater (P = 0.049) IL-10 mRNA levels than Band castrates at 12 h post-castration. Conclusion: Banding castration caused more inflammatory associated gene expression changes to the epididymis and scrotum than burdizzo. Burdizzo caused more severe acute inflammatory responses, in terms of pro-inflammatory cytokine gene expression, in the testis and epididymis than banding.
    • Temporal trends in bulk milk antibodies to Salmonella, Neospora caninum, and Leptospira interrogans serovar hardjo in Irish dairy herds

      O'Doherty, E.; Sayers, Riona; O'Grady, L. (Elsevier, 2012-10-29)
      Bulk milk samples were collected from 309 Irish dairy herds at four time points during 2009 and tested for antibodies to Salmonella spp., N. caninum, and L. hardjo, three abortifacient agents in Irish dairy herds. Of the 312 study herds, 49% vaccinated against Salmonella and 76% vaccinated against L. hardjo. In unvaccinated herds, the overall prevalence of antibody positive herds was 49% for Salmonella, 19% for N. caninum and 86% for L. hardjo. There was no association between both testing positive for and incidence of Salmonella or L. hardjo on sample date and calving season. A significant association was found between sample date and both testing positive for [p = <0.0001 OR = 2.41 (95% CI 1.54–3.80)] and incidence [p = 0.001 OR = 3.10 (95% CI 1.72–5.57)] of N. caninum. No association with region of Ireland was found for either testing positive for or incidence of N. caninum, or L. hardjo. There was however a tendency towards a higher incidence of Salmonella in regions of Ireland with higher cattle densities.
    • Temporal trends in bulk milk antibodies to Salmonella, Neospora caninum, and Leptospira interrogans serovar hardjo in Irish dairy herds

      O'Doherty, Eugene; Sayers, Riona; O'Grady, L. (Elsevier, 2012-10-29)
      Bulk milk samples were collected from 309 Irish dairy herds at four time points during 2009 and tested for antibodies to Salmonella spp., N. caninum, and L. hardjo, three abortifacient agents in Irish dairy herds. Of the 312 study herds, 49% vaccinated against Salmonella and 76% vaccinated against L. hardjo. In unvaccinated herds, the overall prevalence of antibody positive herds was 49% for Salmonella, 19% for N. caninum and 86% for L. hardjo. There was no association between both testing positive for and incidence of Salmonella or L. hardjo on sample date and calving season. A significant association was found between sample date and both testing positive for [p = <0.0001 OR = 2.41 (95% CI 1.54–3.80)] and incidence [p = 0.001 OR = 3.10 (95% CI 1.72–5.57)] of N. caninum. No association with region of Ireland was found for either testing positive for or incidence of N. caninum, or L. hardjo. There was however a tendency towards a higher incidence of Salmonella in regions of Ireland with higher cattle densities.
    • Temporal trends in reproductive performance in Irish dairy herds and associated risk factors

      Mee, John F (Biomed Central, 2004-03-01)
      Irish dairy herd fertility has been declining since the 1980s. The extent, nature and causes of this decline in fertility and the current status of Irish dairy herd fertility were described. An increase in calving interval of approximately one day per year has been recorded. The principal components of this trend have been an increased incidence of postpartum endocrinopathies, reduced expression of oestrus and a fall in conception rate. Both submission rate and calving-to-service interval have increased slightly over time. Significant risk factors associated with these trends have been strain substitution within the Holstein-Friesian breed and single trait selection for milk production. Critically, these changes have been reflected in loss of body condition. Contributory factors included increased herd size and possibly increased use of DIYAI. The most recent Irish study showed that 48% of cows conceived to first service and 14% of cows were not pregnant at the end of the industry-average 15-week spring breeding season. However, the top quartile of herds achieved a first-service conception rate of 59%, illustrating the wide variation between herds. These phenotypic trends were attributed to both genetic and environmental factors and their interactions. Recent Irish dairy herd fertility performance falls short of the targets set for seasonal compact calving.
    • Transcriptome Analysis of CD4+ T Cells in Coeliac Disease Reveals Imprint of BACH2 and IFNγ Regulation

      Quinn, Emma M; Coleman, Ciara; Molloy, Ben; Castro, Patricia Dominguez; Cormican, Paul; Trimble, Valerie; Mahmud, Nasir; McManus, Ross (PLOS, 2015-10-07)
      Genetic studies have to date identified 43 genome wide significant coeliac disease susceptibility (CD) loci comprising over 70 candidate genes. However, how altered regulation of such disease associated genes contributes to CD pathogenesis remains to be elucidated. Recently there has been considerable emphasis on characterising cell type specific and stimulus dependent genetic variants. Therefore in this study we used RNA sequencing to profile over 70 transcriptomes of CD4+ T cells, a cell type crucial for CD pathogenesis, in both stimulated and resting samples from individuals with CD and unaffected controls. We identified extensive transcriptional changes across all conditions, with the previously established CD gene IFNy the most strongly up-regulated gene (log2 fold change 4.6; Padjusted = 2.40x10-11) in CD4+ T cells from CD patients compared to controls. We show a significant correlation of differentially expressed genes with genetic studies of the disease to date (Padjusted = 0.002), and 21 CD candidate susceptibility genes are differentially expressed under one or more of the conditions used in this study. Pathway analysis revealed significant enrichment of immune related processes. Co-expression network analysis identified several modules of coordinately expressed CD genes. Two modules were particularly highly enriched for differentially expressed genes (P<2.2x10-16) and highlighted IFNy and the genetically associated transcription factor BACH2 which showed significantly reduced expression in coeliac samples (log2FC -1.75; Padjusted = 3.6x10-3) as key regulatory genes in CD. Genes regulated by BACH2 were very significantly over-represented among our differentially expressed genes (P<2.2x10-16) indicating that reduced expression of this master regulator of T cell differentiation promotes a pro-inflammatory response and strongly corroborates genetic evidence that BACH2 plays an important role in CD pathogenesis.
    • Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

      O’Loughlin, Aran; Lynn, David J; McGee, Mark; Doyle, Sean; McCabe, Matthew; Earley, Bernadette (Biomed Central, 2012-06-18)
      Background: Weaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessation of the maternal-offspring bond and is often accompanied by housing. While much recent research has focused on the physiological response of the bovine immune system to stress in recent years, little is known about the molecular mechanisms modulating the immune response. Therefore, the objective of this study was to provide new insights into the molecular mechanisms underlying the physiological response to weaning at housing in beef calves using Illumina RNA-seq.Results: The leukocyte transcriptome was significantly altered for at least 7 days following either housing or weaning at housing. Analysis of differentially expressed genes revealed that four main pathways, cytokine signalling, transmembrane transport, haemostasis and G-protein-coupled receptor (GPRC) signalling were differentially regulated between control and weaned calves and underwent significant transcriptomic alterations in response to weaning stress on day 1, 2 and 7. Of particular note, chemokines, cytokines and integrins were consistently found to be up-regulated on each day following weaning. Evidence for alternative splicing of genes was also detected, indicating a number of genes involved in the innate and adaptive immune response may be alternatively transcribed, including those responsible for toll receptor cascades and T cell receptor signalling.Conclusions: This study represents the first application of RNA-Seq technology for genomic studies in bovine leukocytes in response to weaning stress. Weaning stress induces the activation of a number of cytokine, chemokine and integrin transcripts and may alter the immune system whereby the ability of a number of cells of the innate and adaptive immune system to locate and destroy pathogens is transcriptionally enhanced. Stress alters the homeostasis of the transcriptomic environment of leukocytes for at least 7 days following weaning, indicating long term effects of stress exposure in the bovine. The identification of gene signature networks that are stress activated provides a mechanistic framework to characterise the multifaceted nature of weaning stress adaptation in beef calves. Thus, capturing subtle transcriptomic changes provides insight into the molecular mechanisms that underlie the physiological response to weaning stress.