• Comparison of breed of dairy cow under grass-based spring milk production systems.

      Buckley, Frank; Walsh, S.; Dillon, Pat (Teagasc, 2006-01)
      The objective of this study was to investigate the potential differences among different dairy cow breeds across two feeding systems on milk production, udder health, milking characteristics, body weight, body condition score, hormone parameters, ovarian function, survival and overall reproductive efficiency. The breeds investigated included Holstein-Friesian (HF), Montbéliarde (MB), Normande (NM), Norwegian Red (NRF) and Holstein- Friesian × Montbéliarde (MBX) and Holstein- Friesian × Normande (NMX). Selection within the HF breed has, until recently, been predominantly for milk production with little or no direct selection for functional traits other than those correlated with superior type. The MB and the NM have been simultaneously selected for both milk and beef production in the past. The NRF were imported as calves and come from a more balanced total merit index incorporating production and cow functionality since the early 1970s. The dairy cow breeds were grouped into blocks of two within breed groups and randomized across two spring-calving grass-based feeding systems: low concentrate feeding system (LC) and high concentrate feeding system (HC). Those on LC feeding system were offered approximately 530 kg/cow over the total lactation, while those on HC feeding system were offered approximately 1030 kg/cow. There was no genotype by environment interaction observed for any of the milk production, BCS, BW, udder health, milking characteristics, reproductive performance or feed intake/efficiency parameters investigated. Compared to the MB and NM, all other breeds had higher total lactation milk, fat, protein and lactose yield, with the HF having the highest. Animals on the HC feeding system had higher total lactation milk, fat, protein and lactose yield. Compared to the NRF, SCS was higher for the HF, NM, MBX and NMX breed groups, while SCS of the MB was not different. The NM and MB had lower AMF compared to all breeds. The crossbreds achieved the higher AMF. The NM had the lowest PMF, while that of the crossbreds were higher compared to all breeds. Milking duration was not affected by breed. Differences between breeds for AMF, PMF and MD were not apparent after adjustment for milk yield. Animals offered a HC diet had higher AMF, PMF and MD compared to those on the LC feeding system. Somatic cell score did not differ between the feeding systems. The interaction between breed and milk yield influenced SCS, AMF, PMF and MD thus implying that for each unit increase of milk yield by breed, the response in SCS, AMF, PMF and MD was different for some breeds. The response in SCS was similar for the NRF, MBX and NMX, while MD was similar for the MB and MBX. The effect of one unit increase in daily average milk yield caused a favourable decrease in SCS; however a one unit increase in PMF and MD did not influence SCS. No interactions were observed for breed with any milking characteristic on SCS. The HF had the lowest BCS, the MB and NM the highest, while the NRF, MBX and NMX were intermediate. The NRF had the lowest BW; the NM had the highest while the other breeds were intermediate. The NRF had increased likelihood of SR24, PREG1, PREG42 and FINALPR and greater survival compared to the HF. Both MBX and NMX had shorter CSI and CCI and were more likely to be pregnant at the end of the breeding season, thus had higher survival rates compared to the HF; however heterosis estimates for these traits was not significant, likely due to the small data size. Feed system did not influence reproductive performance of the different breeds. Breed of dairy cow did not influence any of the ovarian parameters studied. Breed of dairy cow did not influence insulin or IGF-1 concentrations at any sampling period. Breed significantly effected gestation length, calf birth weight and calving ease score. The NRF had the shortest gestation, lightest calves and least calving difficulty. Genotype had a significant effect on estimated dry matter intake, being highest with the HF, MBX, NMX and lowest with NM and NRF. Genotype also had a significant effect on yield of milk solids per kg of DMI. The highest yield of milk solids per kg of DMI was achieved with the NRF, HF and MBX. Comparisons between genotypes reveal that estimated residual feed intake estimates were lowest (most favourable) for the NRF, compared to other genotypes with the exception of HF.
    • A comparison of energy balance and metabolic profiles of the New Zealand and North American strains of Holstein Friesian dairy cow

      Patton, Joe; Murphy, J.J.; O'Mara, Frank P.; Butler, Stephen T.; National Development Plan Ireland (Cambridge University Press, 2008-06)
      The milk production, energy balance (EB), endocrine and metabolite profiles of 10 New Zealand Holstein Friesian (NZ) cows and 10 North American Holstein Friesian (NA) cows were compared. The NA cows had greater peak milk yields and total lactation milk yields (7387 v. 6208 kg; s.e.d.5359), lower milk fat and similar protein concentrations compared with the NZ cows. Body weight (BW) was greater for NA cows compared with NZ cows throughout lactation (596 v. 544 kg; s.e.d.515.5), while body condition score (BCS) tended to be lower. The NA strain tended to have greater dry matter intake (DMI) (17.2 v. 15.7 kg/day; s.e.d.50.78) for week 1 to 20 of lactation, though DMI as a proportion of metabolic BW was similar for both strains. No differences were observed between the strains in the timing and magnitude of the EB nadir, interval to neutral EB, or mean daily EB for week 1 to 20 of lactation. Plasma concentrations of glucose and insulin were greater for NA cows during the transition period (day 14 pre partum to day 28 post partum). Plasma IGF-I concentrations were similar for the strains at this time, but NZ cows had greater plasma IGF-I concentration from day 29 to day 100 of lactation, despite similar calculated EB. In conclusion, the results of this study do not support the premise that the NZ strain has a more favourable metabolic status during the transition period. The results, however, indicate that NZ cows begin to partition nutrients towards body reserves during mid-lactation, whereas NA cows continue to partition nutrients to milk production.
    • A comparison of finishing strategies to fixed slaughter weights for Holstein Friesian and Belgian Blue × Holstein Friesian steers

      Keane, Michael G. (Teagasc, Oak Park, Carlow, Ireland, 2010)
      Cattle finishing strategies may involve feeding a high energy diet throughout or following a period of moderate growth. The objective of this study was to compare Holstein Friesian (HF) and Belgian Blue × Holstein Friesian (BB) steers (24 per breed type, initial live weight 434 and 431 kg for HF and BB, respectively) finished to 560 kg or 620 kg target slaughter weight, on either a concentrate diet ad libitum from the start of the finishing period (C), or on a concentrate diet ad libitum following an 84-day period on grass silage (SC). Slaughter weights were similar for HF and BB, but kill-out proportion, carcass weight and carcass conformation class were superior (P < 0.001), and carcass fat score was inferior (P < 0.001), for BB. Total concentrate, dry matter and net energy intakes were higher (P < 0.001) for HF, and efficiency of utilization of net energy for carcass-weight gain was lower (P < 0.01). Mean daily live-weight gain was higher for C than SC (P < 0.001) and for slaughter at 560 kg than at 620 kg (P < 0.05). Killout proportion was higher for C than SC (P < 0.05) and for 620 kg compared to 560 kg slaughter weight (P < 0.001). Measures of fatness were unaffected by feeding treatment but all were higher (P < 0.01) for the 620 kg slaughter weight. Net energy required per unit carcass-weight gain was higher for C than SC (P < 0.001) and for 620 kg than for 560 kg slaughter weight (P < 0.001). When slaughtered at 620 kg live weight there was no difference between the feeding treatments in net energy required per unit carcass-weight gain. While both breed types had similar live-weight gain BB had 9% greater (P < 0.01) carcass-weight gain and were 14% more efficient (P < 0.01) in converting feed energy to carcass weight. Neither breed type had commercially acceptable carcasses at 560 kg slaughter weight when finished on SC.
    • Comparison of growth curves of three strains of female dairy cattle

      Berry, Donagh P.; Horan, Brendan; Dillon, Pat (Cambridge University Press, 2005-04)
      The objective of the present study was to compare growth curves for live weight (LW) and body size of three strains of female dairy cattle reared under common environments in Ireland. One strain (HP) was selected from a predominantly North-American/European Holstein-Friesian genetic pool selected for high milk production. The second strain (HD) represented a predominantly North-American/European Holstein-Friesian genetic pool selected for high milk production but with greater selection emphasis on functional non-production traits. The third strain (NZ) consisted of New Zealand Holstein-Friesian females of high genetic merit for profitability in New Zealand. The data consisted of 99 animals (33 animals in each strain) with records on LW, length, girth and height from birth to a minimum of 594 days of age. The von Bertalanffy growth function was fitted to each animal's records separately and least-squares analyses were used to investigate the effect of strain on birth LW/body size, parameters of the growth function and average daily gains. Average mature live weight of the HD animals (591 kg) was significantly larger than that of the HP (566 kg) or NZ (543 kg) strain; the HD strain matured more slowly. The HD (134 cm) and HP (135 cm) strains were significantly taller than the NZ (128 cm) strain. Although the data set was relatively small there are indications that dairy females of North-American genetic origin were heavier at birth, grew faster, and were heavier and taller at maturity than dairy females of New Zealand origin.
    • Comparison of herbage yield, nutritive value and ensilability traits of three ryegrass species evaluated for the Irish Recommended List

      Burns, G. A.; O'Kiely, Padraig; Grogan, D.; Watson, S.; Gilliland, T. J.; Department of Agriculture, Food and the Marine; RSF 07 526 (Teagasc (Agriculture and Food Development Authority), Ireland, 2016-01-13)
      This study examined 169 of the newest varieties of three ryegrass species, perennial (Lolium perenne L.), Italian (Lolium multiflorum Lam.) and hybrid (Lolium boucheanum Kunth), from Recommended List trials in Ireland. The traits examined were yield, dry matter concentration, three nutritive value traits (in vitro dry matter digestibility, water-soluble carbohydrate on a dry matter basis and crude protein concentration) and two ensilability traits (buffering capacity and water soluble carbohydrate concentration on an aqueous phase basis). Varietal monocultures of each species underwent a six cut combined simulated grazing and silage management in each of two years following sowing. Perennial ryegrass yielded less than both other species in one-year-old swards, but less than only Italian ryegrass in two-year-old swards, but generally had the higher in vitro dry matter digestibility and crude protein values. Italian ryegrass displayed the most favourable ensilability characteristics of the three species with perennial ryegrass less favourable and hybrid ryegrass intermediate. Overall, despite the high yields and favourable nutritive value and ensilability traits recorded, the general differences between the three ryegrass species studied were in line with industry expectations. These findings justify assessing the nutritive value and ensilability of ryegrass species, in addition to yield, to allow farmers select species that match farming enterprise requirements.
    • A comparison of machine learning techniques for predicting insemination outcome in Irish dairy cows

      Fenlon, Caroline; O'Grady, Luke; Dunnion, John; Shalloo, Laurence; Butler, Stephen; Doherty, Michael; Dairy Levy Research Trust (AICS, 2016-09)
      Reproductive performance has an important effect on economic efficiency in dairy farms with short yearly periods of breeding. The individual factors affecting the outcome of an artificial insemination have been extensively researched in many univariate models. In this study, these factors are analysed in combination to create a comprehensive multivariate model of conception in Irish dairy cows. Logistic regression, Naive Bayes, Decision Tree learning and Random Forests are trained using 2,723 artificial insemination records from Irish research farms. An additional 4,205 breeding events from commercial dairy farms are used to evaluate and compare the performance of each data mining technique. The models are assessed in terms of both discrimination and calibration ability. The logistic regression model was found to be the most useful model for predicting insemination outcome. This model is proposed as being appropriate for use in decision support and in general simulation of Irish dairy cows.
    • Comparison of pasture and concentrate finishing of Holstein Friesian, Aberdeen Angus × Holstein Friesian and Belgian Blue × Holstein Friesian steers

      Keane, Michael G.; Moloney, Aidan P (Teagasc, Oak Park, Carlow, Ireland, 2010)
      Crossbreeding Holstein Friesian dairy cows with both early and late maturing beef breed bulls is common in Ireland. This study concerned the comparison of spring-born Holstein Friesian (HF), Aberdeen Angus × Holstein Friesian (AA) and Belgian Blue × Holstein Friesian (BB) steers slaughtered directly off pasture in the autumn or following a period of concentrate finishing indoors. Male calves (18 per breed type) were reared together until August of their second year when they were assigned to a 3 (breed type) × 3 (finishing strategy) factorial experiment. The three finishing strategies were (i) pasture only for 94 days to slaughter (PE), (ii) concentrate ad libitum indoors for 94 days to slaughter (CE), and (iii) pasture only for 94 days followed by concentrate ad libitum indoors for 98 days to slaughter (PC). For HF, AA, and BB, mean carcass weight, carcass conformation score and carcass fat score values were 275, 284 and 301 (s.e. 5.1) kg, 1.75, 2.42 and 2.89 (s.e. 0.11), and 2.48, 2.89 and 2.17 (s.e. 0.11), respectively. Pasture alone supported live-weight and carcass-weight gains of approximately 800 g/day and 400 g/day, respectively. Live-weight and carcass-weight gains on concentrate ad libitum were approximately 1400 and 870 g/day, respectively. For PE, CE and PC, mean carcass weight, carcass conformation score and carcass fat score values were 244, 287 and 329 (s.e. 5.1) kg, 1.81, 2.56 and 2.69 (s.e. 0.11), and 1.83, 2.71 and 3.01 (s.e. 0.11), respectively. It is concluded that none of the breed types reached an acceptable carcass weight on PE and only HF had acceptable carcass finish. All breed types were acceptably finished on both concentrate finishing strategies.
    • Comparison of sugar-beet pulp and barley with and without soya bean meal as supplements to silage for growing steers

      Keane, Michael G.; National Development Plan 2000–2006 (Teagasc (Agriculture and Food Development Authority), Ireland, 2005)
      The optimum live-weight gain for growing steers in winter depends on the cost of feed and subsequent compensatory growth. The objectives of this experiment were: (1) to determine the response in growing steers to increasing levels of molassed sugar-beet pulp (MSBP) as a supplement to grass silage, (2) to compare MSBP and barley, and (3) to ascertain if there was a response to the inclusion of soya bean meal as a protein source with both MSBP and barley. Weanling steers (n = 154) were assigned to the following treatments: (1) silage only, (2) silage plus a low level of MSBP, (3) silage plus a low level of MSBP plus soya bean meal, (4) silage plus a high level of MSBP, (5) silage plus a high level of MSBP plus soya bean meal, (6) silage plus a high level of barley, and (7) silage plus a high level of barley plus soya bean meal. Low MSBP, high MSBP and barley levels were 1.5 kg, 3.0 kg and 3.0 kg per head daily, respectively. Where soya bean meal was included it replaced 0.2 kg/day (low) or 0.4 kg/day (high) of MSBP or barley. The duration of the treatments was 125 days (winter) after which the animals grazed together for 148 days. Silage intake decreased linearly (P < 0.001) with increasing MSBP level. Addition of soya bean meal had no effect on silage intake with low MSBP or barley but increased (P < 0.05) intake with high MSBP. Live-weight gain increased both linearly (P < 0.001) and quadratically (P < 0.01) with increasing MSBP. There was a significant live-weight response to the addition of soya bean meal which was greater at the high than at the low MSBP level and was greater for MSBP than barley. Across all treatments, growth rate at pasture was inversely related to growth rate in winter. Final live weights for the treatments as listed were 376, 395, 411, 400, 430, 427 and 428 (s.e. 14.2) kg. It is concluded that there was a curvilinear live-weight gain response to increasing MSBP level. There was no end-of-grazingseason live-weight response to the inclusion of soya bean meal with barley but there was with MSBP, particularly at the high level. MSBP with soya bean meal was equivalent to a similar quantity of barley.
    • A Comparison of the Productivity of Suckler Cows of Different Breed Composition

      Drennan, Michael J; Murphy, B. (Teagasc, 2006-01-01)
      The findings obtained in a comparison of 5 suckler dam breed types {Limousin x Friesian (LF), Limousin x (Limousin x Friesian) (LLF), Limousin (L), Charolais (C) and Simmental x (Limousin x Friesian) (SLF)} and their progeny through to slaughter
    • Confirmation of the Dietary Background of Beef from its Stable Isotope Signature

      Moloney, Aidan P; Bahar, B.; Schmidt, O.; Scrimgeour, C.M.; Begley, I.S.; Monahan, F.J. (Teagasc, 2009-11-01)
      Consumers are increasingly demanding information on the authenticity and source of the food they purchase. Molecular DNA-based technology allows animal identification, but without certification or a “paper-trail” but does not provide information about feed history or the production system under which the animal was reared. The stable isotopes of chemical elements (e.g.13C/12C, 15N/14N) are naturally present in animal tissue and reflect the isotopic composition of the diet. The overall aim of this project was to determine the feasibility of using the stable isotopic composition as an intrinsic, biochemical marker to gain information about feed components used in the production of beef. Factors likely to affect the isotopic signature such as source of tissue, duration of feeding and production systems were examined. It is expected that this highly innovative and original technique will permit the identification of country of origin and dietary history of beef and so greatly assist efforts to market Irish beef, particularly in lucrative European markets. Sequential sampling and stable isotope analysis of bovine tail hair and hoof revealed that the two tissues can provide a detailed and continuous record of animal dietary history. Because hair can be sampled repeatedly and noninvasively, we anticipate that this approach will also prove useful for the investigation of short-term wildlife movements and changes in dietary preferences.
    • Conservation characteristics of baled grass silages differing in duration of wilting, bale density and number of layers of plastic stretch-film

      Keles, G.; O'Kiely, Padraig; Lenehan, J.J.; Forristal, P.D. (Teagasc, Oak Park, Carlow, Ireland, 2009)
      The effects of duration of wilting, bale density and number of layers of plastic stretchfilm used to wrap bales on the conservation characteristics of baled grass silage was investigated. Grass from the primary growth of a Lolium perenne dominant sward was wilted for 24, 48 or 72 h. For each duration of wilting, 54 cylindrical bales (1.2 m nominal diameter) were made with the baler at a high or low density setting for alternate bales. Bales were wrapped with 2, 4 or 6 layers of plastic stretch-film and stored outdoors for 295 days. Two layers of plastic stretch-film resulted in inferior preservation, lower digestibility and extensive mould growth and deteriorated silage. Substantial improvement occurred to each of these characteristics from applying four layers of stretch-film (P<0.05), while six layers of stretch-film brought little further improvement. When four or six layers of stretch-film were used, extensive wilting restricted fermentation and improved the standard of preservation with the apparently difficult-to-preserve herbage used in this experiment. However, under the anaerobic conditions provided by four or six layers of stretch-film neither progressive wilting nor bale density had a major effect on digestibility, or the extent of surface mould growth or deteriorated silage. It can be concluded that a minimum of four layers of conventional black plastic stretch-film were required to achieve suitably anaerobic conditions, and that the additional benefits from six layers were small. Once anaerobic conditions were achieved, extensive wilting improved the conservation characteristics of baled grass silage made from a difficult-to-preserve crop, whereas bale density had little impact.
    • Conservation characteristics of grass and dry sugar beet pulp co-ensiled after different degrees of mixing

      Cummins, B.; O'Kiely, Padraig; Keane, Michael G.; Kenny, David A.; Teagasc Walsh Fellowship Programme (Teagasc, Oak Park, Carlow, Ireland, 2007)
      The objective of this experiment was to quantify the effects of the degree of mixing of dry molassed sugar beet pulp (BP) with grass on silage conservation characteristics. Herbage from a timothy (Phleum pratense) sward was precision chopped and treated with a formic acid based additive (3 l/t grass). Units of 50 kg grass, without or with 2.5kg BP were randomly allocated among four replicates on each of seven treatments. The treatments were (1) no BP (NONE), (2) BP evenly mixed through the grass (EVEN), (3) BP evenly mixed through the lower 25 kg grass (LOWH), (4) BP evenly mixed through the lower 12.5 kg grass (LOWQ), (5) 0.625 kg BP mixed through the top 25 kg grass and 1.875 kg SBP mixed through the lower 25 kg grass (25/75), (6) BP placed in 0.5 kg layers beneath each 10 kg grass (LAYR), and (7) BP placed in a single layer under all of the grass (BOTM). Laboratory silos were filled and sealed, and stored at 15 °C for 163 days. Effluent was collected and weighed from each silo throughout the ensilage period. At opening, silage composition and aerobic stability measurements were made. Total outflow of effluent was reduced (P<0.001) by the addition of BP; LAYR had a greater effect (P<0.001) than any of the other treatments. Effluent dry matter (DM) concentration was highest (P<0.05) for BOTM and lowest (P<0.01) for NONE. All treatments underwent similar lactic-acid dominant fermentations. Incorporation of BP with grass increased silage DM concentration (P<0.001), in vitro DM digestibility (P<0.05) and water soluble carbohydrate (P<0.001) concentration and reduced acid detergent fibre (P<0.001) concentration. Aerobic stability was similar across treatments and aerobic deterioration at 192 h was higher (P<0.05) for LOWQ, 25/75, LAYR and BOTM than for NONE. In conclusion, the incorporation of BP increased silage DM digestibility but had relatively little effect on fermentation or aerobic stability. Placing BP in layers gave the largest and most sustained restriction in effluent output.
    • Consistent mutational paths predict eukaryotic thermostability

      van Noort, Vera; Bradatsch, Bettina; Arumugam, Manimozhiyan; Amlacher, Stefan; Bange, Gert; Creevey, Christopher J.; Falk, Sebastian; Mende, Daniel R; Sinning, Irmgard; Hurt, Ed; Bork, Peer; Deutsche Forschungsgemeinschaft; SFB 638/B2 (Biomed Central, 2013-01-10)
      Background: Proteomes of thermophilic prokaryotes have been instrumental in structural biology and successfully exploited in biotechnology, however many proteins required for eukaryotic cell function are absent from bacteria or archaea. With Chaetomium thermophilum, Thielavia terrestris and Thielavia heterothallica three genome sequences of thermophilic eukaryotes have been published. Results: Studying the genomes and proteomes of these thermophilic fungi, we found common strategies of thermal adaptation across the different kingdoms of Life, including amino acid biases and a reduced genome size. A phylogenetics-guided comparison of thermophilic proteomes with those of other, mesophilic Sordariomycetes revealed consistent amino acid substitutions associated to thermophily that were also present in an independent lineage of thermophilic fungi. The most consistent pattern is the substitution of lysine by arginine, which we could find in almost all lineages but has not been extensively used in protein stability engineering. By exploiting mutational paths towards the thermophiles, we could predict particular amino acid residues in individual proteins that contribute to thermostability and validated some of them experimentally. By determining the three-dimensional structure of an exemplar protein from C. thermophilum (Arx1), we could also characterise the molecular consequences of some of these mutations. Conclusions: The comparative analysis of these three genomes not only enhances our understanding of the evolution of thermophily, but also provides new ways to engineer protein stability.
    • Cow factors affecting the risk of clinical mastitis

      Berry, Donagh P.; Meaney, William J (Teagasc (Agriculture and Food Development Authority), Ireland, 2005)
      The objective of the present study was to identify cow risk factors associated with development of clinical mastitis (CM) in subsequent stages of lactation. A total of 3,309 lactations from spring-calving Holstein-Friesian cows were included in the analysis; parity number ranged from one to three, inclusive. A generalised estimating equations approach with a logit link function was used to account for the binary nature of the data and the unequal number of repeated records per cow. The dependent variable was the probability of developing CM in the subsequent stage of lactation. Independent variables included in the model were chosen using stepwise selection; herd, year of birth, month of calving, parity, period of lactation and previous CM history significantly affected the probability of CM. Two-way interactions between parity and period of lactation and between parity and incidence of CM in the previous lactation were also included in the model. A greater probability of developing CM is expected in cows that experienced CM in the previous lactation and/or previously within the same lactation. The probability of CM occurring in cows that experienced at least one case of CM in the previous lactation was 0.92 to 3.75 times that of a cow that experienced no CM in the previous lactation. It is possible to predict the probability of an animal developing CM in the subsequent stage of lactation when information is available on the parity and month of calving of the animal and its previous history of CM.
    • Cow serum and colostrum immunoglobulin (IgG1) concentration of five suckler cow breed types and subsequent immune status of their calves

      Murphy, B.M.; Drennan, Michael J; O'Mara, Frank P.; Earley, Bernadette; Teagasc Walsh Fellowship Programme (Teagasc (Agriculture and Food Development Authority), Ireland, 2004)
      The objective of this study was to determine the effect of cow breed type on (a) cow serum and colostrum immunoglobulin (IgG1) concentrations and (b) subsequent calf serum IgG1 concentration and zinc sulphate turbidity (ZST) units. Five cow breed types were examined: LF (Limousin × Friesian), LLF (Limousin × (Limousin × Friesian)), L (Limousin), C (Charolais) and SLF (Simmental × (Limousin × Friesian)). Three blood samples were taken by jugular venipuncture from the cows at approximately 90, 60 and 30 days pre partum, at parturition and at 15 days or more post partum and from the calves at 48 (40 to 56) h post partum. Prior to suckling a 20 ml sample of colostrum was obtained. Milk yield was estimated using the weigh-suckleweigh technique. The decrease in serum IgG1 concentration in cows between 90 days pre partum and parturition was greater (P < 0.01) for LF cows than all other breed types, except SLF. There was no difference between LLF, L, C and SLF cows. There was no effect of cow breed type on colostrum IgG1 concentration. Milk yield was higher (P < 0.001) for LF cows than all other breed types, while that of SLF was higher than the three remaining breed types, which were similar. Calf serum IgG1 concentration and ZST units were higher (P < 0.01) for the progeny of LF cows than all others except SLF. There was no difference between the progeny of LLF, L, C and SLF cows. Calf serum IgG1 was affected by cow breed type and showed a positive relationship with cow serum IgG1 decreases in late pregnancy.
    • Cow welfare in grass based milk production systems

      Boyle, Laura; Olmos, G.; Llamas Moya, S.; Palmer, M.A.; Gleeson, David E; O’Brien, Bernadette; Horan, Brendan; Berry, Donagh P.; Arkins, S.; Alonso Gómez, M.; Mee, John F (Teagasc, 2008-08-01)
      Under this project, aspects of pasture based milk production systems, namely different milking frequency and feeding strategies as well as genetic selection for improved fitness using the Irish Economic Breeding Index (EBI) were evaluated in terms of dairy cow behaviour, health, immune function and reproductive performance. Additionally, a typical Irish pasture based system was compared to one in which cows were kept indoors in cubicles and fed a total mixed ration for the duration of lactation in order to elucidate the perceived benefits of pasture based systems for dairy cow welfare.
    • CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software

      Wilkinson, Toby J.; Huws, Sharon A.; Edwards, Joan E.; Kingston-Smith, Alison H.; Siu-Ting, Karen; Hughes, Martin; Rubino, Francesco; Friedersdorff, Maximillian; Creevey, Christopher J.; Biotechnology and Biological Sciences Research Council; BBSRC Institute Strategic Programme; Irish Research Council; BBS/OS/GC/000011B; BB/E/W/10964A01; ELEVATEPD/2014/69 (Frontiers, 2018-05-25)
      Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed “CowPI,” a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome.
    • Cross-Fostering Implications for Pig Mortality, Welfare and Performance

      Calderón Díaz, Julia A.; García Manzanilla, Edgar; Diana, Alessia; Boyle, Laura; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; 14/S/832 (Frontiers, 2018-06-06)
      This study aimed to (1) identify cross-fostering (CF) practices employed on a commercial farm; (2) characterize CF pigs according to litter of origin traits, and (3) investigate the implications of CF practices on pig mortality, performance and welfare. This was an observational study whereby pigs were managed according to normal farming practice. Pigs (n = 1,016) born within 1 week were classified as non-CF (NCF); CF during the first (CFW1) and second or third (CFW2+) weeks of lactation. Pigs were individually weighed and inspected for the presence of tail (TL), ear (EL) and body lesions (BL) at weaning (7.03 ± 1.61 kg) and at the end of the first (12.9 ± 3.03 kg) and second (31.9 ± 5.50 kg) weaner and grower (66.3 ± 9.12 kg) stages. Mortality was recorded through to slaughter (c. 115 kg). At slaughter, TL were scored and carcass characteristics, presence of pleurisy, enzootic pneumonia, pericarditis and heart condemnations were recorded. 40.8% of CF pigs were CFW1; ANOVA tests revealed these were born to sows with a higher number of piglets born alive than NCF pigs (14.6 ± 2.61 and 12.8 ± 2.68, respectively). The remaining 59.2% of CF pigs were CFW2+; these were, on average, 0.14 kg lighter at birth than NCF pigs. Therefore, a nested case control design was retrospectively applied whereby pigs with complete records to slaughter, were matched for these variables to investigate associations between CF weeks, welfare and performance traits. Growth performance did not differ between CF week (P > 0.05); however, CFW2+ carcasses were 4.9 kg lighter (P < 0.05) compared with NCF and CFW1 pigs. EL were more likely in CFW1 compared to NCF and CFW2+ (P < 0.05) pigs. To investigate the effect of CF week on the risk of mortality, all 1,016 pigs were used. CF pigs were at higher risk of death (P < 0.05) with similar odds in CFW1 and CFW2+ pigs compared with NCF pigs, although other underlying factors could contribute to this result. Performance and health traits were similar between CF weeks. Early cross-fostering appeared to influence the presence of ear lesions but the mechanism is likely indirect and difficult to explain.
    • Culicoides species composition and abundance on Irish cattle farms: implications for arboviral disease transmission

      Collins, Áine B; Mee, John F; Doherty, Michael L; Barrett, Damien J; England, Marion E; Teagasc Walsh Fellowship Programme (Biomed Central, 2018-08-17)
      Background Following the emergence of Schmallenberg virus (SBV) in Ireland in 2012, a sentinel herd surveillance program was established in the south of Ireland with the primary aim of investigating the species composition and abundance of Culicoides on livestock farms in the region. Methods Ultraviolet-light trapping for Culicoides was carried out on 10 sentinel farms. Each site was sampled fortnightly over 16 weeks (21st July to 5th November 2014). One Onderstepoort Veterinary Institute UV light trap was run overnight at each site and catches were transferred immediately into 70% ethanol. Culicoides were morphologically identified to species level. Collection site habitats were characterised using the Phase 1 habitat survey technique (Joint Nature Conservation Committee). Results A total of 23,929 individual Culicoides from 20 species was identified, including one species identified in Ireland for the first time, Culicoides cameroni. The most abundant species identified were Culicoides obsoletus/Culicoides scoticus (38%), Culicoides dewulfi (36%), Culicoides pulicaris (9%), Culicoides chiopterus (5%) and Culicoides punctatus (5%), comprising 93% of all Culicoides specimens identified. Collection site habitats were dominated by improved grassland and a combination of broadleaf woodland and native woodland species. Conclusions The most abundant species of Culicoides identified were the putative vectors of bluetongue virus (BTV) and SBV in northern Europe. Their presence and abundance demonstrates the potential for future transmission of arboviruses among livestock in this region.
    • Curating the innate immunity interactome

      Lynn, David J; Chan, Calvin; Naseer, Misbah; Yau, Melissa; Lo, Raymond; Sribnaia, Anastasia; Ring, Giselle; Que, Jaimmie; Wee, Kathleen; Winsor, Geoffrey L; Laird, Matthew R; Breuer, Karin; Foroushani, Amir K; Brinkman, Fiona S. L.; Hancock, Robert EW; Foundation for the National Institutes of Health and the Canadian Institutes of Health Research - Grand Challenges in Global Health Research Initiative (Biomed Central, 2010-08-20)
      Background: The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity. Results: Here, we describe the InnateDB curation project, which is manually annotating the human and mouse innate immunity interactome in rich contextual detail, and present our novel curation software system, which has been developed to ensure interactions are curated in a highly accurate and data-standards compliant manner. To date, over 13,000 interactions (protein, DNA and RNA) have been curated from the biomedical literature. Here, we present data, illustrating how InnateDB curation of the innate immunity interactome has greatly enhanced network and pathway annotation available for systems-level analysis and discuss the challenges that face such curation efforts. Significantly, we provide several lines of evidence that analysis of the innate immunity interactome has the potential to identify novel signalling, transcriptional and post-transcriptional regulators of innate immunity. Additionally, these analyses also provide insight into the cross-talk between innate immunity pathways and other biological processes, such as adaptive immunity, cancer and diabetes, and intriguingly, suggests links to other pathways, which as yet, have not been implicated in the innate immune response. Conclusions: In summary, curation of the InnateDB interactome provides a wealth of information to enable systems-level analysis of innate immunity.