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peer-reviewed The objective of this study was to identify the major electricity and water-consuming components of a pasture-based automatic milking (AM) system and to establish the daily and seasonal consumption trends. Electricity and water meters were installed on 7 seasonal calving pasture-based AM farms across Ireland. Electricity-consuming processes and equipment that were metered for consumption included milk cooling components, air compressors, AM unit(s), auxiliary water heaters, water pumps, lights, sockets, automatic manure scrapers, and so on. On-farm direct water-consuming processes and equipment were metered and included AM unit(s), auxiliary water heaters, tubular coolers, wash-down water pumps, livestock drinking water supply, and miscellaneous water taps. Data were collected and analyzed for the 12-mo period of 2015. The average AM farm examined had 114 cows, milking with 1.85 robots, performing a total of 105 milkings/AM unit per day. Total electricity consumption and costs were 62.6 Wh/L of milk produced and 0.91 cents/L, respectively. Milking (vacuum and milk pumping, within-AM unit water heating) had the largest electrical consumption at 33%, followed by air compressing (26%), milk cooling (18%), auxiliary water heating (8%), water pumping (4%), and other electricity-consuming processes (11%). Electricity costs followed a similar trend to that of consumption, with the milking process and water pumping accounting for the highest and lowest cost, respectively. The pattern of daily electricity consumption was similar across the lactation periods, with peak consumption occurring at 0100, 0800, and between 1300 and 1600 h. The trends in seasonal electricity consumption followed the seasonal milk production curve. Total water consumption was 3.7 L of water/L of milk produced. Water consumption associated with the dairy herd at the milking shed represented 42% of total water consumed on the farm. Daily water consumption trends indicated consumption to be lowest in the early morning period (0300–0600 h), followed by spikes in consumption between 1100 and 1400 h. Seasonal water trends followed the seasonal milk production curve, except for the month of May, when water consumption was reduced due to above-average rainfall. This study provides a useful insight into the consumption of electricity and water on a pasture-based AM farms, while also facilitating the development of future strategies and technologies likely to increase the sustainability of AM systems. We acknowledge funding for this research from the European Union's Seventh Framework Program managed by REA-Research Executive Agency [http://ec.europa.eu/research/rea (FP7/2007-2013), under grant agreement no. SME-2012-2-314879]. The authors also acknowledge the Teagasc Walsh Fellowship program (Ref 2012015), which directly funded the first author.

A bovine colostrum fraction (BCF) was recently shown to enhance the adherence of several commensal organisms to intestinal epithelial cells through modulating the epithelial cell surface. In this study, the main components of the BCF were examined to investigate the active component/s responsible for driving the changes in the intestinal cells. The adherence of various bifidobacteria to HT-29 cells was increased when the intestinal cells were pre-incubated with immunoglobulin G (IgG). Modulation of the intestinal cells by IgG was concentration dependent with 16 mg/mL IgG resulting in a 43-fold increase in the adhesion of Bifidobacterium longum NCIMB 8809 to HT-29 cells. Periodate treatment of colostral IgG prior to performing the colonization studies resulted in a reduction in the adhesion of the strain to the intestinal cells demonstrating that the glycans of IgG may be important in modulating the intestinal cells for enhanced commensal adhesion. IgG isolated from mature milk also resulted in significant increases in adhesion of the Bifidobacterium strains tested albeit at reduced levels (3.9-fold). The impact of IgG on the HT-29 cells was also visualised via scanning electron microscopy. This study builds a strong case for the inclusion of IgG ingredients sourced from cow’s milk in functional foods aimed at increasing numbers of health promoting bacteria in the human gut.

Background Johne’s disease (JD) is a chronic intestinal inflammatory disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) infection in ruminants. Since there are currently no effective vaccine or treatment options available to control JD, genetic selection may be an alternative strategy to enhance JD resistance. Numerous Single Nucleotide Polymorphisms (SNPs) have been reported to be associated with MAP infection status based on published genome-wide association and candidate gene studies. The main objective of this study was to validate these SNPs that were previously identified to be associated with JD by testing their effect on Holstein bulls’ estimated breeding values (EBVs) for milk ELISA test scores, an indirect indicator of MAP infection status in cattle. Results Three SNPs, rs41810662, rs41617133 and rs110225854, located on Bos taurus autosomes (BTA) 16, 23 and 26, respectively, were confirmed as significantly associated with Holstein bulls’ EBVs for milk ELISA test score (FDR Conclusions The findings of this study validate the association of SNPs with JD MAP infection status and highlight the need to further investigate the genomic regions harboring these SNPs.

Nutrient management on grazed grasslands is of critical importance to maintain productivity levels, as grass is the cheapest feed for ruminants and underpins these meat and milk production systems. Many attempts have been made to model the relationships between controllable (crop and soil fertility management) and noncontrollable influencing factors (weather, soil drainage) and nutrient/productivity levels. However, to the best of our knowledge not much research has been performed on modeling the interconnections between the influencing factors on one hand and nutrient uptake/ herbage production on the other hand, by using datadriven modeling techniques. Our paper proposes to use predictive clustering trees (PCT) learned for building models on data from dairy farms in the Republic of Ireland. The PCT models show good accuracy in estimating herbage production and nutrient uptake. They are also interpretable and are found to embody knowledge that is in accordance with existing theoretical understanding of the task at hand. Moreover, if we combine more PCT into an ensemble of PCT (random forest of PCT), we can achieve improved accuracy of the estimates. In practical terms, the number of grazings, which is related proportionally with soil drainage class, is one of the most important factors that moderates the herbage production potential and nutrient uptake. Furthermore, we found the nutrient (N, P, and K) uptake and herbage nutrient concentration to be conservative in fields that had medium yield potential (11 t of dry matter per hectare on average), whereas nutrient uptake was more variable and potentially limiting in fields that had higher and lower herbage production. Our models also show that phosphorus is the most limiting nutrient for herbage production across the fields on these Irish dairy farms, followed by nitrogen and potassium.

peer-reviewed Grazed grass is the cheapest feed available for dairy cows in temperate regions; thus, to maximize profits, dairy farmers must optimize the use of this high-quality feed. Previous research has defined the benefits of including white clover (Trifolium repens L.) in grass swards for milk production, usually at reduced nitrogen usage and stocking rate. The aim of this study was to quantify the responses in milk production of dairy cows grazing tetraploid or diploid perennial ryegrass (Lolium perenne L.; PRG) sown with and without white clover but without reducing stocking rate or nitrogen usage. We compared 4 grazing treatments in this study: tetraploid PRG-only swards, diploid PRG-only swards, tetraploid with white clover swards, and diploid with white clover swards. Thirty cows were assigned to each treatment, and swards were rotationally grazed at a farm-level stocking rate of 2.75 cows/ha and a nitrogen fertilizer rate of 250 kg/ha annually. Sward white clover content was 23.6 and 22.6% for tetraploid with white clover swards and diploid with white clover swards, respectively. Milk production did not differ between the 2 ploidies during this 4-yr study, but cows grazing the PRG-white clover treatments had significantly greater milk yields (+596 kg/cow per year) and milk solid yields (+48 kg/cow per year) compared with cows grazing the PRG-only treatments. The PRG-white clover swards also produced 1,205 kg of DM/ha per year more herbage, which was available for conserving and buffer feeding in spring when these swards were less productive than PRG-only swards. Although white clover is generally combined with reduced nitrogen fertilizer use, this study provides evidence that including white clover in either tetraploid or diploid PRG swards, combined with high levels of nitrogen fertilizer, can effectively increase milk production per cow and per hectare.

The untargeted metabolic profiles of ripened Maasdam cheese samples prepared from milk derived from three herd groups, fed: (1) indoors on total mixed ration (TMR), or outdoors on (2) grass only pasture (GRA) or (3) grass and white clover pasture (CLO) were studied using high resolution nuclear magnetic resonance ( 1H NMR), high resolution magic angle spinning nuclear magnetic resonance ( 1H HRMAS NMR) and headspace (HS) gas chromatography mass spectrometry (GC-MS). A total of 31 compounds were identified using 1H NMR and 32 volatile compounds including 7 acids, 5 esters, 4 alcohols, 4 ketones, 4 sulfur compounds, 2 aldehydes, 3 hydrocarbons, 2 terpenes and a lactone were identified using GC–MS in Maasdam cheeses ripened for 97-d. On comparing the 1H NMR metabolic profiles, TMR-derived cheese had higher levels of citrate compared to GRA-derived cheese. The toluene content of cheese was significantly higher in GRA or CLO compared to TMR cheeses and dimethyl sulfide was identified only in CLO-derived cheese samples as detected using HS GC–MS. These compounds are proposed as indicator compounds for Maasdam cheese derived from pasture-fed milk. Clear differences between outdoor or indoor feeding systems in terms of cheese metabolites were detected in the lipid phase, as indicated by principal component analysis (PCA) from 1H HRMAS NMR spectra, although differences based on PCA of all 1H NMR spectra and HS-GC–MS were less clear. Overall, this study presented the metabolite profile and identified specific compounds which may be useful for discriminating between ripened Maasdam cheese and related cheese varieties manufactured from indoor or outdoor herd-feeding systems.

peer-reviewed The effects of the independent variables protein concentration (4–6%), coagulum cut size (6–18 mm3), and coagulation temperature (28–36°C) on curd moisture loss during in-vat stirring were investigated using response surface methodology. Milk (14 kg) in a cheese vat was rennet coagulated, cut, and stirred as per semihard cheesemaking conditions. During stirring, the moisture content of curd samples was determined every 10 min between 5 and 115 min after cutting. The moisture loss kinetics of curds cut to 6 mm3 followed a logarithmic trend, but the moisture loss of curds from larger cut sizes, 12 or 18 mm3, showed a linear trend. Response surface modeling showed that curd moisture level was positively correlated with cut size and negatively correlated with milk protein level. However, coagulation temperature had a significant negative effect on curd moisture up to 45 min of stirring but not after 55 min (i.e., after cooking). It was shown that curds set at the lower temperature had a slower syneresis rate during the initial stirring compared with curds set at a higher temperature, which could be accelerated by reducing the cut size. This study shows that keeping a fixed cut size at increasing protein concentration decreased the level of curd moisture at a given time during stirring. Therefore, to obtain a uniform curd moisture content at a given stirring time at increasing protein levels, an increased coagulum cut size is required. It was also clear that breakage of the larger curd particles during initial stirring can also significantly influence the curd moisture loss kinetics. Both transmission and scanning electron micrographs of cooked curds (i.e., after 45 min of stirring) showed that the casein micelles were fused at a higher degree in curds coagulated at 36°C compared with 28°C, which confirmed that coagulation temperature causes a marked change in curd microstructure during the earlier stages of stirring. The present study showed the dynamics of curd moisture content during stirring when using protein-concentrated milk at various set temperatures and cut sizes. This provides the basis for achieving a desired curd moisture loss during cheese manufacture using protein-concentrated milk as a means of reducing the effect of seasonal variation in milk for cheesemaking.

peer-reviewed The effect of plant protein inclusion in cooked meat upon in vitro gastro-intestinal (GI) digestion was investigated. Pea protein isolate, rice protein and lentil flour were used to increase the protein content in a meat model system restructured using two transglutaminase enzymes [Activa®EB (TG) and Transgluseen™-M (TS)]. Restructured beef steaks were subjected to simulated GI digestion using the static INFOGEST method. Samples taken at different digestion times were analysed using SDS-PAGE, size exclusion-HPLC, free amino acid analysis and microscopy. SDS-PAGE analysis revealed significant protein hydrolysis during GI digestion. Most soluble peptides had a molecular weight smaller than 500 Da, corresponding to peptides of

peer-reviewed Dietary supplementation of pig diets with exogenous enzymes has been suggested as a strategy to increase nutrient digestibility and improve feed efficiency in grow-finisher pigs. However, inconsistent results are found in the literature. Ingredient composition of the diets is one of the most important sources of variation that may affect enzyme efficacy and consistency of results. A systematic review and a meta-analysis was therefore conducted to determine which exogenous enzymes with which diet type most consistently improve pig growth, nutrient digestibility and feed efficiency. Enzyme type and dietary cereal source were the main explanatory variables included in the models. The mean difference effects of enzyme supplementation on average daily gain (ADG), average daily feed intake (ADFI), gain to feed (G:F), apparent ileal digestibility (AiD) and apparent total tract digestibility (ATTD) of dry matter (DM), crude protein (CP), and gross energy (GE) were calculated for each study and these were used as the effect size estimates in the meta-analysis. A dataset with 139 comparisons from 67 peer-reviewed publications was used in the meta-analysis. In response to enzyme supplementation, G:F was improved in 38 of the 120 comparisons reporting pig growth data, remained un-changed in 78 and deteriorated in 4. Overall, DM and GE AiD, and ATTD were improved by xylanase, xylanase + β-glucanase, mannanase and protease dietary supplementation (P

peer-reviewed Mole (M) and gravel-mole (GM) drainage systems improve the permeability of soils with high clay contents. They collect and carry away infiltrating water during episodic rainfall events. Characterisation of nutrient fluxes (concentration and flows) in overland flow (OF) and in mole drain flow (MF) across sequential rainfall events is important for environmental assessment of such drainage systems. The objective of this study is to assess the impact of drainage systems on soil nutrient losses. Three treatments were imposed on grazed permanent grassland on a clay loam soil in Ireland (52°30′N, 08°12′W) slope 1.48%: undrained control (C), mole drainage (M) and gravel mole drainage (GM). Plots (100 m × 15 m) were arranged in a randomized complete block design with four replicated blocks. Nitrogen (N) and phosphorus (P) concentrations in OF, MF and groundwater (GW) were measured from each plot over 15 consecutive rainfall events. The results showed that M and GM (P

peer-reviewed Potato is highly productive crop and can provide a cheap and nutritionally-rich staple food. Its potential as a cash generator and source of food is much under-utilized in many emerging economies. In this paper we study the impact of an intervention that introduced improved potato technologies in Chencha, Ethiopia on the livelihoods of smallholder farmers. We collected information through in-depth interviews in order to explore possible pathways of impact on farmers’ livelihoods; and used this information as the basis for designing a household survey. The results show changes in agronomic practices and consumption; these changes were most pronounced among wealthy farmers who participated in the intervention. Farmers used the additional income from potato in different ways: wealthier farmers improved their houses and increased their livestock, whereas poor farmers mainly invested in furniture, cooking utensils, tools and in developing small businesses like selling and buying cereals, milk and weaving products in the local markets. Some wealthy farmers, who did not participate in the project, also derived some indirect benefits from the intervention. This underscores: i) interventions that promote uniform farming technologies in themselves are not always sufficient to improve the livelihoods of poor farmers, and ii) the need to broaden the scope of interventions so as to take into account the resources available to farmers in different wealth categories, and the diversity of strategies that they employ for improving their livelihoods. Our approach allows to understand and describe the different developmental effects of a single technological intervention on the different aspects of farmers’ livelihoods.

Recently there has been a considerable rise in the frequency of metabolic diseases, such as obesity, due to changes in lifestyle and resultant imbalances between energy intake and expenditure. Whey proteins are considered as potentially important components of a dietary solution to the obesity problem. However, the roles of individual whey proteins in energy balance remain poorly understood. This study investigated the effects of a high-fat diet (HFD) containing α-lactalbumin (LAB), a specific whey protein, or the non-whey protein casein (CAS), on energy balance, nutrient transporters expression and enteric microbial populations. C57BL/6J mice (n 8) were given an HFD containing either 20 % CAS or LAB as protein sources or a low-fat diet containing CAS for 10 weeks. HFD-LAB-fed mice showed a significant increase in cumulative energy intake (P=0·043), without differences in body weight, energy expenditure, locomotor activity, RER or subcutaneous and epididymal white adipose tissue weight. HFD-LAB intake led to a decrease in the expression of glut2 in the ileum (P=0·05) and in the fatty acid transporter cd36 (PLactobacillus, Parabacteroides and Bifidobacterium were present in significantly higher proportions in the HFD-LAB group. These data indicate a possible functional relationship between gut microbiota, intestinal nutrient transporters and energy balance, with no impact on weight gain.

peer-reviewed Direct supersonic steam injection, direct steam infusion, and indirect tubular heating were each applied to protein-enriched skim milk-based beverages with 4, 6 and 8% (w/w) total protein, and the effect of final heat temperature on the physical properties of these beverages was investigated. Supersonic steam injection resulted in significantly lower levels of denaturation of β-lactoglobulin (34.5%), compared to both infusion (76.3%) and tubular (97.1%) heating technologies. Viscosity, particle size and accelerated physical stability of formulations did not differ significantly between the heating technologies, while noticeable colour differences due to heat treatment (mainly attributed to increasing b* value) were observed, particularly for tubular heating. Overall, the extent of protein denaturation in high-protein dairy products was significantly influenced by the particular heating technology applied. The application of supersonic steam injection technology, with rapid heating and high shear characteristics, may enable differenciated product characteristics for ready-to-drink ambient-delivery high-protein dairy beverages. Industrial relevance: The design and application of novel direct supersonic steam injection technology was comprehensively studied and found to provide significant benefits over direct steam infusion and indirect tubular heating technologies for skim milk-based protein beverages. This type of injection heating system resulted in heat-treated formulations with lower levels of denatured whey proteins, compared to tubular and infusion heating, offering an alternative opportunity to the industry in terms of producing shelf-stable dairy protein beverages.

peer-reviewed Precision livestock farming uses biosensors to measure different parameters of individual animals to support farmers in the decision making process. Although sensor development is advanced, there is still little implementation of sensor-based solutions on commercial farms. Especially on pasture-based dairy systems, the grazing management of cows is largely not supported by technology. A key factor in pasture-based milk production is the correct grass allocation to maximize the grass utilization per cow, while optimizing cow performance. Currently, grass allocation is mostly based on subjective eye measurements or calculations per herd. The aim of this study was to identify possible indicators of insufficient or sufficient grass allocation in the cow grazing behaviour measures. A total number of 30 cows were allocated a restricted pasture allowance of 60% of their intake capacity. Their behavioural characteristics were compared to those of 10 cows (control group) with pasture allowance of 100% of their intake capacity. Grazing behaviour and activity of cows were measured using the RumiWatchSystem for a complete experimental period of 10 weeks. The results demonstrated that the parameter of bite frequency was significantly different between the restricted and the control groups. There were also consistent differences observed between the groups for rumination time per day, rumination chews per bolus and frequency of cows standing or lying.

peer-reviewed The objective of this study was to examine the effect of intravenous infusion of glucose on early embryonic development in lactating dairy cows. Nonpregnant, lactating dairy cows (n = 12) were enrolled in the study (276 ± 17 d in milk). On d 7 after a synchronized estrus, cows were randomly assigned to receive an intravenous infusion of either 750 g/d of exogenous glucose (GLUC; 78 mL/h of 40% glucose wt/vol) or saline (CTRL; 78 mL/h of 0.9% saline solution). The infusion period lasted 7 d and cows were confined to metabolism stalls for the duration of the study. Coincident with the commencement of the infusion on d 7 after estrus, 15 in vitro-produced grade 1 blastocysts were transferred into the uterine horn ipsilateral to the corpus luteum. All animals were slaughtered on d 14 to recover conceptuses, uterine fluid, and endometrial tissue. Glucose infusion increased circulating glucose concentrations (4.70 ± 0.12 vs. 4.15 ± 0.12 mmol/L) but did not affect milk production or dry matter intake. Circulating β-hydroxybutyrate concentrations were decreased (0.51 ± 0.01 vs. 0.70 ± 0.01 mmol/L for GLUC vs. CTRL, respectively) but plasma fatty acids, progesterone, and insulin concentrations were unaffected by treatment. Treatment did not affect either uterine lumen fluid glucose concentration or the mRNA abundance of specific glucose transporters in the endometrium. Mean conceptus length, width, and area on d 14 were reduced in the GLUC treatment compared with the CTRL treatment. A greater proportion of embryos in the CTRL group had elongated to all length cut-off measurements between 11 and 20 mm (measured in 1-mm increments) compared with the GLUC treatment. In conclusion, infusion of glucose into lactating dairy cows from d 7 to d 14 post-estrus during the critical period of conceptus elongation had an adverse impact on early embryonic development.

Sharpea and Kandleria are associated with rumen samples from low-methane-emitting sheep. Four strains of each genus were studied in culture, and the genomes of nine strains were analysed, to understand the physiology of these bacteria. All eight cultures grew equally well with d -glucose, d -fructose, d -galactose, cellobiose, and sucrose supplementation. d -Lactate was the major end product, with small amounts of the mixed acid fermentation products formate, acetate and ethanol. Genes encoding the enzymes necessary for this fermentation pattern were found in the genomes of four strains of Sharpea and five of Kandleria. Strains of Sharpea produced traces of hydrogen gas in pure culture, but strains of Kandleria did not. This was consistent with finding that Sharpea, but not Kandleria, genomes contained genes coding for hydrogenases. It was speculated that, in co-culture with a methanogen, Sharpea and Kandleria might change their fermentation pattern from a predominately homolactic to a predominately mixed acid fermentation, which would result in a decrease in lactate production and an increase in formation of acetate and perhaps ethanol. However, Sharpea and Kandleria did not change their fermentation products when co-cultured with Methanobrevibacter olleyae, a methanogen that can use both hydrogen and formate, and lactate remained the major end product. The results of this study therefore support a hypothesis that explains the link between lower methane yields and larger populations of Sharpea and Kandleria in the rumens of sheep.

peer-reviewed Fatty acids (g/100 g total fatty acids) in M. longissimus thoracis et lumborum (LTL) and total branched chain fatty acids (μg/g fat) in subcutaneous adipose tissue (SAT) of rams and castrates from Scottish Blackface (SB) or Texel × Scottish Blackface (T × SB) lambs, slaughtered at mean ages of 196, 242, 293, 344 or 385 days were determined. Lambs were fed pasture prior to a 36-day finishing period on a barley/maize-based concentrate ration. The intramuscular fat content (IMF; %) was higher (P

peer-reviewed Caseins and whey proteins are known as ‘slow’ and ‘fast’ proteins, respectively, based on their amino acid absorption rate. However, there is limited understanding of the mechanisms controlling their behaviour during gastro-intestinal transit. A protein model system (8% total protein) with varying casein:whey protein ratios (0:100, 20:80, 50:50 and 80:20) were subjected to in vitro gastro-intestinal digestion using a semi-dynamic gastric model, a static intestinal model and an ex vivo absorption model (Ussing chambers). The casein-rich (≥50%) samples showed the formation of solid coagula that were persistent throughout gastric digestion, which caused a delay in nutrient emptying, slower digestion and leucine absorption kinetics. In contrast, whey proteins formed more soluble aggregates during the gastric phase, which led to faster gastric emptying, rapid intestinal hydrolysis, and higher and faster leucine absorption. This work shows the key role of the gastric restructuring for the overall digestive mechanism and kinetics of food, in particular proteins.

Background The control of gastrointestinal nematodes (GIN) of cattle in pasture-based production systems such as Ireland is highly dependent on the availability of efficacious anthelmintics. There is very little information available on the efficacy of the broad-spectrum anthelmintics against GIN of cattle in Ireland and the aim of this study was to determine the prevalence of anthelmintic resistance on dairy calf to beef farms. Results GIN burden was monitored on thirty-six recruited farms by performing herd level faecal egg counts (FEC) every 2 weeks. Of these, nine farms were lost from the study as calves were treated with an anthelmintic for Dictyocaulus viviparus, two were lost as they treated for GIN, one dropped out of the study and on one the herd FEC did not reach the threshold for carrying out the Faecal Egg Count Reduction Test (FECRT). On the remaining 23 farms, once the herd FEC reached 100 eggs per gram, a FECRT was carried out. Pre and post-treatment larval cultures were also performed to identify the GIN to genus level. The efficacy of fenbendazole, levamisole, ivermectin and moxidectin was evaluated on 15, 11, 16 and 11 farms respectively. Resistance to fenbendazole was identified on 9 farms (60%) with resistance suspected on a further farm. Resistance to levamisole, ivermectin and moxidectin was detected on 2 (18%), 16 (100%) and 8 (73%) farms respectively. The predominant genera detected pre and post-treatment were Cooperia and Ostertagia with both genera detected post-treatment with fenbendazole and ivermectin. Due to the low proportion of Ostertagia spp. pre-treatment, the efficacy of levamisole or moxidectin against this genus could not be reliably established. Conclusions Anthelmintic resistance was widespread on the sampled dairy calf to beef farms in Ireland with resistance to benzimidazole, levamisole, ivermectin and moxidectin detected.

Campylobacteriosis is the leading cause of human bacterial gastroenteritis, very often associated with poultry consumption. Thermophilic Campylobacter (Campylobacter jejuni and Campylobacter coli) isolates (n = 158) recovered from broiler neck skin and caecal contents in Ireland over a one-year period, resistant to at least one of three clinically relevant antimicrobial classes, were screened for resistance determinants. All ciprofloxacin-resistant isolates (n = 99) harboured the C257T nucleotide mutation (conferring the Thr-86-Ile substitution) in conjunction with other synonymous and nonsynonymous mutations, which may have epidemiological value. The A2075G nucleotide mutation and amino acid substitutions in L4 and L22 were detected in all erythromycin-resistant isolates (n = 5). The tetO gene was detected in 100% (n = 119) of tetracycline-resistant isolates and three of which were found to harbour the mosaic tetracycline resistance gene tetO/32/O. Two streptomycin-resistant C. jejuni isolates (isolated from the same flock) harboured ant(6)-Ib, located in a multidrug resistance genomic island, containing aminoglycoside, streptothricin (satA) and tetracycline resistance genes (truncated tetO and mosaic tetO/32/O). The ant(6)-Ie gene was identified in two streptomycin-resistant C. coli isolates. This study highlights the widespread acquisition of antimicrobial resistance determinants among chicken-associated Campylobacter isolates, through horizontal gene transfer or clonal expansion of resistant lineages. The stability of such resistance determinants is compounded by the fluidity of mobile genetic element.

Bifidobacteria are known to inhibit, compete with and displace the adhesion of pathogens to human intestinal cells. Previously, we demonstrated that goat milk oligosaccharides (GMO) increased the attachment of Bifidobacterium longum subsp. infantis ATCC 15697 to intestinal cells in vitro. In this study, we aimed to exploit this effect as a mechanism for inhibiting pathogen association with intestinal cells. We examined the synergistic effect of GMO-treated B. infantis on preventing the attachment of a highly invasive strain of Campylobacter jejuni to intestinal HT-29 cells. The combination decreased the adherence of C. jejuni to the HT-29 cells by an average of 42% compared to the control (non-GMO treated B. infantis). Increasing the incubation time of the GMO with the Bifidobacterium strain resulted in the strain metabolizing the GMO, correlating with a subsequent 104% increase in growth over a 24 h period when compared to the control. Metabolite analysis in the 24 h period also revealed increased production of acetate, lactate, formate and ethanol by GMO-treated B. infantis. Statistically significant changes in the GMO profile were also demonstrated over the 24 h period, indicating that the strain was digesting certain structures within the pool such as lactose, lacto-N-neotetraose, lacto-N-neohexaose 3&prime, sialyllactose, 6&prime, sialyllactose, sialyllacto-N-neotetraose c and disialyllactose. It may be that early exposure to GMO modulates the adhesion of B. infantis while carbohydrate utilisation becomes more important after the bacteria have transiently colonised the host cells in adequate numbers. This study builds a strong case for the use of synbiotics that incorporate oligosaccharides sourced from goat&prime, s milk and probiotic bifidobacteria in functional foods, particularly considering the growing popularity of formulas based on goat milk.

peer-reviewed Cattle excreta deposited on grazed pastures are responsible for one fifth of the global anthropogenic nitrous oxide (N2O) emissions. One of the key nitrogen (N) sources is urine deposited from grazing animals, which contributes to very large N loadings within small areas. The main objective of this plot study was to establish whether the application of N fertiliser and urine deposit from dairy cows synergistically interacts and thereby increases N2O emissions, and how such interaction is influenced by the timing of application. The combined application of fertiliser (calcium ammonium nitrate) and urine significantly increased the cumulative N2O emissions as well as the N2O emission factor (EF) from 0.35 to 0.74 % in spring and from 0.26 to 0.52 % in summer. By contrast, EFs were lower when only fertiliser (0.31 % in spring, 0.07 % in summer) or urine was applied (0.33 % in spring, 0.28 % in summer). In autumn, N2O emissions were larger than in other seasons and the emissions from the combined application were not statistically different to those from either the separately applied urine or N fertiliser (EF ranging from 0.72 to 0.83, p-value < 0.05). The absence of significant synergistic effect could be explained by weather conditions, particularly rainfall during the three days prior to and after application in autumn. This study implies that the interactive effects of N fertilisation and urine deposit, as well as the timing of the application on N2O emission need to be taken into account in greenhouse gas emission inventories. Funding for this work was supported by the Walsh fellowship program at Teagasc, Ireland (fellowship number 2014079) and under the project Manipulation and Integration of Nitrogen Emissions (MINE). This research was also financially supported under the National Development Plan, through the Research Stimulus Fund, administered by the Department of Agriculture, Food and the Marine (grant number 15S655).

peer-reviewed Fungi have been used since ancient times in food and beverage-making processes and, more recently, have been harnessed for the production of antibiotics and in processes of relevance to the bioeconomy. Moreover, they are starting to gain attention as a key component of the human microbiome. However, fungi are also responsible for human infections. The incidence of community-acquired and nosocomial fungal infections has increased considerably in recent decades. Antibiotic resistance development, the increasing number of immunodeficiency- and/or immunosuppression-related diseases and limited therapeutic options available are triggering the search for novel alternatives. These new antifungals should be less toxic for the host, with targeted or broader antimicrobial spectra (for diseases of known and unknown etiology, respectively) and modes of actions that limit the potential for the emergence of resistance among pathogenic fungi. Given these criteria, antimicrobial peptides with antifungal properties, i.e., antifungal peptides (AFPs), have emerged as powerful candidates due to their efficacy and high selectivity. In this review, we provide an overview of the bioactivity and classification of AFPs (natural and synthetic) as well as their mode of action and advantages over current antifungal drugs. Additionally, natural, heterologous and synthetic production of AFPs with a view to greater levels of exploitation is discussed. Finally, we evaluate the current and potential applications of these peptides, along with the future challenges relating to antifungal treatments.

The TranSSFor project is comparing conventional thinning in Sitka spruce plantations with two alternative thinning regimes.

peer-reviewed With the cessation of milk quotas in the European Union, dairy herd sizes increased in some countries, including Ireland, with an associated increase in labor requirement. Second to feed costs, labor has been identified as one of the highest costs on pasture-based dairy farms. Compared with other European Union countries, Ireland has historically had low milk production per labor unit; thus, optimization of labor efficiency on farm should be addressed before or concurrently with herd expansion. The objective of this study was to quantify current levels of labor input and labor efficiency on commercial pasture-based dairy farms and to identify the facilities and management practices associated with increased labor efficiency. Thirty-eight dairy farms of varying herd sizes, previously identified as labor-efficient farms, were enrolled on the study and data were collected over 3 consecutive days each month over a 12-mo period, starting in May 2015 and finishing in August of 2016. This was achieved through the use of a smartphone application. For analysis purposes, farms were categorized into 1 of 3 herd size categories (HSC): farms with

peer-reviewed Background Feed accounts for up to 75% of costs in beef production systems, thus any improvement in feed efficiency (FE) will benefit the profitability of this enterprise. Residual feed intake (RFI) is a measure of FE that is independent of level of production. Adipose tissue (AT) is a major endocrine organ and the primary metabolic energy reservoir. It modulates a variety of processes related to FE such as lipid metabolism and glucose homeostasis and thus measures of inter-animal variation in adiposity are frequently included in the calculation of the RFI index. The aim of this study was to determine the effect of phenotypic RFI status and gender on the expression of key candidate genes related to processes involved in energy metabolism within AT. Dry matter intake (DMI) and average daily gain (ADG) were measured over a period of 70 d for 52 purebred Simmental heifers (n = 24) and bulls (n = 28) with an initial BW±SD of 372±39.6 kg and 387±50.6 kg, respectively. Residual feed intake was calculated and animals were ranked within gender by RFI into high (inefficient; n = 9 heifers and n = 8 bulls) and low (efficient; n = 9 heifers and n = 8 bulls) groups. Results Average daily gain ±SD and daily DMI ±SD for heifers and bulls were 1.2±0.4 kg and 9.1±0.5 kg, and 1.8±0.3 kg and 9.5±1 kg respectively. High RFI heifers and bulls consumed 10% and 15% more (P

peer-reviewed The objectives of this study were to (1) evaluate factors associated with variation in circulating anti-Müllerian hormone (AMH) concentrations, (2) establish an optimum AMH threshold predictive of pregnancy to first artificial insemination (P/AI), (3) examine the relationship between AMH and fertility (P/AI, pregnancy loss between 30 and 60 d after artificial insemination, and pregnancy risk up to 250 d postpartum), and (4) identify quantitative trait loci associated with phenotypic variation of AMH concentrations in dairy cows. Serum AMH concentrations (pg/mL) were determined at 7 ± 2.4 d postpartum in 647 lactating Holstein cows (213 primiparous, 434 multiparous) from 1 research and 6 commercial dairy herds in Alberta, Canada. Of these, 589 cows were genotyped on the 26K Bovine BeadChip (Neogen Inc., Lincoln, NE) and subsequently imputed to the Illumina Bovine High Density BeadChip (Illumina, San Diego, CA) for genome-wide association analysis for variation in serum AMH concentrations. Factors associated with variation in serum AMH concentrations and the relationship between categories of AMH and aforementioned fertility outcomes were evaluated only in a subset of 460 cows that had a complete data set available. The overall mean (±standard error of the mean), median, minimum, and maximum AMH concentrations were 191.1 ± 6.3, 151.7, 13.9, and 1,879.0 pg/mL, respectively. The AMH concentrations were not associated with herd, precalving body condition score, postpartum week, and season of sampling; the lactation number, however, had a quadratic relationship with serum AMH concentrations (116.2, 204.9 204.5, and 157.9 pg/mL for first, second, third, and ≥fourth lactation, respectively). The optimum AMH threshold predictive of P/AI could not be established because the receiver operating characteristic curve analysis model was nonsignificant. Categories of AMH [low (285.0 pg/mL; n = 92) based on lowest 20%, intermediate 60%, and highest 20% serum AMH) had no associations with P/AI (34, 43, and 40%), pregnancy loss between 30 and 60 d after artificial insemination (20, 12, and 8%), or pregnancy risk up to 250 d postpartum. One candidate gene associated with AMH production [AMH gene on Bos taurus autosome (BTA) 7] and 4 candidate genes related to embryo development (SCAI and PPP6C genes on BTA11 and FGF18 and EEF2K genes on BTA20 and BTA25, respectively) were in linkage disequilibrium with single nucleotide polymorphisms associated with phenotypic variation in serum AMH in dairy cows.

peer-reviewed 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.

peer-reviewed With the goal of optimising a protein-enriched restructured beef steak targeted at the nutritional and chemosensory requirements of older adults, technological performance of thirty formulations, containing plant-based ingredients, pea protein isolate (PPI), rice protein (RP) and lentil flour (LF) with transglutaminase (TG) to enhance binding of meat pieces, were analysed. Maximal protein content of 28% in cooked product was achieved with PPI, RP and LF. Binding strength was primarily affected by TG, while textural parameters were improved with LF inclusion. Optimal formulation (F) to obtain a protein-enriched steak with lowest hardness values was achieved with TG (2%), PPI (8%), RP (9.35%) and LF (4%). F, F1S (optimal formulation 1 with added seasoning) and control restructured products (not containing plant proteins or seasonings) were scored by 120 consumers' aged over-65 years. Controls were most preferred (P

peer-reviewed Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of Johne's disease in cattle. Johne's disease is a disease of significant economic, animal welfare, and public health concern around the globe. Therefore, understanding the genetic architecture of resistance to MAP infection has great relevance to advance genetic selection methods to breed more resistant animals. The objectives of this study were to perform a genome-wide association study of previously analyzed 50K genotypes now imputed to a high-density single nucleotide polymorphism panel (777K), aiming to validate previously reported associations and potentially identify additional single nucleotide polymorphisms associated with antibody response to MAP infection. A principal component regression-based genome-wide association study revealed 15 putative quantitative trait loci (QTL) associated with the MAP infection phenotype (serum or milk ELISA tests) on 9 different chromosomes (Bos taurus autosomes 5, 6, 7, 10, 14, 15, 16, 20, and 21). These results validated previous findings and identified new QTL on Bos taurus autosomes 15, 16, 20, and 21. The positional candidate genes NLRP3, IFi47, TRIM41, TNFRSF18, and TNFRSF4 lying within these QTL were identified. Further functional validation of these genes is now warranted to investigate their roles in regulating the immune response and, consequently, cattle resistance to MAP infection.

The true prevalence of tet(A), which codes for a tetracycline efflux pump, in thermophilic Camplyobacter spp. requires clarification after reports emerged in Iran (2014) and Kenya (2016) of the novel detection of tet(A) in Campylobacter. During our investigation of antibiotic resistance mechanisms in a sample of Irish thermophilic Campylobacter broiler isolates, it was determined that 100% of tetracycline-resistant isolates (n = 119) harboured tet(O). Accessory tetracycline-resistance mechanisms were considered as tetracycline minimum inhibitory concentrations ranged from 4 to ≥ 64 mg/L. Primers previously reported for the detection of tet(A) in Campylobacter failed to produce an amplicon using a positive control strain (Escherichia coli K12 SK1592 containing the pBR322 plasmid) and a selection of Campylobacter isolates. Accordingly, we designed new tet(A)-targeting primers on SnapGene2.3.2 that successfully generated a 407 bp product from the positive control strain only. Further in silico analysis using BLASTn and SnapGene2.3.2 revealed that previously reported Campylobacter tet(A) sequences deposited on GenBank shared 100% homology with Campylobacter tet(O). We postulate that this gave rise to the erroneous report of a high tet(A) prevalence among a pool of Kenyan broiler Campylobacter isolates that were tested using primers designed based on these apparent tet(A) sequences. In conclusion, further work would be required to determine whether the homology between tet(A) potentially present in Campylobacter and known tet(A) genes would be sufficient to allow amplification using the primers designed in our study. Finally, the existence of tet(A) in thermophilic Campylobacter spp. remains to be demonstrated.

peer-reviewed Oxidative stress contributes to cell injury and aggravates several chronic diseases. Dietary antioxidants help the body to fight against free radicals and, therefore, avoid or reduce oxidative stress. Recently, proteins from milk whey liquid have been described as antioxidants. This review summarizes the evidence that whey products exhibit radical scavenging activity and reducing power. It examines the processing and treatment attempts to increase the antioxidant bioactivity and identifies 1 enzyme, subtilisin, which consistently produces the most potent whey fractions. The review compares whey from different milk sources and puts whey proteins in the context of other known food antioxidants. However, for efficacy, the antioxidant activity of whey proteins must not only survive processing, but also upper gut transit and arrival in the bloodstream, if whey products are to promote antioxidant levels in target organs. Studies reveal that direct cell exposure to whey samples increases intracellular antioxidants such as glutathione. However, the physiological relevance of these in vitro assays is questionable, and evidence is conflicting from dietary intervention trials, with both rats and humans, that whey products can boost cellular antioxidant biomarkers. This work was supported by the Department of Agriculture, Food and the Marine (Dublin, Ireland; FIRM project 13 F 454-WheyGSH). A. R. Corrochano is in receipt of a Teagasc Walsh Fellowship.

peer-reviewed Despite the increasing frequency of integrated automatic milking (AM) and pasture-based systems, there is limited knowledge available on the suitability of different dairy cow breeds to these systems. Thus, the objective of this experiment was to establish the performance of three breeds in a pasture-based AM system with respect to milk production, cow traffic and milking characteristics. The breeds examined were Holstein Friesian (HF), Jersey x HF (JEX) and Norwegian Red x HF (NRX), all of which have been previously identified as being compatible with conventional milking pasture-based systems. The experiment was conducted in mid-lactation and variables measured included milking frequency, -interval, -outcome and -characteristics, milk yield/milking and per day, wait time/visit and per day, return time/visit and the daily distribution of milking events. Data were statistically analysed using least squares means mixed procedure models, while the proportion of different milking events were analysed using the logistics procedure. While there were no significant differences between breeds for milking frequency, or milk production, significant differences did exist for proportion of successful and failed milkings events, with NRX cows recording the highest and lowest proportions, respectively. JEX also recorded a significantly shorter dead time/quarter at 17.6 s/milking compared to the HF and NRX breeds at 28.5 and 27.7 s/milking, respectively. Significant differences also existed with regard to cow traffic, with the NRX breed returning from pasture more quickly and waiting a shorter time both per visit and per day in the pre-milking yard. The distribution of milking events differed between the breeds examined, with the JEX cows recording less milkings in the hour after the pre-selection gate changes of 0000 h and 1600 h. JEX also recorded a significantly greater proportion of milkings than the NRX and HF cows during the hours at which the lowest proportion of total milking events were recorded (0400–0600 h). For the optimisation of the AM system it is important to have an even distribution of milkings throughout the day. Based on the evidence from the current experiment, this may be best achieved by a mixed breed herd rather than a single breed herd. However, the performance of the examined breeds should also be analysed in the context of the whole AM farm system, over an entire lactation, taking into consideration the range of variables that contribute to a profitable farm system.

peer-reviewed Milk protein concentrate (79% protein) reconstituted at 13.5% (w/v) protein was heated (90 °C, 25 min, pH 7.2) with or without added calcium chloride. After fractionation of the casein and whey protein aggregates by fast protein liquid chromatography, the heat stability (90 °C, up to 1 h) of the fractions (0.25%, w/v, protein) was assessed. The heat-induced aggregates were composed of whey protein and casein, in whey protein:casein ratios ranging from 1:0.5 to 1:9. The heat stability was positively correlated with the casein concentration in the samples. The samples containing the highest proportion of caseins were the most heat-stable, and close to 100% (w/w) of the aggregates were recovered post-heat treatment in the supernatant of such samples (centrifugation for 30 min at 10,000 × g). κ-Casein appeared to act as a chaperone controlling the aggregation of whey proteins, and this effect was stronger in the presence of αS- and β-casein. This work was supported by Dairy Levy Research Trust (project MDDT6261 “ProPart”). S. J. Gaspard was funded under the Teagasc Walsh Fellowship Scheme (reference number 2012211)

The gut hormone glucagon-like peptide (GLP)-1 and its analogues represent a new generation of anti-diabetic drugs, which have also demonstrated propensity to modulate host lipid metabolism. Despite this, drugs of this nature are currently limited to intramuscular administration routes due to intestinal degradation. The aim of this study was to design a recombinant microbial delivery vector for a GLP-1 analogue and assess the efficacy of the therapeutic in improving host glucose, lipid and cholesterol metabolism in diet induced obese rodents. Diet-induced obese animals received either Lactobacillus paracasei NFBC 338 transformed to express a long-acting analogue of GLP-1 or the isogenic control microbe which solely harbored the pNZ44 plasmid. Short-term GLP-1 microbe intervention in rats reduced serum low-density lipoprotein cholesterol, triglycerides and triglyceride-rich lipoprotein cholesterol substantially. Conversely, extended GLP-1 microbe intervention improved glucose-dependent insulin secretion, glucose metabolism and cholesterol metabolism, compared to the high-fat control group. Interestingly, the microbe significantly attenuated the adiposity associated with the model and altered the serum lipidome, independently of GLP-1 secretion. These data indicate that recombinant incretin-secreting microbes may offer a novel and safe means of managing cholesterol metabolism and diet induced dyslipidaemia, as well as insulin sensitivity in metabolic dysfunction., Erratum published online 6 February 2020, DOI: 10.1038/s41598-020-59133-w

peer-reviewed Raman spectroscopy and chemometrics were investigated for the prediction of eating quality related physico-chemical traits of Holstein-Friesian bull beef. Raman spectra were collected on the 3rd, 7th and 14th days post-mortem. A frequency range of 1300–2800 cm− 1 was used for partial least squares (PLS) modelling. PLS regression (PLSR) models for the prediction of WBSF and cook loss achieved an R2CV of 0.75 with RMSECV of 6.82 N and an R2CV of 0.77 with RMSECV of 0.97%w/w respectively. For the prediction of intramuscular fat, moisture and crude protein content, R2CV values were 0.85, 0.91 and 0.70 with RMSECV of 0.52%w/w, 0.39%w/w and 0.38%w/w respectively. An R2CV of 0.79 was achieved for the prediction of both total collagen and hydroxyproline content, while for collagen solubility the R2CV was 0.88. All samples (100%) from 15- and 19-month old bulls were correctly classified using PLS discriminant analysis (PLS-DA), while 86.7% of samples from different muscles (longissimus thoracis, semitendinosus and gluteus medius) were correctly classified. In general, PLSR models using Raman spectra on the 3rd day post-mortem had better prediction performance than those on the 7th and 14th days. Raman spectroscopy and chemometrics have potential to assess several beef physical and chemical quality traits.

Expansion of the Irish dairy herd has led to more dairy breed male calves being available for beef production. This study investigated the physico-chemical and sensory characteristics of beef from Holstein-Friesian (HF) and Jersey × HF (JEX) young bulls fed pasture grass only or pasture grass plus 2 kg concentrate during their first grazing season and slaughtered at 15, 19 or 22 mo of age. Longissimus thoracis (LT) muscles were collected from 67 carcasses. Postmortem pH, ultimate pH (pHu), meat colour, chemical composition, collagen content and solubility were evaluated. After ageing for 21 d, Warner-Bratzler shear force and cooking loss were determined, and assessments by a trained sensory panel were conducted. Meat from older animals was darker. The pHu, moisture and ash contents decreased, while residual roast beef flavour length increased with age. However, increasing age to slaughter did not negatively influence tenderness. JEX beef had lower cooking loss, was darker and redder, in addition to having higher sensory scores for initial tenderness and fattiness than HF beef. Warner-Bratzler variables were positively correlated with cooking loss and chewiness and were negatively correlated with intramuscular fat (IMF) content, soluble collagen and initial tenderness. In summary, most young dairy bull beef samples were acceptably tender after 21 d of ageing and half of them had acceptable IMF content. Slaughter age affected beef colour, pHu, chemical composition and flavour length. The eating quality of meat from the JEX breed type was considered to be superior to that of the HF breed type. Diet during the first season had no effect on meat quality traits.

This research was financially supported under the National Development Plan, through the Research Stimulus Fund, administered by the Department of Agriculture, Food and the Marine (Grant numbers RSF10-/RD/SC/716 and RSF11S138) and from the Department of Agriculture, Environment and Rural Affairs for Northern Ireland. The first author gratefully acknowledges funding received from the Teagasc Walsh Fellowship Scheme. peer-reviewed A laboratory and a field study were conducted on a permanent grassland soil in Northern Ireland to investigate the effects of urea in combination with N process inhibitors such as the urease inhibitor N-(butyl) thiophosphoric triamide (NBPT) and/or the nitrification inhibitor dicyandiamide (DCD) on soil N dynamics. Urea enriched with n-butyl 15N to 60 atom % was applied to soil at a rate of 100 μg N g−1 dry soil in the laboratory and 100 kg N ha−1 in the field. A numerical 15N tracing model was used to quantify several simultaneously occurring gross N transformation rates in both studies. The changes in soil nitrate (NO3−) and ammonium (NH4+) concentrations and 15N enrichment over a 25-day period as well as the concentration and 15N enrichment of plant N at harvest were used to model soil gross N transformations. The results showed that the effect of N process inhibitors varied firstly between laboratory and field studies and secondly whether the inhibitors were applied individually or in combination. Overall DCD had a greater effect on the major soil N transformations than NBPT; reducing oxidation of NH4+, total nitrification, net NO3− produced, total mineralisation and the net adsorption of NH4+ at both laboratory and field scale. The effect of DCD was similar for these transformations whether applied alone or co-applied with NBPT. In contrast NBPT had no significant effect on oxidation of NH4+, total nitrification, total mineralisation or total immobilisation compared to urea in the field, while the effect on these transformations in the laboratory was significant. The contrasting effects of inhibitors on gross N transformations between laboratory and field may relate to the differences in experimental conditions, e.g. soil preparation, environmental conditions and the contribution of plant biomass. To obtain a more realistic assessment of gross soil N transformations in situ, it is essential that laboratory experiments are supplemented with field studies. This research was financially supported under the National Development Plan, through the Research Stimulus Fund, administered by the Department of Agriculture, Food and the Marine (Grant numbers RSF10-/RD/SC/716 and RSF11S138) and from the Department of Agriculture, Environment and Rural Affairs for Northern Ireland. The first author gratefully acknowledges funding received from the Teagasc Walsh Fellowship Scheme.

peer-reviewed The purpose of this study was to investigate in vitro the extent to which specific food structures alter gastric behaviour and could therefore impact on nutrient delivery and digestion in the small intestine. Results obtained from a specifically developed gastric digestion model, were compared to results from a previous human study on the same foods. The semi-dynamic model could simulate the main gastric dynamics including gradual acidification, lipolysis, proteolysis and emptying. Two dairy-based foods with the same caloric content but different structure were studied. The semi-solid meal comprised a mixture of cheese and yogurt and the liquid meal was an oil in water emulsion stabilised by milk proteins. Our findings showed similar gastric behaviour to that seen previously in vivo. Gastric behaviour was affected by the initial structure with creaming and sedimentation observed in the case of liquid and semi-solid samples, respectively. Lipid and protein digestion profiles showed clear differences in the amount of nutrients reaching the simulated small intestine and, consequently, the likely bioaccessibility after digestion. The semi-solid sample generated higher nutrient released into the small intestine at an early stage of digestion whereas nutrient accessibility from liquid sample was delayed due to the formation of a cream layer in the gastric phase. This shows the strong effect of the matrix on gastric behaviour, proteolysis and lipolysis, which explains the differences in physiological responses seen previously with these systems in terms of fullness and satiety. This work has funded by the Irish Dairy Levy Research Trust (project number MDDT6261). Ana-Isabel Mulet-Cabero was funded under Teagasc Walsh Fellowship scheme and BBSRC in the UK (grant BB/J004545/1).

peer-reviewed At the catchment scale, a complex mosaic of environmental, hydrogeological and physicochemical characteristics combine to regulate the distribution of groundwater and stream nitrate (NO3−). The efficiency of NO3− removal (via denitrification) versus the ratio of accumulated reaction products, dinitrogen (excess N2) & nitrous oxide (N2O), remains poorly understood. Groundwater was investigated in two well drained agricultural catchments (10 km2) in Ireland with contrasting subsurface lithologies (sandstone vs. slate) and landuse. Denitrification capacity was assessed by measuring concentration and distribution patterns of nitrogen (N) species, aquifer hydrogeochemistry, stable isotope signatures and aquifer hydraulic properties. A hierarchy of scale whereby physical factors including agronomy, water table elevation and permeability determined the hydrogeochemical signature of the aquifers was observed. This hydrogeochemical signature acted as the dominant control on denitrification reaction progress. High permeability, aerobic conditions and a lack of bacterial energy sources in the slate catchment resulted in low denitrification reaction progress (0–32%), high NO3− and comparatively low N2O emission factors (EF5g1). In the sandstone catchment denitrification progress ranged from 4 to 94% and was highly dependent on permeability, water table elevation, dissolved oxygen concentration solid phase bacterial energy sources. Denitrification of NO3 − to N2 occurred in anaerobic conditions, while at intermediate dissolved oxygen; N2O was the dominant reaction product. EF5g1 (mean: 0.0018) in the denitrifying sandstone catchment was 32% less than the IPCC default. The denitrification observations across catchments were supported by stable isotope signatures. Stream NO3− occurrence was 32% lower in the sandstone catchment even though N loading was substantially higher than the slate catchment. Teagasc Walsh Fellowship Programme

The authors would like to acknowledge that the work herein was funded by the Food Institutional Research Measure (FIRM), project number: 10RD/TMFRC/709 administered by the Irish Department of Agriculture, Food & Marine. K. M. Barry was a Teagasc PhD Walsh Fellow supported by this FIRM project. peer-reviewed Extensive enzymatic hydrolysis of milk proteins in reconstituted buttermilk powder was combined with ultrafiltration to generate a phospholipid (PL) enriched fraction with maximum permeation of hydrolysed peptides. Buttermilk, naturally high in PLs, is the ideal substrate for enrichment of these bio- and techno-functionally active compounds. A 7.8 fold increase in PL was achieved in the 50 kDa retentate; 6.16 ± 0.02% total PL compared with 0.79 ± 0.01% in the starting substrate, an increase considerably greater than previously reported. Total lipid content (% dry matter) increased 6.3 fold in the retentate, 43.43 ± 0.61%, from the starting substrate, 6.84 ± 0.17%. This combined strategic approach enabled maximum enrichment of PLs with no transmission of lipid material into the permeate, 0.09 ± 0.02% total lipid, and non-detectable levels of PLs recovered in the permeate, 0.00 ± 0.01% total PL. Teagasc Walsh Fellowship Programme Department of Agriculture, Food and the Marine

The aim of this work was to study the effect of two different pre-treatments, high temperature (100 °C, 5 min) and high pressure (600 MPa, 3 min), on the potential of the enzymes papain, collagenase and Alcalase® to generate bioactive hydrolysates containing dipeptidyl peptidase-IV- (DPP-IV; EC 3.4.14.5) and prolyl endopeptidase- (PEP; EC 3.4.21.26) inhibitory peptides from bovine lung. Both pre-treatments resulted in an increase in the degree of hydrolysis over a 24 h period (P< 0.001) and significantly increased the DPP-IV- and PEP-inhibitory activities of the generated hydrolysates (P< 0.001). Generated hydrolysates included an Alcalase hydrolysate of pressure-treated bovine lung, which was the most active, and showed DPP-IV and PEP half-maximal inhibitory concentration (IC50) values of 1.43 ± 0.06 and 3.62 ± 0.07 mg/ mL, respectively. The major peptides contained in this hydrolysate were determined by liquid chromatography-tandem mass spectrometry, and results demonstrated that bovine lung is a good substrate for the release of bioactive peptides when proper pre-treatment and enzymatic treatment are applied.

peer-reviewed Pulse flours offer nutritional alternatives to wheat flour in the production of baked snacks due to their high protein and fibre levels and low glycaemic index. In this study, broad-bean (Vicia faba), yellow-pea and green-pea (Pisum sativum) flours were each blended with wheat flour at 40% in the formulation of chemically leavened crackers. The effects of flour type and baking time on the physiochemical properties, sensory acceptability, nutritional composition and antioxidant activity of the crackers were observed in comparison with 100% wheat crackers. Broad-bean crackers had the highest protein content and antioxidant activity (13 g per 100 g DM and 38.8 mgAAE per 100 g DM, respectively). Yellow-pea crackers had the highest fibre content (12 g per 100 g DM). Physical dimensions and colour attributes were significantly affected by pulse-flour substitution. Yellow-pea and broad-bean crackers were significantly preferred by consumers compared to the control, demonstrating the potential application of these flours to improve the eating quality and nutritional profile of crackers. Teagasc Walsh Fellowship Programme

Department of Agriculture, Environment and Rural Affairs in Northern Ireland, the Teagasc Walsh Fellowship Scheme peer-reviewed In temperate grassland, urea has been shown to have lower nitrous oxide emissions compared to ammonium nitrate-based fertilizer and is less expensive. However, nitrogen (N) loss via ammonia volatilization from urea raises questions regarding yield performance and efficiency. This study compares the yield and N offtake of grass fertilized with urea, calcium ammonium nitrate (CAN) and urea treated with the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) at six site-years. Five annual fertilizer N rates (100–500 kg N/ha) were applied in five equal splits of 20–100 kg N/ha during the growing season. On average, urea produced slightly better yields than CAN in spring (103.5% of CAN yield) and slightly poorer yields in summer (98.4% of CAN yield). There was no significant difference in annual grass yield between urea, CAN and urea + NBPT. Urea had the lowest cost per tonne of DM grass yield produced. However, the urea treatment had lower N offtake than CAN and this difference was more pronounced as the N rate increased. There was no difference in N offtake between urea + NBPT and CAN. While this study shows that urea produced yields comparable to CAN, urea apparent fertilizer N recovery (AFNR) tends to be lower. Urea selection in place of CAN will increase national ammonia emissions which is problematic for countries with targets to reduce ammonia emissions. Promisingly, NBPT allows the agronomic performance of urea to consistently equal CAN across N rates by addressing the ammonia loss limitations of urea. Department of Agriculture, Environment and Rural Affairs in Northern Ireland Teagasc Walsh Fellowship Programme Department of Agriculture, Food and the Marine

peer-reviewed Farm succession and inheritance is increasingly considered a complex phenomenon which not only affects core dimensions of farm family life but also the agricultural sector more widely. Intergenerational farm transfer in particular is increasingly viewed as fundamental to the sustainability and development of global agriculture. In the majority of EU countries, the average age of farmers is increasing, while the number of farmers under 40 years of age is decreasing. There is growing concern that this demographic trend may have negative impacts on the agricultural industry because it is younger and not older farmers who are associated with more efficient and effective production practices. The question of what motivates decisions to transfer farms is a complex one, and research to date has not apparently enlightened agricultural policy to the extent that current trends towards an ageing farm population are being managed. This research aims to investigate economic and financial aspects of the policy drivers of farm succession and inheritance in Ireland to understand what it is about the policy environment that is failing to stimulate higher levels of farm transfer. It draws on the Teagasc National Farm Survey data which provides Irish data to the Farm Accountancy Data Network in the European Commission. A hypothetical microsimulation model is used to investigate economic factors of farm transfers, with scenarios created to test these factors and their impacts on the transfer process. The Net Present Value (NPV) of income streams for farmers and their successors are calculated to assess which scenarios have the highest/lowest financial effects. The findings illustrate a range of possible scenarios for farm succession/inheritance, with some results indicating that under current policy retaining a farm until death may be more economically beneficial to a farmer than transferring land before death. Royal Dublin Society Teagasc Walsh Fellowship Programme

Defining critical source areas (CSAs) of diffuse pollution in agricultural catchments depends upon the accurate delineation of hydrologically sensitive areas (HSAs) at highest risk of generating surface runoff pathways. In topographically complex landscapes, this delineation is constrained by digital elevation model (DEM) resolution and the influence of microtopographic features. To address this, optimal DEM resolutions and point densities for spatially modelling HSAs were investigated, for onward use in delineating CSAs. The surface runoff framework was modelled using the Topographic Wetness Index (TWI) and maps were derived from 0.25 m LiDAR DEMs (40 bare-earth points m −2 ), resampled 1 m and 2 m LiDAR DEMs, and a radar generated 5 m DEM. Furthermore, the resampled 1 m and 2 m LiDAR DEMs were regenerated with reduced bare-earth point densities (5, 2, 1, 0.5, 0.25 and 0.125 points m −2 ) to analyse effects on elevation accuracy and important microtopographic features. Results were compared to surface runoff field observations in two 10 km 2 agricultural catchments for evaluation. Analysis showed that the accuracy of modelled HSAs using different thresholds (5%, 10% and 15% of the catchment area with the highest TWI values) was much higher using LiDAR data compared to the 5 m DEM (70–100% and 10–84%, respectively). This was attributed to the DEM capturing microtopographic features such as hedgerow banks, roads, tramlines and open agricultural drains, which acted as topographic barriers or channels that diverted runoff away from the hillslope scale flow direction. Furthermore, the identification of ‘breakthrough’ and ‘delivery’ points along runoff pathways where runoff and mobilised pollutants could be potentially transported between fields or delivered to the drainage channel network was much higher using LiDAR data compared to the 5 m DEM (75–100% and 0–100%, respectively). Optimal DEM resolutions of 1–2 m were identified for modelling HSAs, which balanced the need for microtopographic detail as well as surface generalisations required to model the natural hillslope scale movement of flow. Little loss of vertical accuracy was observed in 1–2 m LiDAR DEMs with reduced bare-earth point densities of 2–5 points m −2 , even at hedgerows. Further improvements in HSA models could be achieved if soil hydrological properties and the effects of flow sinks (filtered out in TWI models) on hydrological connectivity are also considered.

This research was supported under the National Development Plan through the Research Stimulus Fund administered by the Department of Agriculture, Food and the Marine (Grants RSF10-/RD/SC/716 and RSF11S138) and from the Department of Agriculture and Rural Development for Northern Ireland and by the Teagasc Walsh Fellowship Scheme. peer reviewed In temperate grasslands, N source influences greenhouse gas emissions. Nitrification and urea hydrolysis inhibitors can reduce these losses. The objective of this study was to evaluate the impact of N source, urease inhibitors, and nitrification inhibitors on temperate grassland yields and N uptake. Experiments were conducted at three locations over 2 years (6 site-years) on the island of Ireland, covering a range of soils and climatic conditions. Results showed that calcium ammonium nitrate (CAN), urea+N-(n-butyl) thiophosphoric triamide (NBPT), urea+NBPT+dicyandiamide (DCD), and urea had equal annual dry matter yield. Urea+DCD had lower dry matter yield than CAN for 3 site-years. Calcium ammonium nitrate and urea+NBPT consistently had the same N uptake, urea+DCD had lower N uptake than CAN in 4 of 6 site-years, urea had lower N uptake than CAN in 2 site-years, and urea+NBPT+DCD had lower N uptake than CAN in 1 site-year. Urea+NBPT is a cost-effective alternative to CAN, which is consistently equal in terms of yield and N uptake in temperate grassland. Teagasc Walsh Fellowship Programme Department of Agriculture and Rural Development for Northern Ireland Department of Agriculture, Food and the Marine

During laboratory assessment of the soil water characteristic curve (SWCC), determining equilibrium at various pressures is challenging. This study establishes a methodological framework to identify appropriate experimental duration at each pressure step for the construction of SWCCs via centrifugation. Three common temporal approaches to equilibrium – 24-, 48- and 72-h – are examined, for a grassland and arable soil. The framework highlights the differences in equilibrium duration between the two soils. For both soils, the 24-h treatment significantly overestimated saturation. For the arable site, no significant difference was observed between the 48- and 72-h treatments. Hence, a 48-h treatment was sufficient to determine ‘effective equilibrium’. For the grassland site, the 48- and 72-h treatments differed significantly. This highlights that a more prolonged duration is necessary for some soils to conclusively determine that effective equilibrium has been reached. This framework can be applied to other soils to determine the optimum centrifuge durations for SWCC construction.

The objective of this study was to investigate the effect of omitting teat preparation prior to milking on the bacterial levels in milk directly after milking and after a period of milk storage. Eighty Holstein–Friesian dairy cows were assigned to two pre-milking teat preparation treatments: (i) washing of teats and drawing of foremilk, followed by drying with paper towels and (ii) no teat preparation. Individual cow measurements included individual quarter somatic cell count (SCC) and teat swabs for the presence of Bacillus cereus sensu lato. On seven monthly occasions, all milk produced over a 24 h period from each treatment group was segregated into a separate tank and sampled. Sub-samples of this milk were stored at 4 °C for 0, 24, 48 and 72 h, and the milk was analysed for total bacterial count (TBC), thermoduric bacterial count and the presence of B. cereus s. I. Individual quarter SCCs were numerically higher for unprepared teats (159,000 cells/mL) compared with those for prepared teats (133,000 cells/mL; P < 0.09). A similar trend was observed for bulk tank SCC, with the unprepared teat treatment tending to have a higher SCC (155,857 cells/mL) compared to the prepared teat treatment (102,286 cells/mL; P< 0.09). The TBC was not significantly higher from unprepared teats (3,152 cfu/ mL) compared with milk from prepared teats (1,678 cfu/mL) (P< 0.10). Milk TBC was significantly higher after storage for 72 h compared with that after 0, 24 and 48 h (P< 0.01). The results of this study indicate that under good hygienic conditions in an outdoor grazing situation, the omission of pre-milking teat preparation has a minimal effect on TBC and SCC.

peer-reviewed ABSTRACT The effect of the addition of caseinomacropeptide (CMP) or desialylated CMP on the heat-induced denaturation and aggregation of whey proteins was investigated in the pH range 3 to 7 after heating at 80°C for 30 min. The rate and temperature of denaturation, the extent of aggregation, and the changes in secondary structure of the whey proteins heated in presence of CMP or desialylated CMP were measured. The sialic acid bound to CMP favored the denaturation and aggregation of whey proteins when the whey proteins were oppositely charged to CMP at pH 4. A transition occurred at pH 6, below which the removal of sialic acid enhanced the stabilizing properties of CMP against the denaturation and aggregation of the whey proteins. At pH >6, the interactions between desialylated CMP and the whey proteins led to more extensive denaturation and aggregation. Sialic acid bound to CMP influenced the denaturation and aggregation behavior of whey proteins in a pH-dependent manner, and this should be considered in future studies on the heat stability of such systems containing CMP.