Now showing items 21-40 of 2210

    • Dairy cow feeding system alters the characteristics of low-heat skim milk powder and processability of reconstituted skim milk

      Gulati, Arunima; Hennessy, Deirdre; O'Donovan, Michael; McManus, Jennifer J.; Fenelon, Mark A.; Guinee, Timothy P.; Department of Agriculture, Food and the Marine; Dairy Levy Trust Co-Operative Society Limited; 11/sf/309 (Elsevier for American Dairy Science Association, 2019-08-01)
      Low-heat skim milk powder (LHSMP) was manufactured on 3 separate occasions in mid lactation (ML, July 4–20) and late lactation (LL, September 27 to October 7) from bulk milk of 3 spring-calving dairy herds on different feeding systems: grazing on perennial ryegrass (Lolium perenne L.) pasture (GRO), grazing on perennial ryegrass and white clover (Trifolium repens L.) pasture (GRC), and housed indoors and offered total mixed ration (TMR). The resultant powders (GRO-SMP, GRC-SMP, and TMR-SMP) were evaluated for composition and color and for the compositional, physicochemical, and processing characteristics of the reconstituted skim milk (RSM) prepared by dispersing the powders to 10% (wt/wt) in water. Feeding system significantly affected the contents of protein and lactose, the elemental composition, and the color of the LHSMP, as well as the rennet gelation properties of the RSM. The GRO and GRC powders had a higher protein content; lower levels of lactose, iodine, and selenium; and a more yellow-green color (lower a* and higher b* color coordinates) than TMR powder. On reconstitution, the GRO-RSM had higher concentrations of protein, casein, and ionic calcium, and lower concentrations of lactose and nonprotein nitrogen (% of total N). It also produced rennet gels with a higher storage modulus (G′) than the corresponding TMR-RSM. These effects were observed over the combined ML and LL period but varied somewhat during the separate ML and LL periods. Otherwise, feeding system had little or no effect on proportions of individual caseins, concentration of serum casein, casein micelle size, casein hydration, heat coagulation time, or ethanol stability of the RSM at pH 6.2 to 7.2, or on the water-holding capacity, viscosity, and flow behavior of stirred yogurt prepared by starter-induced acidification of RSM. The differences in the functionality of the LHSMP may be of greater or lesser importance depending on the application and the conditions applied during the processing of the RSM.
    • Draft Genome Sequences of the Type Strains of Six Macrococcus Species

      Mazhar, Shahneela; Altermann, Eric; Hill, Colin; McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; 2015055 (American Society for Microbiology, 2019-05-09)
      We report here the draft genome sequences of Macrococcus bovicus ATCC 51825T, Macrococcus carouselicus ATCC 51828T, Macrococcus equipercicus ATCC 51831T, Macrococcus brunensis CCM4811T, Macrococcus hajekii CCM4809T, and Macrococcus lamae CCM4815T. The availability of the genome sequences of these species will enable cross-species comparison, which could lead to a more comprehensive understanding of organisms of the Macrococcus genus.
    • Vangl2 disruption alters the biomechanics of late spinal neurulation leading to spina bifida in mouse embryos

      Galea, Gabriel L.; Nychyk, Oleksandr; Mole, Matteo A.; Moulding, Dale; Savery, Dawn; Nikolopoulou, Evanthia; Henderson, Deborah J.; Greene, Nicholas D. E.; Copp, Andrew J. (The Company of Biologists, 2018-03-12)
      Human mutations in the planar cell polarity component VANGL2 are associated with the neural tube defect spina bifida. Homozygous Vangl2 mutation in mice prevents initiation of neural tube closure, precluding analysis of its subsequent roles in neurulation. Spinal neurulation involves rostral-to-caudal ‘zippering’ until completion of closure is imminent, when a caudal-to-rostral closure point, ‘Closure 5’, arises at the caudal-most extremity of the posterior neuropore (PNP). Here, we used Grhl3Cre to delete Vangl2 in the surface ectoderm (SE) throughout neurulation and in an increasing proportion of PNP neuroepithelial cells at late neurulation stages. This deletion impaired PNP closure after the ∼25-somite stage and resulted in caudal spina bifida in 67% of Grhl3Cre/+Vangl2Fl/Fl embryos. In the dorsal SE, Vangl2 deletion diminished rostrocaudal cell body orientation, but not directional polarisation of cell divisions. In the PNP, Vangl2 disruption diminished mediolateral polarisation of apical neuroepithelial F-actin profiles and resulted in eversion of the caudal PNP. This eversion prevented elevation of the caudal PNP neural folds, which in control embryos is associated with formation of Closure 5 around the 25-somite stage. Closure 5 formation in control embryos is associated with a reduction in mechanical stress withstood at the main zippering point, as inferred from the magnitude of neural fold separation following zippering point laser ablation. This stress accommodation did not happen in Vangl2-disrupted embryos. Thus, disruption of Vangl2-dependent planar-polarised processes in the PNP neuroepithelium and SE preclude zippering point biomechanical accommodation associated with Closure 5 formation at the completion of PNP closure.
    • The ability of Listeria monocytogenes to form biofilm on surfaces relevant to the mushroom production environment

      Dygico, Lionel Kenneth; Gahan, Cormac G.M.; Grogan, Helen; Burgess, Catherine; Department of Agriculture, Food and the Marine; 14F881 (Elsevier BV, 2020-03-16)
      Due to its ubiquitous nature, Listeria monocytogenes is a threat to all fresh fruits and vegetables, including mushrooms, which are Ireland's largest horticultural crop. Although fresh cultivated mushrooms (Agaricus bisporus) have not been previously linked with listeriosis outbreaks, the pathogen still poses a threat to the industry, particularly due to its ability to form biofilms. This threat is highlighted by the multiple recalls of mushroom products caused by L. monocytogenes contamination and by previous studies demonstrating that L. monocytogenes is present in the mushroom production environment. In this study, the biofilm formation potential of L. monocytogenes strains isolated from the mushroom production environment was investigated on materials and at temperatures relevant to mushroom production. A preliminary assessment of biofilm formation of 73 mushroom industry isolates was undertaken using a crystal violet assay on polystyrene microtitre plates. The biofilm formation of a subset (n = 7) of these strains was then assessed on twelve different materials, including materials that are representative of the materials commonly found in the mushroom production environments, using the CDC biofilm reactor. Vertical scanning interferometry was used to determine the surface roughness of the chosen materials. All the strains tested using the CDC biofilm reactor were able to form biofilms on the different surfaces tested but material type was found to be a key determining factor on the levels of biofilm formed. Stainless steel, aluminium, rubber, polypropylene and polycarbonate were all able to support biofilm levels in the range of 4–4.9 log10 CFU/cm2, for seven different L. monocytogenes strains. Mushroom industry-specific materials, including growing nets and tarpaulins, were found to support biofilms levels between 4.7 and 6.7 log10 CFU/cm2. Concrete was found to be of concern as it supported 7.7 log10 CFU/cm2 of biofilm for the same strains; however, sealing the concrete resulted in an approximately 2-log reduction in biofilm levels. The surface roughness of the materials varied greatly between the materials (0.7–3.5 log10 Ra) and was found to have a positive correlation with biofilm formation (rs = 0.573) although marginally significant (P = 0.051). The results of this study indicate that L. monocytogenes can readily form biofilms on mushroom industry relevant surfaces, and additionally identifies surfaces of specific concern, where rigorous cleaning and disinfection is required.
    • Draft Genome Sequences of Macrococcus caseolyticus, Macrococcus canis, Macrococcus bohemicus, and Macrococcus goetzii

      Mazhar, Shahneela; Altermann, Eric; Hill, Colin; McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; 2015055 (American Society for Microbiology, 2019-05-09)
      Here, we present the draft genome sequences of 14 strains of 4 species of the genus Macrococcus. These strains were isolated from bovine milk and tongue samples obtained during a screening program.
    • Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory

      Egan, Kevin; Kelleher, Philip; Field, Des; Rea, Mary C.; Ross, R Paul; Cotter, Paul D.; Hill, Colin; Department of Agriculture, Food and the Marine; Science Foundation Ireland; DAFM 13/F/462; et al. (American Society for Microbiology, 2017-10-26)
      This paper reports the full genome sequence of the antimicrobial-producing bacterium Geobacillus stearothermophilus DSM 458, isolated in a sugar beet factory in Austria. In silico analysis reveals the presence of a number of novel bacteriocin biosynthetic genes.
    • Cervico-vaginal mucus (CVM) – an accessible source of immunologically informative biomolecules

      Adnane, Mounir; Meade, Kieran G; O’Farrelly, Cliona; Science Foundation Ireland; Health Research Board; Department of Agriculture, Food and the Marine; 12/Ia/1667; HRA_POR/2012/37; FIRM/ RSF/CoFoRD 2013–2016: ENRICH; FIRM/RSF/CoFoRD 2011-2015 (Springer Science and Business Media LLC, 2018-08-16)
      Cervico-vaginal mucus (CVM), the product of epithelial cells lining the uterus, cervix and vagina, is secreted to facilitate uterine lubrication and microbial clearance. Predominantly composed of water and mucins, CVM also contains high levels of immuno-active proteins such as immunoglobulin A (IgA), lactoferrin and lysozyme which protect against infection by blocking adhesion and mediating microbial killing. The repertoire of cytokines, chemokines and antimicrobial peptides is predominantly generated by the secretions of endometrial epithelial cells into the uterine lumen and concentrated in the CVM. The quantity and relative proportions of these inflammatory biomarkers are affected by diverse factors including the estrus cycle and health status of the animal and therefore potentially provide important diagnostic and prognostic indicators. We propose that measuring molecular signatures in bovine CVM could be a useful approach to identifying and monitoring genital tract pathologies in beef and dairy cows.
    • Investigation of molecular mechanisms underlying tetracycline resistance in thermophilic Campylobacter spp. suggests that previous reports of tet(A)-mediated resistance in these bacteria are premature

      Lynch, Caoimhe; Hawkins, Kayleigh; Lynch, Helen; Egan, John; Bolton, Declan J.; Coffey, Aidan; Lucey, Brigid; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; Ref. 15/F/641; et al. (Springer Science and Business Media LLC, 2019-11-09)
      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.
    • Pig farmers’ willingness to pay for management strategies to reduce aggression between pigs

      Peden, Rachel S. E.; Akaichi, Faical; Camerlink, Irene; Boyle, Laura; Turner, Simon P.; Scotland’s Rural College (Public Library of Science (PLoS), 2019-11-08)
      When deciding whether to invest in an improvement to animal welfare, farmers must trade-off the relative costs and benefits. Despite the existence of effective solutions to many animal welfare issues, farmers’ willingness to pay for them is largely unknown. This study modelled pig farmers’ decisions to improve animal welfare using a discrete choice experiment focused on alleviating aggression between growing/finishing pigs at regrouping. Eighty-two UK and Irish pig farm owners and managers were asked to choose between hypothetical aggression control strategies described in terms of four attributes; installation cost, on-going cost, impact on skin lesions from aggression and impact on growth rate. If they did not like any of the strategies they could opt to keep their current farm practice. Systematic variations in product attributes allowed farmers’ preferences and willingness to pay to be estimated and latent class modelling accounted for heterogeneity in responses. The overall willingness to pay to reduce lesions was low at £0.06 per pig place (installation cost) and £0.01 per pig produced (running cost) for each 1% reduction in lesions. Results revealed three independent classes of farmers. Farmers in Class 1 were unlikely to regroup unfamiliar growing/finishing pigs, and thus were unwilling to adopt measures to reduce aggression at regrouping. Farmers in Classes 2 and 3 were willing to adopt measures providing certain pre-conditions were met. Farmers in Class 2 were motivated mainly by business goals, whilst farmers in Class 3 were motivated by both business and animal welfare goals, and were willing to pay the most to reduce aggression; £0.11 per pig place and £0.03 per pig produced for each 1% reduction in lesions. Farmers should not be considered a homogeneous group regarding the adoption of animal welfare innovations. Instead, campaigns should be targeted at subgroups according to their independent preferences and willingness to pay.
    • Identification and characterisation of capidermicin, a novel bacteriocin produced by Staphylococcus capitis

      Lynch, David; O’Connor, Paula M.; Cotter, Paul D.; Hill, Colin; Field, Des; Begley, Máire; Cork Institute of Technology RISAM PhD scholarship (Public Library of Science (PLoS), 2019-10-16)
      One hundred human-derived coagulase negative staphylococci (CoNS) were screened for antimicrobial activity using agar-based deferred antagonism assays with a range of indicator bacteria. Based on the findings of the screen and subsequent well assays with cell free supernatants and whole cell extracts, one strain, designated CIT060, was selected for further investigation. It was identified as Staphylococcus capitis and herein we describe the purification and characterisation of the novel bacteriocin that the strain produces. This bacteriocin which we have named capidermicin was extracted from the cell-free supernatant of S. capitis CIT060 and purified to homogeneity using reversed-phase high performance liquid chromatography (RP-HPLC). Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric (MS) analysis revealed that the capidermicin peptide has a mass of 5,464 Da. Minimal inhibitory concentration (MIC) experiments showed that capidermicin was active in the micro-molar range against all the Gram-positive bacteria that were tested. Antimicrobial activity was retained over a range of pHs (2–11) and temperatures (10–121°C x 15 mins). The draft genome sequence of S. capitis CIT060 was determined and the genes predicted to be involved in the biosynthesis of capidermicin were identified. These genes included the predicted capidermicin precursor gene, and genes that are predicted to encode a membrane transporter, an immunity protein and a transcriptional regulator. Homology searches suggest that capidermicin is a novel member of the family of class II leaderless bacteriocins.
    • Effect of classroom intervention on student food selection and plate waste: Evidence from a randomized control trial

      Serebrennikov, Dmytro; Katare, Bhagyashree; Kirkham, Lisa; Schmitt, Sara; Indiana State Department of Health (Public Library of Science (PLoS), 2020-01-09)
      Background U.S. children are failing to meet the recommended daily 4 cups of fruits and vegetables. New federal guidelines were implemented for healthier school lunches for the National School Lunch Programs (NSLP). Consequently, students waste large amounts of fruits and vegetables. Several organizations advocate implementation of classroom nutrition education programs as a school nutrition policy. Methods We conducted a randomized control trial to evaluate the effectiveness of a classroom nutrition education on food consumption behavior of public elementary school students. Our intervention was designed to improve students’ preferences for fruits and vegetables. We collected data using digital-photography, and estimated the amount of fruits and vegetables selected and wasted using ordinary least squares. Results The nutrition education program had no impact on the amount of fruits and vegetables selected by the students in the treatment group. We also find no significant difference in the amount of fruits and vegetables wasted by students in the treatment and control group. Conclusion Nutrition education did not change students’ consumption behavior, implying the proposed policy might not be optimal. Inducing a behavioral change in elementary school students is an intricate process and might require more than classroom lessons to change their dietary habits.
    • Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions

      Szoboszlay, Márton; Näther, Astrid; Mullins, Ewen; Tebbe, Christoph C.; European Union; 289706 (Public Library of Science (PLoS), 2019-12-17)
      The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops.
    • Genomic prediction of crown rust resistance in Lolium perenne

      Arojju, Sai Krishna; Conaghan, Patrick; Barth, Susanne; Milbourne, Dan; Casler, Michael D.; Hodkinson, Trevor R.; Michel, Thibauld; Byrne, Stephen L.; Department of Agriculture Food and the Marine; European Union; et al. (Springer Science and Business Media LLC, 2018-05-29)
      Background Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.
    • Long-term effects of prior diets, dietary transition and pregnancy on adipose gene expression in dairy heifers

      Wærp, Hilde K. L.; Waters, Sinead M.; McCabe, Matthew S.; Cormican, Paul; Salte, Ragnar; Research Council of Norway; TINE SA Norwegian dairies; Felleskjøpet agricultural cooperative; Animalia AS; 199448 (Public Library of Science (PLoS), 2019-07-03)
      Adipose tissue is highly involved in whole-body metabolism and is the main site for lipid synthesis, storage and mobilization in ruminants. Therefore, knowledge about adipose tissue responses to different diets is important, especially in growing heifers as the feeding regimes of replacement heifers affect their future success as dairy cows. However, at gene expression level such knowledge is limited. As part of a larger feed trial, adipose tissue biopsies from 24 Norwegian Red heifers were collected at 12 months of age (12MO) and at month seven of gestation (PREG) and analyzed by next-generation mRNA sequencing. Between these two sampling points, all heifers had gone through a successful conception and a feed change from four dietary treatments of high or low energy (HE/LE) and protein (HP/LP) content (treatments LPHE, HPHE, LPLE and HPLE) to a low-energy, low-protein pregnancy feed given to all animals. Gene expression differences between different feed treatments at 12MO are described in an earlier publication from our group. The main objectives of this study were to investigate the long-term effects of diets differing in protein and energy density level on gene expression in adipose tissue of growing replacement dairy heifers. To achieve this, we examined the post-treatment effects between the treatment groups at month seven of gestation; 6 months after the termination of experimental feeding, and the long-term gene expression changes occurring in the adipose tissue between 12MO and PREG. Post-treatment group comparisons showed evidence of long-term effects of dietary treatment on adipose gene expression. Differences between protein treatments were smaller than between energy treatments. Adipose gene expression changes from 12MO to PREG were much larger for the HE than the LE treatments and seemed to mostly be explained by the characteristics of the diet change. 97 genes displayed a unidirectional expression change for all groups from 12MO to PREG, and are considered to be treatment-independent, possibly caused by pregnancy or increased age. This study provides candidate genes and key regulators for further studies on pregnancy preservation (TGFB1, CFD) and metabolic regulation and efficiency (PI3K, RICTOR, MAP4K4,) in dairy cattle.
    • Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of bovine jejunal epithelium

      Keogh, Kate; Waters, Sinead M.; Cormican, Paul; Kelly, Alan K.; Kenny, David A.; Science Foundation Ireland; 09/ RFP/GEN2447 (Public Library of Science (PLoS), 2018-03-19)
      Compensatory growth (CG), an accelerated growth phenomenon which occurs following a period of dietary restriction is utilised worldwide in animal production systems as a management practise to lower feed costs. The objective of this study was to evaluate the contribution of jejunal epithelial to CG in cattle through transcriptional profiling following a period of dietary restriction as well as subsequent re-alimentation induced CG. Sixty Holstein Friesian bulls were separated into two groups; RES and ADLIB, with 30 animals in each. RES animals were offered a restricted diet for 125 days (Period 1) followed by ad libitum feeding for 55 days (Period 2). ADLIB animals had ad libitum access to feed across both periods 1 and 2. At the end of each period, 15 animals from each treatment group were slaughtered, jejunal epithelium collected and RNAseq analysis performed. Animals that were previously diet restricted underwent CG, gaining 1.8 times the rate of their non-restricted counterparts. Twenty-four genes were differentially expressed in RES compared to ADLIB animals at the end of Period 1, with only one gene, GSTA1, differentially expressed between the two groups at the end of Period 2. When analysed within treatment (RES, Period 2 v Period 1), 31 genes were differentially expressed between diet restricted and animals undergoing CG. Dietary restriction and subsequent re-alimentation were associated with altered expression of genes involved in digestion and metabolism as well as those involved in cellular division and growth. Compensatory growth was also associated with greater expression of genes involved in cellular protection and detoxification in jejunal epithelium. This study highlights some of the molecular mechanisms regulating the response to dietary restriction and subsequent re-alimentation induced CG in cattle; however the gene expression results suggest that most of the CG in jejunal epithelium had occurred by day 55 of re-alimentation.
    • Integrated phenotypic-genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei

      Ojha, K. Shikha; Burgess, Catherine; Duffy, Geraldine; Kerry, Joseph P.; Tiwari, Brijesh; Teagasc Walsh Fellowship Programme (Public Library of Science (PLoS), 2018-01-25)
      The lethal effects of soundwaves on a range of microorganisms have been known for almost a century whereas, the use of ultrasound to promote or control their activity is much more recent. Moreover, the fundamental molecular mechanism influencing the behaviour of microorganisms subjected to ultrasonic waves is not well established. In this study, we investigated the influence of ultrasonic frequencies of 20, 45, 130 and 950 kHz on growth kinetics of Lactobacillus sakei. A significant increase in the growth rate of L. sakei was observed following ultrasound treatment at 20 kHz despite the treatment yielding a significant reduction of ca. 3 log cfu/mL in cells count. Scanning electron microscopy showed that ultrasound caused significant changes on the cell surface of L. sakei culture with the formation of pores “sonoporation”. Phenotypic microarrays showed that all ultrasound treated L. sakei after exposure to various carbon, nitrogen, phosphorus and sulphur sources had significant variations in nutrient utilisation. Integration of this phenotypic data with the genome of L. sakei revealed that various metabolic pathways were being influenced by the ultrasound treatments. Results presented in this study showed that the physiological response of L. sakei in response to US is frequency dependent and that it can influence metabolic pathways. Hence, ultrasound treatments can be employed to modulate microbial activity for specialised applications.
    • Functional Land Management: Bridging the Think-Do-Gap using a multi-stakeholder science policy interface

      O’Sullivan, Lilian; Wall, David; Creamer, Rachel; Bampa, Francesca; Schulte, Rogier P. O.; National Development Plan 2007–2013; European Union; 13S468; 635201; 677407 (Springer Science and Business Media LLC, 2017-11-24)
      Functional Land Management (FLM) is proposed as an integrator for sustainability policies and assesses the functional capacity of the soil and land to deliver primary productivity, water purification and regulation, carbon cycling and storage, habitat for biodiversity and recycling of nutrients. This paper presents the catchment challenge as a method to bridge the gap between science, stakeholders and policy for the effective management of soils to deliver these functions. Two challenges were completed by a wide range of stakeholders focused around a physical catchment model—(1) to design an optimised catchment based on soil function targets, (2) identify gaps to implementation of the proposed design. In challenge 1, a high level of consensus between different stakeholders emerged on soil and management measures to be implemented to achieve soil function targets. Key gaps including knowledge, a mix of market and voluntary incentives and mandatory measures were identified in challenge 2.
    • Assessments of Composite and Discrete Sampling Approaches for Water Quality Monitoring

      Cassidy, Rachel; Jordan, Phil; Bechmann, Marianne; Kronvang, Brian; Kyllmar, Katarina; Shore, Mairead (Springer Science and Business Media LLC, 2018-04-12)
      Achieving an operational compromise between spatial coverage and temporal resolution in national scale river water quality monitoring is a major challenge for regulatory authorities, particularly where chemical concentrations are hydrologically dependent. The efficacy of flow-weighted composite sampling (FWCS) approaches for total phosphorus (TP) sampling (n = 26–52 analysed samples per year), previously applied in monitoring programmes in Norway, Sweden and Denmark, and which account for low to high flow discharges, was assessed by repeated simulated sampling on high resolution TP data. These data were collected in three research catchments in Ireland over the period 2010–13 covering a base-flow index range of 0.38 to 0.69. Comparisons of load estimates were also made with discrete (set time interval) daily and sub-daily sampling approaches (n = 365 to >1200 analysed samples per year). For all years and all sites a proxy of the Norwegian sampling approach, which is based on re-forecasting discharge for each 2-week deployment, proved most stable (median TP load estimates of 87–98%). Danish and Swedish approaches, using long-term flow records to set a flow constant, were only slightly less effective (median load estimates of 64–102% and 80–96%, respectively). Though TP load estimates over repeated iterations were more accurate using the discrete approaches, particularly the 24/7 approach (one sample every 7 h in a 24 bottle sampler - median % load estimates of 93–100%), composite load estimates were more stable, due to the integration of multiple small samples (n = 100–588) over a deployment.
    • Associating cow characteristics with mobility scores in pasture-based dairy cows

      O'Connor, A.H.; Bokkers, E.A.M.; de Boer, I.J.M.; Hogeveen, H.; Sayers, Riona; Byrne, Nicky; Ruelle, Elodie; Shalloo, Laurence; Irish Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme (Elsevier for American Dairy Science Association, 2019-07-10)
      The quality of dairy cow mobility can have significant welfare, economic, and environmental consequences that have yet to be extensively quantified for pasture-based systems. The objective of this study was to characterize mobility quality by examining associations between specific mobility scores, claw disorders (both the type and severity), body condition score (BCS), and cow parity. Data were collected for 6,927 cows from 52 pasture-based dairy herds, including mobility score (0 = optimal mobility; 1, 2, or 3 = increasing severities of suboptimal mobility), claw disorder type and severity, BCS, and cow parity. Multinomial logistic regression was used for analysis. The outcome variable was mobility score, and the predictor variables were BCS, type and severity of claw disorders, and cow parity. Three models were run, each with 1 reference category (mobility score 0, 1, or 2). Each model also included claw disorders (overgrown claw, sole hemorrhage, white line disease, sole ulcer, and digital dermatitis), BCS, and cow parity as predictor variables. The presence of most types of claw disorders had odds ratios >1, indicating an increased likelihood of a cow having suboptimal mobility. Low BCS (BCS <3.00) was associated with an increased risk of a cow having suboptimal mobility, and relatively higher parity was also associated with an increased risk of suboptimal mobility. These results confirm an association between claw disorders, BCS, cow parity, and dairy cow mobility score. Therefore, mobility score should be routinely practiced to identify cows with slight deviations from the optimal mobility pattern and to take preventive measures to keep the problem from worsening.
    • An investigation into the factors associated with ewe colostrum production

      Campion, Frank P.; Crosby, Thomas F.; Creighton, Philip; Fahey, Alan G.; Boland, Tommy M.; Teagasc Walsh Fellowship Programme (Elsevier BV, 2019-09)
      The majority of lamb mortality which occurs during the first 24 h post-partum is preventable through providing the lamb with sufficient quantities of high quality colostrum during this time. Data from seven late gestation nutrition experiments carried out at this institute between 2002 and 2014 were collated into a single data set comprising of 415 twin bearing ewes. Analysis was carried out to investigate the key drivers of ewe colostrum production excluding nutrient intake, namely body reserve mobilisation, ewe breed type, ewe age, gestation length and lamb birth weight. The volume of colostrum produced at 1 and 18 h post-partum was significantly lower than the volume recorded at 10 h post-partum (P = 0.01). Multivariate regression analysis indicated that colostrum volume during the first 18 h post-partum was influenced by lamb birth weight (P = 0.01), ewe age (P = 0.01), breed type (P = 0. 01) and gestation length (P = 0.06). Live weight change (P = 0.05) also had a significant influence on the volume of colostrum produced but BCS change did not affect colostrum production (P = 0.25). Further multivariate regression analysis indicated that IgG yield was influenced ewe breed type (P = 0.01), lamb birth weight (P = 0.02), gestation length (P = 0.05) and BCS change (P = 0.04). Live weight change (P = 0.12) and ewe age (P = 0.62) did not influence the quantity of IgG produced. Leicester ewes produced less colostrum per kg lamb birth weight at 1 h post-partum compared to all other ewe breed types (P = 0.01) and less than Suffolk ewes at 10 h post-partum (P = 0.01). The result of this analysis shows the key factors excluding ewe nutrition that drive colostrum production. Ewe breed type in particular appears to play an important role in the ability of the ewe to produce sufficient quantities of adequate quality colostrum. In conclusion the result of this analysis highlights the important factors associated with ewe colostrum volume and IgG yield excluding nutrition. In particular the overall structure of the flock such as breed type and ewe age is important when considering the ability of the flock to meet colostrum demands and hence reduce lamb mortality.