Now showing items 1-20 of 1427

    • Marine Functional Foods Research Initiative (NutraMara)

      Troy, Declan; Tiwari, Brijesh; Hayes, Maria; Ross, R. Paul; Stanton, Catherine; Johnson, Mark; Stengel, Dagmar; O'Doherty, John V.; Fitzgerald, Richard J.; McSorley, Emeir; Kerry, Joseph; Marine Institute; MFFRI/07/01 (Marine Institute, 2017-12)
      The NutraMara – Marine Functional Foods Research Initiative was conceived by Sea Change - A Marine Knowledge, Research and Innovation Strategy for Ireland 2007-2013. The goal was to develop a collaborative funding mechanism that would create new research capacity and build the capabilities required to maximise the potential of Ireland’s extensive marine bioresources. By supporting a strong interdisciplinary research team, capable of exploring marine animals and plants as a sustainable source of materials for use as functional ingredients and foods, the vision for NutraMara was to position Ireland to the fore in use of marine bioresources as health beneficial ingredients. Commencing in 2008 and supported by funds of €5.2 million from the Marine Institute and the Department of Agriculture, Food and the Marine, the research programme was led by Teagasc as the head of a multi-institutional consortium. The NutraMara consortium comprises marine bioresources and bioscience expertise, with food science and technology expertise from University College Cork; University College Dublin; the National University of Ireland Galway; the University of Limerick and Ulster University. Research effort was directed towards exploring Ireland’s marine bioresources – including macro- and microalgae, finfish and shellfish from wild and cultured sources: and discards from processing fish as sources of novel ingredients with bioactive characteristics. This discovery activity involved the collection of over 600 samples from 39 species of algae and fish and the analysis of 5,800 extracts, which resulted in 3,000 positive “hits” for bioactivity. The NutraMara consortium has built a strong research capacity to identify, characterise and evaluate marine-origin bioactives for use as/in functional foods. It further built the capacity to develop model foods enhanced with these marine-origin functional ingredients; providing insights to the processing challenges associated with producing functional ingredients from marine organisms. The consortium was actively engaged in research activities designed to identify and assess bioactive compounds from available marine resources, including polyphenols, proteins/peptides, amino acids, polysaccharides, polyunsaturated fatty acids and materials with antioxidant, probiotic or prebiotic properties. A key component of NutraMara’s activities was the development of human capital. The recruitment of M.Sc. and PhD students and their integration within a dynamic research environment that has strong links to industry, provided lasting expertise and capabilities, which are relevant to the needs of Ireland’s food and marine sectors. NutraMara research led to the awarding of eighteen PhDs and recruitment of 21 post-doctoral researchers over the eight year research programme. In excess of 80 peer reviewed publications resulted from this research and more publications are planned. A further 100 posters and conference presentations were also delivered by NutraMara researchers and Principal Investigators. The development and implementation of training and exchange programmes aimed at providing early stage researchers with inter-disciplinary skills that are critical to their development as researchers, enhanced the research capacity of institutions, the industry sectors and the country as a whole. Principal Investigators involved in leading the NutraMara research programme have secured additional research grants of almost €6 million from national and international sources and are engaged in extensive research collaboration involving marine and food research expertise; an activity which did not exist prior to NutraMara. The dissemination of knowledge and transfer of research results to industry were key activities in the research programme. The research outputs and visibility of NutraMara activity nationally resulted in 10 companies engaging in research and development activity with the consortium. Regular workshops and conferences organised by NutraMara attracted close to five hundred participants from Ireland and overseas. Members of the NutraMara core PI group have contributed to the formulation of new national foods and marine research policy and national research agenda, both during the national prioritisation exercise and in sectoral research strategies. This final project report describes the process by which research targets were identified, and the results of extensive screening and evaluation of compounds extracted from marine bioresources. It also highlights the development of new protocols designed to extract compounds in ways that are food friendly. Evaluating the functional properties, bioactivity and bioavailability of high potential marine compounds involved in vitro and in vivo testing. Pilot animal and human intervention studies yielded further insight to the potential and challenges in developing marine functional ingredients. As a result of work completed within the NutraMara consortium, Ireland is well positioned to continue to contribute to the development of ingredients derived from marine organisms and in doing so support the on-going development of Ireland’s food sector.
    • Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism

      Golubeva, Anna B.; Joyce, Susan A.; Moloney, Gerard; Burokas, Aurelijus; Sherwin, Eoin; Arboyelaya, Silvia; Flynn, Ian; Khochanskiy, Dmitry; Pérez, Angela M.; Peterson, Veronica; REa, Kieran; MUrphy, Kiera; Makarova, Olga; Buravkov, Sergey; Hyland, Niall P.; Stanton, Catherine; Clarke, Gerard; Gahan, Cormac G>M>; Dinan, Timothy G.; Cryan, John F.; Science Foundation Ireland; SFI/12/RC/2273 (2017-09-15)
      Autism spectrum disorder (ASD) is one of the most prevalent neurodevelopmental conditions worldwide. There is growing awareness that ASD is highly comorbid with gastrointestinal distress and altered intestinal microbiome, and that host-microbiome interactions may contribute to the disease symptoms. However, the paucity of knowledge on gut-brain axis signaling in autism constitutes an obstacle to the development of precision microbiota-based therapeutics in ASD. To this end, we explored the interactions between intestinal microbiota, gut physiology and social behavior in a BTBR T+ Itpr3tf/J mouse model of ASD. Here we show that a reduction in the relative abundance of very particular bacterial taxa in the BTBR gut – namely, bile-metabolizing Bifidobacterium and Blautia species, - is associated with deficient bile acid and tryptophan metabolism in the intestine, marked gastrointestinal dysfunction, as well as impaired social interactions in BTBR mice. Together these data support the concept of targeted manipulation of the gut microbiota for reversing gastrointestinal and behavioral symptomatology in ASD, and offer specific plausible targets in this endeavor.
    • A comparison of 4 predictive models of calving assistance and difficulty in dairy heifers and cows

      Fenlon, Caroline; O'Grady, Luke; Mee, John F; Butler, Stephen T.; Doherty, Michael L.; Dunnion, John; Dairy Research Ireland (Elsevier, 21/09/2017)
      The aim of this study was to build and compare predictive models of calving difficulty in dairy heifers and cows for the purpose of decision support and simulation modeling. Models to predict 3 levels of calving difficulty (unassisted, slight assistance, and considerable or veterinary assistance) were created using 4 machine learning techniques: multinomial regression, decision trees, random forests, and neural networks. The data used were sourced from 2,076 calving records in 10 Irish dairy herds. In total, 19.9 and 5.9% of calving events required slight assistance and considerable or veterinary assistance, respectively. Variables related to parity, genetics, BCS, breed, previous calving, and reproductive events and the calf were included in the analysis. Based on a stepwise regression modeling process, the variables included in the models were the dam's direct and maternal calving difficulty predicted transmitting abilities (PTA), BCS at calving, parity; calving assistance or difficulty at the previous calving; proportion of Holstein breed; sire breed; sire direct calving difficulty PTA; twinning; and 2-way interactions between calving BCS and previous calving difficulty and the direct calving difficulty PTA of dam and sire. The models were built using bootstrapping procedures on 70% of the data set. The held-back 30% of the data was used to evaluate the predictive performance of the models in terms of discrimination and calibration. The decision tree and random forest models omitted the effect of twinning and included only subsets of sire breeds. Only multinomial regression and neural networks explicitly included the modeled interactions. Calving BCS, calving difficulty PTA, and previous calving assistance ranked as highly important variables for all 4 models. The area under the receiver operating characteristic curve (ranging from 0.64 to 0.79) indicates that all of the models had good overall discriminatory power. The neural network and multinomial regression models performed best, correctly classifying 75% of calving cases and showing superior calibration, with an average error in predicted probability of 3.7 and 4.5%, respectively. The neural network and multinomial regression models developed are both suitable for use in decision-support and simulation modeling.
    • Ensifer-mediated Arabidopsis thaliana Root Transformation (E-ART): A Protocol to Analyse the Factors that Support Ensifer-mediated Transformation (EMT) of Plant Cells

      Rathore, Deeraj Singh; Doohan, Fiona M.; Mullins, Ewen; Teagasc Walsh Fellowship Programme (Bio-protocol LLC, 2017-10-05)
      Ensifer adhaerens OV14, a soil borne alpha-proteobacteria of the Rhizobiaceae family, fortifies the novel plant transformation technology platform termed ‘Ensifer-mediated transformation’ (EMT). EMT can stably transform both monocot and dicot species, and the host range of EMT is continuously expanding across a diverse range of crop species. In this protocol, we adapted a previously published account that describes the use of Arabidopsis thaliana roots to investigate the interaction of A. thaliana and Agrobacterium tumefaciens. In our laboratory, we routinely use A. thaliana root explants to examine the factors that enhance the utility of EMT. In addition, the E-ART protocol can be used to study the transcriptional response of E. adhaerens and host plant following exposure to explant tissue, the transformability of different Ensifer adhaerens strains/mutants as well as testing the susceptibility of A. thaliana mutant lines as a means to decipher the mechanisms underpinning EMT.
    • Bile acids at the cross-roads of gut microbiome–host cardiometabolic interactions

      Ryan, Paul M; Stanton, Catherine; Caplice, Noel M; Science Foundation Ireland; Enterprise Ireland Commercialization Fund; SFI/12/RC/2273; CF/2013/3030A/B (Biomed Central, 2017-12-28)
      While basic and clinical research over the last several decades has recognized a number of modifiable risk factors associated with cardiometabolic disease progression, additional and alternative biological perspectives may offer novel targets for prevention and treatment of this disease set. There is mounting preclinical and emerging clinical evidence indicating that the mass of metabolically diverse microorganisms which inhabit the human gastrointestinal tract may be implicated in initiation and modulation of cardiovascular and metabolic disease outcomes. The following review will discuss this gut microbiome–host metabolism axis and address newly proposed bile-mediated signaling pathways through which dysregulation of this homeostatic axis may influence host cardiovascular risk. With a central focus on the major nuclear and membrane-bound bile acid receptor ligands, we aim to review the putative impact of microbial bile acid modification on several major phenotypes of metabolic syndrome, from obesity to heart failure. Finally, attempting to synthesize several separate but complementary hypotheses, we will review current directions in preclinical and clinical investigation in this evolving field.
    • Birth delivery method affects expression of immune genes in lung and jejunum tissue of neonatal beef calves

      Surlis, Carla; McNamara, Keelan; O’Hara, Eoin; Waters, Sinead; Beltman, Marijke; Cassidy, Joseph; Kenny, David (Biomed Central, 2017-12-14)
      Background Caesarean section is a routine veterinary obstetrical procedure employed to alleviate dystocia in cattle. However, CS, particularly before the onset of labour, is known to negatively affect neonatal respiration and metabolic adaptation in humans, though there is little published information for cattle. The aim of this study was to investigate the effect of elective caesarean section (ECS) or normal trans-vaginal (TV) delivery, on lung and jejunal gene expression profiles of neonatal calves. Results Paternal half-sib Angus calves (gestation length 278 + 1.8 d) were delivered either transvaginally (TV; n = 8) or by elective caesarean section (ECS; n = 9) and immediately euthanized. Lung and jejunum epithelial tissue was isolated and snap frozen. Total RNA was extracted using Trizol reagent and reverse transcribed to generate cDNA. For lung tissue, primers were designed to target genes involved in immunity, surfactant production, cellular detoxification, membrane transport and mucin production. Primers for jejunum tissue were chosen to target mucin production, immunoglobulin uptake, cortisol reaction and membrane trafficking. Quantitative real-time PCR reactions were performed and data were statistically analysed using mixed models ANOVA. In lung tissue the expression of five genes were affected (p < 0.05) by delivery method. Four of these genes were present at lower (LAP, CYP1A1, SCN11α and SCN11β) and one (MUC5AC) at higher abundance in ECS compared with TV calves. In jejunal tissue, expression of TNFα, Il-1β and 1 l-6 was higher in ECS compared with TV calves. Conclusions This novel study shows that ECS delivery affects the expression of key genes involved in the efficiency of the pulmonary liquid to air transition at birth, and may lead to an increased inflammatory response in jejunal tissue, which could compromise colostral immunoglobulin absorption. These findings are important to our understanding of the viability and management of neonatal calves born through ECS.
    • Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology

      Matthews, Daragh; Diskin, Michael G; Kenny, David A; Creevey, Christopher J; Keogh, Kate; Waters, Sinead M (Biomed Central, 2017-11-09)
      Background Negative energy balance (NEB) is an imbalance between energy intake and energy requirements for lactation and body maintenance affecting high-yielding dairy cows and is of considerable economic importance due to its negative impact on fertility and health in dairy herds. It is anticipated that the cow hypothalamus experiences extensive biochemical changes during the early post partum period in an effort to re-establish metabolic homeostasis. However, there is variation in the tolerance to NEB between individual cows. In order to understand the genomic regulation of ovulation in hypothalamic tissue during NEB, mRNA transcriptional patterns between tolerant and sensitive animals were examined. A short term dietary restriction heifer model was developed which induced abrupt onset of anoestrus in some animals (Restricted Anovulatory; RA) while others maintained oestrous cyclicity (Restricted Ovulatory; RO). A third control group (C) received a higher level of normal feeding. Results A total of 15,295 genes were expressed in hypothalamic tissue. Between RA and C groups 137 genes were differentially expressed, whereas between RO and C, 32 genes were differentially expressed. Differentially expressed genes were involved in the immune response and cellular motility in RA and RO groups, respectively, compared to C group. The largest difference between groups was observed in the comparison between RA and RO heifers, with 1094 genes shown to be significantly differentially expressed (SDE). Pathway analysis showed that these SDE genes were associated with 6 canonical pathways (P < 0.01), of which neuroactive ligand-receptor interaction was the most significant. Within the comparisons the main over-represented pathway functions were immune response including neuroprotection (CXCL10, Q1KLR3, IFIH1, IL1 and IL8; RA v C and RA v RO); energy homeostasis (AgRP and NPY; RA v RO); cell motility (CADH1, DSP and TSP4; RO v C) and prevention of GnRH release (NTSR1 IL1α, IL1β, NPY and PACA; RA v RO). Conclusions This information will assist in understanding the genomic factors regulating the influence of diet restriction on fertility and may assist in optimising nutritional and management systems for the improvement in reproductive performance.
    • A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

      CaoYu; Fanning, Seamus; Proos, Sinead; Jordan, Kieran; Srikumar, Shabarinath; Department of Agriculture, Food and the Marine; SMART-PIF; 13/F/423 (Frontiers, 2017)
      The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.
    • Stabilising effect of α-lactalbumin on concentrated infant milk formula emulsions heat treated pre- or post-homogenisation

      Buggy, Aoife K.; McManus, Jenifer J.; Brodkorb, Andre; McCarthy, Noel; Fenelon, Mark A. (Springer, 2016-11-22)
      Protein type and/or heat treatment pre- or post-homogenisation can affect the physical stability of infant formulations during manufacture. Previous research has described the use of α-lactalbumin addition in infant formulae, but has not demonstrated the effect of heating pre- or post-emulsion formulation during processing. The objective of this study was to evaluate the effect of both of these parameters. Three batches of model 1st-stage infant formula containing differing whey protein ratios (60:40 whey: casein with α-lactalbumin content 12, 30 or 48% of total protein) were prepared. Each batch was split; one half receiving heat treatment pre-homogenisation and the second half homogenised and then heat treated. Emulsion stability was determined by size exclusion chromatography, SDS-PAGE, particle size and viscosity measurements. There was a significant (P < 0.05) reduction in the formation of large soluble aggregates upon increasing α-lac concentration in emulsions heat treated either before or after homogenisation. Heat treatment of formulations post-homogenisation resulted in a higher (P < 0.05) D.v09 within the particle size distribution; increasing α-lactalbumin concentration to 30 or 48% significantly (P < 0.05) reduced the D.v09 within the particle size distribution in these emulsions. The viscosity of concentrates (55 % total solids) containing the 12% α-lactalbumin, heat treated post-homogenisation, was significantly greater (P < 0.05) than the equivalent emulsion heat treated pre-homogenisation; increasing the α-lactalbumin concentration to 30 or 48% significantly (P < 0.05) reduced viscosity. When the α-lactalbumin content was increased to 48% as a percentage of the total protein, heating before or after emulsion formation had no effect on concentrate viscosity. The findings demonstrate the importance of thermal denaturation/aggregation of whey proteins (and in particular, the ratio of α-lactalbumin to β-lactoglobulin) prior to homogenisation of infant formula emulsions.
    • Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites

      Foito, Alexandre; Hackett, Christine A; Stewart, Derek; Velmurugan, Janaki; Milbourne, Dan; Byrne, Stephen L; Barth, Susanne (Biomed Central, 2017-10-10)
      Background Recent advances in the mapping of biochemical traits have been reported in Lolium perenne. Although the mapped traits, including individual sugars and fatty acids, contribute greatly towards ruminant productivity, organic acids and amino acids have been largely understudied despite their influence on the ruminal microbiome. Results In this study, we used a targeted gas-chromatography mass spectrometry (GC-MS) approach to profile the levels of 25 polar metabolites from different classes (sugars, amino acids, phenolic acids, organic acids and other nitrogen-containing compounds) present in a L. perenne F2 population consisting of 325 individuals. A quantitative trait (QTL) mapping approach was applied and successfully identified QTLs regulating seven of those polar metabolites (L-serine, L-leucine, glucose, fructose, myo-inositol, citric acid and 2, 3-hydroxypropanoic acid).Two QTL mapping approaches were carried out using SNP markers on about half of the population only and an imputation approach using SNP and DArT markers on the entire population. The imputation approach confirmed the four QTLs found in the SNP-only analysis and identified a further seven QTLs. Conclusions These results highlight the potential of utilising molecular assisted breeding in perennial ryegrass to modulate a range of biochemical quality traits with downstream effects in livestock productivity and ruminal digestion.
    • Do weaner pigs need in-feed antibiotics to ensure good health and welfare?

      Diana, Alessia; Manzanilla, Edgar G.; Calderon Diaz, Julia A.; Leonard, Finola C.; Boyle, Laura A. (PLOS, 2017-10-05)
      Antibiotics (AB) are used in intensive pig production systems to control infectious diseases and they are suspected to be a major source of antibiotic resistance. Following the ban on AB use as growth promoters in the EU, their prophylactic use in-feed is now under review. The aim of this study was to evaluate the effect of removing prophylactic in-feed AB on pig health and welfare indicators. Every Monday for six weeks, a subset of 70 pigs were weaned, tagged and sorted into two groups of 35 pigs according to weight (9.2 ± 0.6 kg). AB were removed from the diet of one group (NO, n=6) and maintained in the other group (AB, n=6) for nine weeks. Ten focal pigs were chosen per group. After c. five weeks each group was split into two pens of c.17 pigs for the following 4 weeks. Data were recorded weekly. Skin, tail, ear, flank and limb lesions of focal pigs were scored according to severity. The number of animals per group affected by health deviations was also recorded. The number of fights and harmful behaviours (ear, tail bites) per group was counted during 3×5min observations once per week. Data were analysed using mixed model equations and binomial logistic regression. At group level, AB pigs were more likely to have tail (OR=1.70; P=0.05) but less likely to have ear lesions than NO pigs (OR=0.46; P<0.05). The number of ear bites (21.4±2.15 vs. 17.3±1.61; P<0.05) and fights (6.91±0.91 vs. 5.58±0.72; P=0.09) was higher in AB than in NO pigs. There was no effect of treatment on health deviations and the frequency of these was low. Removing AB from the feed of weaner pigs had minimal effects on health and welfare indicators.
    • Insights into the Mode of Action of the Sactibiotic Thuricin CD

      Mathur, Harsh; Fallico, Vicenzo; O'Connor, Paula M.; Rea, Mary C.; Cotter, Paul D.; Hill, Colin; Ross, R. Paul (Frontiers, 2017-04-20)
      Thuricin CD is a two-component bacteriocin, consisting of the peptides Trnα and Trnβ, and belongs to the newly designated sactibiotic subclass of bacteriocins. While it is clear from studies conducted thus far that it is a narrow-spectrum bacteriocin, requiring the synergistic activity of the two peptides, the precise mechanism of action of thuricin CD has not been elucidated. This study used a combination of flow cytometry and traditional culture-dependent assays to ascertain the effects of the thuricin CD peptides on the morphology, physiology and viability of sensitive Bacillus firmus DPC6349 cells. We show that both Trnα and Trnβ are membrane-acting and cause a collapse of the membrane potential, which could not be reversed even under membrane-repolarizing conditions. Furthermore, the depolarizing action of thuricin CD is accompanied by reductions in cell size and granularity, producing a pattern of physiological alterations in DPC6349 cells similar to those triggered by the pore-forming single-component bacteriocin Nisin A, and two-component lacticin 3147. Taken together, these results lead us to postulate that the lytic activity of thuricin CD involves the insertion of thuricin CD peptides into the membrane of target cells leading to permeabilization due to pore formation and consequent flux of ions across the membrane, resulting in membrane depolarization and eventual cell death.
    • From Knowledge to Invention: Exploring User Innovation in Irish Agriculture

      O'Flynn, Patricia; Teagasc Walsh Fellowship Programme (2017-07)
      Improvements in European agriculture are framed in the literature as arising from an Agricultural Knowledge and Innovation System with innovations provided by others for farmers to adopt. The motivators for farmers who invent useful products for themselves, without outside involvement, are not well understood in such developed countries. These inventions, often shared with other farmers rather than introduced to the market, arise from a process of user innovation (von Hippel, 2005). This thesis examines Irish farmers’ motivators in the creation and subsequent sharing or commercialisation of farming artefacts. Their motivators are conceptualised from a sociological perspective, using Bourdieu’s theory of capitals (1986). Employing a multi-perspective research design, methods include a content analysis of 210 inventions, semi-structured interviews with key informants from innovation support organisations, and in-depth interviews with farmer-inventors. The findings indicate that most farmer-inventors get great personal satisfaction from problem-solving and, being generally without higher education, use their tacit knowledge to create inventions that increase efficiency as a means to improve family farm viability. Despite efficiency usually indicating skilful farming, Irish farmer-inventors are frequently derided by other farmers who deem their inventing to be culturally inappropriate. Farmer-inventors with entrepreneurial intentions, willing to withstand such hostility, face financial and temporal constraints, while the help offered by innovation support organisations is often inadequate. As a result, some inventions with commercial potential may never reach the market. Farmer-inventors who share their knowledge and inventions in social learning networks, similar to communities of practice, accrue social capital that leads to the emergence of a shared farmer-inventor identity. This thesis contributes to knowledge about user innovation in developed country agriculture by offering deeper understandings of farmer-inventors’ social, cultural, and economic processes. It proposes farmers to be an underappreciated source of knowledge and inventions, which offer low cost farm-level solutions to support family farm resilience.
    • Evaluation of the Effect of Tocopherols on the Stability of Biodiesel

      Fröhlich, A. (Teagasc, 2005-04-01)
      A comprehensive study was carried out on the effects of naturally occurring tocopherols and carotenoids on the stability of biodiesel-grade methyl esters. Commercially available tocopherols and carotenoids, α-, γ- and δ-tocopherol, carotene and asthaxanthin, were added to destabilised methyl esters and the solutions were exposed to air at 65oC. The stabilising effect of the added tocopherols and carotenoids was determined from the number of days needed to reach the same increase of viscosity as destabilised methyl ester without tocopherols after 1 day. All three tocopherols stabilised methyl esters; γ- being the most effective and α- the least. The stabilising effect of tocopherols increased with concentration up to an optimum level. Concentrations above this level did not improve stability significantly. The stabilising effect of the tocopherols also depended on the composition of the methyl ester; they were most effective in tallow methyl ester, and had the least effect on sunflower methyl ester. Carotene and asthaxanthin had no effect on the stability of the methyl esters. However an unidentified carotenoid in rape methyl ester changed the oxidation pattern by reducing rates of peroxide and viscosity increase, without affecting overall stability.
    • Finishing pigs that are divergent in feed efficiency show small differences in intestinal functionality and structure

      Metzler-Zebeli, Barbara U.; Lawlor, Peadar G; Magowan, Elizabeth; McCormack, Ursula M.; Curiao, Tania; Hollmann, Manfred; Ertl, Reinhardt; Aschenbach, Jorg R.; Zebeli, Qendrim (PLOS, 2017-04-05)
      Controversial information is available regarding the feed efficiency-related variation in intestinal size, structure and functionality in pigs. The present objective was therefore to investigate the differences in visceral organ size, intestinal morphology, mucosal enzyme activity, intestinal integrity and related gene expression in low and high RFI pigs which were reared at three different geographical locations (Austria, AT; Northern Ireland, NI; Republic of Ireland, ROI) using similar protocols. Pigs (n = 369) were ranked for their RFI between days 42 and 91 postweaning and low and high RFI pigs (n = 16 from AT, n = 24 from NI, and n = 60 from ROI) were selected. Pigs were sacrificed and sampled on ~day 110 of life. In general, RFI-related variation in intestinal size, structure and function was small. Some energy saving mechanisms and enhanced digestive and absorptive capacity were indicated in low versus high RFI pigs by shorter crypts, higher duodenal lactase and maltase activity and greater mucosal permeability (P < 0.05), but differences were mainly seen in pigs from AT and to a lesser degree in pigs from ROI. Additionally, low RFI pigs from AT had more goblet cells in duodenum but fewer in jejunum compared to high RFI pigs (P < 0.05). Together with the lower expression of TLR4 and TNFA in low versus high RFI pigs from AT and ROI (P < 0.05), these results might indicate differences in the innate immune response between low and high RFI pigs. Results demonstrated that the variation in the size of visceral organs and intestinal structure and functionality was greater between geographic location (local environmental factors) than between RFI ranks of pigs. In conclusion, present results support previous findings that the intestinal size, structure and functionality do not significantly contribute to variation in RFI of pigs.
    • The bovine paranasal sinuses: Bacterial flora, epithelial expression of nitric oxide and potential role in the in-herd persistence of respiratory disease pathogens

      Murray, Gerard M.; O'Neill, Ronan G.; Lee, Alison M.; McElroy, Maire; More, Simon J.; Monagle, Aisling; Earley, Bernadette; Cassidy, Joseph P. (PLOS, 2017-03-10)
      The bovine paranasal sinuses are a group of complex cavernous air-filled spaces, lined by respiratory epithelium, the exact function of which is unclear. While lesions affecting these sinuses are occasionally reported in cattle, their microbial flora has not been defined. Furthermore, given that the various bacterial and viral pathogens causing bovine respiratory disease (BRD) persist within herds, we speculated that the paranasal sinuses may serve as a refuge for such infectious agents. The paranasal sinuses of clinically normal cattle (n = 99) and of cattle submitted for post-mortem examination (PME: n = 34) were examined by microbial culture, PCR and serology to include bacterial and viral pathogens typically associated with BRD: Mycoplasma bovis, Histophilus somni, Mannheimia haemolytica and Pasteurella multocida, bovine respiratory syncytial virus (BRSV) and bovine parainfluenza-3 virus (BPIV-3). Overall, the paranasal sinuses were either predominantly sterile or did not contain detectable microbes (83.5%: 94.9% of clinically normal and 50.0% of cattle submitted for PME). Bacteria, including BRD causing pathogens, were identified in relatively small numbers of cattle (<10%). While serology indicated widespread exposure of both clinically normal and cattle submitted for PME to BPIV-3 and BRSV (seroprevalences of 91.6% and 84.7%, respectively), PCR identified BPIV-3 in only one animal. To further explore these findings we investigated the potential role of the antimicrobial molecule nitric oxide (NO) within paranasal sinus epithelium using immunohistochemistry. Expression of the enzyme responsible for NO synthesis, inducible nitric oxide synthase (iNOS), was detected to varying degrees in 76.5% of a sub-sample of animals suggesting production of this compound plays a similar protective role in the bovine sinus as it does in humans.
    • Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs

      Horodyska, Justyna; Hamill, Ruth M.; Varley, Patrick F.; Wimmers, Klaus (PLOS, 2017-06-12)
      Feed conversion efficiency is a measure of how well an animal converts feed into live weight and it is typically expressed as feed conversion ratio (FCR). FCR and related traits like growth rate (e.g. days to 110 kg—D110) are of high interest for animal breeders, farmers and society due to implications on animal performance, feeding costs and environmental sustainability. The objective of this study was to identify genomic regions associated with FCR and D110 in pigs. A total of 952 terminal line boars, showing an individual variation in FCR, were genotyped using 60K SNP-Chips. Markers were tested for associations with estimated breeding values (EBV) for FCR and D110. For FCR, the largest number of associated SNPs was located on chromosomes 4 (30 SNPs), 1 (25 SNPs), X (15 SNPs) and 6 (12 SNPs). The most prominent genomic regions for D110 were identified on chromosomes 15 (10 SNPs), 1 and 4 (both 9 SNPs). The most significantly associated SNPs for FCR and D110 mapped 129.8 Kb from METTL11B (chromosome 4) and 32Kb from MBD5 (chromosome 15), respectively. A list of positional genes, closest to significantly associated SNPs, was used to identify enriched pathways and biological functions related to the QTL for both traits. A number of candidate genes were significantly overrepresented in pathways of immune cell trafficking, lymphoid tissue structure, organ morphology, endocrine system function, lipid metabolism, and energy production. After resequencing the coding region of selected positional and functional candidate genes, six SNPs were genotyped in a subset of boars. SNPs in PRKDC, SELL, NR2E1 and AKRIC3 showed significant associations with EBVs for FCR/D110. The study revealed a number of chromosomal regions and candidate genes affecting FCR/D110 and pointed to corresponding biological pathways related to lipid metabolism, olfactory reception, and also immunological status.
    • Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

      McCabe, Matthew Sean; Cormican, Paul; Keogh, Kate; O'Connor, Aaron; O'Hara, Eoin; Palladino, Rafael Alejandro; Kenny, David A.; Waters, Sinead M. (PLOS, 2015-07-30)
      Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.
    • Controlling Blown Pack Spoilage Using Anti-Microbial Packaging

      Reid, Rachael; Bolton, Declan; Tiuftin, Andrey; Kerry, Joe P.; Fanning, Seamus; Whyte, Paul (MDPI, 2017-08-12)
      Active (anti-microbial) packaging was prepared using three different formulations; Auranta FV; Inbac-MDA and sodium octanoate at two concentrations (2.5 and 3.5 times their minimum inhibitory concentration (MIC, the lowest concentration that will inhibit the visible growth of the organisms) against Clostridium estertheticum, DSMZ 8809). Inoculated beef samples were packaged using the active packaging and monitored for 100 days storage at 2 °C for blown pack spoilage. The time to the onset of blown pack spoilage was significantly (p < 0.01) increased using Auranta FV and sodium octanoate (caprylic acid sodium salt) at both concentrations. Moreover, sodium octanoate packs had significantly (p < 0.01) delayed blown pack spoilage as compared to Auranta FV. It was therefore concluded that Auranta FV or sodium octanoate, incorporated into the packaging materials used for vacuum packaged beef, would inhibit blown pack spoilage and in the case of the latter, well beyond the 42 days storage period currently required for beef primals
    • Genome Sequence of Staphylococcus saprophyticus DPC5671, a Strain Isolated from Cheddar Cheese

      Bertuzzi, Andrea; Guinane, Caitriona M.; Crispie, Fiona; Kilcawley, Kieran N; McSweeney, Paul L.H.; Rea, Mary C. (American Society for Microbiology, 2017-04-20)
      The draft genome sequence of Staphylococcus saprophyticus DPC5671, isolated from cheddar cheese, was determined. S. saprophyticus is a common Gram-positive bacterium detected on the surface of smear-ripened cheese and other fermented foods.