Now showing items 21-40 of 2401

    • Human dynamics and the intergenerational farm transfer process in later life: A roadmap for future generational renewal in agriculture policy

      Conway, Shane Francis; McDonagh, John; Farrell, Maura; Kinsella, Anne; National University of Ireland, Galway; Geographical Society of Ireland (International Farm Management Association and Institute of Agricultural Management, 2019)
      The senior generation’s reluctance and indeed resistance to alter the status quo of the existing management and ownership structure of their family farm is undoubtedly strong within the farming community. This phenomenon has resulted in extraordinary socio-economic challenges for young people aspiring to embark on a career in farming. The reasons why older farmers fail to plan effectively and expeditiously for the future are expansive, and range from the potential loss of identity, status and power that may occur as a result of engaging in the process, to the intrinsic multi-level relationship farmers have with their farms. These so-called ‘soft issues’ i.e. the emotional and social dimensions involved, are the issues that distort and dominate the older generation’s decisions on the future trajectory of the farm. These really are the ‘hard issues’. This paper draws on three interrelated journal articles exploring the complex human dynamics influencing the decision-making processes surrounding farm succession and retirement to put forth a series of recommendations that sensitively deal with problematic issues surrounding generational renewal in agriculture, whilst also ensuring farmers’ emotional wellbeing in later life.
    • Mobilising Land Mobility in the European Union: An Under-Researched Phenomenon

      Conway, Shane Francis; Farrell, Maura; McDonagh, John; Kinsella, Anne (International Farm Management Association and Institute of Agricultural Management, 2020)
      Interest in land mobility and its impact on the structural development and economic growth of the agricultural sector has grown considerably amid concerns about the ageing European farming population. There have been calls throughout Europe for structural and institutional deterrents obstructing the passage of farmland from the older to younger generation of farmers to overcome this phenomenon and help facilitate generational renewal in agriculture. Nonetheless, gaining access to land is widely reported to be the single largest barrier facing young people attempting to enter farming. Whilst land mobility is given homogenous importance throughout Europe, this view point paper highlights that policies and regulations relating to land differ considerably across EU Member States. There is also a surprising scarcity of literature and academic discussion on access to land in a European context, despite its crucial role in the survival, continuity and future prosperity of the farming industry and the broader sustainability of rural communities. By focussing on the key policy and structural issues hampering access to agricultural land throughout Europe, and using the Republic of Ireland’s Land Mobility Service as a good practice example of how to help facilitate the process, this paper provides a rationale for why a major European study is required to investigate the factors which influence land mobility in each of the 27 EU Member States in order to inform future Common Agricultural Policy (CAP) Strategic Plans, particularly in relation to generational renewal objectives.
    • Till death do us part: Exploring the Irish farmer-farm relationship in later life through the lens of ‘Insideness’

      Conway, Shane Francis; McDonagh, John; Farrell, Maura; Kinsella, Anne; National University of Ireland, Galway; Geographical Society of Ireland (International Farm Management Association and Institute of Agricultural Management, 2018)
      The senior generation’s unwillingness to relinquish managerial duties and retire is a globally recognized characteristic of intergenerational family farm transfer. This is despite the array of financial incentives put in place to stimulate and entice the process. Applying Rowles’ concept of ‘insideness’ as a theoretical framework, this paper brings into focus the suitability and appropriateness of previous and existing farm transfer policy strategies, by presenting an insightful, nuanced analysis of the deeply embedded attachment older farmers have with their farms, and how such a bond can stifle the necessary hand over of the farm business to the next generation. This research employs a multi-method triangulation design, consisting of a self-administered questionnaire and an Irish adaptation of the International FARMTRANSFERS Survey in conjunction with complimentary Problem-Centred Interviews, to generate a comprehensive insight into the intricate, multi-level farmer-farm relationship in later life. The overriding themes to emerge from the content analysis of the empirical research are farmer’s inherit desire to stay rooted in place in old age and also to maintain legitimate connectedness within the farming community by remaining active and productive on the farm. Additionally, there is a strong sense of nostalgia attributed to the farm, as it is found to represent a mosaic of the farmer’s achievements as well as being a landscape of memories. The paper concludes by suggesting that a greater focus on the farmer-farm relationship has the potential to finally unite farm transfer policy efforts with the mind-set of its targeted audience, after decades of disconnect.
    • Development and validation of a quantitative confirmatory method for 30 β-lactam antibiotics in bovine muscle using liquid chromatography coupled to tandem mass spectrometry

      Di Rocco, Melissa; Moloney, Mary; O’Beirne, T.; Earley, S.; Berendsen, B.; Furey, A.; Danaher, Martin; Department of Agriculture, Food and the Marine; 13/F484 (Elsevier BV, 2017-06)
      A method was developed for the confirmatory and quantitative analysis of 30 β-lactam antibiotic residues in bovine muscle. The method includes 12 penicillins (amoxicillin, ampicillin, cloxacillin, dicloxacillin, mecillinam, methicillin, nafcillin, oxacillin, penicillin G, penicillin V, piperacillin, ticarcillin), 12 cephalosporins (cefacetrile, cefadroxil, cephalexin, cefalonium, cefazolin, cefoperazone, cefotaxime, cefquinome, cefuroxime, desacetyl cephapirin, desfuroylceftiofur cysteine disulfide, desfuroylceftiofur dimer), five carbapenems (biapenem, doripenem, ertapenem, imipenem, meropenem) and faropenem. Samples were extracted using a simple solvent extraction with acetonitrile:water (80:20, v/v) and C18 dispersive solid-phase extraction (d-SPE) clean-up, followed by ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC–MS/MS) detection. Chromatography was performed on a reversed phase CSH C18 column, using a binary gradient separation comprising of 0.01% formic acid and 0.2 mM ammonium acetate in water (mobile phase A) and 0.01% formic acid in acetonitrile (mobile phase B). The mass spectrometer was operated in the positive electrospray ionisation mode (ESI(+)). Validation was performed following the 2002/657/EC guidelines. Trueness ranged between 69% and 143% and precision ranged between 2.0% and 29.9% under within-laboratory reproducibility conditions. The developed method uses minimal sample preparation and 30 test samples can be analysed by a single analyst in a single day. To the best of our knowledge, this is the first method for carbapenems in foodstuff that does not require derivatisation.
    • Improving the chromatographic selectivity of β-lactam residue analysis in milk using phenyl-column chemistry prior to detection by tandem mass spectrometry

      Di Rocco, Melissa; Moloney, Mary; Haren, Deirdre; Gutierrez, Montserrat; Earley, Seán; Berendsen, Bjorn; Furey, Ambrose; Danaher, Martin; Department of Agriculture, Food and the Marine; 13/F484 (Springer Science and Business Media LLC, 2020-05-23)
      Analyte isobaric interferences can limit the development of a comprehensive analytical method for the quantitative liquid chromatography-tandem mass spectrometry profiling of an important cohort of veterinary drugs. In this work, a selective chromatographic separation was developed for the analysis of 32 β-lactam antibiotic residues (12 penicillins, 14 cephalosporins, five carbapenems and faropenem) in milk samples. A range of analytical columns with different stationary phases and mobile phases were evaluated for retention and separation of the β-lactam compounds. Results showed that, among the columns tested, only phenyl-hexyl could adequately separate ampicillin from cephalexin and amoxicillin from cefadroxil, which had shown isobaric interferences on a number of stationary phases. Chromatography was performed using a water/acetonitrile binary gradient with formic acid and ammonium acetate. The β-lactam residues were extracted from the milk samples using a water:acetonitrile solution and purified by C18 dispersive solid-phase extraction (d-SPE) clean-up, followed by concentration under nitrogen and ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) determination. Analytes were monitored in positive electrospray ionisation mode (ESI(+)). Possible interfering matrix effects were overcome by using 13 internal standards. The method was fully validated according to 2002/657/EC guidelines, showing satisfactory performance characteristics. Under within-laboratory reproducibility conditions, trueness and precision ranged from 91 to 130% and from 1.4 to 38.6%, respectively. Decision limits (CCα) were in the range 2.1–133 μg kg−1. Limits of detection (LODs) and quantitation (LOQs) ranged between 0.0090 and 1.5 μg kg−1 and from 0.030 to 5.0 μg kg−1, respectively.
    • Protein quality and quantity influence the effect of dietary fat on weight gain and tissue partitioning via host-microbiota changes

      Nychyk, Oleksandr; Barton, Wiley; Rudolf, Agata M.; Boscaini, Serena; Walsh, Aaron; Bastiaanssen, Thomaz F.S.; Giblin, Linda; Cormican, Paul; Chen, Liang; Piotrowicz, Yolanda; et al. (Elsevier BV, 2021-05-11)
      We investigated how protein quantity (10%–30%) and quality (casein and whey) interact with dietary fat (20%–55%) to affect metabolic health in adult mice. Although dietary fat was the main driver of body weight gain and individual tissue weight, high (30%) casein intake accentuated and high whey intake reduced the negative metabolic aspects of high fat. Jejunum and liver transcriptomics revealed increased intestinal permeability, low-grade inflammation, altered lipid metabolism, and liver dysfunction in casein-fed but not whey-fed animals. These differential effects were accompanied by altered gut size and microbial functions related to amino acid degradation and lipid metabolism. Fecal microbiota transfer confirmed that the casein microbiota increases and the whey microbiota impedes weight gain. These data show that the effects of dietary fat on weight gain and tissue partitioning are further influenced by the quantity and quality of the associated protein, primarily via effects on the microbiota.
    • Gene Expression Pattern in Olive Tree Organs (Olea europaea L.)

      Ramírez-Tejero, Jorge A.; Jiménez-Ruiz, Jaime; Leyva-Pérez, María de la O; Barroso, Juan Bautista; Luque, Francisco; Regional Government of Andalusia; Spanish Ministry of Economy, Industry and Competitiveness; Spanish State Research Agency; European Union; AGR-6038; et al. (MDPI AG, 2020-05-12)
      The olive tree (Olea europaea L.) was one of the first plant species in history to be domesticated. Throughout olive domestication, gene expression has undergone drastic changes that may affect tissue/organ-specific genes. This is an RNA-seq study of the transcriptomic activity of different tissues/organs from adult olive tree cv. “Picual” under field conditions. This analysis unveiled 53,456 genes with expression in at least one tissue, 32,030 of which were expressed in all organs and 19,575 were found to be potential housekeeping genes. In addition, the specific expression pattern in each plant part was studied. The flower was clearly the organ with the most exclusively expressed genes, 3529, many of which were involved in reproduction. Many of these organ-specific genes are generally involved in regulatory activities and have a nuclear protein localization, except for leaves, where there are also many genes with a plastid localization. This was also observed in stems to a lesser extent. Moreover, pathogen defense and immunity pathways were highly represented in roots. These data show a complex pattern of gene expression in different organs, and provide relevant data about housekeeping and organ-specific genes in cultivated olive.
    • Inclusion of Healthy Oils for Improving the Nutritional Characteristics of Dry-Fermented Deer Sausage

      Vargas-Ramella, Márcio; Munekata, Paulo E. S.; Gagaoua, Mohammed; Franco, Daniel; Campagnol, Paulo C. B.; Pateiro, Mirian; Barretto, Andrea Carla da Silva; Domínguez, Rubén; Lorenzo, José M.; CYTED; et al. (MDPI AG, 2020-10-18)
      The influence of partial replacement of animal fat by healthy oils on composition, physicochemical, volatile, and sensory properties of dry-fermented deer sausage was evaluated. Four different batches were manufactured: the control was formulated with animal fat (18.2%), while in the reformulated batches the 50% of animal fat was substituted by olive, canola, and soy oil emulsions immobilized in Prosella gel. The reformulation resulted in a decrease of moisture and fat contents and an increase of protein and ash amount. Moreover, reformulated sausages were harder, darker, and had higher pH values. This fact is related to the lower moisture content in these samples. As expected, the fatty acid composition was changed by the reformulation. The use of soy and canola oils increased polyunsaturated fatty acids and omega-3 content and decreased n-6/n-3 ratio and saturated fatty acids. Thus, the use of these two oils presented the best nutritional benefits. The changes observed in the fatty acids reflected the fatty acid composition of the oils employed in the emulsions. Regarding volatile compounds (VOC), the replacement of animal fat by healthy emulsion gels increased the content of both total VOC and most of individual VOC. However, the lipid-derived VOC did not show this trend. Generally speaking, the control samples presented similar or higher VOC derived from lipid oxidation processes, which could be related to the natural antioxidant compounds present in the vegetable oils. Finally, all reformulated sausages presented higher consumer acceptability than control samples. In fact, the sausage reformulated with soy oil emulsion gel was the most preferred. Thus, as a general conclusion, the reformulation of deer sausages with soy emulsion gel improves both composition and sensory quality of the final product, which could be an excellent strategy to the elaboration of healthy fermented sausages.
    • Genome-Wide Profiling of Enterotoxigenic Staphylococcus aureus Strains Used for the Production of Naturally Contaminated Cheeses

      Macori, Guerrino; Bellio, Alberto; Bianchi, Daniela Manila; Chiesa, Francesco; Gallina, Silvia; Romano, Angelo; Zuccon, Fabio; Cabrera-Rubio, Raúl; Cauquil, Alexandra; Merda, Déborah; et al. (MDPI AG, 2019-12-27)
      Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with emetic activity can be produced by specific strains responsible for staphylococcal food poisoning, one of the most common food-borne diseases. Whole genome sequencing provides a comprehensive view of the genome structure and gene content that have largely been applied in outbreak investigations and genomic comparisons. In this study, six enterotoxigenic S. aureus strains were characterised using a combination of molecular, phenotypical and computational methods. The genomes were analysed for the presence of virulence factors (VFs), where we identified 110 genes and classified them into five categories: adherence (n = 31), exoenzymes (n = 28), genes involved in host immune system evasion (n = 7); iron uptake regulatory system (n = 8); secretion machinery factors and toxins’ genes (n = 36), and 39 genes coding for transcriptional regulators related to staphylococcal VFs. Each group of VFs revealed correlations among the six enterotoxigenic strains, and further analysis revealed their accessory genomic content, including mobile genetic elements. The plasmids pLUH02 and pSK67 were detected in the strain ProNaCC1 and ProNaCC7, respectively, carrying out the genes sed, ser, and selj. The genes carried out by prophages were detected in the strain ProNaCC2 (see), ProNaCC4, and ProNaCC7 (both positive for sea). The strain ProNaCC5 resulted positive for the genes seg, sei, sem, sen, seo grouped in an exotoxin gene cluster, and the strain ProNaCC6 resulted positive for seh, a transposon-associated gene. The six strains were used for the production of naturally contaminated cheeses which were tested with the European Screening Method for staphylococcal enterotoxins. The results obtained from the analysis of toxins produced in cheese, combined with the genomic features represent a portrait of the strains that can be used for the production of staphylococcal enterotoxin-positive cheese as reference material.
    • Efficacy of Woodchip Biochar and Brown Coal Waste as Stable Sorbents for Abatement of Bioavailable Cadmium, Lead and Zinc in Soil

      Amoah-Antwi, C.; Kwiatkowska-Malina, J.; Szara, E.; Thornton, S.; Fenton, Owen; Malina, G.; European Union; 675120 (Springer Science and Business Media LLC, 2020-10-03)
      Organic sorbents alter physicochemical soil properties and mitigate heavy metal (HM) bioavailability. However, some sorbents are labile and, therefore, introduce the risk of HM release into soil after mineralisation. Before field application, new stable organic sorbents such as woodchip biochar (BIO) and brown coal waste (BCW) need to be tested and compared with standard organic amendments like farmyard manure (FYM). An incubated pot experiment was conducted to investigate the efficacy of FYM, BIO and BCW (added to soil in pots at 5 and 10% w/w) to alter soil physicochemical properties and mitigate bioavailability of Cd, Pb and Zn spiked in treatments at different doses (in mg kg−1 ); 0 (not spiked), 1 (1 Cd, 70 Pb, 100 Zn) and 2 (3 Cd, 500 Pb, 700 Zn), and incubated for 9 weeks. At the end of the experiment, the EDTAextractable HM fractions, pH, cation exchange capacity (CEC) and specific surface area (SSA, to check trends) were determined in all treated soils. Results showed that FYM, BCW and BIO generally improved all soil properties (except reduced pH from BCW and apparent SSA reduction from FYM) and accounted for respective maximum abatements of Cd (50.2, 69.9 and 25.5%), Pb (34.2, 64.3 and 17.4%) and Zn (14.9, 17.7 and 11.8%) bioavailability in soil. FYM and BCW were more effective at 10% w/w especially in the low contaminated soil, whereas the highest efficacy for BIO was at 5% w/w and in the high contaminated soil. The efficacies of sorption by the organic sorbents varied for different HMs and were in the orders: BCW > FYM > BIO for Cd, FYM > BCW > BIO for Pb and BIO > BCW > FYM for Zn. Soil pH and CEC were strongly correlated with HM bioavailability in all treatments and implied that immobilisation of HMs occurred via complex formation, ion exchange and pH-dependent specific adsorption. All three sorbents were beneficial as soil amendments, and in terms of HM mitigation, BCW had the highest efficacy, followed by FYM and then BIO. Considering the documented high soil stability of BCW and BIO, these results are promising for further trialling at field scale.
    • Growth performance and hematological changes of weaned beef calves diagnosed with respiratory disease using respiratory scoring and thoracic ultrasonography

      Cuevas-Gómez, Inmaculada; McGee, Mark; McCabe, Matthew; Cormican, Paul; O’Riordan, Edward; McDaneld, Tara; Earley, Bernadette; US-Ireland Tripartite Grant; 2018US-IRL200 (Oxford University Press (OUP), 2020-10-23)
      This study investigated (i) the effect of clinical bovine respiratory disease (BRD) and associated lung consolidations on growth performance and hematological profiles of recently weaned beef calves and (ii) the relationship between clinical respiratory signs and lung consolidation detected by thoracic ultrasonography (TUS). One hundred and fifty-three weaned beef calves (209 (SD; 35.8) days old and 306 (SD; 26.3) kg, at arrival) purchased and transported from auction markets were accommodated indoors in concrete slatted floor pens. Calves were weighed weekly from arrival until d 28 and on d 65 post-arrival. Assessment of BRD and blood sample collection for hematological profiles were performed on scheduled days (at arrival, on d 7, 14 and 28) and on other days upon BRD diagnosis. Animals were assessed for BRD using a total clinical respiratory score (CRS) of five clinical signs (rectal temperature, ear position, cough, nasal secretion and eye secretion with each ranging from normal (0) to abnormal (3)), and TUS scores (normal (0) to lung consolidation ≥ 1 cm2 (2)). Based on CRS, 35% of calves were CRS+ (CRS ≥5) and 65% were CRS- (CRS <5). Although no lung consolidations (TUS-) were detected at arrival, 34% of calves developed lung consolidation (≥ 1 cm2 ) (TUS+) during the first 28 d post-arrival. Only fever (>39.6o C) and nasal discharge were weakly associated (r 0.19, P <0.05) with lung consolidation. On the day of BRD detection, neutrophil number and neutrophil:lymphocyte ratio was 58% and 73% greater, respectively, in BRD calves with lung consolidation compared to healthy calves. From d 0 to 65, calf ADG did not differ (P >0.05) between CRS+ and CRS- calves, but was 0.09 kg/d lower (P <0.05) for TUS+ compared to TUS- calves. Calves classified as BRD (CRS+TUS ≥5) with lung consolidation had lower (P <0.05) ADG from arrival until d 28 than healthy calves and BRD calves without lung consolidation (0.11 ± 0.10 vs. 0.53 ± 0.07 vs. 0.57 ± 0.10 kg/d, respectively); however, no differences in ADG were observed from d 0 to 65. Conventional methods to diagnose BRD failed to detect calves with lung lesions. Thoracic ultrasonography is a useful tool to detect lung lesions and its implementation in combination with CRS should provide a more accurate and early diagnosis of BRD, which is fundamental to successful treatment, animal welfare and growth performance.
    • Strategies to Meet Nutritional Requirements and Reduce Boar Taint in Meat from Entire Male Pigs and Immunocastrates

      Bee, Giuseppe; Quiniou, Nathalie; Maribo, Hanne; Zamaratskaia, Galia; Lawlor, Peadar G. (MDPI AG, 2020-10-23)
      This paper reviews the current knowledge on the nutritional requirements of entire male and immunocastrated pigs to obtain an efficient growth, low boar taint level, and good carcass and meat quality. We present the reasons for offering entire males ad libitum access to the diets in order to optimize their protein deposition potential. Boar taint is one of the major issues in the production of entire males; therefore, the impact of various skatole- and indole-reducing feed ingredients is discussed regarding their efficiency and the possible mechanism affecting skatole and indole production in the hindgut. Entire males have lean carcasses, so their intramuscular fat content can be lower than that of surgical castrates or females and the adipose tissue can be highly unsaturated. The possible nutritional strategies to counteract these effects are summarized. We conclude that immunocastrates can be fed similarly to entire males until the second vaccination. However, due to the metabolic changes occurring shortly after the second vaccination, the requirements for essential amino acids are markedly lower in immunocastrates than in entire males.
    • Therapeutic effects of antibiotics loaded cellulose nanofiber and κ-carrageenan oligosaccharide composite hydrogels for periodontitis treatment

      Johnson, Athira; Kong, Fanbin; Miao, Song; Lin, Hong‑Ting Victor; Thomas, Sabu; Huang, Yi‑Cheng; Kong, Zwe‑Ling (Springer Science and Business Media LLC, 2020-10-22)
      Periodontitis is an infammatory disease that can lead to the periodontal pocket formation and tooth loss. This study was aimed to develop antimicrobials loaded hydrogels composed of cellulose nanofbers (CNF) and κ-carrageenan oligosaccharides (CO) nanoparticles for the treatment of periodontitis. Two antimicrobial agents such as surfactin and Herbmedotcin were selected as the therapeutic agents and the hydrogels were formulated based on the increasing concentration of surfactin. The proposed material has high thermal stability, controlled release, and water absorption capacity. This study was proceeded by investigating the in vitro antibacterial and anti-infammatory properties of the hydrogels. This material has strong antibacterial activity against periodontal pathogens such as Streptococcus mutans, Porphyromonas gingivalis, Fusobacterium nucleatum, and Pseudomonas aeruginosa. Moreover, a signifcant increase in malondialdehyde (MDA) production and a decrease in bioflm formation and metabolic activity of the bacteria was observed in the presence of hydrogel. Besides, it reduced the reactive oxygen species (ROS) generation, transcription factor, and cytokines production in human gingival fbroblast cells (HGF) under infammatory conditions. In conclusion, the hydrogels were successfully developed and proven to have antibacterial and anti-infammatory properties for the treatment of periodontitis. Thus, it can be used as an excellent candidate for periodontitis treatment.
    • Early immune suppression leads to uncontrolled mite proliferation and potent host inflammatory responses in a porcine model of crusted versus ordinary scabies

      Bhat, Sajad A.; Walton, Shelley F.; Ventura, Tomer; Liu, Xiaosong; McCarthy, James S.; Burgess, Stewart T. G.; Mounsey, Kate E.; Australian Research Council; Australian National Health and Medical Research Council; DE120101701; et al. (Public Library of Science (PLoS), 2020-09-04)
      Scabies is a neglected tropical disease of global significance. Our understanding of hostparasite interactions has been limited, particularly in crusted scabies (CS), a severe clinical manifestation involving hyper-infestation of Sarcoptes scabiei mites. Susceptibility to CS may be associated with immunosuppressive conditions but CS has also been seen in cases with no identifiable risk factor or immune deficit. Due to ethical and logistical difficulties with undertaking research on clinical patients with CS, we adopted a porcine model which parallels human clinical manifestations. Transcriptomic analysis using microarrays was used to explore scabies pathogenesis, and to identify early events differentiating pigs with ordinary (OS) and crusted scabies. Pigs with OS (n = 4), CS (n = 4) and non-infested controls (n = 4) were compared at pre-infestation, weeks 1, 2, 4 and 8 post-infestation. In CS relative to OS, there were numerous differentially expressed genes including pro-inflammatory cytokines (IL17A, IL8, IL19, IL20 and OSM) and chemokines involved in immune cell activation and recruitment (CCL20, CCL27 and CXCL6). The influence of genes associated with immune regulation (CD274/PD-L1 and IL27), immune signalling (TLR2, TLR8) and antigen presentation (RFX5, HLA-5 and HLA-DOB) were highlighted in the early host response to CS. We observed similarities with gene expression profiles associated with psoriasis and atopic dermatitis and confirmed previous observations of Th2/17 pronounced responses in CS. This is the first comprehensive study describing transcriptional changes associated with the development of CS and significantly, the distinction between OS and CS. This provides a basis for clinical follow-up studies, potentially identifying new control strategies for this severely debilitating disease
    • MEASURING GHG EMISSIONS ACROSS THE AGRI-FOOD SECTOR VALUE CHAIN: THE DEVELOPMENT OF BIO - A BIO-ECONOMY INPUT-OUTPUT MODEL

      O’Donoghue, Cathal; Chyzheuskaya, Aksana; Grealis, Eoin; Finnegan, William; Goggin, Jamie; Hynes, Stephen; Kilcline, Kevin; Ryan, Mary; Science Foundation Ireland; Teagasc Walsh Fellowship Programme; et al. (INTERNATIONAL JOURNAL ON FOOD SYSTEM DYNAMICS, 2018)
      Sustainable intensification is one of the greatest challenges facing the agri-food sector which needs to produce more food to meet increasing global demand, while minimising negative environmental impacts such as agricultural greenhouse gas (GHG) emissions. Sustainable intensification relates not just to primary production, but also has wider value chain implications. An input-output model is a modelling framework which contains the flows across a value chain within a country. Input-output (IO) models have been disaggregated to have finer granular detail in relation to agricultural sub-sectoral value chains. National IO models with limited agricultural disaggregation have been developed to look at carbon footprints and within agriculture to look at the carbon footprint of specific value chains. In this paper we adapt an agriculturally disaggregated IO model to analyse the source of emissions in different components of agri-food value chains. We focus on Ireland, where emissions from agriculture comprise nearly 30% of national emissions and where there has been a major expansion and transformation in agriculture since the abolition of milk quota restrictions. In a substantial Annex to this paper, we describe the modelling assumptions made in developing this model. Breaking up the value chain into components, we find that most value is generated at the processing stage of the value chain, with greater processing value in more sophisticated value chains such as dairy processing. On the other hand, emissions are in general highest in primary production, albeit emissions from purchased animal feed being higher for poultry than for other value chains, given the lower direct emissions from poultry than from ruminants or sheep. The analysis highlights that emissions per unit of output are much higher for beef and sheep meat value chains than for pig and poultry meat value chains.
    • Developing a microsimulation model for farm forestry planting decisions

      Ryan, Mary; O’Donoghue, Cathal (International Microsimulation Association, 2018)
      There is increasing pressure in Europe to convert land from agriculture to forestry which would enable the sequestration of additional carbon, thereby mitigating agricultural greenhouse gas production. However, there is little or no information available on the drivers of the land use change decision from agriculture to forestry at individual farm level, which is complicated by the inter-temporal nature of the decision.This paper describes a static microsimulation approach which provides a better understanding of the life-cycle relativity of forestry and agricultural incomes, using Ireland as a casestudy. The microsimulation methodology allows for the generation of actual and counterfactual forest and agricultural income streams and for other attributes of utility such as long-term wealth and leisure, for the first time. These attributes are then modelled using purpose built forest models and farm microdata from a 30 year longitudinal dataset. The results show the importance of financial drivers but additionally show that wealth and leisure are also important factors in this inter-temporal land use change decision. By facilitating the examination of the distribution of farms across the farming population, the use of a static microsimulation approach allows us to make a considerable contribution to the literature in relation to the underlying drivers of farm afforestation behaviour. In the broader context of Climate Smart Agriculture and the Grand Challenges facing the intensification of agricultural production, these findings have implications for policies that seek to optimize natural resource use.
    • Current Trends in Proteomic Advances for Food Allergen Analysis

      López-Pedrouso, María; Lorenzo, José M.; Gagaoua, Mohammed; Franco, Daniel; Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo; Axencia Galega de Innovación, Xunta de Galicia, Spain; 119RT0568; IN607A2019/01 (MDPI AG, 2020-08-25)
      Food allergies are a global food challenge. For correct food labelling, the detection and quantification of allergens are necessary. However, novel product formulations and industrial processes produce new scenarios, which require much more technological developments. For this purpose, OMICS technologies, especially proteomics, seemed to be relevant in this context. This review summarises the current knowledge and studies that used proteomics to study food allergens. In the case of the allergenic proteins, a wide variety of isoforms, post-translational modifications and other structural changes during food processing can increase or decrease the allergenicity. Most of the plant-based food allergens are proteins with biological functions involved in storage, structure, and plant defence. The allergenicity of these proteins could be increased by the presence of heavy metals, air pollution, and pesticides. Targeted proteomics like selected/multiple reaction monitoring (SRM/MRM) have been very useful, especially in the case of gluten from wheat, rye and barley, and allergens from lentil, soy, and fruit. Conventional 1D and 2-DE immunoblotting have been further widely used. For animal-based food allergens, the widely used technologies are 1D and 2-DE immunoblotting followed by MALDI-TOF/TOF, and more recently LC-MS/MS, which is becoming useful to assess egg, fish, or milk allergens. The detection and quantification of allergenic proteins using mass spectrometry-based proteomics are promising and would contribute to greater accuracy, therefore improving consumer information.
    • Mitigation of greenhouse gas emissions from beef cattle production systems

      Samsonstuen, Stine; Åby, Bente A.; Crosson, Paul; Beauchemin, Karen A.; Aass, Laila; Norwegian University of Life Sciences (Informa UK Limited, 2020-08-27)
      The whole-farm model HolosNorBeef was used to estimate the efficiency of GHG emission mitigation strategies in Norwegian beef cattle herds. Various mitigation scenarios, involving female reproductive performance (i.e. calf mortality rate and the number of calves produced per cow per year), production efficiency of young bulls for slaughter (i.e. age at slaughter and carcass weight), and supplementation of an inhibitor currently reported as promising for enteric methane (CH4) inhibition (3-nitrooxypropanol; 3-NOP) was investigated in herds of British and Continental breeds. Reducing calf mortality and increasing the number of produced calves per cow per year both reduced emission intensities by 3% across breeds. Continental breeds showed greater potential of reducing emission intensities due to increased carcass production. Combining mitigation options in a best case scenario reduced the total emissions by 11.7% across breeds. The emission intensities could be further reduced by 8.3% with the use of 3-NOP.
    • Is there evidence for bacterial transfer via the placenta and any role in the colonization of the infant gut? – a systematic review

      Gil, Angel; Rueda, Ricardo; Ozanne, Susan E.; van der Beek, Eline M.; van Loo-Bouwman, Carolien; Schoemaker, Marieke; Marinello, Vittoria; Venema, Koen; Stanton, Catherine; Schelkle, Bettina; et al. (Taylor and Francis, 2020-08-05)
      With the important role of the gut microbiome in health and disease, it is crucial to understand key factors that establish the microbial community, including gut colonization during infancy. It has been suggested that the first bacterial exposure is via a placental microbiome. However, despite many publications, the robustness of the evidence for the placental microbiome and transfer of bacteria from the placenta to the infant gut is unclear and hence the concept disputed. Therefore, we conducted a systematic review of the evidence for the role of the placental, amniotic fluid and cord blood microbiome in healthy mothers in the colonization of the infant gut. Most of the papers which were fully assessed considered placental tissue, but some studied amniotic fluid or cord blood. Great variability in methodology was observed especially regarding sample storage conditions, DNA/RNA extraction, and microbiome characterization. No study clearly considered transfer of the normal placental microbiome to the infant gut. Moreover, some studies in the review and others published subsequently reported little evidence for a placental microbiome in comparison to negative controls. In conclusion, current data are limited and provide no conclusive evidence that there is a normal placental microbiome which has any role in colonization of infant gut.
    • Spatial evaluation and trade‐off analysis of soil functions through Bayesian networks

      Vrebos, Dirk; Jones, Arwyn; Lugato, Emanuele; O’Sullivan, Lillian; Schulte, Rogier; Staes, Jan; Meire, Patrick; European Union; 635201 (Wiley, 2020-08-23)
      There is increasing recognition that soils fulfil many functions for society. Each soil can deliver a range of functions, but some soils are more effective at some functions than others due to their intrinsic properties. In this study we mapped four different soil functions on agricultural lands across the European Union. For each soil function, indicators were developed to evaluate their performance. To calculate the indicators and assess the interdependencies between the soil functions, data from continental long‐term simulation with the DayCent model were used to build crop‐specific Bayesian networks. These Bayesian Networks were then used to calculate the soil functions' performance and trade‐offs between the soil functions under current conditions. For each soil function the maximum potential was estimated across the European Union and changes in trade‐offs were assessed. By deriving current and potential soil function delivery from Bayesian networks a better understanding is gained of how different soil functions and their interdependencies can differ depending on soil, climate and management. Highlights When increasing a soil function, how do trade‐offs affect the other functions under different conditions? Bayesian networks evaluate trade‐offs between soil functions and estimate their maximal delivery. Maximizing a soil function has varied effects on other functions depending on soil, climate and management. Differences in trade‐offs make some locations more suitable for increasing a soil function then others.