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.

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.

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.

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.

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.

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.

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.

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.

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.

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.