• A temporal assessment of nematode community structure and diversity in the rhizosphere of cisgenic Phytophthora infestans-resistant potatoes

      Ortiz, Vilma; Phelan, Sinead; Mullins, Ewen; European Union; KBBE.2011.3.5-01 (Biomed Central, 01/12/2016)
      Background Nematodes play a key role in soil processes with alterations in the nematode community structure having the potential to considerably influence ecosystem functioning. As a result fluctuations in nematode diversity and/or community structure can be gauged as a ‘barometer’ of a soil’s functional biodiversity. However, a deficit exists in regards to baseline knowledge and on the impact of specific GM crops on soil nematode populations and in particular in regard to the impact of GM potatoes on the diversity of nematode populations in the rhizosphere. The goal of this project was to begin to address this knowledge gap in regards to a GM potato line, cisgenically engineered for resistance to Phytophthora infestans (responsible organism of the Irish potato famine causing late blight disease). For this, a 3 year (2013, 2014, 2015) field experimental study was completed, containing two conventional genotypes (cvs. Desiree and Sarpo Mira) and a cisgenic genotype (cv. Desiree + Rpi-vnt1). Each potato genotype was treated with different disease management strategies (weekly chemical applications and corresponding no spray control). Hence affording the opportunity to investigate the temporal impact of potato genotype, disease management strategy (and their interaction) on the potato rhizosphere nematode community. Results Nematode structure and diversity were measured through established indices, accounts and taxonomy with factors recording a significant effect limited to the climatic conditions across the three seasons of the study and chemical applications associated with the selected disease management strategy. Based on the metrics studied, the cultivation of the cisgenic potato genotype exerted no significant effect (P > 0.05) on nematode community diversity or structure. The disease management treatments led to a reduction of specific trophic groups (e.g. Predacious c–p = 4), which of interest appeared to be counteracted by a potato genotype with vigorous growth phenotype e.g. cv. Sarpo Mira. The fluctuating climates led to disparate conditions, with enrichment conditions (bacterial feeding c–p = 1) dominating during the wet seasons of 2014 and 2015 versus the dry season of 2013 which induced an environmental stress (functional guild c–p = 2) on nematode communities. Conclusions Overall the functional guild indices in comparison to other indices or absolutes values, delivered the most accurate quantitative measurement with which to determine the occurrence of a specific disturbance relative to the cultivation of the studied cisgenic P. infestans-resistant potatoes.
    • Temporal patterns of inflammatory gene expression in local tissues after banding or burdizzo castration in cattle

      Pang, Wanyong; Earley, Bernadette; Sweeney, Torres; Gath, Vivian; Crowe, Mark A (Biomed Central, 2009-09-23)
      Background: Castration of male cattle has been shown to elicit inflammatory reactions and acute inflammation is initiated and sustained by the participation of cytokines. Methods: Sixty continental × beef bulls (Mean age 12 ± (s.e.) 0.2 months; Mean weight 341 ± (s.e.) 3.0 kg) were blocked by weight and randomly assigned to one of three treatments (n = 20 animals per treatment): 1) untreated control (Con); 2) banding castration at 0 min (Band); 3) Burdizzo castration at 0 min (Burd). Samples of the testis, epididymis and scrotal skin were collected surgically from 5 animals from each group at 12 h, 24 h, 7 d, and 14 d post-treatment, and analysed using real-time PCR. A repeated measurement analysis (Proc GLM) was performed using SAS. If there was no treatment and time interaction, main effects of treatment by time were tested by ANOVA. Results: Electrophoresis data showed that by 7 d post-castration RNA isolated from all the testicle samples of the Burd castrated animals, the epididymis and middle scrotum samples from Band castrates were degraded. Transitory effects were observed in the gene expression of IFN-γ, IL-6, IL-8 and TNF-α at 12 h and 24 h post treatment. Burd castrates had greater (P < 0.05) testicular IFN-γ mRNA levels compared with Band and Con animals, but lower (P < 0.05) testicular TNF-α mRNA levels compared with Con animals. Band castrates had greater (P < 0.05) testicular IL-6 mRNA levels than Burd castrates at 12 h post-castration. Burd castrates had greater (P < 0.05) testicular IL-8 mRNA levels than Band and Con animals at 24 h post-castration. In the epididymis, Burd castrates had greater (P < 0.05) IL-6 mRNA (both at 12 h and 24 h post treatment) and IL-8 mRNA (12 h post treatment) levels compared with Band and Con animals; Burd castrates had greater (P = 0.049) IL-10 mRNA levels than Band castrates at 12 h post-castration. Conclusion: Banding castration caused more inflammatory associated gene expression changes to the epididymis and scrotum than burdizzo. Burdizzo caused more severe acute inflammatory responses, in terms of pro-inflammatory cytokine gene expression, in the testis and epididymis than banding.
    • Temporal trends in reproductive performance in Irish dairy herds and associated risk factors

      Mee, John F (Biomed Central, 2004-03-01)
      Irish dairy herd fertility has been declining since the 1980s. The extent, nature and causes of this decline in fertility and the current status of Irish dairy herd fertility were described. An increase in calving interval of approximately one day per year has been recorded. The principal components of this trend have been an increased incidence of postpartum endocrinopathies, reduced expression of oestrus and a fall in conception rate. Both submission rate and calving-to-service interval have increased slightly over time. Significant risk factors associated with these trends have been strain substitution within the Holstein-Friesian breed and single trait selection for milk production. Critically, these changes have been reflected in loss of body condition. Contributory factors included increased herd size and possibly increased use of DIYAI. The most recent Irish study showed that 48% of cows conceived to first service and 14% of cows were not pregnant at the end of the industry-average 15-week spring breeding season. However, the top quartile of herds achieved a first-service conception rate of 59%, illustrating the wide variation between herds. These phenotypic trends were attributed to both genetic and environmental factors and their interactions. Recent Irish dairy herd fertility performance falls short of the targets set for seasonal compact calving.
    • The significance of the differences in soil phosphorus representation and transport procedures in the SWAT and HSPF models and a comparison of their performance in estimating phosphorus loss from an agriculture catchment in Ireland

      Nasr, Ahmed Elssidig; Bruen, Michael; Moles, Richard; Byrne, Paul; O'Regan, Bernadette (TWRI, 02/07/2012)
      Phosphorus transported from agriculture land has been identified as a major source of water pollution in a large number of Irish catchments. Models of this process are required in order to design and assess management measures. This paper reports on the comparison and assessment of two of the most promising physically-based distributed models, SWAT and HSPF, with particular emphasis on their suitability for Irish conditions. The representation of the overall soil phosphorus cycle is similar in both models but there is a significant difference in the level of detail in describing the chemical and biochemical processes in each model. Also there are differences in modeling the mechanisms by which phosphorus is removed from the soil column and either transported in dissolved form with the runoff water or in particulate form attached to eroded or detached sediment. These differences could have a significant influence on performance when using either of the models to simulate phosphorus loss from any catchment. Both models are applied to estimating the phosphorus concentration at the outlet of the Clarianna catchment in north Tiperrary (Ireland). This catchment is small (23km2) and the landuse is mainly pasture on grey brown podozilic soils. The results of model calibration are presented along with an assessment of the usefulness of the model outputs as a water quality management tool.
    • Transcriptome analysis of porcine M. semimembranosus divergent in intramuscular fat as a consequence of dietary protein restriction

      Hamill, Ruth M; Aslan, Ozlem; Mullen, Anne Maria; O'Doherty, John V.; McBryan, Jean; Morris, Dermot G.; Sweeney, Torres; Department of Agriculture, Food and the Marine, Ireland (Biomed Central, 06/07/2013)
      Background: Intramuscular fat (IMF) content is positively correlated with aspects of pork palatability, including flavour, juiciness and overall acceptability. The ratio of energy to protein in the finishing diet of growing pigs can impact on IMF content with consequences for pork quality. The objective of this study was to compare gene expression profiles of Musculus semimembranosus (SM) of animals divergent for IMF as a consequence of protein dietary restriction in an isocaloric diet. The animal model was derived through the imposition of low or high protein diets during the finisher stage in Duroc gilts. RNA was extracted from post mortem SM tissue, processed and hybridised to Affymetrix porcine GeneChip® arrays. Results: IMF content of SM muscle was increased on the low protein diet (3.60 ± 0.38% versus 1.92 ± 0.35%). Backfat depth was also greater in animals on the low protein diet, and average daily gain and feed conversion ratio were lower, but muscle depth, protein content and moisture content were not affected. A total of 542 annotated genes were differentially expressed (DE) between animals on low and high protein diets, with 351 down-regulated and 191 up-regulated on the low protein diet. Transcript differences were validated for a subset of DE genes by qPCR. Alterations in functions related to cell cycle, muscle growth, extracellular matrix organisation, collagen development, lipogenesis and lipolysis, were observed. Expression of adipokines including LEP, TNFα and HIF1α were increased and the hypoxic stress response was induced. Many of the identified transcriptomic responses have also been observed in genetic and fetal programming models of differential IMF accumulation, indicating they may be robust biological indicators of IMF content. Conclusion: An extensive perturbation of overall energy metabolism in muscle occurs in response to protein restriction. A low protein diet can modulate IMF content of the SM by altering gene pathways involved in lipid biosynthesis and degradation; however this nutritional challenge negatively impacts protein synthesis pathways, with potential consequences for growth.
    • Transcriptome sequencing of Festulolium accessions under salt stress

      Teshome, A.; Byrne, Stephen L.; Didion, T.; De Vega, J.; Jensen, C. S; Klaas, M.; Barth, Susanne; European Union; Marie Sklodowska-Curie Actions; FP7-KBBE-2011-5-289461; et al. (Biomed Central, 2019-05-31)
      Objectives The objective of this study was to establish transcriptome assemblies of Festulolium hybrids under salt stress, and identify genes regulated across the hybrids in response to salt stress. The development of transcriptome assemblies for Festulolium hybrids and cataloguing of genes regulated under salt stress will facilitate further downstream studies. Results Plants were grown at three salt concentrations (0.5%, 1% and 1.5%) and phenotypic and transcriptomic data was collected. Salt stress was confirmed by progressive loss of green leaves as salt concentration increased from 0 to 1.5%. We generated de-novo transcriptome assemblies for two Festulolium pabulare festucoid genotypes, for a single Festulolium braunii genotype, and a single F. pabulare loloid genotype. We also identified 1555 transcripts that were up regulated and 1264 transcripts that were down regulated in response to salt stress in the Festulolium hybrids. Some of the identified transcripts showed significant sequence similarity with genes known to be regulated during salt and other abiotic stresses.
    • Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

      O'Loughlin, Aran; Lynn, David J; McGee, Mark; Doyle, Sean; McCabe, Matthew; Earley, Bernadette; Teagasc Walsh Fellowship Programme (Biomed Central, 2012-06-18)
      Background: Weaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessation of the maternal-offspring bond and is often accompanied by housing. While much recent research has focused on the physiological response of the bovine immune system to stress in recent years, little is known about the molecular mechanisms modulating the immune response. Therefore, the objective of this study was to provide new insights into the molecular mechanisms underlying the physiological response to weaning at housing in beef calves using Illumina RNA-seq.Results: The leukocyte transcriptome was significantly altered for at least 7 days following either housing or weaning at housing. Analysis of differentially expressed genes revealed that four main pathways, cytokine signalling, transmembrane transport, haemostasis and G-protein-coupled receptor (GPRC) signalling were differentially regulated between control and weaned calves and underwent significant transcriptomic alterations in response to weaning stress on day 1, 2 and 7. Of particular note, chemokines, cytokines and integrins were consistently found to be up-regulated on each day following weaning. Evidence for alternative splicing of genes was also detected, indicating a number of genes involved in the innate and adaptive immune response may be alternatively transcribed, including those responsible for toll receptor cascades and T cell receptor signalling.Conclusions: This study represents the first application of RNA-Seq technology for genomic studies in bovine leukocytes in response to weaning stress. Weaning stress induces the activation of a number of cytokine, chemokine and integrin transcripts and may alter the immune system whereby the ability of a number of cells of the innate and adaptive immune system to locate and destroy pathogens is transcriptionally enhanced. Stress alters the homeostasis of the transcriptomic environment of leukocytes for at least 7 days following weaning, indicating long term effects of stress exposure in the bovine. The identification of gene signature networks that are stress activated provides a mechanistic framework to characterise the multifaceted nature of weaning stress adaptation in beef calves. Thus, capturing subtle transcriptomic changes provides insight into the molecular mechanisms that underlie the physiological response to weaning stress.
    • Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes

      Moran, Bruce; Cummins, Sean B; Creevey, Christopher J.; Butler, Stephen T. (Biomed Central, 2016-08-11)
      Background The transition between pregnancy and lactation is a major physiological change for dairy cows. Complex systemic and local processes involving regulation of energy balance, galactopoiesis, utilisation of body reserves, insulin resistance, resumption of oestrous cyclicity and involution of the uterus can affect animal productivity and hence farm profitability. Here we used an established Holstein dairy cow model of fertility that displayed genetic and phenotypic divergence in calving interval. Cows had similar genetic merit for milk production traits, but either very good genetic merit for fertility traits (‘Fert+’; n = 8) or very poor genetic merit for fertility traits (‘Fert-’; n = 8). We used RNA sequencing to investigate gene expression profiles in both liver and muscle tissue biopsies at three distinct time-points: late pregnancy, early lactation and mid lactation (-18, 1 and 147 days relative to parturition, respectively). Results We found 807 and 815 unique genes to be differentially expressed in at least one time-point in liver and muscle respectively, of which 79 % and 83 % were only found in a single time-point; 40 and 41 genes were found differentially expressed at every time-point indicating possible systemic or chronic dysregulation. Functional annotation of all differentially expressed genes highlighted two physiological processes that were impacted at every time-point in the study, These were immune and inflammation, and metabolic, lipid and carbohydrate-binding. Conclusion These pathways have previously been identified by other researchers. We show that several specific genes which are differentially regulated, including IGF-1, might impact dairy fertility. We postulate that an increased burden of reactive oxidation species, coupled with a chronic inflammatory state, might reduce dairy cow fertility in our model.
    • The two peptide lantibiotic lacticin 3147 acts synergistically with polymyxin to inhibit Gram negative bacteria

      Draper, Lorraine A.; Cotter, Paul D.; Hill, Colin; Ross, R Paul; Science Foundation Ireland; 10/IN.1/B3027 (Biomed Central, 26/09/2013)
      Background: The emergence of bacterial drug resistance encourages the re-evaluation of the potential of existing antimicrobials. Lantibiotics are post-translationally modified, ribosomally synthesised antimicrobial peptides with a broad spectrum antimicrobial activity. Here, we focussed on expanding the potential of lacticin 3147, one of the most studied lantibiotics and one which possesses potent activity against a wide range of Gram positive species including many nosocomial pathogens. More specifically, our aim was to investigate if lacticin 3147 activity could be enhanced when combined with a range of different clinical antibiotics. Results: Initial screening revealed that polymyxin B and polymyxin E (colistin) exhibited synergistic activity with lacticin 3147. Checkerboard assays were performed against a number of strains, including both Gram positive and Gram negative species. The resultant fractional inhibitory concentration (FIC) index values established that, while partial synergy was detected against Gram positive targets, synergy was obvious against Gram negative species, including Cronobacter and E. coli. Conclusions: Combining lacticin 3147 with low levels of a polymyxin could provide a means of broadening target specificity of the lantibiotic, while also reducing polymyxin use due to the lower concentrations required as a result of synergy.
    • Update on the development of a novel dry cow therapy using a bismuth-based intramammary teat seal in combination with the bacteriocin lacticin 3147

      Crispie, Fiona; Flynn, James; Ross, R Paul; Hill, Colin; Meaney, William J (Biomed Central, 2004-11-01)
      Public concerns over the widespread prophylactic use of antibiotics have led to a search for alternatives to dry cow therapy for the prevention of intramammary infections. A popular alternative is to infuse a teat seal at drying-off. The teat seal is a viscous non-antibiotic formulation and when it is infused into the teat canal and the teat sinus it forms an internal seal that provides a physical barrier to invasion by mastitis-causing pathogens. Enhancement of teat seal formulations may be achieved using non-antibiotic additives such as bacteriocins, potent proteins produced by some bacteria that have the ability to kill other microorganisms. This paper traces the history of investigations at Moorepark Research Centre into the efficacy of teat seal plus lacticin 3147, a bacteriocin produced by Lactococcus lactis DPC3147, in the prevention of intramammary infections in dry cows. Indications from on-going investigations are that a dry cow formulation combining the two products has considerable potential as a non-antibiotic prophylactic product.
    • Using the Biocheck.UGent™ scoring tool in Irish farrow-to-finish pig farms: assessing biosecurity and its relation to productive performance

      Rodrigues da Costa, Maria; Gasa, Josep; Calderón Díaz, Julia A; Postma, Merel; Dewulf, Jeroen; McCutcheon, Gerard; Manzanilla, Edgar G; Department of Agriculture Food and the Marine; 14/S/832 (Biomed Central, 2019-03-01)
      Background Biosecurity is one of the main factors affecting disease occurrence and antimicrobial use, and it is associated with performance in pig production. However, the importance of specific measures could vary depending on the (national) context. The aim of this study was to describe the biosecurity status in a cohort of Irish pig farms, to investigate which of those biosecurity aspects are more relevant by using the Biocheck.UGent™ scoring system, and to study the impact of such aspects on farm performance. Results External biosecurity score was high compared to most countries due to the characteristics of the Irish pig sector (i.e. purchasing only semen and breeding gilts on farm). The internal biosecurity score was lower and had greater variability among farms than other EU countries. Using multivariable linear regression, the biosecurity practices explained 8, 23, and 16% of variability in piglet mortality, finisher mortality, and average daily gain, respectively. Three clusters of farms were defined based on their biosecurity scores (0 to 100) using principal components and hierarchical clustering analysis. Scores for clusters 1, 2 and 3 were (mean ± SD) 38 ± 7.6, 61 ± 7.0 and 66 ± 9.8 for internal and 73 ± 5.1, 74 ± 5.3 and 86 ± 4.5 for external biosecurity. Cluster 3 had lower piglet mortality (P = 0.022) and higher average daily gain (P = 0.037) when compared to cluster 2. Conclusions Irish farms follow European tendencies with internal biosecurity posing as the biggest liability. Our results suggest that practices related to the environment and region, feed, water and equipment supply, and the management of the different stages, need to be addressed in lower performing farms to improve productive performance. Further studies on the economic impact of these biosecurity practices including complementary data on herd health, gilt rearing, piglet management, vaccination and feeding strategies are needed.
    • Using the EU-SILC to model the impact of the economic crisis on inequality

      O'Donoghue, Cathal; Loughrey, Jason; Morrissey, Karyn (Springer Open, 23/12/2013)
      In this paper we attempted to chart the impact of the early part of Ireland’s economic crisis from 2008–2009 on the distribution of income. In order to decompose the impact of changes in different income components, we utilised a microsimulation methodology and the EU-SILC User Database. This simulation based methodology involved the disaggregation of the 6 main benefit variables in the EU-SILC into 17 variables for our tax-benefit model. Validating, our results were positive, giving us confidence in our methodology. We utilised the framework to model changes in the level of income inequality from the period just before the crisis in 2004 to the depth of the worst year of the crisis in 2009. In terms of the impact of the economic crisis, we found that income inequality fell in the early part of the crisis modelled in this paper. Much of this change was due to rising inequality of market incomes, (even when discounting unemployment). This was due to the differential effect of the downturn on different sectors where some sectors such as the construction and public sectors were significantly hit, while the international traded sectors have been relatively immune from the downturn and have seen continued growth. The impact of the tax-benefit system has been to mitigate this upward pressure, with a gradual rise in the redistributive effect of the tax-benefit system driven by an increase in demand on the benefits side and increased progressivity on the tax side. Jel codes H22, H55, C15
    • Variation in sequences containing microsatellite motifs in the perennial biomass and forage grass, Phalaris arundinacea (Poaceae)

      Barth, Susanne; Jankowska, Marta J; Hodkinson, Trevor R; Vellani, Tia; Klaas, Manfred; European Union; KBBE-2011-5-289461). (Biomed Central, 22/03/2016)
      Forty three microsatellite markers were developed for further genetic characterisation of a forage and biomass grass crop, for which genomic resources are currently scarce. The microsatellite markers were developed from a normalized EST-SSR library. All of the 43 markers gave a clear banding pattern on 3 % Metaphor agarose gels. Eight selected SSR markers were tested in detail for polymorphism across eleven DNA samples of large geographic distribution across Europe. The new set of 43 SSR markers will help future research to characterise the genetic structure and diversity of Phalaris arundinacea, with a potential to further understand its invasive character in North American wetlands, as well as aid in breeding work for desired biomass and forage traits. P. arundinacea is particularly valued in the northern latitude as a crop with high biomass potential, even more so on marginal lands.
    • Veterinary dairy herd fertility service provision in seasonal and non-seasonal dairy industries - a comparison

      Mee, John F (Biomed Central, 2010-04-01)
      The decline in dairy herd fertility internationally has highlighted the limited impact of traditional veterinary approaches to bovine fertility management. Three questionnaire surveys were conducted at buiatrics conferences attended by veterinary practitioners on veterinary dairy herd fertility services (HFS) in countries with a seasonal (Ireland, 47 respondents) and non-seasonal breeding model (The Netherlands, 44 respondents and Portugal, 31 respondents). Of the 122 respondents, 73 (60%) provided a HFS and 49 (40%) did not. The majority (76%) of all practitioners who responded stated that bovine fertility had declined in their practice clients' herds with inadequate cow management, inadequate nutrition and increased milk yield as the most important putative causes. The type of clients who adopted a herd fertility service were deemed more educated than average (70% of respondents), and/or had fertility problems (58%) and/or large herds (53%). The main components of this service were routine postpartum examinations (95% of respondents), fertility records analysis (75%) and ultrasound pregnancy examinations (69%). The number of planned visits per annum varied between an average of four in Ireland, where breeding is seasonal, and 23 in Portugal, where breeding is year-round. The benefits to both the practitioner and their clients from running a HFS were cited as better fertility, financial rewards and job satisfaction. For practitioners who did not run a HFS the main reasons given were no client demand (55%) and lack of fertility records (33%). Better economic evidence to convince clients of the cost-benefit of such a service was seen as a major constraint to adoption of this service by 67% of practitioners.
    • Why do Irish pig farmers use medications? Barriers for effective reduction of antimicrobials in Irish pig production

      Diana, Alessia; Snijders, Sylvia; Rieple, Alison; Boyle, Laura A (Biomed Central, 2021-04-30)
      Abstract Background In addressing the threat of antimicrobial resistance, it is critical to understand the barriers to the uptake of strategies for the reduction of antimicrobial use (AMU) in the pig industry. In several EU countries, factors such as education level, habits and social pressures are recognised as affecting farmers’ decision-making process in relation to AMU. However, there is a lack of information on the Irish scenario. The aim of this study was to investigate pig farmers’ perspectives and their behaviour towards AMU to identify potential barriers to effectively reduce AMU in Irish pig production. We conducted face-to-face semi-structured interviews with 30 pig farmers, 5 pig veterinarians and 4 focus groups of pig farm personnel. We employed qualitative analyses to explore the objective of the study. Results Qualitative analysis revealed six convergent themes as potential barriers: perceptions about the need for AMU on farm, concept of animal welfare and associated management practices, legislation, culture, economics and standards of communication/type of advice-network. Overall, pig farmers believed that there is poor communication between stakeholders (i.e. farmers, vets and advisors) and a lack of reliable people to approach for advice. They considered themselves as operating responsibly in terms of AMU compared to their national and international colleagues and expressed the importance of a so-called ‘Irish solution’ to the problem of AMU because it was associated with what ‘has always been done’ and was therefore considered reliable and safe. Conclusions Barriers and challenges were in line with those identified in other EU countries highlighting similarities in behavioural and attitudinal patterns among pig farmers. Overall, farmers appeared to be more likely to rely on previous experiences or to wait for an imposed change (e.g. legislation) instead of taking personal action. Thus, considerable behavioural and attitudinal changes are needed to adopt a more responsible AMU in Irish pig production and to develop effective intervention strategies.