Now showing items 21-40 of 3620

    • Motivational Interviewing in Veterinary Practice

      Burrell, Alison; Gribben, Laura; Walsh Scholarship (Veterinary Ireland, 2023)
      Previous articles for the Veterinary Ireland Journal have outlined the critical role of the veterinary practitioner as an advocate for behavioural change in relation to antimicrobial resistance and herd health planning (Gribben and Burrell, 2023; Regan and Burrell, 2021). Within the realm of preventative veterinary medicine and herd health planning consults, evidence-based communication strategies which draw on psychological theory and practice have been shown to improve shared decision-making and collaboration between veterinary practitioners and their clients (Bard et al, 2022). In this article, we will describe the relational and technical components of motivational interviewing. The term ‘motivational interviewing’ (MI) might suggest images of someone standing on a stage with a handsfree microphone and an inspirational speech, something which it is not. In short, MI is a collaborative conversation style reflecting person-centred care and is used to elicit and strengthen a person’s own, intrinsic motivation to change. It is used by those working in a helping profession such as counsellors, social workers, doctors, teachers, physiotherapists, psychologists and probation officers. Miller and Rollnick (2013) give the example of a healthcare professional who is supporting a patient to respond to a chronic disease diagnosis. This patient’s future health, quality of life and indeed life expectancy may be determined by their behaviour and lifestyle. The kind of helping conversation that the healthcare professional might have with their patient in this situation can be described as being on a continuum of communication styles. On one side of this continuum is a ‘directing’ style of communication – the practitioner tells the patient what to do and how to do it and this requires adherence and compliance from the patient. On the other side of this communication continuum is ‘following’ – the practitioner merely seeks to understand and does not give any of their own views or advice at all. Motivational interviewing sits in between these two approaches, in a ‘guiding’ style of communication. Millner and Rollnick compare this ‘guiding’ style of communication to being a good tour guide – tourists neither want to be marched around a city being told exactly what to eat and where to go, nor do they want their tour guide to follow them around aimlessly. ‘Guiding’ involves actively listening and providing expertise when asked for. In the case of the healthcare professional and patient, this means exploring what a disease diagnosis means for that person and how they can realistically make the changes required, while incorporating the practitioner’s expertise and knowledge of the disease where needed.
    • Influence of a cattle access point on temporal changes in stream turbidity

      ONeill, M.; Briciu-Burghina, C.; Jennings, E.; Antunes, P.; Ó hUallacháin, D.; Kelly-Quinn, M.; O’Sullivan, M.; Regan, F.; Environmental Protection Agency (Compuscript, 2023)
      Unrestricted cattle access can have negative impacts on aquatic systems, including increases in stream water turbidity and suspended sediment levels. Many agri-environmental policies require the exclusion of livestock from waterbodies; however, data that quantify these impacts are scarce. This study used sensors measuring turbidity, a proxy for suspended sediment, together with motion-detecting cameras, to examine the influence of cattle in-stream activity on water quality in north-east Ireland. Two nephelometers, which automatically measured and logged turbidity, were placed upstream and downstream of a cattle access point in July 2017, while cameras were used to record cattle behaviour. A second deployment was made during February 2018 when cattle were absent. During low flows, frequent short-lived increases in turbidity were recorded at the downstream nephelometer only. These coincided with cattle accessing the water. There was a significant positive relationship between the longitudinal differences (downstream − upstream) in turbidity and the total number of cattle accessing the stream. There was no relationship between turbidity and stream discharge in July (when cattle were present), although that period was dominated by lower flow levels, with only 2 days in which discharge increased above baseflow. In contrast, there were no similar short-lived increases in turbidity in February 2018 when cattle were absent from the field, but there was a strong significant positive relationship between stream discharge and turbidity. These results highlight the consequences of cattle access for water column turbidity levels, particularly during periods of low streamflow, and therefore inform future agri-environmental policy in Ireland.
    • Willingness to consume insects among students in France and Ireland

      Ranga, L.; Vishnumurthy, P.; Dermiki, M.; Connacht-Ulster Alliance Bursary scheme (Compuscript, 2024-01-25)
      Acceptance of insect-containing foods remains low among European consumers. This study aims to explore the factors affecting willingness to consume insects among students in two European countries with different culinary traditions, namely France and Ireland. An online survey was developed and distributed in both countries, with 183 participants (France: n = 103; Ireland: n = 80) included in total. While more participants in France (43.7%) had a positive opinion of entomophagy compared to the ones in Ireland (21.3%), no significant difference was found in their willingness to consume insects for the first time. When given information on the approval of insects as a novel food in Europe, students in France were significantly more willing to consume insects than students in Ireland. For both groups, food neophobia and disgust were impediments to entomophagy. Moreover, males older than 30 yr enrolled in engineering courses, not following a specific diet, more concerned about the environment and health and less about familiarity, culture and religion were the most willing to consume insects. Participants in France and Ireland were more willing to consume insects if they were tasty or disguised (invisible) in another product and not if they were presented in their usual form (‘whole’). This case study shows that entomophagy acceptance is affected by the characteristics of the products, food neophobia, disgust and food choice motives of the consumers, while the impact of information on regulation is country dependent. These findings could be the starting point to guide the development of insect-containing foods acceptable to consumers in Europe.
    • Reassessing the warming impact of methane emissions from Irish livestock using GWP*: historical trends and sustainable futures

      McKenna, P.; Banwart, S. (Compuscript, 2024-01-20)
      Methane from livestock production contributes significantly to Ireland’s greenhouse gas emissions. Methane emissions are generally expressed as carbon dioxide equivalents (CO2e) using the global warming potential (GWP) metric, but this conversion may result in an inaccurate assessment, because methane has a much shorter atmospheric lifespan than CO2. This study calculated the CO2e of methane emissions from Irish livestock using the GWP and GWP* metrics, the latter of which accounts for the short-lived nature of atmospheric methane. Methane emissions from all Irish livestock (1961–2020) were included and three projected scenarios to 2050 were hypothesised: increasing emissions, decreasing emissions and constant emissions. The CO2e of methane from Irish livestock was found to be influenced by changes in the rate of emission over the preceding decades. Using the GWP* metric, declining populations of donkeys and horses from 1961 to 2000 were shown to cause atmospheric removals of methane when expressed as CO2e. Increasing populations of swine and non-dairy cattle (in response to industrial changes and European Union [EU] regulations) saw significant increases in the CO2e of methane emissions from these sources. Milk quotas caused a significant reduction in the CO2e of methane emissions from dairy cows, and atmospheric removals were observed in the years 1990–2012. GWP* indicated that the constant and decreasing future emission scenarios gave more significant reductions in CO2e than the GWP. These results indicate the importance of the effect of emission rate on the CO2e of methane from Irish livestock, which is accounted for using GWP*, but not by the conventional GWP.
    • Ammonia emission factors from cattle production systems in Ireland – a review

      Owusu-Twum, M. Y.; Kelleghan, D.; Gleasure, G.; Forrestal, P.; Lanigan, G. J.; Richards, K. G.; Krol, D. J.; DAFM; 2019R554 (Compuscript, 2024-01-19)
      Ammonia (NH3) emissions from livestock production contribute to environmental pollution. To address this challenge, the European Union (EU) National Emission Reduction Commitments Directive 2016/2284 (NECD) sets NH3 reduction targets for EU member states. In order to achieve these targets, several strategies have been evaluated under Irish conditions. A compilation of emission factors (EFs) from studies which evaluated these strategies is necessary to assess their effectiveness. This paper reports NH3 EFs from cattle production under Irish conditions. The results from the review show that the mean EFs from the deposition of dung, urine and urea applied to urine patches on grasslands were 4%, 9% and 8% total nitrogen (TN), respectively. EFs from the application of urea to urine patches were reduced by 28% after the addition of the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) to urea. The mean EF of 28% TN reported for urea fertiliser was almost 7 times higher than calcium ammonium nitrate (CAN). The inclusion of urease inhibitors with urea fertilisation on grassland led to EF reduction of up to 86%. The mean EFs from cattle houses, concrete yards, slurry storage pits and slurry landspreading were approximately 13%, 35%, 60% and 59% total ammoniacal nitrogen (TAN), respectively. The most effective NH3 abatement strategies for concrete yards and slurry storage were immediate cleaning of concrete floors (up to 89% reduction) after excreta deposition and the application of chemical amendments (sulphuric acid, acetic acid, alum and ferric chloride) to slurry in storage pits (up to 98% reduction), respectively. Low-emission spreading strategies and slurry acidification were effective at abating EFs after slurry application to land.
    • The effect of nitrogen and phosphorus fertiliser application rate and strategy on herbage production and nitrogen response in spring

      Walsh, S.; Bonnard, L.; Ruelle, E.; O’Donovan, M.; McKay, Z.C.; Egan, M. (Compuscript, Ltd., 2024-09-17)
      Maximising herbage yield while reducing nitrogen (N) fertiliser input, particularly in spring, is essential to ensure environmental and economic sustainability on grassland farms. A plot experiment was conducted over 2 yr, comparing three different spring N application rates of 30 (30N), 60 (60N) and 90 (90N) kg N/ha using three different spring application strategies: 0:100 (S1), 50:50 (S2) or a 33:66 (S3) split across February and March, respectively. Half of the plots also received phosphorus (P) fertiliser with the first application of N at a rate of 13 kg P/ha. Nitrogen fertiliser application for the remainder of the year (April–September) was the same for all plots (23 kg N/ha/application). Both spring and cumulative herbage yields were significantly affected (P < 0.05) by N application rate; 90N had the greatest spring and cumulative herbage yield compared to 30N and 60N (10,925, 9,834 and 10,499 kg DM/ha, respectively); however, N response reduced as N application rate increased. Nitrogen application strategy had a significant effect (P < 0.05) on spring herbage yield, with S1 significantly lower than S2 and S3. Applying 13 kg P/ha in spring increased herbage yield at defoliations 2 (23 April) and 3 (15 May) (+133 and 56 kg DM/ha, respectively), relative to no application of P fertiliser, as well as increasing cumulative herbage yield (+241 kg DM/ha). The results of the current study indicate that N should be applied in early February and the strategic application of N and P during spring can increase spring and cumulative herbage yield.
    • Estimating conservation value and natural capital value of land cover classes in the Irish National Land Cover Map and application to a case study area

      Ruas, S.; Finn, J.A.; Ó hUallacháin, D.; Carlier, J.; Doyle, M.; Moran, J.; Department of Agriculture, Food and the Marine; 2019R425 (Compuscript, Ltd., 2024-08-27)
      Conservation science and planning, by measuring proxies of biodiversity and ecosystem services provision, aim to identify priority areas for nature conservation and ecosystem services. In Ireland, fine-scale data on ecosystems functioning and biodiversity are limited, making it challenging to map conservation value (CV) and natural capital value (NCV) accurately. We elicited expert knowledge to rank habitat classes mapped in the recently published National Land Cover Map (NLCM) (EPA and Tailte Éireann, 2023). A scoring system from 0 to 10 was used to score habitats based on their estimated provision of biodiversity (CV) and ecosystem services (NCV). As a case study, we applied this scoring system to a catchment in the south-east of Ireland (>2,000 km2) with land cover information available from the draft NLCM. The expert elicitation showed little overall difference between the scores assigned by the team and the experts invited to validate the CV and NCV scores. However, some scores were revised based on experts’ contributions. Results of the mapping exercise indicated a high correlation between monads with high CV and high NCV scores. Future work should focus on differentiating the weighting assigned to each ecosystem service associated with each land cover class. This could result in changes in the overall NCV scores assigned to each habitat (and monads). Nevertheless, the approach developed here has the potential to identify areas in the landscape that should be targeted for conservation. For reproducibility, we provide the R code for analysis at polygon scale.
    • Exploring the presence of genotype-by-environment interactions between dairy cow herds milking once-a-day or twice-a-day for the entire lactation

      Berry, D.P.; Hilliard, B.; McCarthy, J.; Kennedy, E.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; Vistamilk; 16/RC/3835 (Compuscript, Ltd., 2024-07-05)
      The objective was to explore if the regression of phenotypic performance for six milk production traits on the respective estimate of genetic merit for that trait differed by herd milking frequency; variance components for each trait in the two milking frequency environments were also estimated as well as the genetic correlation between the same trait in both environments. The data used included 12,581 lactations from 5,456 cows in 32 spring-calving once-a-day (OAD) milking herds. Each OAD herd was matched with three contemporary twice-a-day (TAD)-milking herds; 35,823 lactations from 15,188 cows in 96 TAD herds were used. Mean yield was 20% (fat yield) to 31% (milk yield) lower in OAD herds. Milk protein concentration was 11% higher in OAD herds, while milk fat concentration was 16% higher in OAD herds. The mean back-transformed somatic cell score (SCS) was 100,390 cells/mL in OAD herds and 72,493 cells/mL in TAD herds. The association between each milk production trait and its respective estimate of genetic merit differed by herd milking frequency; the estimated regression coefficients were larger in TAD for just milk yield and SCS. The genetic correlation between the same trait in OAD versus TAD was all ≥0.73 with the exception of SCS (genetic correlation of 0.48) which suggests some re-ranking of sires between environments. In conclusion, differences in the scale of the genetic variance were evident for both milking frequencies and possible re-ranking was evident for SCS.
    • The first survey using high-throughput sequencing of cereal and barley yellow dwarf viruses in Irish spring and winter barley crops

      Byrne, S.; Schughart, M.; Ballandras, V.; Carolan, J.C.; Sheppard, L.; McNamara, L.; Teagasc Walsh Scholarships; 2021-A-374 (Compuscript, Ltd., 2024-06-25)
      Yellow dwarf viruses (YDVs) are the most economically important plant viruses impacting cereal production worldwide and include viruses from the genus Luteovirus (e.g., barely yellow dwarf virus (BYDV)-PAV, BYDV-PAS, BYDV-MAV, BYDV-kerII, BYDV-kerIII) and Polerovirus (e.g., cereal yellow dwarf virus (CYDV)-RPV, CYDV-RPS). Until now, much of our knowledge on YDVs infecting Irish barley crops (Hordeum vulgare L.) has come from serological assays; however, due to cross-reactivity it can be difficult to discriminate between viruses of different species. In this study, we have carried out a high-throughput sequencing survey of symptomatic crops, positive with serological assays, to identify YDVs infecting Irish spring and winter barley crops and establish reference genomes to support further development of molecular surveillance tools. In total, RNA was extracted from 45 symptomatic crop samples that were collected across Ireland over 2 yr and sequenced following rRNA depletion. Three samples of barley plants from BYDV-infected aphid colonies were also included. BYDV-MAV was identified in all field samples sequenced. This confirms previous evidence based on serological assays that BYDV-MAV is the dominant YDV in Irish barley crops. We have also identified BYDV-PAS in 29% of symptomatic field samples, the first report of this species in Ireland. In addition, BYDV-PAV was also found, and crop samples with mixed infections were common; although in mixed infections the greatest proportion of YDV reads originated from BYDV-MAV. Finally, CYDV-RPS, the more severe variant of CYDV-RPV belonging to the genus Polerovirus, was identified in a single sample. The complete genomes, assembled from this first sequence-based survey, will enable the development of molecular surveillance tools with greater virus specificity, to further support the Irish aphid and YDV monitoring network.
    • Influence of a cattle access point on temporal changes in stream turbidity

      ONeill, M.; Briciu-Burghina, C.; Jennings, E.; Antunes, P.; Ó hUallacháin, D.; Kelly-Quinn, M.; O’Sullivan, M.; Regan, F.; Environmental Protection Agency (Compuscript, 2023)
      Unrestricted cattle access can have negative impacts on aquatic systems, including increases in stream water turbidity and suspended sediment levels. Many agri-environmental policies require the exclusion of livestock from waterbodies; however, data that quantify these impacts are scarce. This study used sensors measuring turbidity, a proxy for suspended sediment, together with motion-detecting cameras, to examine the influence of cattle in-stream activity on water quality in north-east Ireland. Two nephelometers, which automatically measured and logged turbidity, were placed upstream and downstream of a cattle access point in July 2017, while cameras were used to record cattle behaviour. A second deployment was made during February 2018 when cattle were absent. During low flows, frequent short-lived increases in turbidity were recorded at the downstream nephelometer only. These coincided with cattle accessing the water. There was a significant positive relationship between the longitudinal differences (downstream − upstream) in turbidity and the total number of cattle accessing the stream. There was no relationship between turbidity and stream discharge in July (when cattle were present), although that period was dominated by lower flow levels, with only 2 days in which discharge increased above baseflow. In contrast, there were no similar short-lived increases in turbidity in February 2018 when cattle were absent from the field, but there was a strong significant positive relationship between stream discharge and turbidity. These results highlight the consequences of cattle access for water column turbidity levels, particularly during periods of low streamflow, and therefore inform future agri-environmental policy in Ireland.
    • The sensegiving role of advisors in farmer decision-making

      Hayden, M.T.; Mattimoe, R.; Jack, L.; Teagasc (Compuscript, 2023-11-24)
      In Ireland, and in several other countries around the world, a situation of economic vulnerability exists for many farmers. Alongside this economic vulnerability, the farm management literature acknowledges that most farmers spend little time on financial management. In this context, we argue that farm advisory services have the potential to add value to the farming community by assisting farmers to make informed financial decisions, to combat these economic challenges. In this study, the role of professional advisors in the strategic financial decisionmaking process of farmers is explored to develop an understanding of how farmers avail of advice from, and interact with, farm advisors. A qualitative research approach of 27 semi-structured interviews and a focus group is adopted to explore the strategic financial decision-making process of farmers. The application of sensemaking theory helps us understand how advisors provide a sensegiving role in the farmer’s decision-making process. The evidence gathered identifies numerous professional advice sources that provide this sensegiving role in the strategic financial decision-making process of farmers but contends that two sources, accountants and agricultural consultants, appear most prominent. This study also reveals that the use of specific advice sources is strongly influenced by the type of strategic decision undertaken and the farm type in operation. The results provide an opportunity for policymakers, and those who provide advisory services to farmers, to reflect on how best to create an environment where farmers and farm advisors can work together, to develop sustainable farm enterprises which can contribute to rural development.
    • Labour self-sufficiency on family dairy farms in Ireland: a case study approach considering labour requirement, input and management

      Gormley, M.; Deming, J.; Hogan, C.; O’Brien, B.; Beecher, Marion; Gormley, Martina; Dairy Research Ireland; MKLS0369 (Compuscript, 2023-10-28)
      The efficient use of labour input is essential to the success of farms; however, many countries are experiencing a decreasing family workforce on-farm as a result of perceived labour intensive work and poor work–life balance. Four farms identified from two labour time-use studies were selected as case studies to investigate management of the family dairy farm in terms of herd size, while also meeting the labour requirements and maintaining a satisfactory work–life balance. A mixed methods approach was used; quantitative analysis described the labour profile and characteristics of the farms, while the qualitative interviews provided insights into strategies to achieve labour efficiency. The results demonstrate that a family farm with a herd size of ∼120 cows with appropriate facilities and streamlined practices can operate effectively with a total labour input of 2,986 h/yr. The labour contributed by the farmer and the farm family represented 77.5% of the total annual labour requirement. Contractors or hired employees contributed the remaining labour input, depending on individual circumstances. The annual average working day length for the farmer (excluding breaks) was 7.8 h/d. The analysed narratives of the farmers demonstrated their view that a seasonal, pasture-based spring calving system of production is a key influence in achieving relatively high labour efficiency on-farm, if it is ensured that the peak workload in spring is managed effectively. The study highlights that the overall labour demand can be reduced on Irish family farms through the management of facilities and practices. The farmer and family members can then decide on the degree of self-sufficiency with regard to labour, that is, what proportion of that labour they wish to contribute based on their lifestyle choices, cost and availability of contractors and hired workers.
    • A note on the impact of CYP51 alterations and their combination in the wheat pathogen Zymoseptoria tritici on sensitivity to the azole fungicides epoxiconazole and metconazole

      Kildea, S.; Dooley, H.; Byrne, S.; Teagasc (Compuscript, 2023-10-12)
      Septoria tritici blotch caused by the fungal pathogen Zymoseptoria tritici is the most economically damaging disease of winter wheat in Ireland. As azoles have been intensively used, Z. tritici has developed different means of resisting their toxic effects with multiple alterations now reported in individual strains. Using previously characterised Irish collections of Z. tritici, the relationships between these different alterations have been examined using conditional inference trees and random forest. The results from this study highlight the importance of specific alterations I381V and S524T, with both contributing most to the reductions in epoxiconazole (EPZ) and metconazole (MTZ) sensitivity. As the azole class of fungicides is an extensive and diverse group, it is possible these alterations do not impact other azoles in a similar manner. Further analysis of these and contemporary collections to additional azoles, including mefentrifluconazole, which continues to provide good field control of Z. tritici, is warranted.
    • Utilising commercial farm grass growth data to evaluate long-term dry matter production of perennial ryegrass varieties

      Hearn, C.; Egan, M.; Lynch, M.B.; Tubritt, T.; O’Leary, M.; Geoghegan, A.; O’Donovan, M.; VistaMilk; 16/RC/3835 (Compuscript, 2023-07-08)
      Little data are currently available on either the dry matter (DM) production of perennial ryegrass (PRG) swards as they age beyond 5 yr (i.e. permanent pasture) or the performance of PRG varieties on commercial grassland farms. Previous work has generally assumed a connection between DM production and ground score (GS) and this link has been used as a proxy for variety persistence. The evolution of technology in the form of PastureBase Ireland has led to agronomic data of individual paddocks being made available for analysis over multiple years which has allowed the long-term assessment of varieties sown as monocultures on commercial farms. This technology allowed for the inclusion of eight PRG varieties sown in 649 paddocks across 101 farms in Ireland in the current analysis. The results show little association between GS and variety DM production as varieties age to 7 yr. Dry matter production of 1- to 4-yr-old swards appeared to provide a strong indication of variety DM production in years 5–7 post-sowing (r = 0.72, P < 0.05). The interaction of variety and sward age was not associated with DM production. Generally, varieties which produced the most DM in younger swards also produced the most DM in permanent pasture swards. Over longer-term periods these variety differences can manifest into large differences in DM produced and consumed on farm. The current analysis suggests that the long-term production benefits of utilising improved PRG varieties in pasture reseeding may be underestimated.
    • Genetic and phenotypic trends for carcass traits in Irish beef cattle

      Mulhall, S.A.; Sleator, R.D.; Evans, R.D.; Twomey, A.J.; Irish Department of Agriculture, Food and Marine; DAIRY4BEEF (Compuscript, 2023-07-08)
      Animals subjected to intensive genetic selection require continuous monitoring to observe changes in economically important traits. The focus of this research was to estimate genetic and phenotypic trends for carcass traits for three genotypes: dairy dam and dairy sire (D×D), dairy dam and beef sire (D×B) and beef dam and beef sire (B×B). Linear regression models were used to generate genetic and phenotypic trends for carcass weight, conformation and fat score for both cows and prime animals (i.e. never parented an animal). Phenotypic trends for age at slaughter were also estimated in prime animals. Results indicated that carcass weight increased genetically by 1.1 kg per year for B×B animals, but decreased by 0.14 and 0.39 kg per year for D×B and D×D animals, respectively. Phenotypic trends reflected the genetic trends for carcass weight for D×B and B×B animals, but the decline in genetic trends for carcass weight for D×D animals was not replicated in their phenotypic trends. Carcass conformation declined genetically by 0.02 and 0.05 units per year for D×D and D×B animals, respectively, and increased by 0.05 units per year for B×B animals. Phenotypic trends for conformation were similar to genetic trends. Carcass fat showed a decrease genetically for D×D and B×B, but remained constant for D×B animals, although this was not reflected in the phenotypic trends. Age at slaughter decreased phenotypically for all genotypes. Current breeding programmes have a favourable impact on carcass traits for B×B animals, but an unfavourable trend was observed for D×D and D×B animals.
    • Effect of enhanced plane of nutrition in early life on the transcriptome and proteome of the anterior pituitary gland in Angus heifer calves

      Keogh, Kate; Kelly, Alan K.; Kenny, David A. (2024-08-02)
      Abstract Background Enhanced nutrition during the early calfhood period has been shown to lead to earlier pubertal development in heifer calves. This is of interest as earlier pubertal onset can subsequently facilitate earlier calving which can economically benefit production systems. Reproductive development in heifers is regulated by the hypothalamic-pituitary-ovarian signalling pathway. In particular the anterior pituitary gland is central to reproductive development, through the dynamics of gonadotropic pulsatility. However, despite clear knowledge of the influence of enhanced dietary intake on subsequent reproductive development, the molecular control governing this response in the pituitary gland within the hypothalamic-pituitary-ovarian signalling axis in heifer calves is not fully understood. The objective of this study was to examine the effect of an enhanced plane of nutrition during early life on the anterior pituitary gland of heifer calves through both transcriptomic and proteomic analyses. Between 3 and 21 weeks of age, heifer calves were offered either a high (HI, n = 14) or moderate (MOD, n = 14) plane of nutrition, designed to elicit target growth rates of 1.2 and 0.5 kg/d for HI and MOD groups, respectively. All calves were euthanised at 21 weeks of age and anterior pituitary tissue harvested for subsequent use in global transcriptomic and proteomic analyses. Results Average daily gain was affected by diet (P < 0.001) and was 1.18 and 0.50 kg/day, for HI and MOD calves, respectively. RNAseq analysis resulted in the identification of 195 differentially expressed genes (Padj<0.05; fold change > 1.5), with 277 proteins identified as differentially abundant (Padj<0.05; fold change > 1.5) between contrasting dietary treatment groups. Biochemical pathway analysis of differentially affected genes and proteins revealed an enrichment for both growth hormone and GnRH signalling pathways (Padj.<0.05). Additionally, pathway analysis predicted an effect of enhanced dietary intake on endocrine function within the anterior pituitary gland as well as on reproductive system development and function (Padj.<0.05). Conclusions Results from this study show that an enhanced dietary intake during early calfhood affected the molecular control of the anterior pituitary gland in heifer calves in early life.
    • Transient Carbon Reserves in Barley: Malate, Sucrose and Starch Are the Main Players, Their Quantitative Involvement Being Light Intensity Dependant

      Barros, Kallyne A.; Esteves-Ferreira, Alberto A.; Inaba, Masami; Meally, Helena; Finnan, John; Barth, Susanne; Sulpice, Ronan; Department of Agriculture, Food and the Marine (DAFM); 233005/2014-5; 14/S/819 (Frontiers Media SA, 2020-03-06)
      Under natural environment plants experience different light intensities which can affect photosynthesis and consequently the availability of carbohydrates for daytime growth and their transient storage to supply night growth. We grew a spring barley cultivar, Propino, under three different light intensities under warm days and nights, and evaluated the spatial and diurnal adjustments occurring in the transient carbon stores. Leaves under high light at the end of the day accumulated mainly sucrose (30%) and malate (35%), with lower content of hexoses (5%), starch (15%) and fructans (15%). Under low light, plants presented reduced photosynthesis, with lower metabolite contents at end of day. The malate represented 51% of the total carbon accumulated at end of the day, at the expense of sucrose (12%), other metabolite contributions remaining similar to high light. The percentage of metabolites consumed at night was similar for all light intensities with around 75% of the sucrose and starch being mobilized whilst malate and fructans were only partially mobilized with 56 and 44%, respectively. Altogether, sucrose and malate were the main contributors of the total carbon used at night by barley plants, sucrose being predominant under high light (35% vs. 27%), but malate being the major metabolite used under low light with 40% of the total carbon consumed. Interestingly, light intensity also influenced the location of the C transient stores, the plants under low light prioritizing the accumulation of the metabolites, mostly malate, in the youngest tissues. Therefore, light influences quantitatively, but also qualitatively and spatially the carbon stores in the spring barley cv. Propino, suggesting a tight regulation of the primary metabolism.
    • Diverse Bacteriocins Produced by Strains From the Human Milk Microbiota

      Angelopoulou, Angeliki; Warda, Alicja K.; O’Connor, Paula M.; Stockdale, Stephen R.; Shkoporov, Andrey N.; Field, Des; Draper, Lorraine A.; Stanton, Catherine; Hill, Colin; Ross, R. Paul; et al. (Frontiers Media SA, 2020-05-19)
      Microbial colonization of the infant gut is a convoluted process dependent on numerous contributing factors, including age, mode of delivery and diet among others that has lifelong implication for human health. Breast milk also contains a microbiome which acts as a source of colonizing bacteria for the infant. Here, we demonstrate that human milk harbors a wide diversity of bacteriocin-producing strains with the potential to compete among the developing gut microbiota of the infant. We screened 37 human milk samples and found isolates with antimicrobial activity and distinct cross-immunity profiles. From these isolates, we detected 73 putative gene clusters for bacteriocins of all known sub-classes, including 16 novel prepeptides. More specifically, we detected two novel lantibiotics, four sactibiotics and three class IIa bacteriocins with an unusual modification of the pediocin box that is composed of YDNGI instead of the highly conserved motif YGNGV. Moreover, we identified a novel class IIb bacteriocin, four novel class IIc and two class IId bacteriocins. In conclusion, human milk contains a variety of bacteriocin-producing strains which may provide them a competitive advantage in the colonization of the infant gut and suggests that the milk microbiota is a source of antimicrobial potential.
    • Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics

      Alexa (Oniciuc), Elena A.; Walsh, Calum J.; Coughlan, Laura M.; Awad, Amal; Simon, Cezara A.; Ruiz, Lorena; Crispie, Fiona; Cotter, Paul D.; Alvarez-Ordóñez, Avelino; Science Foundation Ireland (SFI); et al. (American Society for Microbiology, 2020-02-18)
      Here, the role of the dairy-processing chain as a reservoir of antimicrobial resistance (AR) determinants and a source of novel biocontrol quorum-sensing inhibitors is assessed through a functional metagenomics approach. A metagenomic library comprising ∼22,000 recombinant clones was built from DNA isolated from raw milk, raw milk cheeses, and cheese-processing environment swab samples. The high-throughput sequencing of 9,216 recombinant clones showed that lactic acid bacteria (LAB) dominated the microbial communities of raw milk cheese, while Gram-negative microorganisms of animal or soil origin dominated the microbiota of raw milk and cheese-processing environments. Although functional screening of the metagenomic library did not recover potential quorum-sensing inhibitors, in silico analysis using an in-house database built specifically for this study identified homologues to several genes encoding proteins with predicted quorum-quenching activity, among which, the QsdH hydrolase was the most abundant. In silico screening of the library identified LAB, and especially Lactococcus lactis, as a relevant reservoir of AR determinants in cheese. Functional screening of the library allowed the isolation of 13 recombinant clones showing an increased resistance toward ampicillin, which in all cases was accompanied by a reduced susceptibility to a wide range of β-lactam antibiotics. This study shows that the dairy-processing environment is a rich reservoir of AR determinants, which vary by sample source, and suggests that combining next-generation sequencing with functional metagenomics can be of use in overcoming the limitations of both approaches. IMPORTANCE The study shows the potential of functional metagenomics analyses to uncover the diversity of functions in microbial communities prevailing in dairy products and their processing environments, evidencing that lactic acid bacteria (LAB) dominate the cheese microbiota, whereas Gram-negative microorganisms of animal or soil origin dominate the microbiota of milk and cheese-processing environments. The functional and in silico screening of the library allowed the identification of LAB, and especially Lactococcus lactis, as a relevant reservoir of antimicrobial resistance (AR) determinants in cheese. Quorum-quenching (QQ) determinants were not recovered through the execution of wet-lab function-based screenings but were detected through in silico sequencing-based analyses.
    • EUKARYOME: the rRNA gene reference database for identification of all eukaryotes

      Tedersoo, Leho; Hosseyni Moghaddam, Mahdieh S; Mikryukov, Vladimir; Hakimzadeh, Ali; Bahram, Mohammad; Nilsson, R Henrik; Yatsiuk, Iryna; Geisen, Stefan; Schwelm, Arne; Piwosz, Kasia; et al. (Oxford University Press (OUP), 2024-06-12)
      Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers—ITS1, ITS2, 18S V4–V5 and 28S D1–D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding—a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.