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Item A framework for assessing the potential for a double dividend from a policy-induced reduction in alcohol consumption on the economy(Elsevier, 2023-04-13) Sachdev, R.; Roy, G.; Allan, G.Objectives: Tax policies targeted at reducing alcohol consumption are typically understood to be associated with economic losses, including in alcohol production and trade sectors. This study sought to determine whether the overall effect of reduced alcohol consumption might be positive once improvements in productivity associated with reduced alcohol-related consumption are considered. Study design: This study used Computable General Equilibrium economic modelling. Methods: An economic modelling framework was developed for Scotland, which considered the fiscal and economic impacts of alcohol taxation and the economy-wide impacts. Simulation of hypothetical alcohol taxes and improvements in labour productivity calibrated on losses due to absenteeism and presenteeism in Scotland in 2017. Results: The long-run impacts of a five pence increase in taxation alone produce negative economic impacts on jobs and Gross Domestic Product in Scotland (1189 jobs and £71.12 million). These effects are reduced by half e but remain negative e when the revenues from such policy are recycled to the economy through government spending. A small improvement in labour productivity e equivalent to 4.95% of the total productivity gap from absenteeism and presenteeism estimated for Scotland e would be sufficient to turn the economic consequence non-negative. Conclusions: The overall macroeconomic impact of policies targeted at alcohol consumption should include consideration of the potential productivity effect and that impact studies that do not include such mechanisms are likely to overstate the negative economic impacts of alcohol policies.Item A molecular assessment of Ostertagia leptospicularis and Spiculopteragia asymmetrica among wild fallow deer in Northern Ireland and implications for false detection of livestock-associated species(BMC, 2024-03-18) Lyons, Maggie; Brown, Tony L.; Lahuerta-Marin, Angela; Morgan, Eric. R.; Airs, Paul M.; Animal Health and WelfareBackground Wild deer populations utilizing livestock grazing areas risk cross-species transmission of gastrointestinal nematode parasites (GINs), including GINs with anthelmintic resistance (AR) traits. Wild deer have been shown to carry problematic GIN species such as Haemonchus contortus and Trichostrongylus species in the UK, but the presence of livestock GINs in Northern Ireland deer populations is unknown. Also, is it not known whether AR traits exist among GINs of deer such as Ostertagia leptospicularis and Spiculopteragia asymmetrica in pastureland where anthelmintics are heavily used. Methods Adult-stage GIN samples were retrieved from Northern Irish wild fallow deer abomasa. Individual specimens were subject to a species-specific PCR analysis for common sheep and cattle GIN species with ITS-2 sequence analysis to validate species identities. In addition, the beta-tubulin gene was subject to sequencing to identify benzimidazole (BZ) resistance markers. Results ITS-2 sequencing revealed O. leptospicularis and S. asymmetrica, but species-specific PCR yielded false-positive hits for H. contortus, Teladorsagia circimcincta, Trichostrongylus axei, T. colubriformis, T. vitrinus and Ostertagia ostertagi. For beta-tubulin, O. leptospicularis and S. asymmetrica yielded species-specific sequences at the E198 codon, but no resistance markers were identified in either species at positions 167, 198 or 200 of the coding region. Discussion From this report, no GIN species of significance in livestock were identified among Northern Ireland fallow deer. However, false-positive PCR hits for sheep and cattle-associated GINs is concerning as the presence of deer species in livestock areas could impact both deer and livestock diagnostics and lead to overestimation of both GIN burden in deer and the role as of deer as drivers of these pathogens. ITS-2 sequences from both O. leptospicularis and S. asymmetrica show minor sequence variations to geographically distinct isolates. AR has been noted among GINs of deer but molecular analyses are lacking for GINs of wildlife. In producing the first beta-tubulin sequences for both O. leptospicularis and S. asymmetrica, we report no BZ resistance in this cohort. Conclusions This work contributes to genetic resources for wildlife species and considers the implications of such species when performing livestock GIN diagnostics.Item A Review of UK-Registered and Candidate Vaccines for Bovine Respiratory Disease(MDPI, 2021-11-27) Lemon, Joanne; McMenamy, Michael; Animal Health and WelfareVaccination is widely regarded as a cornerstone in animal or herd health and infectious disease management. Nineteen vaccines against the major pathogens implicated in bovine respiratory disease are registered for use in the UK by the Veterinary Medicines Directorate (VMD). However, despite annual prophylactic vaccination, bovine respiratory disease is still conservatively estimated to cost the UK economy approximately £80 million per annum. This review examines the vaccine types available, discusses the surrounding literature and scientific rationale of the limitations and assesses the potential of novel vaccine technologies.Item Allonursing in Wild and Farm Animals: Biological and Physiological Foundations and Explanatory Hypotheses(MDPI, 2021-10-29) Mota-Rojas, Daniel; Marcet-Rius, Míriam; Freitas-de-Melo, Aline; Muns, Ramon; Mora-Medina, Patricia; Domínguez-Oliva, Adriana; Orihuela, AgustínThe dams of gregarious animals must develop a close bond with their newborns to provide them with maternal care, including protection against predators, immunological transference, and nutrition. Even though lactation demands high energy expenditures, behaviors known as allonursing (the nursing of non-descendant infants) and allosuckling (suckling from any female other than the mother) have been reported in various species of wild or domestic, and terrestrial or aquatic animals. These behaviors seem to be elements of a multifactorial strategy, since reports suggest that they depend on the following: species, living conditions, social stability, and kinship relations, among other group factors. Despite their potential benefits, allonursing and allosuckling can place the health and welfare of both non-filial dams and alien offspring at risk, as it augments the probability of pathogen transmission. This review aims to analyze the biological and physiological foundations and bioenergetic costs of these behaviors, analyzing the individual and collective advantages and disadvantages for the dams’ own offspring(s) and alien neonate(s). We also include information on the animal species in which these behaviors occur and their implications on animal welfare.Item An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance(Wiley, 2018-01-24) Tsairidou, S.; Allen, Adrian; Pong-Wong, R.; McBride, S.H.; Wright, D.M.; Matika, O.; Pooley, C.M.; McDowell, Stanley W.J.; Glass, E.J.; Skuce, Robin A.; Bishop, S.C.; Woolliams, J.A.Genetic selection of cattle more resistant to bovine tuberculosis (bTB) may offer a complementary control strategy. Hypothesising underlying non-additive genetic variation, we present an approach using genome-wide high density markers to identify genomic loci with dominance effects on bTB resistance and to test previously published regions with heterozygote advantage in bTB. Our data comprised 1151 Holstein–Friesian cows from Northern Ireland, confirmed bTB cases and controls, genotyped with the 700K Illumina BeadChip. Genome-wide markers were tested for associations between heterozygosity and bTB status using marker-based relationships. Results were tested for robustness against genetic structure, and the genotypic frequencies of a significant locus were tested for departures from Hardy-Weinberg equilibrium. Genomic regions identified in our study and in previous publications were tested for dominance effects. Genotypic effects were estimated through ASReml mixed models. A SNP (rs43032684) on chromosome 6 was significant at the chromosome-wide level, explaining 1.7% of the phenotypic variance. In the controls, there were fewer heterozygotes for rs43032684 (P < 0.01) with the genotypic values suggesting that heterozygosity confers a heterozygote disadvantage. The region surrounding rs43032684 had a significant dominance effect (P < 0.01). SNP rs43032684 resides within a pseudogene with a parental gene involved in macrophage response to infection and within a copy-number-variation region previously associated with nematode resistance. No dominance effect was found for the region on chromosome 11, as indicated by a previous candidate region bTB study. These findings require further validation with large-scale data.Item Analysis of SARS-CoV-2 antibody seroprevalence in Northern Ireland during 2020–2021(Elsevier, 2024-01-10) Greene, Michelle K.; Smyth, Peter; English, Andrew; McLaughlin, Joseph; Bucholc, Magda; Bailie, Janice; McCarroll, Julie; McDonnell, Margaret; Watt, Alison; Barnes, George; Lynch, Mark; Duffin, Kevan; Duffy, Gerard; Lewis, Claire; James, Jacqueline A.; Stitt, Alan W.; Ford, Tom; O’Kane, Maurice; Rai, Taranjit Singh; Bjourson, Anthony J.; Cardwell, Christopher; Elborn, J Stuart; Gibson, David S.; Scott, Christopher J.; Animal Health and WelfareBackground With the spread of SARS-CoV-2 impacting upon public health directly and socioeconomically, further information was required to inform policy decisions designed to limit virus spread during the pandemic. This study sought to contribute to serosurveillance work within Northern Ireland to track SARS-CoV-2 progression and guide health strategy. Methods Sera/plasma samples from clinical biochemistry laboratories were analysed for anti-SARS-CoV-2 antibodies. Samples were assessed using an Elecsys anti-SARS-CoV-2 or anti-SARS-CoV-2 S ECLIA (Roche) on an automated cobas e 801 analyser. Samples were also assessed via an anti-SARS-CoV-2 ELISA (Euroimmun). A subset of samples assessed via the Elecsys anti-SARS-CoV-2 ECLIA were subsequently analysed in an ACE2 pseudoneutralisation assay using a V-PLEX SARS-CoV-2 Panel 7 for IgG and ACE2 (Meso Scale Diagnostics). Results Across three testing rounds (June–July 2020, November–December 2020 and June–July 2021 (rounds 1–3 respectively)), 4844 residual sera/plasma specimens were assayed for anti-SARS-CoV-2 antibodies. Seropositivity rates increased across the study, peaking at 11.6 % (95 % CI 10.4 %–13.0 %) during round 3. Varying trends in SARS-CoV-2 seropositivity were noted based on demographic factors. For instance, highest rates of seropositivity shifted from older to younger demographics across the study period. In round 3, Alpha (B.1.1.7) variant neutralising antibodies were most frequently detected across age groups, with median concentration of anti-spike protein antibodies elevated in 50–69 year olds and anti-S1 RBD antibodies elevated in 70+ year olds, relative to other age groups. Conclusions With seropositivity rates of <15 % across the assessment period, it can be concluded that the significant proportion of the Northern Ireland population had not yet naturally contracted the virus by mid-2021.Item Anti-Campylobacter Probiotics: Latest Mechanistic Insights(Mary Ann Liebert, 2022-07-29) Balta, Igori; Butucel, Eugenia; Stef, Lavinia; Pet, Ioan; Gradisteanu-Pircalabioru, Gratiela; Chifiriuc, Carmen; Gundogdu, Ozan; McCleery, David; Corcionivoschi, NicolaeThe Campylobacter genus is the leading cause of human gastroenteritis, with the consumption of contaminated poultry meat as the main route of infection. Probiotic bacteria, such as Lactobacillus, Bacillus, Escherichia coli Nissle, and Bifidobacterium species, have a great immunomodulatory capacity and exhibit antipathogenic effects through various molecular mechanisms. Reducing Campylobacter levels in livestock animals, such as poultry, will have a substantial benefit to humans as it will reduce disease transmissibility through the food chain. Moreover, probiotic-based strategies might attenuate intestinal inflammatory processes, which consequently reduce the severity of Campylobacter disease progression. At a molecular level, probiotics can also negatively impact on the functionality of various Campylobacter virulence and survival factors (e.g., adhesion, invasion), and on the associated colonization proteins involved in epithelial translocation. The current review describes recent in vitro, in vivo, and preclinical findings on probiotic therapies, aiming to reduce Campylobacter counts in poultry and reduce the pathogen’s virulence in the avian and human host. Moreover, we focused in particular on probiotics with known anti-Campylobacter activity seeking to understand the biological mechanisms involved in their mode of action.Item Antimicrobial Properties of Basidiomycota Macrofungi to Mycobacterium abscessus Isolated from Patients with Cystic Fibrosis(Wolters Kluwer - Medknow, 2019-03-12) Millar, Beverley Cherie; Nelson, David W. V. A.; Moore, Rachel E.; Rao, Juluri R.; Moore, John E.Background: Antimicrobial resistance (AMR) has now emerged as a global public health crisis. Of particular concern is AMR associated with the genus Mycobacterium, including Mycobacterium tuberculosis and the nontuberculous mycobacteria (NTM). Emergence of the NTM, in particular Mycobacterium abscessus, in patients with cystic fibrosis (CF) represents both a diagnostic and a treatment dilemma. Such resistance drives the need to investigate novel sources of antimicrobials. Medicinal fungi have a well‑documented history of use in traditional oriental therapies. Not only is this an ancient practice, but also still today, medical practice in Japan, China, Korea, and other Asian countries continue to rely on fungal‑derived antibiotics. A study was, therefore, undertaken to examine the antimicrobial activity of 23 native macrofungal (mushrooms/ toadstools) taxa, collected from woodlands in Northern Ireland against six clinical (CF) isolates of M. abscessus, as well as M. abscessus National Collection of Type Cultures (NCTC) Reference strain (NCTC 13031). Methods: Free‑growing saprophytic and mycorrhizal macrofungi (n = 23) belonging to the phylum Basidiomycota were collected and were definitively identified employing Polymerase Chain reaction/ITS DNA sequencing. Macrofungal tissues were freeze‑dried and reconstituted before employment in antibiotic susceptibility studies. Results: All macrofungi examined showed varying inhibition of the M. abscessus isolates examined with the exception Russula nigricans. The macrofungi displaying maximum antimycobacterial activity against the clinical isolates were (in descending order) M. giganteus (33.6 mg/ml), Hygrocybe nigrescens (38.5 mg/ml) and Hypholoma fasciculare (25.3 mg/ml). Conclusion: Macrofungi may represent a source of novel antimicrobials against M. abscessus, which have not yet been fully explored nor exploited clinically. This is the first report describing the antimycobacterial properties of extracts of M. giganteus against M. abscessus. Further work is now required to identify the constituents and mode of the inhibitory action of these macrofungi against the M. abscessus. Given the gravity of AMR in the NTMs, particularly M. abscessus and the clinical treatment dilemmas that such AMR present, antibiotic drug discovery efforts should now focus on investigating and developing antibacterial compounds from macrofungi, particularly M. giganteus, where there are no or limited current treatment options.Item Antimicrobial resistance (AMR): significance to food quality and safety(Oxford University Press, 2019-04-09) Nelson, David W. V. A.; Moore, John E.; Rao, Juluri R.Antibiotic resistance presents a significant challenge to clinical, veterinary, and plant health and is now recognized by the World Health Organization (WHO) as a major emerging problem of global significance. As yet, there have been no successful discoveries of classes of novel antibiotics since 1987. There is an antibiotic discovery void, and it is now widely acknowledged that there is an urgent need for the development of novel antimicrobial agents. For economic reasons, many of the largest pharmaceutical companies have abandoned the antibiotic field, and research conducted by academia was scaled back due to funding cuts following the economic crisis. A post-antibiotic era— in which common infections and minor injuries can kill—far from being an apocalyptic fantasy, is indeed a very real possibility for the 21st century.Item The Antioxidant Effect of Natural Antimicrobials in Shrimp Primary Intestinal Cells Infected with Nematopsis messor(MDPI, 2022-05-15) Balta, Igori; Stef, Lavinia; Butucel, Eugenia; Pircalabioru, Gratiela Gradisteanu; Venig, Adelina; Ward, Patrick; Deshaies, Myriam; Pet, Ioan; Stef, Ducu; Koyun, Osman Y.; Callaway, Todd R.; Gundogdu, Ozan; Corcionivoschi, NicolaeNematopsis messor infections severely impact on shrimp’s health with devastating economic consequences on shrimp farming. In a shrimp primary intestinal cells (SGP) model of infection, a sub-inhibitory concentration (0.5%) of natural antimicrobials (Aq) was able to reduce the ability of N. messor to infect (p < 0.0001). To prevent N. messor infection of SGP cells, Aq inhibits host actin polymerization and restores tight junction integrity (TEER) and the expression of Zo-1 and occluding. The oxidative burst, caused by N. messor infection, is attenuated by Aq through the inhibition of NADPH-produced H2O2. Simultaneous to the reduction in H2O2 released, the activity of catalase (CAT) and superoxide dismutase (SOD) were also significantly increase (p < 0.0001). The antimicrobial mixture inactivates the ERK signal transduction pathway by tyrosine dephosphorylation and reduces the expression of DCR2, ALF-A, and ALF-C antimicrobial peptides. The observed in vitro results were also translated in vivo, whereby the use of a shrimp challenge test, we show that in N. messor infected shrimp the mortality rate was 68% compared to the Aq-treated group where the mortality rate was maintained at 14%. The significant increase in CAT and SOD activity in treated and infected shrimp suggested an in vivo antioxidant role for Aq. In conclusion, our study shows that Aq can efficiently reduce N. messor colonization of shrimp’s intestinal cells in vitro and in vivo and the oxidative induced cellular damage, repairs epithelial integrity, and enhances gut immunityItem Antiviral activity of a novel mixture of natural antimicrobials, in vitro, and in a chicken infection model in vivo(Springer Nature, 2020-10-06) Balta, Igori; Stef, Lavinia; Pet, Ioan; Ward, Patrick; Callaway, Todd; Ricke, Steven C.; Gundogdu, Ozan; Corcionivoschi, Nicolae; Animal Health and WelfareThe aim of this study was to test in vitro the ability of a mixture of citrus extract, maltodextrin, sodium chloride, lactic acid and citric acid (AuraShield L) to inhibit the virulence of infectious bronchitis, Newcastle disease, avian influenza, porcine reproductive and respiratory syndrome (PRRS) and bovine coronavirus viruses. Secondly, in vivo, we have investigated its efficacy against infectious bronchitis using a broiler infection model. In vitro, these antimicrobials had expressed antiviral activity against all five viruses through all phases of the infection process of the host cells. In vivo, the antimicrobial mixture reduced the virus load in the tracheal and lung tissue and significantly reduced the clinical signs of infection and the mortality rate in the experimental group E2 receiving AuraShield L. All these effects were accompanied by a significant reduction in the levels of pro-inflammatory cytokines and an increase in IgA levels and short chain fatty acids (SCFAs) in both trachea and lungs. Our study demonstrated that mixtures of natural antimicrobials, such AuraShield L, can prevent in vitro viral infection of cell cultures. Secondly, in vivo, the efficiency of vaccination was improved by preventing secondary viral infections through a mechanism involving significant increases in SCFA production and increased IgA levels. As a consequence the clinical signs of secondary infections were significantly reduced resulting in recovered production performance and lower mortality rates in the experimental group E2.Item Ash Dieback and Other Pests and Pathogens of Fraxinus on the Island of Ireland(Royal Irish Academy, 2022-10-06) Soldi, Erika; Tiley, Anna; O'Hanlon, Richard; Murphy, Brian R.; Hodkinson, Trevor R.; Grassland and Plant ScienceThe common ash (Fraxinus excelsior) is one of the most important native tree species in Ireland but is threatened by the spread of ash dieback (also known as Chalara disease). The disease is caused by the fungal pathogen Hymenoscyphus fraxineus, which is decimating ash in Europe. The first part of this review summarises the scientific discoveries on H. fraxineus, focusing on its origin and infection cycle as well as its impact on Irish forestry. In addition to directly damaging ash, the action of H. fraxineus makes ash trees more vulnerable to attack by other opportunistic secondary pathogens, which accelerate their death. Ireland, as an island, has a natural barrier which slows the spread of pathogens compared to many other countries in the European mainland, but the threat of further pathogen introduction remains real and likely. The second part of this review focuses on the spread of other pathogens of ash, and on their incidence and importance in Ireland.Item Assessing the impact of a test and vaccinate or remove badger intervention project on bovine tuberculosis levels in cattle herds(Cambridge University Press, 2023-07-04) Doyle, Liam Patrick; Gordon, Alan W.; Molloy, Colm; O’Hagan, Maria J. H.; Georgaki, Anastasia; Courcier, Emily A.; Harwood, Roly G.; Menzies, Fraser Duncan; Animal Health and WelfareBovine tuberculosis (bTB) is a chronic, zoonotic infection of domestic and wild animals caused mainly by Mycobacterium bovis. The Test and Vaccinate or Remove (TVR) project was a 5-year intervention (2014–2018) applied to Eurasian badgers (Meles meles) in a 100 km2 area of County Down, Northern Ireland. This observational study used routine bTB surveillance data of cattle to determine if the TVR intervention had any effect in reducing the infection at a herd level. The study design included the TVR treatment area (Banbridge) compared to the three adjacent 100 km2 areas (Dromore, Ballynahinch, and Castlewellan) which did not receive any badger intervention. Results showed that there were statistically lower bTB herd incidence rate ratios in the Banbridge TVR area compared to two of the other three comparison areas, but with bTB herd history and number of bTB infected cattle being the main explanatory variables along with Year. This finding is consistent with other study results conducted as part of the TVR project that suggested that the main transmission route for bTB in the area was cattle-to-cattle spread. This potentially makes any wildlife intervention in the TVR area of less relevance to bTB levels in cattle. It must also be noted that the scientific power of the TVR study (76%) was below the recommended 80%, meaning that results must be interpreted with caution. Even though statistical significance was achieved in two cattle-related risk factors, other potential risk factors may have also demonstrated significance in a larger study.Item Assessing the impact of participatory extension programme membership on farm business performance in Northern Ireland.(MDPI, 2021-09-30) Adenuga, Adewale; Jack, Claire G.; Ashfield, Austen; Wallace, MichaelThis paper evaluates the impact of membership of the Business Development Groups (BDG), a participatory extension programme in Northern Ireland on the economic performance of participating farmers for dairy and sheep enterprise groups. The study employs the conditional difference-in-differences approach which combines a non-parametric matching estimator with a difference-in-differences analytical technique to obtain a credible best-estimates of the causal effect of BDG membership on farmers’ economic performance assuming that BDG participation is as good as random after controlling for observable farm characteristics and that the parallel trends assumption holds between BDG participants and non-participants. The results of the analyses showed that membership in the BDG programme has a statistically significant impact on the economic performance of participating farmers. Specifically, the results showed that farmers who are members of the dairy and sheep BDGs increased their gross margin by £109.10 and £17.10 per head respectively compared to farmers that are non-members of the BDGs. The results of the study provide robust evidence to inform policy development around the area of participatory extension programmes. It also supports the design of efficient agricultural education and extension systems that incorporates the ideas of the farmers themselves through peer-to-peer learning thereby maximising the economic and social benefits accruable from such programmes.Item Assessment and Validation of Globodera pallida as a Novel In Vivo Model for Studying Alzheimer’s Disease(MDPI, 2021-09-19) Althobaiti, Norah A.; Menaa, Farid; Albalawi, Aishah E.; Dalzell, Johnathan; Warnock, Neil; McCammick, Erin M.; Alsolais, Abdulellah; Alkhaibari, Abeer M.; Green, Brian D.Background: Whole transgenic or non-transgenic organism model systems allow the screening of pharmacological compounds for protective actions in Alzheimer’s disease (AD). Aim: In this study, a plant parasitic nematode, Globodera pallida, which assimilates intact peptides from the external environment, was investigated as a new potential non-transgenic model system of AD. Methods: Fresh second-stage juveniles of G. pallida were used to measure their chemosensory, perform immunocytochemistry on their neurological structures, evaluate their survival rate, measure reactive oxygen species, and determine total oxidized glutathione to reduced glutathione ratio (GSSG/GSH) levels, before and after treatment with 100 µM of various amyloid beta (Aβ) peptides (1–40, 1–42, 17–42, 17–40, 1–28, or 1–16). Wild-type N2 C. elegans (strain N2) was cultured on Nematode Growth Medium and directly used, as control, for chemosensory assays. Results: We demonstrated that: (i) G. pallida (unlike Caenorhabditis elegans) assimilates amyloid-β (Aβ) peptides which co-localise with its neurological structures; (ii) pre-treatment with various Aβ isoforms (1–40, 1–42, 17–42, 17–40, 1–28, or 1–16) impairs G. pallida’s chemotaxis to differing extents; (iii) Aβ peptides reduced survival, increased the production of ROS, and increased GSSG/GSH levels in this model; (iv) this unique model can distinguish differences between different treatment concentrations, durations, and modalities, displaying good sensitivity; (v) clinically approved neuroprotective agents were effective in protecting G. pallida from Aβ (1–42) exposure. Taken together, the data indicate that G. pallida is an interesting in vivo model with strong potential for discovery of novel bioactive compounds with anti-AD activity.Item Assessment of Pain and Inflammation in Domestic Animals Using Infrared Thermography: A Narrative Review(MDPI, 2023-06-22) Whittaker, Alexandra L.; Muns, Ramon; Wang, Dehua; Martínez-Burnes, Julio; Hernández-Ávalos, Ismael; Casas-Alvarado, Alejandro; Domínguez-Oliva, Adriana; Mota-Rojas, DanielPain assessment in domestic animals has gained importance in recent years due to the recognition of the physiological, behavioral, and endocrine consequences of acute pain on animal production, welfare, and animal model validity. Current approaches to identifying acute pain mainly rely on behavioral-based scales, quantifying pain-related biomarkers, and the use of devices monitoring sympathetic activity. Infrared thermography is an alternative that could be used to correlate the changes in the superficial temperature with other tools and thus be an additional or alternate acute pain assessment marker. Moreover, its non-invasiveness and the objective nature of its readout make it potentially very valuable. However, at the current time, it is not in widespread use as an assessment strategy. The present review discusses scientific evidence for infrared thermography as a tool to evaluate pain, limiting its use to monitor acute pain in pathological processes and invasive procedures, as well as its use for perioperative monitoring in domestic animals.Item Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1(MDPI, 2022-08-24) Esnault, Gaelle; Earley, Bernadette; Cormican, Paul; Waters, Sinead M.; Lemon, Ken; Cosby, S. Louise; Lagan, Paula; Barry, Thomas; Reddington, Kate; McCabe, Matthew S.Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software.Item Associations between Circulating IGF-1 Concentrations, Disease Status and the Leukocyte Transcriptome in Early Lactation Dairy Cows(MDPI, 2021-11-25) Wathes, D. Claire; Becker, Frank; Buggiotti, Laura; Crowe, Mark A.; Ferris, Conrad; Foldager, Leslie; Grelet, Clément; Hostens, Miel; Ingvartsen, Klaus L.; Marchitelli, Cinzia; Salavati, Mazdak; Signorelli, Federica; Takeda, Haruko; Tang, Lijing; Cheng, Zhangrui; GplusE ConsortiumPeripartum dairy cows commonly experience negative energy balance (EB) and immunosuppression together with high incidences of infectious and metabolic disease. This study investigated mechanisms linking EB status with immune defense in early lactation. Data were collected from multiparous Holstein cows from six herds and leukocyte transcriptomes were analyzed using RNA sequencing. Global gene expression was related to circulating IGF-1 (as a biomarker for EB) by subdividing animals into three groups, defined as IGF-1 LOW (<35 ng/mL, n = 35), MODERATE (35–100 ng/mL, n = 92) or HIGH (>100 ng/mL, n = 43) at 14 ± 4 days in milk (DIM). Differentially expressed genes between groups were identified using CLC Genomics Workbench V21, followed by cluster and KEGG pathway analysis, focusing on the comparison between LOW and HIGH IGF-1 cows. LOW cows were older and had significantly lower dry matter intakes and EB values, whereas HIGH cows produced more milk. During the first 35 DIM, 63% of LOW cows had more than one health problem vs. 26% HIGH cows, including more with clinical mastitis and uterine infections. Gene expression analysis indicated that leukocytes in LOW cows switched energy metabolism from oxidative phosphorylation to aerobic glycolysis (PGM, LDH, and PDK4). Many antimicrobial peptides were up-regulated in LOW cows (e.g., PTX3, DMBT1, S100A8, and S100A9) together with genes associated with inflammation, platelet activation and the complement cascade. HIGH cows had greater expression of genes regulating T and B cell function and the cytoskeleton. Overall, results suggested an ongoing cycle of poor EB and higher infection rates in LOW IGF-1 cows which was reflected in altered leukocyte functionality and reduced milk production.Item ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus(BMC (Springer nature), 2021-01-06) Johnston, Dayle; JaeWoo, Kim; Taylor, Jeremy F.; Earley, Bernadette; McCabe, Matthew S.; Lemon, Ken; Duffy, Catherine; McMenamy, Michael; Cosby, S. Louise; Waters, Sinéad M.Background: Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of the genome, which can be determined using ATAC-Seq. The objectives of this study were to: (i) identify regions of open chromatin in DNA extracted from bronchial lymph nodes (BLN) of healthy dairy calves experimentally challenged with BRSV and compare them with those from non-challenged healthy control calves, (ii) elucidate the chromatin regions that were differentially or uniquely open in the BRSV challenged relative to control calves, and (iii) compare the genes found in regions proximal to the differentially open regions to the genes previously found to be differentially expressed in the BLN in response to BRSV and to previously identified BRD susceptibility loci. This was achieved by challenging clinically healthy Holstein-Friesian calves (mean age 143 ± 14 days) with either BRSV inoculum (n = 12) or with sterile phosphate buffered saline (PBS) (n = 6) and preparing and sequencing ATACSeq libraries from fresh BLN tissues. Results: Using Diffbind, 9,144 and 5,096 differentially accessible regions (P < 0.05, FDR < 0.05) were identified between BRSV challenged and control calves employing DeSeq2 and EdgeR, respectively. Additionally, 8,791 chromatin regions were found to be uniquely open in BRSV challenged calves. Seventy-six and 150 of the genes that were previously found to be differentially expressed using RNA-Seq, were located within 2 kb downstream of the differentially accessible regions, and of the regions uniquely open in BRSV challenged calves, respectively. Pathway analyses within ClusterProfiler indicated that these genes were involved in immune responses to infection and participated in the Th1 and Th2 pathways, pathogen recognition and the anti-viral response. There were 237 differentially accessible regions positioned within 40 previously identified BRD susceptibility loci. Conclusions: The identified open chromatin regions are likely to be involved in the regulatory response of gene transcription induced by infection with BRSV. Consequently, they may contain variants which impact resistance to BRD that could be used in breeding programmes to select healthier, more robust cattle.Item Badger Ecology, Bovine Tuberculosis, and Population Management: Lessons from the Island of Ireland(Wiley-Hindawi, 2024-01-16) Byrne, Andrew W.; Allen, Adrian; Ciuti, Simone; Gormley, Eamonn; Kelly, David J.; Marks, Nikki J.; Marples, Nicola M.; Menzies, Fraser; Montgomery, Ian; Newman, Chris; O’Hagan, Maria; Reid, Neil; Scantlebury, David M.; Stuart, Peter; Tsai, Ming-shan; Animal Health and WelfareThe European badger, Meles meles, is an important wildlife host for Mycobacterium bovis and contributes to the epidemiology of bovine tuberculosis (bTB) in cattle in several countries. The control of zoonotic diseases, such as bTB, is a central component of global One-Health strategies. Such strategies are complicated by human–wildlife conflicts, particularly where wildlife reservoirs are legally protected. The contrasting objectives of disease management and wildlife conservation, therefore, can require significant investment in research to support evidence-based policies. In Britain and Ireland, for example, badgers are a legally protected species but are also subject to lethal control and vaccination for disease management. In this paper, we review recent (2012–2022) advances in research on this wildlife host on the island of Ireland, which is used to underpin national policies and identify research gaps. In recent years, significant advances in estimating key parameters related to badger management and population dynamics have been made, including estimating population abundance at varying scales (local, landscape, and national). Advances in tracking technology, integrated with mark-recapture and modelling tools, have provided significant insights into the movement ecology of badgers and their interactions with cattle. The adaptation of genetic technologies has improved our understanding of the transmission dynamics of M. bovis among different hosts. As a disease management strategy, the culling of badgers to control bTB has reduced badger densities significantly, although this is not considered a sustainable sole long-term solution to the problem of spillback infection. The recent development of vaccination strategies presents an additional approach to control the disease in wild populations. These types of interventions will require significant applied research to ensure they are sustainable and to maximise benefits. It is also expected that focused research efforts will improve human–wildlife coexistence in the context of the broader One-Health strategy.