Roslin Institute

Gastrointestinal nematodes (GIN) can impact on cattle health and welfare as well as cause economic losses associated with lower productivity but are often overlooked by farmers as a sub-clinical issue. Infections are routinely controlled with prophylactic use of anthelmintics but resistance to the available products has been reported. The prevalence of anthelmintic resistance (AR) in cattle GIN is advancing in certain species, making control more challenging. This study shows the current prevalence and diversity of GIN populations in British commercial cattle herds and the extent of infection in traded animals. Faecal samples were collected from 455 cattle herds; 395 from groups being sold through livestock auctions and a further 60 from samples submitted to the Animal and Plant Health Agency (APHA) for monitoring purposes. Faecal egg counts (FEC) were conducted on all samples and nematode eggs recovered for molecular species identification using Illumina MiSeq. Of the traded cattle, 67% had a positive faecal egg count, with a mean FEC of 20 eggs per gram (epg) (95% CI: 11 - 34). Samples from APHA had a mean FEC of 72 epg (95% CI: 56-93). Ostertagia ostertagi and Cooperia oncophora were the most common species identified, with co-infections of these two species found in 87% of samples. A diverse range of additional species were also identified, and these were found to vary with the pedigree status of cattle sampled and geographic location. Our results highlight that most cattle sold at auction were carrying GIN, which included a high prevalence of the pathogenic species O. ostertagi. These findings stress the need for effective biosecurity measures for new and returning cattle to minimise the movement of GIN between farms.

Type I interferon (IFN) induction is a central component of the innate immune response to viral infection, and the cytosolic DNA sensor cyclic GMP-AMP synthase (cGAS) has been identified as a key mediator of IFN production during human cytomegalovirus (HCMV) infection. However, how cGAS detects HCMV remains unresolved, as the viral genome is encapsidated and trafficked directly to the nucleus, limiting cytoplasmic exposure. Here, we show that IFN induction during HCMV infection of primary fibroblasts is largely driven by cGAS recognition of exogenous DNA present in standard laboratory virus preparations rather than the encapsidated viral genome. DNase treatment of AD169 and low-passage TB40/E-GFP viral stocks substantially reduced total DNA content without affecting infectivity, yet markedly abrogated IFN induction, IFN-stimulated gene expression and IRF3 nuclear translocation. Immunofluorescence analysis further revealed cytoplasmic accumulation of DNA in cells infected with untreated virus stocks, which was absent following DNase treatment. Together, these findings demonstrate that contaminating DNA in viral preparations is sufficient to activate cGAS and drive IFN responses during HCMV infection in vitro, highlighting the need for caution when interpreting innate immune sensing mechanisms in experimental infection systems.

Background Generative AI (genAI) has the capacity to create realistic and convincing animal videos, however, it must simplify and reduce behavioural variation to do so, possibly leading to misinformation. Methods We categorised 29 videos in the press release for a specific video genAI engine. Twelve featured animals. We mapped each video to the Five Domains and categorised behaviour and welfare within. Results Negative welfare was rarely seen, ranging from 8% (n = 1) for Nutrition, to 42% (n =5) for Behavioural Interactions. By contrast, Mental State, Environment, and Behavioural Interactions appeared positive in >42% (n = 5) of the videos featured. However, videos were often misleading or did not represent accurate animal behaviour. Limitations This work was limited to a press-release of data and does not explore user experience. Conclusions GenAI videos pose a new route for client confusion and veterinarians need to incorporate genAI misinformation combatting in their practice.

<ns7:p>The well-being of farmed and companion animals is increasingly recognised as integral to sustainable agroecosystems, companionship, and the One Health approach, which emphasises the interconnected health of people, animals, and the environment. The ELIXIR Domestic Animals Genome and Phenome (DAGP) Community supports genome-to-phenome analyses for farmed and companion animal species. Its aim is to coordinate, discuss, and explore the potential of data technology solutions to address key issues in animal welfare, behaviour, health, infectious diseases, metabolism, nutritional efficiency, and the preservation of genetic diversity and the environment. Through consolidating efforts to develop data standards, coordination, workflows, and visualisation, it will enhance the science underpinning rapidly growing fields in domestic animal genomics, including genome-enabled breeding, population genomics, pangenome analysis, functional genomics, genome editing, paleogenomics, phenotyping, and bio-banking. These standards will adhere to the FAIR data principles and leverage established ontologies to promote best practices in data coordination and archiving. This white paper, prepared by the ELIXIR DAGP Focus Group, summarises the current data infrastructure, resources, and tools available for domestic animal genomics and phenomics, and presents community-led plans and priorities to be implemented to meet the requirements of ELIXIR services and the animal science community. We describe how ELIXIR services can be applied in the domestic animal genomics and phenomics fields, and how we can connect projects and infrastructures that are active in the animal sciences domain. We also discuss three key priority areas: i) expanding the FAANG Data Portal for phenotype data with ELIXIR Data Platforms; ii) supporting submissions of new data types across ELIXIR Core Data Resources , including proprietary data from industry partners; and iii) strengthening connections to existing ELIXIR Communities and international consortia. This article provides a set of priorities for a Domestic Animals Genome and Phenome Community in ELIXIR and outlines the next steps to engage across stakeholders and to consolidate data for domestic animal science in Europe.</ns7:p>

ABSTRACT MicroRNAs (miRNAs) are key post-transcriptional regulators of antiviral immunity, controlling gene expression by targeting 3’ UTRs of immune-related transcripts. Despite their importance, the role of miRNAs in viral nervous necrosis (VNN) resistance in European seabass ( Dicentrarchus labrax ) is unexplored. Here, we characterized for the first time the brain miRNome of seabass from three VNN-resistance genotypes (susceptible, intermediate, resistant) across two genetically distinct seabass clusters. Differential expression analyses revealed cluster-specific patterns, with susceptible fish consistently showing overexpression of the differently expressed miRNAs (DEmiRNAs) as compared to the resistant fish. Considering the two genetic clusters in the study, miR–199–5p was differentially expressed between the VNN susceptible and resistant fish. This miRNA was found to be less expressed in the resistant individuals. Functional characterization of the miRNA predicted that it binds to two distinct miRNA recognition elements (MREs) within the ifi27l2a 3’ UTR. These MREs flank a SNP (Chr3:10,082,380) previously associated with VNN survival. A strong negative correlation (r= -0.840) between miR–199–5p expression and ifi27l2a mRNA abundance further supports a post–transcriptional repression mechanism. Together, these results propose a regulatory model in which miR–199–5p modulates ifi27l2a expression, contributing to phenotypic variation in VNN resistance and positioning it as a promising biomarker for seabass aquaculture breeding.

ABSTRACT Purpose Optic fissure closure (OFC) is a critical tissue fusion event in normal eye development and its failure results in ocular coloboma (OC), an inferonasal ocular tissue defect that persists throughout life. Most OC cases lack a genetic diagnosis, reflecting limited understanding of the genes and pathways that regulate OFC. We aimed to determine if OFC gene expression is regulated by the non-coding genome and identify novel candidate loci for OFC/OC. Methods Using the embryonic chicken eye, we performed integrated profiling of accessible chromatin and gene expression patterns during OFC. Matched RNA-seq and ATAC-seq from distinct spatial and temporal eye tissues were utilised with bioinformatic tools to identify regulatory genomic elements and infer gene regulatory networks, and to map synonymous loci in the human genome. Results We revealed domains of accessible chromatin during active fusion and the broader ventral retina that were distinct from those in the dorsal retina, implicating these loci for gene regulation during development and fusion of the optic fissure. In silico analysis using de novo motif enrichment and transcription factor (TF) foot-printing revealed TEAD, ZIC, and SOX TF activity during OFC, and retinoic acid signalling related TF activity in the dorsal eye. A subset of chicken OFC-specific peaks mapped to human cis-regulatory elements near known coloboma genes and OFC candidate genes identified in this study. Conclusions This provides the first evidence for dynamic cis-regulatory activity during OFC, identifies candidate loci for future mutational analysis, and offers new genetic leads for OC cases without a genetic diagnosis.

In many cooperatively breeding species non-breeding individuals help to rear the offspring of breeders. The physiological mechanisms that regulate such cooperative helping behavior are poorly understood, but may have been co-opted, during the evolution of cooperative breeding, from pre-existing mechanisms that regulated parental care. Key among these may be a role for prolactin. Here we investigate whether natural variation in circulating prolactin levels predicts both parental and helper contributions to nestling provisioning in wild cooperatively breeding white-browed sparrow weavers, Plocepasser mahali. In sparrow weaver groups, a dominant pair monopolize reproduction and non-breeding subordinates help with nestling feeding. We show that: (i) among parents, females feed their nestlings at higher rates, make longer provisioning visits, and have higher prolactin levels than males; and (ii) among subordinates, engaged in cooperative helping behavior, those within their natal groups feed nestlings at higher rates and have higher prolactin levels than immigrants. Accordingly, continuous variation in prolactin levels positively predicts nestling provisioning rates and provisioning visit durations when all bird classes are combined. These relationships are principally driven by differences among bird classes; the more limited within-class variation in prolactin and provisioning traits were not evidently correlated, for which a range of potential explanations exist. While these correlative findings are broadly consistent with the hypothesis that parental care and cooperative helping behavior are regulated by a shared mechanism, experiments are now needed to establish whether prolactin plays a causal role, and if so, whether it regulates continuous variation in provisioning rate or simply activates provisioning behavior.

Despite its significant potential, cultivated fat manufacture remains a relatively inefficient process, as it primarily uses source preparations of animal-derived mesenchymal stem/stromal cells (MSC) that are poorly defined and highly heterogenous in nature, containing only relatively minor fractions of bona-fide adipocyte progenitors. The aim of this study was to use RNA-sequencing of clonal MSC populations from cattle to identify cell surface marker(s) of bona-fide pre-adipocytes to be used for efficient enrichment of MSCs, with a view to future cultivated fat applications. Adipose-derived MSC populations (n = 5 animals) were grown clonally from single cells and subsequently tested for adipogenic capacity. Adipogenic (A) and non-adipogenic (N) clones (n = 10/group) thus identified were bulk RNA-sequenced. A total of 35 cluster of differentiation (CD) genes were identified among differentially expressed transcripts, of which CD13, CD141, CD36, CD55 and CD34 were selected for further testing using flow cytometry in bovine MSCs. All antigens except CD13 were detected at negligible levels. FACS was then used to sort MSCs (n = 4 animals) into CD13+ and CD13- fractions. Sorted CD13+ cells were larger and flatter, grew significantly slower, and expressed substantially higher levels of adipogenic regulators (PPARG and CEBPA) compared to CD13- cells. Moreover, on average, adipogenic efficiency was 10.3-fold higher in CD13+ than CD13- cells, as demonstrated by BODIPY staining and confirmed by differential expression of mature adipocyte markers (FABP4, ADIPOQ, LEP), while expression of alternative lineage markers (chondrogenic and osteogenic) and ability to differentiate into bone and cartilage were both similar for CD13+ and CD13- cells. In summary, we identified CD13 as a bona-fide marker of pre-adipocytes in bovine and demonstrated the potential of using CD13-based cell selection for enriching MSC populations for cultivated fat purposes.