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    Transcriptomic in silico analysis of bovine Escherichia coli mastitis highlights its immune-related expressed genes as an effective biomarker.
    (Elsevier B.V., 2021-12) Farmanullah F; Liang X; Khan FA; Salim M; Rehman ZU; Khan M; Talpur HS; Schreurs NM; Gouda M; Khan SU; Shujun Z
    BACKGROUND: Mastitis is one of the major diseases causing economic loss to the dairy industry by reducing the quantity and quality of milk. Thus, the objective of this scientific study was to find new biomarkers based on genes for the early prediction before its severity. METHODS: In the present study, advanced bioinformatics including hierarchical clustering, enrichment analysis, active site prediction, epigenetic analysis, functional domain identification, and protein docking were used to analyze the important genes that could be utilized as biomarkers and therapeutic targets for mastitis. RESULTS: Four differentially expressed genes (DEGs) were identified in different regions of the mammary gland (teat cistern, gland cistern, lobuloalveolar, and Furstenberg's rosette) that resulted in 453, 597, 577, and 636 DEG, respectively. Also, 101 overlapped genes were found by comparing 27 different expressed genes. These genes were associated with eight immune response pathways including NOD-like receptor signaling pathway (IL8, IL18, IL1B, PYDC1) and chemokine signaling pathway (PTK2, IL8, NCF1, CCR1, HCK). Meanwhile, 241 protein-protein interaction networks were developed among overlapped genes. Fifty-seven regulatory events were found between miRNAs, expressed genes, and the transcription factors (TFs) through micro-RNA and transcription factors (miRNA-DEG-TF) regulatory network. The 3D structure docking model of the expressed genes proteins identified their active sites and the binding ligands that could help in choosing the appropriate feed or treatment for affected animals. CONCLUSIONS: The novelty of the distinguished DEG and their pathways in this study is that they can precisely improve the detection biomarkers and treatments techniques of cows' Escherichia coli mastitis disease due to their high affinity with the target site of the mammary gland before appearing the symptoms.
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    Lameness prevalence and management practices on Irish pasture-based dairy farms
    (BioMed Central Ltd, 2022-06-08) Browne N; Hudson CD; Crossley RE; Sugrue K; Kennedy E; Huxley JN; Conneely M
    Background Lameness is a painful disease, which negatively impacts dairy cow production and welfare. The aim of this observational study was to determine herd lameness prevalence, describe current lameness management practices and identify the presence of established risk factors for lameness on Irish pasture-based dairy farms. Farms were visited once during grazing (99 farms) and again during housing (85 farms). Lameness scoring was carried out at each visit (AHDB 0–3 scale); cows were classified as lame if they scored two or three. Farm management practices and infrastructure characteristics were evaluated via farmer questionnaires and direct measurements of farm infrastructure. Results Median herd-level lameness prevalence was 7.9% (interquartile range = 5.6 – 13.0) during grazing and 9.1% (interquartile range = 4.9 – 12.0) during housing; 10.9% of cows were lame at a single visit and 3.5% were lame at both visits (chronically lame or had a repeat episode of lameness). Fifty-seven percent of farmers were not familiar with lameness scoring and only one farm carried out lameness scoring. Only 22% of farmers kept records of lame cows detected, and 15% had a lameness herd health plan. Twenty-eight percent of farmers waited more than 48 h to treat a lame cow, and 21% waited for more than one cow to be identified as lame before treating. Six percent of farmers carried out routine trimming and 31% regularly footbathed (> 12 times per year). Twelve percent put severely lame cows in a closer paddock and 8% stated that they used pain relief to treat severely lame cows. Over 50% of farms had at least one cow track measurement that was classified as rough or very rough, and cow tracks were commonly narrow for the herd size. On 6% of farms, all cubicle beds were bare concrete (no matting or bedding) and on a further 6% of farms, there was a combination of cubicles with and without matting or bedding. On 56% of farms, all pens contained less than 1.1 cubicles per cow and on 28% of farms, a proportion of pens contained less than 1.1 cubicles per cow. Conclusions Overall, this study identified infrastructure and management practices which could be improved upon. The comparatively low lameness prevalence demonstrated, compared to fully housed systems, also highlights the benefits of a pasture-based system for animal welfare; however, there remains scope for improvement.