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Subject: search.filters.subject.300304 Animal protection (incl. pests and pathogens)

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    Towards an in vitro assay : biomarker validation for facial eczema tolerance in sheep : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science [MSc] in Animal Science at Massey University, Manawatū, New Zealand
    (Massey University, 2024) Bramley, Claudia May
    Introduction: Facial eczema (FE) is a photosensitisation disease of grazing ruminant livestock caused by the ingestion of the fungal metabolite sporidesmin which is found in the spores of the fungus Pseudopithomyces chartarum. It is of huge concern to the sheep industry as it effects animal production and welfare. Several strategies to mitigate the effects of FE have been explored, however, breeding for increased tolerance has been recognised as the most effective management strategy. The current practice to test for FE tolerance is to dose rams with a controlled amount of sporidesmin and then observe the effects 21 days later which, from animal welfare and farming perspectives is unsustainable long-term and therefore an alternative test is needed. Recent advances have encouraged the development of an in vitro assay based on easily accessibly samples from individual animals which will remove the risks associated with animal welfare and accelerate FE tolerance in flocks. Aim: The hypothesis for this project was that the differential expression and prognostic values of the nine biomarkers identified during earlier work can be reproduced in a different set of sheep. Materials and methods: Peripheral blood mononuclear cells (PBMCs) were prepared from whole blood samples collected from sheep (n=290) on 13 farms enrolled in the Ramguardᵀᴹ programme, and an in vitro sporidesmin toxicity assay was performed. Total RNA was extracted from the PBMC pellets, subsequent to sporidesmin toxicity assay, using either the Qiagen Kit method or the Zymo Kit method. NanoString analysis of nine genes of interest and three reference genes was performed on 100 RNA samples and statistical analysis was carried out on each target gene between the FE tolerant and susceptible groups. The study animals were categorised into susceptible and tolerant groups based on the change in Gamma-Glutamyl Transferase levels (ΔGGT), before (day 0) and 21 (day 21) days subsequent to in vivo sporidesmin dosing. Results: The change in GGT levels (ΔGGT) was found to be 916.90 ± 489.30 IU/L for susceptible animals and 8.57 ± 9.80 IU/L for tolerant animals. Variability in GGT levels in animals between farms revealed different proportions of tolerant and susceptible rams across farms. There was no difference in RNA yield according to FE status (susceptible or tolerant), however there were differences in RNA yield and ΔGGT between the 13 farms. Of the nine biomarkers1 examined in this study, only four (ACP7, CCL27, LOC106990188 and TXN2) were significantly different between the susceptible and tolerant groups (p<0.05). Sensitivity and specificity were calculated for each of the four biomarkers individually and it was found that CCL27 had high specificity (0.80) and low sensitivity (0.34) while both TXN2 and LOC106990188 had high sensitivity (0.80) and low specificity (0.41). The four biomarkers were also combined in an attempt to improve individual prognostic values, and it was found that ACP7 combined with CCL27 resulted in a sensitivity of 0.37 and a specificity of 0.73. ACP7xCCL27 has a sensitivity of 0.31 and specificity of 0.75. Both ACP7+LOC106990188 and ACP7-TXN2 combinations have a sensitivity of 0.80 however, ACP7+LOC106990188 has a specificity of 0.46 while ACP7-TXN2 has a specificity of 0.23. Conclusion: Of the nine biomarkers investigated, the four markers (ACP7, CCL27, LOC106990188 and TXN2) were differentially expressed between the susceptible and tolerant groups, thereby indicating their potential to be used in a prognostic test for FE tolerance in sheep.
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    Investigation of the microbiomes of sow skin, milk and piglet hind gut : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Animal Science at Massey University, Manawatū, New Zealand
    (Massey University, 2024) Jones, Sophia
    There is a lack of information on the microbiome of sow skin, sow milk and piglet faeces from New Zealand production systems. Therefore, we have a current lack of data on the bacterial populations present and the potential pathways of transmission to colonise the gut of neonatal pigs. Knowledge of these aspects would allow the identification of common probiotics, pathogens and commensal bacteria in pigs and provide information to help identify the pathways of colonisation for bacteria within the gastrointestinal tract of neonatal pigs. Samples were collected from 21 sows (N = 17 milk samples and N = 20 udder skin swabs) and 63 piglets (N = 63 piglet faecal samples) within 72 hours of parturition, on a commercial farrow-to-finish indoor pig farm. The DNA extracted from these samples underwent metabarcoding analysis using the greengenes 16S database and Kraken2 pipeline. The number of reads varied by different samples, even from within the same pen. For example, the milk sample of sow 676 only had 25,000 reads whilst the piglets suckling from this sow had between 125,000 – 160,000 reads. Piglet samples were dominated by populations of Firmicutes and Bacteroidetes bacteria, whilst the sow udder skin and milk samples were dominated by populations of Firmicutes and Proteobacteria bacteria. Milk samples displayed a greater presence of lesser common phyla compared to sow skin or piglet faeces, but these phyla are present at relatively low levels of reads, such as Cyanonbacteria, Chloroflexi and Acidobacteria. There were no reads for Escherichia coli bacteria present in any samples taken for this study which is an unusual but incredibly positive finding. Clostridium, a similar pathogenic bacteria in neonates, was found abundant in piglet faecal samples so we cannot be sure if E. coli did not exist on-farm at all due to upkept disinfection protocols or if the piglets had not yet picked it up. Probiotic bacteria were identified across the piglet faecal samples, namely Pediococcus and Lactococcus, including species of the phyla which are known to increase production and performance, as well as providing a protective function against E. coli bacteria. As probiotic bacteria are typically given as feed additives pre-weaning due to benefits aiding in gut microbiota development, these piglets seem to already have a good basis of these bacteria. The research was successful in what was set out to be completed, despite any limitations that were discovered, and resulted in future recommendations to continue characterising important microbiomes in the New Zealand pork industry, as well as their interactions and pathways of transmission to neonatal piglets.
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    Translating biosecurity world-making : thinking with Mycoplasma bovis in Aotearoa : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Resource and Environmental Planning at Massey University, Manawatū, Aotearoa
    (Massey University, 2023-12-12) McDonald, Deidre Ann
    Aotearoa has one of the strictest biosecurity networks in the world and, at the same time, enacts one of the world’s most export-driven agricultural economies. It was into these dual assemblages that Mycoplasma bovis (M. bovis) first emerged, in July 2017, causing the (then) Biosecurity Minister to declare that M. bovis was Aotearoa’s ‘single biggest biosecurity event’. Consistent with this problematisation, and in a world-first manoeuvre, the government and farming industry bodies decided to try to eradicate the bacteria. This thesis tells the story of that eradication attempt and of M. bovis’ own attempt to fight back. This more-than-human research follows the network translation attempts of five key actors involved with M. bovis’ world-making. These are the eradicators themselves, the scientists enrolled in the programme, the farmers who were impacted by M. bovis (and by the eradicators), the cows who hosted the bacteria and M. bovis, the smallest living organism known to self-replicate. Together these network actors have enacted realities that are significant for the future of farming and biosecurity in Aotearoa. At the time of writing, the eradicators have almost succeeded in protecting and stabilising farming by Othering M. bovis from the network. In doing so, however, the eradicators have reterritorialised a pasture-based farming assemblage that is inherently fragile. Farming’s continual need for complex biological mobilities itself creates the need for ongoing biosecurity practices. Yet, as this thesis will show, these on-farm biosecurity practices are fundamentally incompatible with farming ontologies. There is a precarious misalignment between these two assemblages, each of which are vital for Aotearoa’s economic security. As to M. bovis’ bacterial world-making, this seems to be irrelevant to the human actors, despite their collective interest in non-human health. As a spokesperson for this M. bovis assemblage, I have tried to expose a series of ontological worlds. In doing so, my aim is to create a conceptual space for reimagining farming and biosecurity in Aotearoa.
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    Investigation of lameness and claw disorders in New Zealand dairy goats : a multidisciplinary approach : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Manawatū, New Zealand
    (Massey University, 2022) Jaques, Natasha
    New Zealand dairy goat farmers have problems preventing and treating lameness caused by claw disorders within their herds. There is scarce information about lameness and claw disorders in commercial dairy goat herds nationally and internationally. The two aims of this thesis were: to acquire information on the level of clinical lameness and the types and level of claw disorders present on three dairy goat farms in New Zealand and to explore the epidemiological, productivity, and genetic aspects of lameness and claw disorders. Information on lameness and claw disorders was collected on herds 4 or 5 times between July 2019 and June 2020. Additional information collected were age, stage of lactation, milk production, pedigree, kidding date, and lactation type. The prevalence of clinical lameness and claw disorders fluctuated across the production year at levels that differed on each farm. Farm A had the highest average of clinical lameness (23%), followed by farms B and C (12 and 10%, respectively). For the investigation of claw disorders, the main claw disorders studied were horn separation, granulomas, and rot. Farm C had the highest prevalence of horn separation (83%), while farm A had the highest prevalence of rot and granulomas (19 and 14%). Rot and granulomas increased the odds of clinical lameness (OR= 2.10-7.02). Compared to goats walking normally, severe lameness had the highest milk production losses of 7.10% and 8.56% in extended and seasonal lactation goats, respectively. The average income losses ranged from NZD 26 to 104 per goat. The heritability (h2) estimates for lameness occurrence and susceptibility were 0.07 and 0.13, respectively, and the h2 estimates of claw disorder susceptibilities ranged from 0.02 to 0.23. This thesis identified that clinical lameness caused by claw disorders is a problem on dairy goat farms in New Zealand and reported the negative impact of severe lameness on milk production. Additionally, breeding for resistance or tolerance of clinical lameness and claw disorder may be possible. Further large-scale studies are needed to understand the risk factors of clinical lameness and claw disorders. Small-scale studies are required to investigate effective treatments to manage claw disorders in dairy goats.
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    Fluctuations in population size of Theileria orientalis Ikeda within the tick vector Haemaphysalis longicornis Neumann : an investigation into the life cycle of T. orientalis Ikeda : a thesis presented in partial fulfilment of the requirements for the degree of Masters of Science in Zoology, Massey University, Palmerston North, New Zealand
    (Massey University, 2020) Zhao, Yilin
    Theileria orientalis Ikeda is a protozoan parasite of cattle that causes disease through the destruction of the host's erythrocytes. In 2012, the parasite caused an epidemic of bovine theileriosis in New Zealand at great economic cost to the farming community. As a result, a large number of scientific studies have been undertaken to understand the epidemiology of the T. orientalis Ikeda parasite in the hopes of mitigating the damage done by the parasite. An essential part of the epidemiology of any pathogen is the understanding of its life cycle and this holds true with T. orientalis Ikeda which, like other Theileria parasites, exhibits a complex life cycle involving multiple hosts. In this thesis, fluctuations of T. orientalis Ikeda populations within nymph tick hosts were investigated over the course of six months. By doing so, this investigation highlights a part of the T. orientalis Ikeda lifecycle that is poorly covered in the scientific literature. The population of T. orientalis Ikeda within the tick was determined through qPCR analysis. Analysis of the qPCR results found that populations of T. orientalis Ikeda fluctuated greatly within the ticks over the course of six months. Ticks infected with Theileria were procured through the development of a novel mass tick- rearing protocol: the artificial infestation of a cattle-beast with naïve ticks through the fixation of tick-containing ear-bags. A pilot study of the protocol showed that the fixation of ear-bags onto cattle using Kamar® adhesive did not negatively impact the welfare of the cattle involved. The subsequent field trial of the protocol resulted in the successful engorgement and infection of five thousand naïve tick larva. These results demonstrated a viable method to obtain T. orientalis Ikeda infected ticks that would be suitable for further research. Also described in detail in this thesis are attempts at adapting the protocol of Krober and Guerin (2007) to create a silicone membrane for the artificial feeding of tick larvae on Theileria-infected blood without the involvement of live hosts. Despite multiple attempts, the experiments yielded no successful attachments of ticks onto the synthetic membranes. Failure here was attributed largely to the adapted protocol creating silicone membranes that were too thick for the larval ticks to successfully penetrate with their mouthparts. However, the in vitro feeding of ticks presents itself as a great potential contributor to future tick research. It is hoped that the knowledge gained from the repeated trials of the in vitro feeding apparatus in this experiment may help in the development of successful protocols in the future.