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    Machine learning for predicting climate change impacts on Pseudopithomyces chartarum spore counts: a risk indicator of facial eczema
    (Taylor and Francis Group, 2025-11-09) Wada M; Sagarasaeranee O; Cogger N; Marshall J; Cuttance E; Macara G; Sood A; Vallee E
    Aims To determine the importance of 11 climate variables on pasture spore count of Pseudopithomyces chartarum, a risk indicator of facial eczema (FE), and to forecast spore counts in New Zealand until 2100, using longitudinal P. chartarum pasture spore count data. Methods Between 2010 and 2017, spore counts (n = 6,975) were collected from 862 paddocks spread over 102 farms in the North Island of New Zealand. Historical and projected climate data were obtained from the National Institute of Water and Atmospheric Research. The spore count dataset was merged with climate data from corresponding locations, incorporating time lags of 1–53 weeks. Linear regression models were fitted for describing crude associations, while random forest models were fitted for determining variable importance and predicting future spore counts. Results Mixed-effect linear regression models explained up to 11% of the variance of log-transformed spore counts by a single lagged climate covariate. The best-fit random forest model had a testing accuracy of 80% in classifying low or high FE risk (> 20,000 spores) with an R2 value of 43%. The random forest models suggested time-dependent importance of soil temperature at 10 cm depth, solar radiation, potential evapotranspiration, vapour pressure, soil moisture and minimum temperature, while no or weak evidence of variable importance was found for maximum temperature, rainfall, mean sea level atmospheric pressure, relative humidity and wind speed. Over the next 80 years, our model predicted an increase in the seasonal mean spore counts in the study farms by a mean of 17% (min 6, max 30%) under the high-end greenhouse gas emission scenario (representative concentration pathways (RCP) 8.5). Every decade was associated with an increase in the probability of high-risk spore counts (> 20,000) by 14–22% for the moderate to high emission scenarios (RCP 4.5–8.5). The model indicated increased peak spore counts across most regions over the next 80 years. Specifically, the entire North Island and three districts in the South Island were projected to have high mean peak spore counts by 2100. Conclusions and clinical relevance These findings could be used to target high-risk areas to implement mitigation or adaptation measures for FE. In addition, the study highlights the value of ecological data for forecasting environmental disease risks to enhance preparedness for climate change.
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    The search for biomarkers of facial eczema, following a sporidesmin challenge in dairy cows, using mass spectrometry and nuclear magnetic resonance of serum, urine, and milk : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Sciences at Massey University, Palmerston North, Manawatu, New Zealand
    (Massey University, 2015) Matthews, Zoe Maree
    Facial eczema (FE) is a secondary photosensitisation disease of ruminants that is significant in terms of both its economic importance to New Zealand and its impact on animal welfare. The clinical photosensitivity signs, caused by the retention of phytoporphyrin, occur secondarily to hepatobiliary damage caused by the mycotoxin sporidesmin. Currently it is difficult to diagnose subclinical animals and those in the early stages of the disease. The project was aimed at applying new analytical and statistical techniques, to attempt the early diagnosis of FE in dairy cows following the administration of a single oral dose (0.24 mg/kg) of sporidesmin. Well-established traditional techniques including production parameters, liver enzyme (GGT, GDH) activity measurements, as well as measurements of phytoporphyrin by fluorescence spectroscopy were made for comparison. Serum, urine, and milk were analysed using 1H Nuclear Magnetic Resonance (NMR), multivariate analysis (MVA), and time series statistics. Urine and milk did not prove useful for identification of sporidesmin intoxication. Serum metabolites differed between treated cows before and after administration of the toxin, and could distinguish samples belonging to the clinical group. The metabolites that were identified as being relevant to this classification were a mixture of glycoproteins, carboxylic acids, ketone bodies, amino-acids, glutamate, and glycerol, which were elevated for treated cattle, and acetate, choline, isoleucine, trimethylamine N-oxide, lipids, lipoproteins, cholesterol, and -glucose, which showed decreased concentrations. Citrate was found to be at higher concentration in non-responders and subclinicals only. When serum was analysed using ultra performance liquid chromatography electrospray ionisation mass spectrometry (UPLC/ESI-MS) and UPLC tandem MS (MS/MS), only samples from clinical cows could be discriminated. The molecular ions involved could be tentatively identified as a combination of taurine- and glycine-conjugated bile acids. These bile acids all became elevated. This study confirmed that liver enzyme activities (GGT, GDH) and phytoporphyrin concentrations are not effective as markers of early stage sporidesmin damage. Additionally, the new techniques were unable to detect early stage FE. However, some markers of treated cows were identified. The research does provide a strong foundation for future applications of metabolomics analysis, with MVA and time series statistics, for early stage FE diagnosis.
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    Management of facial eczema : a thesis presented in partial fulfilment of the requirements for the degree of Master of Veterinary Studies in Epidemiology at Massey University, Manawatu, New Zealand
    (Massey University, 2016) Boyd, Emma
    Facial eczema is a hepatogenous photosensitisation of ruminants caused by sporidesmin produced by the saprophytic fungus Pithomyces chartarum. It is of large concern to the dairy industry, both with its effects on production and the significant animal welfare implications of affected stock. In 2011 DairyNZ and Sustainable Farming Fund invested in research initially aimed at trying to get a better understanding behind the natural spore count variability in paddocks, between paddocks and between farms and to try and find alternative ways of managing facial eczema without zinc. After this research was completed in 2013 it was deemed necessary to try and understand to what extent management of facial eczema was breaking down and possible reasons for these breakdowns. The overall aim of this research was to try and help farmers improve their management of this disease and reduce incidence of facial eczema. A study comparing the spore counts from paddocks containing varying quantities of herbs, clovers and tall fescue showed that the addition of chicory, plantain, lucerne and white clover into a ryegrass pasture did not provide any reduction in spore counts. Tall fescue paddocks showed lower spore counts over time than pure swards of ryegrass. A study comparing the application of lime and nitrogen in comparison to control paddocks showed that application of lime before the risk period for facial eczema (in November), application of lime after a spore count rise, (in March) or urea application (in December) did not affect the number of spores produced by Pithomyces chartarum. A study investigating the variability of spore counts within farm, paddock, grass sample and water aliquot showed that if spore counts are to be used for monitoring purposes to identify when to start and finish facial eczema(FE) prevention programmes, at least three aliquots per wash water should be selected. Finally, a study looking at the different types of management of FE used and their effectiveness highlighted that FE management on dairy farms in New Zealand could be substantially improved; principally through farmers getting more information on the success of their FE management programs and responding when tests show that FE management is not effective.
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    Refinement of analytical technologies for detection of biomolecules of importance to the dairy sector : a thesis presented in partial fulfilment of the requirements for the degree of Master of Philosophy in Sciences at Massey University, Palmerston North, New Zealand
    (Massey University, 2011) Sharma, Indu; Sharma, Indu
    There is a continuous push on the dairy industry to enhance livestock productivity to meet with the demands of ever increasing human population. This demand can be achieved by developing rapid and early diagnostic aids to help curtail various problems encountered in the livestock production. The first study of the present thesis was focussed on standardizing initial steps towards development of Surface Plasmon Resonance for progesterone and oestradiol 17- , both of which are critically implicated in animal reproduction. For progesterone, the binding response of two different length linkers, and the antigen-antibody binding response of two different source monoclonal antibodies (P1922 from Sigma vs SE-7720-1430 from Serotec) were evaluated. It was concluded that the long length linker had better binding response than the short length linker. The antibody obtained from Serotec (SE-7720-1430) had greater sensitivity but its binding response was inconsistent. On the other hand, the sensitivity of the monoclonal antibody from Sigma (P1922) was lower, although its binding response was consistent. For oestradiol 17- , antibody procured from Bio-trend (BT70-1020-06) was tested and its binding response was consistently low on all the test days. This study thus suggests that careful testing and selection of antibodies to achieve desired antigen-antibody binding response is a critical step towards development of SPR for progesterone and oestradiol 17- . The second study was undertaken to refine the currently existing fluorescent techniques to measure phytoporphyrin in the peripheral circulation of cows. Phytoporphyrin is implicated in facial eczema (FE), which is a photosensitization disease of high economical importance. This occurs due to disturbances in the chlorophyll metabolism as a result of liver damage and bile duct occlusions caused by fungal toxicity. The present study described new modified fluorescent methods to measure phytoporphyrin in the serum of cows. Further, the absorption and emission spectra of phytoporphyrin were compared with that of other chlorophyll metabolites and thus a currently existing anomaly in the chemical structure of phytoporphyrin was rectified.