Toxoplasma gondii is an economically important parasite that can cause spontaneous abortion in sheep and humans. The importance of the different transmission routes of the parasite is unclear. However, three routes are recognised: (1) shedding of infective oocysts by the definitive host, the cat (2) consumption of undercooked, infected meat and (3) congenital transmission (mother to offspring). Previous work, based on a single farm (Valley Farm, Worcestershire) revealed the controversial finding that congenital transmission may be highly important. In this thesis, I have set out to investigate this in detail and establish more conclusive evidence. A study carried out on a different sheep farm (Heighley Castle Farm, Cheshire) demonstrated congenital transmission was occurring in 44% of pregnancies, thus confirming the importance of the congenital route. A prediction arising from this finding is that different families on a single farm would have different prevalences of T. gondii infection. This hypothesis was tested by investigating infection rates between families of Charollais sheep. A significant difference was found between families (n=27,) both in terms of frequency of abortion (P<0.01) and T. gondii infection (P<0.01). In addition, a significant correlation was found between abortion and infection (correlation co-efficient = 0.89, d.f= 27, (P<0.01)). Furthermore, a study of a large Charollais sheep farm (Foulrice Farm, Yorkshire) showed the same pattern - significantly different frequencies of abortion among different families. This study has shown that one of the principle dogmas of T. gondii research may need revising, namely that sequential abortion and infection does not occur due to acquired immunity. A study of sheep families at Valley Farm demonstrated numerous occurrences of sequential abortion and infection. Taken together, the data presented in this thesis suggests that there are some deficiencies in our understanding of T. gondii epidemiology, and that current sheep husbandry practices may need to be amended.

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Peste des petits ruminants virus (PPRV) produces clinical disease in goats and sheep. PPRV is a morbillivirus, others of which are known to affect the activation of the innate immune response by the actions of their accessory proteins (V&C). A crucial part of normal activation is the induction of interferon β (IFNβ) after pathogen recognition by pattern recognition receptors (PRRs). The presence of viral RNA can be sensed by the cytosolic proteins MDA-5 and RIG-I, starting a signalling cascade that leads to the activation of the IFNβ promoter and the synthesis of IFNβ. The production of IFNβ is a defence mechanism to control the spread of infection to neighbouring cells. Many viruses have evolved to antagonize this cell response. In this thesis I present a study of the induction of IFNβ following PPRV infection in both goat and primate cells, and the effects of infection with PPRV on the induction of IFNβ following MDA-5 and RIG-I mediated activation. Using both reporter assays and direct measurement of IFNβ mRNA, I found that PPRV infection does not induce IFNβ and can block the activation of expression of IFNβ. A study of the interaction of the PPRV accessory proteins with MDA-5 and RIG-I was carried out, including the cloning of goat RIG-I and LGP2. I also generated mutant viruses that lack expression of either accessory protein to characterize the role of these proteins in IFNβ induction during virus infection. Overexpression of V blocks MDA-5 mediated induction of IFNβ, but PPRV lacking V can still block MDA-5 mediated activation of IFNβ. PPRV C bound to neither MDA-5 nor RIG-I, but PPRV lacking C lost the ability to block MDA-5 and RIG-I mediated activation of IFNβ. These results shed new light on the inhibition of the induction of IFNβ by PPRV.

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Methane (CH4) emissions and nitrogen (N) excretion in ruminant production systems are major contributors to atmospheric greenhouse gas accumulation and groundwater pollution. This project aimed to evaluate the effects of dietary (fresh grass, grass silage, pelleted grass and concentrates) and animal (breed and sex) factors on CH4 emissions and N utilisation and to develop prediction models for CH4 emissions and N excretion in sheep. During each measurement period, sheep were fed ad libitum once daily in the morning and were housed in individual pens for 14 d before being transferred to individual respiration chambers for 4 d with feed intake, faeces and urine outputs and CH4 emissions measured. Data were analysed using ANOVA to evaluate the effects of diet and animal factors on feed intake, nutrient digestibility, CH4 emissions and N utilisation. Linear and multiple regression equations for CH4 emissions and N excretion were also developed. Feeding pelleted grass, rather than fresh grass or grass silage, reduced CH4 emissions per kg dry matter intake and shifted N excretion from urine to faeces. Feeding concentrate supplementation by 0.5 kg/d with fresh grass had no effect on CH4 emissions per kg feed intake and N retention. Dry matter intake and N intake were the best single predictors for CH4 emissions and N excretion, respectively. However, adding grass nutrient concentrations as supporting factors improved prediction accuracy. Models based on farm level data (animal liveweight and grass chemical composition) showed satisfactory accuracy for use in practice. Increasing feeding level and grass metabolisable energy and water soluble carbohydrate contents, and decreasing grass N content, could optimise the mitigation of both CH4 emissions and N excretion in grazing sheep. The equations provide an approach to quantify CH4 emissions and N excretion and consequently to develop mitigation strategies to reduce the environmental footprint in sheep production systems.

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