Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at www.rcuk.ac.uk/StudentshipTerminology. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.

This proposal will examine how beef cattle and sheep farmers in upland areas of Northern England and Scotland can improve their resilience to environmental, economic, and social change, and what impact their actions to improve resilience will have on food supplies, natural resources and society. Uplands make up 70% of Scotland, 60% of Wales, 40% of Northern Ireland and 15% of England. Hence over the UK as a whole uplands are a substantial element of the agricultural land resource. The upland regions of Scotland and Northern England have been historically dominated by grazing beef cattle and sheep. Beef cattle and sheep are important to local livelihoods as well as the national food supply and economy. Scotland, for example, has around 2.6 million ewes, 12,700 agricultural holdings, providing the economy with an annual return of £189 million. The UK is a world player when it comes to producing sheep meat. It is the sixth biggest producer globally and exports 36% of output to more than 100 countries. In addition, the UK uplands as a whole - including agricultural land - have a substantial role to play in addressing many wider environmental issues (e.g. flood prevention; biodiversity enhancement; carbon sequestration in upland moorlands, peatlands and forests). Reduced numbers of animals grazing can have positive impacts on biodiversity, but there are equally concerns that reduced grazing can have negative impacts on open habitats in upland landscapes. Farming and other land uses in the uplands is extremely challenging, currently financially unviable, and needing to respond to the challenges such as climate change, livestock diseases and changing demands from society. In this project we will study four upland case study areas in-depth, and work with the people living there, and with organisations working in those areas to understand better what are the critical factors that influence beef cattle and sheep farmers' resilience to change, and what impact changes in beef cattle and sheep farming can have on food supplies locally and globally, the upland environment, local employment opportunities, and local cultures. These four case study areas are Orkney, Lewis and the Isle of Skye, Scottish borders and Yorkshire Dales. The aim of this project is to provide better tools for decision making for policy makers, local authorities and enterprise agencies, non-governmental organisations, food processors and retailers, farmers and farming groups and local people. By understanding better the interactions among different aspects of the food system, we will be able to appreciate who become vulnerable and how, and what actions will make these vulnerabilities better or worse.

Liver fluke is a common parasite that affects sheep and cattle in the UK. It is found throughout the world and in some countries it affects humans too, causing serious and sometimes fatal disease. Fluke infected cattle lose weight, become anaemic, lethargic and stop being productive. This has a serious effect on the welfare of the animal and serious economic consequences for the farmer. It is thought that fluke costs UK agriculture at least £300million pounds a year through direct losses, but real costs are probably much higher. Fluke has become much more common over the past 10 years, due in part to our changing weather patterns, wet summers and mild winters favour the development of the parasite and its vector - a mud snail, found commonly throughout Britain. In a recent study we found 75% of dairy herds had evidence of fluke infection. Future climate change is predicted to have a significant impact on prevalence of infection, changing the epidemiology and increasing incidence of disease. Increased cattle movements and changes to both farm management and environmental schemes are exacerbating the problem. A limited range of drugs is available to control fasciolosis. Only one drug - triclabendazole (TCBZ), is effective against early and late juvenile and adult stages of the parasite and is used extensively for prophylaxis and treatment of disease. There is growing evidence of resistance to TCBZ in fluke populations, moreover the European Medicines Agency has recently revised its advice on drugs used to treat fluke such that they are now contra-indicated in dairy animals. Targeted use of drugs, at specific times of year will slow the development of drug resistance and reduce the overall quantity of drug used, but a better understanding of the epidemiology and transmission of disease is vital if we are to develop control programmes that rely on improved on farm management practises rather than depending solely on drugs. This ultimately will be a sustainable and cost-effective way to control both clinical and sub-clinical disease in cattle and is the express desire of the livestock industry. Specifically requested by the farming industry, the purpose of this project is to produce new, sustainable, bespoke control programmes for beef and dairy farms, to reduce losses associated with fluke infection. In order to achieve this we must first develop diagnostic tests to identify infected herds. We already have good tools that we can use on milk samples to detect infected dairy herds but we need similar tests that are appropriate for beef herds. In addition we are aware of a newly emerging parasite problem, the rumen fluke. It is not clear if this parasite causes disease but it has the potential to interfere with the diagnostic tests we are developing for fluke. Therefore we will also develop a molecular test for rumen fluke. Secondly we will develop a system to categorise snail habitats that can be used to analyse satellite maps on a regional geographic scale to obviate the need to visit every farm to investigate snail habitat. We will also investigate how cow behaviour affects how the parasite gets to a snail host and from the snail host back to the cow. These are risk factors for fluke infection on a farm. Other risk factors, particularly husbandry practices, physical and environmental factors will be obtained from a study of 250 farms and these data fed into statistical and mathematical models to determine theoretically which of these factors are the most important in determining whether a farm has fluke or not. Concurrently we will assess the cost-benefit of changing these practices. Finally we will conduct a trial to evaluate if changing farm practice is effective in reducing levels of infection. We are working in partnership with the Agricultural Levy boards of the UK to implement improved control of fluke infection to benefit animal health, welfare and profitability of livestock farming in the UK.

Ruminant animals, including cattle, sheep and goats, rely on microbial activity in their digestive tract to digest grass and other forages that they consume. A balanced, stable digestion (fermentation) is essential for good growth or milk production. Most livestock producers require productivity higher than that which can be sustained by forage feeding alone, and include some grain in the diet to increase production rates. Gut microbes produce acids more rapidly from the starch in grain than the cellulose in forages, leading to lower pH values prevailing in grain-fed animals. This has adverse effects on the microbes, which require near-neutral pH to perform optimally. This sub-acute ruminal acidosis (SARA) is a major economic and health issue in ruminant livestock production. Animals suffering SARA are less productive, and they suffer from necrosis of the rumen wall, liver abscesses and laminitis. SARA is often difficult for the farmer to detect - it is 'sub-acute' and can only be detected easily at slaughter. SARA is an under-researched condition, such that only a small number of papers have addressed the dietary and microbiological causes of SARA and its underlying pathology, particularly concerning the role of the large intestine. This project aims to understand why SARA is prevalent on some farms but not others, an observation that is common knowledge but not well documented. Farm management conditions and nutrition will be monitored in these farms, and the animals will be followed to slaughter, when the extent of pathological damage will be assessed. Samples of ruminal digesta and wall tissue will be taken for analysis and tissue necrosis, abscesses and laminitis will be scored. SARA also affects some animals but not others within a herd. Remote motion-sensing technology will be used to externally monitor movements, such as rumination activity, that may alert livestock producers to problematic animals. Post mortem analysis will also be carried out on these animals. The root cause of SARA lies in altered gut microbiology. Digesta samples will be taken forward to describe the microbes that are present in the rumen and intestine in susceptible and non-susceptible animals, with the idea that some microbial species may be particularly important in causing the disease while others may be protective. Candidate 'probiotic' bacteria isolated from non-susceptible animals will be investigated with a view to developing them as feed additives. The role of soluble lipopolysaccharide (LPS) in the inflammation will be investigated. LPS is released when bacteria lyse - it is known as 'endotoxin' in human medicine. Materials that may bind soluble LPS to prevent inflammation will also be investigated as potential feed additives. The overall aims are to explain the underlying mechanism of pathogenesis of SARA, to investigate if microbiome analysis can predict the severity of SARA, and to develop simple, non-invasive methods for monitoring animal behaviour relating to SARA and preventing the condition. Three academic partners, three complementary companies, Quality Meat Scotland and DairyCo are involved in the project. The industrial partners will ensure that relevance to the livestock industry is maintained throughout the project and that the pathway to impact will be short and rapid.