Many people are familiar with life in freshwater either from direct experience with angling or from nature documentaries. Most are probably aware that food chains in aquatic habitats differ from those on the ground. However not all are aware of the details of the complex ecosystems found in lakes, or indeed of the links between the lake and its terrestrial catchment. The problems of pollution in lakes are well known as nutrients from fertilisers can enter the water from agricultural land causing plant life to take over the lake (eutrophication) - this issue is regularly highlighted in the media. However the influx of terrestrial carbon into the lake and subsequent utilisation of this resource in lakes is unexpected. Fish are known to eat aquatic insects and plant life - not many people would name peat bog or soil amongst the food groups of the brown trout! We have shown that such terrestrial material does in fact make it's way into the foodchain and therefore fish diet using a technique known as stable isotope analysis. We have also used radiocarbon - more familiar as a dating method - to clarify the importance of terrestrial material in the diet of fish in Irish lakes. Using radiocarbon, or 14C, we can show that a fish is consuming carbon produced by aquatic plants. This 'within-lake' carbon is partly sourced from weathered limestone and is dissolved in the water. This rock weathered carbon does not contain the 14C radio-isotope and as a result artificially appears to be thousands of years old. Most terrestrial carbon on the other hand is in equilibrium with the earth's atmosphere and contains higher levels of radiocarbon - this carbon is 'modern' and can be distinguished from 'within-lake' carbon. Other carbon stored in peat can be 'old'; this can also be found in lakes and we don't yet know what proportions of 'dead', 'modern' and 'old' carbon are used by plants and animals in lakes. We can separate carbon components dissolved in the water which are used by plants, animals and bacteria in the lake. We can measure the stable isotopes in these carbon components as well as their 14C levels and find out where the terrestrial carbon entering the lake goes. We can also measure the 'radiocarbon age' and stable isotope values of the animals and plants living in the lake can show whether they are consuming 'within-lake' carbon or terrestrial ('modern' or 'old') carbon entering from surrounding land. This research is important as the amount of terrestrial material entering a lake can be affected by climate change and land management practices. The consumption of terrestrial carbon by species in the lake can also be affected by invasive species such as the zebra mussel which voraciously consumes 'within-lake carbon' and is rapidly spreading through Irish and U.K. lakes, causing fish to rely more on terrestrial material. Our proposal to combine the use of stable isotopes with radiocarbon in Queen's University Belfast will investigate this important new field of research to shed light on the complicated food webs in freshwater lakes.

The challenge addressed by this project is to unravel the causes of stunting disease in UK broiler chickens. Stunting syndrome has been a production issue in commercial broiler flocks since they became industrialised after the second world war, but is also a problem for small producers in low and middle income countries, such as Nigeria, where women often raise small numbers of chickens to supplement the family income. The stunting problem has many names, including infectious stunting, runting stunting syndrome and malabsorption disease. It pertains to a failure to grow properly despite sufficient feed. Birds typically present with stunting problems around the second to third week post hatching, but clinical signs may be observable earlier. As well as the reduction in weight gain, which can be substantial with severely affected chickens only a fraction of their potential weight for age, there may be other signs such as altered appetite, watery droppings, abnormal feathering and enteritis. We and other groups have evidence that the stunting is caused by infectious agents: chiefly, viral aetiology is suspected and experimental infections at AFBI using specific strains of the endemic, enteric viruses, astroviruses and reoviruses separately have resulted in some of the signs observed during stunting, e.g. weight loss or lesions in the gut mucosa. Other groups have also demonstrated some of the signs of stunting from inoculating birds with single viral strains of these and other viral candidates, e.g. birnavirus; however, none have fully recreated the stunting syndrome, and co-infections with more than one viral agent are considered the more probable aetiology. Moreover, diverse strains of these viruses are in circulation which are known to vary widely in pathogenicity with the majority potentially of low or no pathogenicity and accordingly high levels of these virus may be detected in young, healthy, unaffected birds. Other confounding factors in attributing disease aetiology includes the presence of maternally-derived antibodies, route of transmission (from the hen versus their environment) and the age at which birds become infected, since increasing age appears to confer resistance. All these factors have also hampered the identification of the virus(es) responsible for stunting diseases. The specific aims of the proposal are to: 1) identify a virus or viruses that are actively replicating within the lesions associated with stunting disease and that are present in many similar lesions from clinical cases. Histopathology and laser microdissection will identify and excise lesions from which nucleic acids will be sequenced to determine which virus strain(s) is present at levels indicative of an active infection. 2) confirm that the virus or viruses identified are aetiological agents of stunting; firstly, by cellular and tissue-based methods in the laboratory and secondly, by challenge studies of healthy chickens using purified isolates of the identified virus(es), which will demonstrate the development of hallmark lesions and associated clinical signs typical of stunting disease. These objectives will be achieved through the use of state of the art imaging and genomic methodologies, and through collaboration with the Industry (Moy Park, which is one of UK's top broiler meat producers and St David's Poultry Team, the leading poultry veterinary practice in the country). Currently there are no commercial vaccines to prevent stunting or specific treatments for affected flocks so that affected birds are culled. The results of this project will provide evidence of the causal agents of stunting that will enable improved diagnostics and potential interventions for veterinarians, and for vaccine companies to develop appropriate vaccines.

The Marine Strategy Framework Directive (MSFD) requires 'Good Environmental Status' (GES) in European salt waters, defined as allowing marine ecosystems "to function fully and to maintain their resilience to human-induced environmental change". What measurements are needed to establish that ecosystems in UK seas are fully-functional and resilient, or, if not, to direct what the Directive calls "programmes of measures" to restore GES? Marine ecosystems are largely out of sight, and their biogeochemical cycles and food webs operate in ways that ecological oceanographers are still struggling to understand. Nevertheless, 4 decades of NERC coastal oceanography has mapped the physical features of the seas that overly the UK continental shelf and shone light on the links between physics and biology. This research provides the basis for science-based monitoring of the 'pelagic habitat' as a component of Environmental Status. 'Pelagic habitat' refers to the water column environment and the plankton - the drifting animals and microscopic algae that live here. Defra is the UK government department responsible for the national implementation of the MSFD, and for reporting environmental status to the European Commission. In the case of the pelagic habitat Defra has identified a set of monitoring stations in different physical regimes; one of these sites, in the Firth of Lorn near Oban, is where phytoplankton has been regularly sampled by the Scottish Association for Marine Science since 2000. Observations were first made here in 1970 by SAMS' precursor SMBA. SAMS has already agreed to input current micro-algal data to the Defra programme, and Defra may fund some additional zooplankton work. One of the two main purposes of the present project is to to evaluate, for the purposes of MSFD reporting, the present condition of the Firth of Lorn station in relation to older data and research studies. The second main purpose relates to the methods used for data analysis and reporting. Scrutiny of a water sample containing planktonic micro-algae, or a tow-net sample containing planktonic animals, usually results in a long list of species. The MSFD monitoring programme requires samples to be taken at least 12 times a year, in order to keep track of the seasonal succession of plankton species. One way to simplify this list is to group species into the 'lifeforms' that are the functional units of the plankton. Lifeforms are then grouped in pairs, and the abundance of each of the pair's lifeforms plotted against the horizontal or vertical axis of a graph. A year's worth of samples results in 12 (or more) points on this graph. Over the resulting cloud of points is drawn a 'reference envelope'. The proportion of observations falling outside this envelope is the value of the 'Plankton index' for this lifeform pair and year. Changes in the index can be used to track change in ecosystem condition. Its calculation has been computerized, but the method has so far been used for research rather than routine monitoring. The second purpose of the project is, thus, to assist Defra in the initial application of the method, using the Firth of Lorn data as a test case. While Defra has oversight, the work of sampling, analysis and interpretation is performed by specialized public bodies including those reporting to the devolved administrations in the UK. One of these bodies is AFBI, the 'Agri-Food and Biosciences Institute' in Belfast, which led the consortium charged with designing the strategy for monitoring the pelagic habitat. Although the ultimate benefit of this project falls to the public good, and the designated benficiary is Defra, AFBI will be the immediate partner for SAMS in the proposed 'knowledge exchange'.

Recognition of the enormous costs of ill-health, disease and obesity associated with current UK dietary consumption patterns and the environmental damage inflicted by current food production systems have made the transition to healthy and sustainable diets the key objective of UK food policy for the 21st century. The dietary consumption patterns of all segments of the UK population show large divergences from the UK dietary guidelines for healthy eating, with the poorer sections of the population having the most unhealthy diets. The UK also remains substantially reliant on imports for its food consumption. The transition to healthy and sustainable diets requires a significant shift in consumer preferences and dietary choices that could be induced through a combination of fiscal measures, behavioural, public health, regulatory and supply-side interventions. However, this transition cannot be successfully accomplished without a realignment of UK food production, trade and supply chains consistent with the anticipated shifts in consumer demand and environmental sustainability constraints. This project directly addresses the two overarching questions posed by the Transforming UK Food Systems programme that relate to (1) the changes in dietary consumption, food production and trade patterns that would be required for a transition to healthy and sustainable diets and (2) the interventions that would be needed across government, business and civil society to deliver this transformed food system. The project takes a food systems approach through a simultaneous consideration of consumption, production, trade and supply chain implications of a transition to healthy and sustainable diets and brings together multidisciplinary expertise encompassing: (1) economic modelling of consumer demand and shifts in consumer preferences (2) dietary pattern analysis (3) derivation of environmental sustainability indicators at food product level (3) partial equilibrium modelling of production and trade incorporating environmental impacts of green house gas (GHG) emissions, land use, water use and soil nutrient balances (4) elicitation of consumer preferences using stated preference techniques (discrete choice experiments) (5) trade policy analysis in the context of current and emerging international and regional trade policy regimes (6) structural changes in the supply and value chains for the agri-food sector and (7) co-design approaches for industry-led initiatives - in designing a coherent policy framework for supporting the transition to healthy and sustainable diets. Our analysis will address the complex policy challenges arising from (1) the need to consider the impact of fiscal measures on consumers' entire food baskets rather than on the consumption of individual food products (2) the distributional (equity) impacts of fiscal measures (3) the potential trade-offs between healthy and sustainable diets (4) the constraints imposed on trade policy measures by the architecture of international and regional trade policy regimes and the need to balance the interests of consumers, domestic producers, importers and trading partners in the implementation of trade policy measures (5) food industry incentives for food product development and marketing strategies that may not support the transition to healthy and sustainable diets (6) the socio-culturally embedded nature of dietary patterns that tend to be slow to change and (7) the very limited avenues for restricting consumer dietary choices in a market economy that respects consumer choice. The project aims to develop a blueprint for a coordinated set of fiscal and trade policy interventions along with structural changes to food supply and value chains and industry-led initiatives for supporting the transition to healthy and sustainable diets.

Fasciola hepatica, usually termed "the temperate liver fluke", is a worldwide problem for agriculture. Infections known as fasciolosis, primarily damage ruminant production, and have been reported across many regions of Europe including the UK and Northern Ireland (NI). Fasciolosis as a food-borne disease, results from the consumption of the infective larvae, which greatly reduces global livestock capacity and efficiency. It is estimated that fascioliasis causes annual economic losses in the UK of £110 million, while across Europe the impact is considerably larger, at £524 million. Despite its importance, there is a lack of basic ecological knowledge associated with liver fluke. This includes the diversity and distribution of their snail intermediate hosts integral to the parasite lifecycle. This lack of knowledge limits efforts to successfully assess and combat threats in order to improve animal welfare and productivity. It is unclear what factors drive increased helminth presence and prevalence, but candidates include climate change, decreased interspecies competition among competitors of the intermediate snail host, changes in anthelmintic usage leading to resistance, and high levels of animal movements. Understanding the biodiversity of the helminth and their snail host(s) is key for understanding the ecology of disease transmission. This project will investigate the role of species biodiversity for disease transmission by building an interdisciplinary team. This team will increase research capability and capacity focused on helminth parasites important to UK agriculture. Using a molecular ecology approach, this project will bring together expertise in parasitology, molecular biology and computational biology, ecology, and agricultural management; and will receive input from academic, government and industry partners. The School of Biological Sciences at QUB, has a long history of collaboration with farmers. We have already isolated DNA from the environment (soil), which is known as or eDNA, from farms with a history of helminth disease. While specific assays are being used to look for the presence of suspected known helminth and snail species, we will used new technologies to capture the complete picture of biodiversity at these sites. In this project we will undertake these activities- Use next generation sequencing from eDNA obtained from helminth infected farms in Northern Ireland, to characterise parasite and snail host biodiversity. Determine if helminth and snail biodiversity is correlated with anthelmintic (anti-parasite drug) usage. Lastly, form a research network which uses new sequencing strategies to assess UK agriculture sites for "biodiversity health" as risk factors associated with helminth transmission. The development of these techniques will lead to actionable data that can be applied to the future management of agriculture. Furthermore we will demonstrate that environmental samples, when analysed by molecular methods to determine species biodiversity can answer ecological questions. In considering parasitological, ecological and biodiversity perspectives, invasive species detection, food/water hygiene and biosecurity (anthelmintics in water or bacterial/viral outbreaks) can be managed.