Increases in the number of cattle botulism cases have occurred in the UK within recent years. It is recognised that the mouse is less suceptable to Clostridium botulinum toxins types C and D than the bovine, and diagnostic confirmation of clinically suspect cases using the mouse bioassay has been poor. It has been more successful when used to test intestinal contents than serum which is regarded as the prefered confirmatory test sample. The objective of this project is to replace the mouse a ssay with in vitro assays of improved and better sensitivity, to satisfy a welfare issue and improve the diagnostic rate from clinically suspect cases. The approaches include modifications of monoclonal antibody based sandwich ELISAs for the detection of toxin types C and D, notably the application of immunoPCR to serum samples in particular, and the inclusion of a culture enrichment stage to intestinal contents samples. Improvements in diagnosis from serum test samples is a prime objective, b ut increased confirmation of disease from intestinal contents, which would have to be assessed in relation to the background environmental level of C. botulinum spores, would also improve the existing situation for the testing of field cases.

Abstract Nipah virus (NiV) is a member of the Henipavirus genus (family Paramyxoviridae) and is the causative agent of sporadic outbreaks of respiratory and encephalitic disease in Southeast Asia. During the initial NiV outbreaks in Malaysia and Singapore, most human NiV cases were caused by close contact with pigs. In subsequent outbreaks during 2001 to 2012 in Bangladesh and India, drinking fresh date palm sap, which was contaminated by fruit bat’s droppings, urine and saliva, and close contact with infected humans were found to be the major source of NiV infection. However, pigs are highly susceptible to NiV and generally serve as an amplifying host of the virus. Due to the lethal nature of disease and potential risk of reversion of a live attenuated vaccine to wild-type is not advisable. Therefore, many candidate vaccine for NiV are 'recombinant', where NiV proteins are produced from inserted genes in another safer virus (referred to as the vector). The fusion (F) and (G) proteins of NiV are commonly chosen as they provide an effective immune response in the body. The G protein allows the virus to attach to the cell and the F protein causes fusion of the virus envelope with the cell membrane so that the virus nucelic acid can enter the cell. Recently it has been discovered for several other paramyxovirus that the form of the F protein in the mature virus (post fusion form) is not as good at inducing an immune response as the form of F which occurs when the virus is entering cells (pre-fusion form). The pre-fusion F protein is unstable but we are able to stabilise this by making slight sequence changes. We will use another ‘safe’ member of the Paramyxovirdae, Sendai virus (SeV, a rodent virus) as the vector. We will compare the immune response of the SeV vaccines which produce one of the 2 types of F protein alone or each in combination with the G protein. Increasing evidence indicates that SeV has substantial potential as a vaccine vector in part because the virus uses common sialic acid receptors for cell entry, which facilitates infection of a wide range of cell types from different species including pigs and humans. Although SeV biosafety risks are minimal, we will also develop the system to generate replication-incompetent SeV NiV vaccines that infect host cells and produce the NiV F and G proteins but removes any residual biosafety concerns of a live SeV vector spreading between animals or humans. We hypothesise that novel vaccine approach based on replication-competent and incompetent SeV vectors expressing pre-fusion NiV F protein will provide a significant breakthrough in the generation of highly successful NiV vaccines. We further hypothesise that NiV vaccines based on rSeV expressing pre-fusion NiV F will induce more robust and longer lasting protective immunity than post fusion F vaccines. Used as a pig vaccine these systems will greatly reduce porcine to human transmission. Futhermore, production of non-replicating SeV vaccines addresses biosafety. As Sev also infects human cells, these vaccines could be subsequently trialled for human use.

In 2015, the ecological status of 75-90% of surface waters in NW Europe was reported to be less than good. Diffuse pollution with nitrogen (N) and phosphorus(P) from agriculture, together with point sources of N and P pollution from wastewater plants and industry, are a major cause of this failure to achieve good ecological status. Climate change is likely to exacerbate the pollution risk. Clearly, there is a huge challenge to implement effective mitigation measures to reduce nutrient loadings to air and water to meet desired environmental targets against the background of a changing climate. The synergies and trade-offs between management actions to mitigate climate change and those to mitigate N and P pollution need to be clarified to develop effective local, regional and national policies. Governance arrangements to implement and monitor the necessary actions need to be better integrated, requiring a consistent and coherent set of environmental indicators. The overall objective of NEW-HARMONICA is to assess and co-develop a harmonised systemic approach to prioritizing an effective suite of N and P pollution mitigation measures and indicators to meet local to regional environmental targets. To achieve this objective, an experienced NEW-HARMONICA consortium (4 partners from 3 countries) with complementary expertise, skills and networks will work on 4 N and P-polluted cross-border river basins in NW Europe. All partners are involved in an established NW Europe Policy-Science Working Group (PSWG) who together with local catchment stakeholders play a central role in NEW-HARMONICA. NEW-HARMONICA’s approach is based on a combination of technical assessments, including quantification of N and P flows and load-reduction targets in the study catchments, assessments of governance arrangements, and policy support for the co-development of harmonised environmental policies, based on a strong evidence base and interactions with the PSWG and local stakeholders.

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 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'.